Printable Version of Topic

-Antievolution.org Discussion Board
+--Forum: After the Bar Closes...
+---Topic: Evolution of the horse; a problem for Darwinism? started by Alan Fox


Posted by: Alan Fox on Sep. 18 2007,15:27

I have been posting at < ISCID > and my old friend, Professor Davison, suggested, in his usual forthright style, a fellow poster, Daniel Smith, should try posting here :  

---------------------QUOTE-------------------
Daniel Smith

Better yet, go over to Panda's Thumb and present your views there and see just how far you will get. Look at what is happening to Martin at After The Bar Closes. It is disgusting. I tried to deal with those animals and was banned for life. Like Pharyngula, Panda's Thumb is a closed union shop. Trust me or learn for yourself.
---------------------QUOTE-------------------



So I extended an invitation to Daniel, confident he will receive a warm welcome.

Daniel has stated ( please correct me if I mis-state your view)that Leo Berg in "Nomogenesis" and Otto Schindewolf in "Basic Questions in Paleontology" both produce good arguments against RM and NS using the evolution of the horse as an example.

Hope to hear from you, Daniel.
Posted by: jeannot on Sep. 18 2007,15:57

Hi Alan,

I don't think that anyone here is a paleontologist. So if we're going to defend RM+NS, it will probably be on another ground.
Posted by: skeptic on Sep. 18 2007,16:50

what about Deadman?
Posted by: Steviepinhead on Sep. 18 2007,19:48

deadman is an archaeologist, last I heard.
Posted by: Henry J on Sep. 18 2007,22:39

Evolution? The fossils say neigh!

:p

Henry
Posted by: skeptic on Sep. 19 2007,17:13

I was hoping otherwise but I wasn't sure.  It's been so long since he's been around anyway.  He may not be available.
Posted by: argystokes on Sep. 19 2007,22:56

I think Dr. GH is an archaeologist. Or something. What about afarensis? Deadman's been hanging around iidb, and could probably be lured back here.
Posted by: Daniel Smith on Sep. 20 2007,02:13

Hello to all,

Thanks Alan for the invitation and the thread.  I don't really know what to say here.  The reference to the evolution of the horse was one of many that Schindewolf uses in his book for his position against gradualism.

Berg essentially argues against selection using many examples from modern biological history.

I've also read recently, the excellent books "Evolution: A Theory in Crisis" and "Nature's Destiny" by Michael Denton.

I also respect immensely Dr. John Davison's Prescribed Evolutionary Hypothesis, although I must admit, much of it is over my head.

I myself am no scientist.  As far as formal training, I'm more than ignorant.  What little I know has been self taught. I spent a lot of time on the talk.origins newsgroup sharpening my views, but my positions are not set in stone.  I have not yet decided what I think really happened in the "history of life" on this planet, but I am convinced of one thing: whatever happened was by design.

Also, I must say that I have very little free time to devote to this discussion - probably 1 or 2 hours a week - so there might be some long delays between posts for me.
Posted by: oldmanintheskydidntdoit on Sep. 20 2007,02:48

Quote (Daniel Smith @ Sep. 20 2007,02:13)
I have not yet decided what I think really happened in the "history of life" on this planet, but I am convinced of one thing: whatever happened was by design.
---------------------QUOTE-------------------


As almost every living thing that has ever existed is extinct, why would that be by design? Seems wasteful to me

What's your take on the "designed to go extinct" issue?
Posted by: Alan Fox on Sep. 20 2007,09:17

Hi Daniel,

So you decided to brave the lion's den.

 

---------------------QUOTE-------------------
I myself am no scientist.  As far as formal training, I'm more than ignorant.  What little I know has been self taught. I spent a lot of time on the talk.origins newsgroup sharpening my views, but my positions are not set in stone.
---------------------QUOTE-------------------



There are many posters here who are professional scientists and can answer queries or point you to references.

 

---------------------QUOTE-------------------
I have not yet decided what I think really happened in the "history of life" on this planet, but I am convinced of one thing: whatever happened was by design.
---------------------QUOTE-------------------



Again, I am sure people can supply information and explanation on the scientific evidence. Science does not address anything other than observable, measurable phenomena, however, so the nature and rôle of a supreme being or creator is not available for scientific scrutiny. If you want to claim there is scientific evidence for a designer (intelligent or not) or that "Intelligent Design" can currently claim to be a scientific endeavour, then I expect you may find some disagreement.



 

---------------------QUOTE-------------------
Also, I must say that I have very little free time to devote to this discussion - probably 1 or 2 hours a week - so there might be some long delays between posts for me.
---------------------QUOTE-------------------



I too have to ration my time here. I sometimes wonder if academics have too much free time judging by some people's output.  :D
Posted by: Glen Davidson on Sep. 20 2007,10:39



---------------------QUOTE-------------------
I have not yet decided what I think really happened in the "history of life" on this planet, but I am convinced of one thing: whatever happened was by design.
---------------------QUOTE-------------------



Any chance you could just open your mind to all possibilities?  Otherwise, what's the point of even one or two hours?

Glen D
< http://tinyurl.com/2kxyc7 >
Posted by: C.J.O'Brien on Sep. 20 2007,12:29



---------------------QUOTE-------------------
I have not yet decided what I think really happened in the "history of life" on this planet, but I am convinced of one thing: whatever happened was by design.
---------------------QUOTE-------------------


What has convinced you of this?

The key difference between science and apologetics is that scientific inquiry begins with the data and moves toward the best explanation, while apologetics begins with an "unshakeable" conclusion and finds data to support it. Cherished notions, "common sense," assumptions and "what everybody knows" are all up for examination in science. It's a human activity, so bias and error naturally occur. But because it is a widely distributed activity and its practitioners insist on transparency of method, its explanations converge, ultimately, toward the best available.

Science, therefore, seeks consilience. Whatever explanation is proposed for a set of observations must not only be the best fit for those data, it must also fit within the framework of all the other observations and conclusions drawn in the field. The data used to support preferred conclusions in apologetics are often "cherry-picked," that is, they only support the foregone answer if we ignore other, contrary, observations in the field.

Finally, when all is said and done, a scientist is allowed to return the answer "we still don't know." Intellectual honesty sometimes compels it, though it is usually deeply unsatisfying to admit ignorance when one has worked hard to explain. There are always unsolved problems, and if there weren't, there would be no need for science.

Given all of this, I will echo Glen: If you won't adopt the scientific attitude toward these questions but are instead going to stick to your pre-formed conclusion and labor to keep it "evidence proof," then I don't think there will be much of a meaningful exchange here.
Posted by: VMartin on Sep. 20 2007,13:20



---------------------QUOTE-------------------

Given all of this, I will echo Glen: If you won't adopt the scientific attitude toward these questions but are instead going to stick to your pre-formed conclusion and labor to keep it "evidence proof," then I don't think there will be much of a meaningful exchange here.

---------------------QUOTE-------------------



What is the "scientific attitude" in your comprehension?  Taking darwinian pressupositions to the evolution of horses or what?  Do you mean that "natural selection" had been involved in the phenomenon? Because all the concept of random mutation and natural selection is nothing more as an unproved hypothesis, not the "scientific attitude" as you would like us to believe. Daniel Smith quoted prominent scientists of past like Berg and Schidewolf. Daniel might has been inspired by John Davison's Manifesto, which is an extraordinary anti-darwinian source of information.

I supported the view held by John and Daniel using the research of entomologist Franz Heikertinger who waged  war against proponents of "natural selection" more than 40 years. F. Heikertinger (himself an evolutionist)  refuted "natural selection" as the source of mimicry giving vast number of facts, observations and by darwinists neglected phenomenons.

Those great men were prominent scientists and you have no right to call anyone using their arguments that they use "pre-formed arguments" and not "scientific attitudes".
Posted by: C.J.O'Brien on Sep. 20 2007,13:38



---------------------QUOTE-------------------
Those great men were prominent scientists and you have no right to call anyone using their arguments that they use "pre-formed arguments" and not "scientific attitudes".
---------------------QUOTE-------------------


No right? I beg to differ.

Davison is a crackpot. If Daniel thinks there's any merit to any of his, or your own, output, I will say again, I don't see a meaningful exchange in the future of this thread.

Now that you're here, I see it even less.
Posted by: Alan Fox on Sep. 20 2007,14:41

VMartin:

Thread subject: Horse evolution and whether works by Berg and Schindewolf contain evidence that undermines current evolutionary theory.

Not thread subject: Ladybirds etc.
Posted by: Peter Henderson on Sep. 20 2007,14:52



---------------------QUOTE-------------------
have not yet decided what I think really happened in the "history of life" on this planet, but I am convinced of one thing: whatever happened was by design.
---------------------QUOTE-------------------



Daniel: I assume you have come to these conclusions because of religous convictions ? I have done quite a few conventional science courses in my time (although I don't have a degree yet) but I have progressed to what are known as 3rd level courses in this country (beyond A-Level). I've also worked in the chemistry end of things for over thirty years although I'm now retired:

< http://www.premier-power.co.uk/ >

One thing I've found out about science.....contrary to what groups like AiG claim, it does not try to convert people to Atheism. None of the courses that I have taken have done this, even the ones that had evolutionary concepts like astronomy or geology for example. In fact, in order to be successful in these disciplines they must be approached from an evolutionary viewpoint. Astronomy/cosmology for example, just doesn't make sense when viewed from a YEC perspective despite what people like Dr Jason Lisle say (even he had to learn evolutionary concepts in order to obtain his Phd). What we observe is this field certainly does not confirm a young Earth/Universe.

I've also found that one does not need to abandon conventional/mainstream science (and by that I mean evolution since it encompasses a wide range of subjects, not just biology) when one becomes a Christian. I've mentioned this exceptional lady on more than one occasion as a good example:

< http://www.longman.co.uk/tt_secsci/resources/scimon/jan_01/bell.htm >

< http://www.royalsociety.org/page.asp?tip=1&id=1481 >

< http://www.starcourse.org/jcp/testing_god_3.htm >

 

---------------------QUOTE-------------------
Jocelyn Bell Burnell: One of the things that I can never answer is whether my feeling that there is a god is simply some kind of neurological pattern in my brain. I have no answer to that, I just do not know. But the evidence would lead me to think otherwise, because I’m not the only person who feels this, who has the same experiences. And I can recognise what I call god in other people as well, it’s not just in me.
---------------------QUOTE-------------------



I think I feel the same as the above.

YECism is more likely to convert me to agnosticism rather than conventional science.
Posted by: JAM on Sep. 20 2007,17:43

Quote (Daniel Smith @ Sep. 20 2007,02:13)
I've also read recently, the excellent books "Evolution: A Theory in Crisis" and "Nature's Destiny" by Michael Denton.
---------------------QUOTE-------------------


Didja happen to notice that the latter book walks back from the position taken in the former book?
Posted by: Henry J on Sep. 21 2007,10:58

Quote (JAM @ Sep. 20 2007,17:43)
Didja happen to notice that the latter book walks back from the position taken in the former book?
---------------------QUOTE-------------------


What, somebody went and changed their mind about something? Who'd have thunk it! :p
Posted by: Daniel Smith on Sep. 22 2007,04:07

Quote (C.J.O'Brien @ Sep. 20 2007,12:29)
The key difference between science and apologetics is that scientific inquiry begins with the data and moves toward the best explanation...

Science, therefore, seeks consilience. Whatever explanation is proposed for a set of observations must not only be the best fit for those data, it must also fit within the framework of all the other observations and conclusions drawn in the field.
---------------------QUOTE-------------------


I agree that this is what science should be.  

What then, is your position on the lack of evidence in the fossil record for gradualism?
Posted by: Daniel Smith on Sep. 22 2007,04:11

Quote (JAM @ Sep. 20 2007,17:43)
 
Quote (Daniel Smith @ Sep. 20 2007,02:13)
I've also read recently, the excellent books "Evolution: A Theory in Crisis" and "Nature's Destiny" by Michael Denton.
---------------------QUOTE-------------------


Didja happen to notice that the latter book walks back from the position taken in the former book?
---------------------QUOTE-------------------


Not really.  In the first book, he doesn't really give us an alternative hypothesis; all he does is point out the many deficiencies of the currently held evolutionary theory.

In the second book, he starts to give us his own alternative: a designed universe and directed evolution.

I see no conflict.
Posted by: Daniel Smith on Sep. 22 2007,04:14

Quote (oldmanintheskydidntdoit @ Sep. 20 2007,02:48)
As almost every living thing that has ever existed is extinct, why would that be by design? Seems wasteful to me

What's your take on the "designed to go extinct" issue?
---------------------QUOTE-------------------


I don't know "why" many designers do what they do.  I don't think that in any way negates the fact that their products are designed.  Do you?
Posted by: Wesley R. Elsberry on Sep. 22 2007,04:38



---------------------QUOTE-------------------

What then, is your position on the lack of evidence in the fossil record for gradualism?

---------------------QUOTE-------------------



What meaning of "gradualism" are you interested in? Might it be the "phyletic gradualism" described by Eldredge and Gould in 1972?



---------------------QUOTE-------------------

    In this Darwinian perspective, paleontology formulated its picture for the origin of new taxa. This picture, though rarely articulated, is familiar to all of us. We refer to it here as “phyletic gradualism” and identify the following as its tenets:

   (1) New species arise by the transformation of an ancestral population into its modified descendants.

   (2) The transformation is even and slow.

   (3) The transformation involves large numbers, usually the entire ancestral population.

   (4) The transformation occurs over all or a large part of the ancestral species’ geographic range.

---------------------QUOTE-------------------


Posted by: Daniel Smith on Sep. 22 2007,04:48

Quote (Peter Henderson @ Sep. 20 2007,14:52)
In fact, in order to be successful in these disciplines they must be approached from an evolutionary viewpoint. Astronomy/cosmology for example, just doesn't make sense when viewed from a YEC perspective despite what people like Dr Jason Lisle say (even he had to learn evolutionary concepts in order to obtain his Phd). What we observe is this field certainly does not confirm a young Earth/Universe.
---------------------QUOTE-------------------


There are many things I have yet to make up my mind about.  For instance; I have not made my mind up in regard to the age of the earth/cosmos as I have not seen all the evidence and probably do not have the expertise to rightly interpret it.

My main problem is that I want to see unbiased and unadulterated evidence; not evidence that is made-to-fit the observers viewpoint.  I'm finding that hard to do - since both sides of this issue tend to color the evidence with their own interpretive brush.

The first book I read on the subject (other than my high school science books) was "Scientific Creationism" by Dr. Henry Morris, and, although he makes some good points, I found some of his views to be a bit of a stretch and recognized his attempts to fit science to the bible.

I then spent quite some time on talk.origins and did much research on the internet looking at the case for the currently held theory of evolution.  I found that much of the evidence for the theory was being interpreted under the assumption of the theory.

I decided what I needed was just to see the evidence for myself.

This is the reason I have sought out authors such as Berg, Schindewolf, Denton, Davison and others.  First, they are true scientists - there are no religious views expressed in their books.  Second, they hold to no preconceived paradigm and they have (or had) nothing to gain by publishing their views.  Most were either ridiculed or shunned, or just put on a shelf and forgotten, but their works stand the test of time (at least so far).  These are the type of people I want to get my information from.
Posted by: Daniel Smith on Sep. 22 2007,04:53

Quote (Wesley R. Elsberry @ Sep. 22 2007,04:38)
What meaning of "gradualism" are you interested in?
---------------------QUOTE-------------------


I mean the smooth, gradual, incremental, evolution of forms throughout biological history.
Posted by: Daniel Smith on Sep. 22 2007,04:55

Quote (Wesley R. Elsberry @ Sep. 22 2007,04:38)
Might it be the "phyletic gradualism" described by Eldredge and Gould in 1972?

   

---------------------QUOTE-------------------

    In this Darwinian perspective, paleontology formulated its picture for the origin of new taxa. This picture, though rarely articulated, is familiar to all of us. We refer to it here as “phyletic gradualism” and identify the following as its tenets:

   (1) New species arise by the transformation of an ancestral population into its modified descendants.

   (2) The transformation is even and slow.

   (3) The transformation involves large numbers, usually the entire ancestral population.

   (4) The transformation occurs over all or a large part of the ancestral species’ geographic range.

---------------------QUOTE-------------------


---------------------QUOTE-------------------


Of these I'd pick 1 and 2, but not necessarily 3 or 4.
Posted by: Wesley R. Elsberry on Sep. 22 2007,04:58

Uh, no, it's a package deal. Either you are endorsing all four of the definitional components, or you should be using another term.
Posted by: Wesley R. Elsberry on Sep. 22 2007,05:00



---------------------QUOTE-------------------

What then, is your position on the lack of evidence in the fossil record for gradualism?

---------------------QUOTE-------------------





---------------------QUOTE-------------------

I mean the smooth, gradual, incremental, evolution of forms throughout biological history.

---------------------QUOTE-------------------



So, are you asserting that there are no instances of transitional fossil sequences?
Posted by: jeannot on Sep. 22 2007,05:02

Quote (Daniel Smith @ Sep. 22 2007,04:07)
What then, is your position on the lack of evidence in the fossil record for gradualism?
---------------------QUOTE-------------------


Mine is rather straightforward:
Given the billions of animal and plant species that have existed, we've only collected a very small fraction of them as fossils.

We don't expect to find most transitional forms.
Posted by: Alan Fox on Sep. 22 2007,09:23



---------------------QUOTE-------------------
My main problem is that I want to see unbiased and unadulterated evidence..,
---------------------QUOTE-------------------



This is not a problem, Daniel, this is a good thing. It is always worth trying to look at the primary evidence to see if there is error or bias in interpretation.

 

---------------------QUOTE-------------------
I decided what I needed was just to see the evidence for myself.

This is the reason I have sought out authors such as Berg, Schindewolf, Denton, Davison and others.
---------------------QUOTE-------------------



But should you not then look at the evidence on which they base their hypotheses rather than accepting their interpretations without question? This must be especially so in the case of Berg and Schindewolf as Berg wrote "Nomogenesis" in 1922 and Schindewolf was proposing saltation as a hypothesis in the '30s. A lot of evidence, the elucidation of the genetic code, for instance, was unavailable to them.

I think Berg was quite a polymath, producing works in geography and ichthyology, although there is a question mark as to whether he had some influence on the later disastrous ideas of Trofim Lysenko.

Michael Denton seems to have distanced himself from the Discovery Institute lately, and his current research project seems very laudable.
Posted by: Peter Henderson on Sep. 22 2007,11:43



---------------------QUOTE-------------------
I decided what I needed was just to see the evidence for myself.
---------------------QUOTE-------------------



If you saw 10 clocks Daniel, and 9 of them were reading the same time and the tenth was different which one would you choose ? I know what I would think. I would assume the one that was different was in error.

This is how it is with this debate (if you could call it that). 99.99% of all scientists accept the age of the Earth/evolution. No mainstream scientist that I know of has found evidence of a 6-10,000 year old Earth/Universe. I always wonder why those who question science in favour of YECism don't think about that.
Posted by: Daniel Smith on Sep. 22 2007,14:26

Quote (Wesley R. Elsberry @ Sep. 22 2007,04:58)
Uh, no, it's a package deal. Either you are endorsing all four of the definitional components, or you should be using another term.
---------------------QUOTE-------------------


OK, let me be more specific:
Gradualism is what one would expect to see if the mechanism for evolutionary change were random mutations and natural selection.  If you think that it must entail entire populations and their entire geographical range, then fine - show that by the evidence in the fossil record.
Posted by: Henry J on Sep. 22 2007,14:37



---------------------QUOTE-------------------


    In this Darwinian perspective, paleontology formulated its picture for the origin of new taxa. This picture, though rarely articulated, is familiar to all of us. We refer to it here as ?phyletic gradualism? and identify the following as its tenets:

   (1) New species arise by the transformation of an ancestral population into its modified descendants.

   (2) The transformation is even and slow.

   (3) The transformation involves large numbers, usually the entire ancestral population.

   (4) The transformation occurs over all or a large part of the ancestral species? geographic range.


---------------------QUOTE-------------------



Darwinian? If I recall correctly, Darwin suggested that evolution is apt to occur in a minority of a species, on the fringe of its territory. That stuff about it being the whole species at once was tacked on later by other scientists.

Afaik, only point 1 of those is part of the current theory as phrased above. Number 2 needs a qualifying phrase saying slow relative to the generational span of the species - i.e., that could still be fast relative to geologic eras.

Henry
Posted by: Daniel Smith on Sep. 22 2007,15:01

Quote (jeannot @ Sep. 22 2007,05:02)
         
Quote (Daniel Smith @ Sep. 22 2007,04:07)
What then, is your position on the lack of evidence in the fossil record for gradualism?
---------------------QUOTE-------------------


Mine is rather straightforward:
Given the billions of animal and plant species that have existed, we've only collected a very small fraction of them as fossils.

We don't expect to find most transitional forms.
---------------------QUOTE-------------------


But we have found millions of fossil remains for many types of organisms.  Why then do we still find no evidence of smooth, gradual transitions between types?  

         

---------------------QUOTE-------------------
"As we all know, Darwin's theory of evolutionary descent asserts that organisms evolve slowly and very gradually through the smallest of individual steps, through the accumulation of an infinite number of small transformations.  Consequently, the fossil organic world would have to consist of an uninterrupted, undivided continuum of forms; as Darwin himself said, geological strata must be filled with the remains of every conceivable transitional form between taxonomic groups, between types of organizations and structural designs of differing magnitudes.

Fossil material did not then and, based on the present state of our knowledge, does not today meet this challenge, not by a long shot. It is true that we know of countless lineages with continuous transformation, in as uninterrupted a sequence as could be desired.  However, each time we go back to the beginning of these consistent, abundantly documented series, we stand before an unbridgeable gulf.  The series break off and do not lead beyond the boundaries of their own particular structural type.  The link connecting them is not discernible; the individual structural designs stand apart, beside one another or in sequence, without true transitional forms"

Otto H. Schindewolf, "Basic Questions in Paleontology", pp 102-103
---------------------QUOTE-------------------



And later, when speaking of the sudden appearance of new structural types, Schindewolf comments:
     

---------------------QUOTE-------------------
" And these are by no means just isolated occurrences; these strange new forms are usually also represented by large numbers of individuals.  Nonetheless, there is no connecting link with the stock from which they derived.  The continuity of the other species gives us no reason to suspect interruptions in the deposition of the layers, or subsequent destruction of layers already deposited, which, furthermore, would be revealed by other geological criteria.  Nothing is missing here, and even drastic changes in living conditions are excluded, for the facies remain the same.

Further, when we see this situation repeated in all stratigraphic sequences of the same time period all over the world... we cannot resort to attributing this phenomenon to immigration of the new type from areas not yet investigated, where perhaps a gradual, slowly progressing evolution had taken place. What we have here must be primary discontinuities, natural evolutionary leaps, and not circumstantial accidents of discovery and gaps in the fossil record"

ibid. pp 104-105 (emphasis his)
---------------------QUOTE-------------------


Posted by: Henry J on Sep. 22 2007,15:38



---------------------QUOTE-------------------
No mainstream scientist that I know of has found evidence of a 6-10,000 year old Earth/Universe. I always wonder why those who question science in favour of YECism don't think about that.
---------------------QUOTE-------------------



My guess: Those who do think about that realize that they don't have an evidence based argument, so they don't go around claiming to have one. So the only ones we here from are the ones who didn't think.

Henry
Posted by: jeannot on Sep. 22 2007,15:41

Quote (Daniel Smith @ Sep. 22 2007,15:01)
Quote (jeannot @ Sep. 22 2007,05:02)
         
Quote (Daniel Smith @ Sep. 22 2007,04:07)
What then, is your position on the lack of evidence in the fossil record for gradualism?
---------------------QUOTE-------------------


Mine is rather straightforward:
Given the billions of animal and plant species that have existed, we've only collected a very small fraction of them as fossils.

We don't expect to find most transitional forms.
---------------------QUOTE-------------------


But we have found millions of fossil remains for many types of organisms.  Why then do we still find no evidence of smooth, gradual transitions between types?  
---------------------QUOTE-------------------


No evidence? I doubt it. I'm not a paleontologist, but I heard they can study vicariance with the fossil record. That involve fossil species that are very similar, supporting gradualism.
And I'm not sure we have fossil remains for millions of species.
Let's take hominids. Only rather recently have we discovered many of the forms that separate us from the common ancestor we have with chimps.
Posted by: Wesley R. Elsberry on Sep. 22 2007,17:13

Quote (Daniel Smith @ Sep. 22 2007,14:26)
Quote (Wesley R. Elsberry @ Sep. 22 2007,04:58)
Uh, no, it's a package deal. Either you are endorsing all four of the definitional components, or you should be using another term.
---------------------QUOTE-------------------


OK, let me be more specific:
Gradualism is what one would expect to see if the mechanism for evolutionary change were random mutations and natural selection.  If you think that it must entail entire populations and their entire geographical range, then fine - show that by the evidence in the fossil record.
---------------------QUOTE-------------------


What does it take to convince people that they don't just get to make up their own definitions for terms that are already in use in evolutionary science? I've been running into Humpty-Dumptyism left and right ever since getting involved in these discussions.

"Gradualism" is already in use. Broadly, it means non-saltational change. There's nothing about it that requires that such properties of change occur by particular mechanisms. "Phyletic gradualism" is already in use. It means the conjunction of the four tenets listed already.

You don't have to take my word on it for either of these; consult any competent evolutionary science textbook and you'll find the same thing. That's something that can't be done for the personal connotations of terms, like Daniel's mishmash for "gradualism".

Now, as for "phyletic gradualism" being a term applicable to describing an actual stance on how the fossil record came to look the way it does, I've < long said > that it has a lot of the character of a strawman.

Actually, it is Daniel's claim that the fossil record is in a particular state. I'd be interested to know what experience Daniel has that would underwrite his confidence in his claim. But even more basic than that is getting some concrete idea of what the claim is... that is, I'd like to see some anchors tying the goalposts in place before going any much further with the game. As it stands, Daniel says that one doesn't see something in the fossil record, but he doesn't seem to have any clear notion of just what it is or what actual paleontologists would call it.
Posted by: George on Sep. 22 2007,18:03

Quote (Daniel Smith @ Sep. 22 2007,14:26)
Gradualism is what one would expect to see if the mechanism for evolutionary change were random mutations and natural selection.  If you think that it must entail entire populations and their entire geographical range, then fine - show that by the evidence in the fossil record.
---------------------QUOTE-------------------


You would only expect to see gradualism if natural selection pressures were relatively constant or changed only slowly.  If  selective forces change abruptly, would you not also expect to see rapid evolutionary change (and lots of extinctions)?  For example, we know that the climate in the past has changed very quickly, for example during shifts between ice ages and interglacial periods.
Posted by: Wesley R. Elsberry on Sep. 22 2007,18:51

No, you'd also expect gradualism (i.e., non-saltational change) if any incremental evolutionary process is in play, which would include genetic drift.
Posted by: JAM on Sep. 22 2007,21:05

Quote (Daniel Smith @ Sep. 22 2007,04:11)
Quote (JAM @ Sep. 20 2007,17:43)
   
Quote (Daniel Smith @ Sep. 20 2007,02:13)
I've also read recently, the excellent books "Evolution: A Theory in Crisis" and "Nature's Destiny" by Michael Denton.
---------------------QUOTE-------------------


Didja happen to notice that the latter book walks back from the position taken in the former book?
---------------------QUOTE-------------------


Not really.  In the first book, he doesn't really give us an alternative hypothesis; all he does is point out the many deficiencies of the currently held evolutionary theory.
---------------------QUOTE-------------------


Yes, really. In the first book, he treats the reader to such dishonest misrepresentations as a "purely random process of natural selection," as well as the somewhat more sublime idiocy of his failure to understand basic taxonomic relationships, as well as the idea that conserved amino-acid residues represent functional constraints, in his laughable centerpiece of cytochrome sequences.


---------------------QUOTE-------------------
In the second book, he starts to give us his own alternative: a designed universe and directed evolution.

I see no conflict.
---------------------QUOTE-------------------


That's predictable. Do you see any evidence? I'm struck by the mind-boggling conflict between your claim to be interested in evidence, while simultaneously conflating evidence with opinion.

Have you ever read a paper from the primary biological literature--you know, those ones that have new data in them?

Has Denton ever published any data? If not, why not?
Posted by: Daniel Smith on Sep. 22 2007,21:57

Quote (Peter Henderson @ Sep. 22 2007,11:43)
If you saw 10 clocks Daniel, and 9 of them were reading the same time and the tenth was different which one would you choose ? I know what I would think. I would assume the one that was different was in error.
---------------------QUOTE-------------------


We are talking about people here - not clocks.
If you were in a meeting, and nine out of ten people agreed with everything the boss said, but one disagreed, would you automatically go along with the 9 or listen closely to the 1?
Posted by: Daniel Smith on Sep. 22 2007,22:04

Quote (Wesley R. Elsberry @ Sep. 22 2007,17:13)
Actually, it is Daniel's claim that the fossil record is in a particular state. I'd be interested to know what experience Daniel has that would underwrite his confidence in his claim. But even more basic than that is getting some concrete idea of what the claim is... that is, I'd like to see some anchors tying the goalposts in place before going any much further with the game. As it stands, Daniel says that one doesn't see something in the fossil record, but he doesn't seem to have any clear notion of just what it is or what actual paleontologists would call it.
---------------------QUOTE-------------------


My main source for my argument about paleontology is Otto Schindewolf's "Basic Questions in Paleontology".  

I'm pretty sure Schindewolf qualifies as an "actual paleontologist".  

Did you read the quotes I supplied from that book in any of my posts so far?
Posted by: creeky belly on Sep. 23 2007,00:24



---------------------QUOTE-------------------

We are talking about people here - not clocks.
If you were in a meeting, and nine out of ten people agreed with everything the boss said, but one disagreed, would you automatically go along with the 9 or listen closely to the 1?
---------------------QUOTE-------------------


Except there is no authority here; if you follow the scientific method properly, there is no boss. I wouldn't use the clocks as an example, it reminds me of the fallacy: "50 million Elvis fans can't be wrong". The truth is that most scientists do use some sort of Bayesian approach to new claims, since there is a lot that we already know.
   

---------------------QUOTE-------------------
"As we all know, Darwin's theory of evolutionary descent asserts that organisms evolve slowly and very gradually through the smallest of individual steps, through the accumulation of an infinite number of small transformations.  Consequently, the fossil organic world would have to consist of an uninterrupted, undivided continuum of forms; as Darwin himself said, geological strata must be filled with the remains of every conceivable transitional form between taxonomic groups, between types of organizations and structural designs of differing magnitudes.
---------------------QUOTE-------------------


This assumes that fossilization is a uniform process throughout the lineage of a species. Unfortunately, fossilization is a relatively rare event, and to see such a process is very unlikely. This doesn't mean we see nothing.
   

---------------------QUOTE-------------------

Fossil material did not then and, based on the present state of our knowledge, does not today meet this challenge, not by a long shot. It is true that we know of countless lineages with continuous transformation, in as uninterrupted a sequence as could be desired.  However, each time we go back to the beginning of these consistent, abundantly documented series, we stand before an unbridgeable gulf.  The series break off and do not lead beyond the boundaries of their own particular structural type.  The link connecting them is not discernible; the individual structural designs stand apart, beside one another or in sequence, without true transitional forms"

---------------------QUOTE-------------------


This is demonstrably false. It's like staring at a puzzle after a few pieces have been laid out and saying "We'll never see the picture of Garfield." It's absurd. Look at whale evolution: this use to be trotted out by creationists as an impossible transition only to find that < it existed in the fossil record. >. You can quote this book all you want, but you're in a poor position to rebut considering that the book is about 60 years old. There have been numerous discoveries of transitional forms in fish, birds, and mammals since then, all of which dispute this point. This doesn't even get into disciplines like genetics, where you'll have an even worse time. Please continue, though. I'm interested what this man from the past thinks we'll never find.
Posted by: Daniel Smith on Sep. 23 2007,04:07

Quote (creeky belly @ Sep. 23 2007,00:24)
     

---------------------QUOTE-------------------
"As we all know, Darwin's theory of evolutionary descent asserts that organisms evolve slowly and very gradually through the smallest of individual steps, through the accumulation of an infinite number of small transformations.  Consequently, the fossil organic world would have to consist of an uninterrupted, undivided continuum of forms; as Darwin himself said, geological strata must be filled with the remains of every conceivable transitional form between taxonomic groups, between types of organizations and structural designs of differing magnitudes.
---------------------QUOTE-------------------


This assumes that fossilization is a uniform process throughout the lineage of a species. Unfortunately, fossilization is a relatively rare event, and to see such a process is very unlikely. This doesn't mean we see nothing.
---------------------QUOTE-------------------


Schindewolf was a paleontologist.  He knew how fossilization occurred.  To accuse him of assuming something when (I'm pretty sure) you haven't read the book is presumptuous.  He bases his arguments on a multitude of fossil lineages that are thoroughly understood. He spends 55 pages discussing evolutionary patterns among the Cephalopods and the Stony Corals.  He uses real world examples in support of his arguments.
   

---------------------QUOTE-------------------
and to see such a process is very unlikely.
---------------------QUOTE-------------------

But we do see it (transitional forms) over and over and over again - only they are not transitional between types, but only within types.  Now I ask you: Why is it that only these transitional forms are preserved?
           

---------------------QUOTE-------------------
   

---------------------QUOTE-------------------

Fossil material did not then and, based on the present state of our knowledge, does not today meet this challenge, not by a long shot. It is true that we know of countless lineages with continuous transformation, in as uninterrupted a sequence as could be desired.  However, each time we go back to the beginning of these consistent, abundantly documented series, we stand before an unbridgeable gulf.  The series break off and do not lead beyond the boundaries of their own particular structural type.  The link connecting them is not discernible; the individual structural designs stand apart, beside one another or in sequence, without true transitional forms"

---------------------QUOTE-------------------


This is demonstrably false. It's like staring at a puzzle after a few pieces have been laid out and saying "We'll never see the picture of Garfield." It's absurd. Look at whale evolution: this use to be trotted out by creationists as an impossible transition only to find that < it existed in the fossil record. >. You can quote this book all you want, but you're in a poor position to rebut considering that the book is about 60 years old. There have been numerous discoveries of transitional forms in fish, birds, and mammals since then, all of which dispute this point. This doesn't even get into disciplines like genetics, where you'll have an even worse time. Please continue, though. I'm interested what this man from the past thinks we'll never find.
---------------------QUOTE-------------------


Schindewolf had no arguments against whale evolution to my knowledge.  He did point out that - despite their similar habitats, ichthyosaurs and whales remained reptiles and mammals respectively and did not revert to "the organizations found in fish".  

You have to remember that Schindewolf is no creationist.  He advocated saltational evolution of types, followed by gradual evolution within types.  He did something remarkable: he tailored his views to fit the evidence rather than trying to make the evidence fit his views.
Posted by: oldmanintheskydidntdoit on Sep. 23 2007,04:12

Daniel,
Just to get a feel for your position, if we say that 100% is every living creature that ever existed then what % would you say are represented in the fossil record?

I.E what % of all living creatures fossilize?
Posted by: Daniel Smith on Sep. 23 2007,04:14

Quote (JAM @ Sep. 22 2007,21:05)
Has Denton ever published any data?
---------------------QUOTE-------------------



< Have a look. >

Have you?
Posted by: Daniel Smith on Sep. 23 2007,04:22

Quote (oldmanintheskydidntdoit @ Sep. 23 2007,04:12)
Daniel,
Just to get a feel for your position, if we say that 100% is every living creature that ever existed then what % would you say are represented in the fossil record?

I.E what % of all living creatures fossilize?
---------------------QUOTE-------------------


No idea.  

I have a question for you:
What % of transitional versus non-transitional forms are fossilized?

Is there some difference that makes the transitional forms more resistant to fossilization than their non-transitional counterparts?
Posted by: creeky belly on Sep. 23 2007,05:40



---------------------QUOTE-------------------
Schindewolf was a paleontologist.  He knew how fossilization occurred.  To accuse him of assuming something when (I'm pretty sure) you haven't read the book is presumptuous.  He bases his arguments on a multitude of fossil lineages that are thoroughly understood. He spends 55 pages discussing evolutionary patterns among the Cephalopods and the Stony Corals.  He uses real world examples in support of his arguments.
---------------------QUOTE-------------------


I'm sure he understood the process of fossilization and I've seen his data (although I'm surprised with the amount of life that's inhabited the planet compared to the number of fossils, he would be so shocked to see gaps in the fossil record. I guess he wanted a poster child for the transition). He could have spent 250 pages and it still wouldn't make a difference, this is not 1950. He used the evidence that he had at the time to construct an argument and made a case.  Now we have something like this:

< And here >
       

---------------------QUOTE-------------------

But we do see it (transitional forms) over and over and over again - only they are not transitional between types, but only within types.  Now I ask you: Why is it that only these transitional forms are preserved?
---------------------QUOTE-------------------


Do you mean "archetypes" like he writes on page 411? As he says: "In contrast, we stay with the objective natural data and strive to arrange the morphological steps in the system in their natural sequence." So let's look at fossils that have been discovered since 1950: how about the Therapsid-Mammal transition, are they far enough apart? Try Colbert and Morales (1991) or Strahler(1987). Reptile-Amphibian? < Try here. > Fish-Amphibian? < Try here! >


---------------------QUOTE-------------------
You have to remember that Schindewolf is no creationist.  He advocated saltational evolution of types, followed by gradual evolution within types.  He did something remarkable: he tailored his views to fit the evidence rather than trying to make the evidence fit his views.
---------------------QUOTE-------------------


Sure, and his ideas were shown through observation to be incomplete, and in most cases incorrect.
Posted by: Alan Fox on Sep. 23 2007,06:40



---------------------QUOTE-------------------
We are very lucky to have fossils at all. After an animal dies many conditions have to be met if it is to become a fossil, and one or other of those conditions usually is not met. Personally, I would consider it an honor to be fossilized but I don't have much hope of it. If all the creatures which had ever lived had in fact been fossilized we would be wading knee deep in fossils. The world would be filled with fossils. Perhaps it is just as well that it hasn't happened that way.

Because it is particularly difficult for an animal without a hard skeleton to be fossilized, most of the fossils we find are of animals with hard skeletons - vertebrates with bones, mollusks with their shells, arthropods with their external skeleton. If the ancestors of these were all soft and then same offspring evolved a hard skeleton, the only fossilized animals would be those more recent varieties. Therefore, we expect fossils to appear suddenly in the geologic record and that's one reason groups of animals suddenly appear in the Cambrian Explosion.

There are rare instances in which the soft parts of animals are preserved as fossils. One case is the famous Burgess Shale which is one of the best beds from the Cambrian Era (between 500 million and 600 million years ago) mentioned in this quotation. What must have happened is that the ancestors of these creatures were evolving by the ordinary slow processes of evolution, but they were evolving before the Cambrian when fossilizing conditions were not very good and many of them did not have skeletons anyway. It is probably genuinely true that in the Cambrian there was a very rapid flowering of multicellular life and this may have been when a large number of the great animal phyla did evolve. If they did, their essential divergence during a period of about 10 million years is very fast. However, bearing in mind the Stebbins calculation and the Nilsson calculation, it is actually not all that fast. There is some recent evidence from molecular comparisons among modern animals which suggests that there may not have been a Cambrian explosion at all, anyway. Modern phyla may well have their most recent common ancestors way back in the Precambrian.

As I said, we're actually lucky to have fossils at all. In any case, it is misleading to think that fossils are the most important evidence for evolution. Even if there were not a single fossil anywhere in the earth, the evidence for evolution would still be utterly overwhelming.* We would be in the position of a detective who comes upon a crime after the fact. You can't see the crime being committed because it has already happened. But there is evidence lying all around. To pursue any case, most detectives and most courts of law are happy with 2-3 clues that point in the right direction.
---------------------QUOTE-------------------

(*my emphasis)

< Richard Dawkins >
Posted by: jeannot on Sep. 23 2007,06:44

Quote (oldmanintheskydidntdoit @ Sep. 23 2007,04:12)
Daniel,
Just to get a feel for your position, if we say that 100% is every living creature that ever existed then what % would you say are represented in the fossil record?

I.E what % of all living creatures fossilize?
---------------------QUOTE-------------------


And multiply that by the % of fossils that are actually found by paleontologists.
Posted by: jeannot on Sep. 23 2007,06:49

Quote (Daniel Smith @ Sep. 23 2007,04:07)
But we do see it (transitional forms) over and over and over again - only they are not transitional between types, but only within types.  
---------------------QUOTE-------------------


What do you mean by different "types". Something like fishes and tetrapods, saurians and mammals, dinosaurs and birds...?
Posted by: JAM on Sep. 23 2007,10:31

Quote (Daniel Smith @ Sep. 23 2007,04:14)
Quote (JAM @ Sep. 22 2007,21:05)
Has Denton ever published any data?
---------------------QUOTE-------------------



< Have a look. >
---------------------QUOTE-------------------



No data that pertain to his two books. Why is that, Daniel? If he has any real passion about the subject(s) of his two books, why not test their assumptions, such as his idiotic assumption that conservation of a residue represents a functional constraint?



---------------------QUOTE-------------------
Have you?
---------------------QUOTE-------------------


Of course, and in better journals to boot. More pertinently, I've published more data relevnt to Denton's assumptions than he has. Why is that?
Posted by: JAM on Sep. 23 2007,10:37

Quote (Daniel Smith @ Sep. 22 2007,22:04)
 
Quote (Wesley R. Elsberry @ Sep. 22 2007,17:13)
...As it stands, Daniel says that one doesn't see something in the fossil record, but he doesn't seem to have any clear notion of just what it is or what actual paleontologists would call it.
---------------------QUOTE-------------------


My main source for my argument about paleontology is Otto Schindewolf's "Basic Questions in Paleontology".  
---------------------QUOTE-------------------


But that's a book, not the primary literature. Were you deliberately misleading us when you claimed to be interested in evidence?


---------------------QUOTE-------------------
I'm pretty sure Schindewolf qualifies as an "actual paleontologist".
---------------------QUOTE-------------------


But the opinions of an actual paleontologist aren't actual evidence.  


---------------------QUOTE-------------------
Did you read the quotes I supplied from that book in any of my posts so far?
---------------------QUOTE-------------------


But quotes aren't evidence, either.

You didn't answer my other pointed question: have you ever read a paper from the PRIMARY literature? I mean those papers with actual, new data in them--we real scientists often read them by looking at the figures and tables, because unlike you, we value evidence over opinion.
Posted by: JAM on Sep. 23 2007,10:43

Quote (Daniel Smith @ Sep. 23 2007,04:22)
Quote (oldmanintheskydidntdoit @ Sep. 23 2007,04:12)
Daniel,
Just to get a feel for your position, if we say that 100% is every living creature that ever existed then what % would you say are represented in the fossil record?

I.E what % of all living creatures fossilize?
---------------------QUOTE-------------------


No idea.
---------------------QUOTE-------------------


Then you have no basis for claiming that the incomplete nature of the fossil record represents a problem for modern evolutionary theory. 

I suggest that you look for the relevant evidence. Here's a place to start: passenger pigeons used to be common, now they are extinct. Has anyone ever found a fossilized one?



---------------------QUOTE-------------------
I have a question for you:
What % of transitional versus non-transitional forms are fossilized?
---------------------QUOTE-------------------


You'd have to know the answer, as well as the answer to oldman's question, to come to the conclusion you've already asserted.



---------------------QUOTE-------------------
Is there some difference that makes the transitional forms more resistant to fossilization than their non-transitional counterparts?
---------------------QUOTE-------------------


Are they more "resistant"? How would the concept of "resistance" work anyway, since the issue is one of sampling?
Posted by: Timothy McDougald on Sep. 23 2007,16:36

Quote (Daniel Smith @ Sep. 23 2007,04:07)
Quote (creeky belly @ Sep. 23 2007,00:24)
     

---------------------QUOTE-------------------
"As we all know, Darwin's theory of evolutionary descent asserts that organisms evolve slowly and very gradually through the smallest of individual steps, through the accumulation of an infinite number of small transformations.  Consequently, the fossil organic world would have to consist of an uninterrupted, undivided continuum of forms; as Darwin himself said, geological strata must be filled with the remains of every conceivable transitional form between taxonomic groups, between types of organizations and structural designs of differing magnitudes.
---------------------QUOTE-------------------


This assumes that fossilization is a uniform process throughout the lineage of a species. Unfortunately, fossilization is a relatively rare event, and to see such a process is very unlikely. This doesn't mean we see nothing.
---------------------QUOTE-------------------


Schindewolf was a paleontologist.  He knew how fossilization occurred.  To accuse him of assuming something when (I'm pretty sure) you haven't read the book is presumptuous.  He bases his arguments on a multitude of fossil lineages that are thoroughly understood. He spends 55 pages discussing evolutionary patterns among the Cephalopods and the Stony Corals.  He uses real world examples in support of his arguments.
     

---------------------QUOTE-------------------
and to see such a process is very unlikely.
---------------------QUOTE-------------------

But we do see it (transitional forms) over and over and over again - only they are not transitional between types, but only within types.  Now I ask you: Why is it that only these transitional forms are preserved?
           

---------------------QUOTE-------------------
   

---------------------QUOTE-------------------

Fossil material did not then and, based on the present state of our knowledge, does not today meet this challenge, not by a long shot. It is true that we know of countless lineages with continuous transformation, in as uninterrupted a sequence as could be desired.  However, each time we go back to the beginning of these consistent, abundantly documented series, we stand before an unbridgeable gulf.  The series break off and do not lead beyond the boundaries of their own particular structural type.  The link connecting them is not discernible; the individual structural designs stand apart, beside one another or in sequence, without true transitional forms"

---------------------QUOTE-------------------


This is demonstrably false. It's like staring at a puzzle after a few pieces have been laid out and saying "We'll never see the picture of Garfield." It's absurd. Look at whale evolution: this use to be trotted out by creationists as an impossible transition only to find that < it existed in the fossil record. >. You can quote this book all you want, but you're in a poor position to rebut considering that the book is about 60 years old. There have been numerous discoveries of transitional forms in fish, birds, and mammals since then, all of which dispute this point. This doesn't even get into disciplines like genetics, where you'll have an even worse time. Please continue, though. I'm interested what this man from the past thinks we'll never find.
---------------------QUOTE-------------------


Schindewolf had no arguments against whale evolution to my knowledge.  He did point out that - despite their similar habitats, ichthyosaurs and whales remained reptiles and mammals respectively and did not revert to "the organizations found in fish".  

You have to remember that Schindewolf is no creationist.  He advocated saltational evolution of types, followed by gradual evolution within types.  He did something remarkable: he tailored his views to fit the evidence rather than trying to make the evidence fit his views.
---------------------QUOTE-------------------


See, that is the kind of goal post moving Wesley is talking about. Going from land living artiodactyls to ocean going whales is a significant transition, one, I might add, that we have plenty of evidence for. We show him a transition between orders and he demands one between classes. Okay, the reptile mammal transition, which is quite well documented with transitional forms displaying a wide variety of transitional anatomy.

Although Schindewolf may have been a paleontologist, I doubt he had a very solid understanding of the fossilization process. Taphonomy - the study of fossilization - is a very young science. Efremov coined the term in the 1940's but the field didn't take off till the 1970's and 1980's. This is not to say that paleontologists were ignorant of how fossils form and the way the fossil record can be biased, rather we have progressed a good deal since then.

Daniel is mistaken if he thinks Schindewolf is presenting unbiased and unadulterated evidence. Schindewolf had his own theoretical preconceptions that he used to interpret the evidence. Seems to me that if he really wanted to see the evidence he would be looking at the fossils and not the interpretations of Schindewolf and Berg...
Posted by: Henry J on Sep. 23 2007,17:02



---------------------QUOTE-------------------
Daniel Smith
Is there some difference that makes the transitional forms more resistant to fossilization than their non-transitional counterparts?
---------------------QUOTE-------------------



One problem with trying to answer that is that there is no sharp dividing line between "transitional" and "non-transitional". A species is "transitional" if it (or a close relative) produces descendants significantly different than itself; that isn't even a property of the species itself at the time of fossilization, it's a historical occurance afterward.



---------------------QUOTE-------------------
oldmanintheskydidntdoit, posted 9/23/07 3:12 AM
Daniel,
Just to get a feel for your position, if we say that 100% is every living creature that ever existed then what % would you say are represented in the fossil record?

I.E what % of all living creatures fossilize?
---------------------QUOTE-------------------



I recall reading a few years ago that the number of fossil finds that had been studied was around 250 to 500 million. Since quite a few species have multiple finds, the number of species represented would be a good bit less than that.

I wonder how many species have lived in the last 500 million years - would that be more or less than 500 million?

Henry
Posted by: Henry J on Sep. 23 2007,17:04



---------------------QUOTE-------------------
Are they more "resistant"? How would the concept of "resistance" work anyway, since the issue is one of sampling?
---------------------QUOTE-------------------



Resistance is futile. :p

Henry
Posted by: Daniel Smith on Sep. 23 2007,17:17

Quote (JAM @ Sep. 23 2007,10:37)

But that's a book, not the primary literature.

But the opinions of an actual paleontologist aren't actual evidence.  

But quotes aren't evidence, either.
---------------------QUOTE-------------------


How about opinions quoted from a book by Richard Dawkins?
Posted by: jeannot on Sep. 23 2007,17:34

Quote (Daniel Smith @ Sep. 23 2007,17:17)
 
Quote (JAM @ Sep. 23 2007,10:37)

But that's a book, not the primary literature.

But the opinions of an actual paleontologist aren't actual evidence.  

But quotes aren't evidence, either.
---------------------QUOTE-------------------


How about opinions quoted from a book by Richard Dawkins?
---------------------QUOTE-------------------


They don't constitute original research either, but at least they are arguments. Not like some "John Do says that the fossil record disproves gradualism".
If you want to disprove the current theory, you have to provide some new evidence or a better interpretation of the observations.

You first need to define what you call "transitional species" between "types".
Posted by: jeannot on Sep. 23 2007,17:48

Quote (Henry J @ Sep. 23 2007,17:02)
I recall reading a few years ago that the number of fossil finds that had been studied was around 250 to 500 million. Since quite a few species have multiple finds, the number of species represented would be a good bit less than that.

I wonder how many species have lived in the last 500 million years - would that be more or less than 500 million?

Henry
---------------------QUOTE-------------------


500 million fossils would probably represent at most a million of species, perhaps much less.
Given speciation rates and estimations of current biodiversity, hundreds of billions of species may have lived since the cambrian. I'm not sure if there is an estimation of that number.
What would be interesting is an estimation of the total number of fossil specices for a given group (say animals with skeleton) and a given time range of 1-5 million years. For instance, from -125 to -100 million years. I guess this number is always WAY smaller that the number of known living species of the same group.
Posted by: Erasmus, FCD on Sep. 23 2007,18:29

So I haven't been keeping up so much recently and this is a new thread to me.

Daniel, it seems that you are arguing that there is some bound that constrains evolutionary transition.  I am curious as to why you assume this must be.  As I see it, you either accept that speciation occurs, or it doesn't.  If you accept that it does, then the supposed macro-micro boundary dissolves instantly (indeed, it is a figment of imagination, suriving in the literature because it is a useful fiction for narrative exposition, like any other model).  Why do you invoke boundaries, unless you are wedded to a phenotypical model of evolution?

So you ask about 'transitional forms'.  I can point to several instances of speciation observed and/or reconstructed that do not involve transitional forms.  I would start by pointing out the speciation events that involve contact between lineages of Helianthus sunflowers (see Rieseberg, Nature a few years ago) or the ecological speciation event in Rhagoletis dipterans.  There is no transition.  This does not deny Wesley's point about the gradual process, but it does invoke a question "At what temporal scale do we intend 'gradual' to refer to", I believe this has been addressed above.  The argument against transitional forms or lineages boils down to an assertion that Zeno's Paradox is a true problem.

[Edited to add] And we know that it is not, because I just went to the store.  And I returned as well.

So the saltational opinion can be resolved with the gradualist opinion by virtue of considering that the terms are not necessarily referential to an absolute scale.
Posted by: lkeithlu on Sep. 23 2007,20:18

Daniel wrote:

"I have a question for you:
What % of transitional versus non-transitional forms are fossilized?

Is there some difference that makes the transitional forms more resistant to fossilization than their non-transitional counterparts?"

Does this make sense? The only thing that distinguishes transitional vs non-transitional is order of find, isn't it? A fossil is a fossil; if you find two and then later find a third that seems to be a transition between them, that doesn't make them different as far as fossilization, just how the third fits into the already existing collection. Or am I missing something?
Posted by: Daniel Smith on Sep. 23 2007,22:01

Quote (creeky belly @ Sep. 23 2007,05:40)
I'm sure he understood the process of fossilization and I've seen his data (although I'm surprised with the amount of life that's inhabited the planet compared to the number of fossils, he would be so shocked to see gaps in the fossil record. I guess he wanted a poster child for the transition). He could have spent 250 pages and it still wouldn't make a difference, this is not 1950. He used the evidence that he had at the time to construct an argument and made a case.  Now we have something like this:

< And here >
---------------------QUOTE-------------------


The saltational events that Schindewolf proposed would go where the dotted lines are on your chart - the part subtitled "suggested lines of descent".             

---------------------QUOTE-------------------

Do you mean "archetypes" like he writes on page 411? As he says: "In contrast, we stay with the objective natural data and strive to arrange the morphological steps in the system in their natural sequence." So let's look at fossils that have been discovered since 1950: how about the Therapsid-Mammal transition, are they far enough apart? Try Colbert and Morales (1991) or Strahler(1987). Reptile-Amphibian? < Try here. > Fish-Amphibian? < Try here! >

---------------------QUOTE-------------------


I don't have the book in front of me right now, so I'll have to get back to you on that.
Posted by: k.e on Sep. 23 2007,22:37



---------------------QUOTE-------------------
...so I'll have to get back to you on that.
---------------------QUOTE-------------------



You do that Daniel don't take too long...or change the subject *Snicker*.
Posted by: Daniel Smith on Sep. 24 2007,04:52

Quote (Alan Fox @ Sep. 23 2007,06:40)
       

---------------------QUOTE-------------------
We are very lucky to have fossils at all. After an animal dies many conditions have to be met if it is to become a fossil, and one or other of those conditions usually is not met. Personally, I would consider it an honor to be fossilized but I don't have much hope of it. If all the creatures which had ever lived had in fact been fossilized we would be wading knee deep in fossils. The world would be filled with fossils. Perhaps it is just as well that it hasn't happened that way.

Because it is particularly difficult for an animal without a hard skeleton to be fossilized, most of the fossils we find are of animals with hard skeletons - vertebrates with bones, mollusks with their shells, arthropods with their external skeleton. If the ancestors of these were all soft and then same offspring evolved a hard skeleton, the only fossilized animals would be those more recent varieties. Therefore, we expect fossils to appear suddenly in the geologic record and that's one reason groups of animals suddenly appear in the Cambrian Explosion.

There are rare instances in which the soft parts of animals are preserved as fossils. One case is the famous Burgess Shale which is one of the best beds from the Cambrian Era (between 500 million and 600 million years ago) mentioned in this quotation. What must have happened is that the ancestors of these creatures were evolving by the ordinary slow processes of evolution, but they were evolving before the Cambrian when fossilizing conditions were not very good and many of them did not have skeletons anyway. It is probably genuinely true that in the Cambrian there was a very rapid flowering of multicellular life and this may have been when a large number of the great animal phyla did evolve. If they did, their essential divergence during a period of about 10 million years is very fast. However, bearing in mind the Stebbins calculation and the Nilsson calculation, it is actually not all that fast. There is some recent evidence from molecular comparisons among modern animals which suggests that there may not have been a Cambrian explosion at all, anyway. Modern phyla may well have their most recent common ancestors way back in the Precambrian.

As I said, we're actually lucky to have fossils at all. In any case, it is misleading to think that fossils are the most important evidence for evolution. Even if there were not a single fossil anywhere in the earth, the evidence for evolution would still be utterly overwhelming.* We would be in the position of a detective who comes upon a crime after the fact. You can't see the crime being committed because it has already happened. But there is evidence lying all around. To pursue any case, most detectives and most courts of law are happy with 2-3 clues that point in the right direction.
---------------------QUOTE-------------------

(*my emphasis)

< Richard Dawkins >
---------------------QUOTE-------------------


Of course I am not surprised at all that Dawkins would minimize the importance of the fossil record.  Surely if it teemed with evidence for his theory, he would feel differently about it.

I am a bit surprised that he thinks the theory of evolution via RM+NS is essentially beyond reproach.  I read through his lecture (which I mistakenly referred to as a book earlier) and I looked for this "utterly overwhelming" evidence he speaks of, but did not find it.

From the same lecture:
       

---------------------QUOTE-------------------
These are all domestic dogs (Slide 1) except the top one which is a wolf. The point of it is, as observed by Darwin, how remarkable that we could go by human artificial selection from a wolf ancestor to all these breeds - a Great Dane, a Bulldog, a Whippet, etc. They were all produced by a process analogous to natural selection - artificial selection. Humans did the choosing whereas in natural selection, as you know, it is nature that does the choosing. Nature selects the ones that survive and are good at reproducing, to leave their genes behind. With artificial selection, humans do the choosing of which dogs should breed and with whom they should mate.

These plants (Slide 2) are all members of the same species. They are all descended quite recently from the wild cabbage Brassica olearacea and they are very different cauliflower, brussels sprouts, kale, broccoli, etc. This great variety of vegetables, which look completely different, has been shaped - they have been sculpted - by the process of artificial selection from the same common ancestor.
---------------------QUOTE-------------------


The problem with Dawkins' logic here is that it doesn't match reality:

(As you and I have discussed before), artificial selection is not "analogous to natural selection", as Dawkins argues. Artificial selection only works by shielding organisms from natural selection.

Throw all domesticated dogs back into the wild and watch as all these breeds go away - to be replaced by mutt dogs which will gradually lose many of their unique, bred-for characteristics and more and more closely resemble the wolf from which they came.

The same goes for these cultivated plants.  Throw them back into the wild and eventually they revert back to the original wild cabbage species - all the domesticated varieties would disappear.

These things can be verified in your own back yard.
Posted by: Albatrossity2 on Sep. 24 2007,06:12

Quote (Daniel Smith @ Sep. 24 2007,04:52)
Throw all domesticated dogs back into the wild and watch as all these breeds go away - to be replaced by mutt dogs which will gradually lose many of their unique, bred-for characteristics and more and more closely resemble the wolf from which they came.
---------------------QUOTE-------------------


The fact that dogs under artificial selection have one set of characters, and another set of characters when they are feral and subject to a different kind of selective pressure, is not a problem for evolutionary theory. It is, in fact, a prediction of that theory.

Do you have any testable predictions from your theory (whatever it is at the moment) that would lead to a different outcome than that predicted by evolutionary theory?
Posted by: Erasmus, FCD on Sep. 24 2007,08:44

Daniel, it is also not true.  the genetic milieu is changed by selection (artificial is just another form, and it's not really artificial is it?  unless you are arguing it is sooooopernatcheral).

offspring of different lineages (or hybrids if you will) can have phenotypes that are completely outside the range of variation in the parents.  if there is any positive selective pressure on those traits then they will persist.  if there is then a mate preference, they will diverge.  it is that simple, and 'throwing dogs into the wild and they all turn back into wolves' is just wrong for a litany of reasons.  think about why that might be.  no way can a chihuaha turn 'back into' a wolf.  for one, it never was one.

fancy types of lettuce don't go back to being one single muddy lettuce, there is a quantitative legacy of mutation and selection.  same as the dogs.  new traits can be formed from recombination during contact between different lineages (See the Helianthus sunflower examples, it blows your contentions out of the water in the first paragraph)
Posted by: improvius on Sep. 24 2007,09:12

Quote (Daniel Smith @ Sep. 24 2007,05:52)
(As you and I have discussed before), artificial selection is not "analogous to natural selection", as Dawkins argues. Artificial selection only works by shielding organisms from natural selection.
---------------------QUOTE-------------------


So you actually think that by simply removing natural selection, dogs just magically developed into all of these breeds with very specific purposes?  That's absurd.
Posted by: JAM on Sep. 24 2007,10:58

Quote (Daniel Smith @ Sep. 24 2007,04:52)
     

---------------------QUOTE-------------------
Even if there were not a single fossil anywhere in the earth, the evidence for evolution would still be utterly overwhelming.*
< Richard Dawkins >
---------------------QUOTE-------------------


Of course I am not surprised at all that Dawkins would minimize the importance of the fossil record.
---------------------QUOTE-------------------


You're quote mining, Daniel, and avoiding the real evidence.

He's not minimizing its importance. He's pointing out that evidence from other sources is much more extensive and complete:
 

---------------------QUOTE-------------------
The evidence comes from comparative studies of modern animals. If you look at the millions of modern species and compare them with each other - looking at the comparative evidence of biochemistry, especially molecular evidence - you get a pattern, an exceedingly significant pattern, whereby some pairs of animals like rats and mice are very similar to each other. Other pairs of animals like rats and squirrels are a bit more different. Pairs like rats and porcupines are a bit more different still in all their characteristics. Others like rats and humans are a bit more different still, and so forth. The pattern that you see is a pattern of cousinship; that is the only way to interpret it. Some are close cousins like rats and mice; others are slightly more distant cousins (rats and porcupines) which means they have a common ancestor that lived a bit longer ago. More distinctly different cousins like rats and humans had a common ancestor who lived a bit longer ago still. Every single fact that you can find about animals is compatible with that pattern.
---------------------QUOTE-------------------





---------------------QUOTE-------------------
Surely if it teemed with evidence for his theory, he would feel differently about it.
---------------------QUOTE-------------------


He's saying that other sources are more complete and more than sufficient. That's why creationists generally avoid discussing the sequence evidence, and when they do, they grossly misrepresent it.

How many trees have you constructed from sequences (evidence) using tools like CLUSTAL and BLAST, Daniel?

 

---------------------QUOTE-------------------
I am a bit surprised that he thinks the theory of evolution via RM+NS is essentially beyond reproach.
---------------------QUOTE-------------------



That's because you're afraid of grappling with evidence for yourself. If you any real confidence in your position, you'd be discussing evidence instead of quote mining.

 

---------------------QUOTE-------------------
I read through his lecture (which I mistakenly referred to as a book earlier) and I looked for this "utterly overwhelming" evidence he speaks of, but did not find it.
---------------------QUOTE-------------------


What part of this don't you understand?
 

---------------------QUOTE-------------------
If you look at the millions of modern species and compare them with each other - looking at the comparative evidence of biochemistry, especially molecular evidence - you get a pattern, an exceedingly significant pattern, whereby some pairs of animals like rats and mice are very similar to each other.
---------------------QUOTE-------------------


 

---------------------QUOTE-------------------
The same goes for these cultivated plants.  Throw them back into the wild and eventually they revert back to the original wild cabbage species - all the domesticated varieties would disappear.

These things can be verified in your own back yard.
---------------------QUOTE-------------------


And have you done so?
Posted by: k.e on Sep. 24 2007,11:05

Crikey Daniel has extensive experience 'in the wild'


---------------------QUOTE-------------------
These things can be verified in your own back yard.
---------------------QUOTE-------------------



We don't stand a chance.
Posted by: VMartin on Sep. 24 2007,13:10

Uf, it seems you are having hard time here. Your arguments refuting Adam Smith's opinions are very weak I would say.

1) If you think that Schindewolf was wrong, do you think the same about Gould and Eldredge? You know their conception of Punctuated Equilibria. Do you really think that Schindewolf was as wrong as was Gould?

Gould 1987:

The extreme rarity of transitional forms in the fossil record persist as the trade secret of paleontology. The evolutionary trees that adorn our textbooks have data only at the tips and nodes of their branches; the rest is inference, however reasonable, not the evidence of fossils ….



2) If Dawkins thinks that dogs somehow support evolution in darwinian way, he should show us some speciation. Dogs are only dogs whatever you do with them. You only work with pre-existing variability which are showed up by breeding.

Btw. the great Dawkins seeing the picture from 19 century painted by 17 years old yougster came to this ridiculous conclusion:

   

---------------------QUOTE-------------------

Or a heavyset, thick-coated wolf, strong enough to carry a cask of brandy, that thrives in Alpine passes and might be named after one of them, the St. Bernard?

---------------------QUOTE-------------------



Bernard has never carried a cask of brandy. It is only in Dawkins imagination that he "is strong enough" to carry it. Maybe he would be surprised if he checked it in reality.

Another Dawkins fantasy - I can discuss it in detail at another thread if you like - is his explanation of origin of mimicry. He often offers only his imagination instead of facts .
Posted by: improvius on Sep. 24 2007,14:00

Quote (VMartin @ Sep. 24 2007,14:10)
2) If Dawkins thinks that dogs somehow support evolution in darwinian way, he should show us some speciation. Dogs are only dogs whatever you do with them. You only work with pre-existing variability which are showed up by breeding.
---------------------QUOTE-------------------


It seems obvious that artificial selection pressures have resulted in a wide variation of dog phenotypes in a very short amount of time.  Whether or not these are "species" by any rigorous definition is irrelevant.  The point is that selection pressures can produce physical variation.
Posted by: Daniel Smith on Sep. 24 2007,14:54

Quote (JAM @ Sep. 24 2007,10:58)
 
Quote (Daniel Smith @ Sep. 24 2007,04:52)
         

---------------------QUOTE-------------------
Even if there were not a single fossil anywhere in the earth, the evidence for evolution would still be utterly overwhelming.*
< Richard Dawkins >
---------------------QUOTE-------------------


Of course I am not surprised at all that Dawkins would minimize the importance of the fossil record.
---------------------QUOTE-------------------


You're quote mining, Daniel, and avoiding the real evidence.

---------------------QUOTE-------------------


It wasn't my quote so how could I be "mining" it?
 

---------------------QUOTE-------------------

He's not minimizing its importance. He's pointing out that evidence from other sources is much more extensive and complete:
     

---------------------QUOTE-------------------
The evidence comes from comparative studies of modern animals. If you look at the millions of modern species and compare them with each other - looking at the comparative evidence of biochemistry, especially molecular evidence - you get a pattern, an exceedingly significant pattern, whereby some pairs of animals like rats and mice are very similar to each other. Other pairs of animals like rats and squirrels are a bit more different. Pairs like rats and porcupines are a bit more different still in all their characteristics. Others like rats and humans are a bit more different still, and so forth. The pattern that you see is a pattern of cousinship; that is the only way to interpret it. Some are close cousins like rats and mice; others are slightly more distant cousins (rats and porcupines) which means they have a common ancestor that lived a bit longer ago. More distinctly different cousins like rats and humans had a common ancestor who lived a bit longer ago still. Every single fact that you can find about animals is compatible with that pattern.
---------------------QUOTE-------------------


Big deal.  Things that are alike are built alike - even at the molecular level.  No one disputes this. What the molecular evidence shows, however is not always consistent with RM+NS.  For instance, Denton points out the "Molecular Equidistance of all Eucaryotic Organisms from Bacteria" (in "Evolution: A Theory In Crisis", Figure 12.2, page 280), which is more consistent with the Schindewolf/Berg/Davison et al hypotheses of prescribed/directed/planned/designed evolution.

   

---------------------QUOTE-------------------
Surely if it teemed with evidence for his theory, he would feel differently about it.
---------------------QUOTE-------------------


He's saying that other sources are more complete and more than sufficient. That's why creationists generally avoid discussing the sequence evidence, and when they do, they grossly misrepresent it.

How many trees have you constructed from sequences (evidence) using tools like CLUSTAL and BLAST, Daniel?

---------------------QUOTE-------------------


None.  And in answer to your previous question about the primary literature:  I read what I can online.  I've often searched for articles on google scholar, but most require memberships to read - so I am not nearly as well informed as you I'm sure.
   

---------------------QUOTE-------------------
   

---------------------QUOTE-------------------
I am a bit surprised that he thinks the theory of evolution via RM+NS is essentially beyond reproach.
---------------------QUOTE-------------------



That's because you're afraid of grappling with evidence for yourself. If you any real confidence in your position, you'd be discussing evidence instead of quote mining.

---------------------QUOTE-------------------


I didn't quote mine.  And I'm happy to discuss any evidence you want to discuss.  It may take me awhile to understand what you're getting at sometimes and you may have to bring it down to my level, but don't accuse me of not being willing to discuss evidence when you haven't even given me the chance.

---------------------QUOTE-------------------

     

---------------------QUOTE-------------------
I read through his lecture (which I mistakenly referred to as a book earlier) and I looked for this "utterly overwhelming" evidence he speaks of, but did not find it.
---------------------QUOTE-------------------


What part of this don't you understand?
     

---------------------QUOTE-------------------
If you look at the millions of modern species and compare them with each other - looking at the comparative evidence of biochemistry, especially molecular evidence - you get a pattern, an exceedingly significant pattern, whereby some pairs of animals like rats and mice are very similar to each other.
---------------------QUOTE-------------------


---------------------QUOTE-------------------


I understand all of it.  None of it is inconsistent with Nomogenesis, Orthogenesis, or the PEH.  

---------------------QUOTE-------------------

     

---------------------QUOTE-------------------
The same goes for these cultivated plants.  Throw them back into the wild and eventually they revert back to the original wild cabbage species - all the domesticated varieties would disappear.

These things can be verified in your own back yard.
---------------------QUOTE-------------------


And have you done so?
---------------------QUOTE-------------------


No, but Berg cites many examples of similar types of experiments.  His arguments against evolution via natural selection are very well constructed and empirically based.
Posted by: oldmanintheskydidntdoit on Sep. 24 2007,14:59

Quote (Daniel Smith @ Sep. 24 2007,14:54)
the PEH
---------------------QUOTE-------------------


not the PEH surely?
Posted by: Daniel Smith on Sep. 24 2007,15:02

Quote (creeky belly @ Sep. 23 2007,05:40)
Do you mean "archetypes" like he writes on page 411? As he says: "In contrast, we stay with the objective natural data and strive to arrange the morphological steps in the system in their natural sequence." So let's look at fossils that have been discovered since 1950: how about the Therapsid-Mammal transition, are they far enough apart? Try Colbert and Morales (1991) or Strahler(1987). Reptile-Amphibian? < Try here. > Fish-Amphibian? < Try here! >
---------------------QUOTE-------------------


I'm not sure what you're arguing against here.  The passage you quoted was from the chapter on taxonomy and he was discussing phylogenetic classification (which he deemed subjective) as opposed to morphological classification (which he called objective).  

You seem to be arguing as if he denied common descent or evolution in general.  He denied neither.  His contention was with the mechanism of evolution.

Schindewolf proposed that evolution proceeded according to patterns.  He gave the example of the marsupial and placental wolves.  These obviously unrelated animals developed eerily similar features quite independently of each other.  

He also proposed that evolution proceeded as if constrained by a goal.  He gives the example of the evolution of the one-toed foot on the horse - which began long before the horse moved onto the plains and the one-toed foot became advantageous.

He also proposed that evolution occurred during ontogeny and gave several examples of ammonoid suture and coral septal apparatus evolution to support his views.

Again, I'm not sure what you are arguing against.
Posted by: jeannot on Sep. 24 2007,15:06

Quote (VMartin @ Sep. 24 2007,13:10)
2) If Dawkins thinks that dogs somehow support evolution in darwinian way, he should show us some speciation. Dogs are only dogs whatever you do with them. You only work with pre-existing variability which are showed up by breeding.
---------------------QUOTE-------------------


Martin,
You apparently have access to a broad array of scientific journals. You haven't missed the hundreds of speciation cases that have been studied, then published during the last years, have you?
Posted by: VMartin on Sep. 24 2007,15:14

Quote (jeannot @ Sep. 24 2007,15:06)
Quote (VMartin @ Sep. 24 2007,13:10)
2) If Dawkins thinks that dogs somehow support evolution in darwinian way, he should show us some speciation. Dogs are only dogs whatever you do with them. You only work with pre-existing variability which are showed up by breeding.
---------------------QUOTE-------------------


Martin,
You apparently have access to a broad array of scientific journals. You haven't missed the hundreds of speciation cases that have been studied, then published during the last years, have you?
---------------------QUOTE-------------------


I have somehow missed any speciation from dogs. Or which ones do you have on mind?
Posted by: improvius on Sep. 24 2007,15:21

Quote (VMartin @ Sep. 24 2007,16:14)
Quote (jeannot @ Sep. 24 2007,15:06)
 
Quote (VMartin @ Sep. 24 2007,13:10)
2) If Dawkins thinks that dogs somehow support evolution in darwinian way, he should show us some speciation. Dogs are only dogs whatever you do with them. You only work with pre-existing variability which are showed up by breeding.
---------------------QUOTE-------------------


Martin,
You apparently have access to a broad array of scientific journals. You haven't missed the hundreds of speciation cases that have been studied, then published during the last years, have you?
---------------------QUOTE-------------------


I have somehow missed any speciation from dogs. Or which ones do you have on mind?
---------------------QUOTE-------------------


I'm pretty sure creationists are the only people claiming that there has been massive speciation from dogs over the past few thousand years.
Posted by: Henry J on Sep. 24 2007,15:23

To me it seems at least possible that dog breeders were primarily interesting in getting particular features in their breeds. Obtaining a speciation event was probably not their goal. I wonder if speciation would even be consistent with the usual goals of breeders, since it would limit the possibility of crossing their breed with another in order to import different genes.

Henry
Posted by: C.J.O'Brien on Sep. 24 2007,15:35

The only aspect of "artificial" selection in dogs that's really artificial is the fact that theoretically any breed of canis familiaris can produce viable offspring with any other. We've artficially suppressed speciation.

But how long would it take a population of chihuahuas and a population of great danes to fully speciate in wild conditions?

As a rule, creationists abuse the concept[s] of speciation.
< Ring Species > are illustrative of the complexities that are always ignored in this type of argument.
Posted by: jeannot on Sep. 24 2007,15:38

Quote (C.J.O'Brien @ Sep. 24 2007,15:35)
The only aspect of "artificial" selection in dogs that's really artificial is the fact that theoretically any breed of canis familiaris can produce viable offspring with any other. We've artficially suppressed speciation.

But how long would it take a population of chihuahuas and a population of great danes to fully speciate in wild conditions?
---------------------QUOTE-------------------


That's an instance of mechanical isolation. They certainly can't mate and could be considered as true species.
Posted by: Henry J on Sep. 24 2007,15:47

That's kind of analogous to ring species, but without the geographic aspect of it.

Henry
Posted by: jeannot on Sep. 24 2007,15:50

Quote (VMartin @ Sep. 24 2007,15:14)
Quote (jeannot @ Sep. 24 2007,15:06)
 
Quote (VMartin @ Sep. 24 2007,13:10)
2) If Dawkins thinks that dogs somehow support evolution in darwinian way, he should show us some speciation. Dogs are only dogs whatever you do with them. You only work with pre-existing variability which are showed up by breeding.
---------------------QUOTE-------------------


Martin,
You apparently have access to a broad array of scientific journals. You haven't missed the hundreds of speciation cases that have been studied, then published during the last years, have you?
---------------------QUOTE-------------------


I have somehow missed any speciation from dogs. Or which ones do you have on mind?
---------------------QUOTE-------------------


It seemed to me you were looking for some speciation event, not especially in dogs.

But you remark was irrelevant. Evolution "in Darwinian way" is not synonymous with speciation.
Posted by: jeannot on Sep. 24 2007,15:55

Quote (Henry J @ Sep. 24 2007,15:47)
That's kind of analogous to ring species, but without the geographic aspect of it.

Henry
---------------------QUOTE-------------------


That's what I think.
I wonder if there is a review paper about it. If not, some expert should publish one.
Apparently, speciation in dogs races is hardly studied.
Posted by: JAM on Sep. 24 2007,16:02

Quote (Daniel Smith @ Sep. 24 2007,14:54)
It wasn't my quote so how could I be "mining" it?
---------------------QUOTE-------------------


Very easily.
 

---------------------QUOTE-------------------
 

---------------------QUOTE-------------------
He's not minimizing its importance. He's pointing out that evidence from other sources is much more extensive and complete:
           

---------------------QUOTE-------------------
The evidence comes from comparative studies of modern animals. If you look at the millions of modern species and compare them with each other - looking at the comparative evidence of biochemistry, especially molecular evidence - you get a pattern, an exceedingly significant pattern, whereby some pairs of animals like rats and mice are very similar to each other. Other pairs of animals like rats and squirrels are a bit more different. Pairs like rats and porcupines are a bit more different still in all their characteristics. Others like rats and humans are a bit more different still, and so forth. The pattern that you see is a pattern of cousinship; that is the only way to interpret it. Some are close cousins like rats and mice; others are slightly more distant cousins (rats and porcupines) which means they have a common ancestor that lived a bit longer ago. More distinctly different cousins like rats and humans had a common ancestor who lived a bit longer ago still. Every single fact that you can find about animals is compatible with that pattern.
---------------------QUOTE-------------------


---------------------QUOTE-------------------


Big deal.  Things that are alike are built alike - even at the molecular level.
---------------------QUOTE-------------------


That's not remotely close to what he's saying. He's talking about mathematical analyses of the similarities AND DIFFERENCES. They fit nested hierarchies. The hierarchies of the organisms can be superimposed upon the hierarchies of their components, which are even more complex, because we can see how different proteins are related to each other.

Oh, and Daniel, no set of designed objects has these characteristics, so please save your lying for ignorant lay people.


---------------------QUOTE-------------------
No one disputes this.
---------------------QUOTE-------------------


Which is why you employ it as a straw man.


---------------------QUOTE-------------------
What the molecular evidence shows, however is not always consistent with RM+NS.
---------------------QUOTE-------------------


Obviously, much of it is consistent with drift, which is not RM+NS, and a small subset is consistent with horizontal transfer.

If you had the slightest clue, you'd know that modern evolutionary theory is not limited to RM+NS.


---------------------QUOTE-------------------
For instance, Denton points out the "Molecular Equidistance of all Eucaryotic Organisms from Bacteria" (in "Evolution: A Theory In Crisis", Figure 12.2, page 280), which is more consistent with the Schindewolf/Berg/Davison et al hypotheses of prescribed/directed/planned/designed evolution.
---------------------QUOTE-------------------


No. Denton fundamentally misunderstood evolutionary theory, and has since backtracked on that ignorant claim. MET (particularly drift) predicts that. Denton assumed a ladder, not a bush.


---------------------QUOTE-------------------
None.
---------------------QUOTE-------------------


Why not construct some trees, then, unless you weren't being truthful about your interest in evidence?


---------------------QUOTE-------------------
And in answer to your previous question about the primary literature:  I read what I can online.
---------------------QUOTE-------------------


That doesn't answer my question. Have you ever read a paper from the primary literature?


---------------------QUOTE-------------------
I've often searched for articles on google scholar, but most require memberships to read - so I am not nearly as well informed as you I'm sure.
---------------------QUOTE-------------------


So why do you consider your uninformed conclusions to be more correct than mine?


---------------------QUOTE-------------------
And I'm happy to discuss any evidence you want to discuss.
---------------------QUOTE-------------------


Let's discuss this paper, then:
< http://www.biolbull.org/cgi/content/full/202/2/104 >
...let's start with Figure 2. Note that vertical line length is irrelevant, only the horizontal lines represent sequence divergence.


---------------------QUOTE-------------------
It may take me awhile to understand what you're getting at sometimes and you may have to bring it down to my level, but don't accuse me of not being willing to discuss evidence when you haven't even given me the chance.
---------------------QUOTE-------------------


Sorry, but you're supposed to familiarize yourself with the evidence before reaching a firm conclusion.


---------------------QUOTE-------------------


---------------------QUOTE-------------------
What part of this don't you understand?

---------------------QUOTE-------------------

I understand all of it.  None of it is inconsistent with Nomogenesis, Orthogenesis, or the PEH.      
---------------------QUOTE-------------------


I don't think you understand it at all, since you blew it off as mere similarity.


---------------------QUOTE-------------------
No, but Berg cites many examples of similar types of experiments.  His arguments against evolution via natural selection are very well constructed and empirically based.
---------------------QUOTE-------------------


To know that, you'd have to be familiar with the evidence, not just that someone offered citations. Are you familiar with these data, or are you faking it? Do you realize that science is not about appraising arguments, but about predicting and grappling with the actual evidence, not what anyone says about it?
Posted by: jeannot on Sep. 24 2007,16:38



---------------------QUOTE-------------------
Big deal.  Things that are alike are built alike - even at the molecular level.
---------------------QUOTE-------------------


If you're going to argue for "common design" as we see you coming, you'll have to explain why closely related species share homologies at synonymous or neutral sites, which have nothing to do with "design".
For instance, why do all primates share a non-functional copy of a gene normally involved in the production of vitamin C? And why do the phylogeny of this useless pseudo-gene reflects phylogenies of coding regions?

And also, why are we more genetically close to the coelacanth than it is close to the trout?
The irony is that the fossil record, which according to you disproves the ToE, predicted that.
Posted by: JAM on Sep. 24 2007,16:58

Quote (jeannot @ Sep. 24 2007,16:38)


---------------------QUOTE-------------------
Big deal.  Things that are alike are built alike - even at the molecular level.
---------------------QUOTE-------------------


If you're going to argue for "common design" as we see you coming, you'll have to explain why closely related species share homologies at synonymous or neutral sites, which have nothing to do with "design".
---------------------QUOTE-------------------


That's what I'm trying to do with the cannabinoid receptor paper.


---------------------QUOTE-------------------
For instance, why do all primates share a non-functional copy of a gene normally involved in the production of vitamin C? And why do the phylogeny of this useless pseudo-gene reflects phylogenies of coding regions?
---------------------QUOTE-------------------


That might be too complex, as well as getting into Daniel's likely misconceptions about pseudogenes and "junk" DNA.
Posted by: Reciprocating Bill on Sep. 24 2007,17:58

Holy shit. Another one.

Daniel starts with this admission:
 

---------------------QUOTE-------------------
I myself am no scientist.  As far as formal training, I'm more than ignorant. What little I know has been self taught.
---------------------QUOTE-------------------


Full Stop.

Daniel: based upon your own self-description, we need no longer give the slightest attention to your thoughts on evolutionary biology. You don't know shit from Shinola on the topic, by your own admission. Plus your wingtips stink.

Daniel admits abject ignorance of contemporary evolutionary science, yet nevertheless feels qualified to reject a priori the hard won findings of a community of thousands of scientists laboring over decades in an attempt to better understand the history of life on earth. Moreover, he prefers a priori a handful of crackpots and outliers who "work" outside the scientific community and whose ideas have been ridiculed, shunned, and forgotten by that community. In short, although he claims interest in the work of scientists who themselves operate "free of preconceptions," he freely admits being motivated by the biased assumptions and foregone conclusions of science denial. A position that emerged from his admitted ignorance.  

Daniel: I now invite you to abandon the pretense of "objective, direct consideration of the evidence, free of preconceptions," to which your own self-descriptive statements (and subsequent posts) utterly give the lie, stop holding forth on a topic of which you are self-admittedly utterly ignorant, and tell us what is motivating your anti-science stance.

What commitments and what community identification account for your stance?
Posted by: creeky belly on Sep. 24 2007,18:32



---------------------QUOTE-------------------
I myself am no scientist.  As far as formal training, I'm more than ignorant. What little I know has been self taught.
---------------------QUOTE-------------------


I'm still waiting for him to figure out what advances have been made in molecular genetics since 1950. Oh well.
Posted by: VMartin on Sep. 25 2007,00:03



---------------------QUOTE-------------------

Daniel admits abject ignorance of contemporary evolutionary science, yet nevertheless feels qualified to reject a priori the hard won findings of a community of thousands of scientists laboring over decades in an attempt to better understand the history of life on earth. Moreover, he prefers a priori a handful of crackpots and outliers who "work" outside the scientific community and whose ideas have been ridiculed, shunned, and forgotten by that community. In short, although he claims interest in the work of scientists who themselves operate "free of preconceptions," he freely admits being motivated by the biased assumptions and foregone conclusions of science denial. A position that emerged from his admitted ignorance.

---------------------QUOTE-------------------



These words remind me how Giordano Bruno was wellcommed in Oxford. Pundits there ridiculed him considering themselves to be brilliant scientists. Giordano Bruno was only a layman who knew nothing about movement of planets in their eyes.

I can see the same is now happening to ideas of Schindewolf, Berg and Davison. Their supporters are ridiculed as well. (But you are too ignorant to adress also entomologist Punnett or Heikertinger, who called your alike "Hypothetiker" and who showed that natural selection play no role in evolution of insect forms and coloration).
   

But do not be so sure in your convictions. It doesn't mean if you dismiss their ideas that you are right.

You are operating with very funny arguments:
we are so many, so we are right.
Posted by: blipey on Sep. 25 2007,00:06

What is your argument, VMartin?

That you are anti-establishment, thereby you are right?
Posted by: George on Sep. 25 2007,01:15

Quote (Wesley R. Elsberry @ Sep. 22 2007,18:51)
No, you'd also expect gradualism (i.e., non-saltational change) if any incremental evolutionary process is in play, which would include genetic drift.
---------------------QUOTE-------------------


Not much time to keep up here.  Just like to say that I'm obviously using the terminology incorrectly.  What I was trying to say is that rate of evolution under RM+NS is not necessarily slow and constant.  I was under the impression that this was the model of evolution Daniel was working under.  Periods of rapid gradualistic change might not be captured by the fossil record if resolution is poor, thus resulting in the appearance of saltation.
Posted by: Daniel Smith on Sep. 25 2007,01:58

Quote (Albatrossity2 @ Sep. 24 2007,06:12)
The fact that dogs under artificial selection have one set of characters, and another set of characters when they are feral and subject to a different kind of selective pressure, is not a problem for evolutionary theory. It is, in fact, a prediction of that theory.

---------------------QUOTE-------------------


I didn't know the theory had any predictions.

---------------------QUOTE-------------------

Do you have any testable predictions from your theory (whatever it is at the moment) that would lead to a different outcome than that predicted by evolutionary theory?
---------------------QUOTE-------------------


Since my view holds that selection is a conservative function, my statements about dogs and cabbage would probably qualify as predictions.
Posted by: Daniel Smith on Sep. 25 2007,02:11

Quote (Erasmus @ FCD,Sep. 24 2007,08:44)
Daniel, it is also not true.  the genetic milieu is changed by selection (artificial is just another form, and it's not really artificial is it?  unless you are arguing it is sooooopernatcheral).

---------------------QUOTE-------------------

It's artificial in the sense that it's not natural - man selects the breeding partners - not nature.  

---------------------QUOTE-------------------

offspring of different lineages (or hybrids if you will) can have phenotypes that are completely outside the range of variation in the parents.  if there is any positive selective pressure on those traits then they will persist.  if there is then a mate preference, they will diverge.  it is that simple, and 'throwing dogs into the wild and they all turn back into wolves' is just wrong for a litany of reasons.  think about why that might be.  no way can a chihuaha turn 'back into' a wolf.  for one, it never was one.
---------------------QUOTE-------------------


I never predicted that a chihuahua would "turn into" a wolf.  Chihuahuas and great danes would probably be the first breeds to go extinct - due to a lack of reproductive partners.  Medium sized dogs would have more partners to breed with and dog size would most likely gravitate towards that median.  All the super-specialized breeds would probably also eventually go away - as their gene pool became more and more watered down through breeding as well.

---------------------QUOTE-------------------


fancy types of lettuce don't go back to being one single muddy lettuce, there is a quantitative legacy of mutation and selection.  same as the dogs.  new traits can be formed from recombination during contact between different lineages (See the Helianthus sunflower examples, it blows your contentions out of the water in the first paragraph)
---------------------QUOTE-------------------


No idea what sunflower example you're talking about.  Perhaps a link?
Posted by: Daniel Smith on Sep. 25 2007,02:16

Quote (improvius @ Sep. 24 2007,09:12)

So you actually think that by simply removing natural selection, dogs just magically developed into all of these breeds with very specific purposes?  That's absurd.
---------------------QUOTE-------------------


Come on now.  You're really can't be that dense, can you?
I said artificial selection (that's the part where people actively protect their dogs from breeding with any other breed of dogs) works by shielding (i.e.: protecting) the dogs from natural selection (that is, what would happen if the dogs got out and just ran the streets, breeding with any dog they felt like).
Posted by: oldmanintheskydidntdoit on Sep. 25 2007,02:46

Quote (Daniel Smith @ Sep. 25 2007,01:58)
I didn't know the theory had any predictions.
---------------------QUOTE-------------------


< Predictions >

Start < here >

EDIT: And Darwin himself made predictions about his theory that were later confirmed.
< Here > and < here >

I expect < this > is more to your taste however.
Posted by: Daniel Smith on Sep. 25 2007,03:08

Quote (JAM @ Sep. 24 2007,16:02)
             

---------------------QUOTE-------------------

Big deal.  Things that are alike are built alike - even at the molecular level.
---------------------QUOTE-------------------


That's not remotely close to what he's saying. He's talking about mathematical analyses of the similarities AND DIFFERENCES. They fit nested hierarchies. The hierarchies of the organisms can be superimposed upon the hierarchies of their components, which are even more complex, because we can see how different proteins are related to each other.

---------------------QUOTE-------------------


Nested hierarchies are evidence of "top-down" evolution - where the higher categories are emplaced first - as opposed to evolution by speciation which would not create a nested hierarchy at all but would look more like a road map with lineages wandering aimlessly around.
           

---------------------QUOTE-------------------

Oh, and Daniel, no set of designed objects has these characteristics, so please save your lying for ignorant lay people.
---------------------QUOTE-------------------


Lots of designed objects fit into nested hierarchies.  One could make a nested hierarchy for automobiles - starting with horse drawn carriages and branching out.
               

---------------------QUOTE-------------------
             

---------------------QUOTE-------------------
What the molecular evidence shows, however is not always consistent with RM+NS.
---------------------QUOTE-------------------


Obviously, much of it is consistent with drift, which is not RM+NS, and a small subset is consistent with horizontal transfer.

If you had the slightest clue, you'd know that modern evolutionary theory is not limited to RM+NS.

---------------------QUOTE-------------------

Why do you have to be so mean and accusatory?
               

---------------------QUOTE-------------------
         

---------------------QUOTE-------------------
For instance, Denton points out the "Molecular Equidistance of all Eucaryotic Organisms from Bacteria" (in "Evolution: A Theory In Crisis", Figure 12.2, page 280), which is more consistent with the Schindewolf/Berg/Davison et al hypotheses of prescribed/directed/planned/designed evolution.
---------------------QUOTE-------------------


No. Denton fundamentally misunderstood evolutionary theory, and has since backtracked on that ignorant claim. MET (particularly drift) predicts that. Denton assumed a ladder, not a bush.
---------------------QUOTE-------------------

What claim did he backtrack on?
Denton's last book supports directed evolution.
               

---------------------QUOTE-------------------

Why not construct some trees, then, unless you weren't being truthful about your interest in evidence?
---------------------QUOTE-------------------


So, in order to show that I'm interested in evidence, I must construct trees?
             

---------------------QUOTE-------------------
         

---------------------QUOTE-------------------
And in answer to your previous question about the primary literature:  I read what I can online.
---------------------QUOTE-------------------


That doesn't answer my question. Have you ever read a paper from the primary literature?
---------------------QUOTE-------------------

I guess I don't know what you mean by "primary literature".  Is that only peer-reviewed journals?
         

---------------------QUOTE-------------------
           

---------------------QUOTE-------------------
I've often searched for articles on google scholar, but most require memberships to read - so I am not nearly as well informed as you I'm sure.
---------------------QUOTE-------------------


So why do you consider your uninformed conclusions to be more correct than mine?
---------------------QUOTE-------------------

Well, so far you've mostly called me names, and you haven't (yet) shown me anything that convinces me I'm wrong.
           

---------------------QUOTE-------------------

Let's discuss this paper, then:
< http://www.biolbull.org/cgi/content/full/202/2/104 >
...let's start with Figure 2. Note that vertical line length is irrelevant, only the horizontal lines represent sequence divergence.
---------------------QUOTE-------------------


Alright, I read it.  As I understand it, they found a gene in a fish that would allow it to get high on pot, :D then they sequenced that gene along with the same gene in humans and mice and fed all that info into a couple computer programs that spit out a comparative sequence and a chart that shows a theoretical phylogenetic divergence based on the similarities and differences and... mutation rates I'm guessing?
I'm not sure what I'm supposed to learn from this, but I'm open to whatever it is you think this shows.  You'll just have to spell it out in layman's terms for me.
               

---------------------QUOTE-------------------
           

---------------------QUOTE-------------------
It may take me awhile to understand what you're getting at sometimes and you may have to bring it down to my level, but don't accuse me of not being willing to discuss evidence when you haven't even given me the chance.
---------------------QUOTE-------------------


Sorry, but you're supposed to familiarize yourself with the evidence before reaching a firm conclusion.
---------------------QUOTE-------------------

But I've reached no firm conclusion as of yet.  Unless you are talking about my statement that whatever happened was by design.  In that case, I've yet to see any evidence that doesn't strengthen that conviction.
               

---------------------QUOTE-------------------
               

---------------------QUOTE-------------------

I understand all of it.  None of it is inconsistent with Nomogenesis, Orthogenesis, or the PEH.      
---------------------QUOTE-------------------


I don't think you understand it at all, since you blew it off as mere similarity.
---------------------QUOTE-------------------

Similarities and differences can be mapped out into a neat hierarchal pattern.  What part of that is inconsistent with evolution by law?
               

---------------------QUOTE-------------------
           

---------------------QUOTE-------------------
No, but Berg cites many examples of similar types of experiments.  His arguments against evolution via natural selection are very well constructed and empirically based.
---------------------QUOTE-------------------


To know that, you'd have to be familiar with the evidence, not just that someone offered citations. Are you familiar with these data, or are you faking it? Do you realize that science is not about appraising arguments, but about predicting and grappling with the actual evidence, not what anyone says about it?
---------------------QUOTE-------------------


Berg spent years in the field documenting case after case that confounded those he called "Selectionists".  I respect his findings because they are not arguments but are documented observances.  Many here and at talk.origins who fervently hold to the evolution by RM+NS (and drift and horizontal transfer) seem to be more interested in theoretical arguments than documented field work.
Posted by: Daniel Smith on Sep. 25 2007,03:33

Quote (jeannot @ Sep. 24 2007,16:38)
         

---------------------QUOTE-------------------
Big deal.  Things that are alike are built alike - even at the molecular level.
---------------------QUOTE-------------------


If you're going to argue for "common design" as we see you coming, you'll have to explain why closely related species share homologies at synonymous or neutral sites, which have nothing to do with "design".

---------------------QUOTE-------------------


How about < this? >
         

---------------------QUOTE-------------------
"The new view transforms our view of the genomic fabric," explained Dr Tim Hubbard, from the Wellcome Trust Sanger Institute, "The majority of the genome is copied, or transcribed, into RNA, which is the active molecule in our cells, relaying information from the archival DNA copy to the cellular machinery. This is a remarkable finding, since most prior research suggested only a fraction of the genome was transcribed."

"But it is our new understanding of regulation of genes that stands out. The integrated approach has helped us to identify new regions of gene regulation and altered our view of how gene regulation occurs."...

The team showed that transcription of DNA is pervasive across the genome, and that RNA transcripts overlap known genes and are found in what were previously thought to be gene 'deserts'.(all emphasis mine)
---------------------QUOTE-------------------




I am especially interested in these overlapping coding areas.  What that means, as near as I can tell, is that the coding in DNA is more elaborate and more sophisticated than previously thought - with regions that code for regulatory RNA overlapping (sharing parts of the same code with) regions that code for proteins.

If this is true (and it looks like it is), it would seem to be a nightmare for any theory based on random mutations - since one mutation would have to not only improve the protein produced, but the RNA as well.

Of course those of us who hold to a designed life theory have been predicting that there is no such thing as "junk DNA" all along.

I'm sure, however, that many of you will say that the ToE predicts this as well.
Posted by: oldmanintheskydidntdoit on Sep. 25 2007,05:07

Quote (Daniel Smith @ Sep. 25 2007,03:33)
Of course those of us who hold to a designed life theory have been predicting that there is no such thing as "junk DNA" all along.

I'm sure, however, that many of you will say that the ToE predicts this as well.
---------------------QUOTE-------------------


So, if "junk" DNA is in fact found then that will, to your complete satisfaction, disprove the "designed life theory"?


If not, well you can't have it both ways can you?
Posted by: Reciprocating Bill on Sep. 25 2007,06:51

Quote (VMartin @ Sep. 25 2007,01:03)
But do not be so sure in your convictions. It doesn't mean if you dismiss their ideas that you are right.

You are operating with very funny arguments:
we are so many, so we are right.
---------------------QUOTE-------------------


VMartin: however funny my argument, you failed to grasp it. I'll simplify:

1) Daniel Smith claims to be interested in evidence gathered free of bias and preconception.

2) But Daniel himself, per his own frank and repeated self-description, is operating from a decisive bias (one you appear to endorse), specifically that he prefers to learn from those who have been ignored, laughed at and shunned. This massive bias, and its accompanying a prior assumption that mainstream scientists have nothing to offer to him, renders 1) absurd.

3) I'd like him to publicly abandon 1), given 2). I'd also like him to articulate the origins of his bias. I'm not interested in a reply couched in terms of some biological challenge or other, because he has already confessed his abject ignorance of the field, as well as this self-same bias.

Rather, I'd like to hear about his commitments and community identifications, a description of the non-scientific allegiances from which his biases arise.
Posted by: Erasmus, FCD on Sep. 25 2007,08:25

'junk' is a sloppy term that covers many different phenomenon.  we prefer non-coding.  there is a lot of repetition in there, daniel, and it acts as if it were selectively neutral.  or, as if it were doing nothing but accumulating dust.

sunflower hybrid speciation < here >

punchline?  new traits evolve from lineage contact that promote ecological divergence and reproductive isolation via selection.  you are completely wrong.  

your 'super specialized' breeds have different ecological niches.  chihuahas and terriers would do just fine in a habitat where they could nail mice and dig burrows.  pit bulls hunt in packs.  I, uh, don't know if you have noticed, but every place is not like every other place.  Things vary.  This matters.

It all boils down to my fundamental biologic law:  Shit varies.  It matters.  Sometimes.

Now, we are waiting to hear what makes you doubt the findings of hundreds of thousands of biologists, since it is very clearly not the evidence (perhaps your unfamiliarity with the evidence...).  It could be that you just prefer the German mystical archetype position, but this was refuted in the 20s 30s and 40s (although VMartin may not have access to those journals in the caves he lives in).  Phenotypes may very quickly surpass the range exhibited by parentals, and there is a ton of evidence to show this.  For god's sake look at the work of Dolph Schluter.
Posted by: JAM on Sep. 25 2007,09:09

Quote (Daniel Smith @ Sep. 25 2007,02:11)
All the super-specialized breeds would probably also eventually go away - as their gene pool became more and more watered down through breeding as well.
---------------------QUOTE-------------------


The gene pool would be enriched. Domesticated dogs have high homozygosity from inbreeding, not low.
Posted by: Jim_Wynne on Sep. 25 2007,09:31

Here's a snapshot of Daniel's level of comprehension:
Quote (Daniel Smith @ Sep. 25 2007,03:08)
...evolution by speciation which would not create a nested hierarchy at all but would look more like a road map with lineages wandering aimlessly around.
           
One could make a nested hierarchy for automobiles - starting with horse drawn carriages and branching out.
               
Why do you have to be so mean and accusatory?

Similarities and differences can be mapped out into a neat hierarchal pattern.  What part of that is inconsistent with evolution by law?

Many here and at talk.origins who fervently hold to the evolution by RM+NS (and drift and horizontal transfer) seem to be more interested in theoretical arguments than documented field work.
---------------------QUOTE-------------------


Edit: formatting snafu
Posted by: jeannot on Sep. 25 2007,10:18

Quote (Daniel Smith @ Sep. 25 2007,03:33)
Quote (jeannot @ Sep. 24 2007,16:38)
         

---------------------QUOTE-------------------
Big deal.  Things that are alike are built alike - even at the molecular level.
---------------------QUOTE-------------------


If you're going to argue for "common design" as we see you coming, you'll have to explain why closely related species share homologies at synonymous or neutral sites, which have nothing to do with "design".

---------------------QUOTE-------------------


How about < this? >
---------------------QUOTE-------------------


This has hardly anything to do with my objection. JAM was right about your misconception regarding pseudognes and junk DNA.
Regions of unknown functions (what you like to call “junk”) may actually have some phenotypic effects. And, guess what? This is tested by building phylogenies on those regions, and detecting evidence of selection acting on them.

In a typical gene, synonymous mutations are far more frequent that non-synonymous ones. (To give you an example, the 30 point mutations that separate two species of aphids that I study at a 700 bp locus are all synonymous).
These kinds of observations have been the primary argument of Kimura, who first formulated the neutral theory of evolution.
We know that synonymous mutations lead to the same proteins, and are very unlikely to have a significant effect on the organism. Hence they are not eliminated by natural selection.
Same goes for pseudogenes, once they are knocked-out (typically by a frame shift or a stop mutation), we notice an acceleration of their mutation rates. This is expected if they are no longer active.
So again, why do related species share mutations that have no effect?

And you should think about my second objection: human, lungfish and trout. What does common design predict about their genes?
Posted by: JAM on Sep. 25 2007,10:58

D: Big deal.  Things that are alike are built alike - even at the molecular level.

JAM:That's not remotely close to what he's saying. He's talking about mathematical analyses of the similarities AND DIFFERENCES. They fit nested hierarchies. The hierarchies of the organisms can be superimposed upon the hierarchies of their components, which are even more complex, because we can see how different proteins are related to each other.

D:Nested hierarchies are evidence of "top-down" evolution - where the higher categories are emplaced first - as opposed to evolution by speciation which would not create a nested hierarchy at all but would look more like a road map with lineages wandering aimlessly around.

Please explain how Darwin was wrong when he predicted nested hierarchies, then.
[quote][quote]Oh, and Daniel, no set of designed objects has these characteristics, so please save your lying for ignorant lay people.[/quote]
Lots of designed objects fit into nested hierarchies.[/quote]
They fit into multiple NHs, but one of "these characteristics" that you socleverly omitted was the superimposability of the NH of the assembled objects over any NH independently constructed from their components. Why did you omit that, Daniel? And if you disagree, show me the NHs you can construct from the relationships between lug nuts for GM cars and trucks.
         

---------------------QUOTE-------------------
One could make a nested hierarchy for automobiles - starting with horse drawn carriages and branching out.
---------------------QUOTE-------------------


But it couldn't be superimposed on NHs derived from their components. In fact, virtually none of the components of cars can be organized into nested hierarchies.                            


---------------------QUOTE-------------------


---------------------QUOTE-------------------


---------------------QUOTE-------------------
What the molecular evidence shows, however is not always consistent with RM+NS.
---------------------QUOTE-------------------


Obviously, much of it is consistent with drift, which is not RM+NS, and a small subset is consistent with horizontal transfer. If you had the slightest clue, you'd know that modern evolutionary theory is not limited to RM+NS.

---------------------QUOTE-------------------

Why do you have to be so mean and accusatory?
---------------------QUOTE-------------------


Probably because you have the appealing quality of massive arrogance, made even more appealing by massive ignorance.


---------------------QUOTE-------------------


---------------------QUOTE-------------------


---------------------QUOTE-------------------
For instance, Denton points out the "Molecular Equidistance of all Eucaryotic Organisms from Bacteria" (in "Evolution: A Theory In Crisis", Figure 12.2, page 280), which is more consistent with the Schindewolf/Berg/Davison et al hypotheses of prescribed/directed/planned/designed evolution.
---------------------QUOTE-------------------


No. Denton fundamentally misunderstood evolutionary theory, and has since backtracked on that ignorant claim. MET (particularly drift) predicts that. Denton assumed a ladder, not a bush.
---------------------QUOTE-------------------


What claim did he backtrack on?
---------------------QUOTE-------------------


The ladder part. It's stupid. The equidistance is predicted.


---------------------QUOTE-------------------
Denton's last book supports directed evolution.
---------------------QUOTE-------------------


Evidence supports positions, not books. You don't give a damn about evidence, do you?


---------------------QUOTE-------------------


---------------------QUOTE-------------------
Why not construct some trees, then, unless you weren't being truthful about your interest in evidence?
---------------------QUOTE-------------------


So, in order to show that I'm interested in evidence, I must construct trees?
---------------------QUOTE-------------------


Since the relationships between these sequences represent the overwhelming evidence favoring MET that make fossils unnecessary, it would be the inevitable prediction for someone who claimed an interest in evidence.

---------------------QUOTE-------------------


---------------------QUOTE-------------------


---------------------QUOTE-------------------
And in answer to your previous question about the primary literature:  I read what I can online.
---------------------QUOTE-------------------


That doesn't answer my question. Have you ever read a paper from the primary literature?
---------------------QUOTE-------------------

I guess I don't know what you mean by "primary literature".  Is that only peer-reviewed journals?
---------------------QUOTE-------------------


Within most journals, there are both primary (those with new data) and secondary (reviews). Usually, only the former are peer-reviewed. So I'll ask again: have you ever read a paper from the primary literature--meaning one that reports data that have never been reported before?
                       

---------------------QUOTE-------------------
Well, so far you've mostly called me names, and you haven't (yet) shown me anything that convinces me I'm wrong.
---------------------QUOTE-------------------


Mostly? Show me a single instance in which I called you a name, Daniel.
 

---------------------QUOTE-------------------
 

---------------------QUOTE-------------------
Let's discuss this paper, then:
< http://www.biolbull.org/cgi/content/full/202/2/104 >
...let's start with Figure 2. Note that vertical line length is irrelevant, only the horizontal lines represent sequence divergence.
---------------------QUOTE-------------------


Alright, I read it.  As I understand it, they found a gene in a fish that would allow it to get high on pot, :D then they sequenced that gene along with the same gene in humans and mice
---------------------QUOTE-------------------


No, those were already sequenced.
 

---------------------QUOTE-------------------
and fed all that info into a couple computer programs that spit out a comparative sequence and a chart that shows a theoretical phylogenetic divergence based on the similarities and differences and... mutation rates I'm guessing?
---------------------QUOTE-------------------


Sorry, but you're fudging already. The tree is not theoretical in any way. It is simply a graphic representation of the actual evidence--the identities and differences between the sequences. What do you conclude from these relationships? If CB2 was designed, when was it designed?
 

---------------------QUOTE-------------------
I'm not sure what I'm supposed to learn from this, but I'm open to whatever it is you think this shows.  You'll just have to spell it out in layman's terms for me.
---------------------QUOTE-------------------


It's a starting point for examining the evidence and making predictions, something I predict that you're afraid to do. Where will a reptilian CB2 branch off on this tree? Why do both CB1 and CB2 fit into a single nested hierarchy?
                           

---------------------QUOTE-------------------
But I've reached no firm conclusion as of yet.
---------------------QUOTE-------------------


Read all the conclusions you advanced above.
 

---------------------QUOTE-------------------
Unless you are talking about my statement that whatever happened was by design.  In that case, I've yet to see any evidence that doesn't strengthen that conviction.
---------------------QUOTE-------------------


That's because you haven't looked at evidence. Look at how you misrepresented the tree as "theoretical" above.
Posted by: blipey on Sep. 25 2007,11:07

Daniel Smith:

---------------------QUOTE-------------------
Nested hierarchies are evidence of "top-down" evolution - where the higher categories are emplaced first - as opposed to evolution by speciation which would not create a nested hierarchy at all but would look more like a road map with lineages wandering aimlessly around.
---------------------QUOTE-------------------


You don't know Joe Gallien, do you?  If you don't mind me asking, could you define a nested hierarchy for us?
Posted by: improvius on Sep. 25 2007,13:37

Quote (Daniel Smith @ Sep. 25 2007,03:16)
Quote (improvius @ Sep. 24 2007,09:12)

So you actually think that by simply removing natural selection, dogs just magically developed into all of these breeds with very specific purposes?  That's absurd.
---------------------QUOTE-------------------


Come on now.  You're really can't be that dense, can you?
I said artificial selection (that's the part where people actively protect their dogs from breeding with any other breed of dogs) works by shielding (i.e.: protecting) the dogs from natural selection (that is, what would happen if the dogs got out and just ran the streets, breeding with any dog they felt like).
---------------------QUOTE-------------------


I'm not being dense.  You've completely disregarded the element of selection.  You seem to think that Chihuahuas, Dachshunds, Great Danes, etc. would all eventually spring forth from wolves with no selection whatsoever.  This is ridiculous.
Posted by: VMartin on Sep. 25 2007,15:03



---------------------QUOTE-------------------

It could be that you just prefer the German mystical archetype position, but this was refuted in the 20s 30s and 40s (although VMartin may not have access to those journals in the caves he lives in).  Phenotypes may very quickly surpass the range exhibited by parentals, and there is a ton of evidence to show this.

---------------------QUOTE-------------------



It was refuted only in darwinian heads of course. The tactic is the same - first darwinists pretend that unpleasant facts do not exists. After 50 years they declare their victory over "outdated" facts.
 

This has happend many times. The great research done
by Theodor Eimer (the main proponent of here discussed orthogenesis) and his opus magnum has never been translated into English. Of course observed rules governing the change of color patterns on skin of lizards or evolution of color patterns on butterfly wings has nothing to do with "natural selection".

The same for Franz Heikertinger whose work on mimicry has never been translated into English. His own research and comparisions refuted the darwinian pressupositions about aposematism very clearly.

The research of McAtee from US Department of agriculture where many thousands of birds stomachs was put under scrutiny and shows that all preconceptions of "aposematism" and "mimicry" are often only armchairs theories of "selectionists" that has nothing to do with facts. The research made Poulton very unhappy - but behold, it is forgotten and selectionists continue to spread nowadays their theories of aposematism of ladybirds, wasps etc.. as the research never exist.

I am afraid that in caves live those who do not recognize antiselectionists scientific materials that is older than 1 year.
Posted by: Arden Chatfield on Sep. 25 2007,15:16



---------------------QUOTE-------------------

I am afraid that in caves live those who do not recognize antiselectionists scientific materials that is older than 1 year.
---------------------QUOTE-------------------



Martin, would you share with us what you think the correct explanation is? Any idea at all?

And while you're at it, do you accept common descent between apes and humans?

As someone who supposedly does not live in a cave, I'm sure you're willing to answer.
Posted by: Erasmus, FCD on Sep. 25 2007,15:23

Vmartin, do you recognize the difference between 'selectionist' and 'panadaptationist'?  

you might find that i agree with you that there is no fundamental reason that any particular trait must be adaptive.  but this does nothing to undermine the importance of natural selection.  it sure as hell doesn't imply the existence of a mystical organizing differentiating force.  

Here is my theory.

Shit Varies.  It Matters.  Sometimes.

Now, you could clear up this discussion IMMENSELY and earn your laurel wreaths if you would just get to work and translate Eimer and Heikertinger into English.  But beware the evil darwinist materialist from ATBC conspiracy, they might try to blow up your cave or something.
Posted by: BWE on Sep. 25 2007,15:53

Quote (Daniel Smith @ Sep. 25 2007,01:58)
Quote (Albatrossity2 @ Sep. 24 2007,06:12)
The fact that dogs under artificial selection have one set of characters, and another set of characters when they are feral and subject to a different kind of selective pressure, is not a problem for evolutionary theory. It is, in fact, a prediction of that theory.

---------------------QUOTE-------------------


I didn't know the theory had any predictions.
---------------------QUOTE-------------------


You'd like to think that you're immune, it's so hard
You're gonna have to face it you're addicted to...
Posted by: BWE on Sep. 25 2007,16:00

Quote (Steviepinhead @ Sep. 18 2007,19:48)
 

---------------------QUOTE-------------------
skeptic Posted: Sep. 18 2007,16:50
 

---------------------QUOTE-------------------
jeannot Posted: Sep. 18  
Hi Alan,

I don't think that anyone here is a paleontologist. So if we're going to defend RM+NS, it will probably be on another ground.
---------------------QUOTE-------------------

what about Deadman?
---------------------QUOTE-------------------


deadman is an archaeologist, last I heard.
---------------------QUOTE-------------------


maybe he's a paleontologist now? My neighbor was a banker last year and he's an insurance risk analyzer now.
Posted by: Richardthughes on Sep. 25 2007,16:01

Quote (Peter Henderson @ Sep. 22 2007,11:43)


---------------------QUOTE-------------------
I decided what I needed was just to see the evidence for myself.
---------------------QUOTE-------------------



If you saw 10 clocks Daniel, and 9 of them were reading the same time and the tenth was different which one would you choose ? I know what I would think. I would assume the one that was different was in error.

This is how it is with this debate (if you could call it that). 99.99% of all scientists accept the age of the Earth/evolution. No mainstream scientist that I know of has found evidence of a 6-10,000 year old Earth/Universe. I always wonder why those who question science in favour of YECism don't think about that.
---------------------QUOTE-------------------


Duh! Bible says "don't think".
Posted by: Arden Chatfield on Sep. 25 2007,16:18

Quote (Richardthughes @ Sep. 25 2007,16:01)
Quote (Peter Henderson @ Sep. 22 2007,11:43)


---------------------QUOTE-------------------
I decided what I needed was just to see the evidence for myself.
---------------------QUOTE-------------------



If you saw 10 clocks Daniel, and 9 of them were reading the same time and the tenth was different which one would you choose ? I know what I would think. I would assume the one that was different was in error.

This is how it is with this debate (if you could call it that). 99.99% of all scientists accept the age of the Earth/evolution. No mainstream scientist that I know of has found evidence of a 6-10,000 year old Earth/Universe. I always wonder why those who question science in favour of YECism don't think about that.
---------------------QUOTE-------------------


Duh! Bible says "don't think".
---------------------QUOTE-------------------


FTK solves the problem by accepting massive conspiracies as an everyday fact of life in all the sciences.
Posted by: Richard Simons on Sep. 25 2007,23:56

Daniel said  

---------------------QUOTE-------------------
I didn't know the theory had any predictions.
---------------------QUOTE-------------------


Indeed it does. That is one of the things needed for a theory to be called a theory. It is also one of the reasons why Intelligent Design is not a theory.

Daniel: you seem to be under the impression that artificial selection and natural selection are two quite different processes. What I want to know is how do cabbages, or even dogs, perceive the difference between the two? After all, in both cases they basically breed with whatever partner is available. The only difference is that in one case the available partners are narrowed down by diseases and other stresses, in the other case there's also a person involved saying "By golly, that looks a good un".

With regards to the nested hierarchies, I have some sympathy towards your misunderstanding. The point is that, although it is possible to make a nested hierarchy describing designed objects such as cars and trucks, it would be a forced affair and no two people would come up with the same hierarchy. With evolved organisms, however, not only does everyone come up with essentially the same hierarchy (there will always be a few fuzzy areas) but hierarchies drawn up using just one aspect of an organism (e.g. cytochrome, mitochondrial DNA, reproductive system) will match to an impressive degree.
Posted by: Daniel Smith on Sep. 26 2007,04:39

Quote (jeannot @ Sep. 25 2007,10:18)
       
Quote (Daniel Smith @ Sep. 25 2007,03:33)

How about < this? >
---------------------QUOTE-------------------


This has hardly anything to do with my objection. JAM was right about your misconception regarding pseudognes and junk DNA.
Regions of unknown functions (what you like to call “junk”) may actually have some phenotypic effects. And, guess what? This is tested by building phylogenies on those regions, and detecting evidence of selection acting on them.

In a typical gene, synonymous mutations are far more frequent that non-synonymous ones. (To give you an example, the 30 point mutations that separate two species of aphids that I study at a 700 bp locus are all synonymous).
These kinds of observations have been the primary argument of Kimura, who first formulated the neutral theory of evolution.
We know that synonymous mutations lead to the same proteins, and are very unlikely to have a significant effect on the organism. Hence they are not eliminated by natural selection.
Same goes for pseudogenes, once they are knocked-out (typically by a frame shift or a stop mutation), we notice an acceleration of their mutation rates. This is expected if they are no longer active.
So again, why do related species share mutations that have no effect?
---------------------QUOTE-------------------


First, I don't use the term "junk" to describe any sequence of DNA.  I am against the use of that term - as are most ID proponents.  I've always said that there's no such thing as junk DNA, so saying that I "like to call" it junk is untrue.

Second, I'm arguing that these so-called "junk" regions are important - that they likely do have an effect (something it appears you are noticing too).  The ENCODE study shows that that's true - since it shows that "most" (their word - no idea what the percentage is) of the genome is transcribed.

So to answer your question: Related species share mutations (if that's what they are) that most likely do have an effect.      

---------------------QUOTE-------------------


And you should think about my second objection: human, lungfish and trout. What does common design predict about their genes?
---------------------QUOTE-------------------

Common Design would predict that lungfish and trout would be closer to each other than to humans.  Perhaps, once they get the entire genomes sorted out, they'll find this to be true.  For now, with the concentration seemingly focused on coding regions - it appears not to be true.  I guess we'll have to wait and see.
Posted by: jeannot on Sep. 26 2007,06:01

Thanks for you clarification Daniel. Indeed, you didn't use the term "junk".

I agree that much of this DNA can have a function. However, we do know that many (most) mutations are neutral.
So you're not really answering my question, about the fact that related species tend to share neutral mutations.

Regarding my other objection, I'll get back to it when I have more time.
Posted by: Daniel Smith on Sep. 26 2007,06:01

Quote (JAM @ Sep. 25 2007,10:58)

D:Nested hierarchies are evidence of "top-down" evolution - where the higher categories are emplaced first - as opposed to evolution by speciation which would not create a nested hierarchy at all but would look more like a road map with lineages wandering aimlessly around.

Please explain how Darwin was wrong when he predicted nested hierarchies, then.

---------------------QUOTE-------------------


Can you supply that quote from Darwin?
 

---------------------QUOTE-------------------

They fit into multiple NHs, but one of "these characteristics" that you socleverly omitted was the superimposability of the NH of the assembled objects over any NH independently constructed from their components. Why did you omit that, Daniel? And if you disagree, show me the NHs you can construct from the relationships between lug nuts for GM cars and trucks.
...
But it couldn't be superimposed on NHs derived from their components. In fact, virtually none of the components of cars can be organized into nested hierarchies.

---------------------QUOTE-------------------


That's not true.  Most components can also be organized into nested hierarchies. Speaking from experience (since my job involves troubleshooting and repairing very large, complex, industrial CNC machinery) I can verify that the parts of a machine evolve right along with the machine and can be placed in separate but superimposable NHs.
Right now, the company I work for is talking about rebuilding 8 machines (which are pretty much exact duplicates of one another) - one a year - over an 8 year period.  Even though we'll have the same company come in and do the work, we'll end up with 8 very different machines - since the technology will change every year as the machines go in.
   

---------------------QUOTE-------------------

The ladder part. It's stupid. The equidistance is predicted.

---------------------QUOTE-------------------


Where did Denton assume a ladder?  I don't remember that part.
     

---------------------QUOTE-------------------
     

---------------------QUOTE-------------------

Denton's last book supports directed evolution.

---------------------QUOTE-------------------


Evidence supports positions, not books. You don't give a damn about evidence, do you?

---------------------QUOTE-------------------


Like I said, I'm willing to look at any and all evidence.  I'm less interested in opinions though.
     

---------------------QUOTE-------------------

Since the relationships between these sequences represent the overwhelming evidence favoring MET that make fossils unnecessary, it would be the inevitable prediction for someone who claimed an interest in evidence.

---------------------QUOTE-------------------


Fossils are unnecessary? Wow. You do realize that fossils are empirical, observable evidence don't you?                

---------------------QUOTE-------------------
 
Within most journals, there are both primary (those with new data) and secondary (reviews). Usually, only the former are peer-reviewed. So I'll ask again: have you ever read a paper from the primary literature--meaning one that reports data that have never been reported before?

---------------------QUOTE-------------------


I don't subscribe to the journals and their online articles all seem to require a subscription.  I've been consigned to reading mostly abstracts and summations of these articles.        

---------------------QUOTE-------------------
       

---------------------QUOTE-------------------

Well, so far you've mostly called me names, and you haven't (yet) shown me anything that convinces me I'm wrong.

---------------------QUOTE-------------------


Mostly? Show me a single instance in which I called you a name, Daniel.

---------------------QUOTE-------------------


OK,
       

---------------------QUOTE-------------------

you have the appealing quality of massive arrogance, made even more appealing by massive ignorance... so please save your lying for ignorant lay people.

---------------------QUOTE-------------------


Does that qualify?
       

---------------------QUOTE-------------------
       

---------------------QUOTE-------------------
       

---------------------QUOTE-------------------

Let's discuss this paper, then:
< http://www.biolbull.org/cgi/content/full/202/2/104 >
...let's start with Figure 2. Note that vertical line length is irrelevant, only the horizontal lines represent sequence divergence.

---------------------QUOTE-------------------


Alright, I read it.  As I understand it, they found a gene in a fish that would allow it to get high on pot, :D then they sequenced that gene along with the same gene in humans and mice

---------------------QUOTE-------------------


No, those were already sequenced.

---------------------QUOTE-------------------


OK my bad.
       

---------------------QUOTE-------------------
       

---------------------QUOTE-------------------

and fed all that info into a couple computer programs that spit out a comparative sequence and a chart that shows a theoretical phylogenetic divergence based on the similarities and differences and... mutation rates I'm guessing?

---------------------QUOTE-------------------


Sorry, but you're fudging already. The tree is not theoretical in any way. It is simply a graphic representation of the actual evidence--the identities and differences between the sequences.

---------------------QUOTE-------------------


OK
       

---------------------QUOTE-------------------

What do you conclude from these relationships? If CB2 was designed, when was it designed?

---------------------QUOTE-------------------


When was it designed or when was it implemented?  I have no idea when it was designed, but when it was first implemented can be found out I guess - if you find the earliest fossil evidence for that fish.                

---------------------QUOTE-------------------
       

---------------------QUOTE-------------------

I'm not sure what I'm supposed to learn from this, but I'm open to whatever it is you think this shows.  You'll just have to spell it out in layman's terms for me.

---------------------QUOTE-------------------


It's a starting point for examining the evidence and making predictions, something I predict that you're afraid to do. Where will a reptilian CB2 branch off on this tree? Why do both CB1 and CB2 fit into a single nested hierarchy?

---------------------QUOTE-------------------


I don't know the answers to those questions but I'm not afraid of them - I just need to figure out what you're asking and how you're arriving at your conclusions.  I need to see the evidence for myself - I won't just take your word for it.      
       

---------------------QUOTE-------------------
       

---------------------QUOTE-------------------

Unless you are talking about my statement that whatever happened was by design.  In that case, I've yet to see any evidence that doesn't strengthen that conviction.

---------------------QUOTE-------------------


That's because you haven't looked at evidence. Look at how you misrepresented the tree as "theoretical" above.

---------------------QUOTE-------------------


The tree is theoretical in that it is just a graphic representation of a proposed relationship.  How do you know these genes are not convergent?
Posted by: Reciprocating Bill on Sep. 26 2007,06:24

By the way, Daniel:

1) You claim to be interested in evidence gathered free of bias and preconception.

2) But, per your own frank and repeated self-description, you are operating from a decisive bias, specifically that you prefer a priori to learn from those who have been ignored, laughed at and shunned. This massive bias, and its accompanying assumption that mainstream scientists have nothing to offer to you, renders 1) absurd. Not the least because your self-described ignorance of the field renders you ill-equipped to evaluate the work of these outliers, their methods, and their data.

3) I'd like you to publicly abandon 1), given 2). I'd also like you to articulate the origins of your bias. I'm not interested in a reply couched in terms of some biological challenge or other, because you have already confessed your abject ignorance of the field, as well as this self-same bias.

Rather, I'd like to hear about your commitments and community identifications, a description of the non-scientific allegiances from which your biases arise.

C'mon Daniel - this is the one subject you actually know something about (yourself).
Posted by: Reciprocating Bill on Sep. 26 2007,06:37

Quote (Daniel Smith @ Sep. 26 2007,07:01)
 
Quote (JAM @ Sep. 25 2007,10:58)

D:Nested hierarchies are evidence of "top-down" evolution - where the higher categories are emplaced first - as opposed to evolution by speciation which would not create a nested hierarchy at all but would look more like a road map with lineages wandering aimlessly around.

Please explain how Darwin was wrong when he predicted nested hierarchies, then.

---------------------QUOTE-------------------


Can you supply that quote from Darwin?
---------------------QUOTE-------------------


< Here >.
Posted by: Wesley R. Elsberry on Sep. 26 2007,06:42



---------------------QUOTE-------------------

Fossils are unnecessary? Wow. You do realize that fossils are empirical, observable evidence don't you?

---------------------QUOTE-------------------



<cop drama>

Lt. DS: The lab boys failed to retrieve any fingerprints in this case. We'll have to file it as unsolved.

Lt. JAM: Why would we do that? The lab boys did find the perp's hair at the scene. We got an excellent DNA match to a guy with a motive and no alibi. The fingerprints are unnecessary.

Lt. DS: Fingerprints are unnecessary? Wow. You do realize that fingerprints are empirical, observable evidence don't you?

[Rest of people in room look at Lt. DS, jaws dropping  in amazement.]

</cop drama>
Posted by: Richard Simons on Sep. 26 2007,07:54

Daniel:  

---------------------QUOTE-------------------
Right now, the company I work for is talking about rebuilding 8 machines (which are pretty much exact duplicates of one another) - one a year - over an 8 year period.  Even though we'll have the same company come in and do the work, we'll end up with 8 very different machines - since the technology will change every year as the machines go in.

---------------------QUOTE-------------------


But will any of this new technology be used in any machines made by any other company? Or in any machines made by your company to do other things? Because in biology that is not the case. A new technology, say mammary glands, that is successful in one group of organisms is never picked up by another group, fish for example. You will never find a fern with flowers or a treefrog with dragonfly wings. The one exception is in some micro-organisms, in which the transfer of genetic material is well-established.

BTW, although fossils loom large in the general public's mind (and I include creationists and IDers here) as far as biologists are concerned they form a minor part of the evidence for the theory of evolution. This has been the case right from Origin of Species.
Posted by: improvius on Sep. 26 2007,08:27

Quote (Daniel Smith @ Sep. 26 2007,05:39)


---------------------QUOTE-------------------
And you should think about my second objection: human, lungfish and trout. What does common design predict about their genes?
---------------------QUOTE-------------------

Common Design would predict that lungfish and trout would be closer to each other than to humans.  Perhaps, once they get the entire genomes sorted out, they'll find this to be true.  For now, with the concentration seemingly focused on coding regions - it appears not to be true.  I guess we'll have to wait and see.
---------------------QUOTE-------------------


I love this part.  "Of course the evidence is against me now.  But imaginary, contradictory evidence that has yet to be discovered will certainly support my argument."  This, more than anything else, drives home the hopelessness of trying to reason with creationists.
Posted by: Wesley R. Elsberry on Sep. 26 2007,09:44



---------------------QUOTE-------------------

Common Design would predict that lungfish and trout would be closer to each other than to humans.

---------------------QUOTE-------------------



We don't have to wait to know that Denton's assertion is < incorrect >.
Posted by: JAM on Sep. 26 2007,09:45

[quote]   [quote]Please explain how Darwin was wrong when he predicted nested hierarchies, then.[/quote]
Can you supply that quote from Darwin?[/quote]
Already done. Please explain how his prediction was wrong.
       [quote]  [quote]They fit into multiple NHs, but one of "these characteristics" that you socleverly omitted was the superimposability of the NH of the assembled objects over any NH independently constructed from their components. Why did you omit that, Daniel? And if you disagree, show me the NHs you can construct from the relationships between lug nuts for GM cars and trucks.
...
But it couldn't be superimposed on NHs derived from their components. In fact, virtually none of the components of cars can be organized into nested hierarchies.
[/quote]
That's not true.[/quote]
     

---------------------QUOTE-------------------
 Most components can also be organized into nested hierarchies.
---------------------QUOTE-------------------


No, very few can. As Richard pointed out, many will be identical and others will be outsourced to other companies. We don't see either of those things in biology. We get (allowing for systematic and experimental errors) a single, identically-branching nested hierarchy when we look independently at either functional or nonfunctional differences.
       

---------------------QUOTE-------------------
Speaking from experience (since my job involves troubleshooting and repairing very large, complex, industrial CNC machinery) I can verify that the parts of a machine evolve right along with the machine and can be placed in separate but superimposable NHs.
---------------------QUOTE-------------------


Then show us the data.
       

---------------------QUOTE-------------------
Right now, the company I work for is talking about rebuilding 8 machines (which are pretty much exact duplicates of one another) - one a year - over an 8 year period.  Even though we'll have the same company come in and do the work, we'll end up with 8 very different machines - since the technology will change every year as the machines go in.
---------------------QUOTE-------------------


Yes, but that isn't remotely close to showing that they and their components will fit into a single NH.
             

---------------------QUOTE-------------------
     

---------------------QUOTE-------------------

The ladder part. It's stupid. The equidistance is predicted.

---------------------QUOTE-------------------


Where did Denton assume a ladder?  I don't remember that part.
---------------------QUOTE-------------------


< http://www.talkorigins.org/faqs/denton.html >
Read the last half of part III.
     

---------------------QUOTE-------------------
Like I said, I'm willing to look at any and all evidence.  I'm less interested in opinions though.
---------------------QUOTE-------------------


Then why have you offered nothing but opinions?
     

---------------------QUOTE-------------------
     

---------------------QUOTE-------------------
 

---------------------QUOTE-------------------
Well, so far you've mostly called me names, and you haven't (yet) shown me anything that convinces me I'm wrong.

---------------------QUOTE-------------------


Mostly? Show me a single instance in which I called you a name, Daniel.

---------------------QUOTE-------------------


OK,    

---------------------QUOTE-------------------
you have the appealing quality of massive arrogance, made even more appealing by massive ignorance... so please save your lying for ignorant lay people.
---------------------QUOTE-------------------


Does that qualify?
---------------------QUOTE-------------------


No, because there's not a single name in there.
[quote]    

---------------------QUOTE-------------------
 

---------------------QUOTE-------------------
Sorry, but you're fudging already. The tree is not theoretical in any way. It is simply a graphic representation of the actual evidence--the identities and differences between the sequences.

---------------------QUOTE-------------------


OK
---------------------QUOTE-------------------


Then why do you go back on that below?
   

---------------------QUOTE-------------------
   

---------------------QUOTE-------------------

What do you conclude from these relationships? If CB2 was designed, when was it designed?

---------------------QUOTE-------------------


When was it designed or when was it implemented?  I have no idea when it was designed, but when it was first implemented can be found out I guess - if you find the earliest fossil evidence for that fish.
---------------------QUOTE-------------------


Fossils aren't needed for this. This provides much more detail than fossils. And you can do both design and implementation. Just give me a date that explains the relationships between these sequences. MET explains this beautifully.
   

---------------------QUOTE-------------------
   

---------------------QUOTE-------------------
   

---------------------QUOTE-------------------

I'm not sure what I'm supposed to learn from this, but I'm open to whatever it is you think this shows.  You'll just have to spell it out in layman's terms for me.

---------------------QUOTE-------------------


It's a starting point for examining the evidence and making predictions, something I predict that you're afraid to do. Where will a reptilian CB2 branch off on this tree? Why do both CB1 and CB2 fit into a single nested hierarchy?

---------------------QUOTE-------------------


I don't know the answers to those questions but I'm not afraid of them - I just need to figure out what you're asking and how you're arriving at your conclusions.
---------------------QUOTE-------------------


My conclusions don't matter--what matters is whether your hypothesis can explain this evidence and make predictions about evidence you haven't seen yet.
   

---------------------QUOTE-------------------
I need to see the evidence for myself - I won't just take your word for it.
---------------------QUOTE-------------------


I'm showing you evidence and you are denying that it is evidence.     
   

---------------------QUOTE-------------------
The tree is theoretical in that it is just a graphic representation of a proposed relationship.
---------------------QUOTE-------------------


Daniel, now you're just lying. There is nothing theoretical about that tree; it simply shows the mathematical relationships between the sequences. It is evidence. So, my question is, what hypothesis do YOU advance that explains these relationships and predicts the relationship of other data to these data?
   

---------------------QUOTE-------------------
How do you know these genes are not convergent?
---------------------QUOTE-------------------


If they had converged, they wouldn't be predicted to have this mathematical relationship with each other. However, for you to understand that, you'd have to grasp the concept of NESTED hierarchy, and you clearly don't.

Again, MET explains this relationship and makes predictions about where new sequences will be placed--before we have them.

Your job is to propose a hypothesis. Instead, I predict that you will continue to falsely claim that these trees are theoretical.
Posted by: JAM on Sep. 26 2007,09:47

Quote (Wesley R. Elsberry @ Sep. 26 2007,09:44)


---------------------QUOTE-------------------

Common Design would predict that lungfish and trout would be closer to each other than to humans.

---------------------QUOTE-------------------



We don't have to wait to know that Denton's assertion is < incorrect >.
---------------------QUOTE-------------------


That's a much more lucid explanation than the TO page to which I pointed Daniel, thanks.
Posted by: VMartin on Sep. 26 2007,12:21

Quote (Wesley R. Elsberry @ Sep. 26 2007,06:42)
     

---------------------QUOTE-------------------

Fossils are unnecessary? Wow. You do realize that fossils are empirical, observable evidence don't you?

---------------------QUOTE-------------------



<cop drama>

Lt. DS: The lab boys failed to retrieve any fingerprints in this case. We'll have to file it as unsolved.

Lt. JAM: Why would we do that? The lab boys did find the perp's hair at the scene. We got an excellent DNA match to a guy with a motive and no alibi. The fingerprints are unnecessary.

Lt. DS: Fingerprints are unnecessary? Wow. You do realize that fingerprints are empirical, observable evidence don't you?

[Rest of people in room look at Lt. DS, jaws dropping  in amazement.]

</cop drama>
---------------------QUOTE-------------------




The another drama about fossils proving evolution of man:

Somewhere in England. Medieval castle. JAM is making lecture to an audience standing in front of a big human skull.


JAM: And here we see the skull of the nobleman George Brave.

The audience adjourns to the next room. There is a small skull.  

JAM: And here we see the skull of the nobleman George Brave.

DS: But we have seen it in the previous room!

JAM: Yes, but this the skull when George Brave was a child.
Posted by: Arden Chatfield on Sep. 26 2007,12:23

Martin, since you reject the 'Darwinian' account of the evolution of horses, would you share with us what you think the correct explanation is?
Posted by: jeannot on Sep. 26 2007,12:29

Quote (JAM @ Sep. 26 2007,09:47)
 
Quote (Wesley R. Elsberry @ Sep. 26 2007,09:44)
 

---------------------QUOTE-------------------

Common Design would predict that lungfish and trout would be closer to each other than to humans.

---------------------QUOTE-------------------



We don't have to wait to know that Denton's assertion is < incorrect >.
---------------------QUOTE-------------------


That's a much more lucid explanation than the TO page to which I pointed Daniel, thanks.
---------------------QUOTE-------------------


Still, judging from that page, Cyt C gives some unexpected results. The carp should be closer to us than the lamprey.
And Sordaria is a fungus, isn't it? If so, it should also be closer to us than maize.
Probably, distance-based phylogenies are less reliable than cladistics. Or maybe this has something to do with Cyt C.

EDIT: it's Neurospora, not Sordaria.
Anyway, the problem remains. Yeasts (Saccharomyces) and Neurospora are ascomycetes. They should have a similar genetic distance compared to us. How can maize be between the two?

EDIT2: the problem is solved when considering the distance between Neurospora and yeast (that is quite high however).
Posted by: oldmanintheskydidntdoit on Sep. 26 2007,12:41

Quote (jeannot @ Sep. 26 2007,12:29)
Quote (JAM @ Sep. 26 2007,09:47)
 
Quote (Wesley R. Elsberry @ Sep. 26 2007,09:44)
 

---------------------QUOTE-------------------

Common Design would predict that lungfish and trout would be closer to each other than to humans.

---------------------QUOTE-------------------



We don't have to wait to know that Denton's assertion is < incorrect >.
---------------------QUOTE-------------------


That's a much more lucid explanation than the TO page to which I pointed Daniel, thanks.
---------------------QUOTE-------------------


Still, judging from that page, Cyt C gives some unexpected results. The carp should be closer to us than the lamprey.
And Sordaria is a fungus, isn't it? If so, it should also be closer to us than maize.
Probably, distance-based phylogenies are less reliable than cladistics. Or maybe this has something to do with Cyt C.
---------------------QUOTE-------------------


VMartin, what's your take on that?

:p
Posted by: Tracy P. Hamilton on Sep. 26 2007,15:02

Quote (Daniel Smith @ Sep. 26 2007,06:01)
 
Quote (JAM @ Sep. 25 2007,10:58)

D:Nested hierarchies are evidence of "top-down" evolution - where the higher categories are emplaced first - as opposed to evolution by speciation which would not create a nested hierarchy at all but would look more like a road map with lineages wandering aimlessly around.

Please explain how Darwin was wrong when he predicted nested hierarchies, then.

---------------------QUOTE-------------------


Can you supply that quote from Darwin?
     

---------------------QUOTE-------------------

They fit into multiple NHs, but one of "these characteristics" that you socleverly omitted was the superimposability of the NH of the assembled objects over any NH independently constructed from their components. Why did you omit that, Daniel? And if you disagree, show me the NHs you can construct from the relationships between lug nuts for GM cars and trucks.
...
But it couldn't be superimposed on NHs derived from their components. In fact, virtually none of the components of cars can be organized into nested hierarchies.

---------------------QUOTE-------------------


That's not true.  
---------------------QUOTE-------------------



So you claim.  Can you do it?

Let me choose automobiles, from the present and from the past (since I know nothing of your machines and I can presume you know something about automobiles).

Make a nested hierarchy of

Vega (1971, 1977)
El Camino (1959, 1987)
Model T (1908, 1927)
Model A (1903)
Model A (1927)
Corvair (1960, 1969)
Corvette (1953, 2007)
Porsche 911 (1964)
Altima (1993, 2007)
Avalon (1995, 2007)
S-10 (1982, 2004)
F150 (1948, 2007)
Metropolitan (1954, 1962)
Stanley Steamer (1903, 1923)
Edsel (1958)
Murano (2003, 2007)
Coupe Deville (1949, 1993)
Crossfire (2004, 2007)
Miata (1989, 2007)

Be sure to tell us what it is based on:
safety equipment, engine design, number of doors, etc.
Posted by: Wesley R. Elsberry on Sep. 26 2007,15:17



---------------------QUOTE-------------------

The another drama about fossils proving evolution of man:

---------------------QUOTE-------------------



A fairly major difference between our little dialogues is that I can show the various points of analogy that were retained in mine.
Posted by: jeannot on Sep. 26 2007,15:30

Quote (improvius @ Sep. 26 2007,08:27)
 
Quote (Daniel Smith @ Sep. 26 2007,05:39)
 

---------------------QUOTE-------------------
And you should think about my second objection: human, lungfish and trout. What does common design predict about their genes?
---------------------QUOTE-------------------

Common Design would predict that lungfish and trout would be closer to each other than to humans.  Perhaps, once they get the entire genomes sorted out, they'll find this to be true.  For now, with the concentration seemingly focused on coding regions - it appears not to be true.  I guess we'll have to wait and see.
---------------------QUOTE-------------------


I love this part.  "Of course the evidence is against me now.  But imaginary, contradictory evidence that has yet to be discovered will certainly support my argument."  This, more than anything else, drives home the hopelessness of trying to reason with creationists.
---------------------QUOTE-------------------


Well, he said  

---------------------QUOTE-------------------
I am convinced of one thing: whatever happened was by design.
---------------------QUOTE-------------------

???
Daniel, why not trust the evidence?
From the fossil record, we expected the lungfish and coelacanths to be more closely related to us than they are to the trout and other teleosts.
Why is that? Simply because many transitional fossils undoubtedly indicate that tetrapods descent from earlier sarcopterigian fishes (lungfish, coelacanth) during the devonian, while teleosts (ancestors of the trout and most common fishes) have been existing for a long time. This means they diverged earlier from sarcopterigians.
The fossil record also confirms the molecular phylogeny of human, trout and shark.

The same can be said about cetaceans, which diverged from other (cet)artiodactyls rather recently, and birds that diverged from earlier theropods, resulting also in a bunch of transitional fossils.
So why you think that the fossil record contradicts the current theory, I wonder.

At least, you admit that molecular data contradict you view. Most IDers would have ignored my objection.
I don't expect phylogenies based on non-coding sequences to be different. First, it will be hard do select regions that are conserved enough between those distant taxa.
We already have the complete genomes of human and zebrafish (teleost). I don't know about the lungfish or any other related group.
Posted by: jeannot on Sep. 26 2007,15:36

Quote (VMartin @ Sep. 26 2007,12:21)
The another drama about fossils proving evolution of man:
---------------------QUOTE-------------------


Martin, we'd love to hear your views on the evolution of man in the dedicated thread.
< http://www.antievolution.org/cgi-bin....;t=5188 >
See you there!  :)
Posted by: JAM on Sep. 26 2007,15:52

Quote (Tracy P. Hamilton @ Sep. 26 2007,15:02)
Make a nested hierarchy of

Vega (1971, 1977)...
Be sure to tell us what it is based on:
safety equipment, engine design, number of doors, etc.
---------------------QUOTE-------------------


As a former owner of a '74, I would group the Vega with fecal matter in an evolutionary hierarchy based on a number of common characteristics. Of course, nothing can be grouped with the aluminum engine's legendary oil consumption. I still remember what I said after it was T-boned at an intersection: "God, I hope this thing is totaled."
Posted by: Daniel Smith on Sep. 27 2007,01:54

Quote (Wesley R. Elsberry @ Sep. 26 2007,06:42)
<cop drama>
</cop drama>
---------------------QUOTE-------------------


I have my own cop drama for you.

Lt. DS: The lab boys found the murder weapon with the fingerprints of a known ex-con on it, plus a broken window with size 12 boot prints leading in and out of the house through it.  We'll have to arrest this man for the murder of this woman.

Lt. JAM: Why would we do that? The lab boys also found the husband's DNA all over the house and even on the wife's body.  He had obviously had recent contact with her.  Besides everyone knows that the husband always murders the wife in these cases. The fingerprints, weapon and bootprints are unnecessary.

Lt. DS: Fingerprints are unnecessary? Wow. You do realize that fingerprints are empirical, observable evidence don't you?

Lt. JAM: It doesn't matter - we've got the DNA!

[Rest of people in room look at Lt. JAM, jaws dropping  in amazement at his excellent police work.]

OK, now that we've dispensed with that foolishness, can we get back to talking about the evidence?
Posted by: Daniel Smith on Sep. 27 2007,03:05

Quote (Richard Simons @ Sep. 26 2007,07:54)
Daniel:                          

---------------------QUOTE-------------------
Right now, the company I work for is talking about rebuilding 8 machines (which are pretty much exact duplicates of one another) - one a year - over an 8 year period.  Even though we'll have the same company come in and do the work, we'll end up with 8 very different machines - since the technology will change every year as the machines go in.

---------------------QUOTE-------------------


But will any of this new technology be used in any machines made by any other company? Or in any machines made by your company to do other things?
---------------------QUOTE-------------------


You are right that different designers can have different hierarchies - and so the superimposability will not match exactly.  Many manufacturers tend to stick with the same suppliers for quite some time however, and when they do, you can track the evolution of the various parts - right alongside the evolution of the machine's design.                      

---------------------QUOTE-------------------

Because in biology that is not the case. A new technology, say mammary glands, that is successful in one group of organisms is never picked up by another group, fish for example. You will never find a fern with flowers or a treefrog with dragonfly wings. The one exception is in some micro-organisms, in which the transfer of genetic material is well-established.

---------------------QUOTE-------------------

You will also never find a CD player with a microwave oven in it, or a dresser with a 357 chevy motor... but that's another argument.

A possible reason that the nested hierarchy in nature is more perfect than that of other designed objects is for the simple reason that nature might just be the result of a single designer.  

If every part of a machine was designed by a single designer who could not borrow from any other designs or consult with any other designers, but could only refine and build upon his own ideas, we'd see a set of completely superimposable hierarchies for all the various components of a machine and for the machine itself.

This is what we see in nature - correct?

You are right about biological lineages; they do not borrow from one another (although many arrive at similar places) - they do seem to proceed as though constrained along a certain path though.  Once they get lungs, they don't lose them.  They don't ever revert back to an earlier lung-less state.  Schindewolf made many arguments from the evidence in the fossil record for the irreversibility of evolution and for it's procession down a seemingly defined pathway.  Berg also showed that organisms seem to develop features as if by law - and not through the arbitrary process of minute variations and selection.

If the nested hierarchy proves anything, it proves that higher order taxonomic groups came first, then proceeded to differentiate into lower and lower orders until finally arriving at the species level.  If differentiation started at the species level (as Darwin predicted), the higher orders would come last because - at their root - they would be almost exactly alike.  So you'd have species gradually becoming genuses that would gradually become families, then orders,... etc., until the most recent organisms would define the domain.

This is why the fossil record does not match Darwin's illustration.  The fossil record (from what I've seen, if you remove all the dotted lines - which are theoretical organisms anyway), looks like a grove of bushes - not one single bush.  If you take Darwins illustration and cover up the bottom half, it will look much closer to the graph that creeky belly supplied earlier in this thread.

Let me ask you - and all the other members here:
Does the process of cell differentiation during ontogeny produce superimposable nested hierarchies?

Because I think that ontogeny is a perfect model of how directed evolution would unfurl.

Schindewolf and Davison also championed this view and it makes perfect sense - since it reconciles the rapid differentiation found at the beginning of the fossil record with the overall genetic continuity that flows throughout.

       

---------------------QUOTE-------------------

BTW, although fossils loom large in the general public's mind (and I include creationists and IDers here) as far as biologists are concerned they form a minor part of the evidence for the theory of evolution. This has been the case right from Origin of Species.
---------------------QUOTE-------------------


I'd guess that the fossil record would be a major part of the case for the theory of natural selection if it wasn't so ambiguous in its support of it.
Posted by: Daniel Smith on Sep. 27 2007,03:21

Quote (Wesley R. Elsberry @ Sep. 26 2007,09:44)


We don't have to wait to know that Denton's assertion is < incorrect >.
---------------------QUOTE-------------------


You seem to be saying that the rate of mutational change is the same for all species over time.  Is that correct?

But we know that bacteria, fruit flies and mice - due to their rapid reproduction rates - will have more mutational changes over time than animals with slower reproduction rates.  That's why we use them for such studies isn't it?

So how do you reconcile these two seemingly polar opposite realities?
Posted by: Daniel Smith on Sep. 27 2007,03:24

Quote (Reciprocating Bill @ Sep. 26 2007,06:24)
I'd like to hear about your commitments and community identifications, a description of the non-scientific allegiances from which your biases arise.
---------------------QUOTE-------------------


OK.

You first.
Posted by: Alan Fox on Sep. 27 2007,04:44

Hi Daniel

First, my apologies for being off-topic with my Dawkins quote. I originally only wanted to post the bit in bold:    

---------------------QUOTE-------------------
Even if there were not a single fossil anywhere in the earth, the evidence for evolution would still be utterly overwhelming.
---------------------QUOTE-------------------


as the (for instance) biochemical arguments for common descent are so convincing (to me, at least) and complementary to the fossil evidence, but the surrounding passage seemed quite apt.

You once asked me (of Berg's "Nomogenesis"): "Have you even read the book?" The answer is no. Neither have I read "Origin of Species". But I'll strike a bargain with you. I will get and read a copy of "Nomogenesis" if you will get and read a copy of "The Ancestor's Tale" by Richard Dawkins.

You wrote:    

---------------------QUOTE-------------------
A possible reason that the nested hierarchy in nature is more perfect than that of other designed objects is for the simple reason that nature might just be the result of a single designer.
---------------------QUOTE-------------------



Ignoring for the moment the implication in your remark that a nested hierarchy is an example of a designed object, you appear to suggest that evidence for common descent is also evidence for common design.

The most convincing evidence of common descent for me is at the sub-cellular level: all life-forms based on carbon chemistry, chirality, universal* genetic code, common metabolic pathways, etc,. etc., but I guess you will say this is evidence for a common designer. So finding and presenting evidence will be fruitless if you see design where others see common descent.

(*with a few significant exceptions)
Posted by: Daniel Smith on Sep. 27 2007,05:30

Quote (Reciprocating Bill @ Sep. 25 2007,06:51)
But Daniel himself, per his own frank and repeated self-description, is operating from a decisive bias (one you appear to endorse), specifically that he prefers to learn from those who have been ignored, laughed at and shunned.
---------------------QUOTE-------------------


That's right.  I like scientists who are laughed at and shunned by the majority.  The majority are usually just empty headed sheep anyway. The majority just loves pablum.  Always has, always will.  They're the reason radio stations play the same songs over and over and over - they never want to hear new things.   They suck at the teet of mediocrity.

Me, I've always been this way.  When everyone was listening to ABBA, The Steve Miller Band, and all the other "happy, party, one-beat-fits-all" bands, I was listening to Black Sabbath - a band that cut against the grain and made people uncomfortable.  I liked that.  I was a social outcast and I liked it that way.  People who can't think for themselves gravitate towards the lowest common denominator.  They have to look around and see what everyone else is doing before they'll take a "stand" on anything.  They're afraid of being made fun of and they poke fun at anyone who doesn't "go along".  They're into whatever is "in" at the moment. I hate that.

I don't give a crap what any of you think of me either.  Laugh, shun - who cares.  I don't see any of you coming out with original ideas.  Most of you are probably committed atheists who need science to validate your belief system (or lack thereof).  You not only can't tolerate the thought of "a God", (oh my!), but you must make sure that science never reaches anything but atheistic conclusions.  So you laugh at and shun anyone who dares to bring a different interpretation to the evidence - any interpretation that makes you feel uncomfortable (weez), any interpretation that opens the door - even just a crack - to something remotely theistic.  No, anything like that  has to immediately be ridiculed.  Then you can all pat each other on the back and say "My don't we all think alike!".  It's sad because your minds are closed to anything new or different.  Majority rules!  Better stay safe - stick with whatever the MAJORITY says!

So, yeah, when the majority say one thing, I'm looking for a guy who's saying another.  Guys like Schindewolf, Berg, Davison, Bateson, Goldshmidt, Denton, Spetner - all of them.  These are guys who have the cahonas to take a real stand (without having to look around first).  

I don't think that's a bad way to be.
Posted by: Alan Fox on Sep. 27 2007,05:41

So, shall I cancel my order to Amazon, Daniel?
Posted by: Daniel Smith on Sep. 27 2007,06:35

Quote (JAM @ Sep. 26 2007,09:45)
   

---------------------QUOTE-------------------
 

---------------------QUOTE-------------------
you have the appealing quality of massive arrogance, made even more appealing by massive ignorance... so please save your lying for ignorant lay people.
---------------------QUOTE-------------------


Does that qualify?
---------------------QUOTE-------------------


No, because there's not a single name in there.
---------------------QUOTE-------------------


I guess - since you didn't actually call me an arrogant, ignorant liar, but only implied that I'm an arrogant, ignorant liar - technically I cannot say you called me names.

Please accept my sincerest apologies for accusing you of being a name-caller.  You're obviously only a name-implier.
Posted by: Daniel Smith on Sep. 27 2007,06:38

Quote (Alan Fox @ Sep. 27 2007,05:41)
So, shall I cancel my order to Amazon, Daniel?
---------------------QUOTE-------------------


Leo Berg was a biologist who traveled the world collecting samples and analyzing flora and fauna.  He then proposed his own theory of evolution based on his years of observations in the field.

What has Dawkins done?
Posted by: Reciprocating Bill on Sep. 27 2007,06:52

Quote (Daniel Smith @ Sep. 27 2007,06:30)
...So, yeah, when the majority say one thing, I'm looking for a guy who's saying another...

I don't think that's a bad way to be.
---------------------QUOTE-------------------


You forgot one part:

1) You claim to be interested in evidence gathered free of bias and preconception.

But you are not. You said so before, and you just said so again. You said so loud and clear, undeniably, in statements interpretable by atheists, theists, deists, and fundamentalist Christians alike without the slightest ambiguity: You are committed to a particular, decisive bias motivated by very specific religious preconceptions.

Therefore it is time for you to retract your various statements of 1) above. They are demonstrably, even defiantly false.

BTW, your bias isn't subtle. Because science is essentially a distributed, community activity that is self-correcting by a combination of empirical and consensus-based feedback mechanisms (e.g. public hypothesis testing, peer review), your stance guarantees that you will adopt positions inconsistent with the most secure findings in any given science, and similarly ignore the most compelling evidence.

Thanks for being forthcoming. Take care of that little detail above, and you're done.
Posted by: Reciprocating Bill on Sep. 27 2007,07:10

BTW, Daniel, A 2007 Gallup poll showed that as much as 66% of the US population believe "the idea that God created human beings pretty much in their present form at one time within the last 10,000 years," while another significant segment believe that God was involved in directing evolution or otherwise designing the current state of affairs. Only a minority of Americans (~20%, IIRC) understand and accept our current understanding of biological and human evolution (e.g. as a natural phenomenon), and just a tiny minority describe themselves as atheists.

Why doesn't your defiant nonconformity and disinterest in herd mentality result in your becoming an atheist who accepts evolution?
Posted by: Erasmus, FCD on Sep. 27 2007,07:13

there are examples of lineages that have gained and subsequently lost lungs.  you'll have to look them up.  i'll give you a hint...  nahhh, forget it.  tetrapod is all you get.
Posted by: oldmanintheskydidntdoit on Sep. 27 2007,07:34

Quote (Reciprocating Bill @ Sep. 27 2007,07:10)
Why doesn't your defiant nonconformity and disinterest in herd mentality result in your becoming an atheist who accepts evolution?
---------------------QUOTE-------------------


This is an excellent point. What defines what "herd" you choose the opposite POV of Daniel?
Posted by: Erasmus, FCD on Sep. 27 2007,08:34

Saying you want to be like Bateson is kinda dumb.  Bateson completely misunderstood both Galton's theory (which he attempted to build upon) and the consequences of the discovery of mendelian heredity.  Goldschmidt misunderstood this as well.  Davison is a verified nutcase, there is nothing to see there (I love it so!).

The 'tree of life' is more likely a web.  Bush is perhaps a bit better, but the strict bifurcating model is a bit simplistic because we KNOW that lateral gene transfer is important, not only in bacteria world but in plants and animals (see sunflower example I provided, check out the 50 years of research on Louisana iris hybridization)

You can get out of actually reading any of this, just stop and think about what happens at any branch on the tree:  if lineages split automatically and completely (which they don't, Schindewolf and Bateson and the saltationists were mostly wrong), then you have a branch.  But if the bifurcation takes any amount of time whatsoever, in a sympatric or parapatric population with gene flow, then you have a reticulating pattern.  We know this happens because gene trees show coalescence when considering multiple markers.  We also know this happens from many many many studies in nature:  pay attention and stop whining about the democratic fallacy.  (See Grant and Grant Science 296 Apr 2002).

Trees are NOT THEORETICAL GODDAMMIT.  They are measured relationships from data.  Don't bog the discussion down with whether or not there are theory-free observations.  You have already stated your prediction from common design (lungfish more related to trout), and it is demonstrably wrong.  The burden is upon you to disprove our theory of heredity and to show how these gene trees are incorrect.  I predict you will start pissing and moaning about renegade crackpot biologists from the early 20th century.
Posted by: Wesley R. Elsberry on Sep. 27 2007,09:04

JAM:



---------------------QUOTE-------------------

Since the relationships between these sequences represent the overwhelming evidence favoring MET that make fossils unnecessary, it would be the inevitable prediction for someone who claimed an interest in evidence.

---------------------QUOTE-------------------



Daniel,

I think that your take was not analogous.

However, the point remains that you are interested in phenomena that fossil evidence doesn't provide a complete basis for making conclusions upon. Other forms of evidence, such as DNA sequencing and proteomics, provides evidence that does bear upon the phenomena of interest.

That remains the case no matter what you think of how that point was made.
Posted by: Alan Fox on Sep. 27 2007,11:25

[quote=Daniel Smith,Sep. 27 2007,01:38][/quote]


---------------------QUOTE-------------------
What has Dawkins done?
---------------------QUOTE-------------------



I think it can be demonstrated that Dawkins had a respectable career as a research scientist (ethologist) before embarking on his current work as Charles Simonyi Professor of the Public Understanding of Science. (< Brief bio >). However this is beside the point. It is irrelevant whether a particular person is a paragon of virtue or an utter rotter, it is the idea and whether that idea is based on correct observation, measurement and interpretation that is important. In "The Ancestor's Tale", Dawkins cites authors and evidence, and there is a comprehensive bibliography.

As far as I can tell, Leo Berg was a perfectly respectable and diligent scientist, but it makes no difference to the strength or weakness of his ideas. If you recall, this thread was originally intended for you to show how the evolution of the horse is a problem for the current theory of evolution. I have not seen a great deal of evidence from you, yet.
Posted by: VMartin on Sep. 27 2007,11:37

Excellent Daniel! Folks here have no coherent answers anymore.   

Now - accepting the fact that there are gaps in fossil records, they are trying to turn discussion into DNA.

This is nothing more as an evasion. They wanted by studying macromelecules prove their unfouned hypothesis about natural selection and random mutation as efficient evolutionary forces. They think they know  secrets, what is behind the scene. But they remind more those technicians who studying trasmission of waves or describing details about TV screen think they know more about a broadcasted play. They think they    underestand better a  Shakespeare play, because they know in which frequency it is trasmitted or what is the sequence of bites representing it on CD.    

It was Adolf Portman who in his inauguration speech "Von der Idee des humanen" as rector of Basel University showed that such study is only part of biological work and such study itself is unable to explain evolution.

But I am afraid that his interesting works - especially Biologie und Geist and Neue wege der Biologie -  are also outdated and don't have place in the darwinian Golden library. Or better as folks here call it - it is not "primary literature".
Posted by: Arden Chatfield on Sep. 27 2007,11:42



---------------------QUOTE-------------------

This is nothing more as an evasion.
---------------------QUOTE-------------------



Speaking of people evading things, Martin,

A) what is your alternate explanation for the evolution of horses? Do you even have one?

B) do you believe common descent between apes and humans is true?

Why are you still too much of a coward to answer these questions? Did Davison tell you not to?
Posted by: jeannot on Sep. 27 2007,12:56

Quote (Daniel Smith @ Sep. 27 2007,03:21)
Quote (Wesley R. Elsberry @ Sep. 26 2007,09:44)


We don't have to wait to know that Denton's assertion is < incorrect >.
---------------------QUOTE-------------------


You seem to be saying that the rate of mutational change is the same for all species over time.  Is that correct?

But we know that bacteria, fruit flies and mice - due to their rapid reproduction rates - will have more mutational changes over time than animals with slower reproduction rates.
---------------------QUOTE-------------------


Well, it could be true, but there are many factors to take into account, whether we have sexual reproduction or not, for instance.
Also, if you want to make a comparison between bacteria and multicellular organisms, you need to compare mutation rates per replication, not per generations. There are several cell replications separating the egg cell from the gametes in animals and plants, though I agree, that replication time is usually shorter in prokaryotes.
But more importantly, in absolute time, the relation between substitutions (=fixed mutations) rates and mutation rates (negatively correlated with generation time) is true for neutral sites. Phylogenies involving very distant taxa such as eukaryotes and bacteria are built for genes under very strong selection, namely genes coding for rRNAs.
These are unlikely do evolve by genetic drift, so we don't really expect their substitution rates to depend on generation time, but on other external factors, which may reflect absolute time. I shall add the the molecular clock is not always the rule, especially between very distant lineages. But modern phylogenetic methods don't strictly rely on it.

And lastly, even if you remark is valid, it contradicts Denton's view.

So we're still waiting for you to demonstrate how the fossil record disprove the current theory of evolution.
I showed it was quite the contrary. What is your response to my objection?
Posted by: Erasmus, FCD on Sep. 27 2007,14:51

VMartin, so you do not believe in the material theory of particulate inheritance?  This is what your obfuscation boils down to.  

If you have a better theory of inheritance, let's hear it.

[stage whisper]  His brain vat fluid is getting low and interrupting his interface with the Matrix.  Somebody pee in it!
Posted by: Wesley R. Elsberry on Sep. 27 2007,16:52



---------------------QUOTE-------------------

You seem to be saying that the rate of mutational change is the same for all species over time.  Is that correct?

---------------------QUOTE-------------------



No.
Posted by: Richard Simons on Sep. 27 2007,21:51

Daniel wrote  

---------------------QUOTE-------------------
I'd guess that the fossil record would be a major part of the case for the theory of natural selection if it wasn't so ambiguous in its support of it.
---------------------QUOTE-------------------


Oh aye? Just what are these ambiguities you think are so important? Does this bring you back to the horse evolution that prompted you to come here? Or are you thinking of the old creationist stand-byes, the Cambrian explosion, dinosaur fossils with soft tissue, no intermediate fossils and no fossils with half a fin or half a wing?

Coming back to the nested hierarchies that you seem to persist in misunderstanding; you write
 

---------------------QUOTE-------------------
You will also never find a CD player with a microwave oven in it, or a dresser with a 357 chevy motor
---------------------QUOTE-------------------


But you could find exactly the same electronic chip in a truck, a ship, a railway locomotive, an elevator, a sewing machine and a cash register. On the other hand, not one of the 'ancestors' of these machines would have the same kind of electronic chip, or even anything electrical.

This situation never arises in biology. Whenever organisms share a particular feature you will find that this group of organisms also has other features that are absent in others, or the feature serves the same purpose in each organism but is structurally different (e.g. wings, eyes).

In another post you suggest the same effect could have arisen if there were multiple designers. True. I have often thought it looks as though one god started it off then farmed it out to other gods, who in turn subcontracted to lesser gods - a sort of pyramid scheme of gods ('Here, I've got mammals started off. Now you take a few off to Australia and we'll see how you do. Don't muck around with the basics and no sneaking a look at what gods are doing anywhere else'). How many gods are you suggesting?
Posted by: Henry J on Sep. 27 2007,23:10



---------------------QUOTE-------------------
How many gods are you suggesting?
---------------------QUOTE-------------------



Sounds to me like one per gene pool. :p

Henry
Posted by: Daniel Smith on Sep. 28 2007,02:38

Quote (JAM @ Sep. 25 2007,09:09)
   
Quote (Daniel Smith @ Sep. 25 2007,02:11)
All the super-specialized breeds would probably also eventually go away - as their gene pool became more and more watered down through breeding as well.
---------------------QUOTE-------------------


The gene pool would be enriched. Domesticated dogs have high homozygosity from inbreeding, not low.
---------------------QUOTE-------------------


Yes, but most dogs breeds are too domesticated to survive in the wild.  Surely many have lost the ability to hunt, others will have lost the ability to defend themselves against predators.  Reintroducing them to the wild would probably result in an immediate knockout of many of these breeds - thereby removing much of that enrichment from the gene pool.
Natural selection is a cold mistress.  It works by killing.
As Schindewolf said, "Selection is only a negative principle, an eliminator, and as such is trivial." (pg. 360)
Posted by: oldmanintheskydidntdoit on Sep. 28 2007,02:47

Quote (Daniel Smith @ Sep. 28 2007,02:38)
Quote (JAM @ Sep. 25 2007,09:09)
     
Quote (Daniel Smith @ Sep. 25 2007,02:11)
All the super-specialized breeds would probably also eventually go away - as their gene pool became more and more watered down through breeding as well.
---------------------QUOTE-------------------


The gene pool would be enriched. Domesticated dogs have high homozygosity from inbreeding, not low.
---------------------QUOTE-------------------


Yes, but most dogs breeds are too domesticated to survive in the wild.  Surely many have lost the ability to hunt, others will have lost the ability to defend themselves against predators.  Reintroducing them to the wild would probably result in an immediate knockout of many of these breeds - thereby removing much of that enrichment from the gene pool.
Natural selection is a cold mistress.  It works by killing.
As Schindewolf said, "Selection is only a negative principle, an eliminator, and as such is trivial." (pg. 360)
---------------------QUOTE-------------------


Have you been to the western world lately? There's not many predators that could take on a sausage dog anymore. And there are also cities full of feral cats (descended no doubt from domesticated stock).

And my Siamese cat, bred to the point of insanity, would have no trouble surviving in the wild

"it moved, I caught it, I tried to eat it, Rinse, repeat"
Posted by: Daniel Smith on Sep. 28 2007,03:31

Quote (Alan Fox @ Sep. 27 2007,11:25)
If you recall, this thread was originally intended for you to show how the evolution of the horse is a problem for the current theory of evolution. I have not seen a great deal of evidence from you, yet.
---------------------QUOTE-------------------


You're right.  

In order to keep this thread on topic, I will try to keep my posts focused on the work of Schindewolf and Berg and (at least in the case of Schindewolf) also on the evolution of the horse.

Berg doesn't say a lot about horses other than this from section IV, "Convergence":
               

---------------------QUOTE-------------------
"At the very time when in North America the Equidae were being evolved, forms of the order Litopterna were being elaborated in South America in the plains of the Argentine.  The latter are extinct ungulates, in many respects recalling horses: they had also lost the lateral digits of their limbs, and for progression made use of the median digit; their extremities and neck were likewise lengthened, and in the former, the ball-and-socket joints, by which movements in all directions could be accomplished, were being gradually supplanted by pulley joints, which restricted their limbs to being moved only backwards and forwards; their teeth lengthened and grew more complex (although no cement was present).  This group was extinct in South America before the arrival of horses. The Litopterna, or pseudo-horses, thus copied the horses in many ways.
The same course (as to limbs and teeth) as in horses was followed in the evolution of camels in the New World, and of deer, antelopes, sheep and oxen in the Old"
---------------------QUOTE-------------------

Nomogenesis, pg. 212.

As for Schindewolf's position, why don't I just start by using the same quote I provided for you over at Brainstorms:        

---------------------QUOTE-------------------
To this extent,the one toed horse must be regarded as the ideal running animal of the plains. It's early Tertiary ancestors had four digits on the front feet and three on the hind feet, and low crowned cheek teeth. Since in the later Tertiary, an expansion of plains at the expense of forests has been observed, this change in environmental conditions and the consequent change in the mode of life has been represented as the cause of linear, progressive selection leading up to the modern horse.
However, in the formulation of this view, not enough consideration has been given to the fact that the evolutionary trend of reduction in the number of toes had already been introduced long before the plains were occupied in the early Tertiary by the precursors of the horse; these inhabited dense scrub, meaning that they lived in an environment where the reduction of the primitive five-toed protoungulate foot was not an advantage at all. In the descendants, then, the rest of the lateral toes degenerated and the teeth grew longer step by step... regardless of the mode of life, which... fluctuated repeatedly, with habitats switching around among forests, savannas, shrubby plains, tundra, and so on.
If selection alone were decisive in this specialization trend, we would have to ascribe to it a completely incomprehensible purposefulness...
---------------------QUOTE-------------------

Basic Questions in Paleontology pp. 358-359, (emphasis his)

Both of these men intently studied real examples from nature and the fossil record and came to the same conclusions:
1. That evolution of types happened suddenly - not gradually.
2. That subsequent evolution proceeded as if constrained by laws.
3. That natural selection had nothing to do with the formation of any organ.
Posted by: Daniel Smith on Sep. 28 2007,04:05

Quote (Richard Simons @ Sep. 27 2007,21:51)


Coming back to the nested hierarchies that you seem to persist in misunderstanding; you write
             

---------------------QUOTE-------------------
You will also never find a CD player with a microwave oven in it, or a dresser with a 357 chevy motor
---------------------QUOTE-------------------


But you could find exactly the same electronic chip in a truck, a ship, a railway locomotive, an elevator, a sewing machine and a cash register. On the other hand, not one of the 'ancestors' of these machines would have the same kind of electronic chip, or even anything electrical.
---------------------QUOTE-------------------


That's demonstrably not true.  In electric circuits, the precursors to IC chips were soldered transistor circuit boards, the precursors to those were hand-wired transistor circuit boards, the precursors to those were relay logic and tube circuits, the precursors to those were manually switched electric circuits.   So the ancestors to a modern elevator controlled with IC chips would be an elevator controlled with soldered transistor circuit boards, then one with hand-wired circuit boards, then relays and tubes, then manually operated electric switches.
         

---------------------QUOTE-------------------

This situation never arises in biology. Whenever organisms share a particular feature you will find that this group of organisms also has other features that are absent in others, or the feature serves the same purpose in each organism but is structurally different (e.g. wings, eyes).

---------------------QUOTE-------------------


Every organism has features that are absent in others - even within the same species.  That proves little to nothing.  But it's the similarities in different lineages that are the most troublesome for your theory since many are structurally similar.

Berg's book is filled with examples, but I'll give you one of his brief summations:    

---------------------QUOTE-------------------
The comparative anatomy of animals supplies a number of striking examples of a definite direction in evolution.  Among vertebrates we may mention the evolution of teeth in reptiles and mammals, the gradual ossification of the vertebral column, a reduction in the number of the bones in the skull, the transformation of a two-chambered heart into a three- and four-chambered organ in connection with a corresponding complexity in the circulatory system, the evolution of the brain... the whole subject of comparative anatomy literally bristles with facts exemplifying development in a definite direction
---------------------QUOTE-------------------

Nomogenesis, pg.121
         

---------------------QUOTE-------------------
In another post you suggest the same effect could have arisen if there were multiple designers. True. I have often thought it looks as though one god started it off then farmed it out to other gods, who in turn subcontracted to lesser gods - a sort of pyramid scheme of gods ('Here, I've got mammals started off. Now you take a few off to Australia and we'll see how you do. Don't muck around with the basics and no sneaking a look at what gods are doing anywhere else'). How many gods are you suggesting?
---------------------QUOTE-------------------

You misread me.  I said the nested hierarchy is evidence of a single designer - since the parts and the organisms both make for superimposable nested hierarchies - without the anomalies sometimes seen when parts are produced by multiple designers.
Posted by: Daniel Smith on Sep. 28 2007,04:09

Quote (oldmanintheskydidntdoit @ Sep. 28 2007,02:47)
 
Have you been to the western world lately? There's not many predators that could take on a sausage dog anymore. And there are also cities full of feral cats (descended no doubt from domesticated stock).

And my Siamese cat, bred to the point of insanity, would have no trouble surviving in the wild
---------------------QUOTE-------------------


I've lived in the city and the country.  Your Siamese cat might survive in the wild, but judging by the number of wild barn cats that almost starved to death on our ranch (until we started feeding them), I'd say that's no guarantee.
Posted by: Daniel Smith on Sep. 28 2007,04:12

Quote (oldmanintheskydidntdoit @ Sep. 28 2007,02:47)
 
And there are also cities full of feral cats (descended no doubt from domesticated stock).
---------------------QUOTE-------------------


OH, And the city doesn't really count as "the wild" now does it?
Posted by: Reciprocating Bill on Sep. 28 2007,05:24

Quote (Daniel Smith @ Sep. 28 2007,05:05)
You misread me.  I said the nested hierarchy is evidence of a single designer - since the parts and the organisms both make for superimposable nested hierarchies - without the anomalies sometimes seen when parts are produced by multiple designers.
---------------------QUOTE-------------------


What all this really illustrates is the emptiness of the "designer" hypothesis in a scientific context.

ANY state of affairs in nature can be reconciled with the design hypothesis. Observe nested hierarchy? "Nested hierarchy is evidence of a single designer." DON'T observe nested hierarchy? "A designer is not constrained by common descent" etc. There is NO outcome in nature that cannot be reconciled post hoc with the design hypothesis, with one designer or multiple designers, with good designers or bad designers, and so on.  

It follows that patterns of descent fail to put design to any test; hence nested hierarchy isn't "evidence of a single designer" or of any other design hypothesis.

This may be contrasted with Darwin's predictions: to fail to find nested hierarchy in nature would be to falsify his model of evolution.

(Daniel: Still waiting for you to retract your patently false claim vis interest in data with no biases or preconceptions.)
Posted by: Daniel Smith on Sep. 28 2007,05:45

Quote (Wesley R. Elsberry @ Sep. 26 2007,09:44)
We don't have to wait to know that Denton's assertion is < incorrect >.
---------------------QUOTE-------------------


So what I hear you saying is that the equidistant sequence space between Cytochrome-C among the various groups is more a function of time than anything else.  Is that correct?

If that is correct, then that is completely in keeping with (and in fact would be a prediction of) common descent by design.

Common descent by design would predict that there would be mathematical patterns within the evolution of sequences and that those patterns would be based on time and other internal factors rather than any outside factors - since divergence would occur according to plan - not according to chance, environment, or any other external influences.
Posted by: oldmanintheskydidntdoit on Sep. 28 2007,06:05

Quote (Daniel Smith @ Sep. 28 2007,05:45)
Quote (Wesley R. Elsberry @ Sep. 26 2007,09:44)
We don't have to wait to know that Denton's assertion is < incorrect >.
---------------------QUOTE-------------------


So what I hear you saying is that the equidistant sequence space between Cytochrome-C among the various groups is more a function of time than anything else.  Is that correct?

If that is correct, then that is completely in keeping with (and in fact would be a prediction of) common descent by design.

Common descent by design would predict that there would be mathematical patterns within the evolution of sequences and that those patterns would be based on time and other internal factors rather than any outside factors - since divergence would occur according to plan - not according to chance, environment, or any other external influences.
---------------------QUOTE-------------------


Is there anything that design predicts that evolution does not?

Seems as everything evolution can do, the designer(s) can also do. So your position is essentially meaningless unless you can somehow differentiate the two.

Is there a differentiation somewhere between the two things?

Are there any predictions of design that are not retrospective? I.E make a prediction for a something that's currently unknown that can be tested and the result will unambigiously say "designed" or "evolved".

If not, it seems to be all "design predictions" are worthless if they predict exactly the same things that evolution does.

Pointless.

Can you point me to a list of as yet untested "predictions" that common descent by design makes, or are they only available retrospectively? If the latter, then give up now, you'll never be able to convince anybody.
Posted by: carlsonjok on Sep. 28 2007,06:11

Quote (Daniel Smith @ Sep. 28 2007,04:12)
Quote (oldmanintheskydidntdoit @ Sep. 28 2007,02:47)
 
And there are also cities full of feral cats (descended no doubt from domesticated stock).
---------------------QUOTE-------------------


OH, And the city doesn't really count as "the wild" now does it?
---------------------QUOTE-------------------


For whom?  Certainly, it isn't the wild for humans inasmuch as it consolidates all sorts of things, like grocery stores and homes, for our convenience.  But for feral cats, alas without currency to buy themselves a bag of Friskies or take out a mortgage, it is the wild. Perhaps you would like to define the characteristics of an eco-system and then explain to us how an urban environment is not one?  

Never mind.  After over six pages and you haven't even mentioned a horse and that is the reason you are here, no?
Posted by: Erasmus, FCD on Sep. 28 2007,07:06

daniel's inherent belief as humans distinct and set apart from nature is showing.

cities aren't really the wild, eh?

the edges of deserts aren't really the wild, eh?

tropical oceans aren't really the wild, eh?

a grove of paw paws aren't really the wild, eh?

daniel, natural selection shapes POPULATIONS.  castle showed that selection modified populations beyond the 'regression to the type' that you seem to believe in.  Other than it being a trivial mathematical exercise, you have no reason for continuing to suppose that selection is not a creative force when supplied with a panoply of diversity.  

otherwise, all you are left with is 'The Designer has an inordinate fondness for beetles' and 'The designer likes wolves so much he made a marsupial knockoff model' (that is false from any systematic perspective but since you, like a five year old and VMartin, seem to be stuck on your perception of phenotypes perhaps it makes sense).

and as RBill keeps hammering, your 'design' model is consistent with ANY POSITIVE OR NEGATIVE OBSERVATION.  IT SAYS NOTHING.
Posted by: oldmanintheskydidntdoit on Sep. 28 2007,07:28

yeah, I always liked the beetle point.


---------------------QUOTE-------------------
There are over 370,000 known species of beetle and they are found in every land and freshwater habitat in the world.
---------------------QUOTE-------------------



< National Beetle Week! >

What does the "designed" point of view have to say about the fact there are some many species of beetle?

Daniel, is it your contention that all beetles evolved from a single beetle "kind" on the Ark, or don't you subscribe to that level of idiocy?

If you don't accept the Ark, what does "intelligent design" give as the reason for the sheer numbers other then 'The Designer has an inordinate fondness for beetles'
Posted by: George on Sep. 28 2007,07:44

Quote (Daniel Smith @ Sep. 28 2007,03:31)


---------------------QUOTE-------------------
However, in the formulation of this view, not enough consideration has been given to the fact that the evolutionary trend of reduction in the number of toes had already been introduced long before the plains were occupied in the early Tertiary by the precursors of the horse; these inhabited dense scrub, meaning that they lived in an environment where the reduction of the primitive five-toed protoungulate foot was not an advantage at all. In the descendants, then, the rest of the lateral toes degenerated and the teeth grew longer step by step... regardless of the mode of life, which... fluctuated repeatedly, with habitats switching around among forests, savannas, shrubby plains, tundra, and so on.
If selection alone were decisive in this specialization trend, we would have to ascribe to it a completely incomprehensible purposefulness...
---------------------QUOTE-------------------

Basic Questions in Paleontology pp. 358-359, (emphasis his)
---------------------QUOTE-------------------


So basically Schindewolf is saying that horses developed single-toed hooves regardless of the selection pressures applied?  How does he know what those pressures were?  How does he know the scrub was dense?  Paleoecologists today can identify what species were present in the landscape at a point in time, but have much more difficulty in determining vegetation structure.  This has led to disagreements over what the European landscape of most of the Holocene was.  Yes there were lots of oak trees present, but was it closed forest?  Was it patches of scrub interspersed with grassy plains?  Was it widely spaced parkland-like trees?

In other words, what was the quality of his data and how far is he spreading it with rhetoric?
Posted by: JAM on Sep. 28 2007,07:58

Quote (Daniel Smith @ Sep. 28 2007,02:38)
 
Quote (JAM @ Sep. 25 2007,09:09)
       
Quote (Daniel Smith @ Sep. 25 2007,02:11)
All the super-specialized breeds would probably also eventually go away - as their gene pool became more and more watered down through breeding as well.
---------------------QUOTE-------------------


The gene pool would be enriched. Domesticated dogs have high homozygosity from inbreeding, not low.
---------------------QUOTE-------------------


Yes, but most dogs breeds are too domesticated to survive in the wild.
---------------------QUOTE-------------------


The ones that survive and reproduce (survival isn't sufficient) will tend to be the ones that are less inbred, making the "gene pool" deeper. Your arrow is in the wrong direction.
 

---------------------QUOTE-------------------
Reintroducing them to the wild would probably result in an immediate knockout of many of these breeds - thereby removing much of that enrichment from the gene pool.
---------------------QUOTE-------------------


The loss of the more inbred breeds would enrich the gene pool, not deplete it.
 

---------------------QUOTE-------------------
Natural selection is a cold mistress.  It works by killing.
---------------------QUOTE-------------------


No, it works just as well be preventing reproduction. You can live to 150, but if you leave no children, your fitness is zero.


---------------------QUOTE-------------------
As Schindewolf said, "Selection is only a negative principle, an eliminator, and as such is trivial." (pg. 360)
---------------------QUOTE-------------------


You've forgotten yet again that quotes aren't evidence. Why not admit that you were lying when you claimed an interest in evidence? Look at how you've run away from discussing the massive sequence evidence that makes fossils unnecessary, after you realized that you have no hypothesis that explains the data. BTW, Schindewolf is wrong. Look at how your body normally prevents antibodies that recognize your own antigens from being produced.
Posted by: Richard Simons on Sep. 28 2007,08:19

Daniel

---------------------QUOTE-------------------
So the ancestors to a modern elevator controlled with IC chips would be an elevator controlled with soldered transistor circuit boards, then one with hand-wired circuit boards, then relays and tubes, then manually operated electric switches.

---------------------QUOTE-------------------


But to be equivalent to a nested hierarchy it would have to have exactly the same electronic chip as it does now. So would Cugnot's steam wagon (an ancestral truck), Locomotion (an ancestral railway locomotive) and my Grandmother's treadle sewing machine. That is the only way in a nested hierarchy that the descendents could all have exactly the same feature.
Not only that, but the windshield wipers found on some of these machines would only be found in machines with this specific electronic chip and no others. The windshield wipers on a car with a different chip would be structurally different, although they could look similar and perform a similar function.
Posted by: Peter Henderson on Sep. 28 2007,09:04

The evolution of the horse isn't the only problem for Darwinian evolution. Don't forget about the banana:

< http://www.youtube.com/watch?v=2z-OLG0KyR4 >  

 :)
Posted by: k.e on Sep. 28 2007,10:19

Ftttt d dangbana

there's still hope

< http://www.youtube.com/watch?v=oHnAOgONU6I&NR=1 >

HEY DAVETARD WHENYA GOIN 2DO UR REDNECK TRUCK VIDEO ON UTUBE WITH THE CHAINSAWGUN ISAW A UFO AND MY ASS GOT BIGGER VIDEO VIDEO?
UR MUSHROOMS IS MAKIN MORE NOISE THAN U IS.
Posted by: Tracy P. Hamilton on Sep. 28 2007,13:15

Quote (Daniel Smith @ Sep. 28 2007,05:45)
 
Quote (Wesley R. Elsberry @ Sep. 26 2007,09:44)
We don't have to wait to know that Denton's assertion is < incorrect >.
---------------------QUOTE-------------------


So what I hear you saying is that the equidistant sequence space between Cytochrome-C among the various groups is more a function of time than anything else.  Is that correct?


---------------------QUOTE-------------------



That is incorrect.  Time doesn't come into it, but a nesting based on differences.  It really is quite simple in principle, which is why you should try making one.  Biologists don't have to for extant life, since Linneaus did that hundreds of years ago.

I gave you a list of cars (including first and last years the model was made) to make a nested hierarchy from.  Can you do so on the basis of time?
Posted by: JohnW on Sep. 28 2007,14:11

I love ATBC.

Quote (Reciprocating Bill @ Sep. 28 2007,03:24)

ANY state of affairs in nature can be reconciled with the design hypothesis. Observe nested hierarchy? "Nested hierarchy is evidence of a single designer." DON'T observe nested hierarchy? "A designer is not constrained by common descent" etc. There is NO outcome in nature that cannot be reconciled post hoc with the design hypothesis, with one designer or multiple designers, with good designers or bad designers, and so on.  

---------------------QUOTE-------------------



Twenty-one minutes later:

Quote (Daniel Smith @ Sep. 28 2007,03:45)
If that is correct, then that is completely in keeping with (and in fact would be a prediction of) common descent by design.

---------------------QUOTE-------------------


Posted by: jeannot on Sep. 28 2007,14:21

Quote (Daniel Smith @ Sep. 28 2007,05:45)
Quote (Wesley R. Elsberry @ Sep. 26 2007,09:44)
We don't have to wait to know that Denton's assertion is < incorrect >.
---------------------QUOTE-------------------


So what I hear you saying is that the equidistant sequence space between Cytochrome-C among the various groups is more a function of time than anything else.  Is that correct?

If that is correct, then that is completely in keeping with (and in fact would be a prediction of) common descent by design.
---------------------QUOTE-------------------


Common descent by design?
Can you develop, Daniel?
Posted by: Alan Fox on Sep. 29 2007,04:17

Daniel wrote:

---------------------QUOTE-------------------
In order to keep this thread on topic, I will try to keep my posts focused on the work of Schindewolf and Berg and (at least in the case of Schindewolf) also on the evolution of the horse.
---------------------QUOTE-------------------



OK. (Although it is not a hanging offence to move off topic by gradual steps. Saltational leaps of logic are a different matter.  :) )  

---------------------QUOTE-------------------
Berg doesn't say a lot about horses...
---------------------QUOTE-------------------



So, is there another example that better illustrates Berg's alternative to RM + NS?  

---------------------QUOTE-------------------
As for Schindewolf's position, why don't I just start by using the same quote I provided for you over at Brainstorms...:
---------------------QUOTE-------------------



OK. The RM + NS theory claims that organisms are shaped by their environments. Where a population exists and is subject to change in that environment, selection will result in adaptive change or extinction. Adaptation is not predictive.

From your quote, Schindewolf is claiming that horses began adapting to life on the plains before arriving in that environment. If true, this would indeed be a grave problem for evolution.

How does Schindewolf establish the prevailing climate and vegetation associated with a particular fossil?
Posted by: jeannot on Sep. 29 2007,05:48

Quote (Alan Fox @ Sep. 29 2007,04:17)
Daniel wrote:

---------------------QUOTE-------------------
In order to keep this thread on topic, I will try to keep my posts focused on the work of Schindewolf and Berg and (at least in the case of Schindewolf) also on the evolution of the horse.
---------------------QUOTE-------------------



OK. (Although it is not a hanging offence to move off topic by gradual steps. Saltational leaps of logic are a different matter.  :) )    

---------------------QUOTE-------------------
Berg doesn't say a lot about horses...
---------------------QUOTE-------------------



So, is there another example that better illustrates Berg's alternative to RM + NS?    

---------------------QUOTE-------------------
As for Schindewolf's position, why don't I just start by using the same quote I provided for you over at Brainstorms...:
---------------------QUOTE-------------------



OK. The RM + NS theory claims that organisms are shaped by their environments. Where a population exists and is subject to change in that environment, selection will result in adaptive change or extinction. Adaptation is not predictive.

From your quote, Schindewolf is claiming that horses began adapting to life on the plains before arriving in that environment. If true, this would indeed be a grave problem for evolution.
---------------------QUOTE-------------------


One would have to exclude the possibility of exaptation, though. And that's certainly not straightforward.
Posted by: Alan Fox on Sep. 29 2007,05:57



---------------------QUOTE-------------------
One would have to exclude the possibility of exaptation, though.
---------------------QUOTE-------------------



Using my argument from personal incredulity, what other advantage of loss of digits has been suggested? ???
Posted by: Steverino on Sep. 29 2007,07:25

Daniel, as you use it, Design predicts everything whether it happened or not.  It's not an explanation but, and excuse.
Posted by: Richard Simons on Sep. 29 2007,10:40



---------------------QUOTE-------------------
Using my argument from personal incredulity, what other advantage of loss of digits has been suggested?
---------------------QUOTE-------------------


Less problem with hanging toenails?
Posted by: carlsonjok on Sep. 29 2007,11:02

Quote (Richard Simons @ Sep. 29 2007,10:40)


---------------------QUOTE-------------------
Using my argument from personal incredulity, what other advantage of loss of digits has been suggested?
---------------------QUOTE-------------------


Less problem with hanging toenails?
---------------------QUOTE-------------------


I realize you are making a funny, but I would note that structural problems with hoof wall, which is essentially the equivalent of a toe nail, are quite serious. Severe problems, like acute laminitis (founder), can lead to the horse having to be euthanized.  Remember that the next time you have an ingrown nail. ;)
Posted by: Richard Simons on Sep. 29 2007,11:10

Someotherguy:

---------------------QUOTE-------------------
I had that same problem, but I emailed steve and, presumably, he fixed it for me because the problem went away.

---------------------QUOTE-------------------


On one of the occasions when I was able to get on I posted < here > but I never saw a response so I assumed it was unfixable.

(But thanks to composing this, I've found out why the http key was not working.)
Posted by: Richard Simons on Sep. 29 2007,11:11

Sorry - wrong thread.
Posted by: Richard Simons on Sep. 29 2007,11:18

Carlsonjok:
I did not think of it when I responded about hanging toenails, but now you mention it I remember I've read enough of James Herriott and Dick Francis to know that laminitis can be a severe problem. I've also frequently seen sheep in Wales eating on their knees because of what I gather is laminitis caused by wet conditions.
Posted by: carlsonjok on Sep. 29 2007,11:32

Quote (Richard Simons @ Sep. 29 2007,11:18)
Carlsonjok:
I did not think of it when I responded about hanging toenails, but now you mention it I remember I've read enough of James Herriott and Dick Francis to know that laminitis can be a severe problem. I've also frequently seen sheep in Wales eating on their knees because of what I gather is laminitis caused by wet conditions.
---------------------QUOTE-------------------


I don't know anything about sheep, but with horses the link between wet weather and laminitis is more correlation than causation.  While laminitis can have mechanical causes, it is quite often related to dramatic changes in diet. For example, turnout on lush pasture after a diet of mostly hay can trigger it.  I have a Welsh Pony that has had two bouts of founder, both related to such diet changes during wet spring weather.

So, anyone want to wager whether Daniel will be back or not?
Posted by: JAM on Sep. 29 2007,14:17

Quote (George @ Sep. 28 2007,07:44)
Quote (Daniel Smith @ Sep. 28 2007,03:31)


---------------------QUOTE-------------------
However, in the formulation of this view, not enough consideration has been given to the fact that the evolutionary trend of reduction in the number of toes had already been introduced long before the plains were occupied in the early Tertiary by the precursors of the horse; these inhabited dense scrub, meaning that they lived in an environment where the reduction of the primitive five-toed protoungulate foot was not an advantage at all. In the descendants, then, the rest of the lateral toes degenerated and the teeth grew longer step by step... regardless of the mode of life, which... fluctuated repeatedly, with habitats switching around among forests, savannas, shrubby plains, tundra, and so on.
If selection alone were decisive in this specialization trend, we would have to ascribe to it a completely incomprehensible purposefulness...
---------------------QUOTE-------------------

Basic Questions in Paleontology pp. 358-359, (emphasis his)
---------------------QUOTE-------------------


So basically Schindewolf is saying that horses developed single-toed hooves regardless of the selection pressures applied?
---------------------QUOTE-------------------


Just to clarify, horses don't (yet) have single-toed hooves. Bones (metacarpal/metatarsal) from the two flanking (2 and 4) digits still remain. They serve no useful purpose (they often become inflamed or broken), while the tops of the front ones still form part of a joint:

< http://www.omafra.gov.on.ca/english/livestock/horses/facts/89-093.htm >

If they suggest design, their designer was an idiot. Maybe Daniel can explain the elegance of their design if he disagrees.
Posted by: Daniel Smith on Sep. 30 2007,15:32

Quote (oldmanintheskydidntdoit @ Sep. 28 2007,06:05)
 
Is there anything that design predicts that evolution does not?

Seems as everything evolution can do, the designer(s) can also do. So your position is essentially meaningless unless you can somehow differentiate the two.

Is there a differentiation somewhere between the two things?

---------------------QUOTE-------------------


I could say the same thing about the currently held theory.  Is there anything that will ever be found that you won't somehow make to fit and eventually make to be a prediction of the currently held theory?
Are  protein synthesis, cell division, sexual reproduction, intelligence, speech, flight, sight, hearing, circulatory systems, etc. predicted by the current theory?
Since the current theory predicts "happy accidents", anything useful is then said to be predicted.
ID predicts useful features as well, so we're back to square one aren't we?
   

---------------------QUOTE-------------------

Are there any predictions of design that are not retrospective? I.E make a prediction for a something that's currently unknown that can be tested and the result will unambigiously say "designed" or "evolved".

If not, it seems to be all "design predictions" are worthless if they predict exactly the same things that evolution does.

Pointless.

Can you point me to a list of as yet untested "predictions" that common descent by design makes, or are they only available retrospectively? If the latter, then give up now, you'll never be able to convince anybody.
---------------------QUOTE-------------------


Some predictions (these are my own and in no way represent predictions of the ID movement in general):

Because evolution is proactive, not reactive:

Organisms will show evidence of preparation for anticipated environments; rudiments of organs not yet needed will be found.
When confronted with environmental changes, organisms will adapt using pre-existing features (already coded for in the genome) or will become extinct - no new features will develop slowly over time.
Patterns and laws will be found that govern how evolution works.

From the fossil record:
Lineages will be found to have begun before environments in which they later flourished began.
Mass extinctions will have been preceded by the introduction of new types that would dominate the next phase in earth’s cycle.
Organisms will be found to have begun the adaptive process before adaptation was necessary.
Patterns will be found in the origin, differentiation and eventual extinction of lineages that are not dependent upon environmental factors but exist across all manner of differing environments, geographical locations, types of organisms and ages.

Genetically:
Mathematical patterns not explainable by the current theory will be found when comparing sequences of different organisms.
The genetic code will be found to be more sophisticated and more robust than previously thought.
Embedded and overlapping coding will be found to be more prevalent than previously thought.
Careful examination of genomes will find preparatory and adaptive codes “waiting in the wings” ready to be utilized in case of environmental changes- many just a frame shift away.
Frame shifting will be found to be a more common mechanism for sudden evolutionary change than previously thought.
Every part of the entire genome of any organism will be found to either be used at some time in the organisms life, or be of future use.  There are no unusable “Leftovers”.
No adequate explanation other than design will ever be found for the origin of life’s most basic components - i.e. protein synthesis, cell division, sexual reproduction, etc.

Universally:
Because the earth, and the solar system were specifically designed for life, no life or signs of previous life will be found on any other planets within our field of exploration.
Posted by: Daniel Smith on Sep. 30 2007,15:35

Quote (JAM @ Sep. 29 2007,14:17)
If they suggest design, their designer was an idiot.
---------------------QUOTE-------------------


Many are.
What's your point?
Posted by: Daniel Smith on Sep. 30 2007,15:53

Quote (jeannot @ Sep. 28 2007,14:21)
Common descent by design?
Can you develop, Daniel?
---------------------QUOTE-------------------


Basically common descent by design (or designed descent) is the view the evolution of organisms was planned out in advance.  
I have to clarify here that this was not Schindewolf's view.  He held "mysticism" (as he called it) in contempt and thought that evolution proceeded by internal factors alone - which constrained it along certain paths.  For this reason he also held Darwinism in contempt.
Posted by: jeannot on Sep. 30 2007,15:55

Quote (Daniel Smith @ Sep. 30 2007,15:53)
Quote (jeannot @ Sep. 28 2007,14:21)
Common descent by design?
Can you develop, Daniel?
---------------------QUOTE-------------------


Basically common descent by design (or designed descent) is the view the evolution of organisms was planned out in advance.  
I have to clarify here that this was not Schindewolf's view.  He held "mysticism" (as he called it) in contempt and thought that evolution proceeded by internal factors alone - which constrained it along certain paths.  For this reason he also held Darwinism in contempt.
---------------------QUOTE-------------------


What's your position? Do you support common descent?
Posted by: Daniel Smith on Sep. 30 2007,16:03

Quote (Reciprocating Bill @ Sep. 28 2007,05:24)

This may be contrasted with Darwin's predictions: to fail to find nested hierarchy in nature would be to falsify his model of evolution.
---------------------QUOTE-------------------


But the nested hierarchy was developed to classify organisms before Darwin's time!
Ever heard of Linnaeus?
So how then can it be a prediction of Darwinism?

   

---------------------QUOTE-------------------
(Daniel: Still waiting for you to retract your patently false claim vis interest in data with no biases or preconceptions.)
---------------------QUOTE-------------------


Thanks for continually telling me what I'm thinking and how best I should express my thoughts.  (I bet you're a big hit at parties!)

BTW, do you know what I'm thinking right now?
Posted by: jeannot on Sep. 30 2007,16:13

Quote (Daniel Smith @ Sep. 30 2007,16:03)
Quote (Reciprocating Bill @ Sep. 28 2007,05:24)

This may be contrasted with Darwin's predictions: to fail to find nested hierarchy in nature would be to falsify his model of evolution.
---------------------QUOTE-------------------


But the nested hierarchy was developed to classify organisms before Darwin's time!
Ever heard of Linnaeus?
So how then can it be a prediction of Darwinism?
---------------------QUOTE-------------------


Linné's classification was flawed. His nested hierarchy is largely inconsistent across characters, it is full of contradictions.
And I fail to see how this undermines Darwin's prediction. Linné formulated no hypothesis behind his classification, expect perhaps something similar to common design, which can predict anything (hence nothing).
Posted by: Daniel Smith on Sep. 30 2007,16:15

Quote (carlsonjok @ Sep. 28 2007,06:11)
 
Quote (Daniel Smith @ Sep. 28 2007,04:12)
 
OH, And the city doesn't really count as "the wild" now does it?
---------------------QUOTE-------------------


For whom?  Certainly, it isn't the wild for humans inasmuch as it consolidates all sorts of things, like grocery stores and homes, for our convenience.  But for feral cats, alas without currency to buy themselves a bag of Friskies or take out a mortgage, it is the wild.
---------------------QUOTE-------------------


Well, cats and dogs rely on humans for their sustenance, therefore the cities (which have dumpsters, trash cans and gutters full of food scraps) don't really qualify as an environment of the type where natural selection was proposed to have done all of it's major work now does it?
So, let me rephrase this:
Remove humans from the world and what happens to dogs, cats and cultivated plants?
It is my contention that natural selection will reduce varieties.
 

---------------------QUOTE-------------------
Never mind.  After over six pages and you haven't even mentioned a horse and that is the reason you are here, no?
---------------------QUOTE-------------------


If you go back to Brainstorms, you'll see that the horse was just one example I used in a discussion with Alan Fox while discussing the theory of evolution in general.  I don't know why he decided to start this thread making that the sole subject.  That was not my doing.  Schindewolf's main argument from horse evolution was that the horse developed a single toed foot before it was advantageous to do so.  So far no one has disputed his position with any evidence that shows it to be a false claim.
Posted by: carlsonjok on Sep. 30 2007,16:22

Quote (Daniel Smith @ Sep. 30 2007,16:15)
Quote (carlsonjok @ Sep. 28 2007,06:11)
   
Quote (Daniel Smith @ Sep. 28 2007,04:12)
 
OH, And the city doesn't really count as "the wild" now does it?
---------------------QUOTE-------------------


For whom?  Certainly, it isn't the wild for humans inasmuch as it consolidates all sorts of things, like grocery stores and homes, for our convenience.  But for feral cats, alas without currency to buy themselves a bag of Friskies or take out a mortgage, it is the wild.
---------------------QUOTE-------------------


Well, cats and dogs rely on humans for their sustenance, therefore the cities (which have dumpsters, trash cans and gutters full of food scraps) don't really qualify as an environment of the type where natural selection was proposed to have done all of it's major work now does it?
So, let me rephrase this:
Remove humans from the world and what happens to dogs, cats and cultivated plants?
It is my contention that natural selection will reduce varieties.
   

---------------------QUOTE-------------------
Never mind.  After over six pages and you haven't even mentioned a horse and that is the reason you are here, no?
---------------------QUOTE-------------------


If you go back to Brainstorms, you'll see that the horse was just one example I used in a discussion with Alan Fox while discussing the theory of evolution in general.  I don't know why he decided to start this thread making that the sole subject.  That was not my doing.  Schindewolf's main argument from horse evolution was that the horse developed a single toed foot before it was advantageous to do so.  So far no one has disputed his position with any evidence that shows it to be a false claim.
---------------------QUOTE-------------------


How interesting that you managed to quote my entire post except one sentence.  That sentence read:



---------------------QUOTE-------------------
Perhaps you would like to define the characteristics of an eco-system and then explain to us how an urban environment is not one?

---------------------QUOTE-------------------



I am sure that was an unintentional oversight that you will correct now.
Posted by: jeannot on Sep. 30 2007,16:25

Quote (Daniel Smith @ Sep. 30 2007,16:15)
Quote (carlsonjok @ Sep. 28 2007,06:11)
   
Quote (Daniel Smith @ Sep. 28 2007,04:12)
 
OH, And the city doesn't really count as "the wild" now does it?
---------------------QUOTE-------------------


For whom?  Certainly, it isn't the wild for humans inasmuch as it consolidates all sorts of things, like grocery stores and homes, for our convenience.  But for feral cats, alas without currency to buy themselves a bag of Friskies or take out a mortgage, it is the wild.
---------------------QUOTE-------------------


Well, cats and dogs rely on humans for their sustenance, therefore the cities (which have dumpsters, trash cans and gutters full of food scraps) don't really qualify as an environment of the type where natural selection was proposed to have done all of it's major work now does it?
So, let me rephrase this:
Remove humans from the world and what happens to dogs, cats and cultivated plants?
It is my contention that natural selection will reduce varieties.
---------------------QUOTE-------------------


That's entirely possible in the case of domesticated animals like cats and dogs, who were subject to strong divergent selection. Such divergent selection is probably weaker in the wild.
But does that mean that selection hinders the emergence of new types? The answer is no.
It is demonstrated that natural selection helps speciation.
There are dozens of documented cases of ecological speciation.
Posted by: Daniel Smith on Sep. 30 2007,16:56

Quote (George @ Sep. 28 2007,07:44)
 
Quote (Daniel Smith @ Sep. 28 2007,03:31)
   

---------------------QUOTE-------------------
However, in the formulation of this view, not enough consideration has been given to the fact that the evolutionary trend of reduction in the number of toes had already been introduced long before the plains were occupied in the early Tertiary by the precursors of the horse; these inhabited dense scrub, meaning that they lived in an environment where the reduction of the primitive five-toed protoungulate foot was not an advantage at all. In the descendants, then, the rest of the lateral toes degenerated and the teeth grew longer step by step... regardless of the mode of life, which... fluctuated repeatedly, with habitats switching around among forests, savannas, shrubby plains, tundra, and so on.
If selection alone were decisive in this specialization trend, we would have to ascribe to it a completely incomprehensible purposefulness...
---------------------QUOTE-------------------

Basic Questions in Paleontology pp. 358-359, (emphasis his)
---------------------QUOTE-------------------


So basically Schindewolf is saying that horses developed single-toed hooves regardless of the selection pressures applied?  How does he know what those pressures were?  How does he know the scrub was dense?  Paleoecologists today can identify what species were present in the landscape at a point in time, but have much more difficulty in determining vegetation structure.  This has led to disagreements over what the European landscape of most of the Holocene was.  Yes there were lots of oak trees present, but was it closed forest?  Was it patches of scrub interspersed with grassy plains?  Was it widely spaced parkland-like trees?

In other words, what was the quality of his data and how far is he spreading it with rhetoric?
---------------------QUOTE-------------------


He doesn't go into any details (in this book at least - he may have in others or in one of his papers) about how he knew the environmental conditions were such as he described, so I can't tell you how he determined that.

I'm assuming that the man described in 1965 by Stephen Jay Gould's advisor, Dr. Norman Newell as "the greatest living paleontologist", used the scientific method and the accepted evidence of his day to determine these factors.

You might be in a position to show that he made a false claim, but you must base that on evidence from that time period.
Posted by: Daniel Smith on Sep. 30 2007,18:32

Quote (Alan Fox @ Sep. 29 2007,04:17)

So, is there another example that better illustrates Berg's alternative to RM + NS?    
---------------------QUOTE-------------------


Berg's book is full of examples.  He makes his case on cumulative evidence, making mention of so many species, orders, organs, locations, periods, races, genera, etc. and etc... that I can't remember half of them, (his examples probably average at least one per page, and there are over 400 pages!).  So once again, I'll be unable to provide a "best" example, but I'll give you one example:
           

---------------------QUOTE-------------------
Osborn (1902, 1907), basing his inferences on the study of the teeth of various groups of mammals, comes to the conclusion that teeth have "predispositions" to vary in a definite direction: in the process of the evolution of teeth full development is reached only by what had previously existed in a potential condition.  Therefore, similar characters in teeth appear quite independently in various groups, such as horses, rhinoceroses, Titanotheria.  Nor is this all.  It is possible to detect a similar evolution of the tubercles of the molars in such widely separate groups as Perissodactyla, and Primates (including the Lemuroidea).  Tubercles appear in a strictly definite position, so that there can be no question of chance.  We have to deal here, says Osborn (1902, p.267; 1907, p. 228), with a definite and determined evolution, governed by certain rules.  This may be seen from the following (Osborn, 1902, pp. 267-268; 1907, pp. 235-236):--

1.  Teeth are distinguished by a very singular property, i.e. that they are laid down and formed under the gums.  Consequently use or disuse cannot exert any effect upon their form.  On the contrary, the more they are used, the sooner they wear out.

2.  At the same time, teeth are one of the most progressive organs.

3.  The different families and orders of the Mammalia diverged from one another at the time when their upper molars possessed three tubercles each, the lower from three to five.  Therefore, only those tubercles are homologous which may be compared to the above mentioned primary ones.

4.  New supplementary tubercles are consequently not homologous, but convergent.  At the same time the occurrence of such tubercles is independent of individual variation.

Natural selection could thus play no part in the evolution of teeth in mammals, because they appear in perfectly definite positions.

Had the supplementary tubercles appeared without any definite order, at random, we should then have observed an unusual diversity in the teeth of mammals in all parts of the world.  But such is not the case: as we have seen, the occurrence of new tubercles follows definite rules in various families; in the upper molars from one to eight supplementary tubercles develop at strictly definite points.  We thus unavoidably come to the conclusion that even in the primary tritubercular condition of the molars a tendency has been inherent which to a certain extent predetermines their future variation and evolution (1907, p. 237).
Not only do the teeth, says Osborn, develop independently of chance variations being selected (for tubercles are predetermined); but the skull, the vertebral column and the extremities are subject to the same principle  of development in a definite direction (1907, p. 237)
---------------------QUOTE-------------------

Nomogenesis, pp. 123-124, (emphasis his)
BTW, the "Osborn" quoted above is < Henry Fairfield Osborn >
           

---------------------QUOTE-------------------

OK. The RM + NS theory claims that organisms are shaped by their environments. Where a population exists and is subject to change in that environment, selection will result in adaptive change or extinction. Adaptation is not predictive.

From your quote, Schindewolf is claiming that horses began adapting to life on the plains before arriving in that environment. If true, this would indeed be a grave problem for evolution.

How does Schindewolf establish the prevailing climate and vegetation associated with a particular fossil?
---------------------QUOTE-------------------


I don't know the answer to that.  But normally, when he is about to give a disputed position, he gives the alternate view as well.  He gives no alternate view here, so I'm assuming it was the accepted view at that time.
Posted by: Daniel Smith on Sep. 30 2007,18:55

Quote (jeannot @ Sep. 30 2007,15:55)
   
Quote (Daniel Smith @ Sep. 30 2007,15:53)
   
Quote (jeannot @ Sep. 28 2007,14:21)
Common descent by design?
Can you develop, Daniel?
---------------------QUOTE-------------------


Basically common descent by design (or designed descent) is the view the evolution of organisms was planned out in advance.  
I have to clarify here that this was not Schindewolf's view.  He held "mysticism" (as he called it) in contempt and thought that evolution proceeded by internal factors alone - which constrained it along certain paths.  For this reason he also held Darwinism in contempt.
---------------------QUOTE-------------------


What's your position? Do you support common descent?
---------------------QUOTE-------------------


I'm not sure.  Berg didn't appear to, Schindewolf did.  My opinion is still developing.

I'm interested in the truth - that's all.  My goal is to find out what really happened.
Posted by: Daniel Smith on Sep. 30 2007,18:58

Quote (carlsonjok @ Sep. 30 2007,16:22)
How interesting that you managed to quote my entire post except one sentence.  That sentence read:

   

---------------------QUOTE-------------------
Perhaps you would like to define the characteristics of an eco-system and then explain to us how an urban environment is not one?

---------------------QUOTE-------------------



I am sure that was an unintentional oversight that you will correct now.
---------------------QUOTE-------------------


Well, since it was "the wild" and not "an ecosystem" that I originally specified, perhaps you will now explain to me how the city fits my definition of "the wild"?
Posted by: Henry J on Sep. 30 2007,22:02

Re "Mass extinctions will have been preceded by the introduction of new types that would dominate the next phase in earth?s cycle."

If the previously dominant types became extinct, where else would the dominant types of the next era come from besides those that were non-dominant in the previous era?

Henry
Posted by: Richard Simons on Sep. 30 2007,22:47

Daniel:  

---------------------QUOTE-------------------
But the nested hierarchy was developed to classify organisms before Darwin's time!
Ever heard of Linnaeus?
So how then can it be a prediction of Darwinism?

---------------------QUOTE-------------------


Because the theory of evolution predicted that all aspects of organisms follow the same nested hierarchy. This has proven to be true, even for chemicals such as cytochrome C and DNA that were completely unknown 150 years ago. It is also generally true as regards anatomy, physiology, parasites, diseases and biogeography. That is why it is possible to predict, for example, that bonobos will have the same broken vitamin C gene as we do and elephants will not. That is why researchers looked amongst the apes to find something similar to HIV rather than doing a massive survey of rabbits.

Linnaeus was a creationist, as was virtually everyone of his day, and likely used a nested hierarchy as a tool rather than to indicate genuine relationships. Have you any evidence that he used it to make predictions?
Posted by: carlsonjok on Oct. 01 2007,05:14

Quote (Daniel Smith @ Sep. 30 2007,18:58)
Quote (carlsonjok @ Sep. 30 2007,16:22)
How interesting that you managed to quote my entire post except one sentence.  That sentence read:

     

---------------------QUOTE-------------------
Perhaps you would like to define the characteristics of an eco-system and then explain to us how an urban environment is not one?

---------------------QUOTE-------------------



I am sure that was an unintentional oversight that you will correct now.
---------------------QUOTE-------------------


Well, since it was "the wild" and not "an ecosystem" that I originally specified, perhaps you will now explain to me how the city fits my definition of "the wild"?
---------------------QUOTE-------------------


Well, you haven't defined "the wild" with sufficient rigor other than to imply that an urban environment isn't it because it is an environment where natural selection ceases to operate.  Indeed, "the wild" isn't even a scientific term.  That is why I am asking you to define what an eco-system is and then explain why an urban environment, as experienced by feral animals, is not such a thing.

EDIT: corrected a very badly written sentence.
Posted by: George on Oct. 01 2007,07:22

Quote (Daniel Smith @ Sep. 30 2007,16:56)
Quote (George @ Sep. 28 2007,07:44)
   
Quote (Daniel Smith @ Sep. 28 2007,03:31)
   

---------------------QUOTE-------------------
However, in the formulation of this view, not enough consideration has been given to the fact that the evolutionary trend of reduction in the number of toes had already been introduced long before the plains were occupied in the early Tertiary by the precursors of the horse; these inhabited dense scrub, meaning that they lived in an environment where the reduction of the primitive five-toed protoungulate foot was not an advantage at all. In the descendants, then, the rest of the lateral toes degenerated and the teeth grew longer step by step... regardless of the mode of life, which... fluctuated repeatedly, with habitats switching around among forests, savannas, shrubby plains, tundra, and so on.
If selection alone were decisive in this specialization trend, we would have to ascribe to it a completely incomprehensible purposefulness...
---------------------QUOTE-------------------

Basic Questions in Paleontology pp. 358-359, (emphasis his)
---------------------QUOTE-------------------


So basically Schindewolf is saying that horses developed single-toed hooves regardless of the selection pressures applied?  How does he know what those pressures were?  How does he know the scrub was dense?  Paleoecologists today can identify what species were present in the landscape at a point in time, but have much more difficulty in determining vegetation structure.  This has led to disagreements over what the European landscape of most of the Holocene was.  Yes there were lots of oak trees present, but was it closed forest?  Was it patches of scrub interspersed with grassy plains?  Was it widely spaced parkland-like trees?

In other words, what was the quality of his data and how far is he spreading it with rhetoric?
---------------------QUOTE-------------------


He doesn't go into any details (in this book at least - he may have in others or in one of his papers) about how he knew the environmental conditions were such as he described, so I can't tell you how he determined that.

I'm assuming that the man described in 1965 by Stephen Jay Gould's advisor, Dr. Norman Newell as "the greatest living paleontologist", used the scientific method and the accepted evidence of his day to determine these factors.

You might be in a position to show that he made a false claim, but you must base that on evidence from that time period.
---------------------QUOTE-------------------


You misunderstand me.  I'm not saying he was lying.  I'm questioning how he knew what Tertiary environmental conditions were like and how good were the data he based his conclusions on.  As I said before, it is difficult enough for today's paleoecologists to reconstruct past vegetation.  It would have been much more difficult and imprecise for the ecologists of a century ago.  Palynology, one of the more powerful tools, was only in its infancy.

To summarise:  he may have based his theories on the understanding of the day, but if that understanding is wrong, his ideas crumble.
Posted by: Alan Fox on Oct. 01 2007,07:29

Daniel wrote earlier:  

---------------------QUOTE-------------------
If you go back to Brainstorms, you'll see that the horse was just one example I used in a discussion with Alan Fox while discussing the theory of evolution in general.  I don't know why he decided to start this thread making that the sole subject.
---------------------QUOTE-------------------



My recollection is that you first raised the example < here >:

 

---------------------QUOTE-------------------
   (AF wrote) Would you like to cite your best example?

(DS wrote) There are so many. You really should read the books. Berg and Schindewolf cite hundreds of examples - Berg mostly from modern biology and Schindewolf mostly from the fossil record. It's really does them a disservice to try to pick a "best" example, but I'll give you one that Schindewolf describes:

   quote:To this extent, the one toed horse must be regarded as the ideal running animal of the plains. It's early Tertiary ancestors had four digits on the front feet and three on the hind feet, and low crowned cheek teeth. Since in the later Tertiary, an expansion of plains at the expense of forests has been observed, this change in environmental conditions and the consequent change in the mode of life has been represented as the cause of linear, progressive selection leading up to the modern horse.
   However, in the formulation of this view, not enough consideration has been given to the fact that the evolutionary trend of reduction in the number of toes had already been introduced long before the plains were occupied in the early Tertiary by the precursors of the horse; these inhabited dense scrub, meaning that they lived in an environment where the reduction of the primitive five-toed protoungulate foot was not an advantage at all. In the descendants, then, the rest of the lateral toes degenerated and the teeth grew longer step by step... regardless of the mode of life, which... fluctuated repeatedly, with habitats switching around among forests, savannas, shrubby plains, tundra, and so on.
   If selection alone were decisive in this specialization trend, we would have to ascribe to it a completely incomprehensible purposefulness...

   Basic Questions in Paleontology pp. 358-359, emphasis his.

posted 17. September 2007 12:35
---------------------QUOTE-------------------


Posted by: Alan Fox on Oct. 01 2007,07:31

Daniel wrote:  

---------------------QUOTE-------------------
Some predictions (these are my own and in no way represent predictions of the ID movement in general):

Because evolution is proactive, not reactive:

Organisms will show evidence of preparation for anticipated environments; rudiments of organs not yet needed will be found.
When confronted with environmental changes, organisms will adapt using pre-existing features (already coded for in the genome) or will become extinct - no new features will develop slowly over time.
Patterns and laws will be found that govern how evolution works.

From the fossil record:
Lineages will be found to have begun before environments in which they later flourished began.
Mass extinctions will have been preceded by the introduction of new types that would dominate the next phase in earth’s cycle.
Organisms will be found to have begun the adaptive process before adaptation was necessary.
Patterns will be found in the origin, differentiation and eventual extinction of lineages that are not dependent upon environmental factors but exist across all manner of differing environments, geographical locations, types of organisms and ages.

Genetically:
Mathematical patterns not explainable by the current theory will be found when comparing sequences of different organisms.
The genetic code will be found to be more sophisticated and more robust than previously thought.
Embedded and overlapping coding will be found to be more prevalent than previously thought.
Careful examination of genomes will find preparatory and adaptive codes “waiting in the wings” ready to be utilized in case of environmental changes- many just a frame shift away.
Frame shifting will be found to be a more common mechanism for sudden evolutionary change than previously thought.
Every part of the entire genome of any organism will be found to either be used at some time in the organisms life, or be of future use.  There are no unusable “Leftovers”.
No adequate explanation other than design will ever be found for the origin of life’s most basic components - i.e. protein synthesis, cell division, sexual reproduction, etc.

Universally:
Because the earth, and the solar system were specifically designed for life, no life or signs of previous life will be found on any other planets within our field of exploration.
---------------------QUOTE-------------------



I congratulate you, Daniel, for being so forthright and producing testable predictions.

Re the search for evidence of life on Mars, there are three possible outcomes that I can foresee.

1:Evidence is found for a life-form totally different from anything seen on Earth, say, not even based on carbon, but, for instance, built on silicon.

2: Evidence is found for a life-form bearing distinct similarities to terrestrial lifeforms.

3; No evidence found.

If 1, abiogenesis is almost inevitable on any suitable planet, given enough time.

If 2, lifeforms such as bacterial spores may travel across space as passengers in meteorites. (Panspermia)

If 3, we still don't know.
Posted by: Daniel Smith on Oct. 01 2007,19:37

Quote (George @ Oct. 01 2007,07:22)
You misunderstand me.  I'm not saying he was lying.  I'm questioning how he knew what Tertiary environmental conditions were like and how good were the data he based his conclusions on.  As I said before, it is difficult enough for today's paleoecologists to reconstruct past vegetation.  It would have been much more difficult and imprecise for the ecologists of a century ago.  Palynology, one of the more powerful tools, was only in its infancy.

To summarise:  he may have based his theories on the understanding of the day, but if that understanding is wrong, his ideas crumble.
---------------------QUOTE-------------------


Schindewolf's book was published (originally - in German) in 1950.  While technically that was in the last century, (so was 1999), it wasn't "a century ago".  

This is what he said:
 

---------------------QUOTE-------------------
Since in the later Tertiary, an expansion of plains at the expense of forests has been observed, this change in environmental conditions and the consequent change in the mode of life has been represented as the cause of linear, progressive selection leading up to the modern horse.

---------------------QUOTE-------------------

(emphasis mine)

I assume "has been observed" means that it was well accepted.  Perhaps newer data has proved him wrong, I don't know.
Posted by: Daniel Smith on Oct. 01 2007,19:45

Quote (carlsonjok @ Oct. 01 2007,05:14)
   
Quote (Daniel Smith @ Sep. 30 2007,18:58)
  Well, since it was "the wild" and not "an ecosystem" that I originally specified, perhaps you will now explain to me how the city fits my definition of "the wild"?
---------------------QUOTE-------------------


Well, you haven't defined "the wild" with sufficient rigor other than to imply that an urban environment isn't it because it is an environment where natural selection ceases to operate.  Indeed, "the wild" isn't even a scientific term.  That is why I am asking you to define what an eco-system is and then explain why an urban environment, as experienced by feral animals, is not such a thing.
---------------------QUOTE-------------------




I didn't think I had to define "the wild" when I made my statement.  I think most people here understood what I meant.  

Lets just say "the wild" is what exists outside cities, towns, or anywhere else man dwells.  That was what the ecosystem was like before man arrived on the scene and throughout the majority of natural selection's functional influence.

 

---------------------QUOTE-------------------
EDIT: corrected a very badly written sentence.
---------------------QUOTE-------------------


BTW, How do you edit posts here?
Posted by: Reciprocating Bill on Oct. 01 2007,19:57

Quote (Daniel Smith @ Sep. 30 2007,16:53)
     
Quote (jeannot @ Sep. 28 2007,14:21)
Common descent by design?
Can you develop, Daniel?
---------------------QUOTE-------------------


Basically common descent by design (or designed descent) is the view the evolution of organisms was planned out in advance.  
I have to clarify here that this was not Schindewolf's view.  He held "mysticism" (as he called it) in contempt and thought that evolution proceeded by internal factors alone - which constrained it along certain paths.  For this reason he also held Darwinism in contempt.
---------------------QUOTE-------------------


Planned in advance essentially = frontloading, which presents problems that render the hypothesis unworkable on the face of it.

The processes of adaptation and speciation described in the standard RM+NS model have enabled living organisms to track the countless contingent changes in environments and ecosystems in which those organisms have been embedded over the last 38 million centuries (or so). Even with such tracking a vast majority of species ended in extinction, presumably when these variations become too extreme to track. Indeed, the successes, failures and interactions of some species mold the ecological context for the successes and failures of others, all embedded in a contingently changing physical and environment.  

"Planned in advance" would require storage in advance of the countless adaptations, speciation events, ecoloogical interactions, and even extinction events that have been entailed in the story of the survival of life on earth within this endless succession of changing environments and ecosystems, as well as a program determining in advance the order in which these changes unfold. Yet the environmental transitions with with life has been confronted, and that demand these changes, result from physical processes (planetary, geological, meteorological, astronomical, etc.) that are themselves inherently contingent and unguided and which cannot themselves possibly have been "arranged," "planned," or "predicted." Moreover, we are talking the varied environments and apposite adaptations of every extinct and every extant lineage of descent that have taken their places among the astronomical number of ramifications of the tree of life.

With that in mind, "preplanned" becomes utterly implausible and even absurd, in my view.
Posted by: Daniel Smith on Oct. 01 2007,21:26

Quote (Alan Fox @ Oct. 01 2007,07:31)
Re the search for evidence of life on Mars, there are three possible outcomes that I can foresee.

1:Evidence is found for a life-form totally different from anything seen on Earth, say, not even based on carbon, but, for instance, built on silicon.

2: Evidence is found for a life-form bearing distinct similarities to terrestrial lifeforms.

3; No evidence found.

If 1, abiogenesis is almost inevitable on any suitable planet, given enough time.

If 2, lifeforms such as bacterial spores may travel across space as passengers in meteorites. (Panspermia)

If 3, we still don't know.
---------------------QUOTE-------------------


One other option for #2:

If we find life on another planet that is distinctly similar to our own, it could mean that abiogenesis acts according to laws as well.

Denton's position, as expressed in "Nature's Destiny", was that any life, anywhere else in the universe, would have to be remarkably similar to our own.
Posted by: Daniel Smith on Oct. 01 2007,21:33

Quote (Reciprocating Bill @ Oct. 01 2007,19:57)
Planned in advance essentially = frontloading, which presents problems that render the hypothesis unworkable on the face of it.

The processes of adaptation and speciation described in the standard RM+NS model have enabled living organisms to track the countless contingent changes in environments and ecosystems in which those organisms have been embedded over the last 38 million centuries (or so). Even with such tracking a vast majority of species ended in extinction, presumably when these variations become too extreme to track. Indeed, the successes, failures and interactions of some species mold the ecological context for the successes and failures of others, all embedded in a contingently changing physical and environment.  

"Planned in advance" would require storage in advance of the countless adaptations, speciation events, ecoloogical interactions, and even extinction events that have been entailed in the story of the survival of life on earth within this endless succession of changing environments and ecosystems, as well as a program determining in advance the order in which these changes unfold. Yet the environmental transitions with with life has been confronted, and that demand these changes, result from physical processes (planetary, geological, meteorological, astronomical, etc.) that are themselves inherently contingent and unguided and which cannot themselves possibly have been "arranged," "planned," or "predicted." Moreover, we are talking the varied environments and apposite adaptations of every extinct and every extant lineage of descent that have taken their places among the astronomical number of ramifications of the tree of life.

With that in mind, "preplanned" becomes utterly implausible and even absurd, in my view.
---------------------QUOTE-------------------


Yes.  It would be a remarkable feat wouldn't it?

But the more we learn about DNA, the more remarkable it becomes.  For instance, the embedding and overlapping of coding areas radically changes the amount of information that can be stored in a genome.

Things that seem impossible, might just not be after all.
Posted by: Reciprocating Bill on Oct. 01 2007,21:40

Quote (Daniel Smith @ Oct. 01 2007,22:33)
Quote (Reciprocating Bill @ Oct. 01 2007,19:57)
Planned in advance essentially = frontloading, which presents problems that render the hypothesis unworkable on the face of it.

The processes of adaptation and speciation described in the standard RM+NS model have enabled living organisms to track the countless contingent changes in environments and ecosystems in which those organisms have been embedded over the last 38 million centuries (or so). Even with such tracking a vast majority of species ended in extinction, presumably when these variations become too extreme to track. Indeed, the successes, failures and interactions of some species mold the ecological context for the successes and failures of others, all embedded in a contingently changing physical and environment.  

"Planned in advance" would require storage in advance of the countless adaptations, speciation events, ecoloogical interactions, and even extinction events that have been entailed in the story of the survival of life on earth within this endless succession of changing environments and ecosystems, as well as a program determining in advance the order in which these changes unfold. Yet the environmental transitions with with life has been confronted, and that demand these changes, result from physical processes (planetary, geological, meteorological, astronomical, etc.) that are themselves inherently contingent and unguided and which cannot themselves possibly have been "arranged," "planned," or "predicted." Moreover, we are talking the varied environments and apposite adaptations of every extinct and every extant lineage of descent that have taken their places among the astronomical number of ramifications of the tree of life.

With that in mind, "preplanned" becomes utterly implausible and even absurd, in my view.
---------------------QUOTE-------------------


Yes.  It would be a remarkable feat wouldn't it?

But the more we learn about DNA, the more remarkable it becomes.  For instance, the embedding and overlapping of coding areas radically changes the amount of information that can be stored in a genome.

Things that seem impossible, might just not be after all.
---------------------QUOTE-------------------


Daniel, your response doesn't appear to reflect any comprehension of my objection whatsoever. Read it again.
Posted by: Richard Simons on Oct. 01 2007,23:27



---------------------QUOTE-------------------
I have to clarify here that this was not Schindewolf's view.  He held "mysticism" (as he called it) in contempt and thought that evolution proceeded by internal factors alone - which constrained it along certain paths.

---------------------QUOTE-------------------


How does this differ from the views of Lamark? How do these 'internal factors', whatever they might be, get translated into mutations and changes in gene frequences? Schindewolf, obviously, could not have expressed much of an opinion on the subject as at the time it was not even known what material carried genetic information. However, what is your explanation. Presumably you have thought about it as you are carrying the torch for Schindewolf.

 

---------------------QUOTE-------------------
He also proposed that evolution proceeded as if constrained by a goal.  He gives the example of the evolution of the one-toed foot on the horse - which began long before the horse moved onto the plains and the one-toed foot became advantageous.
---------------------QUOTE-------------------


You say he held mysticism in contempt yet at the same time believed that somehow horses not only knew that at some time in the future they would benefit from having fewer toes but were actually able to evolve towards that state? To me, that is a prime example of mysticism. Again, what mechanism do you propose?
Posted by: Daniel Smith on Oct. 02 2007,02:10

Quote (jeannot @ Sep. 30 2007,16:13)
Linné's classification was flawed. His nested hierarchy is largely inconsistent across characters, it is full of contradictions.
And I fail to see how this undermines Darwin's prediction. Linné formulated no hypothesis behind his classification, expect perhaps something similar to common design, which can predict anything (hence nothing).
---------------------QUOTE-------------------


Linnaeus first published his Systema Naturae in 1738.  How could it not be flawed by today's standards?  Hierarchies and evolutionary trees are still hotly disputed amongst those who classify organisms.
You are right that he formed no new hypothesis based on his hierarchy, but he was an adherent to natural theology - so that would be his "hypothesis" I suppose.
The point is that a nested hierarchy was postulated before Darwin's time so how could it be a prediction?
Posted by: Daniel Smith on Oct. 02 2007,02:25

Quote (Reciprocating Bill @ Oct. 01 2007,21:40)
 
Daniel, your response doesn't appear to reflect any comprehension of my objection whatsoever. Read it again.
---------------------QUOTE-------------------


OK, I see that I missed some of your points (I was at work and answering your post while on a break - so I didn't give it a thorough review).

 
Quote (Reciprocating Bill @ Oct. 01 2007,19:57)
Planned in advance essentially = frontloading, which presents problems that render the hypothesis unworkable on the face of it.

The processes of adaptation and speciation described in the standard RM+NS model have enabled living organisms to track the countless contingent changes in environments and ecosystems in which those organisms have been embedded over the last 38 million centuries (or so). Even with such tracking a vast majority of species ended in extinction, presumably when these variations become too extreme to track. Indeed, the successes, failures and interactions of some species mold the ecological context for the successes and failures of others, all embedded in a contingently changing physical and environment.  

"Planned in advance" would require storage in advance of the countless adaptations, speciation events, ecoloogical interactions, and even extinction events that have been entailed in the story of the survival of life on earth within this endless succession of changing environments and ecosystems, as well as a program determining in advance the order in which these changes unfold.
---------------------QUOTE-------------------


It would not require storage of all of these events.  It would only require knowledge of them by the designer, who would then implement programs that would be set up to anticipate such things.  How do animals anticipate natural disasters?  We don't know, but they do.  Perhaps there is some long-range anticipatory mechanism.
 

---------------------QUOTE-------------------
Yet the environmental transitions with with life has been confronted, and that demand these changes, result from physical processes (planetary, geological, meteorological, astronomical, etc.) that are themselves inherently contingent and unguided and which cannot themselves possibly have been "arranged," "planned," or "predicted."
---------------------QUOTE-------------------


Unless there really is an all knowing God.  

---------------------QUOTE-------------------
 Moreover, we are talking the varied environments and apposite adaptations of every extinct and every extant lineage of descent that have taken their places among the astronomical number of ramifications of the tree of life.

With that in mind, "preplanned" becomes utterly implausible and even absurd, in my view.
---------------------QUOTE-------------------


In your view (which I assume is an atheistic one), pre-planning would seem ridiculous.  In my view, it's perfectly conceptual.
Posted by: oldmanintheskydidntdoit on Oct. 02 2007,02:41

Quote (Daniel Smith @ Oct. 02 2007,02:25)
With that in mind, "preplanned" becomes utterly implausible and even absurd, in my view.[/quote]
In your view (which I assume is an atheistic one), pre-planning would seem ridiculous.  In my view, it's perfectly conceptual.
---------------------QUOTE-------------------


As almost everything that has ever lived is extinct what does that say about the ability of this "designer" to plan?

Why bother to front-load if the organism is going extinct anyway?
Posted by: Daniel Smith on Oct. 02 2007,03:03

Quote (Richard Simons @ Oct. 01 2007,23:27)
   

---------------------QUOTE-------------------
I have to clarify here that this was not Schindewolf's view.  He held "mysticism" (as he called it) in contempt and thought that evolution proceeded by internal factors alone - which constrained it along certain paths.

---------------------QUOTE-------------------


How does this differ from the views of Lamark?
---------------------QUOTE-------------------


Schindewolf did not subscribe at all to Lamarckism:
   

---------------------QUOTE-------------------
an unbiased examination of the fossil material itself also reveals that absolutely no direct response to environmental influences or appropriate adaptations in the Lamarckian sense must necessarily be inferred...
Formerly, in emphasizing the supremacy of the environment, the properties and qualities of organisms were unduly disregarded.  Yet it should be obvious that in such chains of reactions and complexes of conditions the objects themselves must be credited with critical significance.  When I heat two chemical substances together, it is not the rise in temperature but the composition of the original material that is decisive.  The rise in temperature only triggers the reaction; under certain circumstances, it can be replaced by a different physical or chemical action (pressure, catalysts), and the result, determined by the original material, will still be the same.  At most, the environment plays only a similar role with regard to organisms; it can only provoke and set in motion some potential that is already present.
---------------------QUOTE-------------------

Basic Questions in Paleontology, pp. 312-313 (emphasis his)
   
Quote (Richard Simons @ Oct. 01 2007,23:27)
How do these 'internal factors', whatever they might be, get translated into mutations and changes in gene frequences? Schindewolf, obviously, could not have expressed much of an opinion on the subject as at the time it was not even known what material carried genetic information.
---------------------QUOTE-------------------

Schindewolf was familiar with the relatively new science of genetics:
   

---------------------QUOTE-------------------
For our phylogenetic approach, then, we shall take from genetics the basic pair of factors, random mutability and directive selection.
These two factors and their mechanisms provide a satisfactory understanding of microevolution, of the experimentally ascertainable modification of forms of lesser rank.  The changes observed here are usually confined to species and have nothing to do with innovation, with the creation of new organs, but always only with relatively trivial, gradual changes regarding size, shape, number, color, and so on in organs that are already present.
---------------------QUOTE-------------------

ibid., pg. 329 (emphasis his)
 
Quote (Richard Simons @ Oct. 01 2007,23:27)
However, what is your explanation. Presumably you have thought about it as you are carrying the torch for Schindewolf.
---------------------QUOTE-------------------


I have thought about it, but I'm not sure what my explanation is yet.  I fully expect more discoveries to reveal that DNA is deeper than originally thought, and that things like < this > will be found more and more often.
Quote (Richard Simons @ Oct. 01 2007,23:27)


       

---------------------QUOTE-------------------
He also proposed that evolution proceeded as if constrained by a goal.  He gives the example of the evolution of the one-toed foot on the horse - which began long before the horse moved onto the plains and the one-toed foot became advantageous.
---------------------QUOTE-------------------


You say he held mysticism in contempt yet at the same time believed that somehow horses not only knew that at some time in the future they would benefit from having fewer toes but were actually able to evolve towards that state? To me, that is a prime example of mysticism. Again, what mechanism do you propose?
---------------------QUOTE-------------------


He never said horses "knew" any such thing, and I'm not sure how you got that from my posts.  I'm afraid though, that I mischaracterized Schindewolf's views here.  He never used the term "goal" when describing his views - that was my word.
Posted by: Daniel Smith on Oct. 02 2007,03:09

Quote (oldmanintheskydidntdoit @ Oct. 02 2007,02:41)
As almost everything that has ever lived is extinct what does that say about the ability of this "designer" to plan?

Why bother to front-load if the organism is going extinct anyway?
---------------------QUOTE-------------------


Every living thing dies.  Everything.

It would sure seem that natural selection would have overcome that little hiccup by now doesn't it?
Posted by: Occam's Toothbrush on Oct. 02 2007,03:57



---------------------QUOTE-------------------
Things that seem impossible, might just not be after all.
---------------------QUOTE-------------------


Is there any proposition, however illogical and supported by evidence, that this sentence couldn't be used to support?
Posted by: Occam's Toothbrush on Oct. 02 2007,04:01

Quote (Daniel Smith @ Oct. 02 2007,04:09)
 
Quote (oldmanintheskydidntdoit @ Oct. 02 2007,02:41)
As almost everything that has ever lived is extinct what does that say about the ability of this "designer" to plan?

Why bother to front-load if the organism is going extinct anyway?
---------------------QUOTE-------------------


Every living thing dies.  Everything.

It would sure seem that natural selection would have overcome that little hiccup by now doesn't it?
---------------------QUOTE-------------------


It's amazing how convincing one's antintellectual meanderings become, once one simply applies boldfacing, italics, and underlining at the same time.  You do know you can use colored fonts, right?  There's smilies, too!  Then you'd really be proving your invisible and ineffective sky daddy.
Posted by: oldmanintheskydidntdoit on Oct. 02 2007,04:13

Quote (Daniel Smith @ Oct. 02 2007,03:09)
Quote (oldmanintheskydidntdoit @ Oct. 02 2007,02:41)
As almost everything that has ever lived is extinct what does that say about the ability of this "designer" to plan?

Why bother to front-load if the organism is going extinct anyway?
---------------------QUOTE-------------------


Every living thing dies.  Everything.

It would sure seem that natural selection would have overcome that little hiccup by now doesn't it?
---------------------QUOTE-------------------


Humans are still here.

Did the "designer" plan better for them?

I'm not talking about individual organisms, I'm talking about species. As you well know.

Sharks - around alot longer then the Dodo (I presume).

Why the difference? If the intelligent designer is so intelligent why do some species go extinct much much faster then others? Presumably the same amount of effort went into each one.
Posted by: k.e on Oct. 02 2007,04:32



---------------------QUOTE-------------------
Why the difference? If the intelligent designer is so intelligent why do some species go extinct much much faster then others? Presumably the same amount of effort went into each one.

---------------------QUOTE-------------------



Yeah he got rid of those walking, talking snakes pretty damn quick. ** poof  ** overnight they were mute and had to slide on their bellies.

Bwhahahahahaha.

Evolution just isn't intelligent, if it were there would be evidence everywhere that some things weren't designed but evolved instead.

Take for example talking donkeys, obviously designed; autistic donkeys, obviously designed; illiterate donkeys, obviously designed. Remedial schools for autistic illiterate donkeys with donkey speech therapists ....designed!

How can you guys NOT SEE THAT!!!!

The designer designed the lot no evolution necessary.
Posted by: k.e on Oct. 02 2007,04:39



---------------------QUOTE-------------------
Every living thing dies.  Everything.
---------------------QUOTE-------------------



*sniff...snivel...weep ...whine.* ...boo hoo hoo



---------------------QUOTE-------------------

It would sure seem that natural selection would have overcome that little hiccup by now doesn't it?
---------------------QUOTE-------------------



Oh drop dead intelligent ....that was.

Who do you blame for that BTW?

God? After all, he put that talking snake in the garden and er ..entrapped Adam into sinning right?

With friends like that who needs enemies?
Posted by: oldmanintheskydidntdoit on Oct. 02 2007,05:45

Quote (Daniel Smith @ Oct. 02 2007,03:09)
Quote (oldmanintheskydidntdoit @ Oct. 02 2007,02:41)
As almost everything that has ever lived is extinct what does that say about the ability of this "designer" to plan?

Why bother to front-load if the organism is going extinct anyway?
---------------------QUOTE-------------------


Every living thing dies.  Everything.

It would sure seem that natural selection would have overcome that little hiccup by now doesn't it?
---------------------QUOTE-------------------


There's a good case that < HeLa > cells will never die, at least as long as there are labs to be contaminated.
Posted by: Louis on Oct. 02 2007,06:01

Why is dying a hiccup? It isn't.

"Natural selection" isn't "trying" to maximise individual survivability, "natural selection" is "trying" to maximise individual survivability to the point of successful reproduction.

Inverted commas and teleological phraseology are not significant. It's just convenient shorthand to get the point across.

Louis
Posted by: k.e on Oct. 02 2007,06:09



---------------------QUOTE-------------------
There's a good case that HeLa cells will never die, at least as long as there are labs to be contaminated.

---------------------QUOTE-------------------



Imortal eh? So they are Jesus cells.

That HAS TO BE INCONTROVERTABLE PROOF JESUS EXISTS!!!

AND THAT HE IS A CANCER... and a lab WEED.

I'm just starting to get this ID stuff.

Man.... pulling stuff out of your ass and calling its science is EASY, everyone can be a scientist.

Whoever said confusing science with religion made religion look stupid was DEAD WRONG. I JUST PROVED JESUS IS LIVING IN A TEST TUBE NEAR YOU.

Praise the test tube.
Posted by: Albatrossity2 on Oct. 02 2007,06:46

Quote (Daniel Smith @ Oct. 02 2007,03:09)
 
Quote (oldmanintheskydidntdoit @ Oct. 02 2007,02:41)
As almost everything that has ever lived is extinct what does that say about the ability of this "designer" to plan?

Why bother to front-load if the organism is going extinct anyway?
---------------------QUOTE-------------------


Every living thing dies.  Everything.

It would sure seem that natural selection would have overcome that little hiccup by now doesn't it?
---------------------QUOTE-------------------


That is the most ridiculous thing you have written so far (and that covers a lot of ridiculousness).

Besides missing the point that the discussion was about extinction of species, and not the death of organisms, this statement implies an inability to think about the consequences/predictions of one's hypotheses, as well as ignorance of well-known thermodynamic laws governing ecosystem functions.

Think about this for a nanosecond. If natural selection, or any process not involving miracles, was able to produce organisms that overcame death, how long would it take for them to consume all the resources on this planet? And then what? Without death, there is no life as we know it; death provides resources for not just the consumers, but the producers as well.

Death is not just a "little hiccup". If you think that immortality is something that can be achieved by natural selection, or even if you think it is a good thing, then you are not thinking at all. You are taking your theological constructs (the immortal soul) and trying to shoehorn reality into that construct. Sorry, but reality is gonna win this one.
Posted by: Occam's Toothbrush on Oct. 02 2007,06:50

Quote (Daniel Smith @ Oct. 02 2007,04:09)
 
Quote (oldmanintheskydidntdoit @ Oct. 02 2007,02:41)
As almost everything that has ever lived is extinct what does that say about the ability of this "designer" to plan?

Why bother to front-load if the organism is going extinct anyway?
---------------------QUOTE-------------------


Every living thing dies.  Everything.

It would sure seem that natural selection would have overcome that little hiccup by now doesn't it?
---------------------QUOTE-------------------


It's amazing how easily MET can be disproven, simply by posing a rhetorical question.  Clearly, now that scientists are finally faced with this one killer question--one that they've never thought of before and cannot answer--they can all just throw up their hands and admit goddidit.  I'm sure they were getting tired of faking all the evidence, suppressing all the ID research, etc. anyway.  Now they can just go to church for their answers, since DanTard has slain the Darwinist beast with this historic zinger.
Posted by: Reciprocating Bill on Oct. 02 2007,06:52

Quote (Daniel Smith @ Oct. 02 2007,03:25)
Unless there really is an all knowing God.  
     

---------------------QUOTE-------------------
 Moreover, we are talking the varied environments and apposite adaptations of every extinct and every extant lineage of descent that have taken their places among the astronomical number of ramifications of the tree of life.

With that in mind, "preplanned" becomes utterly implausible and even absurd, in my view.
---------------------QUOTE-------------------



In your view (which I assume is an atheistic one), pre-planning would seem ridiculous.  In my view, it's perfectly conceptual.
---------------------QUOTE-------------------


OH, an ALL KNOWING God. *Slaps forehead*. Why didn't you say so in the first place?

At least you're honest about what you are really about, which is more than I can say about most other proponents of views like this:

"An omniscient supernatural being (an all knowing God) with foreknowledge of every environmental shift in every inhabited environment on earth over 3.8 billion years (shifts that resulted from everything from chaotic fluctuations in the sun's output to the Yucatan asteroid) front-loaded into the first prokaryotic life appropriate preplanned sequences of evolutionary transitions (adaptations, speciations, extinction events) for every one of the countless lineages of organisms that would descend from those first organism over those ensuing billions of years."

Now THAT is science - of the same order that marvels at the clean fit between the five-sided banana and the human hand.

You must realize that given that you include extinction events in this scenario, which effectively eliminates any test of this pre-planned fitness, you have effectively rendered this model unfalsifiable and hence ejected it from the domain of science.
Posted by: George on Oct. 02 2007,07:57

Quote (Daniel Smith @ Oct. 01 2007,19:37)
Schindewolf's book was published (originally - in German) in 1950.  While technically that was in the last century, (so was 1999), it wasn't "a century ago".
---------------------QUOTE-------------------

 

My mistake.  I thought you said he worked and wrote in the 1920s.

I wasn't questioning this statement:



---------------------QUOTE-------------------
Since in the later Tertiary, an expansion of plains at the expense of forests has been observed, this change in environmental conditions and the consequent change in the mode of life has been represented as the cause of linear, progressive selection leading up to the modern horse.

---------------------QUOTE-------------------



I was questioning this one:

 

---------------------QUOTE-------------------
However, in the formulation of this view, not enough consideration has been given to the fact that the evolutionary trend of reduction in the number of toes had already been introduced long before the plains were occupied in the early Tertiary by the precursors of the horse; these inhabited dense scrub, meaning that they lived in an environment where the reduction of the primitive five-toed protoungulate foot was not an advantage at all.
---------------------QUOTE-------------------

(emphasis mine)

My question is how did he know the environment at the time was entirely comprised of dense scrub?  If I were to guess, this statement is based on finds of macrofossils or pollen of scrub species coupled with other proxy data that gave clues about climate.  This may have been the prevailing view at the time.  Don't know.  Doesn't matter.  But I suspect hand-waving.

My point is that knowledge of what species were present at the time doesn't give an accurate picture of what the vegetation structure was at the time, especially over large areas.  I presume the ancestors of horses were widely distributed and not confined to a small isolated valley or two.

As you can see as you walk around in "the wild", vegetation structure varies considerably depending on climate, soil and other things, including the activities of grazing animals.  It is extremely unlikely that the landscape where the ancestors of horses evolved was completely dominated by "dense scrub".  It is extremely likely that there were some more open areas where having fewer toes increased fitness.

Schindewolf was overstating the case that the environment required to select for single-toedness was not present in the early Tertiary.  Because of this, he has no grounds for claiming that development of the trait preceeded selection pressure.
Posted by: George on Oct. 02 2007,07:58

Quote (Reciprocating Bill @ Oct. 02 2007,06:52)
"An omniscient supernatural being (an all knowing God) with foreknowledge of every environmental shift in every inhabited environment on earth over 3.8 billion years (shifts that resulted from everything from chaotic fluctuations in the sun's output to the Yucatan asteroid) front-loaded into the first prokaryotic life appropriate preplanned sequences of evolutionary transitions (adaptations, speciations, extinction events) for every one of the countless lineages of organisms that would descend from those first organism over those ensuing billions of years."
---------------------QUOTE-------------------


'Course if you agree with this sentiment, I'm clearly wasting my time.
Posted by: Richard Simons on Oct. 02 2007,08:48

It is interesting that, when asked questions, those who accept the theory of evolution answer in their own words, with links to sources, while those who don't accept it cut and paste more or less lengthy excerpts of other people's writings.

 

---------------------QUOTE-------------------
Schindewolf did not subscribe at all to Lamarckism:

"an unbiased examination of the fossil material itself also reveals that absolutely no direct response to environmental influences or appropriate adaptations in the Lamarckian sense must necessarily be inferred...
Formerly, in emphasizing the supremacy of the environment, the properties and qualities of organisms were unduly disregarded.  Yet it should be obvious that in such chains of reactions and complexes of conditions the objects themselves must be credited with critical significance.  When I heat two chemical substances together, it is not the rise in temperature but the composition of the original material that is decisive.  The rise in temperature only triggers the reaction; under certain circumstances, it can be replaced by a different physical or chemical action (pressure, catalysts), and the result, determined by the original material, will still be the same.  At most, the environment plays only a similar role with regard to organisms; it can only provoke and set in motion some potential that is already present. "

Basic Questions in Paleontology, pp. 312-313 (emphasis his)

---------------------QUOTE-------------------


And this differs from Lamarkism how (your own words, please)? As I see it, he is saying "Lamark claims they adapt to present conditions, I say they adapt to future conditions". This is less mystic and more reasonable because . . . (own words, please)?

 

---------------------QUOTE-------------------
Schindewolf was familiar with the relatively new science of genetics:

---------------------QUOTE-------------------


That does not address the question. The question was "How do these 'internal factors', whatever they might be, get translated into mutations and changes in gene frequences?" In other words, how do the required changes in the DNA (that he could not have known about) take place? What makes a specific alanine change to leucine? Please answer in your own words.

Being able to answer in your own words is significant because it shows that you have thought about the issues to at least some degree.

 

---------------------QUOTE-------------------
Linnaeus first published his Systema Naturae in 1738.  How could it not be flawed by today's standards?  Hierarchies and evolutionary trees are still hotly disputed amongst those who classify organisms.
You are right that he formed no new hypothesis based on his hierarchy, but he was an adherent to natural theology - so that would be his "hypothesis" I suppose.
The point is that a nested hierarchy was postulated before Darwin's time so how could it be a prediction?
---------------------QUOTE-------------------


Hierarchies are hotly disputed? Perhaps at some level, but they are being refined all the time. There is general agreement about the broad outlines and many of the finer details. Could you give an example of a hot dispute in taxonomy?

A nested hierarchy was postulated before Darwin's time? Could we please have a reference.

I think you still have not grasped the significance of a nested hierarchy and are confusing it with Linnaeus' use of a nested hierarchy in his classification scheme. The crucial thing as regards evolution is that it predicts the nested hierarchies will all be the same and that is what is observed.
Posted by: Occam's Toothbrush on Oct. 02 2007,09:20

Is it too late to edit the posting subheading to add the scare quotes DanTard has shown are so appropriate?
   

---------------------QUOTE-------------------
Evolution of the horse; a problem for Darwinism?

For Daniel Smith to present his "argument"
---------------------QUOTE-------------------


Posted by: Erasmus, FCD on Oct. 02 2007,09:53

Schindewolf and the german school are at best mechanist idealists.  They see forms as internally generated by biochemical and physical restraints.  Many of these guys had a completely material theory, but some of them did not.  

Gould says that they have received a bad rap, and that there is an underlying reality to the idea that evolution has constraints.  Of course this is true, but I don't think it is true in the sense that Daniel means it.

Daniel, if you believe that species are not fixed entities (maybe you don't, I dunno, you tell me) then what is the barrier to speciation as an explanation for everything?
Posted by: Darth Robo on Oct. 02 2007,11:15



---------------------QUOTE-------------------
Every living thing dies.  Everything.
---------------------QUOTE-------------------




Isn't God dead?   ;)
Posted by: k.e on Oct. 02 2007,11:28

Quote (Darth Robo @ Oct. 02 2007,19:15)


---------------------QUOTE-------------------
Every living thing dies.  Everything.
---------------------QUOTE-------------------




Isn't God dead?   ;)
---------------------QUOTE-------------------


Yes, and right now he's spinning in his grave.
Posted by: Arden Chatfield on Oct. 02 2007,11:31

Quote (k.e @ Oct. 02 2007,11:28)
Quote (Darth Robo @ Oct. 02 2007,19:15)


---------------------QUOTE-------------------
Every living thing dies.  Everything.
---------------------QUOTE-------------------




Isn't God dead?   ;)
---------------------QUOTE-------------------


Yes, and right now he's spinning in his grave.
---------------------QUOTE-------------------


"If Jesus was alive now, he'd be spinning in his grave!"
Posted by: Tracy P. Hamilton on Oct. 02 2007,13:26

Quote (Daniel Smith @ Oct. 02 2007,02:10)
   
Quote (jeannot @ Sep. 30 2007,16:13)
Linné's classification was flawed. His nested hierarchy is largely inconsistent across characters, it is full of contradictions.
And I fail to see how this undermines Darwin's prediction. Linné formulated no hypothesis behind his classification, expect perhaps something similar to common design, which can predict anything (hence nothing).
---------------------QUOTE-------------------


Linnaeus first published his Systema Naturae in 1738.  How could it not be flawed by today's standards?  
You are right that he formed no new hypothesis based on his hierarchy, but he was an adherent to natural theology - so that would be his "hypothesis" I suppose.
The point is that a nested hierarchy was postulated before Darwin's time so how could it be a prediction?
---------------------QUOTE-------------------



Of course Linnaeus' hierarchy was flawed.  Linnaeus' idea was not flawed.  This is why biology students still have to learn classification.

Predictions:  

Organisms unknown to Linnaeus or Darwin will fit into the nested hierarchy.  That is, we do not have to depend on Linnaeus to make the decisions, and in fact could not have if we call Linneaus' decisions flawed.  A prediction is something that must be true if the theory is correct.

This hierarchy would still hold for the majority of characters not considered originally by Linnaeus.

Extinct organisms will fit into this hierarchy.

Genetics will form the same nested hierarchy.

The mechanism - descent with modification - forms the same kind of pattern.

I took the liberty of moving one sentence to the bottom here:



---------------------QUOTE-------------------
Hierarchies and evolutionary trees are still hotly disputed amongst those who classify organisms.
---------------------QUOTE-------------------



It is trivially true that if one is looking at a statistical process using 95% confidence intervals that you will be wrong about 5% of the time.  The remedy is acquiring more data, which sometimes confirms the conclusion or changes it.
Posted by: Henry J on Oct. 02 2007,21:59

Re "Genetics will form the same nested hierarchy."

There is the exception when horizontal transfers occur, but I gather that's quite rare in animals.

Henry
Posted by: Daniel Smith on Oct. 03 2007,02:06

Quote (Louis @ Oct. 02 2007,06:01)
"Natural selection" isn't "trying" to maximise individual survivability, "natural selection" is "trying" to maximise individual survivability to the point of successful reproduction.

---------------------QUOTE-------------------


Don't those individuals within a species that live longer, reproduce more?  Isn't this exactly what NS is supposed to select for?
       
Quote (Albatrossity2 @ Oct. 02 2007,06:46)
Besides missing the point that the discussion was about extinction of species, and not the death of organisms, this statement implies an inability to think about the consequences/predictions of one's hypotheses, as well as ignorance of well-known thermodynamic laws governing ecosystem functions.

Think about this for a nanosecond. If natural selection, or any process not involving miracles, was able to produce organisms that overcame death, how long would it take for them to consume all the resources on this planet? And then what? Without death, there is no life as we know it; death provides resources for not just the consumers, but the producers as well.
---------------------QUOTE-------------------


OK, so let me get this straight.  Even though all the "tools" necessary to achieve longer life and even immortality are already in every genome - being in use during the developmental and adolescent cycles of every organism...  And even though these tools are able to "cheat" the 2nd law of thermodynamics throughout those periods...  
If an organism gets a mutation that somehow disables the aging process and keeps these processes working - thereby increasing it's progeny considerably - natural selection will look ahead, decide that one species living too long is not good for the planet, and then cause that organism to die early anyway?

You're going to have to explain to me how this unthinking, uncaring, unintelligent force can suddenly show this kind of forethought!  
       

---------------------QUOTE-------------------
Death is not just a "little hiccup". If you think that immortality is something that can be achieved by natural selection, or even if you think it is a good thing, then you are not thinking at all. You are taking your theological constructs (the immortal soul) and trying to shoehorn reality into that construct. Sorry, but reality is gonna win this one.
---------------------QUOTE-------------------


I'm doing no such thing.  It's my contention that everything dies because death is a law which no living (organic) being can violate.
Posted by: Daniel Smith on Oct. 03 2007,02:22

Quote (George @ Oct. 02 2007,07:57)
     
Quote (Daniel Smith @ Oct. 01 2007,19:37)
Schindewolf's book was published (originally - in German) in 1950.  While technically that was in the last century, (so was 1999), it wasn't "a century ago".
---------------------QUOTE-------------------

 

My mistake.  I thought you said he worked and wrote in the 1920s.
---------------------QUOTE-------------------


Perhaps you were thinking of Leo Berg?  He wrote Nomogenesis in 1922.    

---------------------QUOTE-------------------

I wasn't questioning this statement:

       

---------------------QUOTE-------------------
Since in the later Tertiary, an expansion of plains at the expense of forests has been observed, this change in environmental conditions and the consequent change in the mode of life has been represented as the cause of linear, progressive selection leading up to the modern horse.

---------------------QUOTE-------------------



I was questioning this one:

       

---------------------QUOTE-------------------
However, in the formulation of this view, not enough consideration has been given to the fact that the evolutionary trend of reduction in the number of toes had already been introduced long before the plains were occupied in the early Tertiary by the precursors of the horse; these inhabited dense scrub, meaning that they lived in an environment where the reduction of the primitive five-toed protoungulate foot was not an advantage at all.
---------------------QUOTE-------------------

(emphasis mine)

My question is how did he know the environment at the time was entirely comprised of dense scrub?  If I were to guess, this statement is based on finds of macrofossils or pollen of scrub species coupled with other proxy data that gave clues about climate.  This may have been the prevailing view at the time.  Don't know.  Doesn't matter.  But I suspect hand-waving.
---------------------QUOTE-------------------


So, after admitting that you "don't know" what evidence Schindewolf based his argument on, you say that it "doesn't matter", because you "suspect hand-waving".  Is this how science is done?
   

---------------------QUOTE-------------------
My point is that knowledge of what species were present at the time doesn't give an accurate picture of what the vegetation structure was at the time, especially over large areas.  I presume the ancestors of horses were widely distributed and not confined to a small isolated valley or two.

As you can see as you walk around in "the wild", vegetation structure varies considerably depending on climate, soil and other things, including the activities of grazing animals.  It is extremely unlikely that the landscape where the ancestors of horses evolved was completely dominated by "dense scrub".  It is extremely likely that there were some more open areas where having fewer toes increased fitness.

Schindewolf was overstating the case that the environment required to select for single-toedness was not present in the early Tertiary.  Because of this, he has no grounds for claiming that development of the trait preceeded selection pressure.
---------------------QUOTE-------------------


So based on your experience 'walking around in the wild', you've now decided that Schindewolf, one of the premier paleontologists in all of Europe, overstated his case? (a case which, I'm sure, was based on slightly more research than that!)

It's amazing to me how you can delude yourself into thinking you have actually refuted his arguments while presenting no evidence to the contrary from the Tertiary period at all!
Posted by: Daniel Smith on Oct. 03 2007,02:52

Quote (Richard Simons @ Oct. 02 2007,08:48)
It is interesting that, when asked questions, those who accept the theory of evolution answer in their own words, with links to sources, while those who don't accept it cut and paste more or less lengthy excerpts of other people's writings.

---------------------QUOTE-------------------


I can't win!  First I'm told to bring it back to the subject - which was Schindewolf's take on horse evolution - then I'm chided for quoting Schindewolf!  

---------------------QUOTE-------------------

     

---------------------QUOTE-------------------
Schindewolf did not subscribe at all to Lamarckism:

"an unbiased examination of the fossil material itself also reveals that absolutely no direct response to environmental influences or appropriate adaptations in the Lamarckian sense must necessarily be inferred...
Formerly, in emphasizing the supremacy of the environment, the properties and qualities of organisms were unduly disregarded.  Yet it should be obvious that in such chains of reactions and complexes of conditions the objects themselves must be credited with critical significance.  When I heat two chemical substances together, it is not the rise in temperature but the composition of the original material that is decisive.  The rise in temperature only triggers the reaction; under certain circumstances, it can be replaced by a different physical or chemical action (pressure, catalysts), and the result, determined by the original material, will still be the same.  At most, the environment plays only a similar role with regard to organisms; it can only provoke and set in motion some potential that is already present. "

Basic Questions in Paleontology, pp. 312-313 (emphasis his)

---------------------QUOTE-------------------


And this differs from Lamarkism how (your own words, please)? As I see it, he is saying "Lamark claims they adapt to present conditions, I say they adapt to future conditions". This is less mystic and more reasonable because . . . (own words, please)?
---------------------QUOTE-------------------


You want me to explain Schindewolf's position without quoting Schindewolf?
OK, basically, Schindewolf believed that a lineage's evolutionary path was set from the first saltational event that created that type.  He documented what he interpreted as evolutionary patterns throughout the fossil record - which he then used to construct the framework of his "typostrophic theory".  This theory consisted of three stages; "typogenesis", which was the saltational evolution of types; "typostasis", which was a period of gradual development in a way that was constrained by the original typogenetic phase; and finally, "typolysis" which was a period of over-specialization that would usually end in the extinction of the species.
He did not believe that anyone was guiding these processes, he believed them to be totally self-contained.
 

---------------------QUOTE-------------------


     

---------------------QUOTE-------------------
Schindewolf was familiar with the relatively new science of genetics:

---------------------QUOTE-------------------


That does not address the question. The question was "How do these 'internal factors', whatever they might be, get translated into mutations and changes in gene frequences?" In other words, how do the required changes in the DNA (that he could not have known about) take place? What makes a specific alanine change to leucine? Please answer in your own words.
---------------------QUOTE-------------------

He believed that these saltational changes took place during ontogeny.  He cited the many ontogenetic phases documented in the fossils of ammonites, corals, and other lineages in the fossil record as evidence of this.  

---------------------QUOTE-------------------


Being able to answer in your own words is significant because it shows that you have thought about the issues to at least some degree.

     

---------------------QUOTE-------------------
Linnaeus first published his Systema Naturae in 1738.  How could it not be flawed by today's standards?  Hierarchies and evolutionary trees are still hotly disputed amongst those who classify organisms.
You are right that he formed no new hypothesis based on his hierarchy, but he was an adherent to natural theology - so that would be his "hypothesis" I suppose.
The point is that a nested hierarchy was postulated before Darwin's time so how could it be a prediction?
---------------------QUOTE-------------------


Hierarchies are hotly disputed? Perhaps at some level, but they are being refined all the time. There is general agreement about the broad outlines and many of the finer details. Could you give an example of a hot dispute in taxonomy?

A nested hierarchy was postulated before Darwin's time? Could we please have a reference.

I think you still have not grasped the significance of a nested hierarchy and are confusing it with Linnaeus' use of a nested hierarchy in his classification scheme. The crucial thing as regards evolution is that it predicts the nested hierarchies will all be the same and that is what is observed.
---------------------QUOTE-------------------


You just said Linnaeus used a nested hierarchy to classify organisms.  Linnaeus did this more than 100 years before Darwin.  Yet you want me to show that a nested hierarchy was postulated before Darwin's time?
As for your second point.  Maybe you're right.  I'm assuming that nested hierarchies based on morphological characters, or homologous characters, or analogous characters, or genetic sequences will all be different.  I haven't seen how they all line up.
Posted by: Daniel Smith on Oct. 03 2007,02:59

Quote (Erasmus @ FCD,Oct. 02 2007,09:53)
Schindewolf and the german school are at best mechanist idealists.  They see forms as internally generated by biochemical and physical restraints.  Many of these guys had a completely material theory, but some of them did not.  

Gould says that they have received a bad rap, and that there is an underlying reality to the idea that evolution has constraints.  Of course this is true, but I don't think it is true in the sense that Daniel means it.

Daniel, if you believe that species are not fixed entities (maybe you don't, I dunno, you tell me) then what is the barrier to speciation as an explanation for everything?
---------------------QUOTE-------------------


I don't believe that the process of RM+NS has been shown capable of producing anything innovative.
Posted by: oldmanintheskydidntdoit on Oct. 03 2007,03:04

Quote (Daniel Smith @ Oct. 03 2007,02:59)
Quote (Erasmus @ FCD,Oct. 02 2007,09:53)
Schindewolf and the german school are at best mechanist idealists.  They see forms as internally generated by biochemical and physical restraints.  Many of these guys had a completely material theory, but some of them did not.  

Gould says that they have received a bad rap, and that there is an underlying reality to the idea that evolution has constraints.  Of course this is true, but I don't think it is true in the sense that Daniel means it.

Daniel, if you believe that species are not fixed entities (maybe you don't, I dunno, you tell me) then what is the barrier to speciation as an explanation for everything?
---------------------QUOTE-------------------


I don't believe that the process of RM+NS has been shown capable of producing anything innovative.
---------------------QUOTE-------------------


Fine. I don't believe RM+NS could make me a cup of tea either.

Daniel, what do you consider RM+NS able to do?

We can strike innovative off the list, sure.

What can it do, as far as you are concerned?

And, if RM+NS did not create the diversity of biological life, what did?

Are you proposing an alternative method (there are many others) or something non-materialistic (i.e direct intervention by a designer?)?
Posted by: Alan Fox on Oct. 03 2007,05:42

Daniel wrote:

---------------------QUOTE-------------------
Every living thing dies.  Everything.

It would sure seem that natural selection would have overcome that little hiccup by now doesn't it?
---------------------QUOTE-------------------



How does that follow? If (ignoring for the moment the other problems with this scenario) organisms live for ever, and are not replaced by variants, there is nothing for natural selection to work on.
Posted by: k.e on Oct. 03 2007,06:32

Quote (Alan Fox @ Oct. 03 2007,13:42)
Daniel wrote:  

---------------------QUOTE-------------------
Every living thing dies.  Everything.

It would sure seem that natural selection would have overcome that little hiccup by now doesn't it?
---------------------QUOTE-------------------



How does that follow? If (ignoring for the moment the other problems with this scenario) organisms live for ever, and are not replaced by variants, there is nothing for natural selection to work on.
---------------------QUOTE-------------------


OH ......TOO CLEVER BY HALF YOU FRANCOPHONE.

YOUR WHOLE COUNTRY IS PROOF THAT HELL EXISTS.

DON'T YOU SEE?...THE PERFECT WORLD WAS WIPED OUT BY A TALKING SNAKE? RN+NS DOES NOT ALLOW FOR TALKING SNAKES.

IF GOD USED RM+NS TO CREATE TALKING SNAKES THEY WOULD BE RUNNING OUR SCHOOLS RIGHT NOW!!

IN FACT IF GOD USED RM+NS, CANCER AND SLAVERY WOULD NOT EXIST...CAN'T YOU SEE THAT?
Posted by: Alan Fox on Oct. 03 2007,06:32



---------------------QUOTE-------------------
OK, so let me get this straight.  Even though all the "tools" necessary to achieve longer life and even immortality are already in every genome - being in use during the developmental and adolescent cycles of every organism...  And even though these tools are able to "cheat" the 2nd law of thermodynamics throughout those periods...
---------------------QUOTE-------------------



Well, the genome does achieve a sort of immortality by being carried by multiple generations of descendant organisms. The original manuscripts of many ancient texts have long since disappeared, but the words remain by virtue of having been copied and copied again. Far from "all the "tools" necessary to achieve longer life", cell are programmed to commit suicide after a fixed number of divisions, a process referred to as < apoptosis >.
   

---------------------QUOTE-------------------
If an organism gets a mutation that somehow disables the aging process..
---------------------QUOTE-------------------



Breakdown of apoptosis results in uncontrolled cell growth, i.e. cancer.    

---------------------QUOTE-------------------
...and keeps these processes working - thereby increasing it's progeny considerably - natural selection will look ahead, decide that one species living too long is not good for the planet, and then cause that organism to die early anyway?
---------------------QUOTE-------------------



Natural selection cannot and does not look ahead.

   

---------------------QUOTE-------------------
You're going to have to explain to me how this unthinking, uncaring, unintelligent force can suddenly show this kind of forethought!
---------------------QUOTE-------------------



There is no forethought. Perhaps you could explain why you think there needs to be.
Posted by: Reciprocating Bill on Oct. 03 2007,06:37

Quote (Daniel Smith @ Oct. 03 2007,03:06)
If an organism gets a mutation that somehow disables the aging process and keeps these processes working - thereby increasing it's progeny considerably - natural selection will look ahead, decide that one species living too long is not good for the planet, and then cause that organism to die early anyway?

You're going to have to explain to me how this unthinking, uncaring, unintelligent force can suddenly show this kind of forethought!
---------------------QUOTE-------------------


This is a valid objection, and I think Albatrossity could better state his point. Natural selection does not select for the good of the planet, or the future. It operates locally in the present and quite blindly with respect to future consequences.

Generally speaking, long life and certainly immortality are not selected for because opposing the 2nd law is never a passive process; it demands resources devoted to error correction and repair, and those resources will only be present if selected for. But this is unlikely.  Survival until an organism reaches a youthful reproductive run is difficult enough as it is (in most species the a majority of individuals don't survive to reproduce at all), and under those circumstances selective pressures inevitably optimize organisms to survive simply to attain a period of reproductive maturity. Resources diverted to opposing entropy and ensuring a long life beyond this point are increasingly likely to be squandered as time goes by, because death in the wild comes from all directions (accidents, disease, predation etc.), not just entropic breakdown. In such cases resources dedicated to longevity don't have the opportunity to contribute to the organism's reproductive success, and there is a point they become a bad bet and optimizing youthful reproductive success a better bet. This is especially true to the extent that maintaining them reduces the organism's short term reproductive fitness (because fitness resources are finite).  As a result they tend to be selected against in most circumstances, and hence most species are stuck with senescence and death.
Posted by: Albatrossity2 on Oct. 03 2007,06:49

Quote (Daniel Smith @ Oct. 03 2007,02:06)
It's my contention that everything dies because death is a law which no living (organic) being can violate.
---------------------QUOTE-------------------


Even though Alan has touched on these points already, they bear repeating.

Please show me where any reputable biologist alleges that natural selection should favor individuals who "live longer". I've never heard about that before, and I am a professional biologist. Otherwise please understand that either you don't understand evolutionary theory, or you are purposely constructing a strawman.

Please show me where any reputable biologist alleges that living things "cheat" the second law of thermodynamics. Otherwise please understand that you either don't understand thermodynamics, or you are parroting creationist talking points that have been refuted nearly an infinite number of times.

Please show me where any reputable biologist said that natural selection needs to foresee the future in order to avoid tying up all the world's resources in a population of immortal organisms. This is a notion which ignores all of the other organisms on the planet who might also want to eat, and whose populations are also subject to selective pressures. Otherwise please understand that you misunderstand both evolutionary theory and thermodynamics.

I think we can sense a theme here. You don't understand the things that you are attempting to criticize.

As for your last point, you may be right. But that "law" is the second law of thermodynamics. Are you truly so ignorant of biology that you don't understand the use of energy in ensuring the cycling of resources in all ecosystems?
Posted by: Alan Fox on Oct. 03 2007,07:13



---------------------QUOTE-------------------
OH ......TOO CLEVER BY HALF YOU FRANCOPHONE.
---------------------QUOTE-------------------

Well, peut-être vous avez deviné que je suis anglais still gets a laugh, :)

YOUR WHOLE COUNTRY IS PROOF THAT HELL EXISTS.
[/QUOTE]

We'll see at Cardiff on Saturday.
Posted by: George on Oct. 03 2007,07:33

Quote (Alan Fox @ Oct. 03 2007,07:13)


---------------------QUOTE-------------------
OH ......TOO CLEVER BY HALF YOU FRANCOPHONE.
---------------------QUOTE-------------------

Well, peut-être vous avez deviné que je suis anglais still gets a laugh, :)

YOUR WHOLE COUNTRY IS PROOF THAT HELL EXISTS.

---------------------QUOTE-------------------



We'll see at Cardiff on Saturday.[/quote]
Hell (or purgatory?) for Ireland, anyway.  :angry:
Posted by: George on Oct. 03 2007,08:02

Quote (Daniel Smith @ Oct. 03 2007,02:22)

So, after admitting that you "don't know" what evidence Schindewolf based his argument on, you say that it "doesn't matter", because you "suspect hand-waving".  Is this how science is done?
---------------------QUOTE-------------------



It doesn't matter whether Schindewolf's views on the Tertiary environment were widely accepted at the time, because my later points hold regardless.  And I don't know what evidence Schindewolf based his argument on because you haven't said what it is yet.


 

---------------------QUOTE-------------------

So based on your experience 'walking around in the wild' @ you've now decided that Schindewolf,one of the premier paleontologists in all of Europe, overstated his case? (a case which, I'm sure, was based on slightly more research than that
---------------------QUOTE-------------------



Well, I would like to think that I will one day be one of Europe's premier ecologists.  Schindewolf may have been a good paleontologist, but how was he on ecology or paleoecology? What was his research?

 

---------------------QUOTE-------------------

It's amazing to me how you can delude yourself into thinking you have actually refuted his arguments while presenting no evidence to the contrary from the Tertiary period at all!
---------------------QUOTE-------------------



No,I haven't presented any evidence from the Tertiary.  However, I'm not the one proposing a radical departure from evolutionary theory.  You/Schindewolf need to present your evidence that the Tertiary environment was such that there was no selection for single-toedness in ancestral horses.  Invoking a thus-far speculative "dense scrub" engulfing all of Europe isn't evidence.  Without this evidence, your assertion of evolution anticipating selection can't stand.
Posted by: k.e on Oct. 03 2007,09:04



---------------------QUOTE-------------------

Quote (Alan Fox @ Oct. 03 2007,15:13)
 

---------------------QUOTE-------------------
OH ......TOO CLEVER BY HALF YOU FRANCOPHONE.
---------------------QUOTE-------------------

Well, peut-être vous avez deviné que je suis anglais still gets a laugh, :)

YOUR WHOLE COUNTRY IS PROOF THAT HELL EXISTS.

---------------------QUOTE-------------------



We'll see at Cardiff on Saturday.
---------------------QUOTE-------------------


FROMAGE EATING FRENCHMAN.

eAT mY < tUTAI >
Posted by: jeannot on Oct. 03 2007,09:10

Daniel said:

---------------------QUOTE-------------------
Don't those individuals within a species that live longer, reproduce more?  Isn't this exactly what NS is supposed to select for?
---------------------QUOTE-------------------


Natural selection for immortality is an interesting concept.
An allele increasing your life expectancy while your last progeny (assuming you lost your fertility) no longer needs your care would be maladaptive, simply because of kin competition. In other terms, death is adaptive once your children don’t need you anymore. Perhaps spite biased against individuals that are in competition with your descendants would favour a longer lifespan, but that’s a very particular case.

Population sizes being limited mostly because of competition, it would seem there is no clear benefit in extending your fertility in time once you are in competition with your descendants (all else being equal).
But since your progeny will be in competition with others, decreasing their fitness, one would expect that an allele extending fertility be favoured. The only question is: is eternal fertility possible? Apparently no: for instance, cellular respiration produces toxic compounds that are partly responsible for aging. And there is no easy way to prevent that.
Posted by: k.e on Oct. 03 2007,09:23



---------------------QUOTE-------------------
Hell (or purgatory?) for Ireland, anyway.  :angry:
---------------------QUOTE-------------------



Yes, I'm getting carried away on my own petard here.

DANIEL COME BACK AND EXPLAIN WHY YOU ARE SUCH A LOSER
Posted by: Louis on Oct. 03 2007,09:46

Quote (Daniel Smith @ Oct. 03 2007,08:06)
Quote (Louis @ Oct. 02 2007,06:01)
"Natural selection" isn't "trying" to maximise individual survivability, "natural selection" is "trying" to maximise individual survivability to the point of successful reproduction.

---------------------QUOTE-------------------


Don't those individuals within a species that live longer, reproduce more?  Isn't this exactly what NS is supposed to select for?
---------------------QUOTE-------------------


Not necessarily, no. How much, for example, successful sexual reproduction does your grandma accomplish?

I suggest remedial reading on what evolutionary biology actually is before you try to create/find problems with it.

Louis
Posted by: Louis on Oct. 03 2007,09:51

Quote (jeannot @ Oct. 03 2007,15:10)
Daniel said:  

---------------------QUOTE-------------------
Don't those individuals within a species that live longer, reproduce more?  Isn't this exactly what NS is supposed to select for?
---------------------QUOTE-------------------


Natural selection for immortality is an interesting concept.
An allele increasing your life expectancy while your last progeny (assuming you lost your fertility) no longer needs your care would be maladaptive, simply because of kin competition. In other terms, death is adaptive once your children don’t need you anymore. Perhaps spite biased against individuals that are in competition with your descendants would favour a longer lifespan, but that’s a very particular case.

Population sizes being limited mostly because of competition, it would seem there is no clear benefit in extending your fertility in time once you are in competition with your descendants (all else being equal).
But since your progeny will be in competition with others, decreasing their fitness, one would expect that an allele extending fertility be favoured. The only question is: is eternal fertility possible? Apparently no: for instance, cellular respiration produces toxic compounds that are partly responsible for aging. And there is no easy way to prevent that.
---------------------QUOTE-------------------


And don't forget them telomeres!

;-)

Louis
Posted by: k.e on Oct. 03 2007,09:58



---------------------QUOTE-------------------
Not necessarily, no. How much, for example, successful sexual reproduction does your grandma accomplish?
---------------------QUOTE-------------------



Well now...that explains everything.

Forget about RS +NM,  why do ancient Greeks fuck goats?

I rest my Casey!

How much selection could a creationist chuck if he had a baby every year?

The answer is obvious, not enough sex isn't enough for a social Darwinist.
Posted by: mitschlag on Oct. 03 2007,09:59

Quote (Daniel Smith @ Oct. 03 2007,02:06)
Don't those individuals within a species that live longer, reproduce more?  Isn't this exactly what NS is supposed to select for?
---------------------QUOTE-------------------


On the evolutionary significance of grandmothers:  

---------------------QUOTE-------------------
Proc Biol Sci. 2007 Sep 18; [Epub ahead of print]
Testing evolutionary theories of menopause.Shanley DP, Sear R, Mace R, Kirkwood TB.
Henry Wellcome Laboratory for Biogerontology Research, Institute for Ageing and Health, Newcastle University, Newcastle upon Tyne NE4 6BE, UK.

Why do women cease fertility rather abruptly through menopause at an age well before generalized senescence renders child rearing biologically impossible? The two main evolutionary hypotheses are that menopause serves either (i) to protect mothers from rising age-specific maternal mortality risks, thereby protecting their highly dependent younger children from death if the mother dies or (ii) to provide post-reproductive grandmothers who enhance their inclusive fitness by helping to care and provide for their daughters' children. Recent theoretical work indicates that both factors together are necessary if menopause is to provide an evolutionary advantage. However, these ideas need to be tested using detailed data from actual human life histories lived under reasonably 'natural' conditions; for obvious reasons, such data are extremely scarce. We here describe a study based on a remarkably complete dataset from The Gambia. The data provided quantitative estimates for key parameters for the theoretical model, which were then used to assess the actual effects on fitness. Empirically based numerical analysis of this nature is essential if the enigma of menopause is to be explained satisfactorily in evolutionary terms. Our results point to the distinctive (and perhaps unique) role of menopause in human evolution and provide important support for the hypothesized evolutionary significance of grandmothers.
---------------------QUOTE-------------------


Posted by: Louis on Oct. 03 2007,10:00

Quote (k.e @ Oct. 03 2007,15:58)
Forget about RS +NM,  why do ancient Greeks fuck goats?
---------------------QUOTE-------------------


Because they are asking for it those cheeky little slags.

Louis

P.S. Less of the ancient, I'm only 32.
Posted by: k.e on Oct. 03 2007,10:03

Quote (Louis @ Oct. 03 2007,18:00)
Quote (k.e @ Oct. 03 2007,15:58)
Forget about RS +NM,  why do ancient Greeks fuck goats?
---------------------QUOTE-------------------


Because they are asking for it those cheeky little slags.

Louis

P.S. Less of the ancient, I'm only 32.
---------------------QUOTE-------------------


Sorry, I was talking about your grandmother.
Posted by: JAM on Oct. 03 2007,11:37

Quote (Daniel Smith @ Oct. 03 2007,02:52)
   
Quote (Richard Simons @ Oct. 02 2007,08:48)
It is interesting that, when asked questions, those who accept the theory of evolution answer in their own words, with links to sources, while those who don't accept it cut and paste more or less lengthy excerpts of other people's writings.

---------------------QUOTE-------------------


I can't win!  First I'm told to bring it back to the subject - which was Schindewolf's take on horse evolution - then I'm chided for quoting Schindewolf!
---------------------QUOTE-------------------


Daniel,

Scientific arguments aren't about quoting. They are about evidence. If you can't describe the hypothesis, its predictions, and the observations in your own words, you clearly haven't thought it through.

   

---------------------QUOTE-------------------
As for your second point.  Maybe you're right.  I'm assuming that nested hierarchies based on morphological characters, or homologous characters, or analogous characters, or genetic sequences will all be different.
---------------------QUOTE-------------------


This shows your lack of reading comprehension, because I disagreed with your assumption and provided evidence.

Nested hierarchies of designed objects and their components are different. Nested hierarchies of organisms and their components must be superimposable. You simply disagreed with me without explaining why after I patiently explained to you, "The hierarchies of the organisms can be superimposed upon the hierarchies of their components, which are even more complex, because we can see how different proteins are related to each other."

Even worse, you failed to grasp this after I offered a perfect example:

< http://www.biolbull.org/cgi/content-nw/full/202/2/104/F2 >

Do you now see how human and mouse appear in multiple groupings within that tree, and in each clade, the *relative* distances are the same as for the relationships between the whole organisms? For example, look at the CB1 clade--rats and mice are very close, humans and rodents are closer to each other than they are to cats (carnivores). We can add sequences to that and predict where they will branch off, and common design makes no such predictions.
 

---------------------QUOTE-------------------
I haven't seen how they all line up.
---------------------QUOTE-------------------


I was trying to show you that, but predictably, you ran away from discussing evidence. That's because in your very soul, you know that your view won't be supported by the evidence. That's why you desperately quote in lieu of examining the evidence for yourself.
Posted by: Tracy P. Hamilton on Oct. 03 2007,11:54

Quote (Daniel Smith @ Oct. 03 2007,02:52)
       
Quote (Richard Simons @ Oct. 02 2007,08:48)
It is interesting that, when asked questions, those who accept the theory of evolution answer in their own words, with links to sources, while those who don't accept it cut and paste more or less lengthy excerpts of other people's writings.

---------------------QUOTE-------------------


I can't win!  First I'm told to bring it back to the subject - which was Schindewolf's take on horse evolution - then I'm chided for quoting Schindewolf!    

{snip quote}

You want me to explain Schindewolf's position without quoting Schindewolf?
OK, basically, Schindewolf believed that a lineage's evolutionary path was set from the first saltational event that created that type.  He documented what he interpreted as evolutionary patterns throughout the fossil record - which he then used to construct the framework of his "typostrophic theory".  This theory consisted of three stages; "typogenesis", which was the saltational evolution of types; "typostasis", which was a period of gradual development in a way that was constrained by the original typogenetic phase; and finally, "typolysis" which was a period of over-specialization that would usually end in the extinction of the species.
He did not believe that anyone was guiding these processes, he believed them to be totally self-contained.


---------------------QUOTE-------------------



Grasshopper, now you show comprehension.  A kindergardener can cut and paste Einstien's writing - what does that show about their understanding of relativity?

I was talking to my son about his AP history class, and he said that his instructor discouraged the use of quotes.  I told my son that I approved such an attitude.

Why is that?  It places the burden of what you claim on you.  You can't make excuse that because you use some of Einstien's prose that the meaning of that prose read in isolation is something Einstein "said".

Now we can ask:  what do we know now about genetics and development that Schindewolf did not?  We know about HOX genes, and that saltation (the simultaneous multiple mutation model) doesn't work nor is it needed to explain radical morphology changes.
   
     

---------------------QUOTE-------------------


Schindewolf was familiar with the relatively new science of genetics:

---------------------QUOTE-------------------



I.E. Schindewolf knew as little as everybody else, joined a school of thought that turned out to be wrong.  An excellent reason NOT to quote him, eh?

   

---------------------QUOTE-------------------
   

---------------------QUOTE-------------------

That does not address the question. The question was "How do these 'internal factors', whatever they might be, get translated into mutations and changes in gene frequences?" In other words, how do the required changes in the DNA (that he could not have known about) take place? What makes a specific alanine change to leucine? Please answer in your own words.


---------------------QUOTE-------------------

He believed that these saltational changes took place during ontogeny.  He cited the many ontogenetic phases documented in the fossils of ammonites, corals, and other lineages in the fossil record as evidence of this.      
---------------------QUOTE-------------------



So there is no genetic mechanism that explains why the specific mutations (of which many at once are required for saltation) can be ensured.

 

---------------------QUOTE-------------------

 

---------------------QUOTE-------------------

 

---------------------QUOTE-------------------
Linnaeus first published his Systema Naturae in 1738.  How could it not be flawed by today's standards?  Hierarchies and evolutionary trees are still hotly disputed amongst those who classify organisms.
You are right that he formed no new hypothesis based on his hierarchy, but he was an adherent to natural theology - so that would be his "hypothesis" I suppose.
The point is that a nested hierarchy was postulated before Darwin's time so how could it be a prediction?
---------------------QUOTE-------------------


Hierarchies are hotly disputed? Perhaps at some level, but they are being refined all the time. There is general agreement about the broad outlines and many of the finer details. Could you give an example of a hot dispute in taxonomy?

A nested hierarchy was postulated before Darwin's time? Could we please have a reference.

I think you still have not grasped the significance of a nested hierarchy and are confusing it with Linnaeus' use of a nested hierarchy in his classification scheme. The crucial thing as regards evolution is that it predicts the nested hierarchies will all be the same and that is what is observed.
---------------------QUOTE-------------------



You just said Linnaeus used a nested hierarchy to classify organisms.  Linnaeus did this more than 100 years before Darwin.  Yet you want me to show that a nested hierarchy was postulated before Darwin's time?
As for your second point.  Maybe you're right.  I'm assuming that nested hierarchies based on morphological characters, or homologous characters, or analogous characters, or genetic sequences will all be different.  I haven't seen how they all line up.
---------------------QUOTE-------------------



I believe it is I, not Simons who said that Linnean taxonomy is a nested hierarchy.

If you wish to see how they line up, go to www.tolweb.org.  There is text that describes the characteristics used for that level of the family tree.
Posted by: Henry J on Oct. 03 2007,14:15

Quote (Daniel Smith @ Oct. 03 2007,02:06)
Don't those individuals within a species that live longer, reproduce more?  Isn't this exactly what NS is supposed to select for?
---------------------QUOTE-------------------


Depends on the species. But no, that's not what NS selects for - NS selects for a larger number of descendants for the species (or a subset of it), not a maximum number of offspring per individual.

Henry
Posted by: Henry J on Oct. 03 2007,14:16

Quote (Albatrossity2 @ Oct. 03 2007,06:49)
Please show me where any reputable biologist alleges that living things "cheat" the second law of thermodynamics.
---------------------QUOTE-------------------


Maybe it's analogous to how a battery recharger "cheats" the second law when it recharges a battery?

Henry
Posted by: jeannot on Oct. 03 2007,14:24

Im' not a chemist, but claiming that senescence and death are inevitable because of the second law of thermodynamics doesn't makes sense to me.
Posted by: jeannot on Oct. 03 2007,14:31

Quote (Henry J @ Oct. 03 2007,14:15)
But no, that's not what NS selects for - NS selects for a larger number of descendants for the species (or a subset of it), not a maximum number of offspring per individual.
---------------------QUOTE-------------------


No that's not correct, Henry. Species and group selection can't work. That has been proven theoretically and experimentally.
For instance, if NS maximized the number of descendants for a species, sex ratios would be biased toward more females in panmictic populations (if we assume that females invest more in reproduction, which is almost always the case).
What we see in panmictic populations is a 1:1 sex ratio.

NS maximizes the reproductive rate of an allele during a given time span, even if this allele reduces the fitness of its bearers (this can be possible).
Posted by: Albatrossity2 on Oct. 03 2007,16:17

Quote (jeannot @ Oct. 03 2007,14:24)
Im' not a chemist, but claiming that senescence and death are inevitable because of the second law of thermodynamics doesn't makes sense to me.
---------------------QUOTE-------------------


Upon reflection, I'd have to agree. The second law is involved in whatever it was that I was thinking when I wrote that (along with competition and nutrient cycling), but by itself, I don't think that the SLoT makes senescence and death inevitable. And I don't have time to reconstruct (and make more coherent) those thoughts right now.

So thanks for pointing that out. I'll keep working on it and let you know if I can make it concise and/or coherent!
Posted by: Henry J on Oct. 03 2007,16:48

Quote (jeannot @ Oct. 03 2007,14:31)

[...]
NS maximizes the reproductive rate of an allele during a given time span, even if this allele reduces the fitness of its bearers (this can be possible).
---------------------QUOTE-------------------



Yeah, I guess I did oversimplify things too much there.

Henry
Posted by: jeannot on Oct. 03 2007,16:50

Alan was quite right when he said that genomes were immortal (actually, it's not exactly the case because of recombination).
NS is not a matter of individual survival or fecundity, it's a matter of allele frequency in a population.
Non-senescence can be favored only if there is NO tradeoff with other fitness traits, those that influence the reproductive rate of genes. And such tradeoffs are inevitable. You can't reach immortality while remaining as active as your competitor who produces free radicals that damage its cells.
So, an allele extending fertility forever would probably be less fit than another that shorten fertility but gives its bearers a far better competitive aptitude, a larger brood size or an earlier maturity. Of course, all this depends on the environment.

Steve Stearns' "Evolution of Life Histories" is probably the reference book for such questions, though I haven't read it.
Posted by: Henry J on Oct. 03 2007,16:50

Quote (Albatrossity2 @ Oct. 03 2007,16:17)
but by itself, I don't think that the SLoT makes senescence and death inevitable.
---------------------QUOTE-------------------


Not over short time frames, anyway. When the universe is gets old enough for all the stars to have burned out, maybe.

Henry
Posted by: Reciprocating Bill on Oct. 03 2007,17:06

Quote (jeannot @ Oct. 03 2007,15:31)
Quote (Henry J @ Oct. 03 2007,14:15)
But no, that's not what NS selects for - NS selects for a larger number of descendants for the species (or a subset of it), not a maximum number of offspring per individual.
---------------------QUOTE-------------------


No that's not correct, Henry. Species and group selection can't work. That has been proven theoretically and experimentally.
For instance, if NS maximized the number of descendants for a species, sex ratios would be biased toward more females in panmictic populations (if we assume that females invest more in reproduction, which is almost always the case).
What we see in panmictic populations is a 1:1 sex ratio.

NS maximizes the reproductive rate of an allele during a given time span, even if this allele reduces the fitness of its bearers (this can be possible).
---------------------QUOTE-------------------


There's a resurging minority view that argues that group selection can play a role in evolution under certain very specific circumstances (the groups must experience cycles of isolation and merger into the larger population), and that group selection played a role in human evolution. See Sober and Wilson's Unto Others, as an example. GS was radioactive for years after Wynne-Edwards was embarrassed, but that seems to be changing a bit, and the mathematics have been worked out (so say Sober and Wilson - I'm not arguing that position).
Posted by: Richard Simons on Oct. 03 2007,19:25

Quote (Daniel @ Oct. 03 2007,02:52)
You just said Linnaeus used a nested hierarchy to classify organisms.  Linnaeus did this more than 100 years before Darwin.  Yet you want me to show that a nested hierarchy was postulated before Darwin's time?

---------------------QUOTE-------------------


There is a big difference between using a nested hierarchy for convenience and predicting that life will fit into a single nested hierarchy.

It is possible to make a nested hierarchy using any set of items. You could go to the local store and make a nested hierarchy of the things they sell. You could make a nested hierarchy including all the buildings in your city. That is essentially what Linnaeus did.

What the theory of evolution predicted is that there would be just one nested hierarchy, whichever set of criteria you used (avoiding criteria that change readily, such as size and colour). That is not true for items in a store. One, for example, may have rolled oats with breakfast cereals, another with baking goods and a third with bulk items.

I am surprised that you said


---------------------QUOTE-------------------
I'm assuming that nested hierarchies based on morphological characters, or homologous characters, or analogous characters, or genetic sequences will all be different.  I haven't seen how they all line up.
---------------------QUOTE-------------------


The concept of the nested hierarchy is one of the most elementary facts about the theory of evolution. Your not knowing this (and other comments like tells me that you are just starting to find out about the topic, yet you feel confident enough to come to a site where many of the participants have spent years studying the field and make dogmantic statements like "What then, is your position on the lack of evidence in the fossil record for gradualism?" Wow!

You need to spend a year learning all you can about biology, geology and related topics from modern mainstream sources (you already have enough exposure to creationism). Look at rock exposures, especially those with fossils, and think about how they relate to what you’ve read. Better yet, spend a week at somewhere like the Royal Tyrrell Museum where you can participate in a dinosaur dig. Listen to how people tackle questions they can not answer and compare it with the way in which AnswersinGenesis, say, answers questions.

You still did not answer my question "How do these 'internal factors', whatever they might be, get translated into mutations and changes in gene frequences?" I will rephrase it. If it is somehow predetermined that horse ancestors will reduce the number of toes, something has to make the appropriate changes to the DNA at the appropriate time. The difficulty with Schindewolf's work always comes down to the same problem: how and where is the knowledge to make the change to keep on the 'correct' path stored and how is it put into effect? Alternatively, what stops the 'correct' path from being corrupted?

BTW: One of the set of criteria on your list gives a hierarchy that does not fit with the others. Do you know which it is?
Posted by: Richard Simons on Oct. 03 2007,21:02

In the previous post I said

---------------------QUOTE-------------------
(and other comments like tells me that you are just starting
---------------------QUOTE-------------------


I obviously missed out a few words there. I was looking for a phrase I vaguely remembered from earlier when I was interrupted, then had to leave and posted in a hurry. It wasn't an important point.
Posted by: Alan Fox on Oct. 04 2007,02:05

Daniel,

You may be interested in < this article >. It seems there has been parallel (convergent?) interest on horse evolution at < PT >
Posted by: Daniel Smith on Oct. 05 2007,03:24

Well I don't have time to answer everybody right now, so let me just make some comments that will (hopefully) get me caught up with most of your objections.

First, Schindewolf's stand on horse evolution is not well spelled out - and he only devotes a couple pages to it, so it doesn't really do his theory justice to use that example.  What I should have done was brought out his position on the evolution of cephalopods or stony corals - since these are his main areas of expertise and the subject to which he devotes probably a good third of his book.  So maybe we can shift gears as regards Schindewolf?

Now, as to the nested hierarchies (the analogous one was out of place BTW):  I don't know why I started arguing against superimposable nested hierarchies - since that is entirely consistent with designed descent.  I guess it's just the old creationist in me that got me caught up in that.  I do admit that I don't have a real good grasp of the subject, and need to learn more.  Really my main objection to the current theory of evolution is in regards to mechanism.

Which brings me to your questions of what genetic mechanism I would propose for designed descent.  First let me say that we have witnessed a saltational evolutionary event consistent with designed descent in our lifetime - the nylon bug.  That this was saltational is pretty straightforward since an entirely new enzyme was created in one step.  That the code for this enzyme was pre-existing also makes it consistent with designed descent.  I know most of you will probably disagree with my assessment of this, but I believe it could very well be a window into how saltational evolution could occur - especially as genomes are found to contain more embedded, overlapping codes.

I should also mention here Schindewolf's observation that the evolution of cephalopod shells and sutures; and corals' septal developments can be traced to earlier and earlier stages of ontogeny - suggesting an ontogenetic mechanism.  Dr. John Davison's semi-meiotic hypothesis follows this principle.

Next, in an effort to better understand the molecular side of things, I picked up a book called "Patterns in Evolution" by Roger Lewin (who is a Darwinist BTW).  Now, first let me say that I just started reading it and also that it came out in 1997 (I got it at a used bookstore) so it's 10 years old already and may not represent the latest thinking on the subject.  Some of the things he says so far have really struck me though:

First, he contrasts morphological evolution with molecular evolution - saying that morphological evolution proceeds in starts and jumps (my words - not his) due to varying reproduction/replication rates, selective pressures, environments, geological periods, etc., but that molecular evolution remains rather constant across the board due to it's main activity being in neutral, non-coding areas of the genome - thereby largely immune from selective pressure.

He goes on to say that convergent evolution is an issue for both molecular and morphological theory to explain.  He gives the morphological example of the placental and marsupial wolves and gives analogous gene sequences as the molecular example.

So here are my thoughts on the subject so far:
First, if convergent evolution can produce similar genes, then how do we know what's convergent and what isn't?  How also can we tell the distance between analogous sequences - since they are so alike?

Second, molecular evolution is thought to take place at a fairly regular rate because it occurs at mostly neutral, non-coding sites; but what if there aren't any neutral sites (as new research may now show)?  The ENCODE study showed that most of the genome is being transcribed into RNA.  If this RNA is being used (which it most likely is), then isn't it also subject to selective pressure?  And if subject to selection, then wouldn't that pretty much throw the molecular clock right out the window?

Perhaps equidistant sequences represent saltational divergences which produced types whose core structures have changed very little genetically since, (possibly drifting back and forth within certain windows), while their peripheral structures evolved more freely within their own wider constraints.
Posted by: Alan Fox on Oct. 05 2007,04:09



---------------------QUOTE-------------------
First, Schindewolf's stand on horse evolution is not well spelled out - and he only devotes a couple pages to it, so it doesn't really do his theory justice to use that example.  What I should have done was brought out his position on the evolution of cephalopods or stony corals - since these are his main areas of expertise and the subject to which he devotes probably a good third of his book.  So maybe we can shift gears as regards Schindewolf?
---------------------QUOTE-------------------



It does seem to boil down to how clear the evidence is that selective pressure to single toe was occurring before or after horse ancestors were in a savannah or plains environment. If you now concede this evidence is problematic and wish to look at molecular issues, why not start a new thread on the subject when you have marshaled your argument.

     

---------------------QUOTE-------------------
That this was saltational is pretty straightforward since an entirely new enzyme was created in one step.
---------------------QUOTE-------------------



Whilst mutation events are random, in that they are not predictable, some non-lethal mutations occur relatively frequently. Take the mutation that causes achondroplasia (dwarfism). This is a single-point mutation that produces dramatic and extensive changes in the phenotype of the individual with the mutation. This is the result of a single nucleic acid substitution in the genome, the smallest possible change that can happen. The mutation that occured in bacteria enabling them to digest nylon is thought to be a frame shift, caused by the addition or deletion of one* nucleotide. Again the change is as small as can happen, but the consequences are huge, and often catastrophic.

If you define this as saltation then all mutations are saltations.

(* or a larger no. not divisible by three)

(Added in edit)

PS: If I were to play Devil's advocate, I might suggest you have a look at transfer-RNA, and how each specific t-RNA could have evolved to carry its own particular amino acid. :)
Posted by: Reciprocating Bill on Oct. 05 2007,06:38

Quote (Daniel Smith @ Oct. 05 2007,04:24)
Which brings me to your questions of what genetic mechanism I would propose for designed descent.  First let me say that we have witnessed a saltational evolutionary event consistent with designed descent in our lifetime - the nylon bug.  That this was saltational is pretty straightforward since an entirely new enzyme was created in one step.  That the code for this enzyme was pre-existing also makes it consistent with designed descent.  I know most of you will probably disagree with my assessment of this, but I believe it could very well be a window into how saltational evolution could occur - especially as genomes are found to contain more embedded, overlapping codes.
---------------------QUOTE-------------------


Now you would have us include, among the pre-envisioned contingent environmental events for which the genome contains pre-planned, pre-sequenced adaptations, the entire history of cumulative human technological advances, particularly mastery of chemical and manufacturing processes that lead to the introduction of nylon in 1938, and its subsequent widespread use.

Which returns us to:    

"An omniscient supernatural being (an all knowing God) with foreknowledge of every environmental shift in every inhabited environment on earth over 3.8 billion years (shifts that resulted from everything from chaotic fluctuations in the sun's output to the Yucatan asteroid) front-loaded into the first prokaryotic life appropriate preplanned sequences of evolutionary transitions (adaptations, speciations, extinction events) for every one of the countless lineages of organisms that would descend from those first organism over those ensuing billions of years."

Does this fairly summarize your view? The "designer" pre-envisioned Dupont, and planned for it along with the Yucatan asteroid?
Posted by: JAM on Oct. 05 2007,10:05

Quote (Daniel Smith @ Oct. 05 2007,03:24)
Now, as to the nested hierarchies (the analogous one was out of place BTW):  I don't know why I started arguing against superimposable nested hierarchies - since that is entirely consistent with designed descent.  I guess it's just the old creationist in me that got me caught up in that.
---------------------QUOTE-------------------


Yep, creationism requires rank dishonesty.  
 

---------------------QUOTE-------------------
I do admit that I don't have a real good grasp of the subject, and need to learn more.
---------------------QUOTE-------------------


That doesn't explain why you ran away from my offer to explain it to you using the evidence.
 

---------------------QUOTE-------------------
Really my main objection to the current theory of evolution is in regards to mechanism.
---------------------QUOTE-------------------


I don't think so.
 

---------------------QUOTE-------------------
Which brings me to your questions of what genetic mechanism I would propose for designed descent.  First let me say that we have witnessed a saltational evolutionary event consistent with designed descent in our lifetime - the nylon bug.  That this was saltational is pretty straightforward since an entirely new enzyme was created in one step.  That the code for this enzyme was pre-existing also makes it consistent with designed descent.
---------------------QUOTE-------------------


What would be inconsistent with designed descent, Daniel?
 

---------------------QUOTE-------------------
I know most of you will probably disagree with my assessment of this, but I believe it could very well be a window into how saltational evolution could occur
---------------------QUOTE-------------------

How do you explain artificial evolution of random sequences, then?  

---------------------QUOTE-------------------
- especially as genomes are found to contain more embedded, overlapping codes.
---------------------QUOTE-------------------


You're completely misusing the term "code."
 

---------------------QUOTE-------------------
Next, in an effort to better understand the molecular side of things, I picked up a book called "Patterns in Evolution" by Roger Lewin (who is a Darwinist BTW).
---------------------QUOTE-------------------


How can he be a "Darwinist" if much of his book discusses drift, which is non-Darwinian?
 

---------------------QUOTE-------------------
Now, first let me say that I just started reading it and also that it came out in 1997 (I got it at a used bookstore) so it's 10 years old already and may not represent the latest thinking on the subject.
---------------------QUOTE-------------------


If you were being honest, you'd address the evidence, not a book.
 

---------------------QUOTE-------------------
...but that molecular evolution remains rather constant across the board due to it's main activity being in neutral, non-coding areas of the genome - thereby largely immune from selective pressure.
---------------------QUOTE-------------------


That would be the evolution we observe in sequences, but that's not true of the evolution of the functions of the proteins they encode.
 

---------------------QUOTE-------------------
He goes on to say that convergent evolution is an issue for both molecular and morphological theory to explain.
---------------------QUOTE-------------------


I see a strategic omission on your part here.
 

---------------------QUOTE-------------------
He gives the morphological example of the placental and marsupial wolves and gives analogous gene sequences as the molecular example.
---------------------QUOTE-------------------


Convergent sequences won't fit into a superimposable nested hierarchy. Issue addressed!


---------------------QUOTE-------------------
So here are my thoughts on the subject so far:
First, if convergent evolution can produce similar genes, then how do we know what's convergent and what isn't?
---------------------QUOTE-------------------


Convergent sequences won't fit into a superimposable nested hierarchy.     

---------------------QUOTE-------------------
How also can we tell the distance between analogous sequences - since they are so alike?
---------------------QUOTE-------------------


Easily--they aren't identical.
 

---------------------QUOTE-------------------
Second, molecular evolution is thought to take place at a fairly regular rate because it occurs at mostly neutral, non-coding sites; but what if there aren't any neutral sites (as new research may now show)?
---------------------QUOTE-------------------


Daniel, this is a creationist/ID LIE, pure and simple. Showing that 0.01% of the genome has a function does not tell us that 98% of the genome has a function.
 

---------------------QUOTE-------------------
The ENCODE study showed that most of the genome is being transcribed into RNA.  If this RNA is being used (which it most likely is), then isn't it also subject to selective pressure?
---------------------QUOTE-------------------


Why do you think that it is likely? Why not grow some balls and make a prediction instead of hiding from the evidence and making assertions?
Posted by: Daniel Smith on Oct. 05 2007,21:19

Quote (Reciprocating Bill @ Oct. 05 2007,06:38)
 
Quote (Daniel Smith @ Oct. 05 2007,04:24)
Which brings me to your questions of what genetic mechanism I would propose for designed descent.  First let me say that we have witnessed a saltational evolutionary event consistent with designed descent in our lifetime - the nylon bug.  That this was saltational is pretty straightforward since an entirely new enzyme was created in one step.  That the code for this enzyme was pre-existing also makes it consistent with designed descent.  I know most of you will probably disagree with my assessment of this, but I believe it could very well be a window into how saltational evolution could occur - especially as genomes are found to contain more embedded, overlapping codes.
---------------------QUOTE-------------------


Now you would have us include, among the pre-envisioned contingent environmental events for which the genome contains pre-planned, pre-sequenced adaptations, the entire history of cumulative human technological advances, particularly mastery of chemical and manufacturing processes that lead to the introduction of nylon in 1938, and its subsequent widespread use.

Which returns us to:    

"An omniscient supernatural being (an all knowing God) with foreknowledge of every environmental shift in every inhabited environment on earth over 3.8 billion years (shifts that resulted from everything from chaotic fluctuations in the sun's output to the Yucatan asteroid) front-loaded into the first prokaryotic life appropriate preplanned sequences of evolutionary transitions (adaptations, speciations, extinction events) for every one of the countless lineages of organisms that would descend from those first organism over those ensuing billions of years."

Does this fairly summarize your view? The "designer" pre-envisioned Dupont, and planned for it along with the Yucatan asteroid?
---------------------QUOTE-------------------


If you're going to make a list of everything an all-knowing God would know, you've got a long way to go.
(don't forget your birthday! ... and the number of hairs on your head, and ...)
Posted by: Reciprocating Bill on Oct. 05 2007,21:25

Quote (Daniel Smith @ Oct. 05 2007,22:19)
Quote (Reciprocating Bill @ Oct. 05 2007,06:38)
   
Quote (Daniel Smith @ Oct. 05 2007,04:24)
Which brings me to your questions of what genetic mechanism I would propose for designed descent.  First let me say that we have witnessed a saltational evolutionary event consistent with designed descent in our lifetime - the nylon bug.  That this was saltational is pretty straightforward since an entirely new enzyme was created in one step.  That the code for this enzyme was pre-existing also makes it consistent with designed descent.  I know most of you will probably disagree with my assessment of this, but I believe it could very well be a window into how saltational evolution could occur - especially as genomes are found to contain more embedded, overlapping codes.
---------------------QUOTE-------------------


Now you would have us include, among the pre-envisioned contingent environmental events for which the genome contains pre-planned, pre-sequenced adaptations, the entire history of cumulative human technological advances, particularly mastery of chemical and manufacturing processes that lead to the introduction of nylon in 1938, and its subsequent widespread use.

Which returns us to:    

"An omniscient supernatural being (an all knowing God) with foreknowledge of every environmental shift in every inhabited environment on earth over 3.8 billion years (shifts that resulted from everything from chaotic fluctuations in the sun's output to the Yucatan asteroid) front-loaded into the first prokaryotic life appropriate preplanned sequences of evolutionary transitions (adaptations, speciations, extinction events) for every one of the countless lineages of organisms that would descend from those first organism over those ensuing billions of years."

Does this fairly summarize your view? The "designer" pre-envisioned Dupont, and planned for it along with the Yucatan asteroid?
---------------------QUOTE-------------------


If you're going to make a list of everything an all-knowing God would know, you've got a long way to go.
(don't forget your birthday! ... and the number of hairs on your head, and ...)
---------------------QUOTE-------------------


OK - but the question was: Does this fairly summarize your view?
Posted by: Daniel Smith on Oct. 06 2007,03:15

Quote (Reciprocating Bill @ Oct. 05 2007,21:25)
OK - but the question was: Does this fairly summarize your view?
---------------------QUOTE-------------------


Pretty close - yeah.  Of course, I'm not sure if the info was pre-loaded into one or many organisms.

You make it sound so far fetched, but remember, there was a time when it would have seemed far fetched to think that all the info that determines what you will be, and all the info that reveals where you came from, could be contained in one single cell - yet we now know that to be true.
Posted by: oldmanintheskydidntdoit on Oct. 06 2007,04:01

Quote (Daniel Smith @ Oct. 06 2007,03:15)
Quote (Reciprocating Bill @ Oct. 05 2007,21:25)
OK - but the question was: Does this fairly summarize your view?
---------------------QUOTE-------------------


Pretty close - yeah.  Of course, I'm not sure if the info was pre-loaded into one or many organisms.

You make it sound so far fetched, but remember, there was a time when it would have seemed far fetched to think that all the info that determines what you will be, and all the info that reveals where you came from, could be contained in one single cell - yet we now know that to be true.
---------------------QUOTE-------------------


Not all far fetched ideas turn out to be true. Being unlikely in and of itself usually just means it's unlikely to be true, not more likely.

As we've now sequenced some organisms, is it your belief that evidence for "front loading" is present in these sequences waiting to be found?

If so, how do you propose going to look for it?

In the case of flavobacterium Sp. K17 (nylon eating bacteria) would it be logical to expect that if we sequenced "older" versions of the bacteria that the sequences required for making nylonase would be found, even though they were not enabled in that particular strain?

If not, what exactly do you mean by "front loaded" if not "contains instructions for dealing with future events"?

EDIT: Oh, here is "Answers in Genesis" take on it


---------------------QUOTE-------------------
It seems clear that plasmids are designed features of bacteria that enable adaptation to new food sources or the degradation of toxins. The details of just how they do this remains to be elucidated. The results so far clearly suggest that these adaptations did not come about by chance mutations, but by some designed mechanism. This mechanism might be analogous to the way that vertebrates rapidly generate novel effective antibodies with hypermutation in B-cell maturation, which does not lend credibility to the grand scheme of neo-Darwinian evolution.11 Further research will, I expect, show that there is a sophisticated, irreducibly complex, molecular system involved in plasmid-based adaptation—the evidence strongly suggests that such a system exists. This system will once again, as the black box becomes illuminated, speak of intelligent creation, not chance. Understanding this adaptation system could well lead to a breakthrough in disease control, because specific inhibitors of the adaptation machinery could protect antibiotics from the development of plasmid-based resistance in the target pathogenic microbes.
---------------------QUOTE-------------------



Try to avoid sounding like them huh?

< Link >
Posted by: Daniel Smith on Oct. 06 2007,04:26

Quote (Alan Fox @ Oct. 05 2007,04:09)
           

---------------------QUOTE-------------------
First, Schindewolf's stand on horse evolution is not well spelled out - and he only devotes a couple pages to it, so it doesn't really do his theory justice to use that example.  What I should have done was brought out his position on the evolution of cephalopods or stony corals - since these are his main areas of expertise and the subject to which he devotes probably a good third of his book.  So maybe we can shift gears as regards Schindewolf?
---------------------QUOTE-------------------



It does seem to boil down to how clear the evidence is that selective pressure to single toe was occurring before or after horse ancestors were in a savannah or plains environment. If you now concede this evidence is problematic and wish to look at molecular issues, why not start a new thread on the subject when you have marshaled your argument.
---------------------QUOTE-------------------


I'm not saying the evidence is problematic - just that Schindewolf doesn't say much about it.
I did find this:
           

---------------------QUOTE-------------------
The global tropical forest type of ecosystem of the early Tertiary was disrupted by Late Eocene climatic changes, with the extinction of most archaic mammalian lineages and the appearance of most modern families. Later Tertiary trends reflect increasing aridity, with the appearance of open-habitat mammals such as grazing ungulates, although true grasslands probably did not appear until the Late Miocene in the New World and the Pliocene in the Old World....

The relative dryness of the Oligocene (68, 111), as well as evidence from mammalian dental and locomotor adaptations (136, 139, 140) and from paleosols (98), has led to the suggestion that savanna habitats existed in northern latitudes. However, although the faunas were more derived and probably occupied more open habitats than in the Late Eocene, the mammals appear to reflect a woodland rather than a savanna type of community(5 5, 128). The paleosol evidence can be reinterpreted as a dense "woody savanna," without underlying herbs and grasses, a type of vegetation that has no counterpart in modern floras (68).
---------------------QUOTE-------------------

TERTIARY MAMMAL EVOLUTION IN THE CONTEXT OF CHANGING CLIMATES, VEGETATION, AND TECTONIC EVENTS, Christine M. Janis, 1993 Annual Reviews, (Emphasis mine)< (link) >
   

---------------------QUOTE-------------------
   

---------------------QUOTE-------------------
That this was saltational is pretty straightforward since an entirely new enzyme was created in one step.
---------------------QUOTE-------------------



Whilst mutation events are random, in that they are not predictable, some non-lethal mutations occur relatively frequently. Take the mutation that causes achondroplasia (dwarfism). This is a single-point mutation that produces dramatic and extensive changes in the phenotype of the individual with the mutation. This is the result of a single nucleic acid substitution in the genome, the smallest possible change that can happen. The mutation that occured in bacteria enabling them to digest nylon is thought to be a frame shift, caused by the addition or deletion of one* nucleotide. Again the change is as small as can happen, but the consequences are huge, and often catastrophic.

If you define this as saltation then all mutations are saltations.

(* or a larger no. not divisible by three)

(Added in edit)

---------------------QUOTE-------------------


"Saltational" (to my mind) refers to the results - not necessarily the cause.  Dwarfism is morphologically saltational even though it has the smallest of causes.  The same with the frame shift that caused the nylon bug.
If (as I'm alleging) genomes are replete with embedded codes just waiting for a signal, such as a frame shift, to set them in action, then a saltational change can happen with just one substitution.  These substitutions would be non-random of course.
   

---------------------QUOTE-------------------

PS: If I were to play Devil's advocate, I might suggest you have a look at transfer-RNA, and how each specific t-RNA could have evolved to carry its own particular amino acid. :)
---------------------QUOTE-------------------


I just downloaded most of the ENCODE articles and will be spending quite some time trying to digest them.  I don't know if I'll have time for another rabbit trail!
Posted by: Daniel Smith on Oct. 06 2007,04:40

Quote (oldmanintheskydidntdoit @ Oct. 06 2007,04:01)

As we've now sequenced some organisms, is it your belief that evidence for "front loading" is present in these sequences waiting to be found?

---------------------QUOTE-------------------

Yes.    

---------------------QUOTE-------------------

If so, how do you propose going to look for it?
---------------------QUOTE-------------------

I don't know.  It would be difficult to foresee usefulness.  (Although the ENCODE study does mention a "large pool of neutral elements" that "may serve as a 'warehouse' for natural selection".)

---------------------QUOTE-------------------


In the case of flavobacterium Sp. K17 (nylon eating bacteria) would it be logical to expect that if we sequenced "older" versions of the bacteria that the sequences required for making nylonase would be found, even though they were not enabled in that particular strain?
---------------------QUOTE-------------------


That would be logical.    

---------------------QUOTE-------------------

If not, what exactly do you mean by "front loaded" if not "contains instructions for dealing with future events"?

---------------------QUOTE-------------------

That's pretty much exactly what I mean.    

---------------------QUOTE-------------------

EDIT: Oh, here is "Answers in Genesis" take on it
     

---------------------QUOTE-------------------
It seems clear that plasmids are designed features of bacteria that enable adaptation to new food sources or the degradation of toxins. The details of just how they do this remains to be elucidated. The results so far clearly suggest that these adaptations did not come about by chance mutations, but by some designed mechanism. This mechanism might be analogous to the way that vertebrates rapidly generate novel effective antibodies with hypermutation in B-cell maturation, which does not lend credibility to the grand scheme of neo-Darwinian evolution.11 Further research will, I expect, show that there is a sophisticated, irreducibly complex, molecular system involved in plasmid-based adaptation—the evidence strongly suggests that such a system exists. This system will once again, as the black box becomes illuminated, speak of intelligent creation, not chance. Understanding this adaptation system could well lead to a breakthrough in disease control, because specific inhibitors of the adaptation machinery could protect antibiotics from the development of plasmid-based resistance in the target pathogenic microbes.
---------------------QUOTE-------------------



Try to avoid sounding like them huh?

< Link >
---------------------QUOTE-------------------


Never read that, but I can't say that I disagree with it.
Posted by: Reciprocating Bill on Oct. 06 2007,07:42

Quote (Daniel Smith @ Oct. 06 2007,04:15)
   
Quote (Reciprocating Bill @ Oct. 05 2007,21:25)
OK - but the question was: Does this fairly summarize your view?
---------------------QUOTE-------------------


Pretty close - yeah.  Of course, I'm not sure if the info was pre-loaded into one or many organisms.

You make it sound so far fetched, but remember, there was a time when it would have seemed far fetched to think that all the info that determines what you will be, and all the info that reveals where you came from, could be contained in one single cell - yet we now know that to be true.
---------------------QUOTE-------------------


Well, I've stated your thesis, and you've ruled it "pretty close" to summarizing your own views - yet also say that it "sounds far fetched."

I submit to you that I haven't made it "sound" far fetched. It simply IS far fetched.  

And, Daniel, speaking to your preference for outliers and scientific rebels, "being far fetched" is NOT a positive argument - particularly when you YOURSELF find that your position defies credulity when it is compactly stated.
Posted by: improvius on Oct. 06 2007,10:58

oops, wrong thread
Posted by: Daniel Smith on Oct. 06 2007,19:15

Quote (JAM @ Oct. 05 2007,10:05)
Why not grow some balls and make a prediction instead of hiding from the evidence and making assertions?
---------------------QUOTE-------------------


How about this?

I predict that sometime in the near future, the idea that evolutionary constraint is evidence of the functionality of a given sequence - will have to be abandoned.

You can add that prediction to the < list I've already posted. >
Posted by: JAM on Oct. 06 2007,19:27

Quote (Daniel Smith @ Oct. 06 2007,19:15)
Quote (JAM @ Oct. 05 2007,10:05)
Why not grow some balls and make a prediction instead of hiding from the evidence and making assertions?
---------------------QUOTE-------------------


How about this?

I predict that sometime in the near future, the idea that evolutionary constraint is evidence of the functionality of a given sequence - will have to be abandoned.

You can add that prediction to the < list I've already posted. >
---------------------QUOTE-------------------


Daniel,

None of those represent what scientists mean by predictions. Scientific hypotheses don't make predictions about what ideas people will have; they make predictions about the results of discrete experiments or observations that have yet to be made.

< Here is an example of testing a series of predictions in evolutionary biology (not my field). The last paragraph is probably the clearest example. >

IOW, you don't have the balls to do it yet. Front-loading makes plenty of predictions, but you're afraid to.
Posted by: Daniel Smith on Oct. 06 2007,19:55

Quote (Reciprocating Bill @ Oct. 06 2007,07:42)
 
Well, I've stated your thesis, and you've ruled it "pretty close" to summarizing your own views - yet also say that it "sounds far fetched."

I submit to you that I haven't made it "sound" far fetched. It simply IS far fetched.  

And, Daniel, speaking to your preference for outliers and scientific rebels, "being far fetched" is NOT a positive argument - particularly when you YOURSELF find that your position defies credulity when it is compactly stated.
---------------------QUOTE-------------------


You have a way of misinterpreting the meaning of my words.  I didn't say "it sounds far fetched" I said "You make it sound so far fetched".

There's a difference.  

Nowhere did I say it defies credulity, nor do I think that it does.  I think the evidence for design in both the universe and in life's systems is overwhelming.  We are discussing intricate, networked, molecular coding systems that define sophisticated, self-replicating machinery (though the term 'machinery' does not do it justice).  We are talking about cellular systems more complex, more orderly, more efficient, more multi-functional, than anything man can ever hope to invent.  Even the simplest self-replicator had to be more complex than anything man has ever built.  

I work on complex machinery for a living and I see the results of many years of engineering diligence up close and personal every day, yet nothing I've seen at work compares with the type of engineering I've seen in even the simplest bacterial systems or in something as taken-for-granted as the human auditory system.  The more I learn about such systems, the more amazed I am at the mind of God.

Yet you seem fine with dismissing such obvious ingenuity with a simple wave of the hand.  Opting instead for this fairy tale of how happy accidents and the seemingly all-powerful, semi-intelligent, forward-thinking force called "natural selection" designed such complicated efficient structures.

It may sound far fetched to you, that such systems are designed, but it doesn't seem that way at all to those of us who believe in God, nor does it contradict anything we know about designs and designers.

I submit to you that the basis of your objections are not scientific, but atheistic.  Science is your main defense against those pesky thoughts of God that keep popping into your head, and you must do everything in your power to make sure that science cannot reach anything other than atheistic conclusions.
Posted by: Daniel Smith on Oct. 06 2007,20:10

Quote (JAM @ Oct. 06 2007,19:27)
   
Quote (Daniel Smith @ Oct. 06 2007,19:15)
     
Quote (JAM @ Oct. 05 2007,10:05)
Why not grow some balls and make a prediction instead of hiding from the evidence and making assertions?
---------------------QUOTE-------------------


How about this?

I predict that sometime in the near future, the idea that evolutionary constraint is evidence of the functionality of a given sequence - will have to be abandoned.

You can add that prediction to the < list I've already posted. >
---------------------QUOTE-------------------


Daniel,

None of those represent what scientists mean by predictions. Scientific hypotheses don't make predictions about what ideas people will have; they make predictions about the results of discrete experiments or observations that have yet to be made.

< Here is an example of testing a series of predictions in evolutionary biology (not my field). The last paragraph is probably the clearest example. >

IOW, you don't have the balls to do it yet. Front-loading makes plenty of predictions, but you're afraid to.
---------------------QUOTE-------------------


The concept of evolutionary constraint (as I understand it) is based on the theory that mutations are generally rejected in functional sequences because they are usually deleterious, but mutations in neutral sites are not rejected.  Therefore the sequences that have remained alike (are constrained) across related lineages can be inferred to be functional while those that have changed a lot are inferred non-functional (neutral).
My prediction is that there are many functional sequences that are different (even radically so) amongst related lineages - this due to their being of designed, not mutational, origin.
So when I say evolutionary constraint as an indicator of functionality will have to be abandoned, I am expecting my prediction to be experimentally verified.
Posted by: Reciprocating Bill on Oct. 06 2007,20:48



---------------------QUOTE-------------------
You have a way of misinterpreting the meaning of my words.  I didn't say "it sounds far fetched" I said "You make it sound so far fetched".
---------------------QUOTE-------------------


You stated that my little summary more or less fairly represented your view. In fairly summarizing your view I created a passage that sounds far fetched. That seems to speak for itself.

At any rate, your position is that God is the author of the world, including the biological world, in all of its detail, complexity, and apparent design. I appreciate that frankness; so often advocates of ID are coy to the point of dishonesty about the commitments that motivate their position.

However, that isn't a notion amenable to scientific investigation, because God can do anything, in any order, at any time, outside the constraints of natural law, and hence no empirical test can be devised to put this notion to empirical test. This simple fact leaves us no choice but to pursue biological and evolutionary science within the constraints of methodological naturalism, regardless of the personal spiritual beliefs of the investigator. Fortunately this powerful epistemology has yielded countless active and productive lines of research that daily increase our understanding of the history and nature of the biological world - including the facts we all find quite astounding.
Posted by: JAM on Oct. 06 2007,20:52

Quote (Daniel Smith @ Oct. 06 2007,20:10)
The concept of evolutionary constraint (as I understand it) is based on the theory that mutations are generally rejected in functional sequences because they are usually deleterious, but mutations in neutral sites are not rejected.  Therefore the sequences that have remained alike (are constrained) across related lineages can be inferred to be functional while those that have changed a lot are inferred non-functional (neutral).
My prediction is that there are many functional sequences that are different (even radically so) amongst related lineages - this due to their being of designed, not mutational, origin.
---------------------QUOTE-------------------


Daniel,

Much better! I retract and apologize for my insult; it was mainly a strategy to get you to respond in a coherent way. It's also an example of how hypotheses yield new data even when they are incorrect.

The main criterion you're missing is that you need to apply your hypothesis to something more specific. I'm here to help.

One clarification--when you wrote "functional sequences," you meant groups of sequences with the same or similar biological function(s), correct?
 

---------------------QUOTE-------------------
So when I say evolutionary constraint as an indicator of functionality will have to be abandoned, I am expecting my prediction to be experimentally verified.
---------------------QUOTE-------------------


Luckily for you, the "experiment" has already been done. The scientific method works even when the data already exist--the power of the method is in the prediction. Shall we sample a protein family or ten? Any functions that you find particularly interesting?
Posted by: stevestory on Oct. 06 2007,21:25

I'm not up to speed on this thread at all, but let me interject to remind people that personal insults against anyone present won't be tolerated. Keep it as respectful as if you were in a college classroom.
Posted by: Daniel Smith on Oct. 07 2007,05:17

Quote (Reciprocating Bill @ Oct. 06 2007,20:48)
At any rate, your position is that God is the author of the world, including the biological world, in all of its detail, complexity, and apparent design. I appreciate that frankness; so often advocates of ID are coy to the point of dishonesty about the commitments that motivate their position.

However, that isn't a notion amenable to scientific investigation, because God can do anything, in any order, at any time, outside the constraints of natural law, and hence no empirical test can be devised to put this notion to empirical test. This simple fact leaves us no choice but to pursue biological and evolutionary science within the constraints of methodological naturalism, regardless of the personal spiritual beliefs of the investigator. Fortunately this powerful epistemology has yielded countless active and productive lines of research that daily increase our understanding of the history and nature of the biological world - including the facts we all find quite astounding.
---------------------QUOTE-------------------


I sympathize with your frustration over my "goddidit" explanation.  I feel the same way about natural selection:  Often NS is presented as if it can do anything and everything.  If something works, it's because of natural selection; and since pretty much everything works, natural selection becomes this all-powerful entity that can build anything - a lot like God.  In fact the two are essentially interchangeable - they both explain everything and therefore explain nothing.
What's needed are direct observations.  But since we cannot directly observe God or macroevolution, we must look at what we can observe and see if it matches the evidence.  Fortunately for us, natural selection can be observed.  Natural selection needs to be put to the test to assay it's capabilities in the real world.  This is why I have so much respect for scientists like Leo Berg: he spent years, up to his waist, in rivers and streams, observing natural selection in action.  He felt that it was not up to the task.  How many scientists today experimentally verify the ability of NS to produce or conserve innovations?  Probably not many since most take it's capabilities for granted.

Also, when people say that science cannot investigate God or the supernatural, that's not entirely correct.  Science can (and does) investigate claims of supernatural activity - so long as the supernatural activity is supposed to have affected the physical world.  If for example, someone claims that "a ghost" is moving a chair, science can investigate and see if the evidence fits the claim.  More than likely, science will find that some other force is actually moving the chair (if it moves at all), but sometimes they might find no natural explanation.  They can then conclude that the evidence does not rule out the ghost explanation - though they can never actually verify that it is really a ghost.
The same goes for design theories.  If these theories make claims that God affected the natural world, the evidence (the natural world) can be examined to see whether or not it is consistent with such claims.  
One thing that design theories pretty much all do is use the most observed designer - man -  and his designs as a template for what they expect to find when looking for design in nature.  That's what I do.  Of course, if the design theory postulates a God of infinite intelligence, it would expect to find designs that are infinitely more sophisticated than man's.  This is what I expect as well.
So when I examine the evidence, is that what I find?  Yes, that is exactly what I find.  I find complex intricate systems analogous (but far superior) to power plants, factories with automated assembly lines, communication networks, super highway systems, waste management (with recycling!), and on and on.  Does that mean that science has proven there is a God?  No, it only proves that the physical world is consistent with the design theory and that it cannot be ruled out.
Are such systems within the capabilities of RM+NS?  You tell me.
Posted by: oldmanintheskydidntdoit on Oct. 07 2007,05:43

Quote (Daniel Smith @ Oct. 07 2007,05:17)
If these theories make claims that God affected the natural world, the evidence (the natural world) can be examined to see whether or not it is consistent with such claims.
---------------------QUOTE-------------------


Excluding biology for a moment, what other evidence do you claim also shows this proof? Everything?
You say


---------------------QUOTE-------------------
So when I examine the evidence, is that what I find?  Yes, that is exactly what I find.  I find complex intricate systems analogous (but far superior) to power plants, factories with automated assembly lines, communication networks, super highway systems, waste management (with recycling!), and on and on.
---------------------QUOTE-------------------


Is this level of detail also to be found, for instance, in rocks? The sun? The solar system?

Daniel, when you say


---------------------QUOTE-------------------
design theories pretty much all do is use the most observed designer - man -  and his designs as a template for what they expect to find when looking for design in nature
---------------------QUOTE-------------------


Can you apply that template to non-biological entities also?

If so, do you have an example?

If not, well, do you claim there was one designer for biology
one for the mountains
one for the seas
one for the coastline of denmark?

etc etc?
Posted by: Daniel Smith on Oct. 07 2007,05:46

Quote (JAM @ Oct. 06 2007,20:52)
         
Quote (Daniel Smith @ Oct. 06 2007,20:10)
The concept of evolutionary constraint (as I understand it) is based on the theory that mutations are generally rejected in functional sequences because they are usually deleterious, but mutations in neutral sites are not rejected.  Therefore the sequences that have remained alike (are constrained) across related lineages can be inferred to be functional while those that have changed a lot are inferred non-functional (neutral).
My prediction is that there are many functional sequences that are different (even radically so) amongst related lineages - this due to their being of designed, not mutational, origin.
---------------------QUOTE-------------------


Daniel,

Much better! I retract and apologize for my insult; it was mainly a strategy to get you to respond in a coherent way. It's also an example of how hypotheses yield new data even when they are incorrect.

The main criterion you're missing is that you need to apply your hypothesis to something more specific. I'm here to help.

One clarification--when you wrote "functional sequences," you meant groups of sequences with the same or similar biological function(s), correct?
             

---------------------QUOTE-------------------
So when I say evolutionary constraint as an indicator of functionality will have to be abandoned, I am expecting my prediction to be experimentally verified.
---------------------QUOTE-------------------


Luckily for you, the "experiment" has already been done. The scientific method works even when the data already exist--the power of the method is in the prediction. Shall we sample a protein family or ten? Any functions that you find particularly interesting?
---------------------QUOTE-------------------


I think that I need to clarify my position before we can decide how best to test it.

When I say "functional sequences" I mean functional as in "used within the cell".  By this definition, I'd say that anything that is transcribed would qualify as functional - since the cellular machinery is going through the trouble of transcribing it.  So this would include protein coding sequences as well as ncRNA sequences, and anything else that's transcribed.

I also must clarify that I do actually believe that all functional sequences (as I've defined them) are evolutionarily constrained.  It's just that I don't think you can find functionality or constraint by comparing sequences to other lineages (since I posit that there are no truly neutral sites).  If comparing to other lineages, the function must first be known and then the entire sequence that provides that function compared.  However, the only true test of constraint is comparison to ancestral DNA within the same lineage.  

So, with that in mind, how do we go about testing this?
Posted by: Daniel Smith on Oct. 07 2007,05:59

Quote (oldmanintheskydidntdoit @ Oct. 07 2007,05:43)
 
Quote (Daniel Smith @ Oct. 07 2007,05:17)
If these theories make claims that God affected the natural world, the evidence (the natural world) can be examined to see whether or not it is consistent with such claims.
---------------------QUOTE-------------------


Excluding biology for a moment, what other evidence do you claim also shows this proof? Everything?
You say
 

---------------------QUOTE-------------------
So when I examine the evidence, is that what I find?  Yes, that is exactly what I find.  I find complex intricate systems analogous (but far superior) to power plants, factories with automated assembly lines, communication networks, super highway systems, waste management (with recycling!), and on and on.
---------------------QUOTE-------------------


Is this level of detail also to be found, for instance, in rocks? The sun? The solar system?

Daniel, when you say
 

---------------------QUOTE-------------------
design theories pretty much all do is use the most observed designer - man -  and his designs as a template for what they expect to find when looking for design in nature
---------------------QUOTE-------------------


Can you apply that template to non-biological entities also?

If so, do you have an example?

If not, well, do you claim there was one designer for biology
one for the mountains
one for the seas
one for the coastline of denmark?

etc etc?
---------------------QUOTE-------------------


I think similar levels of detail can be found in the earth's various systems in regards to their near perfect fitness for life.  Also, the cosmos, the sun, the moon, all these things are so arranged and physical properties so ordered as to be perfect for life on this planet as well.  Certainly atomic principles and the composition of matter and energy are also remarkable.  The properties of water, carbon, oxygen, hydrogen, light, gravity, etc. are all things which appear to behave as if planned out in advance for the purpose of life on this planet.  I can't think of anything that just appears to be random.  Can you?

So I guess my example would be to compare a human laboratory - where man provides a controlled environment for certain lifeforms to reside - to the earth and its environment.
Posted by: mitschlag on Oct. 07 2007,06:09

Quote (Daniel Smith @ Oct. 07 2007,05:46)
I also must clarify that I do actually believe that all functional sequences (as I've defined them) are evolutionarily constrained.  It's just that I don't think you can find functionality or constraint by comparing sequences to other lineages (since I posit that there are no truly neutral sites).  If comparing to other lineages, the function must first be known and then the entire sequence that provides that function compared.  However, the only true test of constraint is comparison to ancestral DNA within the same lineage.  

So, with that in mind, how do we go about testing this?
---------------------QUOTE-------------------


You are the scientist, DS.  You are responsible for devising the test.
Posted by: oldmanintheskydidntdoit on Oct. 07 2007,06:25

Quote (Daniel Smith @ Oct. 07 2007,05:59)
I think similar levels of detail can be found in the earth's various systems in regards to their near perfect fitness for life.  Also, the cosmos, the sun, the moon, all these things are so arranged and physical properties so ordered as to be perfect for life on this planet as well.  Certainly atomic principles and the composition of matter and energy are also remarkable.  The properties of water, carbon, oxygen, hydrogen, light, gravity, etc. are all things which appear to behave as if planned out in advance for the purpose of life on this planet.  I can't think of anything that just appears to be random.  Can you?

So I guess my example would be to compare a human laboratory - where man provides a controlled environment for certain lifeforms to reside - to the earth and its environment.
---------------------QUOTE-------------------


Well, what about the rest of the known universe. In the entire volume of the known universe this planet hosts the only known lifeforms.

Therefore the composition of "matter and energy" may seem remarkable to you for hosting life as we know it, but to me it seems more remarkable that this same matter and energy configuration appears to only host that life at one particular locus. Why would that be, if that configuration is explicitly designed to foster life as we know it?
More remarkable is the lack of ET then the finding of it here, if indeed our particular solar system is designed and the rules are designed, why not the planet next door? Why is Mars not thriving? It's very earth like, at least as good as we're gonna get anytime soon in person. Hollywood are already there!

If it was all planned out in advance, why for only 1 planet in the known universe?

We've started to identify details about extrasolar planets now. < Photos even. >

What does your theory say about life elsewhere in the universe? Predicts it? Y/N?

I suppose what I'm really asking Daniel, is do you consider the entire known universe intelligently designed for the purpose of hosting life on this planet?

I mean, if the solar system is designed, why stop there?

If it is designed, then why did it appear to end there?
Posted by: Reciprocating Bill on Oct. 07 2007,08:14

Quote (Daniel Smith @ Oct. 07 2007,06:17)
Also, when people say that science cannot investigate God or the supernatural, that's not entirely correct.  Science can (and does) investigate claims of supernatural activity - so long as the supernatural activity is supposed to have affected the physical world...
---------------------QUOTE-------------------


This passage is correct, and also encapsulates the challenge you have set for yourself. I'll sharpen my earlier statement to reflect your comment: "The existence of God is not amenable to scientific investigation, because God can do anything, in any order, at any time, outside the constraints of natural law, and hence no empirical test can be devised to verify God's existence. However, specific claims regarding God's actions in the physical world can be put to empirical test."

One source of assertions regarding God's actions has been the Bible, which makes very specific, testable claims about the world as God created it (e.g. the age of the earth) and his actions within the world (creation of animals and human beings ex nihilo a few thousand years ago; a subsequent world wide flood). One reason why friction has arisen between those who are inclined to Biblical literalism and the advances of the natural sciences is that many Biblical claims about the actions of God CAN be tested, have been tested, and have been found to be obviously false.

However, you are not drawing from Biblical claims about God's actions (although I gather you once did). Your claims are much more sophisticated, and concern the origination of the astounding complexity we observe in the biological world. You don't find current theory about the origination of such complexity believable (for reasons you are happy to enumerate). You claim, instead, that the emergence of biological complexity was accomplished by an all knowing God.

Here you've already gone much beyond the claims of the intelligent design movement generally, as represented by Behe, Dembski, Meyer etc.  They have carefully avoided publicly speculating about the identity and nature of the designer, and have repeatedly declined to make any claims whatsoever regarding the designer's characteristics, modes of action, etc. Because they have been unwilling to propose a model of the design or of the designer, and claim they are solely interested in design detection, that brand of ID has been utterly incapable of generating unique testable predictions about future empirical findings, and fails to rise to the level of a an empirical science.

You've identified the designer. God is the designer. You've also offered some speculations about the manner in which he originated design: he did it by means of "front-loading" information into the genome or genomes of one or more early organisms, front-loading that reflected foreknowledge of the history of the world in all of its detail, as I described above. You see the outcome of that designer's actions in nature - "I find complex intricate systems analogous (but far superior) to power plants, factories with automated assembly lines, communication networks, super highway systems, waste management (with recycling!), and on and on."

OK, now a careful distinction: "Complex intricate systems analogous (but far superior) to power plants, factories with automated assembly lines, communication networks, super highway systems, waste management" are the phenomena that (you say) still demand explanation. Your explanation is that these complex systems were designed by an all knowing God. I think you can see that it would be circular to then point to those self-same "complex intricate systems" as proof that your explanation for their existence is correct - those complex systems that so amaze us all are the very phenomena that call for explanation in the first place. Poring over and expressing amazement at biological complexity, even if that complexity has been elucidated by science, is not itself a scientific activity.  

Rather, to rise to the level of a scientific assertion, your model must make testable empirical predictions that uniquely "put your theory at risk." That is, you must formulate predictions regarding future empirical findings that, if disconfirmed, indicate that the model from which those predictions arose must be modified or discarded. Because you have already asserted that the designer is an omnipotent, all knowing God, you have put yourself in the position of having to make specific predictions regarding God's actions in the world, predictions with power to put your model at risk of disconfirmation.

I think you will agree that this is a problem. It is inherent in the definition of any "God" of sufficient capability to set the entire universe into motion that there are no limitations upon his activities. As I stated earlier, God can do anything, anywhere, anytime, without constraint of the laws of physics. He even specified the laws of physics themselves. Given that, any empirical finding regarding his proposed actions in the world would appear to be compatible with the God hypothesis. Hence it falls to YOU, as you formulate your model of the origins of biological complexity in a scientific manner, to make statements about God's characteristics of sufficient specificity to predict future empirical findings regarding his actions in the world. These assertions must limit God's scope in some way, either based upon constraints (God can do this, but he can't do that) or upon other more intentional characteristics (God would do this, but wouldn't do that). It falls to you to do this before making the relevant observations, in such a way that subsequent disconfirmation would prompt you to conclude, "God does not have the characteristics I proposed."

That's a tall order. In a some respects you've already made some such assertions, although you haven't described how they arise from a specific model of God, or how to test them. Nevertheless, since front-loading is an action in the world, it is potentially testable. I could easily generate some unique testable predictions regarding future empirical findings that arise from front-loading. However, because I find front-loading implausible for reasons I have already described and believe such tests are likely to be a waste of time, it falls to YOU to devise unique empirical predictions that put your theory at risk and then conduct the relevant tests. Ideally, your predictions would put your assertions about God's actions in the world, and hence his characteristics, at risk, as well.

You've got your work cut out for you.
Posted by: JAM on Oct. 07 2007,13:27

Quote (Daniel Smith @ Oct. 07 2007,05:46)
I think that I need to clarify my position before we can decide how best to test it.
---------------------QUOTE-------------------


I feel a breeze.


---------------------QUOTE-------------------
When I say "functional sequences" I mean functional as in "used within the cell".
---------------------QUOTE-------------------


That works for me.


---------------------QUOTE-------------------
By this definition, I'd say that anything that is transcribed would qualify as functional - since the cellular machinery is going through the trouble of transcribing it.
---------------------QUOTE-------------------


That is a prediction of an intelligent design hypothesis, but MET (non-Darwinian) predicts that there will be loads of RNA that has no function.


---------------------QUOTE-------------------
So this would include protein coding sequences as well as ncRNA sequences, and anything else that's transcribed.
---------------------QUOTE-------------------


But if we find anything that's transcribed but not functional, your hypothesis is dead, correct?


---------------------QUOTE-------------------
I also must clarify that I do actually believe that all functional sequences (as I've defined them) are evolutionarily constrained.  It's just that I don't think you can find functionality or constraint by comparing sequences to other lineages (since I posit that there are no truly neutral sites).
---------------------QUOTE-------------------


What if some sites have far greater rates of change over time, Daniel?

What sequences are used for forensic DNA analysis?


---------------------QUOTE-------------------
If comparing to other lineages, the function must first be known and then the entire sequence that provides that function compared.
---------------------QUOTE-------------------


Not a problem.


---------------------QUOTE-------------------
However, the only true test of constraint is comparison to ancestral DNA within the same lineage.
---------------------QUOTE-------------------


Oh-oh...it looks like I'm going to have to retract my retraction. Your prediction:

---------------------QUOTE-------------------
there are many functional sequences that are different (even radically so) amongst related lineages - this due to their being of designed, not mutational, origin.
---------------------QUOTE-------------------


makes clear predictions about the relationships between modern sequences. No ancestral sequences are required.
Posted by: jeannot on Oct. 07 2007,13:47



---------------------QUOTE-------------------
there are many functional sequences that are different (even radically so) amongst related lineages - this due to their being of designed, not mutational, origin.
---------------------QUOTE-------------------


That's unclear. How will you know that differences are not the result of mutations? Drift, positive selection and negative selection can lead to different level of divergence between regions.
And what to you mean by "being of designed origin"? Do new genes appear (from God knows where) instantaneously in a lineage? Or were they front loaded in the first cell?
Posted by: Daniel Smith on Oct. 08 2007,02:18

Quote (JAM @ Oct. 07 2007,13:27)
           
Quote (Daniel Smith @ Oct. 07 2007,05:46)
I think that I need to clarify my position before we can decide how best to test it.
---------------------QUOTE-------------------


I feel a breeze.
             

---------------------QUOTE-------------------
When I say "functional sequences" I mean functional as in "used within the cell".
---------------------QUOTE-------------------


That works for me.
             

---------------------QUOTE-------------------
By this definition, I'd say that anything that is transcribed would qualify as functional - since the cellular machinery is going through the trouble of transcribing it.
---------------------QUOTE-------------------


That is a prediction of an intelligent design hypothesis, but MET (non-Darwinian) predicts that there will be loads of RNA that has no function.
---------------------QUOTE-------------------


Then this is what we need to test.
             

---------------------QUOTE-------------------

             

---------------------QUOTE-------------------
So this would include protein coding sequences as well as ncRNA sequences, and anything else that's transcribed.
---------------------QUOTE-------------------


But if we find anything that's transcribed but not functional, your hypothesis is dead, correct?
---------------------QUOTE-------------------


As for my hypothesis being "dead" if we find anything that conflicts with what I've predicted:  I don't really think that's fair since scientists are constantly finding things they don't expect and simply adjust their hypotheses to fit the evidence when they do.  I will not therefore totally abandon my hypothesis if the results are different, I will simply adjust it (unless the results completely shoot it out of the water).
             

---------------------QUOTE-------------------

             

---------------------QUOTE-------------------
I also must clarify that I do actually believe that all functional sequences (as I've defined them) are evolutionarily constrained.  It's just that I don't think you can find functionality or constraint by comparing sequences to other lineages (since I posit that there are no truly neutral sites).
---------------------QUOTE-------------------


What if some sites have far greater rates of change over time, Daniel?
---------------------QUOTE-------------------


This is precisely the issue.  How do we know the rate if it turns out that there are no neutral sites?  We must first determine that these sites are truly neutral and are actually accumulating mutations.
             

---------------------QUOTE-------------------


What sequences are used for forensic DNA analysis?
---------------------QUOTE-------------------


That's a tough question, and I'm not sure I know the best answer for that.
             

---------------------QUOTE-------------------

             

---------------------QUOTE-------------------
If comparing to other lineages, the function must first be known and then the entire sequence that provides that function compared.
---------------------QUOTE-------------------


Not a problem.
             

---------------------QUOTE-------------------
However, the only true test of constraint is comparison to ancestral DNA within the same lineage.
---------------------QUOTE-------------------


Oh-oh...it looks like I'm going to have to retract my retraction. Your prediction:              

---------------------QUOTE-------------------
there are many functional sequences that are different (even radically so) amongst related lineages - this due to their being of designed, not mutational, origin.
---------------------QUOTE-------------------


makes clear predictions about the relationships between modern sequences. No ancestral sequences are required.
---------------------QUOTE-------------------


I'm not backing off my original prediction, but I think certain terms mean different things to both of us, so I'm just trying to clarify.

I believe that most (if not all) sequences in a genome are functional and therefore resistive to mutation (constrained).  This means there are no neutral sites that are accumulating mutations.

I also believe that macroevolution (when it happens) is not the result of accumulating mutations but is rather; saltational - that is - it creates new types that may have sequences that are radically different from the sequences from which they diverged (hence my earlier prediction).

Therefore, this is what I expect:

1.  Sequence comparisons between related lineages will result in a mixture of like and unlike functional sequences.  

2.  Sequence comparisons within the same lineage will show evolutionary constraint across the board - even in what are presently considered neutral sites.

3.  What are presently considered neutral sites will be found to be "instructional" - that is, they will carry the instructions that tell the various proteins, RNA and enzymes where to go, when to go and what to do when they get there.

Now, the third prediction is more of a guess, but I think it makes sense.  We know about sequences that code for proteins, and we know about sequences that regulate them, but we don't know how a certain protein "knows" where to go, what to do and when to do it.  My guess is that these instructions are carried in what are presently considered neutral sites and - for that reason - these sites resist mutations just like all other evolutionarily constrained sites.

I hope that's clearer.
Posted by: Daniel Smith on Oct. 08 2007,02:34

Quote (oldmanintheskydidntdoit @ Oct. 07 2007,06:25)
 
Quote (Daniel Smith @ Oct. 07 2007,05:59)
I think similar levels of detail can be found in the earth's various systems in regards to their near perfect fitness for life.  Also, the cosmos, the sun, the moon, all these things are so arranged and physical properties so ordered as to be perfect for life on this planet as well.  Certainly atomic principles and the composition of matter and energy are also remarkable.  The properties of water, carbon, oxygen, hydrogen, light, gravity, etc. are all things which appear to behave as if planned out in advance for the purpose of life on this planet.  I can't think of anything that just appears to be random.  Can you?

So I guess my example would be to compare a human laboratory - where man provides a controlled environment for certain lifeforms to reside - to the earth and its environment.
---------------------QUOTE-------------------


Well, what about the rest of the known universe. In the entire volume of the known universe this planet hosts the only known lifeforms.

Therefore the composition of "matter and energy" may seem remarkable to you for hosting life as we know it, but to me it seems more remarkable that this same matter and energy configuration appears to only host that life at one particular locus. Why would that be, if that configuration is explicitly designed to foster life as we know it?
More remarkable is the lack of ET then the finding of it here, if indeed our particular solar system is designed and the rules are designed, why not the planet next door? Why is Mars not thriving? It's very earth like, at least as good as we're gonna get anytime soon in person. Hollywood are already there!

If it was all planned out in advance, why for only 1 planet in the known universe?

We've started to identify details about extrasolar planets now. < Photos even. >

What does your theory say about life elsewhere in the universe? Predicts it? Y/N?

I suppose what I'm really asking Daniel, is do you consider the entire known universe intelligently designed for the purpose of hosting life on this planet?

I mean, if the solar system is designed, why stop there?

If it is designed, then why did it appear to end there?
---------------------QUOTE-------------------


I know it sounds like a cop-out but all designers make choices that many of us don't understand.  If we cannot directly ask a designer why they made certain choices, the best we can hope for is to examine their designs and try to make an educated guess based on what we observe.  

I can't do any more than guess as to "why" God did what he did, but my best guess is that he made life rare in the universe so that; as we delve more deeply into it's intricacies, we might become more keenly aware of the delicate and highly improbable balances required for it's mere existence and might be more deeply in awe of the mind that created - not only life - but the very conditions in which it thrives.

As for there being other lifeforms on other planets; we've already covered that in this thread and I made a couple predictions:

1.  That we won't find other planets with life on them.

and (to cover my butt),

2.  If we do find life elsewhere it will be remarkably similar to life on earth.
Posted by: oldmanintheskydidntdoit on Oct. 08 2007,02:57

Quote (Daniel Smith @ Oct. 08 2007,02:34)
I know it sounds like a cop-out but all designers make choices that many of us don't understand.  If we cannot directly ask a designer why they made certain choices, the best we can hope for is to examine their designs and try to make an educated guess based on what we observe.
---------------------QUOTE-------------------


Then please make an educated guess as to the reason for the huge variety of beetle species.
Posted by: oldmanintheskydidntdoit on Oct. 08 2007,02:59

Quote (Daniel Smith @ Oct. 08 2007,02:34)
1.  That we won't find other planets with life on them.
---------------------QUOTE-------------------


So, as far as you are concerned the entire universe is here for your benefit?

That's some monstrous ego you've got going on there!
Posted by: Daniel Smith on Oct. 08 2007,03:22

Quote (Reciprocating Bill @ Oct. 07 2007,08:14)
         
Quote (Daniel Smith @ Oct. 07 2007,06:17)
Also, when people say that science cannot investigate God or the supernatural, that's not entirely correct.  Science can (and does) investigate claims of supernatural activity - so long as the supernatural activity is supposed to have affected the physical world...
---------------------QUOTE-------------------


This passage is correct, and also encapsulates the challenge you have set for yourself. I'll sharpen my earlier statement to reflect your comment: "The existence of God is not amenable to scientific investigation, because God can do anything, in any order, at any time, outside the constraints of natural law, and hence no empirical test can be devised to verify God's existence. However, specific claims regarding God's actions in the physical world can be put to empirical test."

One source of assertions regarding God's actions has been the Bible, which makes very specific, testable claims about the world as God created it (e.g. the age of the earth) and his actions within the world (creation of animals and human beings ex nihilo a few thousand years ago; a subsequent world wide flood). One reason why friction has arisen between those who are inclined to Biblical literalism and the advances of the natural sciences is that many Biblical claims about the actions of God CAN be tested, have been tested, and have been found to be obviously false.  
---------------------QUOTE-------------------

I am not as quick to abandon biblical claims as you might think, since many biblical claims have not been proven false.  For instance the biblical claims about death and disease, war and poverty, human childbirth, even weeds, all still hold true today.  But that's another subject.          

---------------------QUOTE-------------------


However, you are not drawing from Biblical claims about God's actions (although I gather you once did). Your claims are much more sophisticated, and concern the origination of the astounding complexity we observe in the biological world. You don't find current theory about the origination of such complexity believable (for reasons you are happy to enumerate). You claim, instead, that the emergence of biological complexity was accomplished by an all knowing God.

Here you've already gone much beyond the claims of the intelligent design movement generally, as represented by Behe, Dembski, Meyer etc.  They have carefully avoided publicly speculating about the identity and nature of the designer, and have repeatedly declined to make any claims whatsoever regarding the designer's characteristics, modes of action, etc. Because they have been unwilling to propose a model of the design or of the designer, and claim they are solely interested in design detection, that brand of ID has been utterly incapable of generating unique testable predictions about future empirical findings, and fails to rise to the level of a an empirical science.
---------------------QUOTE-------------------

I can't speak for them but I suspect their reluctance is due to the fact that they are trying to make their theory fit into the realm of naturalistic science - and thus they feel they can't identify the designer as God.
I feel differently.  I feel that we can speculate about how the "mind of God" has affected the physical universe and make testable predictions based on those speculations.          

---------------------QUOTE-------------------


You've identified the designer. God is the designer. You've also offered some speculations about the manner in which he originated design: he did it by means of "front-loading" information into the genome or genomes of one or more early organisms, front-loading that reflected foreknowledge of the history of the world in all of its detail, as I described above. You see the outcome of that designer's actions in nature - "I find complex intricate systems analogous (but far superior) to power plants, factories with automated assembly lines, communication networks, super highway systems, waste management (with recycling!), and on and on."

OK, now a careful distinction: "Complex intricate systems analogous (but far superior) to power plants, factories with automated assembly lines, communication networks, super highway systems, waste management" are the phenomena that (you say) still demand explanation.
---------------------QUOTE-------------------

Yes that's true.      

---------------------QUOTE-------------------
Your explanation is that these complex systems were designed by an all knowing God.
---------------------QUOTE-------------------

Yes that's true also, but I went beyond that - since I first pointed out their analogous qualities with known designs - thereby establishing the precedent of the designer/design as a workable, observable explanation for such systems.      

---------------------QUOTE-------------------
I think you can see that it would be circular to then point to those self-same "complex intricate systems" as proof that your explanation for their existence is correct - those complex systems that so amaze us all are the very phenomena that call for explanation in the first place. Poring over and expressing amazement at biological complexity, even if that complexity has been elucidated by science, is not itself a scientific activity.  
---------------------QUOTE-------------------

That's true, but I've done more than that:  I've suggested a source - an all knowing God that (as you say) "can do anything, in any order, at any time, outside the constraints of natural law", and I hope to show that the evidence actually requires such a being.
I believe that any unbiased look at all the requirements for life on this planet will lead any honest person to rule out chance as a cause.  We are then left with only non-random causes.  My argument is that - once we get to that point - if we examine the delicate balances that exist in nature, and all the intricate complexities of the literally trillions of systems involved in life, a mind of infinite intelligence is the only logical, non-random cause for all of this.      

---------------------QUOTE-------------------


Rather, to rise to the level of a scientific assertion, your model must make testable empirical predictions that uniquely "put your theory at risk." That is, you must formulate predictions regarding future empirical findings that, if disconfirmed, indicate that the model from which those predictions arose must be modified or discarded. Because you have already asserted that the designer is an omnipotent, all knowing God, you have put yourself in the position of having to make specific predictions regarding God's actions in the world, predictions with power to put your model at risk of disconfirmation.

I think you will agree that this is a problem. It is inherent in the definition of any "God" of sufficient capability to set the entire universe into motion that there are no limitations upon his activities. As I stated earlier, God can do anything, anywhere, anytime, without constraint of the laws of physics. He even specified the laws of physics themselves. Given that, any empirical finding regarding his proposed actions in the world would appear to be compatible with the God hypothesis. Hence it falls to YOU, as you formulate your model of the origins of biological complexity in a scientific manner, to make statements about God's characteristics of sufficient specificity to predict future empirical findings regarding his actions in the world. These assertions must limit God's scope in some way, either based upon constraints (God can do this, but he can't do that) or upon other more intentional characteristics (God would do this, but wouldn't do that). It falls to you to do this before making the relevant observations, in such a way that subsequent disconfirmation would prompt you to conclude, "God does not have the characteristics I proposed."

That's a tall order. In a some respects you've already made some such assertions, although you haven't described how they arise from a specific model of God, or how to test them. Nevertheless, since front-loading is an action in the world, it is potentially testable. I could easily generate some unique testable predictions regarding future empirical findings that arise from front-loading. However, because I find front-loading implausible for reasons I have already described and believe such tests are likely to be a waste of time, it falls to YOU to devise unique empirical predictions that put your theory at risk and then conduct the relevant tests. Ideally, your predictions would put your assertions about God's actions in the world, and hence his characteristics, at risk, as well.

You've got your work cut out for you.
---------------------QUOTE-------------------


You are right - and I'm feeling the pressure!
Posted by: Daniel Smith on Oct. 08 2007,03:23

Quote (oldmanintheskydidntdoit @ Oct. 08 2007,02:57)
Quote (Daniel Smith @ Oct. 08 2007,02:34)
I know it sounds like a cop-out but all designers make choices that many of us don't understand.  If we cannot directly ask a designer why they made certain choices, the best we can hope for is to examine their designs and try to make an educated guess based on what we observe.
---------------------QUOTE-------------------


Then please make an educated guess as to the reason for the huge variety of beetle species.
---------------------QUOTE-------------------


God likes beetles?
Posted by: Daniel Smith on Oct. 08 2007,03:32

Quote (jeannot @ Oct. 07 2007,13:47)
 

---------------------QUOTE-------------------
there are many functional sequences that are different (even radically so) amongst related lineages - this due to their being of designed, not mutational, origin.
---------------------QUOTE-------------------


That's unclear. How will you know that differences are not the result of mutations? Drift, positive selection and negative selection can lead to different level of divergence between regions.
And what to you mean by "being of designed origin"? Do new genes appear (from God knows where) instantaneously in a lineage? Or were they front loaded in the first cell?
---------------------QUOTE-------------------


Good questions.
The only fool-proof way to know if differences in sequences are the result of mutations is to study sequences for long periods of time within the same lineage and see if certain areas drift or are changed due to selection.  We can ascertain differences between lineages, but we can't be sure of the mechanism that produced the differences.
As for new genes.  I'd say that at least the template for them was front loaded into the root of every lineage - whether that means one common ancestor or many.

I suspect that that is one of the reasons the entire genome is transcribed - to error check and keep intact these templates.  Another guess.
Posted by: oldmanintheskydidntdoit on Oct. 08 2007,04:11

Quote (Daniel Smith @ Oct. 08 2007,03:23)
Quote (oldmanintheskydidntdoit @ Oct. 08 2007,02:57)
Quote (Daniel Smith @ Oct. 08 2007,02:34)
I know it sounds like a cop-out but all designers make choices that many of us don't understand.  If we cannot directly ask a designer why they made certain choices, the best we can hope for is to examine their designs and try to make an educated guess based on what we observe.
---------------------QUOTE-------------------


Then please make an educated guess as to the reason for the huge variety of beetle species.
---------------------QUOTE-------------------


God likes beetles?
---------------------QUOTE-------------------


That's what you call an "educated guess"?
Posted by: oldmanintheskydidntdoit on Oct. 08 2007,04:12

Quote (Daniel Smith @ Oct. 08 2007,03:22)

---------------------QUOTE-------------------




---------------------QUOTE-------------------
My argument is that - once we get to that point - if we examine the delicate balances that exist in nature, and all the intricate complexities of the literally trillions of systems involved in life, a mind of infinite intelligence is the only logical, non-random cause for all of this.      
---------------------QUOTE-------------------



What's the purpose of AIDS?
Posted by: Daniel Smith on Oct. 08 2007,04:27

Quote (mitschlag @ Oct. 07 2007,06:09)
You are the scientist, DS.  You are responsible for devising the test.
---------------------QUOTE-------------------


Well, I'm not a scientist, but I think I've got an idea for a test:

Take two members of the same species that have been geographically and reproductively isolated for a long period of time (the longer the better), sequence their genomes and compare them.

My prediction is that the coding and non-coding sequences (basically all sequences) will show an equal amount of evolutionary constraint.
Posted by: Reciprocating Bill on Oct. 08 2007,06:51

Quote (Daniel Smith @ Oct. 08 2007,04:23)
Quote (oldmanintheskydidntdoit @ Oct. 08 2007,02:57)
Quote (Daniel Smith @ Oct. 08 2007,02:34)
I know it sounds like a cop-out but all designers make choices that many of us don't understand.  If we cannot directly ask a designer why they made certain choices, the best we can hope for is to examine their designs and try to make an educated guess based on what we observe.
---------------------QUOTE-------------------


Then please make an educated guess as to the reason for the huge variety of beetle species.
---------------------QUOTE-------------------


God likes beetles?
---------------------QUOTE-------------------


Indeed. "The Creator, if He exists, has an inordinate fondness for beetles".

- Haldane
Posted by: Steverino on Oct. 08 2007,06:59

"I know it sounds like a cop-out but all designers make choices that many of us don't understand.  If we cannot directly ask a designer why they made certain choices, the best we can hope for is to examine their designs and try to make an educated guess based on what we observe.  "

While it may not be a cop out, it's BULLSHIT.  It's based on the premise that when we see gaps of information, you feel that God should be included in the discussion until proven otherwise.
Posted by: mitschlag on Oct. 08 2007,07:02

Quote (Daniel Smith @ Oct. 08 2007,04:27)
 
Quote (mitschlag @ Oct. 07 2007,06:09)
You are the scientist, DS.  You are responsible for devising the test.
---------------------QUOTE-------------------


Well, I'm not a scientist, but I think I've got an idea for a test:

Take two members of the same species that have been geographically and reproductively isolated for a long period of time (the longer the better), sequence their genomes and compare them.

My prediction is that the coding and non-coding sequences (basically all sequences) will show an equal amount of evolutionary constraint.
---------------------QUOTE-------------------


Please define "evolutionary constraint."

Predict the expected results that would falsify your hypothesis.
Posted by: Reciprocating Bill on Oct. 08 2007,07:19

Quote (Daniel Smith @ Oct. 08 2007,04:22)
 
Quote (Reciprocating Bill @ Oct. 07 2007,08:14)
...Hence it falls to YOU, as you formulate your model of the origins of biological complexity in a scientific manner, to make statements about God's characteristics of sufficient specificity to predict future empirical findings regarding his actions in the world. These assertions must limit God's scope in some way, either based upon constraints (God can do this, but he can't do that) or upon other more intentional characteristics (God would do this, but wouldn't do that). It falls to you to do this before making the relevant observations, in such a way that subsequent disconfirmation would prompt you to conclude, "God does not have the characteristics I proposed."

...

You've got your work cut out for you.
---------------------QUOTE-------------------


You are right - and I'm feeling the pressure!
---------------------QUOTE-------------------


Just be clear that arguments that originate with speculation about God's characteristics, and the way those characteristics are reflected in the world, are theological arguments, not scientific arguments.  If you endeavor to actually do some science based on theological assertions, I've got some equipment you'll need:

1) Hammer.

2) Box of nails.

3) Tree.

4) Jello.

Now, get to work.
Posted by: Wesley R. Elsberry on Oct. 08 2007,07:49



---------------------QUOTE-------------------

My prediction is that the coding and non-coding sequences (basically all sequences) will show an equal amount of evolutionary constraint.

---------------------QUOTE-------------------



So, why does the term "linkage disequilibrium" seem to get used by geneticists? Wouldn't your prediction mean that we should see the same degree of linkage disequilibrium everywhere we look? If not, what consequences do you think your "prediction" actually has?
Posted by: Patashu on Oct. 08 2007,10:46

Daniel Smith,

Why do four extra kinds of quarks and leptons exist, despite their existence in the universe not effecting the way carbon-based life runs? If the universe is fine-tuned for life, why add in something entirely arbitary? And remember, a perfect god cannot do anything imperfect.

Secondly, how do we know the universe is fine tuned for us? Given that 74% of the universe is dark energy, would it not be a safe bet to assume that the universe was fine tuned to produce as much dark energy as possible?
Posted by: jeannot on Oct. 08 2007,12:17

Quote (Daniel Smith @ Oct. 08 2007,04:27)
My prediction is that the coding and non-coding sequences (basically all sequences) will show an equal amount of evolutionary constraint.
---------------------QUOTE-------------------


Based on your intuition?
Why would that be an evidence for design (assuming you have a clear notion of "evolutionary constraint")?
Please explain.
Posted by: JAM on Oct. 08 2007,13:01

[quote=Daniel Smith,Oct. 08 2007,02:18]     [quote=JAM,Oct. 07 2007,13:27]                   [quote=Daniel Smith,Oct. 07 2007,05:46]By this definition, I'd say that anything that is transcribed would qualify as functional - since the cellular machinery is going through the trouble of transcribing it.[/quote]
That is a prediction of an intelligent design hypothesis, but MET (non-Darwinian) predicts that there will be loads of RNA that has no function.[/quote]
Then this is what we need to test.[/quote]
OK, what do you propose? How about "knocking out" regions using the technology whose developers won the Nobel Prize today?
 [quote]    

---------------------QUOTE-------------------
 

---------------------QUOTE-------------------
So this would include protein coding sequences as well as ncRNA sequences, and anything else that's transcribed.
---------------------QUOTE-------------------


But if we find anything that's transcribed but not functional, your hypothesis is dead, correct?
---------------------QUOTE-------------------


As for my hypothesis being "dead" if we find anything that conflicts with what I've predicted:  I don't really think that's fair since scientists are constantly finding things they don't expect and simply adjust their hypotheses to fit the evidence when they do.[/quote]
That's only true for hypotheses that have a track record. Yours doesn't. I've trashed many hypotheses that I've endorsed in previous publications, for example.
 

---------------------QUOTE-------------------
I will not therefore totally abandon my hypothesis if the results are different, I will simply adjust it (unless the results completely shoot it out of the water).
---------------------QUOTE-------------------


It's your ethical responsibility to state the results that would completely shoot it out of the water.
 

---------------------QUOTE-------------------
 

---------------------QUOTE-------------------
 

---------------------QUOTE-------------------
I also must clarify that I do actually believe that all functional sequences (as I've defined them) are evolutionarily constrained.  It's just that I don't think you can find functionality or constraint by comparing sequences to other lineages (since I posit that there are no truly neutral sites).
---------------------QUOTE-------------------


What if some sites have far greater rates of change over time, Daniel?
---------------------QUOTE-------------------


This is precisely the issue.  How do we know the rate if it turns out that there are no neutral sites?
---------------------QUOTE-------------------


Easily and empirically. We know the mutation rate in the absence of selection. If the rate of change over time is the same as the mutation rate, the only rational inference is the absence of selection. If it is less than the mutation rate, we infer selection.
[quote]

---------------------QUOTE-------------------
We must first determine that these sites are truly neutral and are actually accumulating mutations.
                     

---------------------QUOTE-------------------


What sequences are used for forensic DNA analysis?
---------------------QUOTE-------------------


That's a tough question, and I'm not sure I know the best answer for that.
---------------------QUOTE-------------------


I'm not asking for the "best answer," I'm simply asking for an answer. Certain sequences are used for forensic DNA analysis. What are their characteristics? How polymorphic are they?


---------------------QUOTE-------------------


---------------------QUOTE-------------------


---------------------QUOTE-------------------
If comparing to other lineages, the function must first be known and then the entire sequence that provides that function compared.
---------------------QUOTE-------------------


Not a problem.
                     

---------------------QUOTE-------------------
However, the only true test of constraint is comparison to ancestral DNA within the same lineage.
---------------------QUOTE-------------------


Oh-oh...it looks like I'm going to have to retract my retraction. Your prediction:                      

---------------------QUOTE-------------------
there are many functional sequences that are different (even radically so) amongst related lineages - this due to their being of designed, not mutational, origin.
---------------------QUOTE-------------------


makes clear predictions about the relationships between modern sequences. No ancestral sequences are required.
---------------------QUOTE-------------------


I'm not backing off my original prediction, but I think certain terms mean different things to both of us, so I'm just trying to clarify.
---------------------QUOTE-------------------


Good. Please define "lineage" for starters. Are mice and humans in the same or in different lineages?


---------------------QUOTE-------------------
I believe that most (if not all) sequences in a genome are functional and therefore resistive to mutation (constrained).  This means there are no neutral sites that are accumulating mutations.
---------------------QUOTE-------------------


And the evidence shows that you are wrong.


---------------------QUOTE-------------------
I also believe that macroevolution (when it happens) is not the result of accumulating mutations but is rather; saltational - that is - it creates new types that may have sequences that are radically different from the sequences from which they diverged (hence my earlier prediction).
---------------------QUOTE-------------------


Interesting. Of the ~30,000 protein-encoding genes in the mouse and human genomes, how many do you believe/predict are absent in mouse and present in human, and vice versa?



---------------------QUOTE-------------------
Therefore, this is what I expect:

1.  Sequence comparisons between related lineages will result in a mixture of like and unlike functional sequences.
---------------------QUOTE-------------------

 

I need a rigorous definition of "lineage" before pursuing this one.



---------------------QUOTE-------------------
2.  Sequence comparisons within the same lineage will show evolutionary constraint across the board - even in what are presently considered neutral sites.
---------------------QUOTE-------------------


This is trivially easy to do online. Are you interested or afraid to do so?


---------------------QUOTE-------------------
3.  What are presently considered neutral sites will be found to be "instructional" - that is, they will carry the instructions that tell the various proteins, RNA and enzymes where to go, when to go and what to do when they get there.
---------------------QUOTE-------------------


a) How does that relate to today's Nobel Prize?

b) How about classical genetics--do any homozygous normal inversions exist? If so, doesn't that mean that the sequences disrupted by both breakpoints have no function?



---------------------QUOTE-------------------
Now, the third prediction is more of a guess, but I think it makes sense.  We know about sequences that code for proteins, and we know about sequences that regulate them, but we don't know how a certain protein "knows" where to go, what to do and when to do it.
---------------------QUOTE-------------------


We know a lot about that, Daniel. In fact, it's what I've been working on for the last 16 years, since mouse genetics dumped me into the field.

I'll give you a taste--nothing about the mechanisms involved suggests intelligent design.



---------------------QUOTE-------------------
My guess is that these instructions are carried in what are presently considered neutral sites and - for that reason - these sites resist mutations just like all other evolutionarily constrained sites.

I hope that's clearer.
---------------------QUOTE-------------------


Except for your definition of "lineage," yes. As an introduction to how proteins "know" where to go, you might want to Google "signal sequence" and "nuclear import."

Those are the simple signals intrinsic to the protein. What I study is an order of magnitude or two more complex, fluid, and fuzzy.
Posted by: Henry J on Oct. 09 2007,15:59

Is there a limit on nesting of quotes? I don't see any apparent syntax errors in that last note, but some of the quotes didn't take for some reason.

Henry
Posted by: JAM on Oct. 09 2007,16:20

Quote (Henry J @ Oct. 09 2007,15:59)
Is there a limit on nesting of quotes? I don't see any apparent syntax errors in that last note, but some of the quotes didn't take for some reason.

Henry
---------------------QUOTE-------------------


I don't understand it either.
Posted by: C.J.O'Brien on Oct. 09 2007,17:12



---------------------QUOTE-------------------
So when I examine the evidence, is that what I find?  Yes, that is exactly what I find.  I find complex intricate systems analogous (but far superior) to power plants, factories with automated assembly lines, communication networks, super highway systems, waste management (with recycling!), and on and on.
---------------------QUOTE-------------------


Bob O'H already made this point, but at some length.
For concision: None of that is evidence in the scientific sense. It's a restatement of the question in explicitly teleological terms. To consider this evidence (the result of empirical investigation beyond a cursory glance) is to beg the question.

When you actually get in depth and look at some of that cellular machinery, Daniel, you'll see that it does not resemble at all the products of a rational design process. It rather resembles a Rube Goldberg-type cobbled-together mess eerily similar to the sorts of engineering solutions arrived at by evolutionary algorithms.

Most concise: Analogies are not evidence.

If everybody could understand and accept this basic fact of epistemology, Creationism in all its forms would die a long-overdue and merciful death.
Posted by: JAM on Oct. 09 2007,18:19

Quote (C.J.O'Brien @ Oct. 09 2007,17:12)


---------------------QUOTE-------------------
So when I examine the evidence, is that what I find?  Yes, that is exactly what I find.  I find complex intricate systems analogous (but far superior) to power plants, factories with automated assembly lines, communication networks, super highway systems, waste management (with recycling!), and on and on.
---------------------QUOTE-------------------


Bob O'H already made this point, but at some length.
For concision: None of that is evidence in the scientific sense. It's a restatement of the question in explicitly teleological terms. To consider this evidence (the result of empirical investigation beyond a cursory glance) is to beg the question.
---------------------QUOTE-------------------


Not only that, but most of it is false.

If our superhighway systems were anything like the cell's, trucks crashing into each other (combining their cargos), useless detours, and multiple tractors on the same cargo trailer pulling in different directions would play an integral role in every journey.

If human-designed waste management systems were designed analogously to the cell's, we'd have 20% raw sewage in our drinking water and call it delicious.

The amazing thing is that when you work in these fields, you see massive teleological biases among the scientists, so that extra data are required to overcome these analogies.
Posted by: Daniel Smith on Oct. 09 2007,21:27

Quote (Steverino @ Oct. 08 2007,06:59)
While it may not be a cop out, it's BULLSHIT.  It's based on the premise that when we see gaps of information, you feel that God should be included in the discussion until proven otherwise.
---------------------QUOTE-------------------


No, I'm actually giving God credit for everything - not just the gaps.  You might want to go back and catch up on the previous 10 pages before you jump in and post.
Posted by: Henry J on Oct. 09 2007,21:38



---------------------QUOTE-------------------
1.  That we won't find other planets with life on them.

and (to cover my butt),

2.  If we do find life elsewhere it will be remarkably similar to life on earth.  
---------------------QUOTE-------------------



Seems like either of those would be consistent with current theory. If the density of life-bearing planets is such that no others are within telescope range, it could be a really long time before humans find any.

It seems at least possible that amino acid chains might be the most effective (or at least most reachable) form of organic molecule, and DNA (or something much like it) might be most likely form of hereditary trait "memory". Otoh there might be other chains that work, but could be a while before we discover them.

Henry
Posted by: Daniel Smith on Oct. 10 2007,02:25

Quote (Henry J @ Oct. 09 2007,15:59)
Is there a limit on nesting of quotes? I don't see any apparent syntax errors in that last note, but some of the quotes didn't take for some reason.

Henry
---------------------QUOTE-------------------


There seems to be.  I had the same trouble with an earlier reply and could only rectify it by eliminating some quotes.
Posted by: Daniel Smith on Oct. 10 2007,02:30

Quote (mitschlag @ Oct. 08 2007,07:02)
   
Quote (Daniel Smith @ Oct. 08 2007,04:27)
Take two members of the same species that have been geographically and reproductively isolated for a long period of time (the longer the better), sequence their genomes and compare them.

My prediction is that the coding and non-coding sequences (basically all sequences) will show an equal amount of evolutionary constraint.
---------------------QUOTE-------------------


Please define "evolutionary constraint."

Predict the expected results that would falsify your hypothesis.
---------------------QUOTE-------------------


I am using the term "evolutionary constraint" to mean a sequence that resists or rejects mutations.
As I understand it, this is the common usage of the term.

The results that would falsify my hypothesis would be if the coding sequences showed evolutionary constraint while the non-coding sequences didn't.
Posted by: Daniel Smith on Oct. 10 2007,03:17

Quote (JAM @ Oct. 09 2007,18:19)
             
Quote (C.J.O'Brien @ Oct. 09 2007,17:12)
               

---------------------QUOTE-------------------
So when I examine the evidence, is that what I find?  Yes, that is exactly what I find.  I find complex intricate systems analogous (but far superior) to power plants, factories with automated assembly lines, communication networks, super highway systems, waste management (with recycling!), and on and on.
---------------------QUOTE-------------------


Bob O'H already made this point, but at some length.
For concision: None of that is evidence in the scientific sense. It's a restatement of the question in explicitly teleological terms. To consider this evidence (the result of empirical investigation beyond a cursory glance) is to beg the question.
---------------------QUOTE-------------------


Not only that, but most of it is false.

If our superhighway systems were anything like the cell's, trucks crashing into each other (combining their cargos), useless detours, and multiple tractors on the same cargo trailer pulling in different directions would play an integral role in every journey.

If human-designed waste management systems were designed analogously to the cell's, we'd have 20% raw sewage in our drinking water and call it delicious.

The amazing thing is that when you work in these fields, you see massive teleological biases among the scientists, so that extra data are required to overcome these analogies.
---------------------QUOTE-------------------


I've not seen any descriptions of any biological functions that come across as haphazard and random as you describe them.  In fact I find the opposite to be true.  Whenever I learn the details of how a biological system functions, I'm struck by the sheer brilliance of the system's design (and I'm not going to creationist sources for this info).
Take the process of protein synthesis for example.  Please explain how that process is just a hodgepodge of cobbled together mish-mash that somehow, almost by accident, gets the job done.
Or explain how the brain is just a random lucky accident, or the various visual systems, or the mammalian kidney, or the avian lung, or the central nervous system, or all the various systems of flight, or any other system.  In fact, I challenge you to provide details of how any biological system is just a cobbled together hodge-podge.

Also, explain to me how the qualities observed in an object are not evidence that can be used to determine the object's origin?

What evidence leads us to believe that Stonehenge is designed - if not the qualities of Stonehenge itself?  Do we say it is designed because there were people in the area at that time?  No.  If we did, we'd have to say that every rock, every stone, in fact everything is designed if there are people in the area at the time.  No, it's the organization of the stones and the fact that that organization is analogous to the organization of other designed objects (such as tables, chairs and benches) that leads us to believe that Stonehenge was designed.  This organization is a quality of the object in question - the object that needs explaining.  Yet we can certainly use these qualities to deduce design here.  Why not elsewhere?

Are the qualities of "the thing that needs explaining" and analogies excluded also from random or naturalistic explanations?  Do you not observe the makeup of the organism in question when trying to discern its origin?  Do you not compare the qualities of one object with another?  Do you not say that this sequence is like that one?  Is this not analogy?  If not, then what is it?

And if statements such as mine are not evidence, then why is this statement not challenged equally as vigorously?        
Quote (C.J.O'Brien @ Oct. 09 2007,17:12)
When you actually get in depth and look at some of that cellular machinery, Daniel, you'll see that it does not resemble at all the products of a rational design process. It rather resembles a Rube Goldberg-type cobbled-together mess eerily similar to the sorts of engineering solutions arrived at by evolutionary algorithms.

---------------------QUOTE-------------------



In short, analogies are a form of evidence.  I'm guessing that you just don't like the fact that I'm comparing biological systems to designed systems.
Posted by: Erasmus, FCD on Oct. 10 2007,07:36

Daniel we know people make things like stonehenge.

What designer do we know of that makes cells and platypi and the grand canyon?  People?  Or something else?  I'll wait for your answer.

(sound of wind in trees)
(child farts)
(somewhere a rooster is screwing a guinea hen)
(old men die and babies born)
(cells divide under my toenails)
(republican senator somewhere taps his foot in a bathroom stall)
(snake eats a bullfrog)
(grandmaw fiddles 'Liberty' while dancing on a piece of plywood)
tick tock tick tock

That's Right!!!!  We don't know of any such designer!!!  You Lose!!!
Posted by: JAM on Oct. 10 2007,10:40

Quote (Daniel Smith @ Oct. 10 2007,02:30)
Quote (mitschlag @ Oct. 08 2007,07:02)
     
Quote (Daniel Smith @ Oct. 08 2007,04:27)
Take two members of the same species that have been geographically and reproductively isolated for a long period of time (the longer the better), sequence their genomes and compare them.

My prediction is that the coding and non-coding sequences (basically all sequences) will show an equal amount of evolutionary constraint.
---------------------QUOTE-------------------


Please define "evolutionary constraint."

Predict the expected results that would falsify your hypothesis.
---------------------QUOTE-------------------


I am using the term "evolutionary constraint" to mean a sequence that resists or rejects mutations.
As I understand it, this is the common usage of the term.

The results that would falsify my hypothesis would be if the coding sequences showed evolutionary constraint while the non-coding sequences didn't.
---------------------QUOTE-------------------


By "coding," do you mean more than protein-coding sequences, including things like promoters, enhancers, splicing signals, etc.?

Here's an opposing hypothesis:

Known functional sequences will be evolutionarily conserved. Most sequences will not be conserved. We will continue to find functions for some conserved sequences for which no function has been identified.

What do you think? Shall we look at the evidence to see which hypothesis is better supported?
Posted by: JAM on Oct. 10 2007,11:00

Quote (Daniel Smith @ Oct. 10 2007,03:17)
 
Quote (JAM @ Oct. 09 2007,18:19)
                 
Quote (C.J.O'Brien @ Oct. 09 2007,17:12)
                 

---------------------QUOTE-------------------
So when I examine the evidence, is that what I find?  Yes, that is exactly what I find.  I find complex intricate systems analogous (but far superior) to power plants, factories with automated assembly lines, communication networks, super highway systems, waste management (with recycling!), and on and on.
---------------------QUOTE-------------------


Bob O'H already made this point, but at some length.
For concision: None of that is evidence in the scientific sense. It's a restatement of the question in explicitly teleological terms. To consider this evidence (the result of empirical investigation beyond a cursory glance) is to beg the question.
---------------------QUOTE-------------------


Not only that, but most of it is false.

If our superhighway systems were anything like the cell's, trucks crashing into each other (combining their cargos), useless detours, and multiple tractors on the same cargo trailer pulling in different directions would play an integral role in every journey.

If human-designed waste management systems were designed analogously to the cell's, we'd have 20% raw sewage in our drinking water and call it delicious.

The amazing thing is that when you work in these fields, you see massive teleological biases among the scientists, so that extra data are required to overcome these analogies.
---------------------QUOTE-------------------


I've not seen any descriptions of any biological functions that come across as haphazard and random as you describe them.
---------------------QUOTE-------------------



1) Descriptions aren't evidence. Why not just be honest and admit that you avoid the actual evidence?
2) My descriptions do not imply that these systems are either "haphazard" or "random." I am accurately describing them as extremely fuzzy, with components that are related to each other with partially-overlapping functions. Therefore, they are in no way analogous to systems designed by humans, which was your preposterously ignorant claim.
 

---------------------QUOTE-------------------
In fact I find the opposite to be true.
---------------------QUOTE-------------------


But you depend on descriptions, not evidence.  
 

---------------------QUOTE-------------------
Whenever I learn the details of how a biological system functions, I'm struck by the sheer brilliance of the system's design (and I'm not going to creationist sources for this info).
---------------------QUOTE-------------------


Then show me the evidence you've examined for the cell's recycling systems and I'll show you how you are mistaken. What we real biologists find when examining the real evidence is Rube Goldberg-like, partially-overlapping complexity, with everything borrowed from something else. While this is both incredibly complex and amazing, it is in no way analogous to systems designed by humans.
 

---------------------QUOTE-------------------
Take the process of protein synthesis for example.
---------------------QUOTE-------------------


OK, but you need to explain why you are running away from the examples you initially chose.
 

---------------------QUOTE-------------------
Please explain how that process is just a hodgepodge of cobbled together mish-mash that somehow, almost by accident, gets the job done.
---------------------QUOTE-------------------


First, you are grossly misrepresenting my position by attributing "almost by accident" to me. This is a fundamentally dishonest way to discuss anything.

Second, it is a cobbled-together mish-mash, given the following evidence.

1) Please explain why ribosomal RNA is at the center of the enzymatic active site, when RNA is so much less stable than protein. Since the "RNA World" hypothesis explains this beautifully, explain how a design hypothesis explains this better.

2) Please explain third-base "wobble" and the viability of bacteria carrying amber, ochre, and opal suppressor mutations.

 

---------------------QUOTE-------------------
Or explain how the brain is just a random lucky accident,...
---------------------QUOTE-------------------


You are being dishonest. I am not claiming that the brain is "just a random lucky accident." I am claiming that the brain is not analogous to a designed mechanism.
 

---------------------QUOTE-------------------
... or the various visual systems, or the mammalian kidney, or the avian lung, or the central nervous system, or all the various systems of flight, or any other system.  In fact, I challenge you to provide details of how any biological system is just a cobbled together hodge-podge.
---------------------QUOTE-------------------


As for details, let's use the cell's waste management system. The details show that there is no single pure membranous compartment anywhere in the cell. Even the proteins that help to specify what we call separate compartments overlap with each other.

How's that?
 

---------------------QUOTE-------------------
Also, explain to me how the qualities observed in an object are not evidence that can be used to determine the object's origin?
---------------------QUOTE-------------------


They are. You're just completely wrong about the qualities because you've not bothered to look at real evidence.

Your need to grossly misrepresent my position speaks volumes about your confidence in your own position, too.
 

---------------------QUOTE-------------------
No, it's the organization of the stones and the fact that that organization is analogous to the organization of other designed objects (such as tables, chairs and benches) that leads us to believe that Stonehenge was designed.  This organization is a quality of the object in question - the object that needs explaining.  Yet we can certainly use these qualities to deduce design here.  Why not elsewhere?
---------------------QUOTE-------------------


Then tell me about the qualities of the cell's recycling system that lead you to believe that it was designed. You have to go to the primary data, not anyone's interpretation of them.
 

---------------------QUOTE-------------------
Are the qualities of "the thing that needs explaining" and analogies excluded also from random or naturalistic explanations?
---------------------QUOTE-------------------


Analogies are explanatory devices. They are not evidence.
 

---------------------QUOTE-------------------
Do you not observe the makeup of the organism in question when trying to discern its origin?  Do you not compare the qualities of one object with another?  Do you not say that this sequence is like that one?  Is this not analogy?  If not, then what is it?
---------------------QUOTE-------------------


Mostly, it's homology, not analogy.
 

---------------------QUOTE-------------------
In short, analogies are a form of evidence.  I'm guessing that you just don't like the fact that I'm comparing biological systems to designed systems.
---------------------QUOTE-------------------


We don't like the fact that you are ignoring the actual evidence and promoting fake analogies.
Posted by: C.J.O'Brien on Oct. 10 2007,12:35



---------------------QUOTE-------------------
I've not seen any descriptions of any biological functions that come across as haphazard and random as you describe them.  In fact I find the opposite to be true.  Whenever I learn the details of how a biological system functions, I'm struck by the sheer brilliance of the system's design (and I'm not going to creationist sources for this info).
Take the process of protein synthesis for example.  Please explain how that process is just a hodgepodge of cobbled together mish-mash that somehow, almost by accident, gets the job done.
Or explain how the brain is just a random lucky accident, or the various visual systems, or the mammalian kidney, or the avian lung, or the central nervous system, or all the various systems of flight, or any other system.  In fact, I challenge you to provide details of how any biological system is just a cobbled together hodge-podge.
---------------------QUOTE-------------------


Daniel appears to be running TurboGoalposts v.3:16.

First, we were talking about biochemistry, not how the brain (or anything else) is "just a random lucky accident," which is a straw-man representation of evolutionary theory as well as off the subject.

That there is a certain kind of elegance to biochemical processes is not in question. They work well enough to have sustained evolving life on Earth for billions of years, and are perfectly capable of supporting the functions of big, complex animals like ourselves. So I am not saying that they barely "get the job done." I am saying, though, that all of the highly-touted complexity of the cell, when it is actually investigated, not simply remarked upon, seems to owe its existence to a maddeningly short-sighted designer --one that seems incabable of building a structure or pathway using anything other than pre-existing components, often themselves integral parts of other, fully functioning systems. But you challenged me for examples.

Here is Ken Miller on < the vertebrate blood-clotting cascade >

Here is a TalkOrigins summary of several articles on the evolution of the < Krebs Cycle >

Here is an abstract of a Science paper on the evolution of a < steroid-hormone receptor >
Posted by: mitschlag on Oct. 10 2007,12:47

Quote (Daniel Smith @ Oct. 10 2007,02:30)
The results that would falsify my hypothesis would be if the coding sequences showed evolutionary constraint while the non-coding sequences didn't.
---------------------QUOTE-------------------

There's a fair amount of evidence showing that (contrary to expectation) non-coding sequences have fewer base changes than coding sequences, see, for example:
< http://www.biomedcentral.com/1471-2148/7/66 >


---------------------QUOTE-------------------
The primary result is that the mean rate of intergenic nucleotide substitution is two-thirds that of the synonymous coding data, with an absolute rate estimated to be 1.05 × 10-8 substitutions per site per year. This result holds with alternative nucleotide models (see Methods), and thus does not appear to be solely an issue of estimation procedures.

Slower rates in non-coding regions relative to synonymous sites are becoming a surprisingly frequent observation. For example, a recent study of Drosophila demonstrated that non-coding DNA evolves considerably slower than synonymous sites in terms of both divergence between species and polymorphism within species [16]. By comparing studies, one can also make the case that pseudogenes [32,33] and introns [34,35] evolve more slowly than synonymous sites in apes and other mammals [13,36-38]. Studies of mammalian intergenic regions have also found slower rates than synonymous sites [35,39,40]. Although most of these studies encompass only a handful of genes, an overall picture of relatively slow non-coding rates is emerging.
---------------------QUOTE-------------------


What do you make of that?
Posted by: jeannot on Oct. 10 2007,13:55

Quote (mitschlag @ Oct. 10 2007,12:47)
Quote (Daniel Smith @ Oct. 10 2007,02:30)
The results that would falsify my hypothesis would be if the coding sequences showed evolutionary constraint while the non-coding sequences didn't.
---------------------QUOTE-------------------

There's a fair amount of evidence showing that (contrary to expectation) non-coding sequences have fewer base changes than coding sequences...
---------------------QUOTE-------------------


...at synonymous sites.
Posted by: Henry J on Oct. 10 2007,15:00

What's makes a site synonymous?
Posted by: mitschlag on Oct. 10 2007,15:47

Quote (Henry J @ Oct. 10 2007,15:00)
What's makes a site synonymous?
---------------------QUOTE-------------------


 

---------------------QUOTE-------------------
Nucleotide substitutions in genes coding for proteins can be either synonymous (do not change amino acid), alternatively called silent substitutions, or non-synonymous (changes amino acid). Usually, most non-synonymous changes would be expected to be eliminated by purifying selection, but under certain conditions Darwinian selection may lead to their retention. Investigating the number of synonymous and non-synonymous substitutions may therefore provide information about the degree of selection operating on a system.
---------------------QUOTE-------------------

From < http://pubmlst.org/software/analysis/start/manual/dsdn.shtml >
Posted by: JAM on Oct. 11 2007,11:00

Quote (Daniel Smith @ Oct. 08 2007,02:18)
3.  What are presently considered neutral sites will be found to be "instructional" - that is, they will carry the instructions that tell the various proteins, RNA and enzymes where to go, when to go and what to do when they get there.
---------------------QUOTE-------------------


This is testable. It makes clear predictions about what will happen when we remove the nucleus, for example by cutting off a part of the cell with a laser, creating a cytoplast, or if we sever the axon tethering a neuronal growth cone to its cell body.

It predicts that these proteins will no longer "know what to do." Do you agree, Daniel?
Posted by: Wesley R. Elsberry on Oct. 12 2007,07:35

ISI's Web of Knowledge says, on search for "linkage disequilibrium" in papers of the last 5 years,



---------------------QUOTE-------------------

9,966 results found

---------------------QUOTE-------------------



Hmmm. The crickets seem to have come out.
Posted by: Alan Fox on Oct. 13 2007,03:52



---------------------QUOTE-------------------
Hmmm. The crickets seem to have come out.
---------------------QUOTE-------------------



Daniel tells me that he finds this site "too combative", so I am not sure if he will be continuing here.

I do wonder whether posts can sometimes be a little too waspish, but maybe that's just me.


Posted by: Wesley R. Elsberry on Oct. 13 2007,05:23

Quote (Alan Fox @ Oct. 13 2007,03:52)


---------------------QUOTE-------------------
Hmmm. The crickets seem to have come out.
---------------------QUOTE-------------------



Daniel tells me that he finds this site "too combative", so I am not sure if he will be continuing here.

I do wonder whether posts can sometimes be a little too waspish, but maybe that's just me.
---------------------QUOTE-------------------


The "edit" and "quote" buttons are right next to each other. I ought to wake up sometime along here. Anyway, my reply that I inadvertently dropped into Alan's comment follows:

I asked,

 

---------------------QUOTE-------------------

So, why does the term "linkage disequilibrium" seem to get used by geneticists? Wouldn't your prediction mean that we should see the same degree of linkage disequilibrium everywhere we look? If not, what consequences do you think your "prediction" actually has?

---------------------QUOTE-------------------



After another page of back-and-forth, there was no indication that Smith was going to address work that was highly relevant to his claim. I think the degree of waspishness in my follow-up was quite in line with the context. I think that one can look at Smith's replies and see that he doesn't consider waspishness a bad thing, when he gets to be the wasp.
Posted by: Alan Fox on Oct. 13 2007,05:43



---------------------QUOTE-------------------
I think the degree of waspishness in my follow-up...
---------------------QUOTE-------------------



No, Wesley, I certainly didn't mean you, here. I quoted you thinking you were alluding to Daniel's absence. I don't think I have seen a comment of yours that was in any way less than polite. I was thinking of the name-calling that sometimes seems unnecessary to make a point. It can allow the recipient to avoid the substantive issue.
Posted by: Wesley R. Elsberry on Oct. 13 2007,05:56



---------------------QUOTE-------------------

It can allow the recipient to avoid the substantive issue.

---------------------QUOTE-------------------



That's absolutely right. I've seen that happen a lot.
Posted by: Erasmus, FCD on Oct. 13 2007,13:07

I'd just rather assume that everyone had read Hume and Kant's criticism of arguments from design.  It is rather strange that 200 years later rudimentary errors in reasoning continue to perpetuate themselves.  as fascinating as 'the complexity of life and nature' is, it is only evidence for 'the complexity of life and nature'.

category errors and crap analogies irritate me.  is that waspish?
Posted by: Daniel Smith on Oct. 13 2007,13:22

Quote (Wesley R. Elsberry @ Oct. 12 2007,07:35)
ISI's Web of Knowledge says, on search for "linkage disequilibrium" in papers of the last 5 years,

 

---------------------QUOTE-------------------

9,966 results found

---------------------QUOTE-------------------



Hmmm. The crickets seem to have come out.
---------------------QUOTE-------------------


I've been trying to wrap my head around the concept of linkage disequilibrium but am not having much luck.  It's a bit over my head - which is why I haven't responded to your post yet.  Perhaps if you could explain the concept in layman's terms I could give you an answer.  Either that, or you'll have to wait awhile.
Posted by: JAM on Oct. 13 2007,13:49

Quote (Daniel Smith @ Oct. 13 2007,13:22)
Quote (Wesley R. Elsberry @ Oct. 12 2007,07:35)
ISI's Web of Knowledge says, on search for "linkage disequilibrium" in papers of the last 5 years,

   

---------------------QUOTE-------------------

9,966 results found

---------------------QUOTE-------------------



Hmmm. The crickets seem to have come out.
---------------------QUOTE-------------------


I've been trying to wrap my head around the concept of linkage disequilibrium but am not having much luck.  It's a bit over my head - which is why I haven't responded to your post yet.  Perhaps if you could explain the concept in layman's terms I could give you an answer.  Either that, or you'll have to wait awhile.
---------------------QUOTE-------------------


Maybe while you're trying to wrap your head around linkage disequilibrium, you can point us to a designed mechanism involving large numbers of similar, but not identical, parts, that have only partially overlapping functions.

That mechanism would be analogous to living ones.

Also, you can directly test your hypothesis that noncoding regions are conserved by peeking at the VISTA genome browser:

< http://pipeline.lbl.gov/cgi-bin/gateway2?bg=hg16 >

You're not gonna like what you see, so you probably should blow it off and not try to grapple with any real evidence. Here's an idea--pretend that our calling you out on your false claims is mean, which automatically makes your false claims correct (at least in your mind).
Posted by: Daniel Smith on Oct. 13 2007,13:50

Quote (Erasmus @ FCD,Oct. 10 2007,07:36)
Daniel we know people make things like stonehenge.

What designer do we know of that makes cells and platypi and the grand canyon?  People?  Or something else?  I'll wait for your answer.
That's Right!!!!  We don't know of any such designer!!!  You Lose!!!
---------------------QUOTE-------------------


I'm proposing that the designer is not human but has qualities similar to human qualities (intelligence, free agency, etc.).

I am proposing this entity has infinite intelligence and that it would require intelligence of that kind to design the universe and life.

IOW, if all this is designed (including us), whatever designed it is as far above us intellectually as the cosmos are above us physically.
Posted by: Daniel Smith on Oct. 13 2007,13:53

Quote (mitschlag @ Oct. 10 2007,12:47)
 
Quote (Daniel Smith @ Oct. 10 2007,02:30)
The results that would falsify my hypothesis would be if the coding sequences showed evolutionary constraint while the non-coding sequences didn't.
---------------------QUOTE-------------------

There's a fair amount of evidence showing that (contrary to expectation) non-coding sequences have fewer base changes than coding sequences, see, for example:
< http://www.biomedcentral.com/1471-2148/7/66 >
   

---------------------QUOTE-------------------
The primary result is that the mean rate of intergenic nucleotide substitution is two-thirds that of the synonymous coding data, with an absolute rate estimated to be 1.05 × 10-8 substitutions per site per year. This result holds with alternative nucleotide models (see Methods), and thus does not appear to be solely an issue of estimation procedures.

Slower rates in non-coding regions relative to synonymous sites are becoming a surprisingly frequent observation. For example, a recent study of Drosophila demonstrated that non-coding DNA evolves considerably slower than synonymous sites in terms of both divergence between species and polymorphism within species [16]. By comparing studies, one can also make the case that pseudogenes [32,33] and introns [34,35] evolve more slowly than synonymous sites in apes and other mammals [13,36-38]. Studies of mammalian intergenic regions have also found slower rates than synonymous sites [35,39,40]. Although most of these studies encompass only a handful of genes, an overall picture of relatively slow non-coding rates is emerging.
---------------------QUOTE-------------------


What do you make of that?
---------------------QUOTE-------------------


If this is true, then it would be a confirmation of my hypothesis with better than expected results.
Posted by: Daniel Smith on Oct. 13 2007,14:00

Quote (JAM @ Oct. 10 2007,10:40)

Here's an opposing hypothesis:

Known functional sequences will be evolutionarily conserved. Most sequences will not be conserved. We will continue to find functions for some conserved sequences for which no function has been identified.

What do you think? Shall we look at the evidence to see which hypothesis is better supported?
---------------------QUOTE-------------------


Yes, let's look.  But be warned, I'll be approaching the evidence from a different perspective than you and won't accept any preconceived ideas as part of the interpretation.  What I mean is that the perceived "rate of mutation" is often calculated by a comparison of species that are assumed to have evolved from a common ancestor via an accumulation of random mutations.  Since I am opposing that theory, I won't accept that assumption.  You must show me that the evidence supports this assumed buildup of random mutations first, then we can move on from there.

Fair enough?
Posted by: Daniel Smith on Oct. 13 2007,14:17

Quote (JAM @ Oct. 11 2007,11:00)
 
Quote (Daniel Smith @ Oct. 08 2007,02:18)
3.  What are presently considered neutral sites will be found to be "instructional" - that is, they will carry the instructions that tell the various proteins, RNA and enzymes where to go, when to go and what to do when they get there.
---------------------QUOTE-------------------


This is testable. It makes clear predictions about what will happen when we remove the nucleus, for example by cutting off a part of the cell with a laser, creating a cytoplast, or if we sever the axon tethering a neuronal growth cone to its cell body.

It predicts that these proteins will no longer "know what to do." Do you agree, Daniel?
---------------------QUOTE-------------------


Well, I'm not sure what affect removing the nucleus would have on existing, functioning proteins - since they should already know what to do.  If however, you were able to remove non-coding regions (by this I mean supposed neutral sequences) while leaving the coding sequences intact, then (according to my prediction) the proteins produced would not know what to do.
Posted by: Daniel Smith on Oct. 13 2007,14:41

Quote (C.J.O'Brien @ Oct. 10 2007,12:35)
That there is a certain kind of elegance to biochemical processes is not in question. They work well enough to have sustained evolving life on Earth for billions of years, and are perfectly capable of supporting the functions of big, complex animals like ourselves. So I am not saying that they barely "get the job done." I am saying, though, that all of the highly-touted complexity of the cell, when it is actually investigated, not simply remarked upon, seems to owe its existence to a maddeningly short-sighted designer --one that seems incabable of building a structure or pathway using anything other than pre-existing components, often themselves integral parts of other, fully functioning systems. But you challenged me for examples.

Here is Ken Miller on < the vertebrate blood-clotting cascade >

Here is a TalkOrigins summary of several articles on the evolution of the < Krebs Cycle >

Here is an abstract of a Science paper on the evolution of a < steroid-hormone receptor >
---------------------QUOTE-------------------


The articles and abstracts you cite are just explanations of how such systems theoretically could have evolved - not evidence that these systems are cobbled together "Rube Goldberg" type systems.

I found this item from the article on blood clotting interesting:  

---------------------QUOTE-------------------
If the modern fibrinogen gene really was recruited from a duplicated ancestral gene, one that had nothing to do with blood clotting, then we ought to be able to find a fibrinogen-like gene in an animal that does not possess the vertebrate clotting pathway. In other words, we ought to be able to find a non-clotting fibrinogen protein in an invertebrate. That's a mighty bold prediction, because if it could not be found, it would cast Doolittle's whole evolutionary scheme into doubt.

Not to worry. In 1990, Xun Yu and Doolittle won their own bet, finding a fibrinogen-like sequence in the sea cucumber, an echinoderm. The vertebrate fibrinogen gene, just like genes for the other proteins of the clotting sequence, was formed by the duplication and modification of pre-existing genes.
---------------------QUOTE-------------------


This prediction does not seem that "bold" to me - since we already know that convergent evolution produces analogous sequences in unrelated animals.  In fact, I'll be even bolder and predict that you can take any gene and find something "like it" somewhere in some unrelated organism's genome.
Posted by: jeannot on Oct. 13 2007,14:57

Quote (Daniel Smith @ Oct. 13 2007,13:53)
Quote (mitschlag @ Oct. 10 2007,12:47)
 
Quote (Daniel Smith @ Oct. 10 2007,02:30)
The results that would falsify my hypothesis would be if the coding sequences showed evolutionary constraint while the non-coding sequences didn't.
---------------------QUOTE-------------------

There's a fair amount of evidence showing that (contrary to expectation) non-coding sequences have fewer base changes than coding sequences, see, for example:
< http://www.biomedcentral.com/1471-2148/7/66 >
   

---------------------QUOTE-------------------
The primary result is that the mean rate of intergenic nucleotide substitution is two-thirds that of the synonymous coding data, with an absolute rate estimated to be 1.05 × 10-8 substitutions per site per year. This result holds with alternative nucleotide models (see Methods), and thus does not appear to be solely an issue of estimation procedures.

Slower rates in non-coding regions relative to synonymous sites are becoming a surprisingly frequent observation. For example, a recent study of Drosophila demonstrated that non-coding DNA evolves considerably slower than synonymous sites in terms of both divergence between species and polymorphism within species [16]. By comparing studies, one can also make the case that pseudogenes [32,33] and introns [34,35] evolve more slowly than synonymous sites in apes and other mammals [13,36-38]. Studies of mammalian intergenic regions have also found slower rates than synonymous sites [35,39,40]. Although most of these studies encompass only a handful of genes, an overall picture of relatively slow non-coding rates is emerging.
---------------------QUOTE-------------------


What do you make of that?
---------------------QUOTE-------------------


If this is true, then it would be a confirmation of my hypothesis with better than expected results.
---------------------QUOTE-------------------


Daniel, you still need explain what your hypothesis is.
You merely provided one prediction, which is a totally different thing. Without your hypothesis clearly detailed, a prediction is useless.

I still don't see why you'd expect similar "evolutionary constraint" in coding and non coding sites.
Posted by: Daniel Smith on Oct. 13 2007,14:58

Quote (JAM @ Oct. 13 2007,13:49)
Maybe while you're trying to wrap your head around linkage disequilibrium, you can point us to a designed mechanism involving large numbers of similar, but not identical, parts, that have only partially overlapping functions.

That mechanism would be analogous to living ones.
---------------------QUOTE-------------------


So we're accepting analogies as evidence now?  

---------------------QUOTE-------------------


Also, you can directly test your hypothesis that noncoding regions are conserved by peeking at the VISTA genome browser:

< http://pipeline.lbl.gov/cgi-bin/gateway2?bg=hg16 >

You're not gonna like what you see, so you probably should blow it off and not try to grapple with any real evidence. Here's an idea--pretend that our calling you out on your false claims is mean, which automatically makes your false claims correct (at least in your mind).
---------------------QUOTE-------------------


I went to the vista site, but I'm not sure how to use it.  I'll have to read the help file I guess.

BTW, you are generally mean - but I'm still here.
Your meanness has nothing to do with your rightness.
Posted by: Daniel Smith on Oct. 13 2007,15:02

Quote (Wesley R. Elsberry @ Oct. 13 2007,05:23)
The "edit" and "quote" buttons are right next to each other.
---------------------QUOTE-------------------


I see no "Edit" button with my browser (Mozilla Firefox).  All I see is a question mark (?) next to the "Quote" button - even on my own posts.
Posted by: Daniel Smith on Oct. 13 2007,15:07

Quote (jeannot @ Oct. 13 2007,14:57)
Daniel, you still need explain what your hypothesis is.
You merely provided one prediction, which is a totally different thing. Without your hypothesis clearly detailed, a prediction is useless.

I still don't see why you'd expect similar "evolutionary constraint" in coding and non coding sites.
---------------------QUOTE-------------------


Because my hypothesis - which I have already explained here - is that most (if not all) of the genome is used (non-neutral), and so because of this, there are not a bunch of random mutations accumulating in non-coding (neutral) sites.
I've restated it several times, I'm not sure how I can make it any clearer.
Posted by: jeannot on Oct. 13 2007,15:16

Quote (Daniel Smith @ Oct. 13 2007,15:07)
Quote (jeannot @ Oct. 13 2007,14:57)
Daniel, you still need explain what your hypothesis is.
You merely provided one prediction, which is a totally different thing. Without your hypothesis clearly detailed, a prediction is useless.

I still don't see why you'd expect similar "evolutionary constraint" in coding and non coding sites.
---------------------QUOTE-------------------


Because my hypothesis - which I have already explained here - is that most (if not all) of the genome is used (non-neutral), and so because of this, there are not a bunch of random mutations accumulating in non-coding (neutral) sites.
I've restated it several times, I'm not sure how I can make it any clearer.
---------------------QUOTE-------------------


So what about the fact that mutation rates are far higher at synonymous sites?
Posted by: Wesley R. Elsberry on Oct. 13 2007,16:36



---------------------QUOTE-------------------

I see no "Edit" button with my browser (Mozilla Firefox).

---------------------QUOTE-------------------



You should see an edit button on your own posts, but not other people's posts.

With moderator privileges, the edit button is on every comment.
Posted by: JAM on Oct. 13 2007,17:14

Quote (Daniel Smith @ Oct. 13 2007,14:00)
 
Quote (JAM @ Oct. 10 2007,10:40)

Here's an opposing hypothesis:

Known functional sequences will be evolutionarily conserved. Most sequences will not be conserved. We will continue to find functions for some conserved sequences for which no function has been identified.

What do you think? Shall we look at the evidence to see which hypothesis is better supported?
---------------------QUOTE-------------------


Yes, let's look.  But be warned, I'll be approaching the evidence from a different perspective than you and won't accept any preconceived ideas as part of the interpretation.
---------------------QUOTE-------------------


Daniel, this is why real, honest scientists make predictions BEFORE they get the data.

My hypothesis predicts that when we graph position on the x axis and % identity on the Y axis, we will see this, with the high points representing conserved sequences, which include, but are definitely not limited to, protein-coding sequences:
/\_/\___

Your hypothesis predicts that we will see a flat line wherever we look:

--------------


---------------------QUOTE-------------------
What I mean is that the perceived "rate of mutation" is often calculated by a comparison of species that are assumed to have evolved from a common ancestor via an accumulation of random mutations.
---------------------QUOTE-------------------


Not even remotely close, Daniel. Mutation rates are much more directly measured by quantitating new mutations; for example, we can measure the rate of new cases of autosomal dominant diseases that aren't inherited from parents. No assumptions are necessary to distinguish between our hypotheses. We are simply looking at differences between lineages for orthologous regions of the genome.


---------------------QUOTE-------------------
Since I am opposing that theory, I won't accept that assumption.
---------------------QUOTE-------------------


I'm not making any such assumption, so your desperate evasion won't work. You might want to reread the hypothesis we're testing.


---------------------QUOTE-------------------
You must show me that the evidence supports this assumed buildup of random mutations first, then we can move on from there.
---------------------QUOTE-------------------


Nope. That's not how science works. We use hypotheses to make predictions, and then we look at the evidence to see whether it is consistent or inconsistent.

Only pseudoscientists who have zero confidence in their hypotheses make petulant demands like yours.
Posted by: JAM on Oct. 13 2007,17:22

Quote (Daniel Smith @ Oct. 13 2007,14:58)
   
Quote (JAM @ Oct. 13 2007,13:49)
Maybe while you're trying to wrap your head around linkage disequilibrium, you can point us to a designed mechanism involving large numbers of similar, but not identical, parts, that have only partially overlapping functions.

That mechanism would be analogous to living ones.
---------------------QUOTE-------------------


So we're accepting analogies as evidence now?
---------------------QUOTE-------------------


No, I'm pointing out that the analogy you're offering as evidence is simply wrong.    


---------------------QUOTE-------------------


---------------------QUOTE-------------------
Also, you can directly test your hypothesis that noncoding regions are conserved by peeking at the VISTA genome browser:

< http://pipeline.lbl.gov/cgi-bin/gateway2?bg=hg16 >

You're not gonna like what you see, so you probably should blow it off and not try to grapple with any real evidence. Here's an idea--pretend that our calling you out on your false claims is mean, which automatically makes your false claims correct (at least in your mind).
---------------------QUOTE-------------------


I went to the vista site, but I'm not sure how to use it.  I'll have to read the help file I guess.
---------------------QUOTE-------------------


I suggest clicking the "Go" button to begin.
 

---------------------QUOTE-------------------
BTW, you are generally mean - but I'm still here.
Your meanness has nothing to do with your rightness.
---------------------QUOTE-------------------


Good for you.

I have to admit, though, that I tend to be more mean when I'm right, particularly when dumping evidence on someone as arrogant as you, who pretends to have a better understanding of my life's work than I do. Or someone who claims to have examined evidence, but moves the goalposts to someone else's "descriptions" when challenged.

Do you get a feeling for my perspective?
Posted by: JAM on Oct. 13 2007,17:33

Daniel,

Here's a good VISTA example:

< http://pipeline.lbl.gov/servlet....llbar=0 >

This is mouse against human, dog, rat, and chicken in graphs 1-4 respectively.
Posted by: mitschlag on Oct. 13 2007,18:22

Quote (Daniel Smith @ Oct. 13 2007,13:53)
 
Quote (mitschlag @ Oct. 10 2007,12:47)
     
Quote (Daniel Smith @ Oct. 10 2007,02:30)
The results that would falsify my hypothesis would be if the coding sequences showed evolutionary constraint while the non-coding sequences didn't.
---------------------QUOTE-------------------

There's a fair amount of evidence showing that (contrary to expectation) non-coding sequences have fewer base changes than coding sequences, see, for example:
< http://www.biomedcentral.com/1471-2148/7/66 >
       

---------------------QUOTE-------------------
The primary result is that the mean rate of intergenic nucleotide substitution is two-thirds that of the synonymous coding data, with an absolute rate estimated to be 1.05 × 10-8 substitutions per site per year. This result holds with alternative nucleotide models (see Methods), and thus does not appear to be solely an issue of estimation procedures.

Slower rates in non-coding regions relative to synonymous sites are becoming a surprisingly frequent observation. For example, a recent study of Drosophila demonstrated that non-coding DNA evolves considerably slower than synonymous sites in terms of both divergence between species and polymorphism within species [16]. By comparing studies, one can also make the case that pseudogenes [32,33] and introns [34,35] evolve more slowly than synonymous sites in apes and other mammals [13,36-38]. Studies of mammalian intergenic regions have also found slower rates than synonymous sites [35,39,40]. Although most of these studies encompass only a handful of genes, an overall picture of relatively slow non-coding rates is emerging.
---------------------QUOTE-------------------


What do you make of that?
---------------------QUOTE-------------------


If this is true, then it would be a confirmation of my hypothesis with better than expected results.
---------------------QUOTE-------------------


It's true, all right, but it doesn't confirm your hypothesis.

To learn why, read the cited paper.  Hint: TE=transposable element.

(Sorry that I won't be able to participate in this discussion for the next two weeks due to travel in arcane regions.  In the meantime, I want to commend DS for  his courteous and patient responses to the many challenges that have been addressed to him.)
Posted by: Daniel Smith on Oct. 13 2007,23:01

Quote (jeannot @ Oct. 13 2007,15:16)
So what about the fact that mutation rates are far higher at synonymous sites?
---------------------QUOTE-------------------


As I understand it (and I just learned this) synonymous sites are sites that will accept a substitution with no functional change.  Therefore, there's no reason that these sites wouldn't show higher mutation rates.  The question is: why do sites that are supposedly non-functional show more constraint than synonymous sites?
Posted by: Daniel Smith on Oct. 13 2007,23:32

Quote (JAM @ Oct. 13 2007,17:14)
   
Quote (Daniel Smith @ Oct. 13 2007,14:00)
     
Quote (JAM @ Oct. 10 2007,10:40)

Here's an opposing hypothesis:

Known functional sequences will be evolutionarily conserved. Most sequences will not be conserved. We will continue to find functions for some conserved sequences for which no function has been identified.

What do you think? Shall we look at the evidence to see which hypothesis is better supported?
---------------------QUOTE-------------------


Yes, let's look.  But be warned, I'll be approaching the evidence from a different perspective than you and won't accept any preconceived ideas as part of the interpretation.
---------------------QUOTE-------------------


Daniel, this is why real, honest scientists make predictions BEFORE they get the data.

My hypothesis predicts that when we graph position on the x axis and % identity on the Y axis, we will see this, with the high points representing conserved sequences, which include, but are definitely not limited to, protein-coding sequences:
/\_/\___

Your hypothesis predicts that we will see a flat line wherever we look:

--------------

---------------------QUOTE-------------------


My hypothesis does not predict a flat line - except within a lineage.  By "lineage" I mean either the same species or very closely related species.  As an example I would think something along the lines of the African vs. Asian elephant.  This is why I said that the test needs to be done within the lineage to test my hypothesis.  

---------------------QUOTE-------------------

   

---------------------QUOTE-------------------
What I mean is that the perceived "rate of mutation" is often calculated by a comparison of species that are assumed to have evolved from a common ancestor via an accumulation of random mutations.
---------------------QUOTE-------------------


Not even remotely close, Daniel. Mutation rates are much more directly measured by quantitating new mutations; for example, we can measure the rate of new cases of autosomal dominant diseases that aren't inherited from parents. No assumptions are necessary to distinguish between our hypotheses. We are simply looking at differences between lineages for orthologous regions of the genome.
---------------------QUOTE-------------------

But orthologous regions are regions that are thought to be homologous due to speciation - which is assumed to have occurred by an accumulation of mutations - isn't that correct?  

---------------------QUOTE-------------------

   

---------------------QUOTE-------------------
Since I am opposing that theory, I won't accept that assumption.
---------------------QUOTE-------------------


I'm not making any such assumption, so your desperate evasion won't work. You might want to reread the hypothesis we're testing.
---------------------QUOTE-------------------


Isn't it my hypothesis we're testing?  

---------------------QUOTE-------------------

   

---------------------QUOTE-------------------
You must show me that the evidence supports this assumed buildup of random mutations first, then we can move on from there.
---------------------QUOTE-------------------


Nope. That's not how science works. We use hypotheses to make predictions, and then we look at the evidence to see whether it is consistent or inconsistent.

Only pseudoscientists who have zero confidence in their hypotheses make petulant demands like yours.
---------------------QUOTE-------------------


What demands?  My hypothesis predicts that there is no buildup of random mutations within the genome - even in non-coding sites.  Isn't that what we're testing?
Posted by: Daniel Smith on Oct. 13 2007,23:32

Speaking of predictions, I have another one for you:
It's my prediction that random mutations are only neutral or deleterious - never advantageous.  All advantageous mutations are non-random and are therefore experimentally repeatable.
Therefore, I predict that anytime Acromobacter guttatus Sp. K172 is subjected to an environment where it must consume nylon to survive, the same frame shift will occur, resulting in Flavobacterium Sp. KI72.
Posted by: JAM on Oct. 14 2007,00:01

Quote (Daniel Smith @ Oct. 13 2007,23:32)
My hypothesis does not predict a flat line - except within a lineage.  By "lineage" I mean either the same species or very closely related species.  As an example I would think something along the lines of the African vs. Asian elephant.  This is why I said that the test needs to be done within the lineage to test my hypothesis.
---------------------QUOTE-------------------


I already gave you a URL for such a pair--rat vs. mouse. You, predictably, completely ignored the data.
   

---------------------QUOTE-------------------
But orthologous regions are regions that are thought to be homologous due to speciation - which is assumed to have occurred by an accumulation of mutations - isn't that correct?    
---------------------QUOTE-------------------


Not even close. All orthologs are homologs, but not all homologs are orthologs. Orthologs are not merely homologous, but have the same function. Operationally, we're only really sure about these when we have complete genome sequences or when we rescue a mouse mutant with its human ortholog as a transgene. There are orthologous stretches along huge segments of chromosomes, in which gene order is preserved. This is called synteny. How do you explain that?
     

---------------------QUOTE-------------------
Isn't it my hypothesis we're testing?    
---------------------QUOTE-------------------


We're testing both at once.
     

---------------------QUOTE-------------------
What demands?      

---------------------QUOTE-------------------
You must show me that the evidence supports this assumed buildup of random mutations first, then we can move on from there.
---------------------QUOTE-------------------


---------------------QUOTE-------------------


That's a petulant demand.
     

---------------------QUOTE-------------------
My hypothesis predicts that there is no buildup of random mutations within the genome - even in non-coding sites.  Isn't that what we're testing?
---------------------QUOTE-------------------


Not quite. Your hypothesis predicts that identity will be no different in coding vs. noncoding sites. Predictions are made about observable data, but we both know that you're desperate to avoid that.

You really oughta figure out that "random" only refers to fitness before going on these rants.
 

---------------------QUOTE-------------------
Speaking of predictions, I have another one for you:
It's my prediction that random mutations are only neutral or deleterious - never advantageous.
---------------------QUOTE-------------------


That's not a prediction, it's a hypothesis. Come on, man, this isn't that difficult. Predictions are made ABOUT DIRECTLY OBSERVABLE THINGS.

Let's see if you can grasp this at the second-grade level:
1) The hypothesis that my dog understands the meaning of the word "sit" predicts that that my dog WON'T sit when I say "fit" or "tit" or "sib" or "hit" in the same tone of voice and with the same body language.
2) The hypothesis that my dog does not understand the meaning of the word "sit" predicts that that my dog WILL sit when I say "fit" or "tit" or "sib" or "hit" in the same tone of voice and with the same body language.

Do you get it yet? The prediction is about what you directly observe--whether the dog sits or not.
 

---------------------QUOTE-------------------
All advantageous mutations are non-random and are therefore experimentally repeatable.
---------------------QUOTE-------------------


"Non-random"=/="experimentally repeatable," Daniel. If one does sufficient trials, the random becomes not only repeatable, but predicted. Maybe you should read a primer on the Poisson distribution.
 

---------------------QUOTE-------------------
"Therefore, I predict that anytime Acromobacter guttatus Sp. K172 is subjected to an environment where it must consume nylon to survive, the same frame shift will occur, resulting in Flavobacterium Sp. KI72."
---------------------QUOTE-------------------


That's meaningless without numbers, but that's probably what you were aiming for.
Posted by: Richard Simons on Oct. 14 2007,00:10

Quote (daniel Smith @ Oct. 13 2007,23:32)

By "lineage" I mean either the same species or very closely related species.  As an example I would think something along the lines of the African vs. Asian elephant.
---------------------QUOTE-------------------


I could be wrong, but I thought that African and Asian elephants were considered to be less closely related than humans and chimps. Is this close enough for your purposes, Daniel?
Posted by: Daniel Smith on Oct. 14 2007,10:16

Quote (Wesley R. Elsberry @ Oct. 13 2007,16:36)


---------------------QUOTE-------------------

I see no "Edit" button with my browser (Mozilla Firefox).

---------------------QUOTE-------------------



You should see an edit button on your own posts, but not other people's posts.

With moderator privileges, the edit button is on every comment.
---------------------QUOTE-------------------


I have no Edit button on my posts.  Not with Mozilla, not with IE.
Posted by: Daniel Smith on Oct. 14 2007,10:20

[EDIT]
Speaking of predictions, I have another one for you:
It's my hypothesis that random mutations are only neutral or deleterious - never advantageous.  All advantageous mutations are non-random and are therefore experimentally repeatable and will occurr too rapidly to be random.
Therefore, I predict that anytime Acromobacter guttatus Sp. K172 is subjected to an environment where it must consume nylon to survive, the same frame shift will occur, resulting in Flavobacterium Sp. KI72.

Better?
Posted by: Daniel Smith on Oct. 14 2007,10:37

Quote (JAM @ Oct. 14 2007,00:01)
I already gave you a URL for such a pair--rat vs. mouse. You, predictably, completely ignored the data.
---------------------QUOTE-------------------


I went there, but I'm not sure what I'm looking at.  What I want to see is the rat and mouse genome side by side, sequence by sequence.  That program appears to pick pieces out of the genome and line them up independently of their position in the chromosome.  Basically, I want to start at chromosome 1, bp 1, and see the rat and mouse side by side.  Is that possible?

---------------------QUOTE-------------------

     

---------------------QUOTE-------------------
But orthologous regions are regions that are thought to be homologous due to speciation - which is assumed to have occurred by an accumulation of mutations - isn't that correct?    
---------------------QUOTE-------------------


Not even close. All orthologs are homologs, but not all homologs are orthologs. Orthologs are not merely homologous, but have the same function. Operationally, we're only really sure about these when we have complete genome sequences or when we rescue a mouse mutant with its human ortholog as a transgene. There are orthologous stretches along huge segments of chromosomes, in which gene order is preserved. This is called synteny. How do you explain that?
---------------------QUOTE-------------------

Designed descent.
Posted by: JAM on Oct. 14 2007,10:53

Quote (Daniel Smith @ Oct. 14 2007,10:20)
[EDIT]
Speaking of predictions, I have another one for you:
It's my hypothesis that random mutations are only neutral or deleterious - never advantageous.  All advantageous mutations are non-random and are therefore experimentally repeatable and will occurr too rapidly to be random.
Therefore, I predict that anytime Acromobacter guttatus Sp. K172 is subjected to an environment where it must consume nylon to survive, the same frame shift will occur, resulting in Flavobacterium Sp. KI72.

Better?
---------------------QUOTE-------------------


Better, but you still need numbers. Specifically, "rapidly" is not meaningful, because mutation rates are calculated per individual per generation.

What does your hypothesis predict if a different bacterial species is selected on nylon?

1) Will multiple selections give the same result, and/or
2) Will the enzymes that evolved be the orthologs of the ones that evolved in Achromobacter?

P.S. Did you check out the mouse vs. rat sequences yet?
Posted by: JAM on Oct. 14 2007,11:25

Quote (Daniel Smith @ Oct. 14 2007,10:37)
 
Quote (JAM @ Oct. 14 2007,00:01)
I already gave you a URL for such a pair--rat vs. mouse. You, predictably, completely ignored the data.
---------------------QUOTE-------------------


I went there, but I'm not sure what I'm looking at.
---------------------QUOTE-------------------


I told you that you were looking at mouse vs. rat in line 3, but you ignored me.
 

---------------------QUOTE-------------------
What I want to see is the rat and mouse genome side by side, sequence by sequence.
---------------------QUOTE-------------------


That's exactly what I showed you in line 3.
 

---------------------QUOTE-------------------
That program appears to pick pieces out of the genome and line them up independently of their position in the chromosome.
---------------------QUOTE-------------------


Utterly, totally false. As I plainly explained to you, this lines up orthologous regions only. If you're going to call me a liar, Daniel, at least have the integrity to do so plainly.


---------------------QUOTE-------------------
Basically, I want to start at chromosome 1, bp 1, and see the rat and mouse side by side.  Is that possible?
---------------------QUOTE-------------------


Absolutely, as long as you're not resistant to basic education.
 

---------------------QUOTE-------------------


---------------------QUOTE-------------------
 

---------------------QUOTE-------------------
But orthologous regions are regions that are thought to be homologous due to speciation - which is assumed to have occurred by an accumulation of mutations - isn't that correct?    
---------------------QUOTE-------------------


Not even close. All orthologs are homologs, but not all homologs are orthologs. Orthologs are not merely homologous, but have the same function. Operationally, we're only really sure about these when we have complete genome sequences or when we rescue a mouse mutant with its human ortholog as a transgene. There are orthologous stretches along huge segments of chromosomes, in which gene order is preserved. This is called synteny. How do you explain that?
---------------------QUOTE-------------------

Designed descent.
---------------------QUOTE-------------------


How do you explain the breakpoints between syntenic regions in your design hypothesis, then? How do you explain the extensive synteny that crosses what you idiosyncratically define as "lineages"?
Posted by: Daniel Smith on Oct. 14 2007,14:26

Quote (Wesley R. Elsberry @ Oct. 08 2007,07:49)
 

---------------------QUOTE-------------------

My prediction is that the coding and non-coding sequences (basically all sequences) will show an equal amount of evolutionary constraint.

---------------------QUOTE-------------------



So, why does the term "linkage disequilibrium" seem to get used by geneticists? Wouldn't your prediction mean that we should see the same degree of linkage disequilibrium everywhere we look? If not, what consequences do you think your "prediction" actually has?
---------------------QUOTE-------------------


First, here's a definition of linkage disequilibrium that I can understand:
 

---------------------QUOTE-------------------
The occurrence of some genes together, more often than would be expected. Thus, in the HLA system of histocompatibility antigens, HLA A1 is commonly associated with B8 and DR3 and A2 with B7 and DR2, presumably because the combination confers some selective advantage.
---------------------QUOTE-------------------

< link >
Do you agree with this definition?

Second, if so, I'm not sure how this applies to my hypothesis.  Why would you think that evolutioary constraint of non-coding sites would lead to "the same degree of linkage disequilibrium everywhere we look"?

I guess I'm not understanding the connection.
Posted by: Daniel Smith on Oct. 14 2007,14:34

First, I'm trimming the accusations that I somehow called you a liar because I don't fully understand how VISTA works.    
Quote (JAM @ Oct. 14 2007,11:25)
 

---------------------QUOTE-------------------
 

---------------------QUOTE-------------------
All orthologs are homologs, but not all homologs are orthologs. Orthologs are not merely homologous, but have the same function. Operationally, we're only really sure about these when we have complete genome sequences or when we rescue a mouse mutant with its human ortholog as a transgene. There are orthologous stretches along huge segments of chromosomes, in which gene order is preserved. This is called synteny. How do you explain that?
---------------------QUOTE-------------------

Designed descent.
---------------------QUOTE-------------------


How do you explain the breakpoints between syntenic regions in your design hypothesis, then? How do you explain the extensive synteny that crosses what you idiosyncratically define as "lineages"?
---------------------QUOTE-------------------


The designed descent hypothesis accepts that some genetic regions are passed on intact - while others are changed during the saltational phase of evolution.  I'm not sure how your objection applies.
Posted by: JAM on Oct. 14 2007,14:48

Quote (Daniel Smith @ Oct. 14 2007,14:26)
 
Quote (Wesley R. Elsberry @ Oct. 08 2007,07:49)
     

---------------------QUOTE-------------------

My prediction is that the coding and non-coding sequences (basically all sequences) will show an equal amount of evolutionary constraint.

---------------------QUOTE-------------------



So, why does the term "linkage disequilibrium" seem to get used by geneticists? Wouldn't your prediction mean that we should see the same degree of linkage disequilibrium everywhere we look? If not, what consequences do you think your "prediction" actually has?
---------------------QUOTE-------------------


First, here's a definition of linkage disequilibrium that I can understand:
     

---------------------QUOTE-------------------
The occurrence of some genes together, more often than would be expected. Thus, in the HLA system of histocompatibility antigens, HLA A1 is commonly associated with B8 and DR3 and A2 with B7 and DR2, presumably because the combination confers some selective advantage.
---------------------QUOTE-------------------

< link >
Do you agree with this definition?
---------------------QUOTE-------------------


"Genes" should be "alleles." Do you understand the difference? It's essential for understanding the concept.
 

---------------------QUOTE-------------------
Second, if so, I'm not sure how this applies to my hypothesis.  Why would you think that evolutioary constraint of non-coding sites would lead to "the same degree of linkage disequilibrium everywhere we look"?
---------------------QUOTE-------------------


I'd rephrase what Wesley said and point out that your hypothesis predicts that linkage disequilibrium shouldn't be found at all.
 

---------------------QUOTE-------------------
I guess I'm not understanding the connection.
---------------------QUOTE-------------------


It's interesting that you implicitly claim to understand biology sufficiently to claim that you understand it better than we biologists do, but every time someone points to major problems in reconciling it with the data, you become incredibly modest about your intellect.

Do you not see an inconsistency there?
Posted by: JAM on Oct. 14 2007,14:59

Quote (Daniel Smith @ Oct. 14 2007,14:34)
First, I'm trimming the accusations that I somehow called you a liar because I don't fully understand how VISTA works.
---------------------QUOTE-------------------

 
You were implying that I wasn't honest despite the fact that I explicitly explained to you that line 3 represented mouse vs. rat, and you complained that "What I want to see is the rat and mouse genome side by side, sequence by sequence." That was precisely what I was showing you. Now, I'm asking if you want to see it.
     
Quote (JAM @ Oct. 14 2007,11:25)
     

---------------------QUOTE-------------------
     

---------------------QUOTE-------------------
All orthologs are homologs, but not all homologs are orthologs. Orthologs are not merely homologous, but have the same function. Operationally, we're only really sure about these when we have complete genome sequences or when we rescue a mouse mutant with its human ortholog as a transgene. There are orthologous stretches along huge segments of chromosomes, in which gene order is preserved. This is called synteny. How do you explain that?
---------------------QUOTE-------------------

Designed descent.
---------------------QUOTE-------------------


How do you explain the breakpoints between syntenic regions in your design hypothesis, then? How do you explain the extensive synteny that crosses what you idiosyncratically define as "lineages"?
---------------------QUOTE-------------------


 

---------------------QUOTE-------------------
The designed descent hypothesis accepts that some genetic regions are passed on intact -
---------------------QUOTE-------------------


Hypotheses don't "accept" things, people do. Hypotheses predict. What percentage of the genome do you mean by "some," Daniel?
 

---------------------QUOTE-------------------
... while others are changed during the saltational phase of evolution.  I'm not sure how your objection applies.
---------------------QUOTE-------------------


I didn't offer an objection. I asked you questions that you are evading. Let's try again. Synteny refers to intact gene orders, not intact sequences.

See if you can answer two questions straight up:

1) When considering man/mouse synteny, what proportion of the genome will retain gene orders?

2) Again, with man vs. mouse (but not synteny), each has ~30,000 genes. According to your hypothesis, how many human genes won't have a mouse ortholog and vice versa?

Honest answers will be in numerical form.
Posted by: jeannot on Oct. 14 2007,15:40

Quote (JAM @ Oct. 14 2007,14:48)
I'd rephrase what Wesley said and point out that your hypothesis predicts that linkage disequilibrium shouldn't be found at all.
---------------------QUOTE-------------------


I don't see how Daniel's hypothesis contradicts linkage disequilibrium.

He's not implying that a locus undergoes the same selective pressure whatever its genomic background, he's implying that non-coding regions and genes are subject to the same level of selection, on average.

Of course, this relies on other evolutionary mechanisms (namely genetic epistasis) that Daniel may reject.
Posted by: JAM on Oct. 14 2007,15:43

Quote (jeannot @ Oct. 14 2007,15:40)
Quote (JAM @ Oct. 14 2007,14:48)
I'd rephrase what Wesley said and point out that your hypothesis predicts that linkage disequilibrium shouldn't be found at all.
---------------------QUOTE-------------------


I don't see how Daniel's hypothesis contradicts linkage disequilibrium.

He's not implying that a locus undergoes the same selective pressure whatever its genomic background, he's implying that non-coding regions and genes are subject to the same level of selection, on average. Is that right, Daniel?
---------------------QUOTE-------------------


That all depends on whether "on average" is a part of it, I'd say.
Posted by: jeannot on Oct. 14 2007,15:51

Quote (JAM @ Oct. 14 2007,15:43)
 
Quote (jeannot @ Oct. 14 2007,15:40)
 
Quote (JAM @ Oct. 14 2007,14:48)
I'd rephrase what Wesley said and point out that your hypothesis predicts that linkage disequilibrium shouldn't be found at all.
---------------------QUOTE-------------------


I don't see how Daniel's hypothesis contradicts linkage disequilibrium.

He's not implying that a locus undergoes the same selective pressure whatever its genomic background, he's implying that non-coding regions and genes are subject to the same level of selection, on average. Is that right, Daniel?
---------------------QUOTE-------------------


That all depends on whether "on average" is a part of it, I'd say.
---------------------QUOTE-------------------


Well, it's clear that Daniel is not familiar with recombination and genetic epistasis. He just thinks that a designer would not inject big chunks of useless DNA in our streamlined genome.
If that's his only contention with the ToE, linkage disequilibrium remains.
I'd like to hear his explanation about the Alu sequences, though.

EDIT: I should add that genetic drift leads to linkage disequilibrium if there is population structure. Apparently, Daniel accept that synonymous sites are neutral so I conclude that his hypothesis doesn't say much about drift.
Posted by: David Holland on Oct. 15 2007,15:51

Quote (Daniel Smith @ Oct. 14 2007,10:20)
[EDIT]
Speaking of predictions, I have another one for you:
It's my hypothesis that random mutations are only neutral or deleterious - never advantageous.  All advantageous mutations are non-random and are therefore experimentally repeatable and will occurr too rapidly to be random.
Therefore, I predict that anytime Acromobacter guttatus Sp. K172 is subjected to an environment where it must consume nylon to survive, the same frame shift will occur, resulting in Flavobacterium Sp. KI72.

Better?
---------------------QUOTE-------------------


[QUOTE]

I want to go back to this one for a minute. Suppose I set up a vat with a bazillion Acromobacter guttatus and nylon as the primary source of carbon. If one of the bacteria developes the ability to digest nylon has your hypothesis been supported? Without numbers I can't tell.
Posted by: Henry J on Oct. 15 2007,22:23



---------------------QUOTE-------------------
Suppose I set up a vat with a bazillion Acromobacter guttatus and nylon as the primary source of carbon.
---------------------QUOTE-------------------



I dunno - there might be too many things that could hose that experiment, so I wouldn't put too much stocking into it.

Henry
Posted by: Steverino on Oct. 16 2007,06:36

"The designed descent hypothesis accepts that some genetic regions are passed on intact - while others are changed during the saltational phase of evolution.  I'm not sure how your objection applies."  - Denial Smith

AAHHHH>....Creation thru unidentifiable-all powerful widget.
Posted by: JonF on Oct. 16 2007,07:19

Quote (Daniel Smith @ Oct. 14 2007,11:20)
[EDIT]
Speaking of predictions, I have another one for you:
It's my hypothesis that random mutations are only neutral or deleterious - never advantageous.  All advantageous mutations are non-random and are therefore experimentally repeatable and will occurr too rapidly to be random.
Therefore, I predict that anytime Acromobacter guttatus Sp. K172 is subjected to an environment where it must consume nylon to survive, the same frame shift will occur, resulting in Flavobacterium Sp. KI72.

Better?
---------------------QUOTE-------------------


Better, but still not good enough.  Yuu need to quantify "too rapidly". Numbers.
Posted by: Daniel Smith on Oct. 16 2007,14:00

[quote=David Holland,Oct. 15 2007,15:51]  
Quote (Daniel Smith @ Oct. 14 2007,10:20)
[EDIT]
Speaking of predictions, I have another one for you:
It's my hypothesis that random mutations are only neutral or deleterious - never advantageous.  All advantageous mutations are non-random and are therefore experimentally repeatable and will occurr too rapidly to be random.
Therefore, I predict that anytime Acromobacter guttatus Sp. K172 is subjected to an environment where it must consume nylon to survive, the same frame shift will occur, resulting in Flavobacterium Sp. KI72.

Better?
---------------------QUOTE-------------------




---------------------QUOTE-------------------


I want to go back to this one for a minute. Suppose I set up a vat with a bazillion Acromobacter guttatus and nylon as the primary source of carbon. If one of the bacteria developes the ability to digest nylon has your hypothesis been supported? Without numbers I can't tell.
---------------------QUOTE-------------------


Only if it develops the same exact frame shift and only if it happens consistenty faster than random mutation rates can account for.
BTW, I don't have any idea what those rates are, but I'm sure whoever was doing the test would get that info first.
Posted by: swbarnes2 on Oct. 16 2007,14:34



---------------------QUOTE-------------------
Only if it develops the same exact frame shift
---------------------QUOTE-------------------



Okay, so let's get this straight.

Do you agree that the ability to resist antibiotics is "beneficial"?

If so, you then predict that if 50 labs all over the country screen put every post-doc and lab tech they had to work screening plates for 3 months to find resistant mutants, they will ALL find the exact same mutation?

What if I'm screening for a mutation that cripples a certain pathway, and when I find a colony with the mutation I want, I will keep it and cultivate it for the next 20 years, and all the other ones just get incinerated.

Doesn't that make that mutation beneficial?  You certainly can't claim that its bearers fare worse in their environment than the wild-type kind.
Posted by: JAM on Oct. 16 2007,15:07

Quote (Daniel Smith @ Oct. 16 2007,14:00)
[quote=David Holland,Oct. 15 2007,15:51]  
Quote (Daniel Smith @ Oct. 14 2007,10:20)
[EDIT]
Speaking of predictions, I have another one for you:
It's my hypothesis that random mutations are only neutral or deleterious - never advantageous.  All advantageous mutations are non-random and are therefore experimentally repeatable and will occurr too rapidly to be random.
Therefore, I predict that anytime Acromobacter guttatus Sp. K172 is subjected to an environment where it must consume nylon to survive, the same frame shift will occur, resulting in Flavobacterium Sp. KI72.

Better?
---------------------QUOTE-------------------


 

---------------------QUOTE-------------------


I want to go back to this one for a minute. Suppose I set up a vat with a bazillion Acromobacter guttatus and nylon as the primary source of carbon. If one of the bacteria developes the ability to digest nylon has your hypothesis been supported? Without numbers I can't tell.
---------------------QUOTE-------------------


Only if it develops the same exact frame shift and only if it happens consistenty faster than random mutation rates can account for.
BTW, I don't have any idea what those rates are, but I'm sure whoever was doing the test would get that info first.
---------------------QUOTE-------------------


What does your hypothesis predict if a different bacterial species is selected on nylon?

1) Will multiple selections give the same result, and/or
2) Will the enzymes that evolved be the orthologs of the ones that evolved in Achromobacter?

P.S. Did you check out the mouse vs. rat sequences yet?
Posted by: Daniel Smith on Oct. 16 2007,18:44

[quote=JAM,Oct. 16 2007,15:07]  
Quote (Daniel Smith @ Oct. 16 2007,14:00)
   
Quote (David Holland @ Oct. 15 2007,15:51)
       
Quote (Daniel Smith @ Oct. 14 2007,10:20)
[EDIT]
Speaking of predictions, I have another one for you:
It's my hypothesis that random mutations are only neutral or deleterious - never advantageous.  All advantageous mutations are non-random and are therefore experimentally repeatable and will occurr too rapidly to be random.
Therefore, I predict that anytime Acromobacter guttatus Sp. K172 is subjected to an environment where it must consume nylon to survive, the same frame shift will occur, resulting in Flavobacterium Sp. KI72.

Better?
---------------------QUOTE-------------------


     

---------------------QUOTE-------------------


I want to go back to this one for a minute. Suppose I set up a vat with a bazillion Acromobacter guttatus and nylon as the primary source of carbon. If one of the bacteria developes the ability to digest nylon has your hypothesis been supported? Without numbers I can't tell.
---------------------QUOTE-------------------


Only if it develops the same exact frame shift and only if it happens consistenty faster than random mutation rates can account for.
BTW, I don't have any idea what those rates are, but I'm sure whoever was doing the test would get that info first.
---------------------QUOTE-------------------


What does your hypothesis predict if a different bacterial species is selected on nylon?
---------------------QUOTE-------------------


I've already made my prediction, why are asking me to make another one?    

---------------------QUOTE-------------------


1) Will multiple selections give the same result, and/or
2) Will the enzymes that evolved be the orthologs of the ones that evolved in Achromobacter?

---------------------QUOTE-------------------


My prediction was that exactly the same frame shift will occur - so I'm guessing it will be #1.      

---------------------QUOTE-------------------

P.S. Did you check out the mouse vs. rat sequences yet?
---------------------QUOTE-------------------


I've been there several times.  Let me give you a blow by blow of my most recent visit:
I want to see the mouse and rat genomes side by side so I go to VISTA and select the Mouse Feb. 2006 genome as a base genome, then I figure the best place to start is at the beginning, so I select ch1:1-1000000 and click GO, I get an error saying "No such contig. or chromosome".  This is a bit confusing.  How can the mouse genome not have a chromosome 1?  So then I select ch2:1-1000000 and get the same error. Ch3 and 4 give the same results. So then I decided to try the Rat June 2003 and go with the default chr10:10000001-10100000, which then gives me some results.  I click on Browse alignment so I can see the coding (the Cs, As, Ts, and Gs).  I zoom in on a spot and when I put my mouse over the Rat code, it gives the number 10034062, when I cursor over the Mouse genome in the same spot, it gives the number 5312532.  I'm assuming these are the numbers for the position of that site within the chromosome.  So, (if that's the case) it's not showing me the Rat and Mouse genomes, side by side - starting at position 10000001 and ending at position 10100000.  If it was, they'd both give the number 10034062 - wouldn't they?
So, like I said, I'm not sure what I'm looking at and I'm not sure the correct way to use the site, but it doesn't appear to be giving me what I was looking for.  So, if you have something you want me to see, you'll have to specifically tell me what it is I'm looking at and how it reflects on my hypothesis.
Posted by: Daniel Smith on Oct. 16 2007,18:53

Quote (mitschlag @ Oct. 13 2007,18:22)
 
Quote (Daniel Smith @ Oct. 13 2007,13:53)
     
Quote (mitschlag @ Oct. 10 2007,12:47)
       
Quote (Daniel Smith @ Oct. 10 2007,02:30)
The results that would falsify my hypothesis would be if the coding sequences showed evolutionary constraint while the non-coding sequences didn't.
---------------------QUOTE-------------------

There's a fair amount of evidence showing that (contrary to expectation) non-coding sequences have fewer base changes than coding sequences, see, for example:
< http://www.biomedcentral.com/1471-2148/7/66 >
         

---------------------QUOTE-------------------
The primary result is that the mean rate of intergenic nucleotide substitution is two-thirds that of the synonymous coding data, with an absolute rate estimated to be 1.05 × 10-8 substitutions per site per year. This result holds with alternative nucleotide models (see Methods), and thus does not appear to be solely an issue of estimation procedures.

Slower rates in non-coding regions relative to synonymous sites are becoming a surprisingly frequent observation. For example, a recent study of Drosophila demonstrated that non-coding DNA evolves considerably slower than synonymous sites in terms of both divergence between species and polymorphism within species [16]. By comparing studies, one can also make the case that pseudogenes [32,33] and introns [34,35] evolve more slowly than synonymous sites in apes and other mammals [13,36-38]. Studies of mammalian intergenic regions have also found slower rates than synonymous sites [35,39,40]. Although most of these studies encompass only a handful of genes, an overall picture of relatively slow non-coding rates is emerging.
---------------------QUOTE-------------------


What do you make of that?
---------------------QUOTE-------------------


If this is true, then it would be a confirmation of my hypothesis with better than expected results.
---------------------QUOTE-------------------


It's true, all right, but it doesn't confirm your hypothesis.

To learn why, read the cited paper.  Hint: TE=transposable element.

(Sorry that I won't be able to participate in this discussion for the next two weeks due to travel in arcane regions.  In the meantime, I want to commend DS for  his courteous and patient responses to the many challenges that have been addressed to him.)
---------------------QUOTE-------------------


I read the cited paper.  It was very interesting - a bit over my head - but interesting nonetheless.
Your suggestion to read up on transposable elements was very fruitful as well as now these have piqued my interest.  I, of course, don't believe these to be randomly generated or to be degenerate copies of working genes.  I think they are more likely functional switches for some as yet undefined purpose.  I'm going to read more about them.
Oh and thanks for the commendation.  I appreciate a good civil discussion.  Unfortunately, when things get hostile, I have a tendency to get my guard up and push back a little harder than I have the right to.  Thanks for putting up with that as well.
Posted by: Daniel Smith on Oct. 16 2007,18:55

Quote (swbarnes2 @ Oct. 16 2007,14:34)


---------------------QUOTE-------------------
Only if it develops the same exact frame shift
---------------------QUOTE-------------------



Okay, so let's get this straight.

Do you agree that the ability to resist antibiotics is "beneficial"?

If so, you then predict that if 50 labs all over the country screen put every post-doc and lab tech they had to work screening plates for 3 months to find resistant mutants, they will ALL find the exact same mutation?

What if I'm screening for a mutation that cripples a certain pathway, and when I find a colony with the mutation I want, I will keep it and cultivate it for the next 20 years, and all the other ones just get incinerated.

Doesn't that make that mutation beneficial?  You certainly can't claim that its bearers fare worse in their environment than the wild-type kind.
---------------------QUOTE-------------------


I made a specific prediction.  Why do you want me to modify it to fit your scenario?
Posted by: swbarnes2 on Oct. 16 2007,19:29



---------------------QUOTE-------------------
I made a specific prediction.  Why do you want me to modify it to fit your scenario?
---------------------QUOTE-------------------



If your hypothesis is to be of any value, it has to be applicable to more than just one organism and one survival challange, surely you see that.

So, 50 labs, 5 post-docs and techs a piece, selecting for resistance to a particular antibiotic, for 3 months.

Do you predict that all the resistant strains found will carry the exact same resistance-granting mutation?
Posted by: JAM on Oct. 16 2007,21:44

Quote (Daniel Smith @ Oct. 16 2007,18:44)
   
Quote (JAM @ Oct. 16 2007,15:07)
What does your hypothesis predict if a different bacterial species is selected on nylon?
---------------------QUOTE-------------------


I've already made my prediction, why are asking me to make another one?
---------------------QUOTE-------------------


Because this has already been done!
 

---------------------QUOTE-------------------


---------------------QUOTE-------------------
1) Will multiple selections give the same result, and/or
2) Will the enzymes that evolved be the orthologs of the ones that evolved in Achromobacter?

---------------------QUOTE-------------------


My prediction was that exactly the same frame shift will occur - so I'm guessing it will be #1.
---------------------QUOTE-------------------


Wrong! Completely different, nonhomologous gene. Would you like to see the data?          
 

---------------------QUOTE-------------------
 

---------------------QUOTE-------------------
P.S. Did you check out the mouse vs. rat sequences yet?
---------------------QUOTE-------------------


I've been there several times.  Let me give you a blow by blow of my most recent visit:
I want to see the mouse and rat genomes side by side so I go to VISTA and select the Mouse Feb. 2006 genome as a base genome, then I figure the best place to start is at the beginning,...
---------------------QUOTE-------------------


Probably not. There are repeats, called telomeres, at the ends.
     

---------------------QUOTE-------------------
so I select ch1:1-1000000 and click GO, I get an error saying "No such contig. or chromosome".  This is a bit confusing.  How can the mouse genome not have a chromosome 1?
---------------------QUOTE-------------------


There's probably no contig for that region. The repeats make it complicated.
     

---------------------QUOTE-------------------
So then I select ch2:1-1000000 and get the same error. Ch3 and 4 give the same results. So then I decided to try the Rat June 2003 and go with the default chr10:10000001-10100000, which then gives me some results.
---------------------QUOTE-------------------


Yes, because you're in the middle, away from the junk at the ends that you thought would be conserved.
     

---------------------QUOTE-------------------
I click on Browse alignment so I can see the coding (the Cs, As, Ts, and Gs).  I zoom in on a spot and when I put my mouse over the Rat code, it gives the number 10034062, when I cursor over the Mouse genome in the same spot, it gives the number 5312532.  I'm assuming these are the numbers for the position of that site within the chromosome.
---------------------QUOTE-------------------


Correct, but it's not the same chromosome number. Why do you think that I tried to explain synteny to you?
     

---------------------QUOTE-------------------
So, (if that's the case) it's not showing me the Rat and Mouse genomes, side by side - starting at position 10000001 and ending at position 10100000.  If it was, they'd both give the number 10034062 - wouldn't they?
---------------------QUOTE-------------------


No, because contra your hypothesis, they aren't colinear. The autosomes are numbered according to their length, not their content. In fact, the place in which you were looking on rat chr10 has been inverted, and lines up with a bit of mouse chromosome 16, as VISTA tells you. These relationships are illustrated here:
< http://www.softberry.com/synt_pl....chr_2=* >
and in a different way, as well as conversely, here:
< http://www.informatics.jax.org/reports/homologymap/mouse_rat.shtml >
     

---------------------QUOTE-------------------
So, like I said, I'm not sure what I'm looking at and I'm not sure the correct way to use the site, but it doesn't appear to be giving me what I was looking for.
---------------------QUOTE-------------------


Since your hypothesis is incorrect, what you're looking for doesn't exist. Rat chromosome 10 doesn't align with mouse chromosome 1, it aligns with chunks of mouse chromosomes 16, 17, and 11. Those represent translocations and inversions from the past. Therefore, none of those breakpoints have been conserved, and your hypothesis is incorrect. But all you had to do was look at the graph to see that between rat and mouse, there are big regions of no conservation between the pink lumps that are 80-100% conserved.
   

---------------------QUOTE-------------------
So, if you have something you want me to see, you'll have to specifically tell me what it is I'm looking at and how it reflects on my hypothesis.
---------------------QUOTE-------------------


Why are there gaps between the pink lumps that are the conserved sequences when we align orthologous sequences from two species within the same lineage?
Posted by: Daniel Smith on Oct. 17 2007,18:31

Quote (JAM @ Oct. 16 2007,21:44)
   
Quote (Daniel Smith @ Oct. 16 2007,18:44)
My prediction was that exactly the same frame shift will occur - so I'm guessing it will be #1.
---------------------QUOTE-------------------


Wrong! Completely different, nonhomologous gene. Would you like to see the data?

---------------------QUOTE-------------------

Yes, I would be interested in seeing that.      

---------------------QUOTE-------------------
         
     

---------------------QUOTE-------------------
     

---------------------QUOTE-------------------
P.S. Did you check out the mouse vs. rat sequences yet?
---------------------QUOTE-------------------


I've been there several times.  Let me give you a blow by blow of my most recent visit:
I want to see the mouse and rat genomes side by side so I go to VISTA and select the Mouse Feb. 2006 genome as a base genome, then I figure the best place to start is at the beginning,...
---------------------QUOTE-------------------


Probably not. There are repeats, called telomeres, at the ends.
---------------------QUOTE-------------------

I'd like to see those - just for my own curiosity.      

---------------------QUOTE-------------------
 
         

---------------------QUOTE-------------------
so I select ch1:1-1000000 and click GO, I get an error saying "No such contig. or chromosome".  This is a bit confusing.  How can the mouse genome not have a chromosome 1?
---------------------QUOTE-------------------


There's probably no contig for that region. The repeats make it complicated.
---------------------QUOTE-------------------

What is "contig"?      

---------------------QUOTE-------------------
 
         

---------------------QUOTE-------------------
So then I select ch2:1-1000000 and get the same error. Ch3 and 4 give the same results. So then I decided to try the Rat June 2003 and go with the default chr10:10000001-10100000, which then gives me some results.
---------------------QUOTE-------------------


Yes, because you're in the middle, away from the junk at the ends that you thought would be conserved.
         

---------------------QUOTE-------------------
I click on Browse alignment so I can see the coding (the Cs, As, Ts, and Gs).  I zoom in on a spot and when I put my mouse over the Rat code, it gives the number 10034062, when I cursor over the Mouse genome in the same spot, it gives the number 5312532.  I'm assuming these are the numbers for the position of that site within the chromosome.
---------------------QUOTE-------------------


Correct, but it's not the same chromosome number. Why do you think that I tried to explain synteny to you?
         

---------------------QUOTE-------------------
So, (if that's the case) it's not showing me the Rat and Mouse genomes, side by side - starting at position 10000001 and ending at position 10100000.  If it was, they'd both give the number 10034062 - wouldn't they?
---------------------QUOTE-------------------


No, because contra your hypothesis, they aren't colinear. The autosomes are numbered according to their length, not their content. In fact, the place in which you were looking on rat chr10 has been inverted, and lines up with a bit of mouse chromosome 16, as VISTA tells you. These relationships are illustrated here:
< http://www.softberry.com/synt_pl....chr_2=* >
and in a different way, as well as conversely, here:
< http://www.informatics.jax.org/reports/homologymap/mouse_rat.shtml >
         

---------------------QUOTE-------------------
So, like I said, I'm not sure what I'm looking at and I'm not sure the correct way to use the site, but it doesn't appear to be giving me what I was looking for.
---------------------QUOTE-------------------


Since your hypothesis is incorrect, what you're looking for doesn't exist. Rat chromosome 10 doesn't align with mouse chromosome 1, it aligns with chunks of mouse chromosomes 16, 17, and 11. Those represent translocations and inversions from the past. Therefore, none of those breakpoints have been conserved, and your hypothesis is incorrect. But all you had to do was look at the graph to see that between rat and mouse, there are big regions of no conservation between the pink lumps that are 80-100% conserved.
         

---------------------QUOTE-------------------
So, if you have something you want me to see, you'll have to specifically tell me what it is I'm looking at and how it reflects on my hypothesis.
---------------------QUOTE-------------------


Why are there gaps between the pink lumps that are the conserved sequences when we align orthologous sequences from two species within the same lineage?
---------------------QUOTE-------------------


Thank you for the explanations and the data.  The second page you cited really helped me understand what I was looking at (and not understanding) in the VISTA program.
Let me ask you this:
The rat genome appears to be a re-arrangement of the mouse genome, so how do we know that the "junk" (as you call it) wasn't rearranged in similar manner?  
Does the VISTA program check for this?  
Or does it only compare genes?
Posted by: Daniel Smith on Oct. 17 2007,18:37

Quote (swbarnes2 @ Oct. 16 2007,19:29)
 

---------------------QUOTE-------------------
I made a specific prediction.  Why do you want me to modify it to fit your scenario?
---------------------QUOTE-------------------



If your hypothesis is to be of any value, it has to be applicable to more than just one organism and one survival challange, surely you see that.

So, 50 labs, 5 post-docs and techs a piece, selecting for resistance to a particular antibiotic, for 3 months.

Do you predict that all the resistant strains found will carry the exact same resistance-granting mutation?
---------------------QUOTE-------------------


No I don't.  Mainly because I think bacteria are designed to mutate and evolve quickly - so I'd predict a number of different mutations in that scenario.

Now, if these 50 labs had all started with the same pre-nylon-eating bacteria and subjected all of them to a nylon environment, I'd be surprised if a significant percentage of them didn't develop the same frame shift.

I'm interested to see JAMs data about the nylon though.
Posted by: JAM on Oct. 17 2007,20:35

Quote (Daniel Smith @ Oct. 17 2007,18:31)
Yes, I would be interested in seeing that.      
---------------------QUOTE-------------------

         
< http://jb.asm.org/cgi/reprint/174/24/7948?view=long&pmid=1459943 >

I apologize because I garbled it; unfortunately, it's more bad news for your hypothesis.

It turns out that it was the same bug, Flavobacterium. One of the nylonase genes was deleted, and selection produced a completely new one.
 

---------------------QUOTE-------------------
Thank you for the explanations and the data.  The second page you cited really helped me understand what I was looking at (and not understanding) in the VISTA program.
---------------------QUOTE-------------------


You're most welcome. How's your hypothesis?


---------------------QUOTE-------------------
The rat genome appears to be a re-arrangement of the mouse genome, so how do we know that the "junk" (as you call it) wasn't rearranged in similar manner?
---------------------QUOTE-------------------


It clearly was--it just wasn't conserved, as is clearly shown by the spaces between the pink humps of conserved sequences. Why are you not acknowledging my point about all the breakpoint sequences?
 

---------------------QUOTE-------------------
Does the VISTA program check for this?  
---------------------QUOTE-------------------


Specifically? No, but it answers your question clearly. The spaces between conserved sequences are mostly still there, but they aren't conserved. Do you understand that the spaces in between the conserved pink humps mean that your hypothesis is DOA?


---------------------QUOTE-------------------
Or does it only compare genes?
---------------------QUOTE-------------------


It compares genomes. Genes are only a part of it.
Posted by: JAM on Oct. 17 2007,21:03

Quote (Daniel Smith @ Oct. 17 2007,18:31)
I'd like to see those - just for my own curiosity.  
---------------------QUOTE-------------------

 
< http://en.wikipedia.org/wiki/Telomere >
< http://learn.genetics.utah.edu/features/telomeres/ >
< http://users.rcn.com/jkimbal....es.html >
 

---------------------QUOTE-------------------
What is "contig"?      
---------------------QUOTE-------------------


An assembly of overlapping sequences. Sometimes it's impossible to get overlap.


---------------------QUOTE-------------------
The rat genome appears to be a re-arrangement of the mouse genome,...
---------------------QUOTE-------------------


The human genome just has many more (relative) rearrangements, as one would predict from evolutionary theory:

< http://www.informatics.jax.org/reports/homologymap/mouse_human.shtml >

Are you seeing anything in what I've shown you that is consistent with your hypothesis?
Posted by: Steverino on Oct. 18 2007,06:34

"No I don't.  Mainly because I think bacteria are designed to mutate and evolve quickly - so I'd predict a number of different mutations in that scenario."

You have no proof, evidence or data that the appearance of design, proves design other than you desire to have it be so.

Whenever there is no current explanation for how something happened you play the design card.  I am glad the majority of science is not as lazy or stupid as you.
Posted by: oldmanintheskydidntdoit on Oct. 18 2007,06:40

Quote (Daniel Smith @ Oct. 17 2007,18:37)
Mainly because I think bacteria are designed to mutate and evolve quickly - so I'd predict a number of different mutations in that scenario.
---------------------QUOTE-------------------


To what purpose?

EDIT: E.G I designed a car so I could get around quickly.
I designed a phone so I can stay in touch.
I designed my home so I can live nice.

I designed some bacteria to mutate and evolve quickly so I can....
Posted by: Richard Simons on Oct. 18 2007,08:35

Quote (oldmanintheskydidntdoit @ Oct. 18 2007,06:40)

E.G I designed a car so I could get around quickly.
I designed a phone so I can stay in touch.
I designed my home so I can live nice.

---------------------QUOTE-------------------


That's only partly true. After they were designed, someone had to build them.

Who did (does?) the Great Designer co-opt to do the building, and how did they do it?

Thinking about it more, I suppose the Designer sounds better than the Fabricator.

(edited to correct grammar)
Posted by: oldmanintheskydidntdoit on Oct. 18 2007,08:54

Quote (Richard Simons @ Oct. 18 2007,08:35)
Quote (oldmanintheskydidntdoit @ Oct. 18 2007,06:40)

E.G I designed a car so I could get around quickly.
I designed a phone so I can stay in touch.
I designed my home so I can live nice.

---------------------QUOTE-------------------


That's only partly true. After they were designed, someone had to build them.

Who did (does?) the Great Designer co-opt to do the building, and how did they do it?

Thinking about it more, I suppose the Designer sounds better than the Fabricator.

(edited to correct grammar)
---------------------QUOTE-------------------


Ah, interesting.

Did the designer implement his own designs or did it sub-contract them out?

ID is getting more like Hitchhikers every day :)
Posted by: swbarnes2 on Oct. 18 2007,13:36



---------------------QUOTE-------------------
No I don't.  Mainly because I think bacteria are designed to mutate and evolve quickly - so I'd predict a number of different mutations in that scenario.
---------------------QUOTE-------------------



Don't you understand that when you are trying to prove that bacteria are designed, you can't take that as a given in that proof?

 

---------------------QUOTE-------------------
Now, if these 50 labs had all started with the same pre-nylon-eating bacteria and subjected all of them to a nylon environment, I'd be surprised if a significant percentage of them didn't develop the same frame shift.
---------------------QUOTE-------------------



Oh no.  This is just transparently dishonest.  You previously claimed that you predicted:

 

---------------------QUOTE-------------------
Therefore, I predict that anytime Acromobacter guttatus Sp. K172 is subjected to an environment where it must consume nylon to survive, the same frame shift will occur, resulting in Flavobacterium Sp. KI72.
---------------------QUOTE-------------------



Believe me, we all understand.  Creationists are constantly moving the goalposts.  It's inevitable for them if they want to pretend to be reasonable.  It's totally dishonest, but that's inevitable too.

But to change the goalposts within, what, two days and one page of posts?  That's dishonest and sloppy.  



---------------------QUOTE-------------------
I'm interested to see JAMs data about the nylon though.
---------------------QUOTE-------------------



It's not his data.  It's publicly available.  Surely the abstract, if not the whole paper, is available online.

Why can't you look at the data yourself?

Why didn't you look for the data before you made your claim?

 

---------------------QUOTE-------------------
The rat genome appears to be a re-arrangement of the mouse genome,
---------------------QUOTE-------------------



No, it doesn't appear to be that way.

There was a common ancestor to both mice and rats.  Then those two lineages started evolving separate from each other.  Both lineages started getting both point mutations, and larger chromosomal rearrangments, inversions, duplications, etc.

There are still swaths in both genomes where you can see the orignal sequences much as they were in the common ancestor.  But there are also parts where the mosue genome is unique, and the rat genome is unique.

But to say the the two genomes are the same, but just rearranged is wrong.

You would know that if you looked at the data before deciding what your conclusions were.

 

---------------------QUOTE-------------------
so how do we know that the "junk" (as you call it) wasn't rearranged in similar manner?  

---------------------QUOTE-------------------



Well, why can't you do the BLASTs that would prove this?

Why does everyone else have to do the work to show that your imaginings aren't real?

Honestly, who do you think is responsible for the accuracy of your biology claims?

a) your mommy
b) evil liberals
c) strangers on a message board
d) you

We all think the answer is d.  We all think that if you make a claim about what the geomics of a mouse look like, that it is your responsibility to show that this is the case.

That some people are being nice enough to educate your ignorant self doesn't change that fact.

If you disagree, if you really think that you are not responsible for the truthfulness of your claims, can you explain a bit why you believe this?
Posted by: blipey on Oct. 18 2007,14:01



---------------------QUOTE-------------------
It's not his data.  It's publicly available.  Surely the abstract, if not the whole paper, is available online.

Why can't you look at the data yourself?
---------------------QUOTE-------------------



A. Not particularly interested in doing so?
B. No recent experience looking for "data" so I don't know where to start?
C. Data?  What's that?
Posted by: Henry J on Oct. 18 2007,22:05



---------------------QUOTE-------------------
C. Data?  What's that?
---------------------QUOTE-------------------



The android on Star Trek: TNG.

Henry
Posted by: Daniel Smith on Oct. 19 2007,18:14

Quote (JAM @ Oct. 17 2007,20:35)
       
Quote (Daniel Smith @ Oct. 17 2007,18:31)
Yes, I would be interested in seeing that.      
---------------------QUOTE-------------------

         
< http://jb.asm.org/cgi/reprint/174/24/7948?view=long&pmid=1459943 >

I apologize because I garbled it; unfortunately, it's more bad news for your hypothesis.

It turns out that it was the same bug, Flavobacterium. One of the nylonase genes was deleted, and selection produced a completely new one.
---------------------QUOTE-------------------

While these results are interesting, they don't really meet the criteria of my prediction since they started with the already frame-shifted bacteria.  If you remember, my prediction involved the pre-frame-shifted bacteria Acromobacter guttatus.  My prediction was that if that bacteria was subjected to nylon, the same frame shift would occur.
This study appears to involve a mutation of the Flavobacterium sp. strain KI72 - which already has the plasmid pOAD2 that was the result of the original frame shift.
DISCLAIMER - I'm not calling you a liar or anything - I'm just hoping you can appreciate the difference from my perspective. - END DISCLAIMER
       

---------------------QUOTE-------------------

           

---------------------QUOTE-------------------
Thank you for the explanations and the data.  The second page you cited really helped me understand what I was looking at (and not understanding) in the VISTA program.
---------------------QUOTE-------------------


You're most welcome. How's your hypothesis?
---------------------QUOTE-------------------


It's not in as bad of shape as you think it is.        

---------------------QUOTE-------------------

         

---------------------QUOTE-------------------
The rat genome appears to be a re-arrangement of the mouse genome, so how do we know that the "junk" (as you call it) wasn't rearranged in similar manner?
---------------------QUOTE-------------------


It clearly was--it just wasn't conserved, as is clearly shown by the spaces between the pink humps of conserved sequences. Why are you not acknowledging my point about all the breakpoint sequences?
---------------------QUOTE-------------------


In order to acknowledge that you are correct, I must first determine what exactly you're talking about, (no small task for me!), then I have to know what the parameters of VISTA are (does it ignore the non-coding sites? etc.), and finally I have to interpret these results in the light of designed descent.  If, after careful examination, it appears your evidence falsifies my hypothesis, I'll surely admit it.  I am not going to just throw up my hands and give up because you say so though!      

---------------------QUOTE-------------------

         

---------------------QUOTE-------------------
Does the VISTA program check for this?  
---------------------QUOTE-------------------


Specifically? No, but it answers your question clearly. The spaces between conserved sequences are mostly still there, but they aren't conserved. Do you understand that the spaces in between the conserved pink humps mean that your hypothesis is DOA?
---------------------QUOTE-------------------

No, I don't understand that - because there's no data showing me what those spaces represent.  The only thing I have to go on is your insistence that they falsify my hypothesis.  

What I really need is a program that will...
a.) allow me to select any region (coding or non-coding) of the mouse genome and
b.) search the rat genome for a closely matching sequence.
That's what I'd like to do.  Is there such a program?
       

---------------------QUOTE-------------------

         

---------------------QUOTE-------------------
Or does it only compare genes?
---------------------QUOTE-------------------


It compares genomes. Genes are only a part of it.
---------------------QUOTE-------------------


Obviously I have much more research to do, but I find it extremely hard to believe that you can take a working genome, cut it into pieces, shuffle it around, and come up with another working genome.  It defies credulity.  It's like taking a book, cutting up all the pages, shuffling them around and coming up with an equally coherent story.
I know you'll probably say that millions of years+selection can accomplish this, but where's the data to support that assumption?
Posted by: Daniel Smith on Oct. 19 2007,18:30

Quote (JAM @ Oct. 17 2007,21:03)
 
Quote (Daniel Smith @ Oct. 17 2007,18:31)
I'd like to see those - just for my own curiosity.  
---------------------QUOTE-------------------

 
< http://en.wikipedia.org/wiki/Telomere >
< http://learn.genetics.utah.edu/features/telomeres/ >
< http://users.rcn.com/jkimbal....es.html >

---------------------QUOTE-------------------

Thank you.  Once again I'm amazed at the forethought of God!  Telomeres accomplish two things: they help to conserve genetic information while still guaranteeing that the aging process will eventually take its toll on all of us.  These might seem like contradictory functions to you, but they make perfect sense from my perspective.
   

---------------------QUOTE-------------------
   

---------------------QUOTE-------------------
What is "contig"?      
---------------------QUOTE-------------------


An assembly of overlapping sequences. Sometimes it's impossible to get overlap.
---------------------QUOTE-------------------


No doubt.  The fact that there are such things as overlapping sequences makes me wonder at the mind of God.  

---------------------QUOTE-------------------

   

---------------------QUOTE-------------------
The rat genome appears to be a re-arrangement of the mouse genome,...
---------------------QUOTE-------------------


The human genome just has many more (relative) rearrangements, as one would predict from evolutionary theory:

< http://www.informatics.jax.org/reports/homologymap/mouse_human.shtml >

Are you seeing anything in what I've shown you that is consistent with your hypothesis?
---------------------QUOTE-------------------


Yes I am.  I know that's hard for you to believe, but the more mixed up these genomes are relative to each other, the more confident I am of a designed mechanism for that rearrangement.
Posted by: Daniel Smith on Oct. 19 2007,18:34

Quote (swbarnes2 @ Oct. 18 2007,13:36)


     

---------------------QUOTE-------------------
Now, if these 50 labs had all started with the same pre-nylon-eating bacteria and subjected all of them to a nylon environment, I'd be surprised if a significant percentage of them didn't develop the same frame shift.
---------------------QUOTE-------------------



Oh no.  This is just transparently dishonest.  You previously claimed that you predicted:

     

---------------------QUOTE-------------------
Therefore, I predict that anytime Acromobacter guttatus Sp. K172 is subjected to an environment where it must consume nylon to survive, the same frame shift will occur, resulting in Flavobacterium Sp. KI72.
---------------------QUOTE-------------------



Believe me, we all understand.  Creationists are constantly moving the goalposts.  It's inevitable for them if they want to pretend to be reasonable.  It's totally dishonest, but that's inevitable too.

But to change the goalposts within, what, two days and one page of posts?  That's dishonest and sloppy.  

---------------------QUOTE-------------------


What's the difference between those two predictions?
Posted by: Daniel Smith on Oct. 19 2007,18:54

Quote (swbarnes2 @ Oct. 18 2007,13:36)
   

---------------------QUOTE-------------------
so how do we know that the "junk" (as you call it) wasn't rearranged in similar manner?  

---------------------QUOTE-------------------



Well, why can't you do the BLASTs that would prove this?
---------------------QUOTE-------------------


"BLAST stands for Basic Local Alignment Search Tool. It is used to compare a novel sequence with those contained in nucleotide and protein databases by aligning the novel sequence with previously characterised genes." (emphasis added) < (link) >

I'm not interested in comparing genes.
Posted by: Henry J on Oct. 19 2007,22:06



---------------------QUOTE-------------------
but I find it extremely hard to believe that you can take a working genome, cut it into pieces, shuffle it around, and come up with another working genome.  It defies credulity.
---------------------QUOTE-------------------



Why? Ours is already cut up into forty something pieces.

Henry
Posted by: JAM on Oct. 20 2007,01:00

Quote (Daniel Smith @ Oct. 19 2007,18:14)
 
Quote (JAM @ Oct. 17 2007,20:35)
         
Quote (Daniel Smith @ Oct. 17 2007,18:31)
Yes, I would be interested in seeing that.      
---------------------QUOTE-------------------

         
< http://jb.asm.org/cgi/reprint/174/24/7948?view=long&pmid=1459943 >

I apologize because I garbled it; unfortunately, it's more bad news for your hypothesis.

It turns out that it was the same bug, Flavobacterium. One of the nylonase genes was deleted, and selection produced a completely new one.
---------------------QUOTE-------------------

While these results are interesting, they don't really meet the criteria of my prediction since they started with the already frame-shifted bacteria.  If you remember, my prediction involved the pre-frame-shifted bacteria Acromobacter guttatus.
---------------------QUOTE-------------------


First, if you'll do me the courtesy of rereading what I wrote, I noted that it is still bad news for your HYPOTHESIS, which is an accurate assessment. Your hypothesis makes many testable predictions, and your hypothesis is global, not just about one species.

Second, frameshifts happen to individual genes. The term "frame-shifted bacteria" is gibberish.

 

---------------------QUOTE-------------------
My prediction was that if that bacteria was subjected to nylon, the same frame shift would occur.
---------------------QUOTE-------------------


But your hypothesis makes a very clear prediction in this case, too. Moreover, your prediction was based on a false assumption, because more than one enzyme is involved. In this case, we started without one of the two, and got a completely different new one from a different origin to replace its function. This falsifies your hypothesis.

In case you've forgotten, here's your hypothesis, improperly stated as a prediction:


---------------------QUOTE-------------------
It's my prediction that random mutations are only neutral or deleterious - never advantageous.
---------------------QUOTE-------------------


Posted by: Daniel Smith on Oct. 20 2007,11:43

Quote (JAM @ Oct. 20 2007,01:00)
 
Quote (Daniel Smith @ Oct. 19 2007,18:14)
   
Quote (JAM @ Oct. 17 2007,20:35)
             
Quote (Daniel Smith @ Oct. 17 2007,18:31)
Yes, I would be interested in seeing that.      
---------------------QUOTE-------------------

         
< http://jb.asm.org/cgi/reprint/174/24/7948?view=long&pmid=1459943 >

I apologize because I garbled it; unfortunately, it's more bad news for your hypothesis.

It turns out that it was the same bug, Flavobacterium. One of the nylonase genes was deleted, and selection produced a completely new one.
---------------------QUOTE-------------------

While these results are interesting, they don't really meet the criteria of my prediction since they started with the already frame-shifted bacteria.  If you remember, my prediction involved the pre-frame-shifted bacteria Acromobacter guttatus.
---------------------QUOTE-------------------


First, if you'll do me the courtesy of rereading what I wrote, I noted that it is still bad news for your HYPOTHESIS, which is an accurate assessment. Your hypothesis makes many testable predictions, and your hypothesis is global, not just about one species.
---------------------QUOTE-------------------

What exactly are these predictions?

---------------------QUOTE-------------------


Second, frameshifts happen to individual genes. The term "frame-shifted bacteria" is gibberish.

   

---------------------QUOTE-------------------
My prediction was that if that bacteria was subjected to nylon, the same frame shift would occur.
---------------------QUOTE-------------------


But your hypothesis makes a very clear prediction in this case, too.
---------------------QUOTE-------------------

Which is?

---------------------QUOTE-------------------
Moreover, your prediction was based on a false assumption, because more than one enzyme is involved.
---------------------QUOTE-------------------

Where specifically did I make this "false assumption"?

---------------------QUOTE-------------------
In this case, we started without one of the two, and got a completely different new one from a different origin to replace its function. This falsifies your hypothesis.
---------------------QUOTE-------------------

How does this falsify my hypothesis?

---------------------QUOTE-------------------


In case you've forgotten, here's your hypothesis, improperly stated as a prediction:
 

---------------------QUOTE-------------------
It's my prediction that random mutations are only neutral or deleterious - never advantageous.
---------------------QUOTE-------------------


---------------------QUOTE-------------------


How do you know the mutation was random?
Posted by: JAM on Oct. 20 2007,13:24

Quote (Daniel Smith @ Oct. 20 2007,11:43)
Where specifically did I make this "false assumption"?    
---------------------QUOTE-------------------


When you assumed that only one gene and one mutation was involved.


---------------------QUOTE-------------------


---------------------QUOTE-------------------
 In this case, we started without one of the two, and got a completely different new one from a different origin to replace its function. This falsifies your hypothesis.
---------------------QUOTE-------------------

How does this falsify my hypothesis?  
---------------------QUOTE-------------------


Because your hypothesis predicts that the same mutation will occur in the same gene. It's not limited to frameshifts or a single species. Your hypothesis is about living things in general.


---------------------QUOTE-------------------
How do you know the mutation was random?
---------------------QUOTE-------------------


Because it was different than the initial one, and in an entirely different gene. Your hypothesis predicts that the same mutations will occur every time. You can't honestly weasel out of it by claiming that it only applies to one species and one gene.
Posted by: JAM on Oct. 20 2007,13:25

Quote (Daniel Smith @ Oct. 19 2007,18:34)
What's the difference between those two predictions?
---------------------QUOTE-------------------


One says that the same thing will happen EVERY time, while the other says that the same thing will happen SOME of the time.
Posted by: JAM on Oct. 20 2007,13:27

Quote (Daniel Smith @ Oct. 19 2007,18:54)
I'm not interested in comparing genes.
---------------------QUOTE-------------------


BLAST works for the sequences between genes, too, so your evasion doesn't work. That explanation is probably a holdover from the olden days, in which people were more interested in studying individual genes than they were in genomes. Most people still are more interested in the former, btw, you just wouldn't know it from the lay press.
Posted by: JAM on Oct. 20 2007,14:14

Quote (Daniel Smith @ Oct. 19 2007,18:14)
 
                   

---------------------QUOTE-------------------

                       

---------------------QUOTE-------------------
Thank you for the explanations and the data.  The second page you cited really helped me understand what I was looking at (and not understanding) in the VISTA program.
---------------------QUOTE-------------------


You're most welcome. How's your hypothesis?
---------------------QUOTE-------------------


It's not in as bad of shape as you think it is.
---------------------QUOTE-------------------


Interesting. How could you possibly know, since you claim below that you still don't understand what the VISTA graphs mean?          
       

---------------------QUOTE-------------------
     

---------------------QUOTE-------------------
     

---------------------QUOTE-------------------
The rat genome appears to be a re-arrangement of the mouse genome, so how do we know that the "junk" (as you call it) wasn't rearranged in similar manner?
---------------------QUOTE-------------------


It clearly was--it just wasn't conserved, as is clearly shown by the spaces between the pink humps of conserved sequences. Why are you not acknowledging my point about all the breakpoint sequences?
---------------------QUOTE-------------------


In order to acknowledge that you are correct, I must first determine what exactly you're talking about, (no small task for me!),
---------------------QUOTE-------------------


Then how could you honestly claim that your hypothesis is not in bad shape, Daniel? I don't see how you can flip from certainty to ignorance and retain a shred of credibility.
       

---------------------QUOTE-------------------
then I have to know what the parameters of VISTA are (does it ignore the non-coding sites? etc.),
---------------------QUOTE-------------------


No, it does not ignore non-coding sites. In fact, you were looking at almost entirely non-coding sequences. How's your hypothesis doing?
       

---------------------QUOTE-------------------
...and finally I have to interpret these results in the light of designed descent.
---------------------QUOTE-------------------


No, Daniel, that's utterly dishonest. You make your prediction BEFORE you interpret the data. Remember, you're trying to prevent yourself from fooling yourself.
       

---------------------QUOTE-------------------
If, after careful examination, it appears your evidence falsifies my hypothesis, I'll surely admit it.
---------------------QUOTE-------------------


I don't believe you. Every prediction, explicit and implicit, from your hypotheses has been shown to be wrong, but you claim that it all supports your position.
   

---------------------QUOTE-------------------
   

---------------------QUOTE-------------------
Specifically? No, but it answers your question clearly. The spaces between conserved sequences are mostly still there, but they aren't conserved. Do you understand that the spaces in between the conserved pink humps mean that your hypothesis is DOA?
---------------------QUOTE-------------------

No, I don't understand that - because there's no data showing me what those spaces represent.
---------------------QUOTE-------------------


Yes, there are data--the sequences themselves come up in the browser. What were you thinking they represented?
       

---------------------QUOTE-------------------
The only thing I have to go on is your insistence that they falsify my hypothesis.
---------------------QUOTE-------------------


My only insistence is that you examine the evidence, which you are desperately trying to avoid. Is there some reason why you can't read and/or comprehend the legend in the lower left corner? 


---------------------QUOTE-------------------
What I really need is a program that will...
a.) allow me to select any region (coding or non-coding) of the mouse genome and
b.) search the rat genome for a closely matching sequence.
That's what I'd like to do.  Is there such a program?
---------------------QUOTE-------------------


Yes, VISTA. You're so afraid of what you'll find that you won't explore it. If you need spoonfeeding, here's a larger region:
< http://pipeline.lbl.gov/servlet....llbar=0 >

1) Switch "# rows:" to 1.
2) Read the legend at lower left. See the symbol for genes? This region has four genes: Mtap7, Bclaf1, 260016C23Rik (a putative gene), and Pde7b.
3) Note the color of Exons in the legend: dark blue. See how the exons (protein-coding regions) are within the genes? The exons also are represented on the gene arrows at the top. Exons include all protein-coding regions, but they contain other sequences, such as UTRs, which have function.
4) Look at the scale for the Y axis on the right. It represents % identity.
5) Bonus question: why doesn't the scale go below 50%?
6) Do you see that the exons are highly conserved?
7) Do you see that there is less conservation outside the exons?
7) Look at the mouse vs. rat graph. These species are within the same "lineage" as you defined the term. What do the spaces between the pink bumps represent in that graph?

If you'd like to browse, it's easiest to change chromosome number in the address bar. Here's a gene-rich region:

< http://pipeline.lbl.gov/servlet....llbar=0 >
 

---------------------QUOTE-------------------
Obviously I have much more research to do, but I find it extremely hard to believe that you can take a working genome, cut it into pieces, shuffle it around, and come up with another working genome.  It defies credulity. It's like taking a book, cutting up all the pages, shuffling them around and coming up with an equally coherent story.
---------------------QUOTE-------------------


That's the power of selection. There's no coherent design hypothesis that can explain it.
     

---------------------QUOTE-------------------
I know you'll probably say that millions of years+selection can accomplish this, but where's the data to support that assumption?
---------------------QUOTE-------------------


These *are* the data. There also are data from shorter time periods that, when extrapolated, are consistent with this.
Posted by: JAM on Oct. 20 2007,14:29

Quote (Daniel Smith @ Oct. 19 2007,18:30)
Thank you.  Once again I'm amazed at the forethought of God!
---------------------QUOTE-------------------


Umm...then why did you assume that no telomeres were present, that you could just go in at base pair 1 with VISTA?
 

---------------------QUOTE-------------------
Telomeres accomplish two things: they help to conserve genetic information while still guaranteeing that the aging process will eventually take its toll on all of us.  These might seem like contradictory functions to you, but they make perfect sense from my perspective.
---------------------QUOTE-------------------


Yet your perspective predicted that they didn't exist. Can you name a part of the aging process in which telomeres don't work normally?
 

---------------------QUOTE-------------------
 

---------------------QUOTE-------------------
 

---------------------QUOTE-------------------
What is "contig"?      
---------------------QUOTE-------------------


An assembly of overlapping sequences. Sometimes it's impossible to get overlap.
---------------------QUOTE-------------------


No doubt.  The fact that there are such things as overlapping sequences makes me wonder at the mind of God.
---------------------QUOTE-------------------


How do you figure? Contigs and overlapping sequences merely describe the assembly of sequences by humans.

You'll say anything to avoid testing your own hypotheses against the evidence, won't you?    

---------------------QUOTE-------------------
 

---------------------QUOTE-------------------
Are you seeing anything in what I've shown you that is consistent with your hypothesis?
---------------------QUOTE-------------------


Yes I am.  I know that's hard for you to believe, but the more mixed up these genomes are relative to each other, the more confident I am of a designed mechanism for that rearrangement.
---------------------QUOTE-------------------


How can you be confident when you've predicted the polar opposite in all these cases?
Posted by: Daniel Smith on Oct. 20 2007,18:35

From < Wikipedia >:


---------------------QUOTE-------------------
Recent evidence suggests that "junk DNA" may in fact be employed by proteins created from coding DNA. An experiment concerning the relationship between introns and coded proteins provided evidence for a theory that "junk DNA" is just as important as coding DNA. This experiment consisted of damaging a portion of noncoding DNA in a plant which resulted in a significant change in the leaf structure because structural proteins depended on information contained in introns.
---------------------QUOTE-------------------


Posted by: Daniel Smith on Oct. 20 2007,19:09

Quote (JAM @ Oct. 20 2007,14:14)

Yes, VISTA. You're so afraid of what you'll find that you won't explore it. If you need spoonfeeding, here's a larger region:
< http://pipeline.lbl.gov/servlet....llbar=0 >

1) Switch "# rows:" to 1.
2) Read the legend at lower left. See the symbol for genes? This region has four genes: Mtap7, Bclaf1, 260016C23Rik (a putative gene), and Pde7b.
3) Note the color of Exons in the legend: dark blue. See how the exons (protein-coding regions) are within the genes? The exons also are represented on the gene arrows at the top. Exons include all protein-coding regions, but they contain other sequences, such as UTRs, which have function.
4) Look at the scale for the Y axis on the right. It represents % identity.
5) Bonus question: why doesn't the scale go below 50%?
6) Do you see that the exons are highly conserved?
7) Do you see that there is less conservation outside the exons?
7) Look at the mouse vs. rat graph. These species are within the same "lineage" as you defined the term. What do the spaces between the pink bumps represent in that graph?

If you'd like to browse, it's easiest to change chromosome number in the address bar. Here's a gene-rich region:

< http://pipeline.lbl.gov/servlet....llbar=0 >

---------------------QUOTE-------------------


First, thanks for making it a bit clearer.
Second, if the protein coding regions are dark blue and UTRs are light blue, what are the pink (CNS) regions?
Are these non-coding?  
If so, why are they also so highly conserved between rat and mouse?
Like < this? >        

---------------------QUOTE-------------------


---------------------QUOTE-------------------
Obviously I have much more research to do, but I find it extremely hard to believe that you can take a working genome, cut it into pieces, shuffle it around, and come up with another working genome.  It defies credulity. It's like taking a book, cutting up all the pages, shuffling them around and coming up with an equally coherent story.
---------------------QUOTE-------------------


That's the power of selection. There's no coherent design hypothesis that can explain it.
---------------------QUOTE-------------------

Sure there is.  Every kid who ever rearranged someone else's book report to try to "put it in his own words" knows about it.

BTW, giving credit to "selection" without showing the steps that were selected for is only an assumption and is not grounded in the evidence.  

---------------------QUOTE-------------------

               

---------------------QUOTE-------------------
I know you'll probably say that millions of years+selection can accomplish this, but where's the data to support that assumption?
---------------------QUOTE-------------------


These *are* the data. There also are data from shorter time periods that, when extrapolated, are consistent with this.
---------------------QUOTE-------------------

Isn't that the classic case of using the thing that must be explained as an explanation?  I was told that was taboo around here.
Posted by: Daniel Smith on Oct. 20 2007,19:15

< Another example. >
In this one, the pink regions outside the coding areas, are more highly conserved between rat and mouse than the coding areas.
Posted by: Daniel Smith on Oct. 20 2007,19:18

Oops!  When I click on the links I just provided, they take you to the page JAM originally pointed me to - not the pages I created in VISTA.
I'll have to figure out how to get the correct URL.
Posted by: Daniel Smith on Oct. 20 2007,19:22

Try < this. >
Posted by: Daniel Smith on Oct. 20 2007,21:04

Found it!
CNS = conserved noncoding sequences.
So the pink areas in VISTA are confirmations of my hypothesis.
My, there are quite a lot of them when comparing the rat and mouse genomes!
Posted by: JAM on Oct. 20 2007,23:51

Quote (Daniel Smith @ Oct. 20 2007,18:35)
From < Wikipedia >:
 

---------------------QUOTE-------------------
Recent evidence suggests that "junk DNA" may in fact be employed by proteins created from coding DNA. An experiment concerning the relationship between introns and coded proteins provided evidence for a theory that "junk DNA" is just as important as coding DNA. This experiment consisted of damaging a portion of noncoding DNA in a plant which resulted in a significant change in the leaf structure because structural proteins depended on information contained in introns.
---------------------QUOTE-------------------


---------------------QUOTE-------------------


That passage is bullshit, Daniel. "Junk" DNA is in no way homogeneous, and real scientists don't classify introns as "junk."

The ID approach to "junk" DNA is profoundly dishonest; it ALWAYS depends on equivocating between a tiny fraction of junk and all of the junk.

Every time any IDer talks about it, that dishonesty is displayed. Are you being dishonest or gullible in this case?
Posted by: JAM on Oct. 20 2007,23:59

Quote (Daniel Smith @ Oct. 20 2007,21:04)
Found it!
CNS = conserved noncoding sequences.
So the pink areas in VISTA are confirmations of my hypothesis.
---------------------QUOTE-------------------


No, they are conserved noncoding sequences. Your hypothesis would only be confirmed if there weren't white areas between the pink areas, remember?


---------------------QUOTE-------------------
My, there are quite a lot of them when comparing the rat and mouse genomes!
---------------------QUOTE-------------------


Of course there are! But "quite a lot" of them doesn't fulfill your prediction that there wouldn't be any spaces (nonconserved noncoding sequences) between them at all!
Here's your prediction:
 

---------------------QUOTE-------------------
My prediction is that the coding and non-coding sequences (basically all sequences) will show an equal amount of evolutionary constraint.
---------------------QUOTE-------------------


A lot isn't all, Daniel. Your hypothesis is dead meat. A hefty chunk of noncoding sequences aren't conserved. Did you find any coding sequences that weren't conserved?
Posted by: JAM on Oct. 21 2007,00:11

Quote (Daniel Smith @ Oct. 20 2007,19:09)
First, thanks for making it a bit clearer.
---------------------QUOTE-------------------


You're welcome. Why don't you reread your hypothesis and prediction before replying?
 

---------------------QUOTE-------------------
Second, if the protein coding regions are dark blue and UTRs are light blue, what are the pink (CNS) regions?
Are these non-coding?
---------------------QUOTE-------------------


Yes. 
 

---------------------QUOTE-------------------
If so, why are they also so highly conserved between rat and mouse?
---------------------QUOTE-------------------


By definition. The regions between those regions aren't conserved at all, which falsifies your hypothesis. QED.
 

---------------------QUOTE-------------------
Sure there is.  Every kid who ever rearranged someone else's book report to try to "put it in his own words" knows about it.
---------------------QUOTE-------------------


God's a cheating kid now? What's His motivation?
 

---------------------QUOTE-------------------
BTW, giving credit to "selection" without showing the steps that were selected for is only an assumption and is not grounded in the evidence.    
---------------------QUOTE-------------------


Assuming that there isn't evidence is dishonest, given your inability to grapple with the evidence that's been served up to you.

Daniel, we have observed inversions and translocations in plants, animals, and people, in real time, and we understand how they can survive. In fact, their mere existence falsifies your hypothesis, because they demolish anything functional at the breakpoints.


---------------------QUOTE-------------------


---------------------QUOTE-------------------


---------------------QUOTE-------------------
I know you'll probably say that millions of years+selection can accomplish this, but where's the data to support that assumption?
---------------------QUOTE-------------------


These *are* the data. There also are data from shorter time periods that, when extrapolated, are consistent with this.
---------------------QUOTE-------------------

Isn't that the classic case of using the thing that must be explained as an explanation?
---------------------QUOTE-------------------


No. For example, we use VISTA to design mouse knock-in constructs (the technology leaves small insertions behind, and we place them in between the pink areas). It makes predictions that we then test, in the process of achieving a different goal.
Posted by: JAM on Oct. 21 2007,00:19

Quote (Daniel Smith @ Oct. 20 2007,19:15)
< Another example. >
In this one, the pink regions outside the coding areas, are more highly conserved between rat and mouse than the coding areas.
---------------------QUOTE-------------------


You're cherry-picking, and your hypothesis predicts that all noncoding areas will be pink, not just some of them or most of them.
Posted by: jeannot on Oct. 21 2007,03:16

Quote (JAM @ Oct. 21 2007,00:19)
   
Quote (Daniel Smith @ Oct. 20 2007,19:15)
< Another example. >
In this one, the pink regions outside the coding areas, are more highly conserved between rat and mouse than the coding areas.
---------------------QUOTE-------------------


You're cherry-picking, and your hypothesis predicts that all noncoding areas will be pink, not just some of them or most of them.
---------------------QUOTE-------------------



From your link, this random portion pretty much falsifies your hypothesis, Daniel. Why do exons tend to be more conserved as divergence time increases (from bottom to top : rat, then dog and human vs. mouse)?

Anyway, your hypothesis doesn't follow your theory, if I understand it correctly. That the designer didn't add unnecessary DNA in our genomes doesn't imply similar evolution rates in coding and non coding regions. What if many non coding regions are necessary for DNA structure and stability? Surely you wouldn't expect the same selective pressure that exons undergo.
Posted by: Daniel Smith on Oct. 21 2007,12:53

Quote (JAM @ Oct. 20 2007,23:59)
   
Quote (Daniel Smith @ Oct. 20 2007,21:04)
Found it!
CNS = conserved noncoding sequences.
So the pink areas in VISTA are confirmations of my hypothesis.
---------------------QUOTE-------------------


No, they are conserved noncoding sequences. Your hypothesis would only be confirmed if there weren't white areas between the pink areas, remember?
   

---------------------QUOTE-------------------
My, there are quite a lot of them when comparing the rat and mouse genomes!
---------------------QUOTE-------------------


Of course there are! But "quite a lot" of them doesn't fulfill your prediction that there wouldn't be any spaces (nonconserved noncoding sequences) between them at all!
Here's your prediction:
     

---------------------QUOTE-------------------
My prediction is that the coding and non-coding sequences (basically all sequences) will show an equal amount of evolutionary constraint.
---------------------QUOTE-------------------


A lot isn't all, Daniel. Your hypothesis is dead meat. A hefty chunk of noncoding sequences aren't conserved. Did you find any coding sequences that weren't conserved?
---------------------QUOTE-------------------


Yes!  There are also white spaces amongst the coding sequences.  If you look at the gene markers at the top, you'll see they often extend over white spaces. Like < this. >

As I see it, there is significant constraint amongst coding and noncoding sequences - as well as significant changes.
Nothing here contradicts my hypothesis.
Posted by: Daniel Smith on Oct. 21 2007,12:55

Quote (JAM @ Oct. 21 2007,00:19)
Quote (Daniel Smith @ Oct. 20 2007,19:15)
< Another example. >
In this one, the pink regions outside the coding areas, are more highly conserved between rat and mouse than the coding areas.
---------------------QUOTE-------------------


You're cherry-picking, and your hypothesis predicts that all noncoding areas will be pink, not just some of them or most of them.
---------------------QUOTE-------------------


No it doesn't.  My hypothesis predicts that there will be equal amounts of constraint amongst coding and noncoding areas - not that all of it will be conserved. I never said that!
Posted by: Daniel Smith on Oct. 21 2007,13:29


This wide view of a random portion of the mouse/rat genome illustrates my point.  The fact that there are so many pink regions shows that the noncoding sites are generally conserved just as the coding sites are within lineages.  The question remains as to how closely mice are related to rats, but I don't see anything here that is unexpected from my point of view.  Remember, my hypothesis is that the splitting of lineages is a saltational event.  I would expect big chunks of the genome to be conserved in such an event, but I would also expect some significant changes as well.
Couple this with the significant evidence in the fossil record for adaptive radiation followed by long periods of gradual evolutionary specialization, along with the mounting evidence for non-random mutation and you have the designed descent hypothesis in a nutshell:
Saltational, non-random divergence of types, followed by non-random specialization within types, followed by over-specialization amongst most members of a lineage, resulting in the extinction of the overspecialized members - leaving just those members that have not (for whatever reason) become overly specialized.
From my perspective therefore, concepts such as "evolutionary constraint"  - as they are generally accepted - are meaningless - since all evolutionary events are non-random.
Posted by: Daniel Smith on Oct. 21 2007,13:40



---------------------QUOTE-------------------
Therefore, I predict that anytime Acromobacter guttatus Sp. K172 is subjected to an environment where it must consume nylon to survive, the same frame shift will occur, resulting in Flavobacterium Sp. KI72.
---------------------QUOTE-------------------


           

---------------------QUOTE-------------------
Now, if these 50 labs had all started with the same pre-nylon-eating bacteria and subjected all of them to a nylon environment, I'd be surprised if a significant percentage of them didn't develop the same frame shift.
---------------------QUOTE-------------------



I see here that the wording of my first prediction has caused some confusion.  
When I said:
"anytime Acromobacter guttatus Sp. K172 is subjected to... the same frame shift will occur...",
I didn't mean that the frame shift would occur in every bacteria.  

What I should have said was:
"anytime a colony of Acromobacter guttatus Sp. K172 is subjected to an environment where it must consume nylon to survive, the same frame shift will occur within some members of that colony, resulting in Flavobacterium Sp. KI72".

That would have made my intent clearer.
Posted by: Daniel Smith on Oct. 21 2007,14:09

Let me also say this:

My view is that proteins are essentially the components of biological machinery - therefore I'd expect that coding for proteins would largely be similar amongst related organisms.  The (so-called)* noncoding regions, however, I believe to be instructional regions that determine how these proteins are used.  Hence, I'd expect these regions to show significant differences amongst morphologically different organisms and similarities between morphologically similar organisms.
I also believe there are regions that are designed for adaptation - a kind of "working lab" cooking up non-random adaptive elements (within limits).  I'd expect these regions to change as environments change.

So, to compare this to VISTA:  The dark blue / light blue regions should be similar amongst related organisms; the pink regions should be similar amongst morphologically similar, related organisms and increasingly dissimilar amongst morphologically dissimilar, related organisms; and the white regions should be dissimilar amongst all organisms.

* (I say "so-called noncoding" because I believe these regions actually "code for" something - just not proteins.)
Posted by: oldmanintheskydidntdoit on Oct. 21 2007,14:20

Quote (Daniel Smith @ Oct. 21 2007,13:29)
Saltational, non-random divergence of types, followed by non-random specialization within types
---------------------QUOTE-------------------


If it is true that, as you say

---------------------QUOTE-------------------
all evolutionary events are non-random
---------------------QUOTE-------------------


In what way are you using "non-random"?

I suppose I'll find out what way you are using it if you give me your explanation of the purpose of HIV/AIDS, as per your hypothesis of non-random evolution.

What purpose is evolution being directed towards Daniel? What purpose does HIV serve?
Posted by: oldmanintheskydidntdoit on Oct. 21 2007,14:26

Also, how are these non-random changes being made Daniel? Is it creepy Q type beings from a universe beyond our understanding playing with DNA for some reason? Can we observe it happening or is it off limits, conveniently?
Or some other thing? Non-random = some thing with an plan. Odd way to communicate it! That's Q for ya!
Kinda sounds like a creepy paranoia story Phillip K.Dick style to me.
Posted by: oldmanintheskydidntdoit on Oct. 21 2007,14:28

Quote (Daniel Smith @ Oct. 21 2007,14:09)
My view is that proteins are essentially the components of biological machinery - therefore I'd expect that coding for proteins would largely be similar amongst related organisms.
---------------------QUOTE-------------------


what are atoms called in this scheme? the components of the components of the machinery? What about gluons? Quarks?
Posted by: jeannot on Oct. 21 2007,15:19

Quote (Daniel Smith @ Oct. 21 2007,14:09)
Let me also say this:

My view is that proteins are essentially the components of biological machinery - therefore I'd expect that coding for proteins would largely be similar amongst related organisms.  The (so-called)* noncoding regions, however, I believe to be instructional regions that determine how these proteins are used.  Hence, I'd expect these regions to show significant differences amongst morphologically different organisms and similarities between morphologically similar organisms.
I also believe there are regions that are designed for adaptation - a kind of "working lab" cooking up non-random adaptive elements (within limits).  I'd expect these regions to change as environments change.

So, to compare this to VISTA:  The dark blue / light blue regions should be similar amongst related organisms; the pink regions should be similar amongst morphologically similar, related organisms and increasingly dissimilar amongst morphologically dissimilar, related organisms; and the white regions should be dissimilar amongst all organisms.
---------------------QUOTE-------------------


So you expect to find similarities in non coding region between eutherian and their marsupial counterparts (for instance wolf vs thylacine), and between old world vultures and new world vultures?

These are examples of morphological convergence. You have to correct for relatedness between taxa you compare, as more closely related taxa tend to share a more common ancestor.

EDIT : Interestingly, your view is partially right. Non-coding regions, mostly those adjacent to genes, are important in gene expression and may be the primary target for morphological novelties, according to some. But they are unlikely to represent the majority of the non-coding genome.
Posted by: JAM on Oct. 21 2007,16:45

Quote (Daniel Smith @ Oct. 21 2007,12:53)
 
Quote (JAM @ Oct. 20 2007,23:59)
     
Quote (Daniel Smith @ Oct. 20 2007,21:04)
Found it!
CNS = conserved noncoding sequences.
So the pink areas in VISTA are confirmations of my hypothesis.
---------------------QUOTE-------------------


No, they are conserved noncoding sequences. Your hypothesis would only be confirmed if there weren't white areas between the pink areas, remember?
       

---------------------QUOTE-------------------
My, there are quite a lot of them when comparing the rat and mouse genomes!
---------------------QUOTE-------------------


Of course there are! But "quite a lot" of them doesn't fulfill your prediction that there wouldn't be any spaces (nonconserved noncoding sequences) between them at all!
Here's your prediction:
         

---------------------QUOTE-------------------
My prediction is that the coding and non-coding sequences (basically all sequences) will show an equal amount of evolutionary constraint.
---------------------QUOTE-------------------


A lot isn't all, Daniel. Your hypothesis is dead meat. A hefty chunk of noncoding sequences aren't conserved. Did you find any coding sequences that weren't conserved?
---------------------QUOTE-------------------


Yes!  There are also white spaces amongst the coding sequences.
---------------------QUOTE-------------------


Daniel, this is utterly, totally, completely, spectacularly false.

"Genes" are in no way synonymous with "coding sequences." Only the exons (blue) are coding sequences. Not only that, but I clearly explained that the introns also were marked on the gene arrows as hash marks.

The introns are NONCODING SEQUENCES.
 

---------------------QUOTE-------------------
If you look at the gene markers at the top, you'll see they often extend over white spaces. Like < this. >
---------------------QUOTE-------------------


Yes, those are all the noncoding parts of the genes (introns). Your hypothesis is wrong.
 

---------------------QUOTE-------------------
As I see it, there is significant constraint amongst coding and noncoding sequences - as well as significant changes.
---------------------QUOTE-------------------


Your view has no basis in reality.
 

---------------------QUOTE-------------------
Nothing here contradicts my hypothesis.
---------------------QUOTE-------------------


Your confidence and lack of humility is profoundly un-Christian, given your lack of basic knowledge.

Your hypothesis is dead meat.
Posted by: JAM on Oct. 21 2007,16:57

Quote (Daniel Smith @ Oct. 21 2007,12:55)
 
Quote (JAM @ Oct. 21 2007,00:19)
   
Quote (Daniel Smith @ Oct. 20 2007,19:15)
< Another example. >
In this one, the pink regions outside the coding areas, are more highly conserved between rat and mouse than the coding areas.
---------------------QUOTE-------------------


You're cherry-picking, and your hypothesis predicts that all noncoding areas will be pink, not just some of them or most of them.
---------------------QUOTE-------------------


No it doesn't.  My hypothesis predicts that there will be equal amounts of constraint amongst coding and noncoding areas
---------------------QUOTE-------------------


Daniel, any constraint at all gives you a pink area, so according to your hypothesis, everything should be well above that 50% level. That's why I very pointedly asked you the question about why the bottom of the scale is at 50%--to see if you were thinking at all. You weren't. Your hypothesis makes clear predictions.
 

---------------------QUOTE-------------------
- not that all of it will be conserved. I never said that!
---------------------QUOTE-------------------


 
Quote (Daniel Smith @ Oct. 08 2007,04:27)
My prediction is that the coding and non-coding sequences (basically all sequences) will show an equal amount of evolutionary constraint.
---------------------QUOTE-------------------



What exactly does basically all sequences mean, then?

Don't trip over your feet while you're backpedaling, OK?

And don't forget...
Quote (Daniel Smith @ Oct. 19 2007,18:14)
If, after careful examination, it appears your evidence falsifies my hypothesis, I'll surely admit it.
---------------------QUOTE-------------------


Posted by: David Holland on Oct. 22 2007,16:42

Quote (Daniel Smith @ Oct. 21 2007,13:40)
What I should have said was:
"anytime a colony of Acromobacter guttatus Sp. K172 is subjected to an environment where it must consume nylon to survive, the same frame shift will occur within some members of that colony, resulting in Flavobacterium Sp. KI72".
---------------------QUOTE-------------------


Does it matter how big the colony is? If your hypothesis is correct then I don't think it should matter. If the colony size is one or one bazillion it should evolve into Flavobacterium every time. Does this apply to all bacteria? Should I get the exact same mutations every time I expose E. coli to penicillin? What about animals? Should I get the exact same mutations every time I expose mosquitoes to DDT? I know the conversation has gotten more into the genetic aspects of your hypothesis but I'm still not clear about this part of it.
Posted by: Daniel Smith on Oct. 22 2007,19:26

Quote (JAM @ Oct. 21 2007,16:57)
           

---------------------QUOTE-------------------
- not that all of it will be conserved. I never said that!
---------------------QUOTE-------------------


               
Quote (Daniel Smith @ Oct. 08 2007,04:27)
My prediction is that the coding and non-coding sequences (basically all sequences) will show an equal amount of evolutionary constraint.
---------------------QUOTE-------------------



What exactly does basically all sequences mean, then?

Don't trip over your feet while you're backpedaling, OK?

And don't forget...
           
Quote (Daniel Smith @ Oct. 19 2007,18:14)
If, after careful examination, it appears your evidence falsifies my hypothesis, I'll surely admit it.
---------------------QUOTE-------------------


---------------------QUOTE-------------------


First, why did you take my prediction out of context?

Here's the full prediction:
           
Quote (Daniel Smith @ Oct. 08 2007,04:27)
Take two members of the same species that have been geographically and reproductively isolated for a long period of time (the longer the better), sequence their genomes and compare them.

My prediction is that the coding and non-coding sequences (basically all sequences) will show an equal amount of evolutionary constraint.
---------------------QUOTE-------------------


I also said this:            
Quote (Daniel Smith @ Oct. 06 2007,20:10)
My prediction is that there are many functional sequences that are different (even radically so) amongst related lineages - this due to their being of designed, not mutational, origin.
---------------------QUOTE-------------------


And this:
           
Quote (Daniel Smith @ Oct. 08 2007,02:18)
1.  Sequence comparisons between related lineages will result in a mixture of like and unlike functional sequences.  

2.  Sequence comparisons within the same lineage will show evolutionary constraint across the board - even in what are presently considered neutral sites.

---------------------QUOTE-------------------


Now, I'm not sure how closely related rats and mice are, but I think the data suggests that they're at least closely related species, within the same lineage.  The true test however, (as I've said all along) is to take samples from geographically isolated specimens of the same species and see how close they are.

I've recently learned of two examples where this was done and the results are consistent with my hypothesis.

The first was a study of the Ascension Island green sea turtles.  These turtles, which are notoriously faithful in returning to their breeding grounds every year, have been geographically isolated from other sea turtle populations for 60-80 million years (since the separation of South America and Africa).  A study by Brian Bowen and John Avise < (abstract) > found that the turtles are too genetically similar to other turtles to have been isolated for that length of time.  Their estimate - based on a sequence divergence rate of 2% per million years - was less than 1 million years.  They then go on to postulate that these sea turtles probably interbred with other populations; this despite the fact that sea turtles have never been observed to do so.  In fact, of the 28,000 females tagged over the past 30 years (at another rookery in Costa Rica), none has ever been observed at another nesting site.

Another example is a study done by Scott Baker (from the abstracts on Google Scholar, I was unsure which one corresponds to this study) between Atlantic and Pacific humpback whales - which have been geographically isolated for 3 million years (since the isthmus of Panama separated the two oceans).  Again - based on a sequence divergence rate of 2% per million years - the estimated difference between these two isolated species was 6%.  The actual difference however, was found to be 0.27%.  Again, this forced the scientists to speculate about gene flows occurring between the oceans from time to time, or much slower sequence divergence rates.

In any event, the results in both of these studies are consistent with, and predicted by, my hypothesis, but are not consistent with, or predicted by, the current theory of evolution.  My hypothesis accommodates the known 60-80 million year isolation of the turtles and the known 3 million year isolation of the humpbacks with no extra speculations added to make the data fit!

And, I'll go out on a limb and make another prediction here:
Whenever studies of this type - between geographically isolated members of the same species - are done, the results will be consistent with my hypothesis.
Posted by: JAM on Oct. 22 2007,20:26

Daniel Smith,Oct. 22 2007,19:26:  "- not that all of it will be conserved. I never said that!"

Daniel Smith,Oct. 08 2007,04:27 - "My prediction is that the coding and non-coding sequences (basically all sequences) will show an equal amount of evolutionary constraint."

JAM: What exactly does basically all sequences mean, then?

Here's a question for you. Why didn't you answer that question? You even italicized "all" for emphasis. Now, you didn't mean "all"?
Quote (Daniel Smith @ Oct. 19 2007,18:14)
If, after careful examination, it appears your evidence falsifies my hypothesis, I'll surely admit it.
---------------------QUOTE-------------------


   

---------------------QUOTE-------------------
First, why did you take my prediction out of context?
---------------------QUOTE-------------------


No, first, the evidence falsified your hypothesis and you said that you would admit it.

Instead, your un-Christian pride and your inability to be objective led you to make a patently false claim--that everything within a gene was coding sequence.

                   
Quote (Daniel Smith @ Oct. 08 2007,04:27)
Take two members of the same species that have been geographically and reproductively isolated for a long period of time (the longer the better), sequence their genomes and compare them.

My prediction is that the coding and non-coding sequences (basically all sequences) will show an equal amount of evolutionary constraint.
---------------------QUOTE-------------------


Not a problem. We have loads of sequences from mice that can be crossed with each other, despite the fact that they have been classified as different species, and we have inbred strains of house mice, which have been artificially, and completely, inbred for a century. Take your pick.
   

---------------------QUOTE-------------------
I also said this:                    
Quote (Daniel Smith @ Oct. 06 2007,20:10)
My prediction is that there are many functional sequences that are different (even radically so) amongst related lineages - this due to their being of designed, not mutational, origin.
---------------------QUOTE-------------------


---------------------QUOTE-------------------


Yes, and noting that, I asked you to make a simple prediction in response to a simple question:
     
Quote (JAM @ Oct. 14 2007,14:59)
2) Again, with man vs. mouse (but not synteny), each has ~30,000 genes. According to your hypothesis, how many human genes won't have a mouse ortholog and vice versa?
---------------------QUOTE-------------------


You can make predictions for:
race vs. race
strain vs. strain
mouse vs. man
chimp vs. man, etc.

Your hypothesis makes clear predictions in all those cases, doesn't it? Why did you run away from my simple question?
[quote]And this:
                   
Quote (Daniel Smith @ Oct. 08 2007,02:18)
1.  Sequence comparisons between related lineages will result in a mixture of like and unlike functional sequences.  

2.  Sequence comparisons within the same lineage will show evolutionary constraint across the board - even in what are presently considered neutral sites.

---------------------QUOTE-------------------


Yes, and you've just seen that your hypothesis is dead wrong.
   

---------------------QUOTE-------------------
Now, I'm not sure how closely related rats and mice are, but I think the data suggests that they're at least closely related species, within the same lineage.
---------------------QUOTE-------------------


We can do the same thing for mouse strains, or mouse "species" that interbreed to yield fertile offspring. It's just not as easy as it is with VISTA, where you had to change basic facts, falsifying your promise to admit that your hypothesis was incorrect.
   

---------------------QUOTE-------------------
The true test however, (as I've said all along) is to take samples from geographically isolated specimens of the same species and see how close they are.
---------------------QUOTE-------------------


No, only if you are comparing/contrasting coding and noncoding sequences. You're fudging your hypothesis in addition to the facts now.
   

---------------------QUOTE-------------------
I've recently learned of two examples where this was done and the results are consistent with my hypothesis.

The first was a study of the Ascension Island green sea turtles.  These turtles, which are notoriously faithful in returning to their breeding grounds every year, have been geographically isolated from other sea turtle populations for 60-80 million years (since the separation of South America and Africa).
---------------------QUOTE-------------------


False. That was THE HYPOTHESIS BEING TESTED, for Christ's sake.
   

---------------------QUOTE-------------------
 A study by Brian Bowen and John Avise < (abstract) >
---------------------QUOTE-------------------


Why would you only read/link to the abstract, when the whole paper is freely available?
   

---------------------QUOTE-------------------
found that the turtles are too genetically similar to other turtles to have been isolated for that length of time.  Their estimate - based on a sequence divergence rate of 2% per million years - was less than 1 million years.  They then go on to postulate that these sea turtles probably interbred with other populations; this despite the fact that sea turtles have never been observed to do so.
---------------------QUOTE-------------------


The BS is getting deep.
1) They looked at RFLPs in mitochondrial DNA. That's coding. Do you know what is special about mtDNA, Daniel?
2) Breeding in this species occurs offshore, so "never been observed" is nothing but pure BS to feed your ego. The authors note this clearly.
   

---------------------QUOTE-------------------
In fact, of the 28,000 females tagged over the past 30 years (at another rookery in Costa Rica), none has ever been observed at another nesting site.
---------------------QUOTE-------------------


So what? The males aren't tagged.
   

---------------------QUOTE-------------------
Another example is a study done by Scott Baker (from the abstracts on Google Scholar, I was unsure which one corresponds to this study)
---------------------QUOTE-------------------


Abstracts aren't evidence. You need to look at the DATA, not your misrepresentations of abstracts.

   

---------------------QUOTE-------------------
between Atlantic and Pacific humpback whales - which have been geographically isolated for 3 million years (since the isthmus of Panama separated the two oceans).
---------------------QUOTE-------------------


I'm sorry, Daniel, but that is just a desperate fabrication:
< Humpbacks hang out in Tierra del Fuego. > Can you be more blatantly dishonest than that?
   

---------------------QUOTE-------------------
Again - based on a sequence divergence rate of 2% per million years - the estimated difference between these two isolated species was 6%.  The actual difference however, was found to be 0.27%.  Again, this forced the scientists to speculate about gene flows occurring between the oceans from time to time, or much slower sequence divergence rates.
---------------------QUOTE-------------------


It did, eh? The scientists weren't forced to do anything.
   

---------------------QUOTE-------------------
In any event, the results in both of these studies are consistent with, and predicted by, my hypothesis, but are not consistent with, or predicted by, the current theory of evolution.
---------------------QUOTE-------------------


False on both counts.
   

---------------------QUOTE-------------------
My hypothesis accommodates the known 60-80 million year isolation of the turtles...
---------------------QUOTE-------------------


Daniel, that is a hypothesis, it is not known.
   

---------------------QUOTE-------------------
and the known 3 million year isolation of the humpbacks with no extra speculations added to make the data fit!
---------------------QUOTE-------------------


And that's just a lie. How can humpbacks be isolated given that they are common in Tierra del Fuego?
   

---------------------QUOTE-------------------
And, I'll go out on a limb and make another prediction here:
Whenever studies of this type - between geographically isolated members of the same species - are done, the results will be consistent with my hypothesis.
---------------------QUOTE-------------------


Your limb was gone with the VISTA data. You've proven that you'll fabricate rather than test your hypothesis, Daniel.
Posted by: swbarnes2 on Oct. 22 2007,20:55



---------------------QUOTE-------------------
anytime a colony of Acromobacter guttatus Sp. K172 is subjected to an environment where it must consume nylon to survive, the same frame shift will occur within some members of that colony, resulting in Flavobacterium Sp. KI72".

---------------------QUOTE-------------------



So I take a sample of Acromobacter, I spread it on a plate.  I grow colonies from that.

I replica plate those colonies onto nylon plates, and you claim that there will be a survivor in every colony?

Of every plate, prepped by every lab worker in 50 labs?

Now, claiming that all of the survivors (because, you suppose, there is only a single possible evolutionary solution to the problem, which is ridiculous) would have the exact same mutation, that's at least imaginable.  But what you suggest now is certifiably crazy.  

So yes, you made it clear.  Clear that your understanding of biology is insane.

Well, I guess you weren't interested in hearing the evidence that nylon-eating can be acquired through mutations in other genes after all.  Which makes it a lie when you said you were.  A pretty pathically transparent one at that.
Posted by: Henry J on Oct. 22 2007,22:16



---------------------QUOTE-------------------
They then go on to postulate that these sea turtles probably interbred with other populations; this despite the fact that sea turtles have never been observed to do so.
---------------------QUOTE-------------------



Maybe the turtles are better at doing their mating activities in private than some people think they are?



---------------------QUOTE-------------------
My prediction is that the coding and non-coding sequences (basically all sequences) will show an equal amount of evolutionary constraint.
---------------------QUOTE-------------------



Is that when the groups are in equivalent environments, or different environments? I'm no biologist, but I'd think that in similar environments the current theory would predict similar amount of constraints as well, and that in different environments both current theory and your hypothesis would imply some differences due to the differences in needs in different surroundings.

Henry
Posted by: W. Kevin Vicklund on Oct. 23 2007,15:01



---------------------QUOTE-------------------
The first was a study of the Ascension Island green sea turtles.  These turtles, which are notoriously faithful in returning to their breeding grounds every year, have been geographically isolated from other sea turtle populations for 60-80 million years (since the separation of South America and Africa).  A study by Brian Bowen and John Avise (abstract) found that the turtles are too genetically similar to other turtles to have been isolated for that length of time.  Their estimate - based on a sequence divergence rate of 2% per million years - was less than 1 million years.  They then go on to postulate that these sea turtles probably interbred with other populations; this despite the fact that sea turtles have never been observed to do so.  In fact, of the 28,000 females tagged over the past 30 years (at another rookery in Costa Rica), none has ever been observed at another nesting site.
---------------------QUOTE-------------------



Your claims as to what Bowen and Avise wrote are rather... odd.  Let me guess: you read the abstract, but did not actually read the paper, which is freely avaible from the link you provided.  This is extremely dishonest for anyone who claims to be interested in the evidence.

First, the hypothesized isolation was 40 million years or longer, rather than 60-80 million years.  While this is certainly nitpicking on my part (since 60-80 million years is longer than 40), it suggests that you didn't read the paper - very poor scholarship indeed.  But this is merely a semantic error.  Your other errors are much worse.  For example, the study included a Pacific colony as an outgroup.  The Pacific isolation only occured 3 million years ago (as you yourself noted), yet the Pacific colony showed more changes than the putative 40 million year separation!  Another major error is that you claim they postulated these populations interbred.  This is not quite true - they considered and mostly rejected it, and gave reasons for that rejection.  Rather, they postulated that it was the result of a recent colonization event, and that these events occur periodically.  Bonus question: what is their explanation for why and how periodic colonization events occur?  Finally, you claim that sea turtles have never been observed to change nesting sites.  Yet the paper clearly identifies several instances of this occuring - in the same paragraph they largely rejected the interbreeding argument.

I highly recommend that in the future you read your sources before citing them, if at all possible.  It will help prevent you from making such egregious errors.  Unfortunately, some people never do learn this lesson, and I enjoy rubbing their face in it after the first few times they make that error.  Of course, not all articles are free, and you might find yourself taking a calculated risk to make a point.  Just be prepared for the fall-out if your interpretation of the abstract is incorrect.

For now, I will assume poor scholarship on your part, rather than deliberate dishonesty.  Keep it up, though, and you will soon find yourself being called a pubjacker.
Posted by: W. Kevin Vicklund on Oct. 24 2007,10:10



---------------------QUOTE-------------------
Another example is a study done by Scott Baker (from the abstracts on Google Scholar, I was unsure which one corresponds to this study) between Atlantic and Pacific humpback whales - which have been geographically isolated for 3 million years (since the isthmus of Panama separated the two oceans).  Again - based on a sequence divergence rate of 2% per million years - the estimated difference between these two isolated species was 6%.  The actual difference however, was found to be 0.27%.  Again, this forced the scientists to speculate about gene flows occurring between the oceans from time to time, or much slower sequence divergence rates.
---------------------QUOTE-------------------



I'm going to call shenanigans on this one.  In a 1993 paper, Baker et al. took samples from three major population groups of humpbacked whales.  Geographically, these are located in the North Atlantic, the North Pacific, and the southern oceans.  The results: there was a 3.808% difference in mitochondrial DNA between the North Atlantic and North Pacific populations, which would be the populations affected by the forming of the isthmus.  That's more than 1% per million years, well within the tolerance limit of the very rough 2%/my rule of thumb.  The paper, "Abundant mitochondrial DNA variation and world-wide population structure in humpback whales," can be found at < PubMedCentral >.  Please note: there's a lot of information there which I didn't bother to communicate, but needless to say, it doesn't uphold Daniel's numbers.

My guess is that Daniel found a paper that dealt solely with the southern oceans population, which is sub-divided into 6 groups.  These 6 groups are not geographically isolated, as others have noted.
Posted by: JAM on Oct. 24 2007,11:15

Quote (W. Kevin Vicklund @ Oct. 24 2007,10:10)
 

---------------------QUOTE-------------------
Another example is a study done by Scott Baker (from the abstracts on Google Scholar, I was unsure which one corresponds to this study) between Atlantic and Pacific humpback whales - which have been geographically isolated for 3 million years (since the isthmus of Panama separated the two oceans).  Again - based on a sequence divergence rate of 2% per million years - the estimated difference between these two isolated species was 6%.  The actual difference however, was found to be 0.27%.  Again, this forced the scientists to speculate about gene flows occurring between the oceans from time to time, or much slower sequence divergence rates.
---------------------QUOTE-------------------



I'm going to call shenanigans on this one.  In a 1993 paper, Baker et al. took samples from three major population groups of humpbacked whales.  Geographically, these are located in the North Atlantic, the North Pacific, and the southern oceans.  The results: there was a 3.808% difference in mitochondrial DNA between the North Atlantic and North Pacific populations, which would be the populations affected by the forming of the isthmus.  That's more than 1% per million years, well within the tolerance limit of the very rough 2%/my rule of thumb.  The paper, "Abundant mitochondrial DNA variation and world-wide population structure in humpback whales," can be found at < PubMedCentral >.  Please note: there's a lot of information there which I didn't bother to communicate, but needless to say, it doesn't uphold Daniel's numbers.

My guess is that Daniel found a paper that dealt solely with the southern oceans population, which is sub-divided into 6 groups.  These 6 groups are not geographically isolated, as others have noted.
---------------------QUOTE-------------------


We don't even have to read the paper. All we need to do is look at a globe to see the idiocy of Daniel's claim that the isthmus of Panama separated the two oceans. The fact that humpback whales are prevalent at the junction between them (somewhat south of Panama) is a bonus.
Posted by: Daniel Smith on Oct. 24 2007,20:59

Quote (swbarnes2 @ Oct. 22 2007,20:55)
 

---------------------QUOTE-------------------
anytime a colony of Acromobacter guttatus Sp. K172 is subjected to an environment where it must consume nylon to survive, the same frame shift will occur within some members of that colony, resulting in Flavobacterium Sp. KI72".

---------------------QUOTE-------------------



So I take a sample of Acromobacter, I spread it on a plate.  I grow colonies from that.

I replica plate those colonies onto nylon plates, and you claim that there will be a survivor in every colony?

Of every plate, prepped by every lab worker in 50 labs?

Now, claiming that all of the survivors (because, you suppose, there is only a single possible evolutionary solution to the problem, which is ridiculous) would have the exact same mutation, that's at least imaginable.  But what you suggest now is certifiably crazy.  

So yes, you made it clear.  Clear that your understanding of biology is insane.

Well, I guess you weren't interested in hearing the evidence that nylon-eating can be acquired through mutations in other genes after all.  Which makes it a lie when you said you were.  A pretty pathically transparent one at that.
---------------------QUOTE-------------------


I never said there was only one possible solution to the nylon problem.  I merely said that I would expect the same frame shift to occur more often and more rapidly than random mutations could account for.
Posted by: Daniel Smith on Oct. 24 2007,21:41

Quote (W. Kevin Vicklund @ Oct. 23 2007,15:01)
Your claims as to what Bowen and Avise wrote are rather... odd.  Let me guess: you read the abstract, but did not actually read the paper, which is freely avaible from the link you provided.  This is extremely dishonest for anyone who claims to be interested in the evidence.

First, the hypothesized isolation was 40 million years or longer, rather than 60-80 million years.  While this is certainly nitpicking on my part (since 60-80 million years is longer than 40), it suggests that you didn't read the paper - very poor scholarship indeed.  But this is merely a semantic error.  Your other errors are much worse.  For example, the study included a Pacific colony as an outgroup.  The Pacific isolation only occured 3 million years ago (as you yourself noted), yet the Pacific colony showed more changes than the putative 40 million year separation!  Another major error is that you claim they postulated these populations interbred.  This is not quite true - they considered and mostly rejected it, and gave reasons for that rejection.  Rather, they postulated that it was the result of a recent colonization event, and that these events occur periodically.  Bonus question: what is their explanation for why and how periodic colonization events occur?  Finally, you claim that sea turtles have never been observed to change nesting sites.  Yet the paper clearly identifies several instances of this occuring - in the same paragraph they largely rejected the interbreeding argument.

I highly recommend that in the future you read your sources before citing them, if at all possible.  It will help prevent you from making such egregious errors.  Unfortunately, some people never do learn this lesson, and I enjoy rubbing their face in it after the first few times they make that error.  Of course, not all articles are free, and you might find yourself taking a calculated risk to make a point.  Just be prepared for the fall-out if your interpretation of the abstract is incorrect.

For now, I will assume poor scholarship on your part, rather than deliberate dishonesty.  Keep it up, though, and you will soon find yourself being called a pubjacker.
---------------------QUOTE-------------------


You are right.  I did not read the paper.  My source was a book I've been reading called "Patterns in Evolution" by Roger Lewin.  I decided that it would be better to try to find a link when I posted it; so I found the abstract and just linked to it.
Now that I've read the paper, I see that it's not exactly what I characterized it to be.  I was however, struck by their hypothesis that sea turtles do not accumulate mutations in their mitochondrial DNA as fast as they had expected - and even the 3 million year Atlantic/Pacific separation produced far less variation than the 2% per million years that has generally been accepted.

I must say also here that I've been a bit presumptuous in declaring my "hypothesis" - since (as I said when I first arrived here) my ideas are still in development.  My main goal is to find out what really happened.  I will go wherever the data leads.  So I don't really have a hypothesis that's set in stone.  I have more in the way of expectations due to my variant interpretation of the data.

One thing I've learned recently (from the same book) is that; even among interbreeding populations, sequence divergence can vary widely (one study found a species of skink with an 8% divergence and a subwren species with 0.1% sequence divergence in the same Australian environment).

This has led me to re-evaluate my views.

I'm thinking that perhaps these divergence percentages correlate to Schindewolf's proposed three-stage evolutionary theory; with the "typolosis" (or degenerative, over-specialized) phase corresponding to the species with the lowest sequence diversity.

I'll have to do more study.
Posted by: Richard Simons on Oct. 25 2007,00:00

Back to Schindewolf! I am not sure why a hypothesis that has been essentially dead for 50 years holds so much fascination for you. However, given that it does perhaps you could explain how the information to constrain an organism's evolutionary pathway is held. What conceivable mechanism could stop evolution from taking place, or enable parts to evolve before they became useful?

I am also curious about the saltational events. Do you see these as creating a new genus, order, phylum or what? What actually occurs during a saltational event? How does the DNA get changed and how does it know what to become, as I gather it is preparing for the next few million years of evolution and changing conditions? When did the last saltational event take place? I don't even know if the proposal is that one day a dinosaur chick hatched that had feathers and wings or if the process was spread over many generations, which might make it little different from the rapid evolution phase of punctuated equilibrium.

I'm looking forward to your answers.
Posted by: Albatrossity2 on Oct. 25 2007,06:01

Quote (Richard Simons @ Oct. 25 2007,00:00)
I'm looking forward to your answers.
---------------------QUOTE-------------------


I'm not.

It's already clear that the conclusion is more important than the data. Merely looking for an alternative path to the conclusion is a sure sign that the conclusion is hardwired in Daniel's psyche. Unless he shows signs of looking at the evidence and then forming a conclusion, his next post will be just as unsatisfactory as the rest of them have been.
Posted by: Richard Simons on Oct. 25 2007,08:39

Quote (Albatrossity2 @ Oct. 25 2007,06:01)
 
Quote (Richard Simons @ Oct. 25 2007,00:00)
I'm looking forward to your answers.
---------------------QUOTE-------------------


I'm not.

It's already clear that the conclusion is more important than the data. Merely looking for an alternative path to the conclusion is a sure sign that the conclusion is hardwired in Daniel's psyche. Unless he shows signs of looking at the evidence and then forming a conclusion, his next post will be just as unsatisfactory as the rest of them have been.
---------------------QUOTE-------------------


Perhaps I should have phrased it more carefully. I would like to see answers but I think the questions are mostly unanswerable. I expect that either they will be ignored or there will be a lot of beating of bushes that fails to provide answers. I have noticed (but I have not followed everything in detail) that he seems to be following the usual Creationist/ID tactic of scouring the literature for something that could superficially be seen to support his views and pouncing on it, rather than looking at the evidence as a whole and seeing where it leads.
Posted by: Daniel Smith on Oct. 25 2007,13:50

Quote (Richard Simons @ Oct. 25 2007,00:00)
Back to Schindewolf! I am not sure why a hypothesis that has been essentially dead for 50 years holds so much fascination for you. However, given that it does perhaps you could explain how the information to constrain an organism's evolutionary pathway is held. What conceivable mechanism could stop evolution from taking place, or enable parts to evolve before they became useful?

I am also curious about the saltational events. Do you see these as creating a new genus, order, phylum or what? What actually occurs during a saltational event? How does the DNA get changed and how does it know what to become, as I gather it is preparing for the next few million years of evolution and changing conditions? When did the last saltational event take place? I don't even know if the proposal is that one day a dinosaur chick hatched that had feathers and wings or if the process was spread over many generations, which might make it little different from the rapid evolution phase of punctuated equilibrium.

I'm looking forward to your answers.
---------------------QUOTE-------------------


I don't know.
Posted by: swbarnes2 on Oct. 25 2007,14:36



---------------------QUOTE-------------------
I never said there was only one possible solution to the nylon problem.
---------------------QUOTE-------------------



And I never said you claimed that.  Why are you lying about what I said?

Your posts are perfectly easy to look up.  

You said:

 

---------------------QUOTE-------------------
anytime a colony of Acromobacter guttatus Sp. K172 is subjected to an environment where it must consume nylon to survive, the same frame shift will occur within some members of that colony, resulting in Flavobacterium Sp. KI72.

---------------------QUOTE-------------------



It means what it says.  You predict that a replica experiment will result in every colony re-establishing itself on the nylon plate because every colony will have a member with that frameshift.

I'm sorry if your prediction is stupid, but that's your responsibility.  You write it.

 

---------------------QUOTE-------------------
I merely said that I would expect the same frame shift to occur more often and more rapidly than random mutations could account for.
---------------------QUOTE-------------------



No, you said what I quoted above.  

Every colony exposed gets the frameshift.

We understand, believe me, we do.

You have already concluded that evolution is wrong because you don't like it, so you are "predicting" that the evidence will show that it doesn't happen.

But you don't honetly care about the content of your predictions.  They aren't relevant.  That's why you can't keep them straight over the course of two days.

This is really one of those cases where you are better off with the truth, because lies are too hard to keep straight.

People who care about the evidence look it up first, and then draw their conclusions.  Do you honestly think that anyone reading this board would call you a "look at the data first" kind of person?

So embrace the truth about yourself.  You like your Creationism for reasons that have nothing to do with the evidence (since you don't know what any of it is).

Then you can stop making posts that make you look like a braindead moron, or a pathetic liar.
Posted by: Steverino on Oct. 25 2007,17:44

Denial Smith, CG, FTK....they all never remember what they said but, will be the first to tell you that you have misquoted them.
Posted by: Daniel Smith on Oct. 25 2007,20:56

Quote (swbarnes2 @ Oct. 25 2007,14:36)
       

---------------------QUOTE-------------------
I never said there was only one possible solution to the nylon problem.
---------------------QUOTE-------------------



And I never said you claimed that.  Why are you lying about what I said?
---------------------QUOTE-------------------


I was referring to this:
       
Quote (swbarnes2 @ Oct. 22 2007,20:55)
Now, claiming that all of the survivors (because, you suppose, there is only a single possible evolutionary solution to the problem, which is ridiculous) would have the exact same mutation, that's at least imaginable.
---------------------QUOTE-------------------


Now that I re-read it, I can see that you weren't really saying that I supposed there to be "only a single possible evolutionary solution to the problem" (although it came across that way when I first read it).  So I misinterpreted.
Sorry I'm such a "liar".
       

---------------------QUOTE-------------------

Your posts are perfectly easy to look up.  

You said:

           

---------------------QUOTE-------------------
anytime a colony of Acromobacter guttatus Sp. K172 is subjected to an environment where it must consume nylon to survive, the same frame shift will occur within some members of that colony, resulting in Flavobacterium Sp. KI72.

---------------------QUOTE-------------------



It means what it says.  You predict that a replica experiment will result in every colony re-establishing itself on the nylon plate because every colony will have a member with that frameshift.

I'm sorry if your prediction is stupid, but that's your responsibility.  You write it.

---------------------QUOTE-------------------


You got me there.  I guess I'll have to stick with the prediction until it's proven wrong.
       

---------------------QUOTE-------------------

           

---------------------QUOTE-------------------
I merely said that I would expect the same frame shift to occur more often and more rapidly than random mutations could account for.
---------------------QUOTE-------------------



No, you said what I quoted above.  
---------------------QUOTE-------------------

Here's the full context of that quote:
       
Quote (Daniel Smith @ Oct. 14 2007,10:20)
Speaking of predictions, I have another one for you:
It's my hypothesis that random mutations are only neutral or deleterious - never advantageous.  All advantageous mutations are non-random and are therefore experimentally repeatable and will occurr too rapidly to be random.
Therefore, I predict that anytime Acromobacter guttatus Sp. K172 is subjected to an environment where it must consume nylon to survive, the same frame shift will occur, resulting in Flavobacterium Sp. KI72. (emphasis added)
---------------------QUOTE-------------------

So, as you can see, I actually said both things.        

---------------------QUOTE-------------------


Every colony exposed gets the frameshift.

We understand, believe me, we do.

You have already concluded that evolution is wrong because you don't like it, so you are "predicting" that the evidence will show that it doesn't happen.
---------------------QUOTE-------------------


I have concluded that the currently held theory of evolution is wrong because I have yet to see any convincing evidence of it's mechanism.        

---------------------QUOTE-------------------


But you don't honetly care about the content of your predictions.  They aren't relevant.  That's why you can't keep them straight over the course of two days.

This is really one of those cases where you are better off with the truth, because lies are too hard to keep straight.

People who care about the evidence look it up first, and then draw their conclusions.
---------------------QUOTE-------------------

Is that what you did?

---------------------QUOTE-------------------
 Do you honestly think that anyone reading this board would call you a "look at the data first" kind of person?
---------------------QUOTE-------------------

Maybe not.  I don't really care what the readers of this board think of me.  The truth is, I was invited here.  I was supposed to come here and discuss Berg and Schindewolf, but I was immediately told that the fossil record doesn't matter because molecular evidence outweighs it.  I was then challenged to produce a hypothesis and predictions - so I did.  I probably shouldn't have jumped in so quickly, but oh well.  Now that we're here, let's see how it turns out.  Of all the predictions I've made, how many have been shown false?        

---------------------QUOTE-------------------


So embrace the truth about yourself.  You like your Creationism for reasons that have nothing to do with the evidence (since you don't know what any of it is).
---------------------QUOTE-------------------


I'll admit that my belief in God greatly weighs against any belief in random causes.  In fact what I'm actually advocating is Natural Theology - the belief that the study of nature reveals the mind and qualities of God.  I don't try to hide that.  I started this journey as a young earth creationist, but I've changed much about what I believe because of the evidence.  I refuse, however, to be an unthinking, uncritical lemming.  I will not blindly accept a theory for which there is very little in the way of true evidence.  Much of what I've seen of the case for the theory of evolution is circular.  It presupposes it's conclusion.  In fact the conclusion is a foregone one.  It's very hard sometimes to sift through the evidence without being caught up in the tautology in which it is interpreted.    

---------------------QUOTE-------------------


Then you can stop making posts that make you look like a braindead moron, or a pathetic liar.
---------------------QUOTE-------------------


Thanks.
Posted by: Daniel Smith on Oct. 25 2007,21:06

And, another thing:

If I were really only interested in reaffirming my own ideas with no concerns for opposing data or evidence, why on earth would I come here?!?!
Posted by: IanBrown_101 on Oct. 25 2007,22:57

Quote (Daniel Smith @ Oct. 26 2007,03:06)
And, another thing:

If I were really only interested in reaffirming my own ideas with no concerns for opposing data or evidence, why on earth would I come here?!?!
---------------------QUOTE-------------------


1. I don't recall anyone saying you were here to reaffirm your beliefs, they said you were rock steady in them.

2. In order to convince us you are right, because you subconsciously think this will work, since you clearly think that they trump absolutely anything we can throw at them. Whenever someone gets an idea they believe is totally impervious to attack they immediately want to test it on the opposition because they expect them to fall on their knees and shield their eyes from it's brilliance. It's that simple, if you seriously think that your idea is absolutely, no matter what right, then you think deep down we will, eventually succumb to it.
Posted by: oldmanintheskydidntdoit on Oct. 26 2007,02:50

Quote (Daniel Smith @ Oct. 25 2007,20:56)
In fact what I'm actually advocating is Natural Theology - the belief that the study of nature reveals the mind and qualities of God.
---------------------QUOTE-------------------


And what have you found out so far?

You've presumably been studying nature for a while now.

What has Natural Theology revealed so far about the mind and qualities of God?

Anything?
Posted by: Henry J on Oct. 26 2007,11:17

Quote (oldmanintheskydidntdoit @ Oct. 26 2007,02:50)
What has Natural Theology revealed so far about the mind and qualities of God?
---------------------QUOTE-------------------


A fondness for beetles? :p
Posted by: Daniel Smith on Oct. 26 2007,13:48

Quote (oldmanintheskydidntdoit @ Oct. 26 2007,02:50)
 
Quote (Daniel Smith @ Oct. 25 2007,20:56)
In fact what I'm actually advocating is Natural Theology - the belief that the study of nature reveals the mind and qualities of God.
---------------------QUOTE-------------------


And what have you found out so far?

You've presumably been studying nature for a while now.

What has Natural Theology revealed so far about the mind and qualities of God?

Anything?
---------------------QUOTE-------------------


I've learned that God is an infinitely brilliant chemist, physisict and engineer.
I still might not know much about how or why he did what he did (who does?), but I can surely see the elegance of it.
Posted by: Louis on Oct. 26 2007,13:50

Quote (Daniel Smith @ Oct. 26 2007,19:48)
I've learned that God is an infinitely brilliant chemist...
---------------------QUOTE-------------------


I call bullshit! Since the synthesis of azadirachtin I think we can conclude that Steve Ley is an infinitely brilliant chemist!

Louis
Posted by: Daniel Smith on Oct. 26 2007,13:51

Quote (IanBrown_101 @ Oct. 25 2007,22:57)
   
Quote (Daniel Smith @ Oct. 26 2007,03:06)
And, another thing:

If I were really only interested in reaffirming my own ideas with no concerns for opposing data or evidence, why on earth would I come here?!?!
---------------------QUOTE-------------------


1. I don't recall anyone saying you were here to reaffirm your beliefs, they said you were rock steady in them.

2. In order to convince us you are right, because you subconsciously think this will work, since you clearly think that they trump absolutely anything we can throw at them. Whenever someone gets an idea they believe is totally impervious to attack they immediately want to test it on the opposition because they expect them to fall on their knees and shield their eyes from it's brilliance. It's that simple, if you seriously think that your idea is absolutely, no matter what right, then you think deep down we will, eventually succumb to it.
---------------------QUOTE-------------------


There might be some truth to #2.
Posted by: Daniel Smith on Oct. 26 2007,13:56

Quote (Louis @ Oct. 26 2007,13:50)
Quote (Daniel Smith @ Oct. 26 2007,19:48)
I've learned that God is an infinitely brilliant chemist...
---------------------QUOTE-------------------


I call bullshit! Since the synthesis of azadirachtin I think we can conclude that Steve Ley is an infinitely brilliant chemist!

Louis
---------------------QUOTE-------------------


Where did he get the idea for azadirachtin?
Posted by: Albatrossity2 on Oct. 26 2007,13:59

Quote (Daniel Smith @ Oct. 26 2007,13:56)
Where did he get the idea for azadirachtin?
---------------------QUOTE-------------------


From pixies.

Prove that he didn't!
Posted by: Louis on Oct. 26 2007,14:11

Quote (Albatrossity2 @ Oct. 26 2007,19:59)
Quote (Daniel Smith @ Oct. 26 2007,13:56)
Where did he get the idea for azadirachtin?
---------------------QUOTE-------------------


From pixies.

Prove that he didn't!
---------------------QUOTE-------------------


WAS NOT!

It was leprechauns.

PROVE ME WRONG!!!!! (All science so far)

Louis
Posted by: Albatrossity2 on Oct. 26 2007,14:27

Quote (Louis @ Oct. 26 2007,14:11)
WAS NOT!

It was leprechauns.

PROVE ME WRONG!!!!! (All science so far)

Louis
---------------------QUOTE-------------------


Had to be pixies; leprechauns don't live in south Asia so they don't have a clue (or even a gut feeling) about azadirachtin.

Ha!  I've run rings around you logically. Now you must fall down and weep over the total collapse of your world view.
Posted by: Louis on Oct. 26 2007,14:44

Quote (Albatrossity2 @ Oct. 26 2007,20:27)
Quote (Louis @ Oct. 26 2007,14:11)
WAS NOT!

It was leprechauns.

PROVE ME WRONG!!!!! (All science so far)

Louis
---------------------QUOTE-------------------


Had to be pixies; leprechauns don't live in south Asia so they don't have a clue (or even a gut feeling) about azadirachtin.

Ha!  I've run rings around you logically. Now you must fall down and weep over the total collapse of your world view.
---------------------QUOTE-------------------


{Looks briefly like being about to fall down and weep, but then...}

AH! But the leprechauns were on an exchange holiday with the pixies and thus had a MASSIVE grounding in what azadirachtin is and then they went to Cambridge to see Steve Ley where they did all the lab work (hmmm that's frighteningly close to reality!).

Anyway, my leprechauns don;t have to match your pixetic level of detail.

Go Leprechauns!

Louis
Posted by: Albatrossity2 on Oct. 26 2007,15:49

Quote (Louis @ Oct. 26 2007,14:44)
{Looks briefly like being about to fall down and weep, but then...}

AH! But the leprechauns were on an exchange holiday with the pixies and thus had a MASSIVE grounding in what azadirachtin is and then they went to Cambridge to see Steve Ley where they did all the lab work (hmmm that's frighteningly close to reality!).

Anyway, my leprechauns don;t have to match your pixetic level of detail.

Go Leprechauns!

Louis
---------------------QUOTE-------------------


I’m going to try to ignore everything I’ve read and go with my gut, because there have been so many debates between Behe/Miller pixies and leprechauns, and articles written on this issue that it borders on insanity.  It doesn’t seem to me that there is any kind of consensus as to who is right and who is wrong.

On the basis of this incredibly brilliant logic and non-evidence based thinking, I declare pixies the winner!!!one 1110

I will now post all of this (minus the illogical bits, of course) on YoungCosmos, where Sal will certainly understand that pixiesdidit, and he will tell his mom about it while she irons his shirts and balances his equations.
Posted by: swbarnes2 on Oct. 26 2007,15:52

[quote=Daniel Smith,Oct. 25 2007,20:56]


---------------------QUOTE-------------------
Now that I re-read it, I can see that you weren't really saying that I supposed there to be "only a single possible evolutionary solution to the problem" (although it came across that way when I first read it).  So I misinterpreted.
Sorry I'm such a "liar".

---------------------QUOTE-------------------



Oh no.

If your behavior on this board had been such that you had demonstrated honesty, others would be much more willing to atribute an occasional wrong step to accident.

But you have chosen to be dishonest on this board time and time again, so you don't get to claims "oops, you all are mean for thinking that my innocent mistake was malicious".

You made your bed here, now you have to lie in it.



---------------------QUOTE-------------------
You got me there.  I guess I'll have to stick with the prediction until it's proven wrong.
---------------------QUOTE-------------------



So you admit you wer telling untruths about your position.

Wonderful.  At last, a little progress.  Thought if you'd said so at the start, there wouldn't be a whole sub-thread about how stupid/dishonest you are.  But that's the way you wanted it, so I suppose you are happy with the outcome.

Your "prediction" has already been proved false.  If you do a replica plate of anything onto a hostile medium, you will not get survivors from every colony, as you predict.  Even if survival can be gained with only a single point mutation, as oppsoed to a frame-shift, you won't see every single colony containing a survivor.



---------------------QUOTE-------------------
I'll admit that my belief in God greatly weighs against any belief in random causes.
---------------------QUOTE-------------------



We know that.  

Just like a belief in God weighs in for many agaisnt beleiving that the planet is billions of years old.

Or round.

You are no different.



---------------------QUOTE-------------------
In fact what I'm actually advocating is Natural Theology - the belief that the study of nature reveals the mind and qualities of God.
---------------------QUOTE-------------------



So you believe that the persistant adaptiveness of parasites that kill a hundred thousand children a year reveals...what, exactly about God?

Please, be specific.

Or, you can say nothing, and we'll all understand why.

You want to believe that you are special, and that someone powerful loves you.  So you will rationalize that however you can, and if you can pretend that biology provesit, then you are satisfied.

You are starting with the conclusion you want (god is looking out for me), and rationalizing afterwards.

Unfortunately, the evidence doesn't support your cherished desire.  You can deal with reality, or you can continue to look like a liar/moron as your pathetic arguments get ripped to shreds.



---------------------QUOTE-------------------
I started this journey as a young earth creationist, but I've changed much about what I believe because of the evidence.
---------------------QUOTE-------------------



But your core belief, that a Big Sky Daddy loves you and is looking out for you, you won't question.  So you keep straining to prove to the rest of us that it's so, when the evidence just doesn't support it.

And again, if you really cared about the evidence, you would have consulted it before you made your stupid predictions.  You didn't therefore, you don't.



---------------------QUOTE-------------------
I refuse, however, to be an unthinking, uncritical lemming.
---------------------QUOTE-------------------



Your ignorance of biology makes it impossible for you to be anything but.

Learn some things, then you can start thinking and criticizing.



---------------------QUOTE-------------------
I will not blindly accept a theory for which there is very little in the way of true evidence.
---------------------QUOTE-------------------



But you don't know the evidence.



---------------------QUOTE-------------------
It presupposes its conclusion.
---------------------QUOTE-------------------



No, it doesn't.  You say that becuase you wish it were true  (because if evolution is false, then your Big Sky Daddy must love you), and because you don't know what the evidence is.

And you will never learn, because you are too busy making up stupid predictions and lying about them later, and announcing that the evidence is all circular, without bothering to know what it is.

I have a question for you...do you think that anyone on this board could honestly lay out what you perceive the evidence against evolution to be?  I'm pretty sure lots of people can.

Do you honestly believe that you are capable of explaining what other people on this board believe to be the evidence in favor of evolution?

Because I and everyone else on this board know that you can't, but I'm curious to know if you think so.
Posted by: Daniel Smith on Oct. 28 2007,13:08

I'm going to ignore most of your post because it is laced with personal insults which have little or nothing to do with the subject.  You have attempted to make this thread about me, when it should be about the evidence.  Something you have devoted almost no time to discussing.  For instance, you say that my prediction about Acromobacter guttatus Sp. K172 has been falsified, but where is the cited study?  What specific parameters were used?  How many plates were used?  Were all the bacteria on each plate Acromobacter guttatus Sp. K172?  In short, where is your evidence?

 
Quote (swbarnes2 @ Oct. 26 2007,15:52)
So you believe that the persistant adaptiveness of parasites that kill a hundred thousand children a year reveals...what, exactly about God?

Please, be specific.

Or, you can say nothing, and we'll all understand why.
---------------------QUOTE-------------------


I will address this one thing you brought up, because it keeps getting asked (in one form or another - "Why HIV/AIDS ?", etc.).

The standard theological answer as to why there is disease and death, is due to the "Curse".  I don't know if you're familiar with Christian doctrine or not, but disease and death are expected from this theological perspective.
Posted by: Daniel Smith on Oct. 28 2007,13:10

What is your explanation as to why disease and death continue?
Posted by: Daniel Smith on Oct. 28 2007,13:20

Quote (Louis @ Oct. 26 2007,14:11)
   
Quote (Albatrossity2 @ Oct. 26 2007,19:59)
   
Quote (Daniel Smith @ Oct. 26 2007,13:56)
Where did he get the idea for azadirachtin?
---------------------QUOTE-------------------


From pixies.

Prove that he didn't!
---------------------QUOTE-------------------


WAS NOT!

It was leprechauns.

PROVE ME WRONG!!!!! (All science so far)

Louis
---------------------QUOTE-------------------


I'd argue that he got the idea from azadirachtin.

Arguing that Steve Ley is an "infinitely brilliant chemist", because he figured out how to synthesize something that already exists in a natural form, is like arguing that a cover band is brilliant because they can play someone else's music.  They might be great musicians, but they have not shown any creativity or originality by merely copying someone else's work.  They (and he) surely have not shown "infinite brilliance"!
Posted by: Daniel Smith on Oct. 28 2007,15:22

Back to another prediction I made:
   
Quote (Daniel Smith @ Sep. 30 2007,15:32)

The genetic code will be found to be more sophisticated and more robust than previously thought.
Embedded and overlapping coding will be found to be more prevalent than previously thought.

---------------------QUOTE-------------------



In researching the phenomena of overlapping genes, I found that their initial discovery in < bacteriophages > was followed by speculation that perhaps they evolved due to a lack of informational space in small genomes.  Their subsequent discovery in < viruses >  seemed to confirm this hypothesis.  
They were then discovered in mammalian mitochondrial DNA < (example) > - which led to speculation that they might be more common than previously thought.
They are.  I found < this article. > which shows that not only are overlapping genes fairly common in mammalian genomes, but there are even triple and quadruple overlaps! < (Table of triple overlaps for human and mouse genomes) >
And:
   

---------------------QUOTE-------------------
In the human genome we also found a segment with four exon overlapping genes: LOC338549, IDI2, HT009, and IDI1.
---------------------QUOTE-------------------



So it would seem, from a cursory browsing of the scientific literature, that my prediction is holding true so far.  Of course, one could argue that this data was already available when I made the prediction - so my prediction was dishonest.  Of course such an accusation would fly in the face of your collective observation regarding my complete lack of knowledge on the subjects of which I speak!  So either I'm much more cunning and aware than I let on, or my prediction is (for the time being at least) a good one.
Posted by: oldmanintheskydidntdoit on Oct. 28 2007,16:16

Quote (Daniel Smith @ Oct. 28 2007,15:22)
Back to another prediction I made:
       
Quote (Daniel Smith @ Sep. 30 2007,15:32)

The genetic code will be found to be more sophisticated and more robust than previously thought.
Embedded and overlapping coding will be found to be more prevalent than previously thought.

---------------------QUOTE-------------------



In researching the phenomena of overlapping genes, I found that their initial discovery in < bacteriophages > was followed by speculation that perhaps they evolved due to a lack of informational space in small genomes.  Their subsequent discovery in < viruses >  seemed to confirm this hypothesis.  
They were then discovered in mammalian mitochondrial DNA < (example) > - which led to speculation that they might be more common than previously thought.
They are.  I found < this article. > which shows that not only are overlapping genes fairly common in mammalian genomes, but there are even triple and quadruple overlaps! < (Table of triple overlaps for human and mouse genomes) >
And:
     

---------------------QUOTE-------------------
In the human genome we also found a segment with four exon overlapping genes: LOC338549, IDI2, HT009, and IDI1.
---------------------QUOTE-------------------



So it would seem, from a cursory browsing of the scientific literature, that my prediction is holding true so far.  Of course, one could argue that this data was already available when I made the prediction - so my prediction was dishonest.  Of course such an accusation would fly in the face of your collective observation regarding my complete lack of knowledge on the subjects of which I speak!  So either I'm much more cunning and aware than I let on, or my prediction is (for the time being at least) a good one.
---------------------QUOTE-------------------


Not really. It's like saying "there is more to find out" and when more is found out, it confirms your prediction.

Make a specific prediction, and then maybe crow about it when it comes true. I don't see the word "overlapping" in there.

The genetic code will be found to be more sophisticated and more robust than previously thought.

The < daleks > will be found to be more sophisticated and more robust than previously thought.

And look, they are! Prediction came true.
Posted by: JAM on Oct. 28 2007,16:58

Quote (Daniel Smith @ Oct. 28 2007,15:22)
Back to another prediction I made:
     
Quote (Daniel Smith @ Sep. 30 2007,15:32)

The genetic code will be found to be more sophisticated and more robust than previously thought.
Embedded and overlapping coding will be found to be more prevalent than previously thought.

---------------------QUOTE-------------------



In researching the phenomena of overlapping genes, I found that their initial discovery in < bacteriophages > was followed by speculation that perhaps they evolved due to a lack of informational space in small genomes.  Their subsequent discovery in < viruses >  seemed to confirm this hypothesis.  
They were then discovered in mammalian mitochondrial DNA < (example) > - which led to speculation that they might be more common than previously thought.
---------------------QUOTE-------------------


So your predictions, in addition to being horseshit because they aren't about anything in particular, have no ability to distinguish between evolutionary theory and whatever it is you think.

What do any of the data have to do with the genetic code, which really isn't very complex? What's so complex about coding for 20 amino acids, start, and stop in 64 codons? Or were you just using "genetic code" in a profoundly ignorant way? If not, would you mind commenting on the intelligence of having the same codon that starts protein synthesis also encoding the amino acid methionine?

I ask because it seems really, really stupid to me; I can improve the design with my measly human intelligence. Does that therefore make me smarter than God? Why would one want to worship an unintelligent God? Do you see how the ID movement is bad theology slathered onto nonexistent science?

Since your hypothesis about noncoding DNA was dead wrong, what's your revised hypothesis?
Posted by: Mark Iosim on Oct. 28 2007,18:35

I am puzzled with random mutation, because it reminds me the protein folding paradox that states: if a protein were to fold by randomly sampling of all possible conformations, it would take about 10E10 years to finish folding.

Can any body help me to find a source of information that explains how random mutation able to produce adaptive changes. What kind of statistical calculations supports this theory?

Thanks
Posted by: Richardthughes on Oct. 28 2007,19:40

Empirical observation shows it, as does Genetic Algorithms ability to solve seemingly intractable problems.
Posted by: JAM on Oct. 29 2007,00:10

Quote (Mark Iosim @ Oct. 28 2007,18:35)
I am puzzled with random mutation, because it reminds me the protein folding paradox that states: if a protein were to fold by randomly sampling of all possible conformations, it would take about 10E10 years to finish folding.

Can any body help me to find a source of information that explains how random mutation able to produce adaptive changes. What kind of statistical calculations supports this theory?

Thanks
---------------------QUOTE-------------------


Random mutation doesn't do it by itself. You've bought into the lie that evolution is random, just because a part of it (mutation) is random only in a very limited way (wrt fitness). Why would you buy into such an obvious lie?

Also, the amount of time it takes a protein to fold is irrelevant to your question, as is the computational time required to predict it. It folds.

How do you explain the fact that starting with a random sequence, we can use mutation and selection to evolve a function in real time?
Posted by: swbarnes2 on Oct. 29 2007,13:52



---------------------QUOTE-------------------
You have attempted to make this thread about me, when it should be about the evidence.
---------------------QUOTE-------------------



But the point is that you are immune to the evidence, because you aren't reasoning from evidence to conclusion.

You are starting with your conclusion, and looking for evidence to fit your conclusion, which is that a powerful God is looking out for you.

That is the key divide between yourself and the other people on this board, and until you see that, no oe can convince you of anything.

You already demonstrated that, when you looked at a presentation of the raw data, which showed that coding DNA was much more conserved than non-coding DNA, and you concluded that it showed the opposite.

There's just no point showing you evidence when your unacknowledged bias prevents you from seeing it properly.

 

---------------------QUOTE-------------------
For instance, you say that my prediction about Acromobacter guttatus Sp. K172 has been falsified, but where is the cited study?
---------------------QUOTE-------------------



Why the hell can't you look it up yourself?  Why is everyone but yourself responsible for the accuracy of your claims?

 

---------------------QUOTE-------------------
The standard theological answer as to why there is disease and death, is due to the "Curse".
---------------------QUOTE-------------------



Oh no.

You are lying again.

You said that nature reveals things about God, not about something else.

If you meant to say "100,000 dead children per year tell me that my god created world that was guarenteed to get horrible broken, and he refuses to lift a finger to help innocent children suffer and die becuase of that", then you should have been honest enough to say that.

Or if you meant "the great adaptability of the malaria parasite tells me that God thought it was a good idea to supernaturally aid the evolution of an organism that kills 100,000 children a year", you should have written that.

But saying that "I look at nature to tell me about God, and I conclude that this unpleasent bit of nature tells me nothing about God, but only confirms the story I already believe about a curse" is dishonest.

And I'm sorry that you object to that label, but all you have to do is stop posting dishonestly.

For starters, if you really, really think that the evolution of malaria, both in its ability to evade the human immune system, and its ability to resist drug treatments, both of which allow it to kill 1000,000 children a year tells you something about God, then tell us exactly what that something is.  (Hint: it has to start with "This tells me that God..." and that '...' has to be something other than "is so inscrutable that I refuse to conclude anything")
Posted by: swbarnes2 on Oct. 29 2007,14:07

Quote (Mark Iosim @ Oct. 28 2007,18:35)
I am puzzled with random mutation, because it reminds me the protein folding paradox that states: if a protein were to fold by randomly sampling of all possible conformations, it would take about 10E10 years to finish folding.

---------------------QUOTE-------------------



First of all, who told you that was true?  Does the source have any idea what they are talking about?

What you are saying is something like saying there's no way for the Colorado River to flow, because the water would have to test every single possible path from its source to the sea, and that would take longer thatn the earth has existed.

Well, first, the Colorado River does flow.  So saying that it can't without supernatural help is just crazy.  Second, the river flows the path it does because water goes downhill.  No supernatural influence necessary.

Proteins fold mostly the same way.  They fold in the way that their amnio acids naturally want to be arranged.  

 

---------------------QUOTE-------------------
Can any body help me to find a source of information that explains how random mutation able to produce adaptive changes.
---------------------QUOTE-------------------



DNA changes happen.  That's empirical fact.  Some of them help their bearers survive better.  That's also empirical fact.  Do you want papers where these empirical facts were observed?

 

---------------------QUOTE-------------------
What kind of statistical calculations supports this theory?
---------------------QUOTE-------------------



Rather than asking everyone here to re-invent the wheel for you, why don't you find a paper on this topic in PubMed, and come back here with any particular points which you feel are inadequately supported in that paper.

PLOS, or PNAS, or some other publically available journal would be best, of course.  But I'm sure that somone here will have a subscription to whatever peer-reviewed journal you choose to consult.
Posted by: Mark Iosim on Oct. 29 2007,19:57



---------------------QUOTE-------------------
JAM:
“Random mutation doesn't do it by itself. You've bought into the lie that evolution is random, just because a part of
it (mutation) is random only in a very limited way (wrt fitness). Why would you buy into such an obvious lie?”
---------------------QUOTE-------------------


It could be that inadvertently I was brainwashed or misunderstood the following passage from Wikipedia about adaptation:  
“Although the vast majority of genetic variants arising from errors of DNA replication or recombination do not confer any advantage to an individual organism, the multitude of variation contained within the collective genomes of a species provides much material for natural selection to work upon allowing many adaptations to be manifest.”
If  “errors of DNA replication or recombination” are not random, the only option remains is that mutation of DNA is directed by some mechanisms that I am not aware of. Do you know anything about these mechanisms?


---------------------QUOTE-------------------
JAM:
“Also, the amount of time it takes a protein to fold is irrelevant to your question, as is the computational time required to predict it. It folds.”
---------------------QUOTE-------------------


It is very relevant, because Levinthal paradox simply serves as reminder that purely random search may not succeed. Later were indeed found the specialized proteins, called chaperones, whose functions are to aid in the folding of other proteins.


---------------------QUOTE-------------------
JAM:
“How do you explain the fact that starting with a random sequence, we can use mutation and selection to evolve a function in real time?”
---------------------QUOTE-------------------


I don't know. Do you?



---------------------QUOTE-------------------
swbarnes2:
“What you are saying is something like saying there's no way for the Colorado River to flow, because the water would have to test every single possible path from its source to the sea, and that would take longer that the earth has existed.
Well, first, the Colorado River does flow.  So saying that it can't without supernatural help is just crazy.  Second, the river flows the path it does because water goes downhill.  No supernatural influence necessary.
Proteins fold mostly the same way.  They fold in the way that their amnio acids naturally want to be arranged.”
---------------------QUOTE-------------------


Interesting point. I have an answer, but it is long and  irrelevant to the topic of this thread as well as your question.

P.S. For the record, I have no problem with Darwin and his theory. For his time it was an enormous achievement.  I just have a problem that some scientists do not admit that the mechanism of biological evolution is still a mystery. And it remains a  mystery not only because we are separated from it by a million years; it remains a mystery even we are staring at a colony of microorganism adapting to harmful conditions created in a laboratory.

Also about one comment about dishonesty.
From Wikipedia:
“There are three basic mechanisms of evolutionary change: natural selection, genetic drift, and gene flow. Natural selection favors genes that improve capacity for survival and reproduction.”
The authors of this articles forgot to include the main mechanism of evolutionary change that is called UNKNOWN. And absence of this admission is a very relevant to subject of dishonesty.
Posted by: Erasmus, FCD on Oct. 29 2007,20:09

.

---------------------QUOTE-------------------
mutation of DNA is directed by some mechanisms that I am not aware of. Do you know anything about these mechanisms?
---------------------QUOTE-------------------



do you?  RB has postulated the existence of tiny little dudes called 'Behes' that snip away at Things with directions from Thing-Think upstairs.  Is that how you view evolution?  

of course random means unplanned, random with respect to an organism's 'need'.  

of course it's not 'random' as in 'anyfuckingthingcouldhappenhere'.

what can happen is constrained by what has happened.  what can happen is constrained by what could happen.  read gould and the river analogy.  and stop being redundantly ignorant
Posted by: Henry J on Oct. 29 2007,22:55



---------------------QUOTE-------------------
It could be that inadvertently I was brainwashed or misunderstood the following passage from Wikipedia about adaptation:  

?Although the vast majority of genetic variants arising from errors of DNA replication or recombination do not confer any advantage to an individual organism, the multitude of variation contained within the collective genomes of a species provides much material for natural selection to work upon allowing many adaptations to be manifest.?

If ?errors of DNA replication or recombination? are not random, the only option remains is that mutation of DNA is directed by some mechanisms that I am not aware of. Do you know anything about these mechanisms?
---------------------QUOTE-------------------



The anwswer to that question was right there in what you quoted: "provides much material for natural selection to work upon allowing many adaptations to be manifest".

Henry
Posted by: Richard Simons on Oct. 30 2007,08:22



---------------------QUOTE-------------------
If  “errors of DNA replication or recombination” are not random, the only option remains is that mutation of DNA is directed by some mechanisms that I am not aware of.
---------------------QUOTE-------------------


No. Errors of DNA replication are not random because some changes are easier to make than others. There is no evidence of any directing agency, either in the DNA changes that occur or in the resulting changes to the phenotype (if any).
Posted by: swbarnes2 on Oct. 30 2007,11:42

Quote (Mark Iosim @ Oct. 29 2007,19:57)
Also
From Wikipedia:
“There are three basic mechanisms of evolutionary change: natural selection, genetic drift, and gene flow. Natural selection favors genes that improve capacity for survival and reproduction.”
The authors of this articles forgot to include the main mechanism of evolutionary change that is called UNKNOWN. And absence of this admission is a very relevant to subject of dishonesty.
---------------------QUOTE-------------------



First of all, Wikipedia is hardly the be-all-end-all of evolutionary theory.  It's just a Wiki.

What defines a scientific theory is what's written in the peer-reviewed journal articles.  

If you think that the Wiki is wrong, find us a peer-reviewed paper that you think supports your case.

For instance, point us to the paper in which something is obsserved that is not explicable by the current theory.

It would be preferable to use a journal like PLOS or PNAS, because then everyone can read along, but if the paper is somewhere else, I'm sure that someone here will be able to read it and comment on it.

Second, just because you are unhappy with what you think the current theory of evolution is doesn't mean that there is a serious void in the current theory.

Certainly, you just saying so with absolutely no evidence is convincing to absolutely no one.

You want to impress us?  Stop citing Wikis, start reading and citing peer-reviewed papers.
Posted by: VMartin on Oct. 30 2007,12:00

Erasmus
     

---------------------QUOTE-------------------

what can happen is constrained by what has happened.  what can happen is constrained by what could happen.  read gould and the river analogy.  and stop being redundantly ignorant.

---------------------QUOTE-------------------



Yes, if you like to be bored and sleepy read Gould. If you want something intelligent read Franz Heikertinger and especially Adolf Portmann and Zdenek Neubauer. These prominent scientists published in peer-reviewed journals - the last one in Nature - and were/are no way darwinists.

Evolution is a process little bit more complicated as your weird idea how  natural selection created human or mimicry of ants. Your sentence above: "what can happen is constrained by what has happened " is an extraordinary vague darwinian nonsense.
Posted by: Erasmus, FCD on Oct. 30 2007,12:10

Vicky



---------------------QUOTE-------------------
Your sentence above: "what can happen is constrained by what has happened " is an extraordinary vague darwinian nonsense.
---------------------QUOTE-------------------



I suppose we could substitute your preference:


Posted by: Erasmus, FCD on Oct. 30 2007,12:29

I looked up Neubauer.  Wonder why none of his 'Rivista' articles have ever been cited?

Could it be because the magical 'morphogenetic field' is a kooky harebrained idea with no evidence behind this?

Hasn't PZ spanked you enough about this?
Posted by: Erasmus, FCD on Oct. 30 2007,12:35

Martin are you the translator for the wiki german page into english?



---------------------QUOTE-------------------
Another time and again in Port's research and publications occurring theme is the external shape of animals, particularly in his work "The animal shape", "camouflage in the animal kingdom" and "New Ways of biology." Portland man is here already to his lifetime hotly disputed theory that the design of the surface is not readily from their adaptive value annulled. S His empirically and theoretically well criticism of extremely adaptionistischen ideas is currently also for those left to deal with his concept of "presentation value" is not liked.
---------------------QUOTE-------------------


Posted by: VMartin on Oct. 30 2007,12:53

Quote (Erasmus @ FCD,Oct. 30 2007,12:29)
I looked up Neubauer.  Wonder why none of his 'Rivista' articles have ever been cited?

Could it be because the magical 'morphogenetic field' is a kooky harebrained idea with no evidence behind this?

Hasn't PZ spanked you enough about this?
---------------------QUOTE-------------------


I suppose your knowledge of foreign languages other than English is limited. Otherwise you would read some materials before babbling nonsense about professor Zdenek Neubauer.
Posted by: Erasmus, FCD on Oct. 30 2007,13:00

If it was worth a damn, in 2007, it would be translated.  This is not a monk growing peas here.

Martin, is there a material explanation for your 'morphic fields'?  If not, why do you disagree with your german structuralist predecessors who were strongly convinced that there WAS a material explanation?

Gould is not as hard on them as he could have been.  I wonder if you understand why that is.

< More of Vicky's shenanigans, elsewhere, same effect >
Posted by: Daniel Smith on Oct. 30 2007,13:52

Quote (oldmanintheskydidntdoit @ Oct. 28 2007,16:16)
 
Quote (Daniel Smith @ Oct. 28 2007,15:22)
Back to another prediction I made:
         
Quote (Daniel Smith @ Sep. 30 2007,15:32)

The genetic code will be found to be more sophisticated and more robust than previously thought.
Embedded and overlapping coding will be found to be more prevalent than previously thought.

---------------------QUOTE-------------------




---------------------QUOTE-------------------


Not really. It's like saying "there is more to find out" and when more is found out, it confirms your prediction.

Make a specific prediction, and then maybe crow about it when it comes true. I don't see the word "overlapping" in there.
---------------------QUOTE-------------------


You must've missed it.
Posted by: Daniel Smith on Oct. 30 2007,13:59

Quote (JAM @ Oct. 29 2007,00:10)
Random mutation doesn't do it by itself. You've bought into the lie that evolution is random, just because a part of it (mutation) is random only in a very limited way (wrt fitness). Why would you buy into such an obvious lie?
---------------------QUOTE-------------------

You're right.  Evolution is not random.

---------------------QUOTE-------------------
How do you explain the fact that starting with a random sequence, we can use mutation and selection to evolve a function in real time?
---------------------QUOTE-------------------


My guess is that it has to do with the selection criteria.  With a specific goal in mind, random solutions can be consecutively selected until they actually build something useful.

The main reason these types of selection algorithms work is because they select for potential.

Natural selection is not so kind.
Posted by: IanBrown_101 on Oct. 30 2007,14:18

Is it just me, or are you Daniel trying to force God into some real science?

I mean when you say things like it's your "guess" that structures are being designed by evolution, aren't you just saying that since the general direction of evolution after stages a and b seems to be towards z, therefore something designed it to be z?

Seems like a whole lot of straw clutching there.
Posted by: C.J.O'Brien on Oct. 30 2007,14:19



---------------------QUOTE-------------------
My guess is that it has to do with the selection criteria.  With a specific goal in mind, random solutions can be consecutively selected until they actually build something useful.

The main reason these types of selection algorithms work is because they select for potential.

Natural selection is not so kind.
---------------------QUOTE-------------------



You're wrong, Daniel.
See
< here > and < here > for an object lesson in Evolutionary Computation.
Posted by: oldmanintheskydidntdoit on Oct. 30 2007,14:22

Quote (Daniel Smith @ Oct. 30 2007,13:52)
Quote (oldmanintheskydidntdoit @ Oct. 28 2007,16:16)
 
Quote (Daniel Smith @ Oct. 28 2007,15:22)
Back to another prediction I made:
           
Quote (Daniel Smith @ Sep. 30 2007,15:32)

The genetic code will be found to be more sophisticated and more robust than previously thought.
Embedded and overlapping coding will be found to be more prevalent than previously thought.

---------------------QUOTE-------------------




---------------------QUOTE-------------------


Not really. It's like saying "there is more to find out" and when more is found out, it confirms your prediction.

Make a specific prediction, and then maybe crow about it when it comes true. I don't see the word "overlapping" in there.
---------------------QUOTE-------------------


You must've missed it.
---------------------QUOTE-------------------


Permalink? Not that I don't trust you or anything, but I am willing to be proven wrong.
Posted by: JAM on Oct. 30 2007,15:05

Quote (Daniel Smith @ Oct. 30 2007,13:59)
 

---------------------QUOTE-------------------
How do you explain the fact that starting with a random sequence, we can use mutation and selection to evolve a function in real time?
---------------------QUOTE-------------------


My guess is that it has to do with the selection criteria.
---------------------QUOTE-------------------


There was a single criterion in the case to which I'm referring: reproduction. Does that help?
 

---------------------QUOTE-------------------
With a specific goal in mind, random solutions can be consecutively selected until they actually build something useful.
---------------------QUOTE-------------------


But there was no specific goal in this case, just reproduction.
 

---------------------QUOTE-------------------
The main reason these types of selection algorithms work is because they select for potential.
---------------------QUOTE-------------------


There was no selection for potential in this case. I'm amazed at the way you view your speculations as more relevant than reality.
 

---------------------QUOTE-------------------
Natural selection is not so kind.
---------------------QUOTE-------------------


This was no different, with the exception of the elimination of competition from outside the initial pool. How do you explain it? More importantly, why would you attempt to explain it when you don't have a clue to begin with?
Posted by: Daniel Smith on Oct. 31 2007,18:20

Quote (IanBrown_101 @ Oct. 30 2007,14:18)
Is it just me, or are you Daniel trying to force God into some real science?

I mean when you say things like it's your "guess" that structures are being designed by evolution, aren't you just saying that since the general direction of evolution after stages a and b seems to be towards z, therefore something designed it to be z?

Seems like a whole lot of straw clutching there.
---------------------QUOTE-------------------


I'm talking about computer simulations - not real evolution.
Posted by: Daniel Smith on Oct. 31 2007,18:25

Quote (C.J.O'Brien @ Oct. 30 2007,14:19)


---------------------QUOTE-------------------
My guess is that it has to do with the selection criteria.  With a specific goal in mind, random solutions can be consecutively selected until they actually build something useful.

The main reason these types of selection algorithms work is because they select for potential.

Natural selection is not so kind.
---------------------QUOTE-------------------



You're wrong, Daniel.
See
< here > and < here > for an object lesson in Evolutionary Computation.
---------------------QUOTE-------------------


He doesn't give us his selection algorithm, so how can we know if it selects for potential?
Posted by: Daniel Smith on Oct. 31 2007,18:27

Quote (oldmanintheskydidntdoit @ Oct. 30 2007,14:22)
Quote (Daniel Smith @ Oct. 30 2007,13:52)
Quote (oldmanintheskydidntdoit @ Oct. 28 2007,16:16)
   
Quote (Daniel Smith @ Oct. 28 2007,15:22)
Back to another prediction I made:
           
Quote (Daniel Smith @ Sep. 30 2007,15:32)

The genetic code will be found to be more sophisticated and more robust than previously thought.
Embedded and overlapping coding will be found to be more prevalent than previously thought.

---------------------QUOTE-------------------




---------------------QUOTE-------------------


Not really. It's like saying "there is more to find out" and when more is found out, it confirms your prediction.

Make a specific prediction, and then maybe crow about it when it comes true. I don't see the word "overlapping" in there.
---------------------QUOTE-------------------


You must've missed it.
---------------------QUOTE-------------------


Permalink? Not that I don't trust you or anything, but I am willing to be proven wrong.
---------------------QUOTE-------------------


< Permalink >
Posted by: Daniel Smith on Oct. 31 2007,18:35

Quote (JAM @ Oct. 30 2007,15:05)
 
Quote (Daniel Smith @ Oct. 30 2007,13:59)
     

---------------------QUOTE-------------------
How do you explain the fact that starting with a random sequence, we can use mutation and selection to evolve a function in real time?
---------------------QUOTE-------------------


My guess is that it has to do with the selection criteria.
---------------------QUOTE-------------------


There was a single criterion in the case to which I'm referring: reproduction. Does that help?
     

---------------------QUOTE-------------------
With a specific goal in mind, random solutions can be consecutively selected until they actually build something useful.
---------------------QUOTE-------------------


But there was no specific goal in this case, just reproduction.
   

---------------------QUOTE-------------------
The main reason these types of selection algorithms work is because they select for potential.
---------------------QUOTE-------------------


There was no selection for potential in this case. I'm amazed at the way you view your speculations as more relevant than reality.
     

---------------------QUOTE-------------------
Natural selection is not so kind.
---------------------QUOTE-------------------


This was no different, with the exception of the elimination of competition from outside the initial pool. How do you explain it? More importantly, why would you attempt to explain it when you don't have a clue to begin with?
---------------------QUOTE-------------------


The more you say, the less I understand you.

If you want specific, detailed answers, why don't you try starting with a specific example - rather than a vague question?
This:


---------------------QUOTE-------------------
How do you explain the fact that starting with a random sequence, we can use mutation and selection to evolve a function in real time?
---------------------QUOTE-------------------


Gives us no information.  I was forced to speculate that you were referring to computer simulations of evolution.  Is that what you were talking about?  Or were you referring to something else?  If a simulation, please show me the info - including the selection algorithm - so I can get a better idea how it works.  
If you're not willing to give any more info, then be satisfied with general answers.
Posted by: C.J.O'Brien on Oct. 31 2007,18:35

Here you go Daniel. Find me the potential. < FORTRAN Code for Dave Thomas's Steiner Tree GA >
Posted by: C.J.O'Brien on Oct. 31 2007,18:38

Note also, that in a strict and very real sense these are not "simulations of evolution."

GA's like these we are speaking of are instantiations of real, no-kidding, actual Darwinian processes.

Hope that clears up your misunderstanding of JAM's post.
Posted by: Daniel Smith on Oct. 31 2007,19:08

More confirmation:

From the paper, "Unbiased Mapping of Transcription Factor Binding Sites along Human Chromosomes 21 and 22 Points to Widespread Regulation of Noncoding RNAs"
< link >
         

---------------------QUOTE-------------------
To further explore properties of the transcriptome and to identify functional attributes of the noncoding transcripts, binding sites for a collection of transcription factors have been mapped along chromosomes 21 and 22 in an unbiased approach, as a means of identifying possible regulatory regions for a wide variety of cellular RNAs. Interestingly, only 22% of the transcription factor binding sites (TFBS) are located at the canonical 5? termini of well-characterized protein-coding genes, while 36% lie within of immediately 3? to well-characterized genes and are significantly correlated with noncoding RNAs. A number of these noncoding RNAs are regulated in response to retinoic acid stimulation, and coregulation of overlapping pairs of protein-coding and noncoding RNAs occurs at a frequency significantly greater than chance. These data point to evidence that protein coding and noncoding genes have similar functional attributes regarding (1) the existence of common transcription factors in their promoter regions and (2) their ability to respond to environmental and developmental conditions, which together suggest that that they may be controlled by the same transcriptional regulatory machinery. These functional attributes argue against the idea that these noncoding RNAs merely represent transcriptional noise, but instead suggest that they may have biological functions. (my emphasis)
---------------------QUOTE-------------------

And...        

---------------------QUOTE-------------------
Additionally, overlapping novel transcripts from the genes encoding nuclear protein UBASH3A (Supplemental Figures S2A and S2B), phosphatidylinositol transfer-like protein SEC14L2 (Supplemental Figures S2C and S2D), TBC/rabGAP domain protein EPI64 (Supplemental Figures S2E and S2F), guanine-nucleotide exchange factor TIAM1 (Supplemental Figures S2G and S2H), KIAA0376 protein (Supplemental Figures S2I and S2J), and GTSE1 (Supplemental Figures S2K and S2L) were verified by RT-PCR and/or Northern blot analyses (Supplemental Figure S3). In many of these cases, the TFBS that are located on the 3? end of the well-characterized gene appear to be located 5? of the overlapping novel transcript, which suggests that these transcripts may be regulated by these factors and in precisely the same way as protein coding genes. (my emphasis)
---------------------QUOTE-------------------



So not only is the myth of "junk DNA" being systematically shattered, but they are also finding evidence that coding and non-coding sequences not only overlap each other, but also share regulatory factors.
Posted by: JAM on Oct. 31 2007,19:09

Quote (C.J.O'Brien @ Oct. 31 2007,18:38)
Note also, that in a strict and very real sense these are not "simulations of evolution."

GA's like these we are speaking of are instantiations of real, no-kidding, actual Darwinian processes.

Hope that clears up your misunderstanding of JAM's post.
---------------------QUOTE-------------------


Actually, I wasn't talking about computers at all, but real biology.
Posted by: JAM on Oct. 31 2007,19:17

Quote (Daniel Smith @ Oct. 31 2007,18:35)
 
Quote (JAM @ Oct. 30 2007,15:05)
     
Quote (Daniel Smith @ Oct. 30 2007,13:59)
         

---------------------QUOTE-------------------
How do you explain the fact that starting with a random sequence, we can use mutation and selection to evolve a function in real time?
---------------------QUOTE-------------------


My guess is that it has to do with the selection criteria.
---------------------QUOTE-------------------


There was a single criterion in the case to which I'm referring: reproduction. Does that help?
         

---------------------QUOTE-------------------
With a specific goal in mind, random solutions can be consecutively selected until they actually build something useful.
---------------------QUOTE-------------------


But there was no specific goal in this case, just reproduction.
       

---------------------QUOTE-------------------
The main reason these types of selection algorithms work is because they select for potential.
---------------------QUOTE-------------------


There was no selection for potential in this case. I'm amazed at the way you view your speculations as more relevant than reality.
         

---------------------QUOTE-------------------
Natural selection is not so kind.
---------------------QUOTE-------------------


This was no different, with the exception of the elimination of competition from outside the initial pool. How do you explain it? More importantly, why would you attempt to explain it when you don't have a clue to begin with?
---------------------QUOTE-------------------


The more you say, the less I understand you.
---------------------QUOTE-------------------


You have to do that, otherwise you might have to give up your fantasies for the truth.


---------------------QUOTE-------------------
If you want specific, detailed answers, why don't you try starting with a specific example - rather than a vague question?
---------------------QUOTE-------------------


Because there are many such cases. I'm asking for your explanation, and you came back with nothing but false suppositions.



---------------------QUOTE-------------------
This:
   

---------------------QUOTE-------------------
How do you explain the fact that starting with a random sequence, we can use mutation and selection to evolve a function in real time?
---------------------QUOTE-------------------


Gives us no information.  I was forced to speculate that you were referring to computer simulations of evolution.  Is that what you were talking about?
---------------------QUOTE-------------------


Not at all! I can see why you would assume that I wasn't talking about actual biology, though. ;-)

Why wouldn't you ask before spouting nonsense?


---------------------QUOTE-------------------
Or were you referring to something else? If a simulation, please show me the info - including the selection algorithm - so I can get a better idea how it works.
---------------------QUOTE-------------------


It's biology. You delete a gene with an essential function. You replace it with random sequence. You go through cycles of genetic variation (random wrt fitness) and selection (only reproduction).

You end up with a functional sequence that is nothing like the designed/evolved one that it replaced.

How do you explain that?



---------------------QUOTE-------------------
If you're not willing to give any more info, then be satisfied with general answers.
---------------------QUOTE-------------------


You didn't give any answers, just false suppositions. You're afraid of the truth.

Here's another question: how long does it take to evolve multiple, different, incredibly specific, functional, new protein-protein binding sites, using nothing but genetic variation and selection?
Posted by: JAM on Oct. 31 2007,19:26

Quote (Daniel Smith @ Oct. 31 2007,19:08)
More confirmation:
---------------------QUOTE-------------------


Of what?

Did you read this?



---------------------QUOTE-------------------
By combining chromatin immunoprecipitation and high-density oligonucleotide arrays interrogating the [bold]nonrepeat[/bold] genomic sequences of chromosomes 21 and 22 at 35 base pair (bp) resolution (Kapranov et al., 2002), the positions of binding for three human transcription factors (TFs), cMyc, Sp1, and p53, were determined within two cell lines (cMyc and Sp1 in Jurkat, p53 in HCT1116).
---------------------QUOTE-------------------



What does "nonrepeat" mean, Daniel? What proportion of "junk" is repeat, and what proportion is nonrepeat (unique)?



---------------------QUOTE-------------------
So not only is the myth of "junk DNA" being systematically shattered, but they are also finding evidence that coding and non-coding sequences not only overlap each other, but also share regulatory factors.
---------------------QUOTE-------------------



How much DNA was reclassified as something other than the provisional classification of "junk" in this case?

What proportion of the genome? Be precise and systematic.

What proportion of the genome did they throw out when they only looked at "nonrepeat" sequences? Be precise and systematic.

You lie like a rug, Daniel. The fact that you're lying to yourself doesn't excuse your behavior.
Posted by: Daniel Smith on Oct. 31 2007,19:42

Quote (C.J.O'Brien @ Oct. 31 2007,18:38)
Note also, that in a strict and very real sense these are not "simulations of evolution."

GA's like these we are speaking of are instantiations of real, no-kidding, actual Darwinian processes.
---------------------QUOTE-------------------


Therein lies the difference.  "Darwinian processes", when coupled with strict selection criteria (which conform to a specific goal), can take any random sequence and eventually meet that goal.

Real Darwinian evolution however, has no goal.  Reproductive fitness is seen as a valid section criteria, but it cannot be the reason for the variety of lifeforms we see.  If reproductive fitness was the goal, nothing beyond bacteria would have ever evolved - since they are probably the fittest reproducers on the planet.

So, if you want to postulate a mechanism for evolution, you must show one that is capable of producing vast complexity without a goal.

Therein lies the conundrum for your theory.
Posted by: IanBrown_101 on Oct. 31 2007,19:57

Quote (Daniel Smith @ Nov. 01 2007,01:42)
Quote (C.J.O'Brien @ Oct. 31 2007,18:38)
Note also, that in a strict and very real sense these are not "simulations of evolution."

GA's like these we are speaking of are instantiations of real, no-kidding, actual Darwinian processes.
---------------------QUOTE-------------------


Therein lies the difference.  "Darwinian processes", when coupled with strict selection criteria (which conform to a specific goal), can take any random sequence and eventually meet that goal.

Real Darwinian evolution however, has no goal.  Reproductive fitness is seen as a valid section criteria, but it cannot be the reason for the variety of lifeforms we see.  If reproductive fitness was the goal, nothing beyond bacteria would have ever evolved - since they are probably the fittest reproducers on the planet.

So, if you want to postulate a mechanism for evolution, you must show one that is capable of producing vast complexity without a goal.

Therein lies the conundrum for your theory.
---------------------QUOTE-------------------


Errr.....No.


They are indeed fittest, but only for their niche. If one happened to spawn various things which put it on a track to (eventually) become multicellular, then these would have distinct advantage, in certain conditions. You can't put all animals on one scale of "fitness", that would be simplistic.

And idiotic.
Posted by: swbarnes2 on Oct. 31 2007,20:05

Quote (Daniel Smith @ Oct. 31 2007,19:08)
So not only is the myth of "junk DNA" being systematically shattered,
---------------------QUOTE-------------------



I'm curious...do you honestly think that the authors who wrote this paper think that they have shattered major parts of the theory of evolution, as you think this paper has?

If not, why do you think that we should take your grossly ignorant opnion over theirs?
Posted by: David Holland on Oct. 31 2007,21:11

Quote (Daniel Smith @ Oct. 31 2007,19:42)
Real Darwinian evolution however, has no goal.  Reproductive fitness is seen as a valid section criteria, but it cannot be the reason for the variety of lifeforms we see.  If reproductive fitness was the goal, nothing beyond bacteria would have ever evolved - since they are probably the fittest reproducers on the planet.
---------------------QUOTE-------------------



If I have a petri dish with bacteria that are reproducing once an hour and add something to the petri dish that only reproduces once a day but eats the bacteria, will that new organism flourish? Of course it will. It is exploiting an empty niche in the petri dish. There is more to fitness that speed of reproduction.
Posted by: JAM on Oct. 31 2007,21:43

Quote (swbarnes2 @ Oct. 31 2007,20:05)
Quote (Daniel Smith @ Oct. 31 2007,19:08)
So not only is the myth of "junk DNA" being systematically shattered,
---------------------QUOTE-------------------



I'm curious...do you honestly think that the authors who wrote this paper think that they have shattered major parts of the theory of evolution, as you think this paper has?

If not, why do you think that we should take your grossly ignorant opnion over theirs?
---------------------QUOTE-------------------


In addition, why aren't these discoveries being made by ID proponents...like, um, at the Discovery Institute?

Why aren't discoveries like these motivating people like you to start careers in science?

You know you're desperately spinning this, and you don't even believe your own spin.
Posted by: Henry J on Oct. 31 2007,22:08

I'd think having a specific goal would probably produce less diversity than what we see on this planet. As it is, the effective goal of the members of a population is to out produce their relatives in their current environment - and the environment is different for every species, since every species is part of the environment of all their neighbors.

I'd also think that much of the complexity is a result of dealing with the neighbors (i.e., predators, prey, competitors, or pests that arne't in those other categories), and needing lots of different strategies to do that.

Henry
Posted by: VMartin on Nov. 01 2007,02:59

Quote (Henry J @ Oct. 31 2007,22:08)
I'd think having a specific goal would probably produce less diversity than what we see on this planet. As it is, the effective goal of the members of a population is to out produce their relatives in their current environment - and the environment is different for every species, since every species is part of the environment of all their neighbors.

I'd also think that much of the complexity is a result of dealing with the neighbors (i.e., predators, prey, competitors, or pests that arne't in those other categories), and needing lots of different strategies to do that.

Henry
---------------------QUOTE-------------------


I suppose it was Gould who noticed that higher intelligence must have had liking in beetles because there are so many beetles species. Anyway the same argument can be used for "natural selection" -  Natural selection must have had liking in forming beetles because there are so many species.

Obviously even greatest darwinian  fantasy could not explain some weird creatures like Bocydium, Sphongorus - species, Cyphonia . No wonder that "natural selection" make wrong conclusions as to the nature of many cases of mimicry as discussed elsewhere.
Posted by: oldmanintheskydidntdoit on Nov. 01 2007,03:49

Quote (VMartin @ Nov. 01 2007,02:59)
Obviously even greatest darwinian  fantasy could not explain some weird creatures like Bocydium, Sphongorus - species, Cyphonia . No wonder that "natural selection" make wrong conclusions as to the nature of many cases of mimicry as discussed elsewhere.
---------------------QUOTE-------------------


That's a very astute observation VMartin.

I don't suppose you'd care to note the "correct" conclusion in this case if "natural selection" is not the answer?

I'm surprised you don't have your own lab already VMartin, and a research team.

Your cutting insights sure leave these poor darwinists gasping for words.

Your forward looking thinking puts Dawkins, Gould etc to shame. I can't wait to read your book, your first book that is, as no doubt your eventual output will rival Dawkins etc.

I look forward to your receiving the Nobel, when they recognize your so-far hidden genius. You deserve it.
Posted by: Daniel Smith on Nov. 01 2007,19:29

Quote (JAM @ Oct. 31 2007,19:17)
It's biology. You delete a gene with an essential function. You replace it with random sequence. You go through cycles of genetic variation (random wrt fitness) and selection (only reproduction).

You end up with a functional sequence that is nothing like the designed/evolved one that it replaced.

How do you explain that?
---------------------QUOTE-------------------


Be more specific.  Show me the paper that describes this experiment.  I will no longer answer your questions unless you provide complete explanations with references.
Posted by: JAM on Nov. 01 2007,19:37

Quote (Daniel Smith @ Nov. 01 2007,19:29)
Quote (JAM @ Oct. 31 2007,19:17)
It's biology. You delete a gene with an essential function. You replace it with random sequence. You go through cycles of genetic variation (random wrt fitness) and selection (only reproduction).

You end up with a functional sequence that is nothing like the designed/evolved one that it replaced.

How do you explain that?
---------------------QUOTE-------------------


Be more specific.  Show me the paper that describes this experiment.  I will no longer answer your questions unless you provide complete explanations with references.
---------------------QUOTE-------------------


Your petulant demand is pretty damn funny, coming from a guy who claims that a paper in which the authors explicitly told him that they weren't looking at repeated sequences has something global to say about junk DNA. Moreover, you don't have the integrity to address that problem when I pointed it out to you.

OK, I'll give in to your whining, but you have to answer a question first.

What level reduction do you consider to represent lack of function? For example, if your heart rate was reduced a million-fold, to ~1 beat every 10 days, you'd be dead. Would you agree that your heart failed to function--that it was not meeting design criteria, so to speak?
Posted by: Daniel Smith on Nov. 01 2007,19:48

Quote (JAM @ Oct. 31 2007,19:26)
 
Quote (Daniel Smith @ Oct. 31 2007,19:08)
More confirmation:
---------------------QUOTE-------------------


Of what?

Did you read this?
---------------------QUOTE-------------------


Yes I did.
 

---------------------QUOTE-------------------

   

---------------------QUOTE-------------------
By combining chromatin immunoprecipitation and high-density oligonucleotide arrays interrogating the [bold]nonrepeat[/bold] genomic sequences of chromosomes 21 and 22 at 35 base pair (bp) resolution (Kapranov et al., 2002), the positions of binding for three human transcription factors (TFs), cMyc, Sp1, and p53, were determined within two cell lines (cMyc and Sp1 in Jurkat, p53 in HCT1116).
---------------------QUOTE-------------------



What does "nonrepeat" mean, Daniel?
---------------------QUOTE-------------------

Just what it says.  

---------------------QUOTE-------------------
What proportion of "junk" is repeat, and what proportion is nonrepeat (unique)?
---------------------QUOTE-------------------

There is no junk  

---------------------QUOTE-------------------


   

---------------------QUOTE-------------------
So not only is the myth of "junk DNA" being systematically shattered, but they are also finding evidence that coding and non-coding sequences not only overlap each other, but also share regulatory factors.
---------------------QUOTE-------------------



How much DNA was reclassified as something other than the provisional classification of "junk" in this case?
---------------------QUOTE-------------------

They didn't specifically mention "junk".  

---------------------QUOTE-------------------


What proportion of the genome? Be precise and systematic.

---------------------QUOTE-------------------

Since they didn't refer to any portion of the genome as junk, I cannot answer that.  

---------------------QUOTE-------------------

What proportion of the genome did they throw out when they only looked at "nonrepeat" sequences? Be precise and systematic.
---------------------QUOTE-------------------

I could not find that information in the paper.   Are you equating repeat sequences with "junk"?  

---------------------QUOTE-------------------


You lie like a rug, Daniel. The fact that you're lying to yourself doesn't excuse your behavior.
---------------------QUOTE-------------------


I know: "Liar, liar - pants on fire!"
What are we - in 3rd grade here?
You may be a smart, educated guy - but you're socially retarded.
Posted by: Daniel Smith on Nov. 01 2007,19:50

Quote (JAM @ Nov. 01 2007,19:37)
 
Quote (Daniel Smith @ Nov. 01 2007,19:29)
   
Quote (JAM @ Oct. 31 2007,19:17)
It's biology. You delete a gene with an essential function. You replace it with random sequence. You go through cycles of genetic variation (random wrt fitness) and selection (only reproduction).

You end up with a functional sequence that is nothing like the designed/evolved one that it replaced.

How do you explain that?
---------------------QUOTE-------------------


Be more specific.  Show me the paper that describes this experiment.  I will no longer answer your questions unless you provide complete explanations with references.
---------------------QUOTE-------------------


Your petulant demand is pretty damn funny, coming from a guy who claims that a paper in which the authors explicitly told him that they weren't looking at repeated sequences has something global to say about junk DNA. Moreover, you don't have the integrity to address that problem when I pointed it out to you.

OK, I'll give in to your whining, but you have to answer a question first.

What level reduction do you consider to represent lack of function? For example, if your heart rate was reduced a million-fold, to ~1 beat every 10 days, you'd be dead. Would you agree that your heart failed to function--that it was not meeting design criteria, so to speak?
---------------------QUOTE-------------------


No more games.  Show me the paper.
Posted by: Erasmus, FCD on Nov. 01 2007,19:54

Vicky

It was Haldane.  You know even less than you think.
Posted by: JAM on Nov. 01 2007,20:02

Quote (Daniel Smith @ Nov. 01 2007,19:48)
   
Quote (JAM @ Oct. 31 2007,19:26)
 What proportion of "junk" is repeat, and what proportion is nonrepeat (unique)?
---------------------QUOTE-------------------

There is no junk
---------------------QUOTE-------------------


I'm sorry, but I don't understand your sentence fragment.
 

---------------------QUOTE-------------------
 

---------------------QUOTE-------------------


---------------------QUOTE-------------------
So not only is the myth of "junk DNA" being systematically shattered, but they are also finding evidence that coding and non-coding sequences not only overlap each other, but also share regulatory factors.
---------------------QUOTE-------------------


How much DNA was reclassified as something other than the provisional classification of "junk" in this case?
---------------------QUOTE-------------------

They didn't specifically mention "junk".
---------------------QUOTE-------------------


Of course not! YOU did, and you said that THIS PAPER was the evidence. Which one of us is the tard here?
 

---------------------QUOTE-------------------
 

---------------------QUOTE-------------------
What proportion of the genome? Be precise and systematic.

---------------------QUOTE-------------------

Since they didn't refer to any portion of the genome as junk, I cannot answer that.
---------------------QUOTE-------------------


The answer isn't in the paper. You'd have to know the answer before concluding that this was evidence supporting your claim that "junk DNA" was:

1) a myth, and
2) being "systematically shattered."

You're just lying, Daniel. Hell, the VISTA output showed you what proportion is made up of repeats, so you've already been shown the relevant evidence in detail, but as usual, you ignore it in favor of wishful thinking and rank dishonesty.
    
 

---------------------QUOTE-------------------
 

---------------------QUOTE-------------------
What proportion of the genome did they throw out when they only looked at "nonrepeat" sequences? Be precise and systematic.
---------------------QUOTE-------------------

I could not find that information in the paper.
---------------------QUOTE-------------------


I didn't say it was in the paper. Having that information is a prerequisite for your claim, though, if you thought that this was evidence supporting it.

Wishful thinking doesn't excuse lying.
 

---------------------QUOTE-------------------
Are you equating repeat sequences with "junk"?
---------------------QUOTE-------------------


No, obviously, I'm not. This paper explicitly dealt with nonrepeat sequences. If I ask you the simple question, "How much of what is classified as "junk DNA" is made up of repeats?" it's pretty damn obvious to anyone who isn't socially retarded that I am very well aware that some is made up of repeats, and some isn't. For you to use this as evidence for your fantasy hypothesis, you need to know the proportions. Not only don't you know, you are afraid to learn.   
 

---------------------QUOTE-------------------
 

---------------------QUOTE-------------------
You lie like a rug, Daniel. The fact that you're lying to yourself doesn't excuse your behavior.
---------------------QUOTE-------------------


I know: "Liar, liar - pants on fire!"
---------------------QUOTE-------------------


No, you already falsely accused me of namecalling. I am accusing you of specific lies. For all I know, you might be a paragon of honesty, but I doubt it.

What does the Bible say about bearing false witness? What does it say about judging on the basis of mere hearsay?
 

---------------------QUOTE-------------------
What are we - in 3rd grade here?
---------------------QUOTE-------------------


No, I'd say you're at about 6th grade in terms of biology.
 

---------------------QUOTE-------------------
You may be a smart, educated guy - but you're socially retarded.
---------------------QUOTE-------------------


Does that make you feel better? How would it excuse your relentless lying?
Posted by: JAM on Nov. 01 2007,20:08

Quote (Daniel Smith @ Nov. 01 2007,19:50)
Quote (JAM @ Nov. 01 2007,19:37)
   
Quote (Daniel Smith @ Nov. 01 2007,19:29)
     
Quote (JAM @ Oct. 31 2007,19:17)
It's biology. You delete a gene with an essential function. You replace it with random sequence. You go through cycles of genetic variation (random wrt fitness) and selection (only reproduction).

You end up with a functional sequence that is nothing like the designed/evolved one that it replaced.

How do you explain that?
---------------------QUOTE-------------------


Be more specific.  Show me the paper that describes this experiment.  I will no longer answer your questions unless you provide complete explanations with references.
---------------------QUOTE-------------------


Your petulant demand is pretty damn funny, coming from a guy who claims that a paper in which the authors explicitly told him that they weren't looking at repeated sequences has something global to say about junk DNA. Moreover, you don't have the integrity to address that problem when I pointed it out to you.

OK, I'll give in to your whining, but you have to answer a question first.

What level reduction do you consider to represent lack of function? For example, if your heart rate was reduced a million-fold, to ~1 beat every 10 days, you'd be dead. Would you agree that your heart failed to function--that it was not meeting design criteria, so to speak?
---------------------QUOTE-------------------


No more games.  Show me the paper.
---------------------QUOTE-------------------


I'm not playing games. I'm anticipating your predictably dishonest and cowardly game, Daniel.
Posted by: mitschlag on Nov. 02 2007,05:08

Quote (JAM @ Oct. 31 2007,19:17)
It's biology. You delete a gene with an essential function. You replace it with random sequence. You go through cycles of genetic variation (random wrt fitness) and selection (only reproduction).

You end up with a functional sequence that is nothing like the designed/evolved one that it replaced.
---------------------QUOTE-------------------


Hey JAM, I'm curious, too.  What's the reference for your claim?
Posted by: W. Kevin Vicklund on Nov. 02 2007,11:43

I believe I know of the paper JAM is referring to - it came up last month (hint: 10^6 is not the same as six-fold).  I haven't read it myself, though.

I think we can safely assume that Daniel will maintain that even a million-fold reduction in function is still functional.
Posted by: JAM on Nov. 02 2007,20:24

Quote (W. Kevin Vicklund @ Nov. 02 2007,11:43)
I believe I know of the paper JAM is referring to - it came up last month (hint: 10^6 is not the same as six-fold).  I haven't read it myself, though.

I think we can safely assume that Daniel will maintain that even a million-fold reduction in function is still functional.
---------------------QUOTE-------------------


Yup. Even if it's his heart.
Posted by: Daniel Smith on Nov. 03 2007,16:05

Quote (JAM @ Nov. 02 2007,20:24)
Quote (W. Kevin Vicklund @ Nov. 02 2007,11:43)
I believe I know of the paper JAM is referring to - it came up last month (hint: 10^6 is not the same as six-fold).  I haven't read it myself, though.

I think we can safely assume that Daniel will maintain that even a million-fold reduction in function is still functional.
---------------------QUOTE-------------------


Yup. Even if it's his heart.
---------------------QUOTE-------------------


Still waiting...
Posted by: Daniel Smith on Nov. 03 2007,16:47

Meanwhile, here's a graphic description of the overwhelming complexity within the multi-layered encoding within genomes:

   

---------------------QUOTE-------------------
Figure 2. Transcriptional complexity of a gene. Hypothetical gene cluster with detailed zoom-in for highlighted gene demonstrates that a single gene can have multiple transcriptional start sites (TSSs) as well as many interleaved coding and noncoding transcripts. Exons are shown as red boxes and TSSs are green right-angled arrows. Known short RNAs such as snoRNAs and miRNAs can be processed from intronic sequences and novel species of short RNAs that cluster around the beginning and ends of genes have recently been discovered (see text).

---------------------QUOTE-------------------



From the paper < Origin of phenotypes: Genes and transcripts. >

Although this illustration is hypothetical, it represents what the author expects to find and indeed what the ENCODE scientists did find, in their recent groundbreaking research.  This prompted the author to make this statement:  

---------------------QUOTE-------------------
Thus, in light of this overlapping interleaved network of protein-coding and noncoding transcripts, it seems appropriate to reconsider the concept of gene in describing the relationship of a portion of a genome to a phenotype.
---------------------QUOTE-------------------


Posted by: JAM on Nov. 03 2007,20:17

Quote (Daniel Smith @ Nov. 03 2007,16:05)
 
Quote (JAM @ Nov. 02 2007,20:24)
 
Quote (W. Kevin Vicklund @ Nov. 02 2007,11:43)
I believe I know of the paper JAM is referring to - it came up last month (hint: 10^6 is not the same as six-fold).  I haven't read it myself, though.

I think we can safely assume that Daniel will maintain that even a million-fold reduction in function is still functional.
---------------------QUOTE-------------------


Yup. Even if it's his heart.
---------------------QUOTE-------------------


Still waiting...
---------------------QUOTE-------------------


Yes, I am too. Did you notice that Kevin predicted your weaseling perfectly?



---------------------QUOTE-------------------
Meanwhile, here's a graphic description of the overwhelming complexity within the multi-layered encoding within genomes:
---------------------QUOTE-------------------


In what way is it "overwhelming" if it can be so concisely described? Is it more overwhelming than the fluidity and fuzziness of endocytic pathways, for example?


---------------------QUOTE-------------------
Quote
Figure 2. Transcriptional complexity of a gene.
---------------------QUOTE-------------------


And how is that more overwhelming than the complexity of the multitude of functions of the product of that gene? What about alternative splicing?

And why were you lying and claiming that this says anything about junk DNA?


---------------------QUOTE-------------------
Although this illustration is hypothetical, it represents what the author expects to find...
---------------------QUOTE-------------------


But the author isn't a creationist. Why didn't you find what YOU predicted you'd find? Why did you go off searching for something else to cherry-pick and misrepresent instead of revising or discarding your hypothesis about coding vs. noncoding conservation?


---------------------QUOTE-------------------
... and indeed what the ENCODE scientists did find, in their recent groundbreaking research.
---------------------QUOTE-------------------


But none of those scientists are creationists either, and no creationist or ID proponent predicted this, so your attempt to spin it after the fact is just plain dishonest. If you aren't predicting, it ain't science.


---------------------QUOTE-------------------
This prompted the author to make this statement:
---------------------QUOTE-------------------


Quotes aren't data. You struck out when we dragged you kicking and screaming to the actual data.


---------------------QUOTE-------------------
Thus, in light of this overlapping interleaved network of protein-coding and noncoding transcripts, it seems appropriate to reconsider the concept of gene in describing the relationship of a portion of a genome to a phenotype.
---------------------QUOTE-------------------


We've already reconsidered it (successfully) several times in my lifetime, every time in an evolutionary context, so I don't see this as helping you out. Can you offer more than platitudes about how overwhelming it is to you?
Posted by: Assassinator on Nov. 04 2007,04:34

Sorry to break in guys, i'm just new here, but i've got a few questions for Daniel.
First of all, what do you want Daniel? I don't get it, are you interested in reality of are you interested in confirming you're own thoughts? Because if it is the latter, that's not what science is about. I also read you were more interested in the scientists who were shunned by the scientific world, the one's who were laughed at etc etc. But also, that's not where it is about, it's pure about evidence. Hell, it doesn't matter if correct statements are brought by a light-blue, Satan worshipping fairy with daisy's sprouting out of it's head: evidence is evidence, no matter who brought it up. Persons do not matter, and so does your own thoughts about this subject. If you want to learn, let those things go. I don't have the idea you want to learn, but only want to confirm you're own thoughts, that there must be some form of design, designer or end-goal. I think you have emotionally attached yourself to your own idea about reality, i wonder why.
This may be a lot for me to ask, because i'm new, but maybe you could give a little summary about what you think Daniel. Maybe this would help the discussion in general, it's getting a little out of hand because people start ignoring important parts of posts from eachother.
Posted by: Daniel Smith on Nov. 04 2007,12:50

Quote (Assassinator @ Nov. 04 2007,04:34)
Sorry to break in guys, i'm just new here, but i've got a few questions for Daniel.
First of all, what do you want Daniel? I don't get it, are you interested in reality of are you interested in confirming you're own thoughts? Because if it is the latter, that's not what science is about. I also read you were more interested in the scientists who were shunned by the scientific world, the one's who were laughed at etc etc. But also, that's not where it is about, it's pure about evidence. Hell, it doesn't matter if correct statements are brought by a light-blue, Satan worshipping fairy with daisy's sprouting out of it's head: evidence is evidence, no matter who brought it up. Persons do not matter, and so does your own thoughts about this subject. If you want to learn, let those things go. I don't have the idea you want to learn, but only want to confirm you're own thoughts, that there must be some form of design, designer or end-goal. I think you have emotionally attached yourself to your own idea about reality, i wonder why.
This may be a lot for me to ask, because i'm new, but maybe you could give a little summary about what you think Daniel. Maybe this would help the discussion in general, it's getting a little out of hand because people start ignoring important parts of posts from eachother.
---------------------QUOTE-------------------


First of all, we all have preconceived ideas we are hoping to verify.  Many here have a preconceived notion that there is no God.  They are not even willing to consider that option.  In fact many will say that such an option is outside the realm of science.  So even if there really is a God, they are forced to find another explanation - no matter how ridiculous.  Is that "seeking the truth"?
I think I've laid out my thoughts and goals pretty straightforwardly throughout the 18 pages of this thread.  I'm willing to let go of anything I believe - provided the evidence against it is convincing.  So far, I've seen nothing convincing here.  The fossil record and the molecular evidence are both consistent with a belief that God designed and implemented life on this planet.
The fossil record shows "explosions" of lifeforms suddenly appearing and then diversifying.
The molecular evidence shows an extremely complex, sophisticated, multi-layered coding system that defies any unguided evolutionary explanation.  If you notice, most of the more recent papers don't even bother to speculate anymore as to how such a system evolved.  It's beyond explanation.
In fact, the more I learn, the more convinced I am of the infinite intelligence of the designing God.
Now, I could take your questions and turn them around and ask them of you:  What is your goal?  What are your preconceived ideas?  Are you willing to let them go and consider the possibility of a designing God?
Posted by: Assassinator on Nov. 04 2007,13:05

I agree that lots of people also have preconcieved ideas about a god. But there is also something else, it looks like you're emotionally attached to your preconcieved ideas. Note that the word "God" doesn't mean anything by itself, it's rather a coat rack (i hope i translate that correctly) on wich people put there own image of the word "God". The word "God" is thus worthless to science. Science can only work with certain images of the word "God". It's so easy to modify that image. Not even that long ago, and even today, people still beleive that God created and designed everything around us, but not in the way you would beleive it. The role of God has changed, it's like the God of the Gaps.


---------------------QUOTE-------------------
The fossil record and the molecular evidence are both consistent with a belief that God designed and implemented life on this planet.
---------------------QUOTE-------------------


Explain yourself. Because i don't see why. I'm only seeing a certain interpretation of the available evidence so the evidence fits in your beleifs. But is that interpretation in agreement with reality? Ofcourse, you can ask the same with other interpretations.


---------------------QUOTE-------------------
The fossil record shows "explosions" of lifeforms suddenly appearing and then diversifying.
---------------------QUOTE-------------------


You shouldn't take the world "explosion" too literally. It still took several millions of years, and that's VERY long and LOTS of generations fit into that.


---------------------QUOTE-------------------
The molecular evidence shows an extremely complex, sophisticated, multi-layered coding system that defies any unguided evolutionary explanation.
---------------------QUOTE-------------------


No, it does not. It's complex in your eyes, nothing more. Hell, we may meet aliens who laugh at our simple planet with our simple lifeforms. It's simply not an argument to say it's complex compared what we can do. The fact that we don't get it, is no argument for design, it's only an argument for our limited knowledge.


---------------------QUOTE-------------------
Now, I could take your questions and turn them around and ask them of you:  What is your goal?  What are your preconceived ideas?  Are you willing to let them go and consider the possibility of a designing God?
---------------------QUOTE-------------------


My goal? To learn more about reality. My preconcieved ideas? No idea, i don't give a ratsass if our planet was made by a God, erupted out of natural laws or made by aliens from starsystems thousands of lightyears away for an experiment. I just care about what's true. Ofcourse i consider the possibility of a designing God, but as i sad before there is no evidence or objective sign for such a being.
Posted by: Daniel Smith on Nov. 04 2007,13:05

Quote (Assassinator @ Nov. 04 2007,04:34)
I also read you were more interested in the scientists who were shunned by the scientific world, the one's who were laughed at etc etc. But also, that's not where it is about, it's pure about evidence. Hell, it doesn't matter if correct statements are brought by a light-blue, Satan worshipping fairy with daisy's sprouting out of it's head: evidence is evidence, no matter who brought it up.
---------------------QUOTE-------------------


Let me also add; these scientists have theories that have never been falsified.
Their ideas were ridiculed - because they did not fit the current paradigm, but I've seen no convincing evidence against them.  The Prescribed Evolutionary Hypothesis (PEH) of Dr. John Davison is a good example. < (link) > Many here and elsewhere have ridiculed Dr. Davison for his personal habits, grumpiness, lack of civility, etc., or they have ridiculed his hypothesis from afar, but how many have systematically and thoroughly reviewed it and presented convincing evidence against it?  I've not seen any.
The same can be said about the theories of Berg and Schindewolf I've presented (albeit limitedly) here.  No one has presented any evidence against them.  Most of it was just preconceived suppositions that they must somehow be wrong because they didn't fit the current paradigm!  In fact there's been an almost complete lack of willingness to discuss their ideas - with some frantic subject-changing going on.
So... Yes... I do look for those on the fringes who have presented differing ideas.  If their ideas have been shown wrong, I don't give them much weight, but if it's just that they were made fun of, that doesn't hold much sway with me.
Posted by: Assassinator on Nov. 04 2007,13:12

I don't know if they're not falsified, so i'm asking other people now if they do know if they're falsified and if they can post links to papers and other stuff about it. (and please, no ad hominems on that :) )
Posted by: Erasmus, FCD on Nov. 04 2007,13:25

Schindewolf's theories were devastated by particulate inheritance and the mathematical synthesis.  

it makes no sense whatsoever to have reserve genetic material, in advance of adaptive radiations, sitting around in the genome.

unless we now have a function for noncoding DNA?  not seen that advanced but it would still be a greatly different take from schindewolf.
Posted by: Assassinator on Nov. 04 2007,13:35

Thanks, do you have links to articles about that? Would be nice ;) (just here to learn :D)
Posted by: Daniel Smith on Nov. 04 2007,13:36

Quote (Assassinator @ Nov. 04 2007,13:05)
I agree that lots of people also have preconcieved ideas about a god. But there is also something else, it looks like you're emotionally attached to your preconcieved ideas. Note that the word "God" doesn't mean anything by itself, it's rather a coat rack (i hope i translate that correctly) on wich people put there own image of the word "God". The word "God" is thus worthless to science. Science can only work with certain images of the word "God". It's so easy to modify that image. Not even that long ago, and even today, people still beleive that God created and designed everything around us, but not in the way you would beleive it. The role of God has changed, it's like the God of the Gaps.
         

---------------------QUOTE-------------------
The fossil record and the molecular evidence are both consistent with a belief that God designed and implemented life on this planet.
---------------------QUOTE-------------------


Explain yourself. Because i don't see why. I'm only seeing a certain interpretation of the available evidence so the evidence fits in your beleifs. But is that interpretation in agreement with reality? Ofcourse, you can ask the same with other interpretations.
         

---------------------QUOTE-------------------
The fossil record shows "explosions" of lifeforms suddenly appearing and then diversifying.
---------------------QUOTE-------------------


You shouldn't take the world "explosion" too literally. It still took several millions of years, and that's VERY long and LOTS of generations fit into that.
         

---------------------QUOTE-------------------
The molecular evidence shows an extremely complex, sophisticated, multi-layered coding system that defies any unguided evolutionary explanation.
---------------------QUOTE-------------------


No, it does not. It's complex in your eyes, nothing more. Hell, we may meet aliens who laugh at our simple planet with our simple lifeforms. It's simply not an argument to say it's complex compared what we can do. The fact that we don't get it, is no argument for design, it's only an argument for our limited knowledge.
         

---------------------QUOTE-------------------
Now, I could take your questions and turn them around and ask them of you:  What is your goal?  What are your preconceived ideas?  Are you willing to let them go and consider the possibility of a designing God?
---------------------QUOTE-------------------


My goal? To learn more about reality. My preconcieved ideas? No idea, i don't give a ratsass if our planet was made by a God, erupted out of natural laws or made by aliens from starsystems thousands of lightyears away for an experiment. I just care about what's true. Ofcourse i consider the possibility of a designing God, but as i sad before there is no evidence or objective sign for such a being.
---------------------QUOTE-------------------


You are right. I am emotionally attached to my preconceived ideas - and I will only let go of them when convinced otherwise.
And (I've said this before), I am not advocating a "god of the gaps", I am advocating a "God of all that is".  I give him credit for everything - even those things that man thinks he has explained.  Just because we can explain something doesn't mean we have eliminated design from the argument.  I can explain many of the systems at work within my car, does that mean it wasn't designed?  Obviously not.  It only means I have gained an understanding of the designer's systems.
So... my definition of God is that of an eternal, infinitely intelligent, cognitive agent that exists in a parallel dimension to our own.
Thus, he is a being not bound by time and capable of doing anything.  Now, I realize that that last part seems like a cop-out, since someone who can do anything also explains everything, but let me also point out that - if life were created by a being of infinite intelligence - we would expect to find certain things within life.
Let's use your aliens as an example.  If we were to find an object that we believed to be created by an alien race more intelligent than our own, we would expect to find technology superior to our own within that object.
The fact that we find technology superior to our own within the mechanisms of life can be used as an argument that the designer of life was at least orders of magnitude more intelligent than us.
Now some will argue that the molecular mechanisms - in all their sophistication - are the result of natural processes, but then isn't it up to them to show that these natural processes can create such sophistication and elegance?
So far, I've seen no convincing evidence that natural processes can produce complex, functional systems such as we have in life.  None.
Posted by: Daniel Smith on Nov. 04 2007,13:40

Quote (Erasmus @ FCD,Nov. 04 2007,13:25)
Schindewolf's theories were devastated by particulate inheritance and the mathematical synthesis.  
---------------------QUOTE-------------------

Yes, please provide links to those papers and please elaborate as to how these things "devastated" Schindewolf's theory.

---------------------QUOTE-------------------
it makes no sense whatsoever to have reserve genetic material, in advance of adaptive radiations, sitting around in the genome.
---------------------QUOTE-------------------

It makes perfect sense from a front-loading perspective.

---------------------QUOTE-------------------

unless we now have a function for noncoding DNA?  not seen that advanced but it would still be a greatly different take from schindewolf.
---------------------QUOTE-------------------

I have no idea what this sentence means.
Posted by: Assassinator on Nov. 04 2007,13:43

And because you are emotionally attached to your views, you won't accept evidence. Before you would, you would first try to fit in that evidence in your own picture of reality. Also, you're giving your own images about reality too much credit: Face it: they're unimportant, the universe doesn't give a rats ass about your views and also about mine and any other human.
But again, it's complex in YOUR eyes. Take for example sea urchins. We humans share 70% of our DNA with sea urchins. Now you can say 2 things: either sea urchins are VERY complex, proving your point, or you can say that we are VERY simple because we're still that similair with sea urchins. Now who is right? The choice is completly made on personal taste, and has nothing to do with science. It's simply not an argument. You're using all kinds of emotional words, like "elegance" and "sophistication" but those words mean nothing. They're all bound to your emotions, and your emotions are worthless here just like mine. I don't think you want to learn about reality, because you've already made up your mind on nothing more then personal preferences. What's left to discuss then?
Posted by: Assassinator on Nov. 04 2007,13:53

Another thing, i do understand your point-of-view a bit. Because it's ages old. Hundreds of years ago people saw lightening, it made no sense to them, they were overwhelmed and simply didn't know what it was. The most reasonable thought: something greater then us is causing it. It's exactly the same as we're having with the developement from life on earth: we don't fully understand, and some people totally don't understand (again: evolution has a VERY big PR problem) because they don't understand the science behind it.
I've got the same, when i watch at the stars at night (when the ratchet Dutch weather allows me) i find it so incredibly beautifull, but i know my personal feelings have nothing to do what's out there. I know what i'm watching it, nothing more then huge balls of gas billions of lightyears away. But that knowledge is making it more spectaculair for me, i'm realising that i'm watching light erupted thousands if not millions of years ago, a downright timemachine! I'm so amazed by what i'm watching, but again it has nothing to do with science. My personal feelings about the universe don't say anything about the universe itself. It's exactly the same as what you're having with life on earth.
Posted by: swbarnes2 on Nov. 04 2007,14:01

Quote (Daniel Smith @ Nov. 04 2007,12:50)

Many here have a preconceived notion that there is no God.
---------------------QUOTE-------------------



No, many people here have concluded from the evidence that there is no evidence for God, and are operating under the perfectly reasonable paradigm that it is a bad idea to believe in things for which there is no evidence.

For you to say what you said means that you are clueless, or a liar.

Gee, why is it that almost everything you post here can easily be construed as a lie?

 

---------------------QUOTE-------------------
They are not even willing to consider that option.
---------------------QUOTE-------------------



Good grief, you are pathological.  There is a whole thread active right now about "What would you do if you discoverd that you were wrong about the existance/non-existance of God?"

And guess who has declared that they are utterly incapable of even imagining that scenario?  It's not the atheists, its the theist.  

And in your warped brain, this means that it is the atheists who are intractable.

And I won't even start on the fact that you arguments aren't even convincing to theists.

 

---------------------QUOTE-------------------
I think I've laid out my thoughts and goals pretty straightforwardly throughout the 18 pages of this thread.
---------------------QUOTE-------------------



Lying is the farthest thing from straightforward.  And you have lied here.  You admitted it.

And look, you just lied again.

I honestly can't imagine it.  If I had been caught lying over and over again a message board, I would have died of embarassment.  But you integrity means nothing to you.  The fact that you keep posting lies here proves it.

 

---------------------QUOTE-------------------
I'm willing to let go of anything I believe - provided the evidence against it is convincing.
---------------------QUOTE-------------------



Your posts demonstrate that this is not true.  The VISTA data proves that you were wrong, and you insisted pretended that it justified your claims!  You made claims about the results of replica plating experiments, and those claims are wildly wrong, but you believe them still.

 

---------------------QUOTE-------------------
The fossil record and the molecular evidence are both consistent with a belief that God designed and implemented life on this planet.
---------------------QUOTE-------------------



See, again.  The goal of this board was for you to prove that this is true.  But you have failed. No one here is convinced.  But since you will not allow any evidence or argument to convince you that you are wrong, you you take the existance of 18 pages of 'unconvincing' counter-argumetn to mean that you are right.

But you aren't.  The evidence simply doesn't support what you wish it did.

 

---------------------QUOTE-------------------
If you notice, most of the more recent papers don't even bother to speculate anymore as to how such a system evolved.  It's beyond explanation.

---------------------QUOTE-------------------



You are dreaming.

 

---------------------QUOTE-------------------
In fact, the more I learn, the more convinced I am of the infinite intelligence of the designing God.
---------------------QUOTE-------------------



So, why don't you tell us what the 100,000 children who die from malaria tell us about God?

Oh, that's right, you can't.  You never will.  

 

---------------------QUOTE-------------------
Are you willing to let them go and consider the possibility of a designing God?
---------------------QUOTE-------------------



Sure, if the evidence were there.  It just isn't.

You showing a pretty picture of all the complex things that can go on around a coding transcript (when about 80% of the genome is intergenic) isn't evidence of a designing God.
Posted by: JAM on Nov. 04 2007,15:00

Quote (Daniel Smith @ Nov. 04 2007,12:50)
First of all, we all have preconceived ideas we are hoping to verify.
---------------------QUOTE-------------------


But scientists TEST their preconceived ideas. They try to falsify them. You don't do that.


---------------------QUOTE-------------------
Many here have a preconceived notion that there is no God.
---------------------QUOTE-------------------


I'd say that NO ONE here had such a preconceived notion. More accurately, some here have decided that, AFTER looking at the evidence.

BTW, I don't have that notion, so if you are referring to me, you're once again showing your utter contempt for the Ninth Commandment.


---------------------QUOTE-------------------
So even if there really is a God, they are forced to find another explanation - no matter how ridiculous.  Is that "seeking the truth"?
---------------------QUOTE-------------------


Why don't you look in the mirror?

To falsely claim that you've seen no evidence to refute your preconceptions, you've blatantly lied about the classification of noncoding sequences within genes (primarily introns). Not only that, but your lies contradict each other!

1) When looking at VISTA, you lied and claimed that noncoding sequences within genes were coding regions.

2) Just above, you lied again, claiming that noncoding sequences within genes were classified as "junk."

3) In reality, noncoding sequences within genes (promoters, 5' and 3' UTRs, and introns have NEVER been classified as "junk."

Now, even if you refuse to believe #3, #1 and #2 are complete contradictions.



---------------------QUOTE-------------------
I think I've laid out my thoughts and goals pretty straightforwardly throughout the 18 pages of this thread.  I'm willing to let go of anything I believe - provided the evidence against it is convincing.
---------------------QUOTE-------------------


That's a lie. You've chosen to lie about the evidence instead.


---------------------QUOTE-------------------
So far, I've seen nothing convincing here.  The fossil record and the molecular evidence are both consistent with a belief that God designed and implemented life on this planet.
---------------------QUOTE-------------------


So how can introns be both coding sequences and junk sequences in your addled mind?


---------------------QUOTE-------------------
The molecular evidence shows an extremely complex, sophisticated, multi-layered coding system that defies any unguided evolutionary explanation.
---------------------QUOTE-------------------


You're lying again.


---------------------QUOTE-------------------
If you notice, most of the more recent papers don't even bother to speculate anymore as to how such a system evolved.  It's beyond explanation.
---------------------QUOTE-------------------


And again.


---------------------QUOTE-------------------
In fact, the more I learn, the more convinced I am of the infinite intelligence of the designing God.
---------------------QUOTE-------------------


How does studying nonrepeat sequences within and near genes reclassify "junk" DNA, then?


---------------------QUOTE-------------------
Now, I could take your questions and turn them around and ask them of you:  What is your goal?  What are your preconceived ideas?  Are you willing to let them go and consider the possibility of a designing God?
---------------------QUOTE-------------------


Absolutely. But I've looked at and produced far more evidence than you have, and the NATURE of the complexity (particularly related, but nonidentical parts with partially-overlapping functions) I see and grapple with every day doesn't even remotely suggest intelligent design.

And, unlike you, I'm honest about the evidence.

For example, if God designed your body, He clearly understands the concept of plumbing. Why is there nothing analogous within cells, then? Why do cells use a system analogous to throwing lipid water balloons full of food and sewage around (allowing them to fuse and ripping them apart) instead of having simple plumbing? Is your God stupid? Mine sure isn't.
Posted by: Richard Simons on Nov. 04 2007,15:30



---------------------QUOTE-------------------
Yes, please provide links to those papers and please elaborate as to how these things "devastated" Schindewolf's theory.
---------------------QUOTE-------------------


When I asked you about some aspects of Schindewolf's theory your response was

Quote (Daniel Smith @ Oct. 25 2007,13:50)
 
Quote (Richard Simons @ Oct. 25 2007,00:00)
Back to Schindewolf! I am not sure why a hypothesis that has been essentially dead for 50 years holds so much fascination for you. However, given that it does perhaps you could explain how the information to constrain an organism's evolutionary pathway is held. What conceivable mechanism could stop evolution from taking place, or enable parts to evolve before they became useful?

I am also curious about the saltational events. Do you see these as creating a new genus, order, phylum or what? What actually occurs during a saltational event? How does the DNA get changed and how does it know what to become, as I gather it is preparing for the next few million years of evolution and changing conditions? When did the last saltational event take place? I don't even know if the proposal is that one day a dinosaur chick hatched that had feathers and wings or if the process was spread over many generations, which might make it little different from the rapid evolution phase of punctuated equilibrium.

I'm looking forward to your answers.
---------------------QUOTE-------------------


I don't know.
---------------------QUOTE-------------------


How do you expect us to respond when you can't even tell us some of the basics of the theory?
Posted by: Assassinator on Nov. 04 2007,17:19

Then i'm also curious why you're (directing at Daniel here, ofcourse) so sure of those theory's because apperantly you don't know a lot about them. Is it really just because Shindewolf was mocked at by the scientific community? You do know that that has absolutly nothing to do with the vality of his theory, right?
Posted by: Daniel Smith on Nov. 04 2007,20:08

Quote (Richard Simons @ Nov. 04 2007,15:30)
       

---------------------QUOTE-------------------
Yes, please provide links to those papers and please elaborate as to how these things "devastated" Schindewolf's theory.
---------------------QUOTE-------------------


When I asked you about some aspects of Schindewolf's theory your response was

         
Quote (Daniel Smith @ Oct. 25 2007,13:50)
         
Quote (Richard Simons @ Oct. 25 2007,00:00)
Back to Schindewolf! I am not sure why a hypothesis that has been essentially dead for 50 years holds so much fascination for you. However, given that it does perhaps you could explain how the information to constrain an organism's evolutionary pathway is held. What conceivable mechanism could stop evolution from taking place, or enable parts to evolve before they became useful?

I am also curious about the saltational events. Do you see these as creating a new genus, order, phylum or what? What actually occurs during a saltational event? How does the DNA get changed and how does it know what to become, as I gather it is preparing for the next few million years of evolution and changing conditions? When did the last saltational event take place? I don't even know if the proposal is that one day a dinosaur chick hatched that had feathers and wings or if the process was spread over many generations, which might make it little different from the rapid evolution phase of punctuated equilibrium.

I'm looking forward to your answers.
---------------------QUOTE-------------------


I don't know.
---------------------QUOTE-------------------


How do you expect us to respond when you can't even tell us some of the basics of the theory?
---------------------QUOTE-------------------


Schindewolf didn't cover many of the questions you asked.  His theory was based on the fossil record - not genetics.  If you had asked me what evidence exists in the fossil record to support his threefold theory of typogenesis, typostasis and typolysis, I could answer you.

I will say this: Davison's < PEH > does attempt to answer many of your questions.
     

---------------------QUOTE-------------------
perhaps you could explain how the information to constrain an organism's evolutionary pathway is held.
---------------------QUOTE-------------------

It is contained in the first individual of a new type, and is maintained by sexual reproduction and/or selection.      

---------------------QUOTE-------------------
What conceivable mechanism could stop evolution from taking place
---------------------QUOTE-------------------

Sexual reproduction, selection, extinction...      

---------------------QUOTE-------------------
or enable parts to evolve before they became useful?
---------------------QUOTE-------------------

Semi-meiotic reproduction.      

---------------------QUOTE-------------------
I am also curious about the saltational events. Do you see these as creating a new genus, order, phylum or what?
---------------------QUOTE-------------------

Schindewolf called them "types".  I have no idea what current category that conforms to.    

---------------------QUOTE-------------------
What actually occurs during a saltational event?
---------------------QUOTE-------------------

According to Davison's semi-meiotic hypothesis, the structural reordering of genetic information within the chromosomes.      

---------------------QUOTE-------------------
How does the DNA get changed and how does it know what to become, as I gather it is preparing for the next few million years of evolution and changing conditions?
---------------------QUOTE-------------------

See above.      

---------------------QUOTE-------------------
When did the last saltational event take place?
---------------------QUOTE-------------------

Again, according to Davison - the evolution of humans was the last saltational event.

Now, I have to restate the fact that I don't know the answers to any of your questions, and Schindewolf did not address most of them, so I was not "lying", nor was I unsupportive of Schindewolf's theory.
Posted by: Jim_Wynne on Nov. 04 2007,20:57

Quote (Daniel Smith @ Nov. 04 2007,20:08)
 

---------------------QUOTE-------------------
I am also curious about the saltational events. Do you see these as creating a new genus, order, phylum or what?
---------------------QUOTE-------------------

Schindewolf called them "types".  I have no idea what current category that conforms to.
---------------------QUOTE-------------------


I'm guessing "kinds."
Posted by: Richard Simons on Nov. 04 2007,23:19



---------------------QUOTE-------------------

perhaps you could explain how the information to constrain an organism's evolutionary pathway is held.

- It is contained in the first individual of a new type, and is maintained by sexual reproduction and/or selection.      
---------------------QUOTE-------------------


The problem is not what stops the organism from changing but rather what determines that it evolves in a particular way. You quoted Schindewolf as saying that changes in horse anatomy anticipated changes in the environment, therefore 'selection' is not an option.
       

---------------------QUOTE-------------------
What conceivable mechanism could stop evolution from taking place

- Sexual reproduction, selection, extinction...
---------------------QUOTE-------------------


Selection could only stop evolution if the organism were perfectly adapted to an unchanging environment.
       

---------------------QUOTE-------------------
 
or enable parts to evolve before they became useful?

- Semi-meiotic reproduction.
---------------------QUOTE-------------------


Throwing out a phrase does not answer the question. My point was how could the organism know what it is to become? How does this knowledge get incorporated into the genome?  
     

---------------------QUOTE-------------------
I am also curious about the saltational events. Do you see these as creating a new genus, order, phylum or what?  

- Schindewolf called them "types".  I have no idea what current category that conforms to.
---------------------QUOTE-------------------


The problem is probably that Schindewolf had no idea either.
       

---------------------QUOTE-------------------
What actually occurs during a saltational event?  

- According to Davison's semi-meiotic hypothesis, the structural reordering of genetic information within the chromosomes.
---------------------QUOTE-------------------

 
       

---------------------QUOTE-------------------
How does the DNA get changed and how does it know what to become, as I gather it is preparing for the next few million years of evolution and changing conditions?

- See above.
---------------------QUOTE-------------------


I could not see anything in his hypothesis that comes remotely close to explaining how the DNA knows what it should become.
       

---------------------QUOTE-------------------
When did the last saltational event take place?  

- Again, according to Davison - the evolution of humans was the last saltational event.
---------------------QUOTE-------------------


Where in < this series > would the saltational event have happened?

BTW. What is your explanation for Davison's hypothesis having gone nowhere in the last 20 years?
Posted by: JAM on Nov. 05 2007,00:37

Quote (Daniel Smith @ Nov. 04 2007,13:05)
Let me also add; these scientists have theories that have never been falsified.
---------------------QUOTE-------------------


Let me add that whether they've been falsified is irrelevant, when they have never been TESTED.

Therefore, you were bearing false witness (check that Ninth Commandment!) when you called them "theories." Theories are hypotheses that have a long track record of withstanding tests designed to falsify them. None of your heroes are willing to do that.


---------------------QUOTE-------------------
Their ideas were ridiculed - because they did not fit the current paradigm,
---------------------QUOTE-------------------


The fact that they are ridiculed doesn't make them right. If they are being ridiculed, they should get to work testing their hypotheses.

Virologists ridiculed Stan Prusiner and his prion hypothesis in the early '80s, too. Did Prusiner blog or write books aimed at lay people? No, he tested his hypothesis inside and out. In 1997, he won the Nobel.


---------------------QUOTE-------------------
but I've seen no convincing evidence against them.
---------------------QUOTE-------------------


We've seen how you can ignore blatant evidence when it's right in front of your face, Daniel. Your credibility is zero.


---------------------QUOTE-------------------
...how many have systematically and thoroughly reviewed it and presented convincing evidence against it?  I've not seen any.
---------------------QUOTE-------------------


It's not our responsibility to "present convincing evidence" against anything, you goof. It's DAVISON'S responsibility to TEST his hypothesis, but he won't. That's the main reason why real scientists ridicule Davison and Behe.


---------------------QUOTE-------------------
The same can be said about the theories of Berg and Schindewolf I've presented (albeit limitedly) here.  No one has presented any evidence against them.
---------------------QUOTE-------------------


Again, you can't be bothered to look at the evidence after you make a prediction. You see just what you want to see, and you tell blatant lies. Make a prediction. Do an experiment. Make an observation. Produce new data.
Posted by: oldmanintheskydidntdoit on Nov. 05 2007,02:48



---------------------QUOTE-------------------
...how many have systematically and thoroughly reviewed it and presented convincing evidence against it?  I've not seen any.
---------------------QUOTE-------------------


Nor have I seen systematic evidence against the moon being made of green cheese.

I can propose anything I like, I don't expect the world to jump on it and disprove it. It's up to me to provide positive proof in the first instance.
Posted by: VMartin on Nov. 05 2007,23:59

JAM

 

---------------------QUOTE-------------------

It's not our responsibility to "present convincing evidence" against anything, you goof. It's DAVISON'S responsibility to TEST his hypothesis, but he won't. That's the main reason why real scientists ridicule Davison and Behe.

---------------------QUOTE-------------------



Unbelievable. John Davison supported his ideas presented in his Manifesto by thoughts of Berg, Broom, Schindewolf, Punnet, Grasse. All of them were real scientists. Grasse was president of French academy of science!
It is utterly ridiculous when you call "real scientists" only your neodarwinian cronies.



---------------------QUOTE-------------------

The fact that they are ridiculed doesn't make them right. If they are being ridiculed, they should get to work testing their hypotheses.

---------------------QUOTE-------------------



Neodarwinists with their babbling about "evolution in action"  and "natural selection" are ridiculous as well. They should better test their hypothesis. Especially considering the fact that evolution is over - how real scientists as Davison, Broom and Grasse claimed.

(that evolution of mammalian orders is finished is admitted fact also by you. You only claim that there are no "empty niches" anymore.)
Posted by: IanBrown_101 on Nov. 06 2007,02:16

Quote (VMartin @ Nov. 06 2007,05:59)
JAM

 

---------------------QUOTE-------------------

It's not our responsibility to "present convincing evidence" against anything, you goof. It's DAVISON'S responsibility to TEST his hypothesis, but he won't. That's the main reason why real scientists ridicule Davison and Behe.

---------------------QUOTE-------------------



Unbelievable. John Davison supported his ideas presented in his Manifesto by thoughts of Berg, Broom, Schindewolf, Punnet, Grasse. All of them were real scientists. Grasse was president of French academy of science!
It is utterly ridiculous when you call "real scientists" only your neodarwinian cronies.
---------------------QUOTE-------------------


Quoting people isn't data (incidentally, how many of these scientists published all/most of their work before 1950?) dumbass.

If it was, I could "prove" there was a god by quoting various religious leaders or, even better, religious scientists.

You're either insane or unbelievably, incurably, ridiculously stupid.
Posted by: Assassinator on Nov. 06 2007,02:58



---------------------QUOTE-------------------
Neodarwinists with their babbling about "evolution in action"  and "natural selection" are ridiculous as well. They should better test their hypothesis.
---------------------QUOTE-------------------


Ya know Martin, it would be nice if you would actually do something more then just rant.
Posted by: oldmanintheskydidntdoit on Nov. 06 2007,03:06

Quote (VMartin @ Nov. 05 2007,23:59)
Especially considering the fact that evolution is over - how real scientists as Davison, Broom and Grasse claimed.
---------------------QUOTE-------------------


If it's the case that "real scientists" only mutter to themselves on ISCID then yes, Davidson is a real scientist.
Posted by: Daniel Smith on Nov. 06 2007,13:58

Quote (oldmanintheskydidntdoit @ Nov. 05 2007,02:48)
I can propose anything I like, I don't expect the world to jump on it and disprove it. It's up to me to provide positive proof in the first instance.
---------------------QUOTE-------------------


Davison cites experimental evidence showing that semi-meiotic reproduction is possible even amongst sexually reproductive animals.

But where is the "positive proof" (you say) you require for the assumed mechanisms of gradual evolution?
Posted by: oldmanintheskydidntdoit on Nov. 06 2007,14:14

Quote (Daniel Smith @ Nov. 06 2007,13:58)
 
Quote (oldmanintheskydidntdoit @ Nov. 05 2007,02:48)
I can propose anything I like, I don't expect the world to jump on it and disprove it. It's up to me to provide positive proof in the first instance.
---------------------QUOTE-------------------


Davison cites experimental evidence showing that semi-meiotic reproduction is possible even amongst sexually reproductive animals.

But where is the "positive proof" (you say) you require for the assumed mechanisms of gradual evolution?
---------------------QUOTE-------------------


 

---------------------QUOTE-------------------
Allen MacNeill
Sources of Heritable Variation (both genotypic and phenotypic) Among Individuals in Populations

Gene Structure (in DNA)
• single point mutations
• deletion and insertion (“frame shift”) mutations
• inversion and translocation mutations
Gene Expression in Prokaryotes
• changes in promoter or terminator sequences (increasing or decreasing binding)
• changes in repressor binding (in prokaryotes); increasing or decreasing binding to operator sites
• changes in repressor binding (in prokaryotes); increasing or decreasing binding to inducers
• changes in repressor binding (in prokaryotes); increasing or decreasing binding to corepressors
Gene Expression in Eukaryotes
• changes in activation factor function in eukaryotes (increasing or decreasing binding to promoters)
• changes in intron length, location, and/or editing by changes in specificity of SNRPs
• changes in interference/antisense RNA regulation (increasing or decreasing binding to sense RNAs)
Gene Interactions
• changes in substrates or products of biochemical pathways
• addition or removal of gene products (especially enzymes) from biochemical pathways
• splitting or combining of biochemical pathways
• addition or alteration of pleiotropic effects, especially in response to changes in other genes/traits
Eukaryotic Chromosome Structure
• gene duplication within chromosomes
• gene duplication in multiple chromosomes
• inversions involving one or more genes in one chromosome
• translocations involving one or more genes between two or more chromosomes
• deletion/insertion of one or more genes via transposons
• fusion of two or more chromosomes or chromosome fragments
• fission of one chromosome into two or more fragments
• changes in chromosome number via nondisjunction (aneuploidy)
• changes in chromosome number via autopolyploidy (especially in plants)
• changes in chromosome number via allopolyploidy (especially in plants)
Eukaryotic Chromosome Function
• changes in regulation of multiple genes in a chromosome as a result of the foregoing structural changes
• changes in gene expression as result of DNA methylation
• changes in gene expression as result of changes in DNA-histone binding
Genetic Recombination
• the exchange of non-identical genetic material between two or more individuals (i.e. sex)
• lateral gene transfer via plasmids and episomes (especially in prokaryotes)
• crossing-over (reciprocal and non-reciprocal) between sister chromatids in meiosis
• crossing-over (non-reciprocal) between sister chromatids in mitosis
• Mendelian independent assortment during meiosis
• hybridization
Genome Structure and Function
• genome reorganization and/or reintegration
• partial or complete genome duplication
• partial or complete genome fusion
Development (among multicellular eukaryotes, especially animals)
• changes in tempo and timing of gene regulation, especially in eukaryotes
• changes in homeotic gene regulation in eukaryotes
• genetic imprinting, especially via hormone-mediated DNA methylation
Symbiosis
• partial or complete endosymbiosis
• partial or complete incorporation of unrelated organisms as part of developmental pathways (especially larval forms)
• changes in presence or absence of mutualists, commensals, and/or parasites
Behavior/Neurobiology
• changes in behavioral anatomy, histology, and/or physiology in response to changes in biotic community
• changes in behavioral anatomy, histology, and/or physiology in response to changes in abiotic environment
• learning (including effects of use and disuse)
Physiological Ecology
• changes in anatomy, histology, and/or physiology in response to changes in biotic community
• changes in anatomy, histology, and/or physiology in response to changes in abiotic environment
---------------------QUOTE-------------------



Which particular assumed mechanism are you interested in?
< creationist and id strawman >
Posted by: JAM on Nov. 07 2007,09:10

Quote (Daniel Smith @ Nov. 06 2007,13:58)
Quote (oldmanintheskydidntdoit @ Nov. 05 2007,02:48)
I can propose anything I like, I don't expect the world to jump on it and disprove it. It's up to me to provide positive proof in the first instance.
---------------------QUOTE-------------------


Davison cites experimental evidence showing that semi-meiotic reproduction is possible even amongst sexually reproductive animals.

But where is the "positive proof" (you say) you require for the assumed mechanisms of gradual evolution?
---------------------QUOTE-------------------


Daniel, I take issue with omitsddi's use of the term "proof," but plenty of positive evidence is available from VISTA. That's why you felt compelled to lie and claim that noncoding regions in genes (introns and 5' and 3' UTRs) were "coding regions."

Again, get this through your thick head. It's not about CITING evidence. It's about PRODUCING NEW EVIDENCE by TESTING YOUR OWN HYPOTHESIS.

Surely you're not so stupid that you can't see the immense difference between those criteria. Are you so dishonest that you cant acknowledge it?
Posted by: Daniel Smith on Nov. 09 2007,13:51

Quote (JAM @ Nov. 07 2007,09:10)
Quote (Daniel Smith @ Nov. 06 2007,13:58)
 
Quote (oldmanintheskydidntdoit @ Nov. 05 2007,02:48)
I can propose anything I like, I don't expect the world to jump on it and disprove it. It's up to me to provide positive proof in the first instance.
---------------------QUOTE-------------------


Davison cites experimental evidence showing that semi-meiotic reproduction is possible even amongst sexually reproductive animals.

But where is the "positive proof" (you say) you require for the assumed mechanisms of gradual evolution?
---------------------QUOTE-------------------


Daniel, I take issue with omitsddi's use of the term "proof," but plenty of positive evidence is available from VISTA. That's why you felt compelled to lie and claim that noncoding regions in genes (introns and 5' and 3' UTRs) were "coding regions."

Again, get this through your thick head. It's not about CITING evidence. It's about PRODUCING NEW EVIDENCE by TESTING YOUR OWN HYPOTHESIS.

Surely you're not so stupid that you can't see the immense difference between those criteria. Are you so dishonest that you cant acknowledge it?
---------------------QUOTE-------------------


I'm still waiting for a paper from you.
Posted by: JAM on Nov. 09 2007,15:03

Quote (Daniel Smith @ Nov. 09 2007,13:51)
     
Quote (JAM @ Nov. 07 2007,09:10)
       
Quote (Daniel Smith @ Nov. 06 2007,13:58)
         
Quote (oldmanintheskydidntdoit @ Nov. 05 2007,02:48)
I can propose anything I like, I don't expect the world to jump on it and disprove it. It's up to me to provide positive proof in the first instance.
---------------------QUOTE-------------------


Davison cites experimental evidence showing that semi-meiotic reproduction is possible even amongst sexually reproductive animals.

But where is the "positive proof" (you say) you require for the assumed mechanisms of gradual evolution?
---------------------QUOTE-------------------


Daniel, I take issue with omitsddi's use of the term "proof," but plenty of positive evidence is available from VISTA. That's why you felt compelled to lie and claim that noncoding regions in genes (introns and 5' and 3' UTRs) were "coding regions."

Again, get this through your thick head. It's not about CITING evidence. It's about PRODUCING NEW EVIDENCE by TESTING YOUR OWN HYPOTHESIS.

Surely you're not so stupid that you can't see the immense difference between those criteria. Are you so dishonest that you cant acknowledge it?
---------------------QUOTE-------------------


I'm still waiting for a paper from you.
---------------------QUOTE-------------------


I'm still waiting for you to answer some questions, starting with your predictions for the paper:
------------
How do you explain the fact that starting with a random sequence, we can use mutation and selection to evolve a function in real time?

What level reduction do you consider to represent lack of function? For example, if your heart rate was reduced a million-fold, to ~1 beat every 10 days, you'd be dead. Would you agree that your heart failed to function--that it was not meeting design criteria, so to speak?

------------
And some others:
-------
In addition, why aren't these discoveries being made by ID proponents...like, um, at the Discovery Institute?

Why aren't discoveries like these motivating people like you to start careers in science?

What do any of the data have to do with the genetic code, which really isn't very complex?

What's so complex about coding for 20 amino acids, start, and stop in 64 codons?

Or were you just using "genetic code" in a profoundly ignorant way?

...would you mind commenting on the intelligence of having the same codon that starts protein synthesis also encoding the amino acid methionine?

I ask because it seems really, really stupid to me; I can improve the design with my measly human intelligence. Does that therefore make me smarter than God? Why would one want to worship an unintelligent God? Do you see how the ID movement is bad theology slathered onto nonexistent science?

Here's another question: how long does it take to evolve multiple, different, incredibly specific, functional, new protein-protein binding sites, using nothing but genetic variation and selection?

What does "nonrepeat" mean, Daniel? What proportion of "junk" is repeat, and what proportion is nonrepeat (unique)?

How much DNA was reclassified as something other than the provisional classification of "junk" in this case? What proportion of the genome? Be precise and systematic.

What proportion of the genome did they throw out when they only looked at "nonrepeat" sequences? Be precise and systematic.

So how can introns be both coding sequences and junk sequences?

How does studying nonrepeat sequences within and near genes reclassify "junk" DNA?

For example, if God designed your body, He clearly understands the concept of plumbing. Why is there nothing analogous within cells?

Why do cells use a system analogous to throwing lipid water balloons full of food and sewage around (allowing them to fuse and ripping them apart) instead of having simple plumbing?

According to your hypothesis, how many human genes won't have a mouse ortholog and vice versa?

You can start with the bolded ones.
Posted by: Daniel Smith on Nov. 09 2007,22:05

Quote (oldmanintheskydidntdoit @ Nov. 06 2007,14:14)
 
Quote (Daniel Smith @ Nov. 06 2007,13:58)
   
Quote (oldmanintheskydidntdoit @ Nov. 05 2007,02:48)
I can propose anything I like, I don't expect the world to jump on it and disprove it. It's up to me to provide positive proof in the first instance.
---------------------QUOTE-------------------


Davison cites experimental evidence showing that semi-meiotic reproduction is possible even amongst sexually reproductive animals.

But where is the "positive proof" (you say) you require for the assumed mechanisms of gradual evolution?
---------------------QUOTE-------------------


   

---------------------QUOTE-------------------
Allen MacNeill
Sources of Heritable Variation (both genotypic and phenotypic) Among Individuals in Populations

Gene Structure (in DNA)
• single point mutations
• deletion and insertion (“frame shift”) mutations
• inversion and translocation mutations
Gene Expression in Prokaryotes
• changes in promoter or terminator sequences (increasing or decreasing binding)
• changes in repressor binding (in prokaryotes); increasing or decreasing binding to operator sites
• changes in repressor binding (in prokaryotes); increasing or decreasing binding to inducers
• changes in repressor binding (in prokaryotes); increasing or decreasing binding to corepressors
Gene Expression in Eukaryotes
• changes in activation factor function in eukaryotes (increasing or decreasing binding to promoters)
• changes in intron length, location, and/or editing by changes in specificity of SNRPs
• changes in interference/antisense RNA regulation (increasing or decreasing binding to sense RNAs)
Gene Interactions
• changes in substrates or products of biochemical pathways
• addition or removal of gene products (especially enzymes) from biochemical pathways
• splitting or combining of biochemical pathways
• addition or alteration of pleiotropic effects, especially in response to changes in other genes/traits
Eukaryotic Chromosome Structure
• gene duplication within chromosomes
• gene duplication in multiple chromosomes
• inversions involving one or more genes in one chromosome
• translocations involving one or more genes between two or more chromosomes
• deletion/insertion of one or more genes via transposons
• fusion of two or more chromosomes or chromosome fragments
• fission of one chromosome into two or more fragments
• changes in chromosome number via nondisjunction (aneuploidy)
• changes in chromosome number via autopolyploidy (especially in plants)
• changes in chromosome number via allopolyploidy (especially in plants)
Eukaryotic Chromosome Function
• changes in regulation of multiple genes in a chromosome as a result of the foregoing structural changes
• changes in gene expression as result of DNA methylation
• changes in gene expression as result of changes in DNA-histone binding
Genetic Recombination
• the exchange of non-identical genetic material between two or more individuals (i.e. sex)
• lateral gene transfer via plasmids and episomes (especially in prokaryotes)
• crossing-over (reciprocal and non-reciprocal) between sister chromatids in meiosis
• crossing-over (non-reciprocal) between sister chromatids in mitosis
• Mendelian independent assortment during meiosis
• hybridization
Genome Structure and Function
• genome reorganization and/or reintegration
• partial or complete genome duplication
• partial or complete genome fusion
Development (among multicellular eukaryotes, especially animals)
• changes in tempo and timing of gene regulation, especially in eukaryotes
• changes in homeotic gene regulation in eukaryotes
• genetic imprinting, especially via hormone-mediated DNA methylation
Symbiosis
• partial or complete endosymbiosis
• partial or complete incorporation of unrelated organisms as part of developmental pathways (especially larval forms)
• changes in presence or absence of mutualists, commensals, and/or parasites
Behavior/Neurobiology
• changes in behavioral anatomy, histology, and/or physiology in response to changes in biotic community
• changes in behavioral anatomy, histology, and/or physiology in response to changes in abiotic environment
• learning (including effects of use and disuse)
Physiological Ecology
• changes in anatomy, histology, and/or physiology in response to changes in biotic community
• changes in anatomy, histology, and/or physiology in response to changes in abiotic environment
---------------------QUOTE-------------------



Which particular assumed mechanism are you interested in?
---------------------QUOTE-------------------


I don't care.  Pick one and lets look at the experimental evidence showing it's capabilities towards creating complex functional systems.
Posted by: Jim_Wynne on Nov. 09 2007,22:22



---------------------QUOTE-------------------
Pick one and lets look at the experimental evidence showing it's capabilities towards creating complex functional systems.
---------------------QUOTE-------------------


Define "complex" and tell us how we can identify it, and what the delimiter is between complex and not-complex.  While you're at it, you might also want to tell us what you think a "functional system" is.
Posted by: Daniel Smith on Nov. 09 2007,23:32

OK, only because you're going to keep acting as if I'm the one who's stalling the discussion, I'll attempt to answer your questions.              
Quote (JAM @ Nov. 09 2007,15:03)
How do you explain the fact that starting with a random sequence, we can use mutation and selection to evolve a function in real time?
---------------------QUOTE-------------------


I don't know.  I don't know that it is possible.  I'd predict that it isn't.  But first, don't we have to agree what a "function" is?                  

---------------------QUOTE-------------------
What level reduction do you consider to represent lack of function? For example, if your heart rate was reduced a million-fold, to ~1 beat every 10 days, you'd be dead. Would you agree that your heart failed to function--that it was not meeting design criteria, so to speak?
---------------------QUOTE-------------------


This is silly.  Are you asking for a general level for "lack of function"?  Or are you just concerned about the heart?  I would agree that a heart that beats once every ten days would be considered "non-functional" for a human - or any other known animal.  What does that have to do with the paper you refuse to show me?                  

---------------------QUOTE-------------------
In addition, why aren't these discoveries being made by ID proponents...like, um, at the Discovery Institute?
---------------------QUOTE-------------------


I don't know.                  

---------------------QUOTE-------------------
Why aren't discoveries like these motivating people like you to start careers in science?
---------------------QUOTE-------------------


I don't know.  I can't speak for "people like me".  I can only speak for myself.  Science for me, is a hobby.  I already have a career.                  

---------------------QUOTE-------------------
What do any of the data have to do with the genetic code, which really isn't very complex?

What's so complex about coding for 20 amino acids, start, and stop in 64 codons?

Or were you just using "genetic code" in a profoundly ignorant way?
---------------------QUOTE-------------------


Apparently I was.  You are right, the code is simple, what it codes for isn't.                  

---------------------QUOTE-------------------
...would you mind commenting on the intelligence of having the same codon that starts protein synthesis also encoding the amino acid methionine?
---------------------QUOTE-------------------


Is this a problem?                  

---------------------QUOTE-------------------
I ask because it seems really, really stupid to me; I can improve the design with my measly human intelligence.
---------------------QUOTE-------------------


Then why don't you?                    

---------------------QUOTE-------------------
Does that therefore make me smarter than God?
---------------------QUOTE-------------------


No.                  

---------------------QUOTE-------------------

Why would one want to worship an unintelligent God?
---------------------QUOTE-------------------


One wouldn't.                  

---------------------QUOTE-------------------
Do you see how the ID movement is bad theology slathered onto nonexistent science?
---------------------QUOTE-------------------


No.                  

---------------------QUOTE-------------------
Here's another question: how long does it take to evolve multiple, different, incredibly specific, functional, new protein-protein binding sites, using nothing but genetic variation and selection?
---------------------QUOTE-------------------


I don't know.                  

---------------------QUOTE-------------------
What does "nonrepeat" mean, Daniel?
---------------------QUOTE-------------------


I would guess it means "doesn't consist of repeating sequences".                  

---------------------QUOTE-------------------

What proportion of "junk" is repeat, and what proportion is nonrepeat (unique)?

How much DNA was reclassified as something other than the provisional classification of "junk" in this case? What proportion of the genome? Be precise and systematic.

What proportion of the genome did they throw out when they only looked at "nonrepeat" sequences? Be precise and systematic.

So how can introns be both coding sequences and junk sequences?

How does studying nonrepeat sequences within and near genes reclassify "junk" DNA?
---------------------QUOTE-------------------


Since you've never given me a definition for "junk" DNA, I had to do a google search.  I found this < here > (at the first page I looked at):
 

---------------------QUOTE-------------------
#  Less than 2% of the genome codes for proteins.
# Repeated sequences that do not code for proteins ("junk DNA") make up at least 50% of the human genome.
---------------------QUOTE-------------------



Do you agree with this definition: "Repeated sequences that do not code for proteins = junk DNA"?

If that's the "provisional definition" of junk DNA, then studying non-repeat sequences doesn't have anything to do with junk (as so defined) and I was wrong to argue that it did.

I guess the answer to the other question would be that they "threw out" 50% of the genome when they didn't look at repeat sequences.

I'm curious though, when I asked; "Are you equating repeat sequences with "junk"?", you replied "No, obviously, I'm not.".  So, I'm guessing that this isn't exactly your definition of junk.  Why don't you just tell me what your definition is?
           

---------------------QUOTE-------------------
For example, if God designed your body, He clearly understands the concept of plumbing. Why is there nothing analogous within cells?
---------------------QUOTE-------------------


You mean like pumps?                  

---------------------QUOTE-------------------
Why do cells use a system analogous to throwing lipid water balloons full of food and sewage around (allowing them to fuse and ripping them apart) instead of having simple plumbing?
---------------------QUOTE-------------------


I don't know.  It seems to work just fine though.                  

---------------------QUOTE-------------------
According to your hypothesis, how many human genes won't have a mouse ortholog and vice versa?
---------------------QUOTE-------------------


I don't have a specific number.  Did you have one before you found out the actual number?

Now, will you show me the paper?
Posted by: Daniel Smith on Nov. 09 2007,23:42

Quote (Jim_Wynne @ Nov. 09 2007,22:22)
 

---------------------QUOTE-------------------
Pick one and lets look at the experimental evidence showing it's capabilities towards creating complex functional systems.
---------------------QUOTE-------------------


Define "complex" and tell us how we can identify it, and what the delimiter is between complex and not-complex.  While you're at it, you might also want to tell us what you think a "functional system" is.
---------------------QUOTE-------------------


< Suggested reading. >
Posted by: JAM on Nov. 10 2007,01:05

Quote (Daniel Smith @ Nov. 09 2007,23:32)
OK, only because you're going to keep acting as if I'm the one who's stalling the discussion, I'll attempt to answer your questions.                  
Quote (JAM @ Nov. 09 2007,15:03)
How do you explain the fact that starting with a random sequence, we can use mutation and selection to evolve a function in real time?
---------------------QUOTE-------------------


I don't know.  I don't know that it is possible.  I'd predict that it isn't.  But first, don't we have to agree what a "function" is?
---------------------QUOTE-------------------


In this case, protein-protein binding.


---------------------QUOTE-------------------


---------------------QUOTE-------------------
What level reduction do you consider to represent lack of function? For example, if your heart rate was reduced a million-fold, to ~1 beat every 10 days, you'd be dead. Would you agree that your heart failed to function--that it was not meeting design criteria, so to speak?
---------------------QUOTE-------------------


This is silly.
---------------------QUOTE-------------------


Yes, the standard creationist response to this paper is profoundly silly, which is why I'm asking ahead of time.


---------------------QUOTE-------------------
Are you asking for a general level for "lack of function"?
---------------------QUOTE-------------------


No, I'm just asking if a million-fold reduction crosses the line for you.


---------------------QUOTE-------------------
Or are you just concerned about the heart?  I would agree that a heart that beats once every ten days would be considered "non-functional" for a human - or any other known animal.
---------------------QUOTE-------------------


Good.


---------------------QUOTE-------------------
What does that have to do with the paper you refuse to show me?
---------------------QUOTE-------------------


I'm not refusing to show you; I'm just heading off an evasive, dishonest response.

< http://www.springerlink.com/content/hhcx0pur3545x7v3/ >
Posted by: JAM on Nov. 10 2007,01:06



---------------------QUOTE-------------------


---------------------QUOTE-------------------
In addition, why aren't these discoveries being made by ID proponents...like, um, at the Discovery Institute?
---------------------QUOTE-------------------


I don't know.
---------------------QUOTE-------------------


My hypothesis is a lack of faith.


---------------------QUOTE-------------------


---------------------QUOTE-------------------
Why aren't discoveries like these motivating people like you to start careers in science?
---------------------QUOTE-------------------


I don't know.  I can't speak for "people like me".  I can only speak for myself.  Science for me, is a hobby.  I already have a career.
---------------------QUOTE-------------------


People change careers all the time, and I think that I can confidently say that science is not a hobby for you.


---------------------QUOTE-------------------
Apparently I was.  You are right, the code is simple, what it codes for isn't.
---------------------QUOTE-------------------


Thanks for admitting that. I'm impressed.


---------------------QUOTE-------------------


---------------------QUOTE-------------------
...would you mind commenting on the intelligence of having the same codon that starts protein synthesis also encoding the amino acid methionine?
---------------------QUOTE-------------------


Is this a problem?
---------------------QUOTE-------------------


Wouldn't you agree that not combining the stop signal with an amino acid is an intelligent move, given that functional proteins end in all sorts of different aa residues?

Now, since functional proteins BEGIN with many different residues, what does that say about the intelligence of combining start with methionine?

It's really not a difficult question. There's a perfect control to demonstrate the alleged intelligence of the designer!



---------------------QUOTE-------------------


---------------------QUOTE-------------------
I ask because it seems really, really stupid to me; I can improve the design with my measly human intelligence.
---------------------QUOTE-------------------


Then why don't you?
---------------------QUOTE-------------------


Huh?
 

---------------------QUOTE-------------------
 

---------------------QUOTE-------------------
Does that therefore make me smarter than God?
---------------------QUOTE-------------------


No.                    
---------------------QUOTE-------------------


Why not?
 

---------------------QUOTE-------------------
 

---------------------QUOTE-------------------
Why would one want to worship an unintelligent God?
---------------------QUOTE-------------------


One wouldn't.
---------------------QUOTE-------------------


I agree. So why do creationists attribute biological design to God, since so much of it is so obviously unintelligent?
 

---------------------QUOTE-------------------
 

---------------------QUOTE-------------------
Do you see how the ID movement is bad theology slathered onto nonexistent science?
---------------------QUOTE-------------------


No.
---------------------QUOTE-------------------


Have you considered opening your eyes to the NATURE of biological complexity, and avoiding the dishonest arguments about its presence and extent?
Posted by: JAM on Nov. 10 2007,01:07



---------------------QUOTE-------------------
   

---------------------QUOTE-------------------
Here's another question: how long does it take to evolve multiple, different, incredibly specific, functional, new protein-protein binding sites, using nothing but genetic variation and selection?
---------------------QUOTE-------------------


I don't know.
---------------------QUOTE-------------------


Two weeks.
   

---------------------QUOTE-------------------
Since you've never given me a definition for "junk" DNA, I had to do a google search.
---------------------QUOTE-------------------


But you're the one that brought it up! Why would I be responsible for defining it?
   

---------------------QUOTE-------------------
   

---------------------QUOTE-------------------
#  Less than 2% of the genome codes for proteins.
# Repeated sequences that do not code for proteins ("junk DNA") make up at least 50% of the human genome.
---------------------QUOTE-------------------


Do you agree with this definition: "Repeated sequences that do not code for proteins = junk DNA"?
---------------------QUOTE-------------------


Not at all, primarily because I can point you to repeated sequences that do not code for proteins that have a known function and that no one considers to be junk: ribosomal RNA genes.

Junk is mostly repeated and some nonrepeated DNA that has no known function and is very polymorphic. The classification, being negative, is clearly provisional.
   

---------------------QUOTE-------------------
If that's the "provisional definition" of junk DNA,...
---------------------QUOTE-------------------


No, the definition isn't provisional, the classification of a certain sequence as junk is. There's a huge difference.
   

---------------------QUOTE-------------------
then studying non-repeat sequences doesn't have anything to do with junk (as so defined) and I was wrong to argue that it did.
---------------------QUOTE-------------------


Your conclusion is correct, even though the definition wasn't.
   

---------------------QUOTE-------------------
I guess the answer to the other question would be that they "threw out" 50% of the genome when they didn't look at repeat sequences.
---------------------QUOTE-------------------


More like 90-95%.
   

---------------------QUOTE-------------------
   

---------------------QUOTE-------------------
For example, if God designed your body, He clearly understands the concept of plumbing. Why is there nothing analogous within cells?
---------------------QUOTE-------------------


You mean like pumps?
---------------------QUOTE-------------------


Yes, but more like pipes and valves that separate dirty from clean water.


---------------------QUOTE-------------------
   

---------------------QUOTE-------------------
Why do cells use a system analogous to throwing lipid water balloons full of food and sewage around (allowing them to fuse and ripping them apart) instead of having simple plumbing?
---------------------QUOTE-------------------


I don't know.  It seems to work just fine though.
---------------------QUOTE-------------------


That all depends on your definition of "just fine." It's laughable as an example of intelligent design. Why not just put structures that serve as pipes and valves in there?
   

---------------------QUOTE-------------------
   

---------------------QUOTE-------------------
According to your hypothesis, how many human genes won't have a mouse ortholog and vice versa?
---------------------QUOTE-------------------


I don't have a specific number.  Did you have one before you found out the actual number?
---------------------QUOTE-------------------


A range will do: thousands, hundreds, dozens, or <10?

My prediction was too high.

BTW, I did an experiment today that had a really exciting result. My prediction was wrong.
   

---------------------QUOTE-------------------
Now, will you show me the paper?
---------------------QUOTE-------------------


See the link to the abstract above.
Posted by: Jim_Wynne on Nov. 10 2007,10:04

Quote (Daniel Smith @ Nov. 09 2007,23:42)
Quote (Jim_Wynne @ Nov. 09 2007,22:22)
   

---------------------QUOTE-------------------
Pick one and lets look at the experimental evidence showing it's capabilities towards creating complex functional systems.
---------------------QUOTE-------------------


Define "complex" and tell us how we can identify it, and what the delimiter is between complex and not-complex.  While you're at it, you might also want to tell us what you think a "functional system" is.
---------------------QUOTE-------------------


< Suggested reading. >
---------------------QUOTE-------------------


I've done my reading, and unlike you, I've actually learned from it.  Unless you're willing to define your terms in your own words, we have no way of knowing what you're talking about, and you are free to move the goalposts at will. So I'll ask again:
1) What do you mean by "complex," how do you identify it, and what are the empirical delimiters between "complex" and not-complex?
2) How do you define "functional system"?
Posted by: Daniel Smith on Nov. 10 2007,10:45

Quote (JAM @ Nov. 10 2007,01:05)
< http://www.springerlink.com/content/hhcx0pur3545x7v3/ >
---------------------QUOTE-------------------


Thank you.

I was not able to read the entire paper, but only the abstract:
 

---------------------QUOTE-------------------
Abstract

To explore the possibility that an arbitrary sequence can evolve towards acquiring functional role when fused with other pre-existing protein modules, we replaced the D2 domain of the fd-tet phage genome with the soluble random polypeptide RP3-42. The replacement yielded an fd-RP defective phage that is six-order magnitude lower infectivity than the wild-type fd-tet phage. The evolvability of RP3-42 was investigated through iterative mutation and selection. Each generation consists of a maximum of ten arbitrarily chosen clones, whereby the clone with highest infectivity was selected to be the parent clone of the generation that followed. The experimental evolution attested that, from an initial single random sequence, there will be selectable variation in a property of interest and that the property in question was able to improve over several generations. fd-7, the clone with highest infectivity at the end of the experimental evolution, showed a 240-fold increase in infectivity as compared to its origin, fd-RP. Analysis by phage ELISA using anti-M13 antibody and anti-T7 antibody revealed that about 37-fold increase in the infectivity of fd-7 was attributed to the changes in the molecular property of the single polypeptide that replaced the D2 domain of the g3p protein. This study therefore exemplifies the process of a random polypeptide generating a functional role in rejuvenating the infectivity of a defective bacteriophage when fused to some preexisting protein modules, indicating that an arbitrary sequence can evolve toward acquiring a functional role. Overall, this study could herald the conception of new perspective regarding primordial polypeptides in the field of molecular evolution.
---------------------QUOTE-------------------


This is an interesting experiment.  I have a couple questions:
1.  Why did they use artificial selection as opposed to natural selection?
2.  My math isn't the greatest so when they say that the replacement phage had "six-order magnitude lower infectivity" than the original phage, and the newly evolved phage "showed a 240-fold increase in infectivity as compared to its origin, fd-RP", they're talking about 0.00024 less infectivity than the original wild phage - correct?
Posted by: Daniel Smith on Nov. 10 2007,11:05

Quote (JAM @ Nov. 10 2007,01:07)
 

---------------------QUOTE-------------------
       

---------------------QUOTE-------------------
Here's another question: how long does it take to evolve multiple, different, incredibly specific, functional, new protein-protein binding sites, using nothing but genetic variation and selection?
---------------------QUOTE-------------------


I don't know.
---------------------QUOTE-------------------


Two weeks.
---------------------QUOTE-------------------

Is this information in the paper you linked to?  

---------------------QUOTE-------------------

       

---------------------QUOTE-------------------
Since you've never given me a definition for "junk" DNA, I had to do a google search.
---------------------QUOTE-------------------


But you're the one that brought it up! Why would I be responsible for defining it?
       

---------------------QUOTE-------------------
       

---------------------QUOTE-------------------
#  Less than 2% of the genome codes for proteins.
# Repeated sequences that do not code for proteins ("junk DNA") make up at least 50% of the human genome.
---------------------QUOTE-------------------


Do you agree with this definition: "Repeated sequences that do not code for proteins = junk DNA"?
---------------------QUOTE-------------------


Not at all, primarily because I can point you to repeated sequences that do not code for proteins that have a known function and that no one considers to be junk: ribosomal RNA genes.

Junk is mostly repeated and some nonrepeated DNA that has no known function and is very polymorphic. The classification, being negative, is clearly provisional.
---------------------QUOTE-------------------

My expectation then is that the provisional definition of "junk DNA" will continually evolve until it no longer includes any portion of the genome.  

---------------------QUOTE-------------------

       

---------------------QUOTE-------------------
If that's the "provisional definition" of junk DNA,...
---------------------QUOTE-------------------


No, the definition isn't provisional, the classification of a certain sequence as junk is. There's a huge difference.
       

---------------------QUOTE-------------------
then studying non-repeat sequences doesn't have anything to do with junk (as so defined) and I was wrong to argue that it did.
---------------------QUOTE-------------------


Your conclusion is correct, even though the definition wasn't.
       

---------------------QUOTE-------------------
I guess the answer to the other question would be that they "threw out" 50% of the genome when they didn't look at repeat sequences.
---------------------QUOTE-------------------


More like 90-95%.
---------------------QUOTE-------------------

Are you saying that 90-95% of the human genome is repeats?  

---------------------QUOTE-------------------

       

---------------------QUOTE-------------------
       

---------------------QUOTE-------------------
For example, if God designed your body, He clearly understands the concept of plumbing. Why is there nothing analogous within cells?
---------------------QUOTE-------------------


You mean like pumps?
---------------------QUOTE-------------------


Yes, but more like pipes and valves that separate dirty from clean water.
   

---------------------QUOTE-------------------
       

---------------------QUOTE-------------------
Why do cells use a system analogous to throwing lipid water balloons full of food and sewage around (allowing them to fuse and ripping them apart) instead of having simple plumbing?
---------------------QUOTE-------------------


I don't know.  It seems to work just fine though.
---------------------QUOTE-------------------


That all depends on your definition of "just fine." It's laughable as an example of intelligent design. Why not just put structures that serve as pipes and valves in there?
---------------------QUOTE-------------------

I don't know why most designers do what they do - that is not an argument against design.  It might be an effective argument against the competency of the designer, provided you can come up with a better workable system.  

---------------------QUOTE-------------------

       

---------------------QUOTE-------------------
       

---------------------QUOTE-------------------
According to your hypothesis, how many human genes won't have a mouse ortholog and vice versa?
---------------------QUOTE-------------------


I don't have a specific number.  Did you have one before you found out the actual number?
---------------------QUOTE-------------------


A range will do: thousands, hundreds, dozens, or <10?

My prediction was too high.

---------------------QUOTE-------------------

I have no idea.  My hypothesis doesn't really work that way.  What I mean is; since I view each of the multitude of evolutionary events between mouse and man as saltational, there's no way to predict the number of orthologs.  

My main contention is that the genomic sequences of organisms will be found to be fully functional and evolutionarily constrained within species - leaving the only possible mechanisms for the true evolution of new species saltational ones.  

---------------------QUOTE-------------------

BTW, I did an experiment today that had a really exciting result. My prediction was wrong.
     
---------------------QUOTE-------------------

So a wrong prediction is not "lying" then I take it?  ;)
Posted by: Daniel Smith on Nov. 10 2007,11:26

Quote (JAM @ Nov. 10 2007,01:06)

     

---------------------QUOTE-------------------
     

---------------------QUOTE-------------------
...would you mind commenting on the intelligence of having the same codon that starts protein synthesis also encoding the amino acid methionine?
---------------------QUOTE-------------------


Is this a problem?
---------------------QUOTE-------------------


Wouldn't you agree that not combining the stop signal with an amino acid is an intelligent move, given that functional proteins end in all sorts of different aa residues?

Now, since functional proteins BEGIN with many different residues, what does that say about the intelligence of combining start with methionine?

It's really not a difficult question. There's a perfect control to demonstrate the alleged intelligence of the designer!
---------------------QUOTE-------------------


Not necessarily.  Many genomic sequences are multi-functional - containing overlapping coding and non-coding functional sequences.  Perhaps we just don't know the functional advantage for combining the codon that starts protein synthesis and methionine.    

---------------------QUOTE-------------------

     

---------------------QUOTE-------------------
     

---------------------QUOTE-------------------
I ask because it seems really, really stupid to me; I can improve the design with my measly human intelligence.
---------------------QUOTE-------------------


Then why don't you?
---------------------QUOTE-------------------


Huh?
---------------------QUOTE-------------------

Why don't you engineer a better design and show it to the world?    

---------------------QUOTE-------------------

       

---------------------QUOTE-------------------
       

---------------------QUOTE-------------------
Does that therefore make me smarter than God?
---------------------QUOTE-------------------


No.                    
---------------------QUOTE-------------------


Why not?
---------------------QUOTE-------------------

It just means you think you're smarter than God.  You have to make a workable system to actually show yourself smarter than God.    

---------------------QUOTE-------------------

       

---------------------QUOTE-------------------
       

---------------------QUOTE-------------------
Why would one want to worship an unintelligent God?
---------------------QUOTE-------------------


One wouldn't.
---------------------QUOTE-------------------


I agree. So why do creationists attribute biological design to God, since so much of it is so obviously unintelligent?
---------------------QUOTE-------------------

So now that you have mastered all the various elements of biological design, you are prepared to say that anyone who was able to design it all would have to be unintelligent and that you could have come up with a better design?  That's a mighty big boast.  Good luck in your new venture (creating an alternate (and improved) form of life)!    

---------------------QUOTE-------------------

       

---------------------QUOTE-------------------
       

---------------------QUOTE-------------------
Do you see how the ID movement is bad theology slathered onto nonexistent science?
---------------------QUOTE-------------------


No.
---------------------QUOTE-------------------


Have you considered opening your eyes to the NATURE of biological complexity, and avoiding the dishonest arguments about its presence and extent?
---------------------QUOTE-------------------

I am attempting to "open my eyes" to anything and everything. Please explain (or link to) anything that will help me better understand "the NATURE of biological complexity".
Posted by: Daniel Smith on Nov. 10 2007,11:29

I have a question for anyone who wants to take a shot at it:

In the human genome, what percentage of genomic sequence would you say is likely to be transcribed as nuclear primary transcripts?
Posted by: Daniel Smith on Nov. 10 2007,11:40

Quote (Jim_Wynne @ Nov. 10 2007,10:04)
Unless you're willing to define your terms in your own words, we have no way of knowing what you're talking about, and you are free to move the goalposts at will. So I'll ask again:
1) What do you mean by "complex," how do you identify it, and what are the empirical delimiters between "complex" and not-complex?
2) How do you define "functional system"?
---------------------QUOTE-------------------


Fair enough.

"Complex" means "composed of many interconnected parts".
As a general rule: more parts = more complex.

"Functional system" means "an assemblage of parts which work together towards the same purpose or function"
Posted by: VMartin on Nov. 10 2007,11:42

Quote (Erasmus @ FCD,Nov. 01 2007,19:54)
Vicky

It was Haldane.  You know even less than you think.
---------------------QUOTE-------------------


Haldane was as perplexed by the concept of "Natural selection" as you are now.  

Haldane:
   

---------------------QUOTE-------------------

"Now this process of 'racial senescence' was not peculiar to the Ammonites . . . It seems to have occurred also in the Graptolites, Foraminifera, and other groups . . . It is not very easy to reconcile with evolution by natural selection."

---------------------QUOTE-------------------



and

   

---------------------QUOTE-------------------

"fallacy that natural selection will always make an organism fitter in its struggle with the environment"
(p. 119) and that variations "which possess survival value for the individual may lead to degeneration and extinction of the species"

---------------------QUOTE-------------------



But obviouisly the species can be eliminated only if all their individuals are eliminated. But those are not eliminated because they posses "survival value".

Btw McAtee who pointed out (and obviously ridiculed)  conception of Natural selection in darwinian heads also addressed the problem of evolution of horses from his point of view:

 

---------------------QUOTE-------------------

Horses, reintroduced, thrive in the wild in both North and South America on ranges where their fossil analogues
abounded. Such cases convincingly indicate that the causes of extinction were internal to the organisms concerned and not external or selective.

---------------------QUOTE-------------------




< https://kb.osu.edu/dspace/bitstream/1811/3985/1/V52N06_339.pdf >
Posted by: Arden Chatfield on Nov. 10 2007,12:25

Quote (VMartin @ Nov. 10 2007,11:42)
Quote (Erasmus @ FCD,Nov. 01 2007,19:54)
Vicky

It was Haldane.  You know even less than you think.
---------------------QUOTE-------------------


Haldane was as perplexed by the concept of "Natural selection" as you are now.  

Haldane:
   

---------------------QUOTE-------------------

"Now this process of 'racial senescence' was not peculiar to the Ammonites . . . It seems to have occurred also in the Graptolites, Foraminifera, and other groups . . . It is not very easy to reconcile with evolution by natural selection."

---------------------QUOTE-------------------



and

   

---------------------QUOTE-------------------

"fallacy that natural selection will always make an organism fitter in its struggle with the environment"
(p. 119) and that variations "which possess survival value for the individual may lead to degeneration and extinction of the species"

---------------------QUOTE-------------------



But obviouisly the species can be eliminated only if all their individuals are eliminated. But those are not eliminated because they posses "survival value".

Btw McAtee who pointed out (and obviously ridiculed)  conception of Natural selection in darwinian heads also addressed the problem of evolution of horses from his point of view:

 

---------------------QUOTE-------------------

Horses, reintroduced, thrive in the wild in both North and South America on ranges where their fossil analogues
abounded. Such cases convincingly indicate that the causes of extinction were internal to the organisms concerned and not external or selective.

---------------------QUOTE-------------------




< https://kb.osu.edu/dspace/bitstream/1811/3985/1/V52N06_339.pdf >
---------------------QUOTE-------------------


Hey Marty, what's YOUR explanation on the development of the horse? Were all the different varieties on Noah's Ark?
Posted by: Daniel Smith on Nov. 10 2007,12:30

Quote (JAM @ Nov. 05 2007,00:37)
     
Quote (Daniel Smith @ Nov. 04 2007,13:05)
Let me also add; these scientists have theories that have never been falsified.
---------------------QUOTE-------------------


Let me add that whether they've been falsified is irrelevant, when they have never been TESTED.
---------------------QUOTE-------------------


Schindewolf based his theory on the observed fossil record as well as observed biological evidence.  His theory was an attempt to explain all the evidence.

Berg based his theory on years and years of his own observations in the field, as well as the documented observations of countless others.

Both of these men were scientists of the highest regard in their respective fields who based their theories on observed, documented phenomena.

Davison took their work and expanded upon it - suggesting a workable mechanism.  This mechanism (semi-meiotic reproduction) has been experimentally verified possible < here >,
< here >,
and < here >.

   

---------------------QUOTE-------------------
Gynogenetic reproduction, employing the inhibtion of meiosis I1 and yielding diploid rather than triploid progeny, can be used to map G-K distances as well as
to develop “inbred” strains*. This mode of reproduction is known in several natural populations of invertebrates and vertebrates (SUOMALAINEN 1950; WHITE 1948, 1970; OLSEN 1962; CARSON 1967) and has been produced experimentally in vertebrates when the appropriate meiotic events are altered (TYLER 1955; BEATTY 1967; GRAHAM 1970; TARKOWSKI, WITKOWSKA, and NOWICKA 1970).
(Emphasis mine)
---------------------QUOTE-------------------



A search for the terms parthenogenesis, gynogenesis, and hybridogenesis reveals more data in this area.

I have no idea why these scientists are ignored, but my guess is that their views don't fit the paradigm, and - based on my own observations - scientists whose ideas don't fit are generally ostracized, lose funding, and eventually relegated to the sidelines.

No one wants to lose their position over such things, so they stick to the paradigm.

That's my guess.
Posted by: mitschlag on Nov. 10 2007,12:50

Quote (Daniel Smith @ Nov. 10 2007,11:05)
My expectation then is that the provisional definition of "junk DNA" will continually evolve until it no longer includes any portion of the genome.
---------------------QUOTE-------------------


So natural selection (new data) will elicit mutations (deletions) in the definition of "junk DNA."

Another nail in the coffin of Darwinism.
Posted by: mitschlag on Nov. 10 2007,13:06

Quote (Daniel Smith @ Nov. 10 2007,12:30)
Davison took their work and expanded upon it - suggesting a workable mechanism.  This mechanism (semi-meiotic reproduction) has been experimentally verified possible < here >,
< here >,
and < here >.

             

---------------------QUOTE-------------------
Gynogenetic reproduction, employing the inhibtion of meiosis I1 and yielding diploid rather than triploid progeny, can be used to map G-K distances as well as
to develop “inbred” strains*. This mode of reproduction is known in several natural populations of invertebrates and vertebrates (SUOMALAINEN 1950; WHITE 1948, 1970; OLSEN 1962; CARSON 1967) and has been produced experimentally in vertebrates when the appropriate meiotic events are altered (TYLER 1955; BEATTY 1967; GRAHAM 1970; TARKOWSKI, WITKOWSKA, and NOWICKA 1970).
(Emphasis mine)
---------------------QUOTE-------------------



A search for the terms parthenogenesis, gynogenesis, and hybridogenesis reveals more data in this area.
---------------------QUOTE-------------------


That's not the issue.  The issue is not whether semi-meiotic reproduction can occur.  The issue is whether that is the driving mechanism of evolution, as Davison claims.

Furthermore, let's assume that Davison is correct in that claim.  How would that logically entail "front-loading"?
     

---------------------QUOTE-------------------
I have no idea why these scientists are ignored, but my guess is that their views don't fit the paradigm, and - based on my own observations - scientists whose ideas don't fit are generally ostracized, lose funding, and eventually relegated to the sidelines.

No one wants to lose their position over such things, so they stick to the paradigm.

That's my guess.
---------------------QUOTE-------------------


My guess is that their findings (not their "views," whatever they may be, not having been expressed in the papers you cited), are not RELEVANT to the paradigm.  It's survival of the fittest out there.  (Your case is not strengthened by such gratuitous ad hominems.)
Posted by: Daniel Smith on Nov. 10 2007,15:51

Quote (mitschlag @ Nov. 10 2007,13:06)
     
Quote (Daniel Smith @ Nov. 10 2007,12:30)
Davison took their work and expanded upon it - suggesting a workable mechanism.  This mechanism (semi-meiotic reproduction) has been experimentally verified possible < here >,
< here >,
and < here >.

                   

---------------------QUOTE-------------------
Gynogenetic reproduction, employing the inhibtion of meiosis I1 and yielding diploid rather than triploid progeny, can be used to map G-K distances as well as
to develop “inbred” strains*. This mode of reproduction is known in several natural populations of invertebrates and vertebrates (SUOMALAINEN 1950; WHITE 1948, 1970; OLSEN 1962; CARSON 1967) and has been produced experimentally in vertebrates when the appropriate meiotic events are altered (TYLER 1955; BEATTY 1967; GRAHAM 1970; TARKOWSKI, WITKOWSKA, and NOWICKA 1970).
(Emphasis mine)
---------------------QUOTE-------------------



A search for the terms parthenogenesis, gynogenesis, and hybridogenesis reveals more data in this area.
---------------------QUOTE-------------------


That's not the issue.  The issue is not whether semi-meiotic reproduction can occur.  The issue is whether that is the driving mechanism of evolution, as Davison claims.

Furthermore, let's assume that Davison is correct in that claim.  How would that logically entail "front-loading"?
---------------------QUOTE-------------------

These saltational events are too extensive to be random.  This is what implies front-loading.    

---------------------QUOTE-------------------

             

---------------------QUOTE-------------------
I have no idea why these scientists are ignored, but my guess is that their views don't fit the paradigm, and - based on my own observations - scientists whose ideas don't fit are generally ostracized, lose funding, and eventually relegated to the sidelines.

No one wants to lose their position over such things, so they stick to the paradigm.

That's my guess.
---------------------QUOTE-------------------


My guess is that their findings (not their "views," whatever they may be, not having been expressed in the papers you cited), are not RELEVANT to the paradigm.  It's survival of the fittest out there.  (Your case is not strengthened by such gratuitous ad hominems.)
---------------------QUOTE-------------------


I wasn't aware that I was using "gratuitous ad hominems".  I based my statements on observed incidents such as < this one >; where a proponent of ID decides to sever his ties (at least publicly) to the movement because he was accepted into a graduate program at Johns Hopkins University.  This after being advised that he "may expect possible complications" for his public involvement with ID.

Dr. Davison suffered extensive < repurcusions > at the University of Vermont.

What I'm describing here is not imaginary, but a real palpable fear of losing that for which you've worked all your life if you don't embrace the currently held theory.
Posted by: Erasmus, FCD on Nov. 10 2007,16:15

Daniel, is Sal Cordova an ID'er or a Young Earth Creationist?

Are the two the same?

toodles, sweetums....
Posted by: Assassinator on Nov. 10 2007,16:39



---------------------QUOTE-------------------
These saltational events are too extensive to be random.
---------------------QUOTE-------------------


Wich "saltational" events? You mean like the Cambrian Explosion? That still took several millions of years, and that's one HELL of a long time.
Posted by: mitschlag on Nov. 10 2007,17:08

Quote (Daniel Smith @ Nov. 10 2007,15:51)
These saltational events are too extensive to be random.  This is what implies front-loading.
---------------------QUOTE-------------------


I've read Davison's < Evolutionary Manifesto >

Please quote where in that document he makes that point.

And please state the criteria that would distinguish "too extensive" from "random," citing data upon which you base your claim.
Posted by: Wesley R. Elsberry on Nov. 10 2007,17:12



---------------------QUOTE-------------------

What I'm describing here is not imaginary, but a real palpable fear of losing that for which you've worked all your life if you don't embrace the currently held theory.

---------------------QUOTE-------------------



Scientific advancement is, broadly speaking, based on merit.

How does one distinguish between simple incompetence that is fully deserving of worsening one's standing in science, and exploration of alternative theories in a competent fashion, which should not be penalized?

Bear in mind that we have plenty of examples of both sorts that we can check your answer against.
Posted by: mitschlag on Nov. 10 2007,17:14

Quote (Daniel Smith @ Nov. 10 2007,15:51)
I wasn't aware that I was using "gratuitous ad hominems".  I based my statements on observed incidents such as this one; where a proponent of ID decides to sever his ties (at least publicly) to the movement because he was accepted into a graduate program at Johns Hopkins University.  This after being advised that he "may expect possible complications" for his public involvement with ID.
---------------------QUOTE-------------------


The persecution complexes of evolution deniers are legion, on this thread and throughout the blogosphere.

Can you tell the difference between anecdote and reality?

The more you pile on crap like this, the more you undermine your credibility.
Posted by: Jim_Wynne on Nov. 10 2007,17:39

Quote (Daniel Smith @ Nov. 10 2007,11:40)
Quote (Jim_Wynne @ Nov. 10 2007,10:04)
Unless you're willing to define your terms in your own words, we have no way of knowing what you're talking about, and you are free to move the goalposts at will. So I'll ask again:
1) What do you mean by "complex," how do you identify it, and what are the empirical delimiters between "complex" and not-complex?
2) How do you define "functional system"?
---------------------QUOTE-------------------


Fair enough.

"Complex" means "composed of many interconnected parts".
As a general rule: more parts = more complex.

"Functional system" means "an assemblage of parts which work together towards the same purpose or function"
---------------------QUOTE-------------------


Please reread the first question, and try again. What about boundaries? You need to be able to describe (with more rigor than "I know it when I see it") the difference between complex and not-complex.
Posted by: mitschlag on Nov. 10 2007,18:47

Quote (Daniel Smith @ Nov. 10 2007,15:51)
Dr. Davison suffered extensive < repurcusions > at the University of Vermont.
---------------------QUOTE-------------------


Try to put yourself in the position of authority.  You have a tenured faculty member who has become scientifically unproductive (check publications and grants lists) and is making a public spectacle of himself.

You can't fire him.  What do you do?  (Cue < Lehigh > and Behe.)
Posted by: VMartin on Nov. 11 2007,03:15

Quote (mitschlag @ Nov. 10 2007,18:47)
Quote (Daniel Smith @ Nov. 10 2007,15:51)
Dr. Davison suffered extensive < repurcusions > at the University of Vermont.
---------------------QUOTE-------------------


Try to put yourself in the position of authority.  You have a tenured faculty member who has become scientifically unproductive (check publications and grants lists) and is making a public spectacle of himself.

You can't fire him.  What do you do?  (Cue < Lehigh > and Behe.)
---------------------QUOTE-------------------


Interesting link.



---------------------QUOTE-------------------

It is our collective position that intelligent design has no basis in science, has not been tested experimentally, and should not be regarded as scientific.

---------------------QUOTE-------------------



I think you would agree 500 years ago also with:



---------------------QUOTE-------------------

It is our collective position that hermetism has no basis in science, has not been tested experimentally, and should not be regarded as scientific.

---------------------QUOTE-------------------



Surely true and yet it was the faked work of Hermes Trismegistus and his worshipping of the Sun, that led Giordano Bruno to support solar system of Copernikus (who in his drawing of new Solar system used Hermes Trismegistus name as well).  From bad pressupositions good results.

And it is utterly weird to use your "letter" against anti-darwinist Pierre Grasse mentioned in John Davison's Manifesto. Grasse was president of French academy of science, you know.
Posted by: mitschlag on Nov. 11 2007,06:29

Quote (VMartin @ Nov. 11 2007,03:15)
 

---------------------QUOTE-------------------

It is our collective position that hermetism has no basis in science, has not been tested experimentally, and should not be regarded as scientific.

---------------------QUOTE-------------------



Surely true and yet it was the faked work of Hermes Trismegistus and his worshipping of the Sun, that led Giordano Bruno to support solar system of Copernikus (who in his drawing of new Solar system used Hermes Trismegistus name as well).  From bad pressupositions good results.
---------------------QUOTE-------------------


The Lord works in mysterious ways, VMartin.
Posted by: VMartin on Nov. 11 2007,07:49

Quote (mitschlag @ Nov. 11 2007,06:29)
           
Quote (VMartin @ Nov. 11 2007,03:15)
             

---------------------QUOTE-------------------

It is our collective position that hermetism has no basis in science, has not been tested experimentally, and should not be regarded as scientific.

---------------------QUOTE-------------------



Surely true and yet it was the faked work of Hermes Trismegistus and his worshipping of the Sun, that led Giordano Bruno to support solar system of Copernikus (who in his drawing of new Solar system used Hermes Trismegistus name as well).  From bad pressupositions good results.
---------------------QUOTE-------------------


The Lord works in mysterious ways, VMartin.
---------------------QUOTE-------------------



My point was that at the root of the modern science stood men of Rennaisance who had a much more complex view of the reality than reductionism  so common today. Nowadays it is biologist professor Zdenek Neubauer in Czech republic, an extraordinary educated scholar and philosopher with such a stance. He dismissed in his latest books neodarwinism using harsh words. Of course reductionists flocked together in their atheistic Czech circle for science "Sisyphos" became angry. But no one of them has so strong reputation and background in Czech republic and on the radio discussions with him they sounds very naive and plain. So there was no tendency to create any letter of dissociation at the department of Charles University  Prague which he headed some times ago.

No one of his most interesting books have been translated into English yet (maybe he disagree, I don't know. He doesn't publish in English anymore. He writes now only in Czech and Italian, even though he is fluent in German, Latin and English and helped translate some neo-platonic works from Greek). But his friend and colleague Komarek wrote a book on history of mimicry which has been translated and is available in English. Komarek no way take seriously neodarwinian explanation of many cases of so-called mimicry. But it is no reason for his colleagues at Uni Prague to flock together and scribble a letter of dissociation.

You know these letter of dissociation are very funny in the area of Central Europe. Such letters make often only more sympathy for your stance.

Of course I am very well aware of the fact that influnce of Behe is differenet than those scientists I mentioned above. Anyway  Davison's work in my opinion goes more deeply into secrets of evolution than the work of Behe.
Posted by: Erasmus, FCD on Nov. 11 2007,08:28

Publishing in the Rivista journal doesn't help.  I hear that it comes in a brown paper bag.

martin your ideas about what makes ideas valid and what constitutes a proper defense from criticism sure are interesting.  

much in the same way that i dig through bear shit to see what he has been eating.  and also flipping over dead possums and looking for Nicrophorus.  you are a curiosity much like bloody stool.  now please tell us what you intend to replace-a da darwismus with, since you have been unable to demonstrate that it is wrong beyond handwaving and quotemining.
Posted by: mitschlag on Nov. 11 2007,08:46

Quote (VMartin @ Nov. 11 2007,07:49)
My point was that at the root of the modern science stood men of Rennaisance who had a much more complex view of the reality than reductionism  so common today.
---------------------QUOTE-------------------


Maybe they were just confused.
Posted by: VMartin on Nov. 11 2007,11:38

I don't have time to google for mitschlag and Erasmus  all scientific articles regarding microbiology by professor Zden?k Neubauer. Here is the abstract of his article he published as a 24 year old microbiologist in the Nature 1967.

< Nature 1967: Brief consideration of the Meaning of the Lysogenic Conversion in Salmonella anatum Phage System >

and then as a co-author working at the International Laboratory of Genetics and Biophysics, Naples


< Nature 1970: The Antirepressor: a New Element in the Regulation of Protein Synthesis >


Did anyone of you published so young in the Nature (if you have ever published there something)  that entitles you to dismiss your antidarwinian adersaries who  published there as "confused"?
Posted by: Erasmus, FCD on Nov. 11 2007,12:16

indeed if we look at the progression of any body of theory at the basal branches you will find a plurality of alternative theories (see S Naeem Ecology 2006 or 2007 paper for a discussion of this dialectical progression in ecology).  the reasons for the trimming of the branches are varied, but ultimately empirical support is the criterion.

and there is no theoretical nor empirical support for your ideas Martin, and this is the same as for Daniel.  saltational orthogenetical views must deny heredity.  if you believe that speciation is independent of phylogenesis or the arisal of new forms, you must have another mechanism.  i've not read all of davison's manifesto yet so i'll withhold judgment about his proposed mechanisms, but it suffices to say that the discovery and advent of DNA based phylogenetics destroyed any possibility that schindewolf et al could be right because it showed the mechanism for divergence between populations and a workable theoretical framework for constructing hypotheses about nested hierarchies.

schindewolf was right about some things, namely the effects of canalization as a constraint.  but there is no support for the idea of reservoirs of variation, unless you are going to follow daniels lead and claim that this is what non-coding DNA is.  JAM is doing a much better job than I could with refuting that view, so I will simply ask:  do you have a new mechanism?  do you have a testable theory?
Posted by: Daniel Smith on Nov. 11 2007,12:36

Quote (Jim_Wynne @ Nov. 10 2007,17:39)
   
Quote (Daniel Smith @ Nov. 10 2007,11:40)
     
Quote (Jim_Wynne @ Nov. 10 2007,10:04)
Unless you're willing to define your terms in your own words, we have no way of knowing what you're talking about, and you are free to move the goalposts at will. So I'll ask again:
1) What do you mean by "complex," how do you identify it, and what are the empirical delimiters between "complex" and not-complex?
2) How do you define "functional system"?
---------------------QUOTE-------------------


Fair enough.

"Complex" means "composed of many interconnected parts".
As a general rule: more parts = more complex.

"Functional system" means "an assemblage of parts which work together towards the same purpose or function"
---------------------QUOTE-------------------


Please reread the first question, and try again. What about boundaries? You need to be able to describe (with more rigor than "I know it when I see it") the difference between complex and not-complex.
---------------------QUOTE-------------------


You can count can't you?

What part of "more parts = more complex" doesn't make sense?

Complexity is a matter of degree - the only boundary is that it requires more than 1 part.

After that it's not, "this is complex and that isn't"; it's, "this is more complex than that".

Remember we're talking about biological systems here.  If you can point to one that you'd say is not a "complex functional system", go ahead and eliminate that one from the discussion.

I'd like to see some experimental evidence that any one of the myriads of suggested mechanisms for evolution can produce systems that are at least as complex and functional as known biological systems.

Here, I'll make it easy for you:  I'll give you on of the most basic biological system in life; one on which all life depends:  Protein Synthesis.

Now, take any of the mechanisms you like (or any combination of them) and show me experimental evidence that a product very much like protein synthesis can be constructed utilizing those mechanisms.
Posted by: Daniel Smith on Nov. 11 2007,12:52

Quote (mitschlag @ Nov. 10 2007,17:08)
     
Quote (Daniel Smith @ Nov. 10 2007,15:51)
These saltational events are too extensive to be random.  This is what implies front-loading.
---------------------QUOTE-------------------


I've read Davison's < Evolutionary Manifesto >

Please quote where in that document he makes that point.

And please state the criteria that would distinguish "too extensive" from "random," citing data upon which you base your claim.
---------------------QUOTE-------------------


He doesn't make that point in the Manifesto.  He does make it in his many postings on the web since that time.  The only place in his manifesto where he hints at it is here:
     

---------------------QUOTE-------------------
While it is true that the existence of a Creator, while a logical necessity, has never been rigorously proved and perhaps never can be, it is also true that neither has been the spontaneous generation of life. (emphasis mine)
---------------------QUOTE-------------------


If one reads the various works on which he builds his hypothesis: the writings of William Bateson, Leo S. Berg, Robert Broom, Richard B. Goldschmidt, Pierre Grassé, and Otto Schindewolf, (of which I've only read one work apiece for Berg and Schindewolf, and just started one from Bateson), you find that this need for front-loading (or some type of divine guidance) is necessary (or at least implied) for evolution of the saltational type they espouse to happen.

So, as to the data on which I base my claim, I'll just point you to the < Vista Genome Browser >, where you can compare the genomes of like organisms and see the multitude of differences for yourself.  If these differences are the result of a small number of saltational events, they could not be random and still produce working, living organisms.
Posted by: Daniel Smith on Nov. 11 2007,12:55

Quote (Wesley R. Elsberry @ Nov. 10 2007,17:12)
 

---------------------QUOTE-------------------

What I'm describing here is not imaginary, but a real palpable fear of losing that for which you've worked all your life if you don't embrace the currently held theory.

---------------------QUOTE-------------------



Scientific advancement is, broadly speaking, based on merit.

How does one distinguish between simple incompetence that is fully deserving of worsening one's standing in science, and exploration of alternative theories in a competent fashion, which should not be penalized?

Bear in mind that we have plenty of examples of both sorts that we can check your answer against.
---------------------QUOTE-------------------


I would say one would distinguish between these two types of individuals by careful analysis of their claims via the scientific method.
Posted by: JAM on Nov. 11 2007,13:05

Quote (Daniel Smith @ Nov. 10 2007,10:45)

This is an interesting experiment.  I have a couple questions:
1.  Why did they use artificial selection as opposed to natural selection?
---------------------QUOTE-------------------


So that they could analyze the phage after each generation. You're desperately looking for a reason to discount this; how predictable.


---------------------QUOTE-------------------
2.  My math isn't the greatest so when they say that the replacement phage had "six-order magnitude lower infectivity" than the original phage, and the newly evolved phage "showed a 240-fold increase in infectivity as compared to its origin, fd-RP", they're talking about 0.00024 less infectivity than the original wild phage - correct?
---------------------QUOTE-------------------


But that increase was obtained in just seven generations, so that doesn't work as a justification for discounting the data.
Posted by: Erasmus, FCD on Nov. 11 2007,13:07

Daniel may I recommend a book to you?  it's short.  


< book >

you might get a broader perspective of galton bateson and devries and why their ideas were wrong.  it has something to do with mendel.
Posted by: JAM on Nov. 11 2007,13:25

Quote (Daniel Smith @ Nov. 10 2007,11:05)
   
Quote (JAM @ Nov. 10 2007,01:07)
 

---------------------QUOTE-------------------
 

---------------------QUOTE-------------------
Here's another question: how long does it take to evolve multiple, different, incredibly specific, functional, new protein-protein binding sites, using nothing but genetic variation and selection?
---------------------QUOTE-------------------


I don't know.
---------------------QUOTE-------------------


Two weeks.
---------------------QUOTE-------------------

Is this information in the paper you linked to?
---------------------QUOTE-------------------


No. It's a completely different case.
 

---------------------QUOTE-------------------
My expectation then is that the provisional definition of "junk DNA" will continually evolve until it no longer includes any portion of the genome.
---------------------QUOTE-------------------


Junk isn't a provisional DEFINITION, it is a provisional CLASSIFICATION. Let's take one of the most prevalent types of junk in our genomes: LINE repeats. Just to be clear, you're claiming that if you have 9 LINE repeats and I have 10 at a particular genomic position, you are predicting that the difference will have functional relevance, correct?


---------------------QUOTE-------------------
Are you saying that 90-95% of the human genome is repeats?
---------------------QUOTE-------------------


Don't ask me, look at VISTA. That multicolored line shows the major (not all) families of repeats.  See the legend at lower left.


---------------------QUOTE-------------------
I don't know why most designers do what they do - that is not an argument against design.
---------------------QUOTE-------------------


Baloney. It demolishes any human's claim that life LOOKS designed, exposing it as dishonest cherry-picking.


---------------------QUOTE-------------------
It might be an effective argument against the competency of the designer, provided you can come up with a better workable system.      
---------------------QUOTE-------------------


It's the same designer that understands the value of plumbing. The point is that you can't recognize design in the cell's "plumbing" at all.


---------------------QUOTE-------------------


---------------------QUOTE-------------------
According to your hypothesis, how many human genes won't have a mouse ortholog and vice versa?
---------------------QUOTE-------------------


...I have no idea.  My hypothesis doesn't really work that way.  What I mean is; since I view each of the multitude of evolutionary events between mouse and man as saltational, there's no way to predict the number of orthologs.
---------------------QUOTE-------------------


So, in your hypothesis, saltational events have nothing whatsoever to do with new genes and proteins? WTF do these saltational events involve, then?  


---------------------QUOTE-------------------
My main contention is that the genomic sequences of organisms will be found to be fully functional and evolutionarily constrained within species - leaving the only possible mechanisms for the true evolution of new species saltational ones.      
---------------------QUOTE-------------------


So why wouldn't such mechanisms involve new proteins and genes encoding them? I'm not following your exclusion of the fundamental nuts & bolts of biology.


---------------------QUOTE-------------------
So a wrong prediction is not "lying" then I take it?  ;)
---------------------QUOTE-------------------


Not as long as one admits it. Responding to a question about testing a hypothesis with a long list of things that don't constitute testing is, IMO. ;-)
Posted by: Daniel Smith on Nov. 11 2007,13:38

Quote (Erasmus @ FCD,Nov. 11 2007,12:16)
indeed if we look at the progression of any body of theory at the basal branches you will find a plurality of alternative theories (see S Naeem Ecology 2006 or 2007 paper for a discussion of this dialectical progression in ecology).  the reasons for the trimming of the branches are varied, but ultimately empirical support is the criterion.

and there is no theoretical nor empirical support for your ideas Martin, and this is the same as for Daniel.  saltational orthogenetical views must deny heredity.  if you believe that speciation is independent of phylogenesis or the arisal of new forms, you must have another mechanism.  i've not read all of davison's manifesto yet so i'll withhold judgment about his proposed mechanisms, but it suffices to say that the discovery and advent of DNA based phylogenetics destroyed any possibility that schindewolf et al could be right because it showed the mechanism for divergence between populations and a workable theoretical framework for constructing hypotheses about nested hierarchies.

schindewolf was right about some things, namely the effects of canalization as a constraint.  but there is no support for the idea of reservoirs of variation, unless you are going to follow daniels lead and claim that this is what non-coding DNA is.  JAM is doing a much better job than I could with refuting that view, so I will simply ask:  do you have a new mechanism?  do you have a testable theory?
---------------------QUOTE-------------------



< Definition > of phylogenesis:
     

---------------------QUOTE-------------------
phylogenesis - (biology) the sequence of events involved in the evolutionary development of a species or taxonomic group of organisms
---------------------QUOTE-------------------


Saltational evolution is not "independent of phylogenesis or the arisal of new forms", nor does it "deny heredity" (as in inheritance) ; it is just another explanation for these things.  One more fully supported by the fossil record (especially the many observed gaps followed by intense adaptive radiations).

While "the mechanism for divergence between populations and a workable theoretical framework for constructing hypotheses about nested hierarchies" may be sufficient to explain variations within species, it has never (to my knowledge) been shown a capable mechanism for the arisal of new forms, or unique new biological systems.

Saltational evolution is just an attempt to better explain the observed progression of organisms in the fossil record.

If "the mechanism for divergence between populations" was the mechanism that created new forms, families, orders, etc., we'd surely see a much more diverse and continuous progression in the fossil record than we do.
Posted by: JAM on Nov. 11 2007,13:44

Quote (Daniel Smith @ Nov. 10 2007,11:26)
 
Quote (JAM @ Nov. 10 2007,01:06)
...would you mind commenting on the intelligence of having the same codon that starts protein synthesis also encoding the amino acid methionine? ...
---------------------QUOTE-------------------


Not necessarily.  Many genomic sequences are multi-functional - containing overlapping coding and non-coding functional sequences.
---------------------QUOTE-------------------


That has absolutely nothing to do with my question, and I suspect that you know it.


---------------------QUOTE-------------------
Perhaps we just don't know the functional advantage for combining the codon that starts protein synthesis and methionine.      
---------------------QUOTE-------------------


So you aren't capable of recognizing intelligent design?
       

---------------------QUOTE-------------------
       

---------------------QUOTE-------------------
I ask because it seems really, really stupid to me; I can improve the design with my measly human intelligence.
---------------------QUOTE-------------------


Then why don't you?
---------------------QUOTE-------------------


Huh?[/quote]Why don't you engineer a better design and show it to the world?      [/quote]
Switch one of the present serine codons to "start." That provides huge efficiency and energy savings.
         

---------------------QUOTE-------------------
         

---------------------QUOTE-------------------
Does that therefore make me smarter than God?
---------------------QUOTE-------------------


No.                    
---------------------QUOTE-------------------


Why not?[/quote]It just means you think you're smarter than God.[/quote]
That's completely dishonest of you, given that I don't claim that God designed protein synthetic machinery. YOU claim that life was intelligently designed. I don't.


---------------------QUOTE-------------------
So now that you have mastered all the various elements of biological design, you are prepared to say that anyone who was able to design it all would have to be unintelligent and that you could have come up with a better design?
---------------------QUOTE-------------------


Again, your argumentative tactics are completely dishonest. YOU claim to be able to recognize intelligent design in biology. I don't. I'm pointing you to a well-controlled example in which one aspect of design is unequivocally unintelligent RELATIVE to another aspect within the SAME mechanism.


---------------------QUOTE-------------------


---------------------QUOTE-------------------
Have you considered opening your eyes to the NATURE of biological complexity, and avoiding the dishonest arguments about its presence and extent?
---------------------QUOTE-------------------

I am attempting to "open my eyes" to anything and everything. Please explain (or link to) anything that will help me better understand "the NATURE of biological complexity".
---------------------QUOTE-------------------


Similar, but not identical, components with partially-overlapping functions.

Name a designed object that has those characteristics.
Posted by: Daniel Smith on Nov. 11 2007,13:50

Quote (Erasmus @ FCD,Nov. 11 2007,13:07)
Daniel may I recommend a book to you?  it's short.  


< book >

you might get a broader perspective of galton bateson and devries and why their ideas were wrong.  it has something to do with mendel.
---------------------QUOTE-------------------


I'll tell you what, after I'm done reading Bateson, I'll let you tell me everything that's wrong with him.  I'd rather read his works myself first if you don't mind.
Posted by: JAM on Nov. 11 2007,13:53

Quote (Daniel Smith @ Nov. 10 2007,12:30)
 
Quote (JAM @ Nov. 05 2007,00:37)
       
Quote (Daniel Smith @ Nov. 04 2007,13:05)
Let me also add; these scientists have theories that have never been falsified.
---------------------QUOTE-------------------


Let me add that whether they've been falsified is irrelevant, when they have never been TESTED.
---------------------QUOTE-------------------


Schindewolf based his theory on the observed fossil record as well as observed biological evidence.  His theory was an attempt to explain all the evidence.
---------------------QUOTE-------------------


First, you're not familiar with all the evidence, so you can't make such a claim in good faith. Second, attempting to explain all the evidence isn't enough; it's about making and testing predictions. That's what "testing a hypothesis" means.
 

---------------------QUOTE-------------------
Berg based his theory on years and years of his own observations in the field, as well as the documented observations of countless others.
---------------------QUOTE-------------------


Why not just admit that he never tested his hypothesis?
 

---------------------QUOTE-------------------
Both of these men were scientists of the highest regard in their respective fields who based their theories on observed, documented phenomena.
---------------------QUOTE-------------------


You're lying again. It's not a theory unless it's been tested many, many times, and they are definitely not held in high regard if they don't test their own hypotheses. This is the very essence of science, Dan, and you reject it.
 

---------------------QUOTE-------------------
Davison took their work and expanded upon it - suggesting a workable mechanism.  This mechanism (semi-meiotic reproduction) has been experimentally verified possible < here >,
< here >,
and < here >.
---------------------QUOTE-------------------


None of those things verifies his mechanism. He hasn't tested it, which means that it isn't science at all.
 

---------------------QUOTE-------------------
I have no idea why these scientists are ignored, but my guess is that their views don't fit the paradigm, and - based on my own observations - scientists whose ideas don't fit are generally ostracized, lose funding, and eventually relegated to the sidelines.
---------------------QUOTE-------------------


Baloney. They are ignored because they don't test their hypotheses.
 

---------------------QUOTE-------------------
No one wants to lose their position over such things, so they stick to the paradigm.
---------------------QUOTE-------------------


That's simply a lie, as the way to become famous in science is to overturn dogma. One needs data to do that, though.
 

---------------------QUOTE-------------------
That's my guess.
---------------------QUOTE-------------------


No, it isn't. That's disregard for the truth coupled with wishful thinking.
Posted by: Daniel Smith on Nov. 11 2007,13:54

Quote (JAM @ Nov. 11 2007,13:05)
 
Quote (Daniel Smith @ Nov. 10 2007,10:45)

This is an interesting experiment.  I have a couple questions:
1.  Why did they use artificial selection as opposed to natural selection?
---------------------QUOTE-------------------


So that they could analyze the phage after each generation. You're desperately looking for a reason to discount this; how predictable.
---------------------QUOTE-------------------

Not at all.  I will never discount experimental evidence, but I was curious whether natural selection would have made the same choices they did.  That's all.

---------------------QUOTE-------------------

 

---------------------QUOTE-------------------
2.  My math isn't the greatest so when they say that the replacement phage had "six-order magnitude lower infectivity" than the original phage, and the newly evolved phage "showed a 240-fold increase in infectivity as compared to its origin, fd-RP", they're talking about 0.00024 less infectivity than the original wild phage - correct?
---------------------QUOTE-------------------


But that increase was obtained in just seven generations, so that doesn't work as a justification for discounting the data.
---------------------QUOTE-------------------

I'm not discounting it, I was only asking if my math was right.  Now that I have the full paper, I should be able to answer these questions for myself.  Thanks.
Posted by: JAM on Nov. 11 2007,13:57

Quote (Daniel Smith @ Nov. 11 2007,12:55)
I would say one would distinguish between these two types of individuals by careful analysis of their claims via the scientific method.
---------------------QUOTE-------------------


In real science, we don't analyze the claims (hypotheses) of others. We are responsible for analyzing our own claims (testing our hypotheses) and disseminating the data generated by our efforts.

Has any one of your heroes produced a single new datum after advancing the hypotheses with which you agree?
Posted by: Daniel Smith on Nov. 11 2007,14:58

Quote (JAM @ Nov. 11 2007,13:25)
             
Quote (Daniel Smith @ Nov. 10 2007,11:05)
                   
Quote (JAM @ Nov. 10 2007,01:07)
                 

---------------------QUOTE-------------------
                 

---------------------QUOTE-------------------
Here's another question: how long does it take to evolve multiple, different, incredibly specific, functional, new protein-protein binding sites, using nothing but genetic variation and selection?
---------------------QUOTE-------------------


I don't know.
---------------------QUOTE-------------------


Two weeks.
---------------------QUOTE-------------------

Is this information in the paper you linked to?
---------------------QUOTE-------------------


No. It's a completely different case.
               

---------------------QUOTE-------------------
My expectation then is that the provisional definition of "junk DNA" will continually evolve until it no longer includes any portion of the genome.
---------------------QUOTE-------------------


Junk isn't a provisional DEFINITION, it is a provisional CLASSIFICATION. Let's take one of the most prevalent types of junk in our genomes: LINE repeats. Just to be clear, you're claiming that if you have 9 LINE repeats and I have 10 at a particular genomic position, you are predicting that the difference will have functional relevance, correct?
---------------------QUOTE-------------------

Yes.  I have no idea what the functional difference will be.  Line repeats may just be placeholders - similar to the spaces between words in a sentence, so the functional difference may be small, but I expect there to be one.            

---------------------QUOTE-------------------

               

---------------------QUOTE-------------------
Are you saying that 90-95% of the human genome is repeats?
---------------------QUOTE-------------------


Don't ask me, look at VISTA. That multicolored line shows the major (not all) families of repeats.  See the legend at lower left.
---------------------QUOTE-------------------

What percentage of these repeats are thought to be functional?            

---------------------QUOTE-------------------

               

---------------------QUOTE-------------------
I don't know why most designers do what they do - that is not an argument against design.
---------------------QUOTE-------------------


Baloney. It demolishes any human's claim that life LOOKS designed, exposing it as dishonest cherry-picking.
---------------------QUOTE-------------------

I call "Baloney" on that one.  Virtually all evolutionary scientists will tell you that they are trying to explain the apparent design of life.  If it doesn't look designed, what are they talking about?            

---------------------QUOTE-------------------

               

---------------------QUOTE-------------------
It might be an effective argument against the competency of the designer, provided you can come up with a better workable system.      
---------------------QUOTE-------------------


It's the same designer that understands the value of plumbing. The point is that you can't recognize design in the cell's "plumbing" at all.
---------------------QUOTE-------------------

I don't know enough about it to give an answer "Yes" or "No".  My expectation though, is that I will recognize much more design in it than you give credit for.            

---------------------QUOTE-------------------

               

---------------------QUOTE-------------------
               

---------------------QUOTE-------------------
According to your hypothesis, how many human genes won't have a mouse ortholog and vice versa?
---------------------QUOTE-------------------


...I have no idea.  My hypothesis doesn't really work that way.  What I mean is; since I view each of the multitude of evolutionary events between mouse and man as saltational, there's no way to predict the number of orthologs.
---------------------QUOTE-------------------


So, in your hypothesis, saltational events have nothing whatsoever to do with new genes and proteins?
---------------------QUOTE-------------------

They do, but only the necessary genes are retained, while others are reordered.  What's retained is retained.  You'd have to know the function of each gene in order to answer your question.  You'd also have to know how many saltational events took place between mouse and man.  I don't have that knowledge.  Maybe it can be answered - I don't know - I know I can't answer it.            

---------------------QUOTE-------------------
 
               

---------------------QUOTE-------------------
My main contention is that the genomic sequences of organisms will be found to be fully functional and evolutionarily constrained within species - leaving the only possible mechanisms for the true evolution of new species saltational ones.      
---------------------QUOTE-------------------


So why wouldn't such mechanisms involve new proteins and genes encoding them? I'm not following your exclusion of the fundamental nuts & bolts of biology.
---------------------QUOTE-------------------

I'm not excluding them, just saying that I don't know how one (at least with my knowledge) could predict them.            

---------------------QUOTE-------------------

               

---------------------QUOTE-------------------
So a wrong prediction is not "lying" then I take it?  ;)
---------------------QUOTE-------------------


Not as long as one admits it. Responding to a question about testing a hypothesis with a long list of things that don't constitute testing is, IMO. ;-)
---------------------QUOTE-------------------


You know, I began this discussion expecting to talk about Schindewolf, Berg, and the fossil record.  I was almost immediately sidetracked with molecular arguments - so I took the bait and waded right in - figuring that design would show in that arena as well.  

I began that discussion with a severely limited knowledge of genetics - only knowing that there were genes (which I assumed to be regions that only coded for proteins) and non-coding regions between them (which I assumed to be what-is-commonly-referred-to-as "junk DNA").  With this limited knowledge, I made several predictions indicating what I'd expect to find molecularly - including increasing complexity and overlapping and embedded codes.

As I delved in, I found all this and more.  While my view of genes as solely protein coding regions was wrong, as well as my definition of "junk", my expectations as to the complexity of the genome was confirmed many times over.  I learned that many, many transcriptions (both coding and non-coding) overlap each other - with differing reading frames on the same strand, overlapping transcriptions on opposite strands, and overlapping transcriptions in opposite directions on either the same strand or the opposite strand.  

Such things as sense and anti-sense transcriptions, ribosomal {r}RNAs, transfer (t)RNAs, small nuclear (sn)RNAs, small nucleolar (sno)RNAs, microRNAs (miRNAs) and exogenous small interfering RNAs (siRNAs), were all unheard of for me.  Couple that with the newly minted classification "Transcripts of unknown function" (TUFs), and you're talking about a world of complexity I'd never dreamed of when I made those predictions.

Now, maybe you feel that all these things are easily explained by the suggested mechanisms of evolution and that my wonder at it all is just a matter of my own ignorance.  You might be right - I don't know - (I was definitely ignorant coming into this molecular discussion!), but, I feel vindicated in my own mind by what I've found.

I will probably never convince you or anyone else on this board of design, but I'm more fully convinced now than I was when I came here.
Posted by: Daniel Smith on Nov. 11 2007,15:09

Quote (JAM @ Nov. 11 2007,13:57)
Quote (Daniel Smith @ Nov. 11 2007,12:55)
I would say one would distinguish between these two types of individuals by careful analysis of their claims via the scientific method.
---------------------QUOTE-------------------


In real science, we don't analyze the claims (hypotheses) of others. We are responsible for analyzing our own claims (testing our hypotheses) and disseminating the data generated by our efforts.

Has any one of your heroes produced a single new datum after advancing the hypotheses with which you agree?
---------------------QUOTE-------------------


I'm not sure what you mean by "produced a single new datum", but you can look up the papers written by Berg and Schindewolf on Google Scholar for yourself and see if any of it meets your criteria.
Unfortunately most of Schindewolf's papers are in German.
Posted by: JAM on Nov. 11 2007,16:11

[quote=Daniel Smith,Nov. 11 2007,14:58]      

---------------------QUOTE-------------------

Junk isn't a provisional DEFINITION, it is a provisional CLASSIFICATION. Let's take one of the most prevalent types of junk in our genomes: LINE repeats. Just to be clear, you're claiming that if you have 9 LINE repeats and I have 10 at a particular genomic position, you are predicting that the difference will have functional relevance, correct?
---------------------QUOTE-------------------


Yes.  I have no idea what the functional difference will be.  Line repeats may just be placeholders - similar to the spaces between words in a sentence, so the functional difference may be small, but I expect there to be one.[/quote]
So if one is intelligently designing a spacing mechanism, why in heaven's name (literally) would one use tandem repeats, which expand and contract (via recombination) at ridiculously high frequencies? Wouldn't unique sequence be the far more intelligent choice?
   

---------------------QUOTE-------------------
What percentage of these repeats are thought to be functional?  
---------------------QUOTE-------------------


As families, zero. However, evolutionary theory predicts that copies near/inside genes will be coopted.
   

---------------------QUOTE-------------------
   

---------------------QUOTE-------------------
   

---------------------QUOTE-------------------
I don't know why most designers do what they do - that is not an argument against design.
---------------------QUOTE-------------------


Baloney. It demolishes any human's claim that life LOOKS designed, exposing it as dishonest cherry-picking.
---------------------QUOTE-------------------

I call "Baloney" on that one.  Virtually all evolutionary scientists will tell you that they are trying to explain the apparent design of life.
---------------------QUOTE-------------------


Virtually all evolutionary scientists? Quote ten of them. The reality is that the ones who say things like that tend not to study evolution.
   

---------------------QUOTE-------------------
If it doesn't look designed, what are they talking about?
---------------------QUOTE-------------------


They are talking about the parts that are apparently designed. Can you find a single instance of a scientist referring to the design of endocytic (plumbing) pathways?
   

---------------------QUOTE-------------------
   

---------------------QUOTE-------------------
 

---------------------QUOTE-------------------
It might be an effective argument against the competency of the designer, provided you can come up with a better workable system.      
---------------------QUOTE-------------------


It's the same designer that understands the value of plumbing. The point is that you can't recognize design in the cell's "plumbing" at all.
---------------------QUOTE-------------------

I don't know enough about it to give an answer "Yes" or "No".
---------------------QUOTE-------------------


Then how can you have any confidence if you've only been exposed to creationist spoonfeeding of quote mines?

And above, you tried to weasel with "provided you can come up with a better workable system." The problem is that I can point to the fact that the SAME DESIGNER (according to you) came up with a much more intelligently-designed system. I don't have to; I only need to point out the contrasts.

   

---------------------QUOTE-------------------
My expectation though, is that I will recognize much more design in it than you give credit for.                
---------------------QUOTE-------------------


Then go for it. Explain the intelligence in the design of endocytic pathways, particularly their superiority to more conventional plumbing, as observed from the very same designer in our very own bodies. Be sure to explain the rationale behind the choice of so many similar, closely-related components with partially-overlapping (neither separate nor redundant) pathways.
   

---------------------QUOTE-------------------
   

---------------------QUOTE-------------------
 

---------------------QUOTE-------------------
 

---------------------QUOTE-------------------
According to your hypothesis, how many human genes won't have a mouse ortholog and vice versa?
---------------------QUOTE-------------------


...I have no idea.  My hypothesis doesn't really work that way.  What I mean is; since I view each of the multitude of evolutionary events between mouse and man as saltational, there's no way to predict the number of orthologs.
---------------------QUOTE-------------------


So, in your hypothesis, saltational events have nothing whatsoever to do with new genes and proteins?
---------------------QUOTE-------------------


They do, but only the necessary genes are retained, while others are reordered.  What's retained is retained.
---------------------QUOTE-------------------


And what's lost/discarded is lost/discarded. So what's the ratio of the two classes after a typical saltational event?
 

---------------------QUOTE-------------------
You'd have to know the function of each gene in order to answer your question.
---------------------QUOTE-------------------


Not at all. You're weaseling because you have no faith in your position.
 

---------------------QUOTE-------------------
You'd also have to know how many saltational events took place between mouse and man.
---------------------QUOTE-------------------


For grins, let's say just one. How many genes?
 

---------------------QUOTE-------------------
I don't have that knowledge.  Maybe it can be answered - I don't know - I know I can't answer it.                  
---------------------QUOTE-------------------


I'm not expecting you to ANSWER, I'm expecting you to PREDICT. There's a world of difference that you can't bring yourself to acknowledge.
 

---------------------QUOTE-------------------
 

---------------------QUOTE-------------------
 

---------------------QUOTE-------------------
My main contention is that the genomic sequences of organisms will be found to be fully functional and evolutionarily constrained within species - leaving the only possible mechanisms for the true evolution of new species saltational ones.      
---------------------QUOTE-------------------


So why wouldn't such mechanisms involve new proteins and genes encoding them? I'm not following your exclusion of the fundamental nuts & bolts of biology.
---------------------QUOTE-------------------

I'm not excluding them, just saying that I don't know how one (at least with my knowledge) could predict them.
---------------------QUOTE-------------------


You don't need knowledge--you have a hypothesis that makes predictions. Let it go and do science! It's the most reliable way to gain useful knowledge about the world.
Posted by: mitschlag on Nov. 11 2007,16:12

Quote (VMartin @ Nov. 11 2007,11:38)
Did anyone of you published so young in the Nature (if you have ever published there something)  that entitles you to dismiss your antidarwinian adersaries who  published there as "confused"?
---------------------QUOTE-------------------


Yes, yes, and yes.
Posted by: mitschlag on Nov. 11 2007,16:20

Quote (Daniel Smith @ Nov. 11 2007,12:52)
 
Quote (mitschlag @ Nov. 10 2007,17:08)
         
Quote (Daniel Smith @ Nov. 10 2007,15:51)
These saltational events are too extensive to be random.  This is what implies front-loading.
---------------------QUOTE-------------------


I've read Davison's < Evolutionary Manifesto >

Please quote where in that document he makes that point.

---------------------QUOTE-------------------


He doesn't make that point in the Manifesto.  He does make it in his many postings on the web since that time.  The only place in his manifesto where he hints at it is here:
         

---------------------QUOTE-------------------
While it is true that the existence of a Creator, while a logical necessity, has never been rigorously proved and perhaps never can be, it is also true that neither has been the spontaneous generation of life. (emphasis mine)
---------------------QUOTE-------------------


.
---------------------QUOTE-------------------


Coherence is evidently not one of Davison's strong suits.
Posted by: mitschlag on Nov. 11 2007,16:28

Quote (Daniel Smith @ Nov. 11 2007,12:52)
If these differences are the result of a small number of saltational events, they could not be random and still produce working, living organisms.
---------------------QUOTE-------------------


If wishes were horses, beggars would ride.

One more time: At what point, quantitatively, does a "small number of saltational events" equal "could not be random"?
Posted by: JAM on Nov. 11 2007,16:32

[quote=Daniel Smith,Nov. 11 2007,14:58][quote=JAM,Nov. 11 2007,13:25]               [quote=Daniel Smith,Nov. 10 2007,11:05]                     [quote=JAM,Nov. 10 2007,01:07]                   [quote]                    

---------------------QUOTE-------------------

You know, I began this discussion expecting to talk about Schindewolf, Berg, and the fossil record.  I was almost immediately sidetracked with molecular arguments - so I took the bait and waded right in - figuring that design would show in that arena as well.
---------------------QUOTE-------------------


It wasn't bait; the molecular evidence is much more massive. 


---------------------QUOTE-------------------
I began that discussion with a severely limited knowledge of genetics - only knowing that there were genes (which I assumed to be regions that only coded for proteins) and non-coding regions between them (which I assumed to be what-is-commonly-referred-to-as "junk DNA").  With this limited knowledge, I made several predictions indicating what I'd expect to find molecularly - including increasing complexity and overlapping and embedded codes.
---------------------QUOTE-------------------


No, that wasn't your original prediction, and it's not even remotely scientific. Your original prediction was wrong, and you lied and claimed that introns were coding to save it.


---------------------QUOTE-------------------
As I delved in, I found all this and more.  While my view of genes as solely protein coding regions was wrong,...
---------------------QUOTE-------------------


That's only an issue relating to your lack of honesty. What you've strategically omitted are your actual predictions:

"My hypothesis does not predict a flat line - except within a lineage."
There was no flat line, even within what you defined as a lineage.

"My hypothesis predicts that there is no buildup of random mutations within the genome - even in non-coding sites."
Yet the data showed you that there was much higher divergence in noncoding regions.

"My prediction is that the coding and non-coding sequences (basically all sequences) will show an equal amount of evolutionary constraint."
VISTA showed that within or outside what you define as a "lineage," this was utterly false. Yet your hypothesis didn't change!

"I believe that most (if not all) sequences in a genome are functional and therefore resistive to mutation (constrained).  This means there are no neutral sites that are accumulating mutations."
Utterly wrong, yet your confidence is increased? How can that be?

"I also believe that macroevolution (when it happens) is not the result of accumulating mutations but is rather; saltational - that is - it creates new types that may have sequences that are radically different from the sequences from which they diverged (hence my earlier prediction)."
So assuming at least one saltational event between mouse and man, how many orthologs of 30K would you predict to be missing or "radically different"?

"I'd say that anything that is transcribed would qualify as functional - since the cellular machinery is going through the trouble of transcribing it."
How does this one stand?


---------------------QUOTE-------------------
as well as my definition of "junk", my expectations as to the complexity of the genome was confirmed many times over.
---------------------QUOTE-------------------


Evolutionary mechanisms are great at producing complexity. The existence of complexity has nothing to do with inferring intelligent design.


---------------------QUOTE-------------------
Now, maybe you feel that all these things are easily explained by the suggested mechanisms of evolution and that my wonder at it all is just a matter of my own ignorance.
---------------------QUOTE-------------------


No, I think that I can speak for the others and say that we share your wonder. What we don't share is your lack of curiosity, and your insistence that you understand it all already, even when you get caught in blatant falsehoods.
Posted by: mitschlag on Nov. 11 2007,16:34

Quote (Daniel Smith @ Nov. 11 2007,14:58)
You know, I began this discussion expecting to talk about Schindewolf, Berg, and the fossil record.  I was almost immediately sidetracked with molecular arguments - so I took the bait and waded right in - figuring that design would show in that arena as well.  

I began that discussion with a severely limited knowledge of genetics - only knowing that there were genes (which I assumed to be regions that only coded for proteins) and non-coding regions between them (which I assumed to be what-is-commonly-referred-to-as "junk DNA").  With this limited knowledge, I made several predictions indicating what I'd expect to find molecularly - including increasing complexity and overlapping and embedded codes.

As I delved in, I found all this and more.  While my view of genes as solely protein coding regions was wrong, as well as my definition of "junk", my expectations as to the complexity of the genome was confirmed many times over.  I learned that many, many transcriptions (both coding and non-coding) overlap each other - with differing reading frames on the same strand, overlapping transcriptions on opposite strands, and overlapping transcriptions in opposite directions on either the same strand or the opposite strand.  

Such things as sense and anti-sense transcriptions, ribosomal {r}RNAs, transfer (t)RNAs, small nuclear (sn)RNAs, small nucleolar (sno)RNAs, microRNAs (miRNAs) and exogenous small interfering RNAs (siRNAs), were all unheard of for me.  Couple that with the newly minted classification "Transcripts of unknown function" (TUFs), and you're talking about a world of complexity I'd never dreamed of when I made those predictions.
---------------------QUOTE-------------------


Aren't you glad you came here, then?
Posted by: JAM on Nov. 11 2007,16:42

Quote (Daniel Smith @ Nov. 11 2007,15:09)
 
Quote (JAM @ Nov. 11 2007,13:57)
   
Quote (Daniel Smith @ Nov. 11 2007,12:55)
I would say one would distinguish between these two types of individuals by careful analysis of their claims via the scientific method.
---------------------QUOTE-------------------


In real science, we don't analyze the claims (hypotheses) of others. We are responsible for analyzing our own claims (testing our hypotheses) and disseminating the data generated by our efforts.

Has any one of your heroes produced a single new datum after advancing the hypotheses with which you agree?
---------------------QUOTE-------------------


I'm not sure what you mean by "produced a single new datum",
---------------------QUOTE-------------------


What don't you understand about it? Prusiner tested his prion hypothesis and generated hundreds of papers worth of data. I've tested my own hypotheses, often found them to be wrong, and still published plenty of papers with new data. Hypotheses only have value when they are tested, and they retain this value even when they are wrong. Those who aren't willing to test their hypotheses are frauds and cranks.
 

---------------------QUOTE-------------------
...but you can look up the papers written by Berg and Schindewolf on Google Scholar for yourself and see if any of it meets your criteria.
---------------------QUOTE-------------------


I didn't see any with data that corresponded with what you were citing.
 

---------------------QUOTE-------------------
Unfortunately most of Schindewolf's papers are in German.
---------------------QUOTE-------------------


Not a problem, as the data are almost always in tables and figures. Why not just come clean and admit that none of your heroes have sufficient faith to test their hypotheses?
Posted by: JAM on Nov. 11 2007,16:43

Quote (VMartin @ Nov. 11 2007,11:38)
Did anyone of you published so young in the Nature (if you have ever published there something)  that entitles you to dismiss your antidarwinian adersaries who  published there as "confused"?
---------------------QUOTE-------------------


Yes, yes, and yes, too.

And you?
Posted by: mitschlag on Nov. 12 2007,14:07

The evolution of the horse:



No gradualism here, nossir.  All saltational, yessir.

Fig. 4 from < Davison's Manifesto >.
Posted by: Arden Chatfield on Nov. 12 2007,14:26

Quote (VMartin @ Nov. 11 2007,07:49)
My point was that at the root of the modern science stood men of Rennaisance who had a much more complex view of the reality than reductionism  so common today. Nowadays it is biologist professor Zdenek Neubauer in Czech republic, an extraordinary educated scholar and philosopher with such a stance. He dismissed in his latest books neodarwinism using harsh words.
---------------------QUOTE-------------------


Harsh Czech words. Wow. Heavy duty shit, Marty.

What's Neubauer's alternative to Neodarwinism, Marty? Or is he like you and not have one?

 

---------------------QUOTE-------------------
Of course reductionists flocked together in their atheistic Czech circle for science "Sisyphos" became angry.
---------------------QUOTE-------------------



Why is atheism relevant to this, Marty?
Posted by: Arden Chatfield on Nov. 12 2007,14:28

Quote (JAM @ Nov. 11 2007,16:43)
Quote (VMartin @ Nov. 11 2007,11:38)
Did anyone of you published so young in the Nature (if you have ever published there something)  that entitles you to dismiss your antidarwinian adersaries who  published there as "confused"?
---------------------QUOTE-------------------


Yes, yes, and yes, too.

And you?
---------------------QUOTE-------------------


Yes, Marty, share your publication record and 'brutal research' with us, so we'll be more inclined to take you seriously.
Posted by: Daniel Smith on Nov. 12 2007,21:25

Quote (JAM @ Nov. 11 2007,13:57)
In real science, we don't analyze the claims (hypotheses) of others. We are responsible for analyzing our own claims (testing our hypotheses) and disseminating the data generated by our efforts.
---------------------QUOTE-------------------


So only Darwin can test his theory?
Posted by: Daniel Smith on Nov. 12 2007,22:15

Quote (JAM @ Nov. 11 2007,16:32)
         

---------------------QUOTE-------------------

You know, I began this discussion expecting to talk about Schindewolf, Berg, and the fossil record.  I was almost immediately sidetracked with molecular arguments - so I took the bait and waded right in - figuring that design would show in that arena as well.
---------------------QUOTE-------------------


It wasn't bait; the molecular evidence is much more massive.
---------------------QUOTE-------------------

More massive than the millions and millions of fossils collected over several hundred years?          

---------------------QUOTE-------------------

           

---------------------QUOTE-------------------
With this limited knowledge, I made several predictions indicating what I'd expect to find molecularly - including increasing complexity and overlapping and embedded codes.
---------------------QUOTE-------------------


No, that wasn't your original prediction, and it's not even remotely scientific.
---------------------QUOTE-------------------

Why not?          

---------------------QUOTE-------------------
Your original prediction was wrong, and you lied and claimed that introns were coding to save it.
---------------------QUOTE-------------------

Did not. (Que the obligatory 3rd grade "Did too!" retort machine)        

---------------------QUOTE-------------------

           

---------------------QUOTE-------------------
As I delved in, I found all this and more.  While my view of genes as solely protein coding regions was wrong,...
---------------------QUOTE-------------------


That's only an issue relating to your lack of honesty. What you've strategically omitted are your actual predictions:

"My hypothesis does not predict a flat line - except within a lineage."
There was no flat line, even within what you defined as a lineage.
---------------------QUOTE-------------------

I don't remember defining Rat and Mouse as a lineage.  I think you did that for me.        

---------------------QUOTE-------------------


"My hypothesis predicts that there is no buildup of random mutations within the genome - even in non-coding sites."
Yet the data showed you that there was much higher divergence in noncoding regions.
---------------------QUOTE-------------------

How do you know this "divergence" is the result of a buildup of random mutations?          

---------------------QUOTE-------------------


"My prediction is that the coding and non-coding sequences (basically all sequences) will show an equal amount of evolutionary constraint."
VISTA showed that within or outside what you define as a "lineage," this was utterly false. Yet your hypothesis didn't change!
---------------------QUOTE-------------------

First, I have no idea what VISTA's parameters are or how it does what it does.  You say it proves me wrong, fine.  I'll defer to you that VISTA proves me wrong as far as you understand my hypothesis.  I just would rather find out for myself if you don't mind.          

---------------------QUOTE-------------------


"I believe that most (if not all) sequences in a genome are functional and therefore resistive to mutation (constrained).  This means there are no neutral sites that are accumulating mutations."
Utterly wrong, yet your confidence is increased? How can that be?
---------------------QUOTE-------------------

I still don't understand how VISTA shows that the mechanism for the differences between genomes was an accumulation of random mutations.  Will you please explain how you know this?          

---------------------QUOTE-------------------


"I also believe that macroevolution (when it happens) is not the result of accumulating mutations but is rather; saltational - that is - it creates new types that may have sequences that are radically different from the sequences from which they diverged (hence my earlier prediction)."
So assuming at least one saltational event between mouse and man, how many orthologs of 30K would you predict to be missing or "radically different"?
---------------------QUOTE-------------------

I can only make a rough guess, but obviously all the genes that make for mammals would be retained, as well as the placental ones, then you'd have the genes for two eyes, two ears, one mouth, four limbs, etc. - How many is that?  
As for differences; obviously the genes that control intelligence, speech, opposing thumbs, walking upright, shape of the skull, lack of a tail, etc. -  How many is that?        

---------------------QUOTE-------------------


"I'd say that anything that is transcribed would qualify as functional - since the cellular machinery is going through the trouble of transcribing it."
How does this one stand?
---------------------QUOTE-------------------

I've been systematically reading through several of the ENCODE consortium's papers, and I feel very confident of that one.   I'll also predict that soon it will be found that pseudogenes are much more functional than previously thought.  My guess is that they are used as a sort of redundant blueprint for regulation of their true gene counterpart.  I'd also not be the least bit surprised if repeat sequences were found to be functional - would you be?      

---------------------QUOTE-------------------

           

---------------------QUOTE-------------------
as well as my definition of "junk", my expectations as to the complexity of the genome was confirmed many times over.
---------------------QUOTE-------------------


Evolutionary mechanisms are great at producing complexity. The existence of complexity has nothing to do with inferring intelligent design.
---------------------QUOTE-------------------

I'm not talking about random complexity, I'm talking about overlapping codes, running in opposite directions on both strands of DNA.  Does your theory predict that?  (If so, point me to the paper where the prediction was made before such things were discovered.)          

---------------------QUOTE-------------------

           

---------------------QUOTE-------------------
Now, maybe you feel that all these things are easily explained by the suggested mechanisms of evolution and that my wonder at it all is just a matter of my own ignorance.
---------------------QUOTE-------------------


No, I think that I can speak for the others and say that we share your wonder. What we don't share is your lack of curiosity, and your insistence that you understand it all already, even when you get caught in blatant falsehoods.
---------------------QUOTE-------------------


I've never claimed that I understand it all.  Talk about blatant falsehoods!
Posted by: Daniel Smith on Nov. 12 2007,22:35

Quote (mitschlag @ Nov. 11 2007,16:28)
One more time: At what point, quantitatively, does a "small number of saltational events" equal "could not be random"?
---------------------QUOTE-------------------


First, the number of saltational events doesn't have anything to do with it.  

Second, I think "saltational evolution", by definition, excludes random causes - in that there are two many successful changes all at once.  Maybe I'm wrong.
Posted by: Daniel Smith on Nov. 12 2007,22:59

Quote (mitschlag @ Nov. 12 2007,14:07)
The evolution of the horse:

No gradualism here, nossir.  All saltational, yessir.

Fig. 4 from < Davison's Manifesto >.
---------------------QUOTE-------------------


The horse is used as an example of evolution in a determined direction - not as an example of saltational change.  The caption reads: "Phyletic size increase in the horse". and is used in the section entitled "Are there laws governing evolution?"
Davison (and Schindewolf before him) saw evolution of new types as a saltational event. What followed was a series of constrained variations within that type which usually resulted in over-specialization and extinction.  Oversized organisms were often a sign of this last stage.
Did the fact that this illustration was Schindewolf's own - from his book "Basic Questions in Paleontology" - escape you?
Posted by: JAM on Nov. 13 2007,01:19

Quote (Daniel Smith @ Nov. 12 2007,22:15)
[the molecular evidence is] More massive than the millions and millions of fossils collected over several hundred years?            
---------------------QUOTE-------------------


Yes! That's why dishonest IDers/creationists want to talk about fossils instead. It's easier to obfuscate.
   

---------------------QUOTE-------------------
   

---------------------QUOTE-------------------
"My hypothesis does not predict a flat line - except within a lineage."
There was no flat line, even within what you defined as a lineage.
---------------------QUOTE-------------------

I don't remember defining Rat and Mouse as a lineage.  I think you did that for me.        
---------------------QUOTE-------------------


You're being incredibly dishonest, Dan.

YOU defined a lineage as containing both African and Asian elephants, two different genuses within the same family. Rats and mice have the same relationship, so you've got no wriggle room.
   

---------------------QUOTE-------------------
First, I have no idea what VISTA's parameters are or how it does what it does.
---------------------QUOTE-------------------


So you were lying when you claimed that what you saw on VISTA supported your hypothesis. I'm glad we cleared that up!
   

---------------------QUOTE-------------------
   

---------------------QUOTE-------------------
"I believe that most (if not all) sequences in a genome are functional and therefore resistive to mutation (constrained).  This means there are no neutral sites that are accumulating mutations."
Utterly wrong, yet your confidence is increased? How can that be?
---------------------QUOTE-------------------

I still don't understand how VISTA shows that the mechanism for the differences between genomes was an accumulation of random mutations.
---------------------QUOTE-------------------


Your prediction is all about which regions accumulate mutations. You're frantically invoking the Big Creationist Lie of randomness. Do you even have a clue that the "random" in "random mutation" is extremely limited? That mutations don't occur at random places? That they are only random wrt fitness, not truly random in any other way?
   

---------------------QUOTE-------------------
   

---------------------QUOTE-------------------
"I also believe that macroevolution (when it happens) is not the result of accumulating mutations but is rather; saltational - that is - it creates new types that may have sequences that are radically different from the sequences from which they diverged (hence my earlier prediction)."
So assuming at least one saltational event between mouse and man, how many orthologs of 30K would you predict to be missing or "radically different"?
---------------------QUOTE-------------------

I can only make a rough guess, but obviously all the genes that make for mammals would be retained, as well as the placental ones, then you'd have the genes for two eyes, two ears, one mouth, four limbs, etc. - How many is that?
---------------------QUOTE-------------------


You tell me. Do you realize that you've stumbled into making an easily testable prediction?
   

---------------------QUOTE-------------------
As for differences; obviously the genes that control intelligence, speech, opposing thumbs, walking upright, shape of the skull, lack of a tail, etc. -  How many is that?        
---------------------QUOTE-------------------


You tell me! You're the one predicting that such genes even exist. Let's get to a more specific prediction: do you predict that whales are lacking "hind leg genes"? What sort of "hind leg genes" or "opposing thumbs genes" do you predict will exist?
 

---------------------QUOTE-------------------
I've been systematically reading through several of the ENCODE consortium's papers, and I feel very confident of that one ["anything that is transcribed would qualify as functional"].
---------------------QUOTE-------------------


Good! Let's take that into a more specific case. I have a gene, and both mice and humans homozygous for the null allele die shortly after birth. Since according to you, transcription implies function, when I look at transcription of that gene, will it be turned on:
1) right before the age of death in the null mutants,
2) right before or at the time at which mutants can be distinguished from wild-type individuals, or
3) more than a month before 1 or 2?
[quote]  

---------------------QUOTE-------------------
I'll also predict that soon it will be found that pseudogenes are much more functional than previously thought.
---------------------QUOTE-------------------


Again, "much more functional than previously thought" is not a scientific prediction. Scientific predictions are not dependent on anyone's opinion, they must be predictions about what is actually observed.


---------------------QUOTE-------------------
My guess is that they are used as a sort of redundant blueprint for regulation of their true gene counterpart.
---------------------QUOTE-------------------


Great! Are you willing to bet your house on it?


---------------------QUOTE-------------------
I'd also not be the least bit surprised if repeat sequences were found to be functional - would you be?        
---------------------QUOTE-------------------


I think only someone who is dishonest, an idiot, or both would ask such a question, as I JUST TOLD YOU OF A CLASS OF FUNCTIONAL REPEATS--rRNA genes. Are you drunk, Dan?

I wouldn't be so arrogant and stupid as to lump all classes of repeats together, and I also just told you which repeats MET predicts will be functional.

Now, why would an intelligent designer use repeats as spacers, when repeats expand and contract all the time because of unequal crossing over? An intelligent designer would use unique sequence as a spacer.
Posted by: JAM on Nov. 13 2007,01:26

Quote (Daniel Smith @ Nov. 12 2007,21:25)
Quote (JAM @ Nov. 11 2007,13:57)
In real science, we don't analyze the claims (hypotheses) of others. We are responsible for analyzing our own claims (testing our hypotheses) and disseminating the data generated by our efforts.
---------------------QUOTE-------------------


So only Darwin can test his theory?
---------------------QUOTE-------------------


No. Is this the best you can do? How does "Darwin is responsible for testing his own hypothesis" imply "only Darwin can test his hypothesis"? Do you not see the utter cowardice of expecting others to present evidence to refute your hypothesis when you are too lazy to use it to make and test its predictions yourself?

Do you realize that it wasn't a theory when Darwin proposed it (accompanied by more new data than have been produced by the entire ID movement by testing their own hypotheses in the 150 years since)?
Posted by: mitschlag on Nov. 13 2007,08:13

Quote (Daniel Smith @ Nov. 12 2007,22:35)
     
Quote (mitschlag @ Nov. 11 2007,16:28)
One more time: At what point, quantitatively, does a "small number of saltational events" equal "could not be random"?
---------------------QUOTE-------------------


First, the number of saltational events doesn't have anything to do with it.
---------------------QUOTE-------------------


Thanks for your response.
 

---------------------QUOTE-------------------
(Daniel Smith @ Nov. 11 2007,12:52)
If these differences are the result of a small number of saltational events, they could not be random and still produce working, living organisms.
---------------------QUOTE-------------------

(My emphasis)
So now a "small number" of saltational events becomes "any number," because:    

---------------------QUOTE-------------------
Second, I think "saltational evolution", by definition, excludes random causes - in that there are two many successful changes all at once.  Maybe I'm wrong.
---------------------QUOTE-------------------

Yes, the only way one could claim that "saltation" excludes "random" in this context is by definition.  Unless you can cite relevent empirical evidence.

Bearing in mind that "random" means "undirected" in this context.
Posted by: mitschlag on Nov. 13 2007,08:29

Quote (Daniel Smith @ Nov. 12 2007,22:59)
     
Quote (mitschlag @ Nov. 12 2007,14:07)
The evolution of the horse:

No gradualism here, nossir.  All saltational, yessir.

Fig. 4 from < Davison's Manifesto >.
---------------------QUOTE-------------------


The horse is used as an example of evolution in a determined direction - not as an example of saltational change.  The caption reads: "Phyletic size increase in the horse". and is used in the section entitled "Are there laws governing evolution?"

---------------------QUOTE-------------------


I am well aware of the way Davison was using his Fig. 4.  I quoted it sarcastically for the purpose of showing that the data make the case for gradualism.
   

---------------------QUOTE-------------------
Davison (and Schindewolf before him) saw evolution of new types as a saltational event. What followed was a series of constrained variations within that type which usually resulted in over-specialization and extinction.  Oversized organisms were often a sign of this last stage.
---------------------QUOTE-------------------

Understood.  Interesting ideas.  Any reason to accept them without cocking a skeptical eye and asking for some confirmatory evidence?.  


---------------------QUOTE-------------------
Did the fact that this illustration was Schindewolf's own - from his book "Basic Questions in Paleontology" - escape you?
---------------------QUOTE-------------------

You underestimate my reading comprehension, Dan.  Now please let go of my leg.
Posted by: mitschlag on Nov. 13 2007,08:43

An update on Schindewolf from
< Sciencemag >:

     

---------------------QUOTE-------------------
Adaptive radiation of a beloved icon. Phylogeny, geographic distribution, diet, and body sizes of the Family Equidae over the past 55 My. The vertical lines represent the actual time ranges of equid genera or clades.
---------------------QUOTE-------------------


Posted by: JAM on Nov. 13 2007,11:00

Quote (Daniel Smith @ Nov. 11 2007,14:58)
I began that discussion with a severely limited knowledge of genetics - only knowing that there were genes (which I assumed to be regions that only coded for proteins) and non-coding regions between them (which I assumed to be what-is-commonly-referred-to-as "junk DNA").  With this limited knowledge, I made several predictions indicating what I'd expect to find molecularly - including increasing complexity and overlapping and embedded codes.
---------------------QUOTE-------------------


I don't see how the fact that you didn't know that introns were within genes and are non-coding preserves your hypothesis against the inescapable fact that introns, whether one looks within species, between races, between species within a genus, between genuses within a family (which met YOUR definition of "within a lineage"), or between phyla, diverge more than exons.

It seems to me that your saltational hypothesis still makes an utterly false prediction.
 

---------------------QUOTE-------------------
...I feel vindicated in my own mind by what I've found.

I will probably never convince you or anyone else on this board of design, but I'm more fully convinced now than I was when I came here.
---------------------QUOTE-------------------


Good! Then you'll have no problem explaining how your hypothesis treats non-coding regions within genes completely differently from non-coding regions outside genes.
Posted by: Daniel Smith on Nov. 15 2007,15:39

Quote (JAM @ Nov. 13 2007,11:00)
 
Quote (Daniel Smith @ Nov. 11 2007,14:58)
I began that discussion with a severely limited knowledge of genetics - only knowing that there were genes (which I assumed to be regions that only coded for proteins) and non-coding regions between them (which I assumed to be what-is-commonly-referred-to-as "junk DNA").  With this limited knowledge, I made several predictions indicating what I'd expect to find molecularly - including increasing complexity and overlapping and embedded codes.
---------------------QUOTE-------------------


I don't see how the fact that you didn't know that introns were within genes and are non-coding preserves your hypothesis against the inescapable fact that introns, whether one looks within species, between races, between species within a genus, between genuses within a family (which met YOUR definition of "within a lineage"), or between phyla, diverge more than exons.

It seems to me that your saltational hypothesis still makes an utterly false prediction.
     

---------------------QUOTE-------------------
...I feel vindicated in my own mind by what I've found.

I will probably never convince you or anyone else on this board of design, but I'm more fully convinced now than I was when I came here.
---------------------QUOTE-------------------


Good! Then you'll have no problem explaining how your hypothesis treats non-coding regions within genes completely differently from non-coding regions outside genes.
---------------------QUOTE-------------------


Let me just say this:

I am still not convinced that the evidence you showed me from VISTA contradicts my hypothesis.  Until I know what VISTA does and how it does it, I'll have to reserve judgment on it.

You are convinced (based on VISTA) that I am wrong.  That's fine - I very well may be wrong!  After all, I'm trying to guess what God was thinking when he designed life.  I'll probably be wrong more than I'm right.

All I'm saying is, I'm not seeing what you're seeing (yet at least).  I have a lot less knowledge in this area than you so I'm not able to just look at a chart of colors and immediately know what they all represent and how they confirm or falsify my predictions.  Please be patient with me and please stop accusing me of lying whenever I make ignorant statements!

Thank you.
Posted by: Daniel Smith on Nov. 15 2007,15:52

Meanwhile, I just found out about an hypothesis that < another code > exists of which it is said, it "considerably
extends the information potential of the genetic code".
Evidence supporting this "histone code" was also recently found < here >:  

---------------------QUOTE-------------------
The identification of these characteristic signatures associated with active regulatory elements, particularly promoters, suggests that there is a strong correlation between the histone modifications and biological activity. This lends support to the idea that there is a histone code associated with the activity of these elements, although perhaps not a completely deterministic one.
---------------------QUOTE-------------------


I have not read the first paper yet.  I found out about it by reading the second paper - so this post is just an FYI.
Posted by: mitschlag on Nov. 15 2007,16:14

Quote (Daniel Smith @ Nov. 15 2007,15:39)
You are convinced (based on VISTA) that I am wrong.  That's fine - I very well may be wrong!  After all, I'm trying to guess what God was thinking when he designed life.  I'll probably be wrong more than I'm right.
---------------------QUOTE-------------------


Hi, Dan,

I hope you don't mind me kibitzing here, since you and JAM have this thing going between yourselves, but it seems to me, based on my sectarian Christian education, that the answer is in the Catechism.

Why waste energy on all this sciency stuff?
Posted by: swbarnes2 on Nov. 15 2007,17:30

Quote (Daniel Smith @ Nov. 15 2007,15:39)

I am still not convinced that the evidence you showed me from VISTA contradicts my hypothesis.
---------------------QUOTE-------------------



This says a great deal about your dishonesty, inability to understand the data, and pathological unwillingness to admit that you don't know what you are talking about.

It says nothing about biology.

 

---------------------QUOTE-------------------
After all, I'm trying to guess what God was thinking when he designed life.
---------------------QUOTE-------------------



Why don't you start with something smaller?

Why don't you tell us what God had in mind when he designed the malaria parasite that kills 100,00 children every year?

 

---------------------QUOTE-------------------
I will probably never convince you or anyone else on this board of design,
---------------------QUOTE-------------------



No, you won't.  Because we won't be convinced without evidence that actually supports the conclusions.  

We understand that you don't operate that way.  We understand that you are convinced of things because of your faith, and that you don't care what the evidence says.  You just admitted as such.  You don't understand what VISTA says, so you will continue believing what you want until you understand VISTA, but you will never bother to learn it, so you will never change your mind.

So basically, nothing we could possibly show you will change your mind, beucase you will tell yourself you don't understand it, and you won't change you mind until you do, and you won't ever choose to do so.

Do you really not understand the general comtempt that this attitude will earn you on a board about science?

Or do you just not care?

 

---------------------QUOTE-------------------
All I'm saying is, I'm not seeing what you're seeing (yet at least).
---------------------QUOTE-------------------



Of course not.  We are looking at evidence we understand.  You are seeing what you want to see.

How can you not understand that those are two entirely different things?

 

---------------------QUOTE-------------------
I have a lot less knowledge in this area than you so I'm not able to just look at a chart of colors and immediately know what they all represent and how they confirm or falsify my predictions.
---------------------QUOTE-------------------



There is a lot you don't understand about biology.

That is why almost everything substantial you have predicted is flat-out wrong.

And you have demonstrated that you really don't care.

Do you think that you have convinced a single person on this board that you are capable of honestly analyzing data?  Do you think that anyone on this board thinks that you are capable of examining any kind of tough question honestly?
Posted by: Daniel Smith on Nov. 16 2007,18:50

One thing I find interesting here is that most of you have shown no interest in any of the various papers I've cited from the < ENCODE > project.

These papers clearly show a multi-layered, overlapping, multi-directional "coding" scheme within the human genome.  (I put "coding" in quotes since most of the genome "codes" for things other than proteins and so is currently classified as "non-coding").

They also show quite clearly that most of the human genome is transcribed and functional.

These scientists are suggesting that a re-defining of the most basic term in genetics - the gene - is necessary.

I'll ask again:  When did any of your various theories or hypotheses predict such a complex interwoven tapestry within our genome (or any other)?
And...
Is that why none of you want to talk about it?  Does it cause difficulties for you?
Posted by: oldmanintheskydidntdoit on Nov. 16 2007,18:55

Quote (Daniel Smith @ Nov. 16 2007,18:50)
One thing I find interesting here is that most of you have shown no interest in any of the various papers I've cited from the < ENCODE > project.

These papers clearly show a multi-layered, overlapping, multi-directional "coding" scheme within the human genome.  (I put "coding" in quotes since most of the genome "codes" for things other than proteins and so is currently classified as "non-coding").

They also show quite clearly that most of the human genome is transcribed and functional.

These scientists are suggesting that a re-defining of the most basic term in genetics - the gene - is necessary.

I'll ask again:  When did any of your various theories or hypotheses predict such a complex interwoven tapestry within our genome (or any other)?
And...
Is that why none of you want to talk about it?  Does it cause difficulties for you?
---------------------QUOTE-------------------


yeah yeah, we know, god did it. what further is there to discuss?
Posted by: Daniel Smith on Nov. 16 2007,19:01

Quote (oldmanintheskydidntdoit @ Nov. 16 2007,18:55)
Quote (Daniel Smith @ Nov. 16 2007,18:50)
One thing I find interesting here is that most of you have shown no interest in any of the various papers I've cited from the < ENCODE > project.

These papers clearly show a multi-layered, overlapping, multi-directional "coding" scheme within the human genome.  (I put "coding" in quotes since most of the genome "codes" for things other than proteins and so is currently classified as "non-coding").

They also show quite clearly that most of the human genome is transcribed and functional.

These scientists are suggesting that a re-defining of the most basic term in genetics - the gene - is necessary.

I'll ask again:  When did any of your various theories or hypotheses predict such a complex interwoven tapestry within our genome (or any other)?
And...
Is that why none of you want to talk about it?  Does it cause difficulties for you?
---------------------QUOTE-------------------


yeah yeah, we know, god did it. what further is there to discuss?
---------------------QUOTE-------------------


No, the "ENCyclopedia Of DNA Elements Consortium" did it.

Have you read any of it?
Posted by: mitschlag on Nov. 17 2007,07:25

Quote (Daniel Smith @ Nov. 16 2007,18:50)
One thing I find interesting here is that most of you have shown no interest in any of the various papers I've cited from the < ENCODE > project.

These papers clearly show a multi-layered, overlapping, multi-directional "coding" scheme within the human genome.  (I put "coding" in quotes since most of the genome "codes" for things other than proteins and so is currently classified as "non-coding").

They also show quite clearly that most of the human genome is transcribed and functional.

These scientists are suggesting that a re-defining of the most basic term in genetics - the gene - is necessary.

I'll ask again:  When did any of your various theories or hypotheses predict such a complex interwoven tapestry within our genome (or any other)?
And...
Is that why none of you want to talk about it?  Does it cause difficulties for you?
---------------------QUOTE-------------------


One thing I find interesting is that when he can't provide answers to standing questions, Daniel changes the subject.

It's not that we are afraid to talk about it.  We just don't see it as being a problem.  And especially not as evidence for a Designer.

Why should we be shocked to learn something new?   That's the way it goes in science, in which empirical data trump previous belief.  And the pace of discovery keeps accelerating.

So it is irrelevant whether anyone predicted or did not predict new findings.  The excitement is in learning new things and in overthrowing the existent paradigm...whenever possible.

You might understand better if you would read < The Structure of Scientific Revolutions >.
Posted by: JAM on Nov. 17 2007,10:30

Quote (Daniel Smith @ Nov. 16 2007,18:50)
One thing I find interesting here is that most of you have shown no interest in any of the various papers I've cited from the < ENCODE > project.
These papers clearly show a multi-layered, overlapping, multi-directional "coding" scheme within the human genome.
---------------------QUOTE-------------------


Why would the human genome be so different from the Drosophila genome?

And if it's a scheme, why don't you understand it? And if it supports your hypothesis, why didn't you predict it?




---------------------QUOTE-------------------
(I put "coding" in quotes since most of the genome "codes" for things other than proteins and so is currently classified as "non-coding").
---------------------QUOTE-------------------


You don't know what you're talking about. Given that, how can you ethically reach the conclusion that we don't know what we are talking about?


---------------------QUOTE-------------------
They also show quite clearly that most of the human genome is transcribed and functional.
---------------------QUOTE-------------------


Now you're just lying. You haven't shown that transcription necessarily implies function. I already asked you to make a prediction about the relationship between the time transcription of an essential gene begins and the time at which the null mutant has a phenotype, but you ran away.


---------------------QUOTE-------------------
These scientists are suggesting that a re-defining of the most basic term in genetics - the gene - is necessary.
---------------------QUOTE-------------------


So what? That does absolutely nothing to support a design hypothesis.


---------------------QUOTE-------------------
I'll ask again:  When did any of your various theories or hypotheses predict such a complex interwoven tapestry within our genome (or any other)?
---------------------QUOTE-------------------


1) MET makes clear, testable predictions about the mechanisms by which the messy, fuzzy nature of our genome came about.
2) As for any other, similar phenomena were shown in the Drosophila bithorax complex FIVE YEARS AGO. Therefore, we predicted similar complexity in the human genome.


---------------------QUOTE-------------------
And...
Is that why none of you want to talk about it?  Does it cause difficulties for you?
---------------------QUOTE-------------------


It doesn't address any of your predictions--it's just the same ol' post hoc spin to try and conceal the fact that you are dishonest, because you won't change or abandon your hypothesis when its predictions are shown to be false.

Bearing false witness is a sin in my Bible, Daniel.
Posted by: JAM on Nov. 17 2007,13:31

Quote (Daniel Smith @ Nov. 15 2007,15:39)
Quote (JAM @ Nov. 13 2007,11:00)
   
Quote (Daniel Smith @ Nov. 11 2007,14:58)
I began that discussion with a severely limited knowledge of genetics - only knowing that there were genes (which I assumed to be regions that only coded for proteins) and non-coding regions between them (which I assumed to be what-is-commonly-referred-to-as "junk DNA").  With this limited knowledge, I made several predictions indicating what I'd expect to find molecularly - including increasing complexity and overlapping and embedded codes.
---------------------QUOTE-------------------


I don't see how the fact that you didn't know that introns were within genes and are non-coding preserves your hypothesis against the inescapable fact that introns, whether one looks within species, between races, between species within a genus, between genuses within a family (which met YOUR definition of "within a lineage"), or between phyla, diverge more than exons.

It seems to me that your saltational hypothesis still makes an utterly false prediction.
       

---------------------QUOTE-------------------
...I feel vindicated in my own mind by what I've found.

I will probably never convince you or anyone else on this board of design, but I'm more fully convinced now than I was when I came here.
---------------------QUOTE-------------------


Good! Then you'll have no problem explaining how your hypothesis treats non-coding regions within genes completely differently from non-coding regions outside genes.
---------------------QUOTE-------------------


Let me just say this:

I am still not convinced that the evidence you showed me from VISTA contradicts my hypothesis.
---------------------QUOTE-------------------


What should convince you, assuming that you were an honest person, was that your prediction was dead wrong. This is why we have the scientific method.


---------------------QUOTE-------------------
Until I know what VISTA does and how it does it, I'll have to reserve judgment on it.
---------------------QUOTE-------------------


It takes you right down to the sequences themselves, Dan. What more is there to know?


---------------------QUOTE-------------------
You are convinced (based on VISTA) that I am wrong.
---------------------QUOTE-------------------


No, I know from decades of professional experience that you are wrong. I merely chose VISTA as a way to present the evidence.


---------------------QUOTE-------------------
That's fine - I very well may be wrong!  After all, I'm trying to guess what God was thinking when he designed life.  I'll probably be wrong more than I'm right.
---------------------QUOTE-------------------


You already know that you are wrong. That's why you are afraid to pursue the predictions you made in your last response to me.

Do you predict that whales will be missing a hind-leg gene? Do you predict that monkeys have a tail gene that humans lack? Both of these stream from your guess as to what God was thinking when he designed, but you are afraid to pursue it, because you have no real faith. This is why ID is first and foremost bad theology.


---------------------QUOTE-------------------
All I'm saying is, I'm not seeing what you're seeing (yet at least).
---------------------QUOTE-------------------

Have you considered opening your eyes to what God Himself has written in the book of nature?


---------------------QUOTE-------------------
 I have a lot less knowledge in this area than you so I'm not able to just look at a chart of colors and immediately know what they all represent and how they confirm or falsify my predictions.
---------------------QUOTE-------------------

 
So how do you explain why you believe your bottom line more than mine, given your lack of knowledge?


---------------------QUOTE-------------------
Please be patient with me and please stop accusing me of lying whenever I make ignorant statements!
---------------------QUOTE-------------------


Then please don't pretend to know things that you don't know. That's lying.
Posted by: oldmanintheskydidntdoit on Nov. 17 2007,19:10

Quote (Daniel Smith @ Nov. 16 2007,19:01)
Quote (oldmanintheskydidntdoit @ Nov. 16 2007,18:55)
 
Quote (Daniel Smith @ Nov. 16 2007,18:50)
One thing I find interesting here is that most of you have shown no interest in any of the various papers I've cited from the < ENCODE > project.

These papers clearly show a multi-layered, overlapping, multi-directional "coding" scheme within the human genome.  (I put "coding" in quotes since most of the genome "codes" for things other than proteins and so is currently classified as "non-coding").

They also show quite clearly that most of the human genome is transcribed and functional.

These scientists are suggesting that a re-defining of the most basic term in genetics - the gene - is necessary.

I'll ask again:  When did any of your various theories or hypotheses predict such a complex interwoven tapestry within our genome (or any other)?
And...
Is that why none of you want to talk about it?  Does it cause difficulties for you?
---------------------QUOTE-------------------


yeah yeah, we know, god did it. what further is there to discuss?
---------------------QUOTE-------------------


No, the "ENCyclopedia Of DNA Elements Consortium" did it.

Have you read any of it?
---------------------QUOTE-------------------


all of it.
Posted by: Lou FCD on Nov. 18 2007,06:09



   

---------------------QUOTE-------------------
< Urinal at The Fire, by highstrungloner @ Flickr >
---------------------QUOTE-------------------



There's been a bit of clean up, < Find it here. >
Posted by: oldmanintheskydidntdoit on Nov. 18 2007,10:46

Quote (Daniel Smith @ Nov. 16 2007,18:50)
One thing I find interesting here is that most of you have shown no interest in any of the various papers I've cited from the < ENCODE > project.

These papers clearly show a multi-layered, overlapping, multi-directional "coding" scheme within the human genome.  (I put "coding" in quotes since most of the genome "codes" for things other than proteins and so is currently classified as "non-coding").

They also show quite clearly that most of the human genome is transcribed and functional.

These scientists are suggesting that a re-defining of the most basic term in genetics - the gene - is necessary.

I'll ask again:  When did any of your various theories or hypotheses predict such a complex interwoven tapestry within our genome (or any other)?
And...
Is that why none of you want to talk about it?  Does it cause difficulties for you?
---------------------QUOTE-------------------


Very well Daniel. We can't have you thinking that "darwinists" are scared of your layman point of view. I'm a lay person here too.

And as such, here are my questions (conditions, if you like, for further discussion to take place. I'm not a moderator here but I won't bother to engage  again if you don't make a reasonable attempt to answer. Most other people it seems have stopped bothering already).

1) Could you please show me the specific prediction that "darwinism" makes that specifies that multi-layered, overlapping, multi-directional "coding" schemes within the human genome should not exist?

2) Could you please show me the specific prediction that "darwinism" makes that  most of the human genome should not be transcribed and functional.

3) Could you please show me the specific prediction that "darwinism" makes that predicts such a complex interwoven tapestry within our genome (or any other) cannot exist?



---------------------QUOTE-------------------
Is that why none of you want to talk about it?  Does it cause difficulties for you?
---------------------QUOTE-------------------



I suspect you are confusing "scientists were surprised at what they found" with "scientists found something that they  predicted was impossible" or suchlike.

What is it exactly that you want to talk about? So what if scientists are suggesting redefining the gene. How does that in any what whatsoever support the idea that a deity was necessary at any stage along the way. In fact, lets make that question four.

4) How does redefining the gene suggest a supernatural intervention was required? Specifically?
Posted by: VMartin on Nov. 18 2007,12:47

JAM

 

---------------------QUOTE-------------------

So if one is intelligently designing a spacing mechanism, why in heaven's name (literally) would one use tandem repeats, which expand and contract (via recombination) at ridiculously high frequencies? Wouldn't unique sequence be the far more intelligent choice?

---------------------QUOTE-------------------



As a layman I dont know what you and Daniel are meaning by "tandem repeats". Are those repeats  "tandem duplication" or pure "repeated sequences"?

In the second case I don't see how how the difference in the structure of repeated sequences between different species proves Daniel theory by saltus as wrong. It may  have been induced by some unknown mechanism during John Davison's chromosome rearrangements, no? As far as I know repeated sequences by two sisters species are sometimes very different. But they are also different from those of the ancestor species.

This phenomenon is very hard to explain without special mechanism that after speciation causes parallel differentiation of repeated sequences in all locuses of genome. There must be obviously also some process of homogenization of repeated sequences. These repeated sequences are often identical in new species and have sometimes hundered thousands copies.  

So there must be process of  differentiation of repeated sequences in daughter species from mother species and at the same time homogenization of all these repeated sequences to new ones.

Wouldn't be it more simple to assume that such  repeated sequences are for each new species created de novo by saltus?

If the phenomenon is to be explained by molecular drive as I have read elsewhere it would mean that by such process (molecular drive) would be affected many individuals of population simultaneously. It would assume some kind of synchronized evolution of repeated sequences.

Generalizing molecular drive to all genome we are dealing with synchronized evolution, something proposed by Leo Berg (with which John Davison disagree btw).
Posted by: Daniel Smith on Nov. 18 2007,15:08

Quote (JAM @ Nov. 17 2007,10:30)
1) MET makes clear, testable predictions about the mechanisms by which the messy, fuzzy nature of our genome came about.
---------------------QUOTE-------------------


As far as I can see, the only thing messy or fuzzy about our genome is our understanding of it.
Posted by: Daniel Smith on Nov. 18 2007,15:10

Quote (oldmanintheskydidntdoit @ Nov. 17 2007,19:10)
 
Quote (Daniel Smith @ Nov. 16 2007,18:50)

No, the "ENCyclopedia Of DNA Elements Consortium" did it.

Have you read any of it?
---------------------QUOTE-------------------


all of it.
---------------------QUOTE-------------------


All 29 papers?
Posted by: JAM on Nov. 18 2007,15:30

Quote (Daniel Smith @ Nov. 18 2007,15:08)
Quote (JAM @ Nov. 17 2007,10:30)
1) MET makes clear, testable predictions about the mechanisms by which the messy, fuzzy nature of our genome came about.
---------------------QUOTE-------------------


As far as I can see, the only thing messy or fuzzy about our genome is our understanding of it.
---------------------QUOTE-------------------


Mine's a helluvalot less fuzzy than yours. May I take it that you conceded all of the other points in choosing a one-liner? I'm particularly interested in your answers to these questions:

A) Do you predict that whales will be missing a hind-leg gene? Do you predict that monkeys have a tail gene that humans lack? Both of these stream from your guess as to what God was thinking when he designed, but you are afraid to pursue it, because you have no real faith (Note that this relates to the fuzziness that you lack the integrity to address).

B) I have a gene, and both mice and humans homozygous for the null allele die shortly after birth (with essentially the same phenotype). Since according to you, transcription implies function, when I look at transcription of that gene, will it be turned on:
1) right before the age of death in the null mutants,
2) right before or at the time at which mutants can be distinguished from wild-type individuals, or
3) more than a month before 1 or 2?

C) Why is it that you are so breathtakingly arrogant that you believe that God causes millions of children to suffer and die as a lesson to people like you, but getting you to make predictions is like pulling teeth?
Posted by: Henry J on Nov. 18 2007,18:14



---------------------QUOTE-------------------
Wouldn't be it more simple to assume that such repeated sequences are for each new species created de novo by saltus?
---------------------QUOTE-------------------



Wouldn't the simplest assumption be that a series of repeats was caused by a duplication type mutation? If so, that could occur independently in closely related species. (In which case it would presumably be repetitions of a different sequence, in a different location of the genome.)

Henry
Posted by: Daniel Smith on Nov. 18 2007,18:35

Quote (oldmanintheskydidntdoit @ Nov. 18 2007,10:46)
   
Quote (Daniel Smith @ Nov. 16 2007,18:50)
One thing I find interesting here is that most of you have shown no interest in any of the various papers I've cited from the < ENCODE > project.

These papers clearly show a multi-layered, overlapping, multi-directional "coding" scheme within the human genome.  (I put "coding" in quotes since most of the genome "codes" for things other than proteins and so is currently classified as "non-coding").

They also show quite clearly that most of the human genome is transcribed and functional.

These scientists are suggesting that a re-defining of the most basic term in genetics - the gene - is necessary.

I'll ask again:  When did any of your various theories or hypotheses predict such a complex interwoven tapestry within our genome (or any other)?
And...
Is that why none of you want to talk about it?  Does it cause difficulties for you?
---------------------QUOTE-------------------


Very well Daniel. We can't have you thinking that "darwinists" are scared of your layman point of view. I'm a lay person here too.

And as such, here are my questions (conditions, if you like, for further discussion to take place. I'm not a moderator here but I won't bother to engage  again if you don't make a reasonable attempt to answer. Most other people it seems have stopped bothering already).

1) Could you please show me the specific prediction that "darwinism" makes that specifies that multi-layered, overlapping, multi-directional "coding" schemes within the human genome should not exist?

2) Could you please show me the specific prediction that "darwinism" makes that  most of the human genome should not be transcribed and functional.

3) Could you please show me the specific prediction that "darwinism" makes that predicts such a complex interwoven tapestry within our genome (or any other) cannot exist?

     

---------------------QUOTE-------------------
Is that why none of you want to talk about it?  Does it cause difficulties for you?
---------------------QUOTE-------------------



I suspect you are confusing "scientists were surprised at what they found" with "scientists found something that they  predicted was impossible" or suchlike.

What is it exactly that you want to talk about? So what if scientists are suggesting redefining the gene. How does that in any what whatsoever support the idea that a deity was necessary at any stage along the way. In fact, lets make that question four.

4) How does redefining the gene suggest a supernatural intervention was required? Specifically?
---------------------QUOTE-------------------


First, I'm not aware of any predictions "darwinism" has made about these types of things so I'll have to give you my take on what "darwinism" might predict:

If I understand it correctly, the modern evolutionary theory hypothesizes that morphological change has occurred as a result of millions of years of accumulated mutations within the genomes of organisms.  These random mutations mostly accumulate in non-coding / non-functional areas within the genome.  They will thus eventually create a new genetic sequence or modify an existing functional sequence to the point that a new or improved feature is developed.  That feature then becomes fixed in the genome due to selection.  Of course, there's a whole lot more to it than that, and many others here will no doubt chime in with their take on the mechanisms of evolution, but that's my "nutshell" version.

Now, if that's the case, then we should see some evidence in every genome of millions of years of these accumulated random mutations in non-functional (and functional) areas of the genome.  

What would you expect to see and how does it compare to what we do see?

Of course, if there are no (or very few) non-functional areas in the genome (as I believe), then there would be no place for random mutations to accumulate.  I think what we are actually observing and discovering about genomes is more in line with this approach.

Which brings me to your last question:
At some point; after we realize that whole genomes are functional; after we've discovered bewildering complexity within them; and after we've pretty much eliminated random causes for such things; we have to explore the possibility that intelligence was involved in the design of such a system.  I predict science will some day soon arrive at that point.
Posted by: Daniel Smith on Nov. 18 2007,18:43

Quote (VMartin @ Nov. 18 2007,12:47)
JAM

       

---------------------QUOTE-------------------

So if one is intelligently designing a spacing mechanism, why in heaven's name (literally) would one use tandem repeats, which expand and contract (via recombination) at ridiculously high frequencies? Wouldn't unique sequence be the far more intelligent choice?

---------------------QUOTE-------------------



As a layman I dont know what you and Daniel are meaning by "tandem repeats". Are those repeats  "tandem duplication" or pure "repeated sequences"?

In the second case I don't see how how the difference in the structure of repeated sequences between different species proves Daniel theory by saltus as wrong. It may  have been induced by some unknown mechanism during John Davison's chromosome rearrangements, no? As far as I know repeated sequences by two sisters species are sometimes very different. But they are also different from those of the ancestor species.

This phenomenon is very hard to explain without special mechanism that after speciation causes parallel differentiation of repeated sequences in all locuses of genome. There must be obviously also some process of homogenization of repeated sequences. These repeated sequences are often identical in new species and have sometimes hundered thousands copies.  

So there must be process of  differentiation of repeated sequences in daughter species from mother species and at the same time homogenization of all these repeated sequences to new ones.

Wouldn't be it more simple to assume that such  repeated sequences are for each new species created de novo by saltus?

If the phenomenon is to be explained by molecular drive as I have read elsewhere it would mean that by such process (molecular drive) would be affected many individuals of population simultaneously. It would assume some kind of synchronized evolution of repeated sequences.

Generalizing molecular drive to all genome we are dealing with synchronized evolution, something proposed by Leo Berg (with which John Davison disagree btw).
---------------------QUOTE-------------------


Very astute observations Martin.  

I've often wondered "Why repeats?", "Why not random 'gibberish'?"

It seems to me that millions of years of accumulated random mutations in non-functional areas would have to result in random base pairs - as opposed to repeat sequences.

But then again, I don't understand the logic behind the theory of evolution anywhere near as well as the rest of them say they do.
Posted by: Daniel Smith on Nov. 18 2007,19:19

Quote (JAM @ Nov. 18 2007,15:30)
           
Quote (Daniel Smith @ Nov. 18 2007,15:08)
             
Quote (JAM @ Nov. 17 2007,10:30)
1) MET makes clear, testable predictions about the mechanisms by which the messy, fuzzy nature of our genome came about.
---------------------QUOTE-------------------


As far as I can see, the only thing messy or fuzzy about our genome is our understanding of it.
---------------------QUOTE-------------------


Mine's a helluvalot less fuzzy than yours. May I take it that you conceded all of the other points in choosing a one-liner?
---------------------QUOTE-------------------


No.            

---------------------QUOTE-------------------
I'm particularly interested in your answers to these questions:

A) Do you predict that whales will be missing a hind-leg gene?
---------------------QUOTE-------------------

Not necessarily - though I predict it will be suppressed as to it's full development.  IOW, the non-coding "support cast" for that gene will be markedly different from animals that have fully developed hind legs.            

---------------------QUOTE-------------------
Do you predict that monkeys have a tail gene that humans lack?
---------------------QUOTE-------------------

No.  I predict that their "tail gene(s)" (at least the protein coding parts) may be similar to ours, but all their various regulatory and support elements will be markedly different from ours.  Theirs will have much more activity and development in these non-coding areas - possibly evidenced by a markedly higher level of histone activity.  Ours will be suppressed.      

---------------------QUOTE-------------------
Both of these stream from your guess as to what God was thinking when he designed, but you are afraid to pursue it, because you have no real faith (Note that this relates to the fuzziness that you lack the integrity to address).
---------------------QUOTE-------------------

Why does every response from you have to be so peppered with accusations?  It gets tiring after awhile.  I feel like I'm answering you not so much because I have to defend my positions, but rather because I have to defend my character.        

---------------------QUOTE-------------------
B) I have a gene, and both mice and humans homozygous for the null allele die shortly after birth (with essentially the same phenotype). Since according to you, transcription implies function, when I look at transcription of that gene, will it be turned on:
1) right before the age of death in the null mutants,
2) right before or at the time at which mutants can be distinguished from wild-type individuals, or
3) more than a month before 1 or 2?
---------------------QUOTE-------------------

I'm not sure what you mean by "when I look at transcription of that gene, will it be turned on".  Do you mean "will transcription of that gene be turned on", or will "the gene itself be turned on"?  
Because I think transcription of the gene will always be happening,  but as to when exactly the gene gets turned on, I have no clue.      

---------------------QUOTE-------------------


C) Why is it that you are so breathtakingly arrogant that you believe that God causes millions of children to suffer and die as a lesson to people like you, but getting you to make predictions is like pulling teeth?
---------------------QUOTE-------------------


The suffering of these children (and everything else that happens in life) is a lesson for us all - not just for "people like me".
Posted by: stevestory on Nov. 18 2007,19:33

Quote (Daniel Smith @ Nov. 18 2007,20:19)
I'm not sure what you mean by "when I look at transcription of that gene, will it be turned on".  Do you mean "will transcription of that gene be turned on", or will "the gene itself be turned on"?  
Because I think transcription of the gene will always be happening,  but as to when exactly the gene gets turned on, I have no clue.
---------------------QUOTE-------------------


Dan, we will send you some intro biology textbooks, if you want to learn about biology. You don't understand the basic terminology and concepts. If you're interested in learning, send a PM to Lou FCD or Albatrossity with a mailing address and we will send you some freshman-level textbooks to start with.
Posted by: Arden Chatfield on Nov. 18 2007,21:47

Quote (Daniel Smith @ Nov. 18 2007,18:43)
Quote (VMartin @ Nov. 18 2007,12:47)
JAM

       

---------------------QUOTE-------------------

So if one is intelligently designing a spacing mechanism, why in heaven's name (literally) would one use tandem repeats, which expand and contract (via recombination) at ridiculously high frequencies? Wouldn't unique sequence be the far more intelligent choice?

---------------------QUOTE-------------------



As a layman I dont know what you and Daniel are meaning by "tandem repeats". Are those repeats  "tandem duplication" or pure "repeated sequences"?

In the second case I don't see how how the difference in the structure of repeated sequences between different species proves Daniel theory by saltus as wrong. It may  have been induced by some unknown mechanism during John Davison's chromosome rearrangements, no? As far as I know repeated sequences by two sisters species are sometimes very different. But they are also different from those of the ancestor species.

This phenomenon is very hard to explain without special mechanism that after speciation causes parallel differentiation of repeated sequences in all locuses of genome. There must be obviously also some process of homogenization of repeated sequences. These repeated sequences are often identical in new species and have sometimes hundered thousands copies.  

So there must be process of  differentiation of repeated sequences in daughter species from mother species and at the same time homogenization of all these repeated sequences to new ones.

Wouldn't be it more simple to assume that such  repeated sequences are for each new species created de novo by saltus?

If the phenomenon is to be explained by molecular drive as I have read elsewhere it would mean that by such process (molecular drive) would be affected many individuals of population simultaneously. It would assume some kind of synchronized evolution of repeated sequences.

Generalizing molecular drive to all genome we are dealing with synchronized evolution, something proposed by Leo Berg (with which John Davison disagree btw).
---------------------QUOTE-------------------


Very astute observations Martin.  
---------------------QUOTE-------------------


VMartin has also stated that "if a reptile hatched a bird there is no ancestor in common view." Is that astute, too?
Posted by: Henry J on Nov. 18 2007,22:37



---------------------QUOTE-------------------
VMartin has also stated that "if a reptile hatched a bird there is no ancestor in common view." Is that astute, too?

---------------------QUOTE-------------------



Of course, cladistically speaking, birds are reptiles. ;)

Henry
Posted by: VMartin on Nov. 18 2007,23:50

Quote (stevestory @ Nov. 18 2007,19:33)
           
Quote (Daniel Smith @ Nov. 18 2007,20:19)
I'm not sure what you mean by "when I look at transcription of that gene, will it be turned on".  Do you mean "will transcription of that gene be turned on", or will "the gene itself be turned on"?  
Because I think transcription of the gene will always be happening,  but as to when exactly the gene gets turned on, I have no clue.
---------------------QUOTE-------------------


Dan, we will send you some intro biology textbooks, if you want to learn about biology. You don't understand the basic terminology and concepts. If you're interested in learning, send a PM to Lou FCD or Albatrossity with a mailing address and we will send you some freshman-level textbooks to start with.
---------------------QUOTE-------------------


Maybe you can describe the mechanism of gradual homologization of repeated sequences in new species which everybody know about from "intro biolology text books" and which is different from the molecular drive? Otherwise I am afraid that you are as great expert in the evolutionary biology as Erasmus is an "expert" in the problem of aposematism at another thread.
Posted by: Arden Chatfield on Nov. 19 2007,00:18

Quote (VMartin @ Nov. 18 2007,23:50)
Quote (stevestory @ Nov. 18 2007,19:33)
             
Quote (Daniel Smith @ Nov. 18 2007,20:19)
I'm not sure what you mean by "when I look at transcription of that gene, will it be turned on".  Do you mean "will transcription of that gene be turned on", or will "the gene itself be turned on"?  
Because I think transcription of the gene will always be happening,  but as to when exactly the gene gets turned on, I have no clue.
---------------------QUOTE-------------------


Dan, we will send you some intro biology textbooks, if you want to learn about biology. You don't understand the basic terminology and concepts. If you're interested in learning, send a PM to Lou FCD or Albatrossity with a mailing address and we will send you some freshman-level textbooks to start with.
---------------------QUOTE-------------------


Maybe you can describe the mechanism of gradual homologization of repeated sequences in new species which everybody know about from "intro biolology text books" and which is different from the molecular drive? Otherwise I am afraid that you are as great expert in the evolutionary biology as Erasmus is an "expert" in the problem of aposematism at another thread.
---------------------QUOTE-------------------


What exactly are you an expert in, 'Martin'?
Posted by: JAM on Nov. 19 2007,00:38

[quote=Daniel Smith,Nov. 18 2007,19:19]  [quote=JAM,Nov. 18 2007,15:30]                
Quote (Daniel Smith @ Nov. 18 2007,15:08)
                 
Quote (JAM @ Nov. 17 2007,10:30)
1) MET makes clear, testable predictions about the mechanisms by which the messy, fuzzy nature of our genome came about.
---------------------QUOTE-------------------


As far as I can see, the only thing messy or fuzzy about our genome is our understanding of it.
---------------------QUOTE-------------------


Mine's a helluvalot less fuzzy than yours. May I take it that you conceded all of the other points in choosing a one-liner?[/quote]
No.[/quote]
Then maybe you should respond.


---------------------QUOTE-------------------


---------------------QUOTE-------------------
I'm particularly interested in your answers to these questions:
A) Do you predict that whales will be missing a hind-leg gene?
---------------------QUOTE-------------------

Not necessarily - though I predict it will be suppressed as to it's full development.
---------------------QUOTE-------------------


Genes don't "develop." Organisms and organs do.
Please define "it" in this context. Does your hypothesis predict that there will be anything that we humans could call a "hind-leg gene" based on analogies with our own designs?


---------------------QUOTE-------------------
IOW, the non-coding "support cast" for that gene will be markedly different from animals that have fully developed hind legs.
---------------------QUOTE-------------------


Please define "markedly" in this context. It's important.


---------------------QUOTE-------------------


---------------------QUOTE-------------------
Do you predict that monkeys have a tail gene that humans lack?
---------------------QUOTE-------------------

No.  I predict that their "tail gene(s)" (at least the protein coding parts) may be similar to ours, but all their various regulatory and support elements will be markedly different from ours.
---------------------QUOTE-------------------


Does your hypothesis predict that there will be anything that we humans could call a "tail gene" based on analogies with our own designs?  


---------------------QUOTE-------------------
Theirs will have much more activity and development
---------------------QUOTE-------------------


Again, the term "development" is gibberish in this context, and "activity" means transcriptional activity in this context. Is that what you mean?


---------------------QUOTE-------------------
in these non-coding areas - possibly evidenced by a markedly higher level of histone activity.
---------------------QUOTE-------------------


What do you mean by "histone activity"? Again, it's important.


---------------------QUOTE-------------------
Ours will be suppressed.
---------------------QUOTE-------------------


Our what, exactly? It has to be measurable. Please provide units.


---------------------QUOTE-------------------


---------------------QUOTE-------------------
Both of these stream from your guess as to what God was thinking when he designed, but you are afraid to pursue it, because you have no real faith (Note that this relates to the fuzziness that you lack the integrity to address).
---------------------QUOTE-------------------

Why does every response from you have to be so peppered with accusations?
---------------------QUOTE-------------------


Sit down and take a deep breath. Think, as a Christian, for a moment about what YOU are accusing me and the other scientists of doing here. YOU are accusing US of gross incompetence, and in direct contradiction of clear Biblical guidance, you have made this accusation on the basis of nothing but hearsay.


---------------------QUOTE-------------------
It gets tiring after awhile.
---------------------QUOTE-------------------


Put yourself in my shoes, Dan. I've spent most of my life doing biology, and you come along. Would you describe your claims as humble ones?


---------------------QUOTE-------------------
I feel like I'm answering you not so much because I have to defend my positions, but rather because I have to defend my character.
---------------------QUOTE-------------------


What sort of character makes grandiose claims without evidence, and then discounts the evidence?


---------------------QUOTE-------------------


---------------------QUOTE-------------------
B) I have a gene, and both mice and humans homozygous for the null allele die shortly after birth (with essentially the same phenotype). Since according to you, transcription implies function, when I look at transcription of that gene, will it be turned on:
1) right before the age of death in the null mutants,
2) right before or at the time at which mutants can be distinguished from wild-type individuals, or
3) more than a month before 1 or 2?
---------------------QUOTE-------------------

I'm not sure what you mean by "when I look at transcription of that gene, will it be turned on".  Do you mean "will transcription of that gene be turned on", or will "the gene itself be turned on"?
---------------------QUOTE-------------------


The former.


---------------------QUOTE-------------------
Because I think transcription of the gene will always be happening,
---------------------QUOTE-------------------


Why would you think that? WTF do transcription factors do?
 

---------------------QUOTE-------------------
 but as to when exactly the gene gets turned on, I have no clue.
---------------------QUOTE-------------------


Why not? Wouldn't an intelligent designer design it so transcription was turned on when (and where) it was needed, and not before or in other tissues?


---------------------QUOTE-------------------


---------------------QUOTE-------------------
C) Why is it that you are so breathtakingly arrogant that you believe that God causes millions of children to suffer and die as a lesson to people like you, but getting you to make predictions is like pulling teeth?
---------------------QUOTE-------------------


The suffering of these children (and everything else that happens in life) is a lesson for us all - not just for "people like me".
---------------------QUOTE-------------------


I'm sorry, but I don't see what the children who suffer and die are learning. Why shouldn't you and your children be suffering and dying?
Posted by: IanBrown_101 on Nov. 19 2007,07:35

Quote (JAM @ Nov. 19 2007,06:38)


---------------------QUOTE-------------------
The suffering of these children (and everything else that happens in life) is a lesson for us all - not just for "people like me".
---------------------QUOTE-------------------


I'm sorry, but I don't see what the children who suffer and die are learning. Why shouldn't you and your children be suffering and dying?
---------------------QUOTE-------------------


Because their life will be bad anyway, so it's a mercy.

By this logic we should commit multiple genocides in Africa to end their suffering.
Posted by: Richard Simons on Nov. 19 2007,08:17



---------------------QUOTE-------------------
The suffering of these children (and everything else that happens in life) is a lesson for us all - not just for "people like me".
---------------------QUOTE-------------------


Only if you are aware of it. In which case, wouldn't it be more instructive if it happened in the developed world where communications are so much better, rather than in Third World villages where TV cameras rarely penetrate?
Posted by: Erasmus, FCD on Nov. 19 2007,08:36

I suppose that 'being an expert' in something is sufficiently attained when you know enough about something to point out the flaws in another's reasoning.  like the guts of 80,000 birds being a controlled experiment, or something.

now, i don't know enough about molecular drives and it seems that what daniel is predicting is not very different, at least from the root concepts, from the evolutionary explanation.  

minus the assumption of saltation, which if my contention is above is correct is thus a non-parsimonious explanation. co-opting predictions post hoc is certainly a hallmark of crankery.  gene copy number varies within populations so i don't see what someone's point is...
Posted by: Henry J on Nov. 20 2007,11:26

If saltation doesn't work, try pepper-ation...  :p
Posted by: Daniel Smith on Nov. 20 2007,18:58

Quote (Richard Simons @ Nov. 19 2007,08:17)
 

---------------------QUOTE-------------------
The suffering of these children (and everything else that happens in life) is a lesson for us all - not just for "people like me".
---------------------QUOTE-------------------


Only if you are aware of it. In which case, wouldn't it be more instructive if it happened in the developed world where communications are so much better, rather than in Third World villages where TV cameras rarely penetrate?
---------------------QUOTE-------------------


You know, my wife just lost her mother after years and years of progressive debilitation due to complications of diabetes.  We watched a healthy, beautiful woman disintegrate before our eyes.  When she died, at the young age of 65, she looked like she was 90.  This happened in the most developed nation on earth, with the best medical care available.  Suffering is not restricted to 3rd world countries - nor is it restricted to children.  We all see it.
Posted by: Daniel Smith on Nov. 20 2007,19:20

Quote (mitschlag @ Nov. 17 2007,07:25)
One thing I find interesting is that when he can't provide answers to standing questions, Daniel changes the subject.
---------------------QUOTE-------------------


Some of you get on me for not answering every question thrown at me here.  You make it out that, if I don't answer your questions, it's because I'm "running away", or "avoiding real questions", or "changing the subject", (even though I'm only one man and there are many of you, firing many questions at me).

I started out talking about the fossil record, Schindewolf, Berg and natural selection, yet most of you wanted to "change the subject" to molecular evidence.

I asked about the multi-layered complexity of the human genome and most of you dismissed it with a shrug of the shoulders as if it was "old news".

I brought up the "histone code" but - no comments.

And, no one even tried to answer this question I posted:        
Quote (Daniel Smith @ Nov. 10 2007,11:29)

In the human genome, what percentage of genomic sequence would you say is likely to be transcribed as nuclear primary transcripts?
---------------------QUOTE-------------------



So.  Are you all running away? (Or does that only apply to me?)
Posted by: mitschlag on Nov. 21 2007,06:42

Quote (Daniel Smith @ Nov. 20 2007,19:20)
And, no one even tried to answer this question I posted:              
Quote (Daniel Smith @ Nov. 10 2007,11:29)

In the human genome, what percentage of genomic sequence would you say is likely to be transcribed as nuclear primary transcripts?
---------------------QUOTE-------------------


So.  Are you all running away? (Or does that only apply to me?)
---------------------QUOTE-------------------


But, but, but hasn't a start in obtaining data that answer your question been obtained by the < ENCODE Project >?

And hasn't this just been discussed (e.g. JAM Nov. 17 2007,10:30, among others)?

Looks to me like the ball is in your court to make whatever you want to make out of the data.
Posted by: mitschlag on Nov. 21 2007,07:19

In case memories need to be refreshed, here is Figure 4 of < Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project >


Three different technologies (integrated annotation from GENCODE, RACE-array experiments (RxFrags) and PET tags) were used to assess the presence of a nucleotide in a primary transcript. Use of these technologies provided the opportunity to have multiple observations of each finding. The proportion of genomic bases detected in the ENCODE regions associated with each of the following scenarios is depicted: detected by all three technologies, by two of the three technologies, by one technology but with multiple observations, and by one technology with only one observation. Also indicated are genomic bases without any detectable coverage of primary transcripts.
Posted by: JAM on Nov. 21 2007,11:05

Quote (JAM @ Nov. 17 2007,10:30)
 
Quote (Daniel Smith @ Nov. 16 2007,18:50)
One thing I find interesting here is that most of you have shown no interest in any of the various papers I've cited from the < ENCODE > project.
These papers clearly show a multi-layered, overlapping, multi-directional "coding" scheme within the human genome.
---------------------QUOTE-------------------


Why would the human genome be so different from the Drosophila genome?

And if it's a scheme, why don't you understand it? And if it supports your hypothesis, why didn't you predict it?


 

---------------------QUOTE-------------------
(I put "coding" in quotes since most of the genome "codes" for things other than proteins and so is currently classified as "non-coding").
---------------------QUOTE-------------------


You don't know what you're talking about. Given that, how can you ethically reach the conclusion that we don't know what we are talking about?
 

---------------------QUOTE-------------------
They also show quite clearly that most of the human genome is transcribed and functional.
---------------------QUOTE-------------------


Now you're just lying. You haven't shown that transcription necessarily implies function. I already asked you to make a prediction about the relationship between the time transcription of an essential gene begins and the time at which the null mutant has a phenotype, but you ran away.
 

---------------------QUOTE-------------------
These scientists are suggesting that a re-defining of the most basic term in genetics - the gene - is necessary.
---------------------QUOTE-------------------


So what? That does absolutely nothing to support a design hypothesis.
 

---------------------QUOTE-------------------
I'll ask again:  When did any of your various theories or hypotheses predict such a complex interwoven tapestry within our genome (or any other)?
---------------------QUOTE-------------------


1) MET makes clear, testable predictions about the mechanisms by which the messy, fuzzy nature of our genome came about.
2) As for any other, similar phenomena were shown in the Drosophila bithorax complex FIVE YEARS AGO. Therefore, we predicted similar complexity in the human genome.
 

---------------------QUOTE-------------------
And...
Is that why none of you want to talk about it?  Does it cause difficulties for you?
---------------------QUOTE-------------------


It doesn't address any of your predictions--it's just the same ol' post hoc spin to try and conceal the fact that you are dishonest, because you won't change or abandon your hypothesis when its predictions are shown to be false.

Bearing false witness is a sin in my Bible, Daniel.
---------------------QUOTE-------------------


Daniel, by what twisted logic do you describe this post as running away?

YOU are the one running away.

Also, please convey my deepest sympathies to your wife on the loss of her mother, but let's realize that her death is not relevant to your theologically twisted claim that God is causing children to be poor and dying of malaria just to teach people like you and me a lesson.

Do you not realize that your position implicitly claims that you are much more important in God's sight than those millions of children? If God's goal was to teach you a lesson (because you are so special), wouldn't the lesson be far more effective if he caused YOUR OWN child (or wife or mother) to die of malaria?
Posted by: J-Dog on Nov. 21 2007,12:25

Quote (JAM @ Nov. 21 2007,11:05)
Do you not realize that your position implicitly claims that you are much more important in God's sight than those millions of children? If God's goal was to teach you a lesson (because you are so special), wouldn't the lesson be far more effective if he caused YOUR OWN child (or wife or mother) to die of malaria?
---------------------QUOTE-------------------


Daniel - Since God is All Powerful, he could put words on your forhead that magically apppear when you look in the mirror, and they would say:  "HaHa, You Have Malaria!"

What a fun guy He is!

Bow down and worship him.

Amen
Posted by: Daniel Smith on Nov. 21 2007,22:44

Quote (JAM @ Nov. 17 2007,10:30)
         
Quote (Daniel Smith @ Nov. 16 2007,18:50)
One thing I find interesting here is that most of you have shown no interest in any of the various papers I've cited from the < ENCODE > project.
These papers clearly show a multi-layered, overlapping, multi-directional "coding" scheme within the human genome.
---------------------QUOTE-------------------


Why would the human genome be so different from the Drosophila genome?
---------------------QUOTE-------------------

     

---------------------QUOTE-------------------
1) MET makes clear, testable predictions about the mechanisms by which the messy, fuzzy nature of our genome came about.
2) As for any other, similar phenomena were shown in the Drosophila bithorax complex FIVE YEARS AGO. Therefore, we predicted similar complexity in the human genome.
---------------------QUOTE-------------------

     

---------------------QUOTE-------------------
It doesn't address any of your predictions--it's just the same ol' post hoc spin to try and conceal the fact that you are dishonest, because you won't change or abandon your hypothesis when its predictions are shown to be false.
---------------------QUOTE-------------------


I hope you don't misinterpret this as "accusing" you of something, but...

How is the complexity of the human genome a prediction of your theory - when you are "predicting" it based on the complexity of the Drosophila genome?  

So both genomes are complex--how does that confirm or falsify the mechanisms of your theory?  

What specific mechanism of the MET is tested by this "prediction"?

And how does this "prediction" differ from what you call, "post hoc spin"?
Posted by: oldmanintheskydidntdoit on Nov. 22 2007,03:00

Quote (Daniel Smith @ Nov. 21 2007,22:44)
Quote (JAM @ Nov. 17 2007,10:30)
         
Quote (Daniel Smith @ Nov. 16 2007,18:50)
One thing I find interesting here is that most of you have shown no interest in any of the various papers I've cited from the < ENCODE > project.
These papers clearly show a multi-layered, overlapping, multi-directional "coding" scheme within the human genome.
---------------------QUOTE-------------------


Why would the human genome be so different from the Drosophila genome?
---------------------QUOTE-------------------

       

---------------------QUOTE-------------------
1) MET makes clear, testable predictions about the mechanisms by which the messy, fuzzy nature of our genome came about.
2) As for any other, similar phenomena were shown in the Drosophila bithorax complex FIVE YEARS AGO. Therefore, we predicted similar complexity in the human genome.
---------------------QUOTE-------------------

     

---------------------QUOTE-------------------
It doesn't address any of your predictions--it's just the same ol' post hoc spin to try and conceal the fact that you are dishonest, because you won't change or abandon your hypothesis when its predictions are shown to be false.
---------------------QUOTE-------------------


I hope you don't misinterpret this as "accusing" you of something, but...

How is the complexity of the human genome a prediction of your theory - when you are "predicting" it based on the complexity of the Drosophila genome?  

So both genomes are complex--how does that confirm or falsify the mechanisms of your theory?  

What specific mechanism of the MET is tested by this "prediction"?

And how does this "prediction" differ from what you call, "post hoc spin"?
---------------------QUOTE-------------------


We could ask you exactly the same questions, based upon your previous answer to me.

Now are you beginning to see?
Posted by: IanBrown_101 on Nov. 22 2007,07:18

"
What specific mechanism of the MET is tested by this "prediction"?

And how does this "prediction" differ from what you call, "post hoc spin"?"

It's testing the idea of descent with modification, since if they were totally different then it would be a little....hard to explain, shall we say.

It isn't post hoc because, shockingly, it wasn't developed post hoc, and actually relied on a prediction made before the results were found.

You DO understand what post hoc means, don't you?
Posted by: Daniel Smith on Nov. 22 2007,09:35

Quote (IanBrown_101 @ Nov. 22 2007,07:18)
"
What specific mechanism of the MET is tested by this "prediction"?

And how does this "prediction" differ from what you call, "post hoc spin"?"

It's testing the idea of descent with modification, since if they were totally different then it would be a little....hard to explain, shall we say.

It isn't post hoc because, shockingly, it wasn't developed post hoc, and actually relied on a prediction made before the results were found.

You DO understand what post hoc means, don't you?
---------------------QUOTE-------------------


My hypothesis embraces "descent with modification" as well.  It just suggests that the modifications are constrained and directed.  So I could just as easily have made the same prediction.  So this prediction says nothing about the actual mechanism that produces these modifications.

Let me give you an example:
Lets say I have an hypothesis that says my house was built by aliens.  I examine my house and find that it contains many complex wall structures - including "rooms within rooms" (closets, bathrooms).  I then predict that my neighbor's house will be also contain rooms within rooms.  I examine his house and find that it does contain rooms within rooms.  I declare my hypothesis verified.

Now, you can see that the prediction had nothing to do with how my house came to contain rooms within rooms.  You could have virtually any hypothesis as to the mechanism - since the observations of rooms within rooms are not relevant to the cause.

So the post hoc part was that the prediction was made after complex genome structure was already discovered in Drosophila.  It says nothing about how genomes get complex in the first place and therefore says nothing about the mechanisms of evolution.
Posted by: oldmanintheskydidntdoit on Nov. 22 2007,09:47

Quote (Daniel Smith @ Nov. 22 2007,09:35)
My hypothesis embraces "descent with modification" as well.  It just suggests that the modifications are constrained and directed.
---------------------QUOTE-------------------


Unless your "hypothesis" defines how the modifications are directed it's simply worthless.

Daniel, what mechanism does your god use to poke at DNA? Magic sticks? Gluon storms? Quark Storms? Quantum probability manipulation? Zero-point energy?



---------------------QUOTE-------------------
My hypothesis embraces "descent with modification" as well.
---------------------QUOTE-------------------



So your contention is as follows, correct me if i'm wrong.

"Evolution is 100% correct, except mutations are not random but directed"

Is that it?
Posted by: Daniel Smith on Nov. 22 2007,09:59

Quote (JAM @ Nov. 21 2007,11:05)
Also, please convey my deepest sympathies to your wife on the loss of her mother, but let's realize that her death is not relevant to your theologically twisted claim that God is causing children to be poor and dying of malaria just to teach people like you and me a lesson.

Do you not realize that your position implicitly claims that you are much more important in God's sight than those millions of children? If God's goal was to teach you a lesson (because you are so special), wouldn't the lesson be far more effective if he caused YOUR OWN child (or wife or mother) to die of malaria?
---------------------QUOTE-------------------


Thank you for your sympathy.  I don't think that anyone on this planet is "better" than anyone else.  I certainly don't think that God's goal is to teach me a lesson through the suffering of others because I am "so special" (as you put it).  I think that (and have already given an example from close to home) that anyone can experience suffering and death.  We've all witnessed it.  It doesn't only happen in far away places.  I am of the opinion that those of us who are not currently suffering can learn form the suffering of others because it could very easily happen to us!.  It is not a matter of God killing children in a poverty stricken country so that the fortunate ones in a rich land can get an object lesson in life.  It's a matter of the fact that suffering and death are common to us all and we all can learn from it.  I have learned that death is not the end.  In fact, it is only the beginning. If you can grasp the concept of eternity, and see our place in it, suffering and death becomes less frightening.

I've also learned that suffering and death do not negate the fact that God is good and merciful.  Don't forget that (according to Christian theology) God himself is familiar with suffering and death.  The bible says that God has a special place in his heart for the poor and suffering (remember the parable of Lazarus and the rich man?), and that there is a special place for them in the kingdom of heaven.  It's those of us who haven't suffered, and who aren't poor that have more to worry about eternally.
Posted by: JAM on Nov. 22 2007,10:08

Quote (Daniel Smith @ Nov. 21 2007,22:44)
 
Quote (JAM @ Nov. 17 2007,10:30)
1) MET makes clear, testable predictions about the mechanisms by which the messy, fuzzy nature of our genome came about.
---------------------QUOTE-------------------


---------------------QUOTE-------------------


Daniel, please reread this and explain how your questions below are anything but straw men.
 

---------------------QUOTE-------------------
 

---------------------QUOTE-------------------
2) As for any other, similar phenomena were shown in the Drosophila bithorax complex FIVE YEARS AGO. Therefore, we predicted similar complexity in the human genome.
---------------------QUOTE-------------------

         

---------------------QUOTE-------------------
It doesn't address any of your predictions--it's just the same ol' post hoc spin to try and conceal the fact that you are dishonest, because you won't change or abandon your hypothesis when its predictions are shown to be false.
---------------------QUOTE-------------------


I hope you don't misinterpret this as "accusing" you of something, but...

How is the complexity of the human genome a prediction of your theory - when you are "predicting" it based on the complexity of the Drosophila genome?
---------------------QUOTE-------------------


It's predicting the phenomena based on common descent with modification.

How does your theory predict the NATURE of the complexity we observe in life--similar, but not identical components performing PARTIALLY-overlapping functions? Your failure to address this important point demonstrates why fondness for ID correlates so highly with ignorance about biology. It also illustrates the hypocrisy of abandoning analogies when they don't support your predetermined conclusion.

 

---------------------QUOTE-------------------
So both genomes are complex--how does that confirm or falsify the mechanisms of your theory?
---------------------QUOTE-------------------


It's about the mechanisms that generate the complexity (mutational mechanisms, natural selection and drift), not the mere existence of complexity. Do you realize how intellectually shallow your behavior is when you keep ranting about complexity, but run away from any discussions of its nature?
 

---------------------QUOTE-------------------
What specific mechanism of the MET is tested by this "prediction"?
---------------------QUOTE-------------------


Combinations of natural selection and drift, particularly the utter disgregard for efficiency (the antithesis of intelligent design) when the lack thereof doesn't affect fitness.
 

---------------------QUOTE-------------------
And how does this "prediction" differ from what you call, "post hoc spin"?
---------------------QUOTE-------------------


Because it was made pre, not post. Do you not comprehend this important distinction and its relevance to intellectual honesty?
Posted by: Daniel Smith on Nov. 22 2007,10:21

Quote (oldmanintheskydidntdoit @ Nov. 22 2007,09:47)
       
Quote (Daniel Smith @ Nov. 22 2007,09:35)
My hypothesis embraces "descent with modification" as well.  It just suggests that the modifications are constrained and directed.
---------------------QUOTE-------------------


Unless your "hypothesis" defines how the modifications are directed it's simply worthless.

Daniel, what mechanism does your god use to poke at DNA? Magic sticks? Gluon storms? Quark Storms? Quantum probability manipulation? Zero-point energy?
---------------------QUOTE-------------------


I don't know.  Based on recent readings, I'd say perhaps histone with intricately designed tails.      

---------------------QUOTE-------------------


         

---------------------QUOTE-------------------
My hypothesis embraces "descent with modification" as well.
---------------------QUOTE-------------------



So your contention is as follows, correct me if i'm wrong.

"Evolution is 100% correct, except mutations are not random but directed"

Is that it?
---------------------QUOTE-------------------


Correct, and natural selection has little to nothing to do with it.  Evolution is based on internal mechanisms, is constrained along certain paths (convergent), and is directed (as in prescribed).  The creation of new types is saltational (happens all at once), is most likely the result of chromosome reordering and is also prescribed in advance.  This view is consistent with the fossil record, (as Schindewolf so eloquently documented), observations in the wild (see Berg's Nomogenesis), and genetics (See virtually any recent paper describing the molecular workings within genomes) and has a workable, testable mechanism (See Davison's Semi-meiotic hypothesis).

In short, I don't see any evidence that random mutations coupled with natural selection can produce complex genomes and all the other elegant complexities within life.  I don't see a fossil record consistent with that, nor do I see that nature works that way in real time.  So, I have embraced instead the evolutionary theories that don't rely on that mechanism.
Posted by: oldmanintheskydidntdoit on Nov. 22 2007,10:26



---------------------QUOTE-------------------
In short, I don't see any evidence that random mutations coupled with natural selection can produce complex genomes and all the other elegant complexities within life.  I don't see a fossil record consistent with that, nor do I see that nature works that way in real time.  So, I have embraced instead the evolutionary theories that don't rely on that mechanism.
---------------------QUOTE-------------------



And your contention is that these "alternate theory's" are better supported by physical evidence then "standard evolution" ? Please list such evidence. If it exists.

Tell me Daniel, is there *any* evidence that random mutations coupled with natural selection *cannot* produce complex genomes and all the other elegant complexities within life?

Links please.
Posted by: oldmanintheskydidntdoit on Nov. 22 2007,10:32

Quote (Daniel Smith @ Nov. 22 2007,10:21)
I don't know.  Based on recent readings, I'd say perhaps histone with intricately designed tails.
---------------------QUOTE-------------------


Do you have any references?

I found this

< http://homepage.ntlworld.com/malcolmbowden/histones.htm >



---------------------QUOTE-------------------
These investigations into Cortical Inheritance were not popular because evolutionists seek a random mechanism that can bring about changes. This is why Mendel's work on peas was well known to the scientific world, but was deliberately ignored until the mechanism of random mutations was discovered.
Because Cortical Inheritance similarly demonstrated that the information that can bring about many changes in any organism is already within the cell, and that no chance mutation was involved, work on this subject was stopped.
---------------------QUOTE-------------------



Is this what you are using as a basis for your claim? Or something more mainstream?
Posted by: Daniel Smith on Nov. 22 2007,10:57

Quote (JAM @ Nov. 22 2007,10:08)
         
Quote (Daniel Smith @ Nov. 21 2007,22:44)
             
Quote (JAM @ Nov. 17 2007,10:30)
1) MET makes clear, testable predictions about the mechanisms by which the messy, fuzzy nature of our genome came about.
---------------------QUOTE-------------------


---------------------QUOTE-------------------


Daniel, please reread this and explain how your questions below are anything but straw men.
             

---------------------QUOTE-------------------
             

---------------------QUOTE-------------------
2) As for any other, similar phenomena were shown in the Drosophila bithorax complex FIVE YEARS AGO. Therefore, we predicted similar complexity in the human genome.
---------------------QUOTE-------------------

                     

---------------------QUOTE-------------------
It doesn't address any of your predictions--it's just the same ol' post hoc spin to try and conceal the fact that you are dishonest, because you won't change or abandon your hypothesis when its predictions are shown to be false.
---------------------QUOTE-------------------


I hope you don't misinterpret this as "accusing" you of something, but...

How is the complexity of the human genome a prediction of your theory - when you are "predicting" it based on the complexity of the Drosophila genome?
---------------------QUOTE-------------------


It's predicting the phenomena based on common descent with modification.

How does your theory predict the NATURE of the complexity we observe in life--similar, but not identical components performing PARTIALLY-overlapping functions?
---------------------QUOTE-------------------

If the mechanisms for the production of new types is the reordering of the chromosomal structure of existing types, then we'd expect to see modifications of old types within the new.  I fully expect (as I've stated in the past) to see similar components in organisms.  You seem to be arguing against de-novo creationism more than my stated views.          

---------------------QUOTE-------------------


             

---------------------QUOTE-------------------
So both genomes are complex--how does that confirm or falsify the mechanisms of your theory?
---------------------QUOTE-------------------


It's about the mechanisms that generate the complexity (mutational mechanisms, natural selection and drift), not the mere existence of complexity. Do you realize how intellectually shallow your behavior is when you keep ranting about complexity, but run away from any discussions of its nature?
---------------------QUOTE-------------------

I'm perfectly willing to discuss the nature of complexity.  I am wide open for your explanations as to how mutational mechanisms, natural selection and drift create such things.  Do you have any specific cases you want to discuss?  I'm trying to steer you toward the wealth of papers produced by the ENCODE consortium with the hope that maybe we can get specific and you can explain to me how mutational mechanisms, natural selection and drift produced the systems found within our genome.          

---------------------QUOTE-------------------

             

---------------------QUOTE-------------------
What specific mechanism of the MET is tested by this "prediction"?
---------------------QUOTE-------------------


Combinations of natural selection and drift, particularly the utter disgregard for efficiency (the antithesis of intelligent design) when the lack thereof doesn't affect fitness.
---------------------QUOTE-------------------

Is "the utter disgregard for efficiency" the mechanism tested in the experiment you cited earlier?
Because I seem to remember the selection criteria being based on the efficiency of infectivity:
   

---------------------QUOTE-------------------
Each generation consists of a maximum of ten arbitrarily chosen clones, whereby the clone with highest infectivity was selected to be the parent clone of the generation that followed.
"Can an Arbitrary Sequence Evolve Towards Acquiring a Biological Function" J Mol Evol (2003) 56:162–168 (emphasis mine)
---------------------QUOTE-------------------

       

---------------------QUOTE-------------------

             

---------------------QUOTE-------------------
And how does this "prediction" differ from what you call, "post hoc spin"?
---------------------QUOTE-------------------


Because it was made pre, not post. Do you not comprehend this important distinction and its relevance to intellectual honesty?
---------------------QUOTE-------------------


It was not made preDrosophila.  If you could show me where interwoven, sense, anti-sense, overlapping, and embedded "coding" was predicted before it was actually discovered, I'd call that a prediction.  This was made afterwards and is thus a postdiction.  All you've shown by this is that the same mechanism is responsible for both the Drosophila genome and the human genome.  That's it.  You have not made a prediction that tests a certain mechanism.
Posted by: oldmanintheskydidntdoit on Nov. 22 2007,11:01



---------------------QUOTE-------------------
you can explain to me how mutational mechanisms, natural selection and drift produced the systems found within our genome.
---------------------QUOTE-------------------



Don't you think you'd be better off going to university, studying these issues and them coming back with a firmer grasp of the issues? Rather then expecting people here to educate you in the basics?

I mean, if mainstream understanding is so utterly wrong then why don't you write a letter to Nature spelling out your case?

Or write a paper?

Or

Or

Or

Or

Or
Posted by: mitschlag on Nov. 22 2007,11:25

Quote (Daniel Smith @ Nov. 22 2007,10:57)
I'm trying to steer you toward the wealth of papers produced by the ENCODE consortium with the hope that maybe we can get specific and you can explain to me how mutational mechanisms, natural selection and drift produced the systems found within our genome.          
---------------------QUOTE-------------------


Steer away.



And please explain how the data (specific citations would be helpful) show that  "mutational mechanisms, natural selection and drift [could not have] produced the systems found within our genome."
Posted by: mitschlag on Nov. 22 2007,11:35

Quote (Daniel Smith @ Nov. 22 2007,10:21)
Correct, and natural selection has little to nothing to do with it.  Evolution is based on internal mechanisms, is constrained along certain paths (convergent), and is directed (as in prescribed).  The creation of new types is saltational (happens all at once), is most likely the result of chromosome reordering and is also prescribed in advance.  This view is consistent with the fossil record, (as Schindewolf so eloquently documented), observations in the wild (see Berg's Nomogenesis), and genetics (See virtually any recent paper describing the molecular workings within genomes) and has a workable, testable mechanism (See Davison's Semi-meiotic hypothesis).
---------------------QUOTE-------------------


And so, after two months, we're back here with the original claims, still supported only by references to "authorities."

Let's try one: Davison's semi-meiotic hypothesis that you say is testable.  How so?
Posted by: mitschlag on Nov. 22 2007,11:53

A quote from Schindewolf, by Daniel,  < here >:
 

---------------------QUOTE-------------------
"And these are by no means just isolated occurrences; these strange new forms are usually also represented by large numbers of individuals.  Nonetheless, there is no connecting link with the stock from which they derived.  The continuity of the other species gives us no reason to suspect interruptions in the deposition of the layers, or subsequent destruction of layers already deposited, which, furthermore, would be revealed by other geological criteria.  Nothing is missing here, and even drastic changes in living conditions are excluded, for the facies remain the same.

Further, when we see this situation repeated in all stratigraphic sequences of the same time period all over the world... we cannot resort to attributing this phenomenon to immigration of the new type from areas not yet investigated, where perhaps a gradual, slowly progressing evolution had taken place. What we have here must be primary discontinuities, natural evolutionary leaps, and not circumstantial accidents of discovery and gaps in the fossil record"

ibid. pp 104-105 (emphasis his)
---------------------QUOTE-------------------


How so?  (How does his belief make it so?)
Posted by: VMartin on Nov. 22 2007,12:52

mitschlag

       

---------------------QUOTE-------------------

And please explain how the data (specific citations would be helpful) show that  "mutational mechanisms, natural selection and drift [could not have] produced the systems found within our genome."

---------------------QUOTE-------------------



Natural selection doesn't play any any role in evolution, it removes only extremities. See the thread about "mimicry and aposematism" where I put many arguments refuting it.
("Mimicry" is beloved child of selectionists, you know).

I am afraid that neutral drift plays no role either. Do you know that in two separated population the migration of 1 or 2 individuals per one generation will prevent genetic differentiation caused by genetic drift? No matter if population has 1.000.000 members or 100.000.000 or 100 - gene flow due one migrant per one generation annules differentiation caused by"genetic drift" (This theoretical conclusion done by Sewall Wright and also by Fisher has been proved experimentally by Schamber and Muir 2001) .  Such a small migration ( 1 individual per one generation) easily escapes attention of any terrain biologist. Neverthenless an armchair neodarwinist will insist that genetic drift is a real evolutionary force even in cases where migration amongst populations is obvious (I mean birds, insects etc...)
Posted by: Arden Chatfield on Nov. 22 2007,12:54



---------------------QUOTE-------------------
Natural selection doesn't play any any role in evolution, it removes only extremities.
---------------------QUOTE-------------------





---------------------QUOTE-------------------
I am afraid that neutral drift plays no role either.
---------------------QUOTE-------------------



What does drive evolution, Marty?
Posted by: Arden Chatfield on Nov. 22 2007,13:00

Quote (VMartin @ Nov. 18 2007,23:50)
 
Quote (stevestory @ Nov. 18 2007,19:33)
               
Quote (Daniel Smith @ Nov. 18 2007,20:19)
I'm not sure what you mean by "when I look at transcription of that gene, will it be turned on".  Do you mean "will transcription of that gene be turned on", or will "the gene itself be turned on"?  
Because I think transcription of the gene will always be happening,  but as to when exactly the gene gets turned on, I have no clue.
---------------------QUOTE-------------------


Dan, we will send you some intro biology textbooks, if you want to learn about biology. You don't understand the basic terminology and concepts. If you're interested in learning, send a PM to Lou FCD or Albatrossity with a mailing address and we will send you some freshman-level textbooks to start with.
---------------------QUOTE-------------------


Maybe you can describe the mechanism of gradual homologization of repeated sequences in new species which everybody know about from "intro biolology text books" and which is different from the molecular drive? Otherwise I am afraid that you are as great expert in the evolutionary biology as Erasmus is an "expert" in the problem of aposematism at another thread.
---------------------QUOTE-------------------


What exactly are you an expert in, Marty?
Posted by: oldmanintheskydidntdoit on Nov. 22 2007,14:07

Quote (VMartin @ Nov. 22 2007,12:52)
mitschlag

       

---------------------QUOTE-------------------

And please explain how the data (specific citations would be helpful) show that  "mutational mechanisms, natural selection and drift [could not have] produced the systems found within our genome."

---------------------QUOTE-------------------



Natural selection doesn't play any any role in evolution, it removes only extremities. See the thread about "mimicry and aposematism" where I put many arguments refuting it.
("Mimicry" is beloved child of selectionists, you know).

I am afraid that neutral drift plays no role either. Do you know that in two separated population the migration of 1 or 2 individuals per one generation will prevent genetic differentiation caused by genetic drift? No matter if population has 1.000.000 members or 100.000.000 or 100 - gene flow due one migrant per one generation annules differentiation caused by"genetic drift" (This theoretical conclusion done by Sewall Wright and also by Fisher has been proved experimentally by Schamber and Muir 2001) .  Such a small migration ( 1 individual per one generation) easily escapes attention of any terrain biologist. Neverthenless an armchair neodarwinist will insist that genetic drift is a real evolutionary force even in cases where migration amongst populations is obvious (I mean birds, insects etc...)
---------------------QUOTE-------------------


Oh wise one. Tell us more of the things that do not drive evolution!

How about:

The distance to the nearest solar system
The number of atoms in a kilo of lead
The snapping point of a nylon rope 2mm in diameter.
Posted by: Richard Simons on Nov. 22 2007,16:36

Quote (Daniel Smith @ Nov. 22 2007,10:21)
Evolution is based on internal mechanisms, is constrained along certain paths (convergent), and is directed (as in prescribed).  The creation of new types is saltational (happens all at once), is most likely the result of chromosome reordering and is also prescribed in advance.  This view is consistent with the fossil record, (as Schindewolf so eloquently documented), observations in the wild (see Berg's Nomogenesis), and genetics (See virtually any recent paper describing the molecular workings within genomes) and has a workable, testable mechanism (See Davison's Semi-meiotic hypothesis).
---------------------QUOTE-------------------


But you have still not suggested any possible internal mechanism that could constrain evolution or direct it, or any mechanism by which the organism could foresee the future and know what adaptations it will need. As far as I can tell, Schindewolf and Davison are just as barren of ideas for this as you are. The semi-meiotic hypothesis has nothing to do with how the path of evolution is constrained or pre-ordained. Whether evolution procedes by saltation or continuously is a different issue from the mechanism for storing and imposing the constraints.
Posted by: oldmanintheskydidntdoit on Nov. 22 2007,17:22

Quote (Richard Simons @ Nov. 22 2007,16:36)
Quote (Daniel Smith @ Nov. 22 2007,10:21)
Evolution is based on internal mechanisms, is constrained along certain paths (convergent), and is directed (as in prescribed).  The creation of new types is saltational (happens all at once), is most likely the result of chromosome reordering and is also prescribed in advance.  This view is consistent with the fossil record, (as Schindewolf so eloquently documented), observations in the wild (see Berg's Nomogenesis), and genetics (See virtually any recent paper describing the molecular workings within genomes) and has a workable, testable mechanism (See Davison's Semi-meiotic hypothesis).
---------------------QUOTE-------------------


But you have still not suggested any possible internal mechanism that could constrain evolution or direct it, or any mechanism by which the organism could foresee the future and know what adaptations it will need. As far as I can tell, Schindewolf and Davison are just as barren of ideas for this as you are. The semi-meiotic hypothesis has nothing to do with how the path of evolution is constrained or pre-ordained. Whether evolution procedes by saltation or continuously is a different issue from the mechanism for storing and imposing the constraints.
---------------------QUOTE-------------------


In addition, the most significant issue (to my mind) - *why* - is left untouched.

To what purpose is this directed evolution being driven?

One might imagine that this same being/force/thing who is directing evolution over millions of years could direct cancer or AIDS not to be quite so nasty. If it wanted to. Which it evidently does not.

I believe Daniel has addressed this point previously (IIRC) by saying "I don't know". Do correct me if I'm wrong.

Seems pointless to talk about "directions" in evolution if you've no idea what direction that is. If no direction can be differentiated from any other direction, does not that say something to you Daniel?
Posted by: oldmanintheskydidntdoit on Nov. 22 2007,17:27

Quote (Daniel Smith @ Nov. 22 2007,10:21)
and has a workable, testable mechanism (See Davison's Semi-meiotic hypothesis).
---------------------QUOTE-------------------


Daniel,
Why, if it's testable, has it not been tested?

That good old Darwinian conspiracy theory? That the reason?

Can you describe, in your own words, an test that could be done to prove the issue one way or the other?
Posted by: JAM on Nov. 22 2007,18:21

Quote (Daniel Smith @ Nov. 22 2007,10:57)
If the mechanisms for the production of new types is the reordering of the chromosomal structure of existing types,
---------------------QUOTE-------------------


Daniel, AFAIK, there is ZERO evidence that the reordering of chunks of chromosomes by inversions, translocations, etc. had anything to do with the "production of new types," whatever the hell "types" means in this context. We know that heterozygosity for inversions and translocations is selected against (leading to rapid fixation), but there's not a lick of evidence that any of the inversions or translocations increased fitness when homozygous.

You grossly underestimate the complexity of the genome. Do you not see any irony in that?

 

---------------------QUOTE-------------------
... then we'd expect to see modifications of old types within the new.  I fully expect (as I've stated in the past) to see similar components in organisms.
---------------------QUOTE-------------------


Then you also would predict that they have functional significance. Where's your evidence?
     

---------------------QUOTE-------------------
You seem to be arguing against de-novo creationism more than my stated views.          
---------------------QUOTE-------------------


Daniel, you really need to reduce your misrepresentations of the views of others (as well as your far more egregious misrepresentations of the evidence itself) before accusing others.
     

---------------------QUOTE-------------------
     

---------------------QUOTE-------------------
     

---------------------QUOTE-------------------
So both genomes are complex--how does that confirm or falsify the mechanisms of your theory?
---------------------QUOTE-------------------


It's about the mechanisms that generate the complexity (mutational mechanisms, natural selection and drift), not the mere existence of complexity. Do you realize how intellectually shallow your behavior is when you keep ranting about complexity, but run away from any discussions of its nature?
---------------------QUOTE-------------------


I'm perfectly willing to discuss the nature of complexity.
---------------------QUOTE-------------------


ORLY?
1) Does your hypothesis predict that there will be anything that we humans could reasonably call a "hind-leg gene" based on analogies with our own intelligent designs?

2) Does your hypothesis predict that there will be anything that we humans could reasonably call a "tail gene" based on analogies with our own intelligent designs?

3) What do you mean by "histone activity"?

4) Why would you think that transcription of a particular gene is always happening? WTF do transcription factors do?

5) Wouldn't an intelligent designer design genes so that their transcription was turned on ONLY when (and where) the presence of the gene product is necessary?

6) an you find a single instance of a scientist referring to the design of endocytic (intracellular plumbing) pathways?

7) Explain the intelligence in the design of endocytic pathways, particularly their superiority to more conventional plumbing, as observed from the very same designer in our very own bodies. Be sure to explain the rationale behind the choice of so many similar, closely-related components with partially-overlapping (neither separate nor redundant) pathways.

8) According to your hypothesis, how many human genes won't have a mouse ortholog and vice versa?

   

---------------------QUOTE-------------------
D: ...I have no idea.  My hypothesis doesn't really work that way.  What I mean is; since I view each of the multitude of evolutionary events between mouse and man as saltational, there's no way to predict the number of orthologs.

J: So, in your hypothesis, saltational events have nothing whatsoever to do with new genes and proteins?

D: They do, but only the necessary genes are retained, while others are reordered.  What's retained is retained.

J: And what's lost/discarded is lost/discarded. So what's the ratio of the two classes after a typical saltational event?
---------------------QUOTE-------------------



Get busy, Dan. ALL of these questions relate DIRECTLY to the NATURE of the complexity you claim to be so convincing, yet you've dodged them.
   

---------------------QUOTE-------------------
I am wide open for your explanations as to how mutational mechanisms, natural selection and drift create such things.  Do you have any specific cases you want to discuss?
---------------------QUOTE-------------------


See above.
   

---------------------QUOTE-------------------
I'm trying to steer you toward the wealth of papers produced by the ENCODE consortium with the hope that maybe we can get specific and you can explain to me how mutational mechanisms, natural selection and drift produced the systems found within our genome.            
---------------------QUOTE-------------------


The ENCODE data are pretty nonspecific so far.
 

---------------------QUOTE-------------------
 

---------------------QUOTE-------------------
 

---------------------QUOTE-------------------
What specific mechanism of the MET is tested by this "prediction"?
---------------------QUOTE-------------------


Combinations of natural selection and drift, particularly the utter disgregard for efficiency (the antithesis of intelligent design) when the lack thereof doesn't affect fitness.
---------------------QUOTE-------------------

Is "the utter disgregard for efficiency" the mechanism tested in the experiment you cited earlier?
Because I seem to remember the selection criteria being based on the efficiency of infectivity:
           

---------------------QUOTE-------------------
Each generation consists of a maximum of ten arbitrarily chosen clones, whereby the clone with highest infectivity was selected to be the parent clone of the generation that followed.
"Can an Arbitrary Sequence Evolve Towards Acquiring a Biological Function" J Mol Evol (2003) 56:162–168 (emphasis mine)
---------------------QUOTE-------------------

 
---------------------QUOTE-------------------


Yes, Dan. Reread the sentence you are pretending to challenge. See the word "drift"? What does it mean? The paper I sent you was about the power of selection to produce function from a random sequence.
   

---------------------QUOTE-------------------
   

---------------------QUOTE-------------------
   

---------------------QUOTE-------------------
And how does this "prediction" differ from what you call, "post hoc spin"?
---------------------QUOTE-------------------


Because it was made pre, not post. Do you not comprehend this important distinction and its relevance to intellectual honesty?
---------------------QUOTE-------------------


It was not made preDrosophila.
---------------------QUOTE-------------------


Why did Rob and Ed choose to do what they did in Drosophila, then, if they weren't testing a hypothesis? What do you hypothesize that the intragenic RNAs code for?

Do you see your hypocrisy here? Your IDers claim to have made all these predictions, but are afraid to invest time, effort and money to test any of them, while when biologists invest time, effort, and money to test a prediction, and you deny, from a position of aggressive, utter ignorance, that they weren't testing a hypothesis. Sheesh.
 

---------------------QUOTE-------------------
If you could show me where interwoven, sense, anti-sense, overlapping, and embedded "coding" was predicted before it was actually discovered, I'd call that a prediction.  This was made afterwards and is thus a postdiction.  All you've shown by this is that the same mechanism is responsible for both the Drosophila genome and the human genome.
---------------------QUOTE-------------------


No, I haven't. You are so far from understanding the data that it isn't even funny.
 

---------------------QUOTE-------------------
 That's it.  You have not made a prediction that tests a certain mechanism.
---------------------QUOTE-------------------


They predicted a certain mechanism, and AFAIK, their data are consistent with it. That mechanism isn't a part of your hypothesis nor your ridiculously vague predictions.
Posted by: VMartin on Nov. 23 2007,12:16

Neodarwinists here didn't answer my questions. The problem of homologization of repeated sequences in new species hasn't been addressed yet. The problem of annulation of "genetic drift"  due gene flow (or migration) hasn't been answered either.

But folks here still insist  that John Davison's and Daniel's concept is wrong and they are right.

Even if there is an estimation that 90% - 98% of speciation is connected with the change of karyotype (WHITE 1978). Some biologists think that mutation of chromosomes play the key role in speciation (Jaroslav  Flegr,  Department of Parasitology and Hydrobiology, Charles University, Prague, Czech Republic: Evolutionary biology 2006, page 401 -  in Czech.)
Posted by: Arden Chatfield on Nov. 23 2007,12:40

An article in Czech. Thanks a bunch, Marty. I'm sure it'll prove all the points you don't make.

So, since the Stalinist Darwinismus is so bad, what does cause variation and change of karyotype, Marty?

And what are you an expert in?
Posted by: JAM on Nov. 23 2007,13:02

Quote (VMartin @ Nov. 18 2007,12:47)
JAM  

---------------------QUOTE-------------------

So if one is intelligently designing a spacing mechanism, why in heaven's name (literally) would one use tandem repeats, which expand and contract (via recombination) at ridiculously high frequencies? Wouldn't unique sequence be the far more intelligent choice?

---------------------QUOTE-------------------



As a layman I dont know what you and Daniel are meaning by "tandem repeats". Are those repeats  "tandem duplication" or pure "repeated sequences"?
---------------------QUOTE-------------------


It's a purely descriptive term. It simply means that the repeats read in the same direction, in contrast to inverted repeats, in which they read in opposite directions.
 

---------------------QUOTE-------------------
In the second case I don't see how how the difference in the structure of repeated sequences between different species proves Daniel theory by saltus as wrong. It may  have been induced by some unknown mechanism during John Davison's chromosome rearrangements, no?
---------------------QUOTE-------------------


We can't distinguish between your alternatives, because we know that tandem repeats expand and contract at very high frequencies, IN REAL TIME, by unequal crossing-over during both mitosis and meiosis. IOW, tandem repeats aren't very stable, so it would be stupid to employ them as spacers if one is designing a genome.
Posted by: Henry J on Nov. 23 2007,13:20

Re "The problem of annulation of "genetic drift" due gene flow (or migration) hasn't been answered either."

What problem?

Of course interbreeding populations are going to eventually drift the same way. Isn't that what the current theory says?

Re "The problem of homologization of repeated sequences in new species hasn't been addressed yet."

Is that referring to a chromosome containing several identical copies of some sequence? I thought a single duplication type mutation event could cause that. Unless you're referring to something else.

Henry
Posted by: Daniel Smith on Nov. 23 2007,13:41

Quote (mitschlag @ Nov. 22 2007,11:53)
A quote from Schindewolf, by Daniel,  < here >:
     

---------------------QUOTE-------------------
"And these are by no means just isolated occurrences; these strange new forms are usually also represented by large numbers of individuals.  Nonetheless, there is no connecting link with the stock from which they derived.  The continuity of the other species gives us no reason to suspect interruptions in the deposition of the layers, or subsequent destruction of layers already deposited, which, furthermore, would be revealed by other geological criteria.  Nothing is missing here, and even drastic changes in living conditions are excluded, for the facies remain the same.

Further, when we see this situation repeated in all stratigraphic sequences of the same time period all over the world... we cannot resort to attributing this phenomenon to immigration of the new type from areas not yet investigated, where perhaps a gradual, slowly progressing evolution had taken place. What we have here must be primary discontinuities, natural evolutionary leaps, and not circumstantial accidents of discovery and gaps in the fossil record"

ibid. pp 104-105 (emphasis his)
---------------------QUOTE-------------------


How so?  (How does his belief make it so?)
---------------------QUOTE-------------------


Schindewolf based his theory on some of the most abundant fossils that appear in the fossil record - cephalopods and stony corals.  These fossils are so abundant they are used as index fossils.  He extensively documented the changes within lineages among these organisms.  He came to his conclusions based on this evidence.  His belief has nothing to do with it.  

So when he says something like this (from your quote above (emphasis mine)):
"The continuity of the other species gives us no reason to suspect interruptions in the deposition of the layers, or subsequent destruction of layers already deposited, which, furthermore, would be revealed by other geological criteria. Nothing is missing here, and even drastic changes in living conditions are excluded, for the facies remain the same."
... he's making a case for the continuity of the fossil record within which these "leaps" between types are found.

Again, it has nothing whatsoever to do with "belief", it is an observation - made by one of Europe's leading Paleontologists.
Posted by: Daniel Smith on Nov. 23 2007,13:47

Quote (JAM @ Nov. 22 2007,18:21)
...

1) Does your hypothesis predict that there will be anything that we humans could reasonably call a "hind-leg gene" based on analogies with our own intelligent designs?

2) Does your hypothesis predict that there will be anything that we humans could reasonably call a "tail gene" based on analogies with our own intelligent designs?

3) What do you mean by "histone activity"?

4) Why would you think that transcription of a particular gene is always happening? WTF do transcription factors do?

5) Wouldn't an intelligent designer design genes so that their transcription was turned on ONLY when (and where) the presence of the gene product is necessary?

6) an you find a single instance of a scientist referring to the design of endocytic (intracellular plumbing) pathways?

7) Explain the intelligence in the design of endocytic pathways, particularly their superiority to more conventional plumbing, as observed from the very same designer in our very own bodies. Be sure to explain the rationale behind the choice of so many similar, closely-related components with partially-overlapping (neither separate nor redundant) pathways.

8) According to your hypothesis, how many human genes won't have a mouse ortholog and vice versa?
---------------------QUOTE-------------------


I'll do my best to answer your questions if you'll do your best to answer this question:
In the human genome, what percentage of genomic sequence would you predict is likely to be transcribed as nuclear primary transcripts?

I think it's only fair that you put your hypothesis on the line as well.  Besides, I'd be interested to know what your answer is.  (No one else has been willing to touch it!)
Posted by: Daniel Smith on Nov. 23 2007,14:29

Quote (oldmanintheskydidntdoit @ Nov. 22 2007,10:26)
     

---------------------QUOTE-------------------
In short, I don't see any evidence that random mutations coupled with natural selection can produce complex genomes and all the other elegant complexities within life.  I don't see a fossil record consistent with that, nor do I see that nature works that way in real time.  So, I have embraced instead the evolutionary theories that don't rely on that mechanism.
---------------------QUOTE-------------------



And your contention is that these "alternate theory's" are better supported by physical evidence then "standard evolution" ? Please list such evidence. If it exists.

---------------------QUOTE-------------------


OK.

Among Cephalopods (from Schindewolf):
1. The "explosion" of Nautiloid types in the lower Ordovician.
2. The  "explosion" of the Goniatitacea in the lower Carboniferous.
3. The  "explosion" of the Ammonitacea in the lower Carboniferous.

Convergent evolution (from Schindewolf and Berg):
1. Multiple instances among marsupial and placental mammals - most notably the wolf.
2. Spermatozoa and parasitic flagellates.
3. Among insects.
4. Between vertebrates and invertebrates.
5. Among amphioxus, lampreys and fishes.
6. Between dinosaurs, crocodiles and birds.
7. Among theromorpha.
8. Between lemurs and apes.
9. Among the ratitae or "keel-less birds
10. Between monocotyledons and dicotyledons.

That's a small portion of the evidence brought forth in the two books I've read.  The list goes on and on, but I'm not going to list it all here - since the books are available.
   

---------------------QUOTE-------------------

Tell me Daniel, is there *any* evidence that random mutations coupled with natural selection *cannot* produce complex genomes and all the other elegant complexities within life?

Links please.
---------------------QUOTE-------------------


Since almost anything is possible, I don't see how anyone can prove that negative.  I would say though that the lack of experimental evidence that random mutations coupled with natural selection can produce complex genomes and all the other elegant complexities within life, is a strong case against such a mechanism.
Posted by: mitschlag on Nov. 23 2007,16:44

Quote (Daniel Smith @ Nov. 23 2007,13:41)
Schindewolf based his theory on some of the most abundant fossils that appear in the fossil record - cephalopods and stony corals.  These fossils are so abundant they are used as index fossils.  He extensively documented the changes within lineages among these organisms.  He came to his conclusions based on this evidence.  His belief has nothing to do with it.  

So when he says something like this (from your quote above (emphasis mine)):
"The continuity of the other species gives us no reason to suspect interruptions in the deposition of the layers, or subsequent destruction of layers already deposited, which, furthermore, would be revealed by other geological criteria. Nothing is missing here, and even drastic changes in living conditions are excluded, for the facies remain the same."
... he's making a case for the continuity of the fossil record within which these "leaps" between types are found.

Again, it has nothing whatsoever to do with "belief", it is an observation - made by one of Europe's leading Paleontologists.
---------------------QUOTE-------------------


Schindewolf's theory and conclusions are not equivalent to observation or evidence.  Theory and conclusions may or may not be based on evidence.  If you can't distinguish fundamental categories, you'll continue to be confused.  And your arguments will be futile.

Appeals to authority are also futile: Schindewolf's eminence in paleontology is long gone and was limited to the special circumstances existing at the time (50 years ago!) in German academia.  Outside of Germany, his theory had no traction and it is now a minor footnote in the history of paleontology.
Posted by: Assassinator on Nov. 23 2007,16:46

Have you got any idea how long those "explosions" took?
Furthermore, convergent evolution isn't a piece of evidence for directed evolution. It's simply an unsupported interpretation of it. I'll simply quote the Wiki about convergent evolution:
[quote]In evolutionary biology, convergent evolution is the process whereby organisms not closely related (not monophyletic), independently evolve similar traits as a result of having to adapt to similar environments or ecological niches[1]. It is the opposite of divergent evolution, where related species evolve different traits.[/
Posted by: oldmanintheskydidntdoit on Nov. 23 2007,17:49

Quote (Daniel Smith @ Nov. 23 2007,14:29)
I would say though that the lack of experimental evidence that random mutations coupled with natural selection can produce complex genomes and all the other elegant complexities within life, is a strong case against such a mechanism.
---------------------QUOTE-------------------


Obviously you have to discount the main body of experimental evidence that does support the idea that random mutations coupled with natural selection can produce complex genomes and all the other elegant complexities within life.

Namely every living thing on the planet. Of course, that's presupposing the conclusion. So lets skip that.

 

---------------------QUOTE-------------------
the lack of experimental evidence that random mutations coupled with natural selection can produce complex genomes
---------------------QUOTE-------------------


Would you also hold that  random mutations coupled with natural selection cannot produce simple genomes?
 

---------------------QUOTE-------------------
all the other elegant complexities within life
---------------------QUOTE-------------------


These words mean nothing. Are worn out knees elegant? Please define elegant complexities so that it means something tangible. Do you think that what initially appears to us to be inelegant, will on further examination (possibly from a ID point of view) turn out to be elegant after all? Otherwise it seems to me a single example of "inelegant" design falsifies your theory.
 

---------------------QUOTE-------------------
is a strong case against such a mechanism.
---------------------QUOTE-------------------


Is a strong case? Not a watertight case? Not 100% proof? Daniel, for a moment take the position of the other side in this argument. Now argue against your own case for a moment. Expand further on this "strong" case, and explain why it's not definitive proof.

And lastly, please define "explosion" as already requested, and put some numbers on those
 

---------------------QUOTE-------------------
1. The "explosion" of Nautiloid types in the lower Ordovician.
---------------------QUOTE-------------------


Wikipedia notes
 

---------------------QUOTE-------------------
Nautiloids remained at the height of their range of adaptations and variety of forms throughout the Ordovician, Silurian, and Devonian periods, with various straight, curved and coiled shell forms coexisting at the same time. Several of the early orders became extinct over that interval, but others rose to prominence.

Nautiloids began to decline in the Devonian, perhaps due to competition with their descendants and relatives the Ammonoids and Coleoids, with only the Nautilida holding their own (and indeed increasing in diversity). Their shells became increasingly tightly coiled, while both numbers and variety of non-Nautilid species continued to decrease throughout the Carboniferous and Permian.
---------------------QUOTE-------------------



At what point did this "explosion" take place exactly, what caused it and why don't you go and edit the wikipedia article to reflect that?
Posted by: Daniel Smith on Nov. 24 2007,11:13

Quote (oldmanintheskydidntdoit @ Nov. 23 2007,17:49)
   

---------------------QUOTE-------------------
all the other elegant complexities within life
---------------------QUOTE-------------------


These words mean nothing. Are worn out knees elegant? Please define elegant complexities so that it means something tangible. Do you think that what initially appears to us to be inelegant, will on further examination (possibly from a ID point of view) turn out to be elegant after all? Otherwise it seems to me a single example of "inelegant" design falsifies your theory.
---------------------QUOTE-------------------


The phrase "all the other elegant complexities within life" is - yours!  I just copied and pasted it directly from your original question.
< Permalink >
When you're done digesting the delicious irony of the situation, get back to me!
Posted by: Daniel Smith on Nov. 24 2007,11:19

Quote (mitschlag @ Nov. 23 2007,16:44)
 
Quote (Daniel Smith @ Nov. 23 2007,13:41)
Schindewolf based his theory on some of the most abundant fossils that appear in the fossil record - cephalopods and stony corals.  These fossils are so abundant they are used as index fossils.  He extensively documented the changes within lineages among these organisms.  He came to his conclusions based on this evidence.  His belief has nothing to do with it.  

So when he says something like this (from your quote above (emphasis mine)):
"The continuity of the other species gives us no reason to suspect interruptions in the deposition of the layers, or subsequent destruction of layers already deposited, which, furthermore, would be revealed by other geological criteria. Nothing is missing here, and even drastic changes in living conditions are excluded, for the facies remain the same."
... he's making a case for the continuity of the fossil record within which these "leaps" between types are found.

Again, it has nothing whatsoever to do with "belief", it is an observation - made by one of Europe's leading Paleontologists.
---------------------QUOTE-------------------


Schindewolf's theory and conclusions are not equivalent to observation or evidence.  Theory and conclusions may or may not be based on evidence.  If you can't distinguish fundamental categories, you'll continue to be confused.  And your arguments will be futile.

Appeals to authority are also futile: Schindewolf's eminence in paleontology is long gone and was limited to the special circumstances existing at the time (50 years ago!) in German academia.  Outside of Germany, his theory had no traction and it is now a minor footnote in the history of paleontology.
---------------------QUOTE-------------------


OK.  Because you said so, I'll abandon my affinity for Schindewolf's theory.  This in spite of the fact that you have provided no evidence or observations to contradict it.  

I am abandoning it because you said, "Appeals to authority are also futile".  

That convinced me!
Posted by: Daniel Smith on Nov. 24 2007,11:25

Quote (Assassinator @ Nov. 23 2007,16:46)
Have you got any idea how long those "explosions" took?
Furthermore, convergent evolution isn't a piece of evidence for directed evolution. It's simply an unsupported interpretation of it. I'll simply quote the Wiki about convergent evolution:
 

---------------------QUOTE-------------------
In evolutionary biology, convergent evolution is the process whereby organisms not closely related (not monophyletic), independently evolve similar traits as a result of having to adapt to similar environments or ecological niches[1]. It is the opposite of divergent evolution, where related species evolve different traits.
---------------------QUOTE-------------------


---------------------QUOTE-------------------


OK, via Occam's razor, the simplest explanation for convergent evolution is that evolution is constrained by laws down similar paths.  Postulating that random mutations coupled with natural selection can produce the same happy accident numerous times is a much more complicated explanation.
Posted by: Assassinator on Nov. 24 2007,11:53

It ain't no happy accident! Natural selection and bio-chemistry aren't random. Besides, simple doesn't mean correct.
Posted by: IanBrown_101 on Nov. 24 2007,12:28



---------------------QUOTE-------------------
happy accident numerous times is a much more complicated explanation.
---------------------QUOTE-------------------



This shows you have absolutely o idea what you are talking about.

Swing and a miss....
Posted by: mitschlag on Nov. 24 2007,12:51

Quote (Daniel Smith @ Nov. 24 2007,11:19)
OK.  Because you said so, I'll abandon my affinity for Schindewolf's theory.  This in spite of the fact that you have provided no evidence or observations to contradict it.  

I am abandoning it because you said, "Appeals to authority are also futile".  

That convinced me!
---------------------QUOTE-------------------


This charming outburst is not reasonable or logical, so I take it as sarcasm.

I intended no offense.  My admittedly sharp remark about argumentum ad verecundiam was directed at your statement:  "Again, it has nothing whatsoever to do with "belief", it is an observation - made by one of Europe's leading Paleontologists."

Do you not agree that it's the quality of Schindewolf's argument that is at issue, not his credentials?

That he was an expert in the paleontology of cephalopods and stony corals is not at issue.  His work in those areas may well have stood the test of time.  The current issue is, I believe, whether his ideas about saltation and orthogenesis are valid.

Since Schindewolf's ideas about saltation and orthogenesis are interpretations of the evidence, they can only be challenged by alternative interpretations, as provided in the modern synthesis.  

But let's assume for fun that saltation and orthogenesis are valid.  Is there any compelling reason to assert that these supposed mechanisms are not "natural"?  Is there any compelling reason to think that a supernatural agency had to bring them about?

The same goes for Davison's semi-meiosis, by the way.
Posted by: Alan Fox on Nov. 24 2007,12:59

Quote (Daniel Smith @ Nov. 24 2007,06:13)
   
Quote (oldmanintheskydidntdoit @ Nov. 23 2007,17:49)
       

---------------------QUOTE-------------------
all the other elegant complexities within life
---------------------QUOTE-------------------


These words mean nothing. Are worn out knees elegant? Please define elegant complexities so that it means something tangible. Do you think that what initially appears to us to be inelegant, will on further examination (possibly from a ID point of view) turn out to be elegant after all? Otherwise it seems to me a single example of "inelegant" design falsifies your theory.
---------------------QUOTE-------------------


The phrase "all the other elegant complexities within life" is - yours!  I just copied and pasted it directly from your original question.
< Permalink >
When you're done digesting the delicious irony of the situation, get back to me!
---------------------QUOTE-------------------


[delurks]

Well played, Daniel!!! (Sorry, Oldman, but you gotta smile)

[/delurks]
Posted by: Reciprocating Bill on Nov. 24 2007,13:54

Quote (Daniel Smith @ Nov. 24 2007,12:13)
   
Quote (oldmanintheskydidntdoit @ Nov. 23 2007,17:49)
         

---------------------QUOTE-------------------
all the other elegant complexities within life
---------------------QUOTE-------------------


These words mean nothing. Are worn out knees elegant? Please define elegant complexities so that it means something tangible. Do you think that what initially appears to us to be inelegant, will on further examination (possibly from a ID point of view) turn out to be elegant after all? Otherwise it seems to me a single example of "inelegant" design falsifies your theory.
---------------------QUOTE-------------------


The phrase "all the other elegant complexities within life" is - yours!  I just copied and pasted it directly from your original question.
< Permalink >
When you're done digesting the delicious irony of the situation, get back to me!
---------------------QUOTE-------------------


Just lurking here, Daniel. But you better look a bit harder at the oldman post you've linked to. His use of this phrase was in implicit quotation of YOU:



---------------------QUOTE-------------------
In short, I don't see any evidence that random mutations coupled with natural selection can produce complex genomes and all the other elegant complexities within life.  I don't see a fossil record consistent with that, nor do I see that nature works that way in real time.  So, I have embraced instead the evolutionary theories that don't rely on that mechanism.
---------------------QUOTE-------------------



Found within the block of quoted text found within Oldman's post.

One man's irony is another man's crow, Daniel.
Posted by: oldmanintheskydidntdoit on Nov. 24 2007,14:07

Quote (Daniel Smith @ Nov. 22 2007,10:21)
In short, I don't see any evidence that random mutations coupled with natural selection can produce complex genomes and all the other elegant complexities within life.  I don't see a fossil record consistent with that, nor do I see that nature works that way in real time.  So, I have embraced instead the evolutionary theories that don't rely on that mechanism.
---------------------QUOTE-------------------


< Permalink >
 

---------------------QUOTE-------------------
When you're done digesting the delicious irony of the situation, get back to me!
---------------------QUOTE-------------------


Digested.
Posted by: oldmanintheskydidntdoit on Nov. 24 2007,14:08

Quote (Reciprocating Bill @ Nov. 24 2007,13:54)
Quote (Daniel Smith @ Nov. 24 2007,12:13)
     
Quote (oldmanintheskydidntdoit @ Nov. 23 2007,17:49)
         

---------------------QUOTE-------------------
all the other elegant complexities within life
---------------------QUOTE-------------------


These words mean nothing. Are worn out knees elegant? Please define elegant complexities so that it means something tangible. Do you think that what initially appears to us to be inelegant, will on further examination (possibly from a ID point of view) turn out to be elegant after all? Otherwise it seems to me a single example of "inelegant" design falsifies your theory.
---------------------QUOTE-------------------


The phrase "all the other elegant complexities within life" is - yours!  I just copied and pasted it directly from your original question.
< Permalink >
When you're done digesting the delicious irony of the situation, get back to me!
---------------------QUOTE-------------------


Just lurking here, Daniel. But you better look a bit harder at the oldman post you've linked to. His use of this phrase was in implicit quotation of YOU:



---------------------QUOTE-------------------
In short, I don't see any evidence that random mutations coupled with natural selection can produce complex genomes and all the other elegant complexities within life.  I don't see a fossil record consistent with that, nor do I see that nature works that way in real time.  So, I have embraced instead the evolutionary theories that don't rely on that mechanism.
---------------------QUOTE-------------------



Found within the block of quoted text found within Oldman's post.

One man's irony is another man's crow, Daniel.
---------------------QUOTE-------------------


Indeed Sir, Indeed :)
Posted by: Reciprocating Bill on Nov. 24 2007,14:25

Daniel's original use of this phrase is found < here >.
Posted by: mitschlag on Nov. 24 2007,16:46

Quote (Daniel Smith @ Nov. 23 2007,14:29)
   

---------------------QUOTE-------------------

Tell me Daniel, is there *any* evidence that random mutations coupled with natural selection *cannot* produce complex genomes and all the other elegant complexities within life?

Links please.
---------------------QUOTE-------------------


Since almost anything is possible, I don't see how anyone can prove that negative.  I would say though that the lack of experimental evidence that random mutations coupled with natural selection can produce complex genomes and all the other elegant complexities within life, is a strong case against such a mechanism.
---------------------QUOTE-------------------


You were not asked to "prove a negative."  You were asked for evidence.

See also < here > where mitschlag asks for data:    

---------------------QUOTE-------------------
And please explain how the data (specific citations would be helpful) show that  "mutational mechanisms, natural selection and drift [could not have] produced the systems found within our genome."
---------------------QUOTE-------------------


You are not the first person to choose to answer the question you would like to answer instead of the question you were asked.  

Care to try again?
Posted by: Erasmus, FCD on Nov. 24 2007,19:45

The entire sociological aspect of the saltational theory has been neglected.  Daniel and VickyMartin and his heroes Berg and Schindewolf and Bateson etc fit quite neatly into a box that Gould has discussed extensively under the heading of formalism.  There is a certain logic that is a property of this school that Gould feels is not entirely discardable, but refers to the discussion about constraints from history or development that ensued after the paper I can't remember the name of now.  1970s or so I think.  

What is interesting is why this notion has stuck around, even in the halls of crankdom, and how it has done so.  the major theme as far as i can tell, following JAD and these guys around the interwebz, has been to construct a 'theory' that is empirically equivalent to the MET.  following this, the strategy is to raise obtuse and irrelevant objections to the MET, then use the argument from authority plus false dichotomy to attempt to build support for the crackpot theory.  frontloading is EXACTLY this argument.  How would one falsify such a beast?  Not from the first principles of the cough cough splutter ptoooowee 'Theory'.  NO sir, not at all, and this is the platform from which ad hoc and post hoc explanations are constructed.

There are no first principles from the formalist camp, except that there is 'some law' that evolution must follow.  Despite 150+ years of evidence, one would assume that all it would take would be one single meta-analysis to derive such relationships.  

and here is my FUNDAMENTAL law of evolution.  Take it to the bank Daniel.  This is as much of a law as you can get (Bob O'Hare I think this trumps your anarchist guide to ecology... for I place ecology as a subset of all living things.  Toodles!!!)



---------------------QUOTE-------------------
Shit Varies.  It Matters.  Sometimes.
---------------------QUOTE-------------------


Posted by: Richard Simons on Nov. 24 2007,20:11

Quote (Daniel Smith @ Nov. 24 2007,11:25)
OK, via Occam's razor, the simplest explanation for convergent evolution is that evolution is constrained by laws down similar paths.  Postulating that random mutations coupled with natural selection can produce the same happy accident numerous times is a much more complicated explanation.
---------------------QUOTE-------------------


No it isn't. See, I can produce unevidenced assertions just as well as you can.

Perhaps you would like to tell us what these laws are and how they specify the paths. The only way I can imagine you see it is that somewhere in the cells of primitive wolves, hyaenas and marsupial wolves (presumably in all of the cells, unless it somehow gets restricted to the eggs and/or sperm) there is a little instruction saying 'Your descendents shall become ever more dog-like'. I can't imagine how this is stored or implemented. Could you please elucidate?
Posted by: Erasmus, FCD on Nov. 24 2007,20:14

Richard you have very succintly pointed out how, at the bottom of the neo-creationist sciency sounding talk, it is still "POOF".

infinte wavelength energy and all that.  front loading in ways that we, due to our fallen nature contemporary ignorance and the ingenuity of the designer complexity of the genome, can't understand.
Posted by: Alan Fox on Nov. 25 2007,05:00

@ Oldman

Very sorry, my excuse being I haven't been following along very closely. I feel like < Abu Hassan > now.

@ Daniel

Thanks for making me look a prat :angry:
Posted by: oldmanintheskydidntdoit on Nov. 25 2007,05:17

Quote (Alan Fox @ Nov. 25 2007,05:00)
@ Oldman

Very sorry, my excuse being I haven't been following along very closely. I feel like < Abu Hassan > now.

@ Daniel

Thanks for making me look a prat :angry:
---------------------QUOTE-------------------


No problem whatsoever Alan.
Posted by: oldmanintheskydidntdoit on Nov. 25 2007,05:35

The most amusing aspect of this for me is it illustrates the level and quality of research that Daniel is capable of.

If you click the "all" button then every page in the thread is loaded at once. If I was going to crow over somebody's "mistake" I'd be certain to make sure I'd checked the "all" page to see where the first appearance of the "mistake" was. In this case, as RB points out, the original usage of the words was in the message from Daniel that I quoted! So no need to even search the entire thread. And yet it was missed.

Daniel, Daniel, Daniel. I think you've just blown your chance at tenure.  :D
Posted by: Daniel Smith on Nov. 25 2007,12:56

Quote (oldmanintheskydidntdoit @ Nov. 25 2007,05:35)
The most amusing aspect of this for me is it illustrates the level and quality of research that Daniel is capable of.

If you click the "all" button then every page in the thread is loaded at once. If I was going to crow over somebody's "mistake" I'd be certain to make sure I'd checked the "all" page to see where the first appearance of the "mistake" was. In this case, as RB points out, the original usage of the words was in the message from Daniel that I quoted! So no need to even search the entire thread. And yet it was missed.

Daniel, Daniel, Daniel. I think you've just blown your chance at tenure.  :D
---------------------QUOTE-------------------


I'm embarrassed now.  ???
Posted by: Daniel Smith on Nov. 25 2007,13:18

Quote (mitschlag @ Nov. 24 2007,12:51)
   
Quote (Daniel Smith @ Nov. 24 2007,11:19)
OK.  Because you said so, I'll abandon my affinity for Schindewolf's theory.  This in spite of the fact that you have provided no evidence or observations to contradict it.  

I am abandoning it because you said, "Appeals to authority are also futile".  

That convinced me!
---------------------QUOTE-------------------


This charming outburst is not reasonable or logical, so I take it as sarcasm.

I intended no offense.  My admittedly sharp remark about argumentum ad verecundiam was directed at your statement:  "Again, it has nothing whatsoever to do with "belief", it is an observation - made by one of Europe's leading Paleontologists."

Do you not agree that it's the quality of Schindewolf's argument that is at issue, not his credentials?

That he was an expert in the paleontology of cephalopods and stony corals is not at issue.  His work in those areas may well have stood the test of time.  The current issue is, I believe, whether his ideas about saltation and orthogenesis are valid.

Since Schindewolf's ideas about saltation and orthogenesis are interpretations of the evidence, they can only be challenged by alternative interpretations, as provided in the modern synthesis.  

But let's assume for fun that saltation and orthogenesis are valid.  Is there any compelling reason to assert that these supposed mechanisms are not "natural"?  Is there any compelling reason to think that a supernatural agency had to bring them about?

The same goes for Davison's semi-meiosis, by the way.
---------------------QUOTE-------------------


Actually Schindewolf saw these mechanisms as 100% natural - not supernatural in any way.

It's me who sees the supernatural mind behind it all.

It's a matter of perspective.  I approach the evidence from a theological perspective - something most of you have probably never done.  If you approach the evidence from a purely naturalist perspective - not allowing for the possibility of the supernatural - it forces you to seek purely natural explanations for everything.  Sometimes this works, sometimes it doesn't.  For instance, no one can give me a detailed theoretical pathway for the initial creation of even the simplest, most fundamental molecular machinery - protein synthesis - via a purely natural pathway.  Now maybe that's because we just don't know enough.  But there's also the possibility that it just can't be done.

As a believer, I expect to see intricate designs in life - because I believe life came from God.  I am not surprised to find overlapping, multi-directional coding within genomes - I fully expect such things.  I can't explain how such things came to be either - but I'm not surprised by them.

So what am I saying?  Am I suggesting we cancel all research, throw in the towel and just say "goddidit"?  Not at all.  I think we should delve into these mysteries and try to solve them.  No matter what perspective we begin from, there is still much to discover - a never ending (infinite) supply.  Some of us will see such marvels as technology of the highest order - a glimpse inside the mind of God if you will.  Others will see it as the product of natural causes.  Either way, the research should continue.
Posted by: Erasmus, FCD on Nov. 25 2007,14:31



---------------------QUOTE-------------------
I approach the evidence from a theological perspective - something most of you have probably never done.
---------------------QUOTE-------------------



speak for thyself, kemosabe.

minus all the breathless bits about design in life, etc (don't get me wrong, i love Ralph Waldo Emerson as much as anyone) I'm not sure there is too much to disagree with here.  THAT IS, as long as design is some meta-induction that you would conclude no matter what evidence you see (which is ultimately the question, no?) then you won't be led down the wrong track.

I think, personally and on a bellybutton gazing note, that there are some interesting nuts to crack at the root of the divide between the saltational notion and the evolutionary theory.

Operationally, however, you are in an intractable mess.  I'm open to the suggestion that it is the (oft)reductionist nature of scientific investigation that has muddied the water.  But in order to clear off the table, you need some testable first principles.  And I don't think I have seen any.  Perhaps I missed them.  

The business about 'interpretations' is a sunken road straight into the po-mo solipcist dungeon and it wouldn't behoove ANYONE to take that route.  See for example the FTK Thread.  

At the heart of that criticism is a valid (I think) objection:  induction is always a second or third order process and is always, IMO by definition, a valid (although often superfluous) criticism.  But if that is true, then you must have an operationally sound alternative.  And for my two cents, I don't see that happening here.
Posted by: Steverino on Nov. 25 2007,14:58

Daniel,

"...Now maybe that's because we just don't know enough.  But there's also the possibility that it just can't be done."

This is basis of your, ID's and Creationists argument. Boiled down it's the standard "God of the Gaps" argument.

When one gap is explained you abandon that point like rats leaving the sinking ship and move on to the next gap.  You (IDiots/Creationists) never admit that it was you that was wrong in your thinking.

It's disingenuous at best because no matter how much Science proves, there will always be a gap for you and yours to hide in.
Posted by: mitschlag on Nov. 25 2007,16:40

Quote (Daniel Smith @ Nov. 25 2007,13:18)
Actually Schindewolf saw these mechanisms as 100% natural - not supernatural in any way.

It's me who sees the supernatural mind behind it all.
---------------------QUOTE-------------------


Thank you, Daniel.  Your honesty is exemplary.

And for me, this chapter in the unending conflict between science and religion closes on a welcome conciliatory note.
Posted by: JAM on Nov. 26 2007,13:18

Quote (Daniel Smith @ Nov. 23 2007,13:47)
 
Quote (JAM @ Nov. 22 2007,18:21)
...

1) Does your hypothesis predict that there will be anything that we humans could reasonably call a "hind-leg gene" based on analogies with our own intelligent designs?

2) Does your hypothesis predict that there will be anything that we humans could reasonably call a "tail gene" based on analogies with our own intelligent designs?

3) What do you mean by "histone activity"?

4) Why would you think that transcription of a particular gene is always happening? WTF do transcription factors do?

5) Wouldn't an intelligent designer design genes so that their transcription was turned on ONLY when (and where) the presence of the gene product is necessary?

6) an you find a single instance of a scientist referring to the design of endocytic (intracellular plumbing) pathways?

7) Explain the intelligence in the design of endocytic pathways, particularly their superiority to more conventional plumbing, as observed from the very same designer in our very own bodies. Be sure to explain the rationale behind the choice of so many similar, closely-related components with partially-overlapping (neither separate nor redundant) pathways.

8) According to your hypothesis, how many human genes won't have a mouse ortholog and vice versa?
---------------------QUOTE-------------------


I'll do my best to answer your questions if you'll do your best to answer this question:
---------------------QUOTE-------------------


I have trouble buying that, as those are questions that I have already asked you, but what the hey:
 

---------------------QUOTE-------------------
In the human genome, what percentage of genomic sequence would you predict is likely to be transcribed as nuclear primary transcripts?
---------------------QUOTE-------------------


Among unique sequence, most (70-90%). Among repeats, less, and I'd predict that the probability of transcription increases with proximity to genes for both repeats and nonrepeats.

Of course, you aren't being upfront about your unsupported belief that transcription implies function. I predict that no function will be found for the vast majority of those transcripts. The next largest class will be those in which the transcript has no function, but the transcription does (can you grasp this important distinction?). Again, the probability that a transcript or transcription serves some function will be highly correlated with proximity to genes.
Posted by: Assassinator on Nov. 26 2007,13:22



---------------------QUOTE-------------------
Among unique sequence, most (70-90%). Among repeats, less, and I'd predict that the probability of transcription increases with proximity to genes for both repeats and nonrepeats.
---------------------QUOTE-------------------


At biology class we calculated that about 1.7% of the whole human genome is for coding. Is that correct?
Posted by: Daniel Smith on Nov. 26 2007,13:56

Quote (Steverino @ Nov. 25 2007,14:58)
Daniel,

"...Now maybe that's because we just don't know enough.  But there's also the possibility that it just can't be done."

This is basis of your, ID's and Creationists argument. Boiled down it's the standard "God of the Gaps" argument.

When one gap is explained you abandon that point like rats leaving the sinking ship and move on to the next gap.  You (IDiots/Creationists) never admit that it was you that was wrong in your thinking.

It's disingenuous at best because no matter how much Science proves, there will always be a gap for you and yours to hide in.
---------------------QUOTE-------------------


I've already answered your "god of the gaps" objection once - don't you remember?
Let me just nutshell it for you:
Even though man can explain certain things, it doesn't mean they weren't designed.  I can explain many of the systems at work within my car.  Does that mean they weren't designed?
Posted by: oldmanintheskydidntdoit on Nov. 26 2007,16:02

Quote (Daniel Smith @ Nov. 26 2007,13:56)
Quote (Steverino @ Nov. 25 2007,14:58)
Daniel,

"...Now maybe that's because we just don't know enough.  But there's also the possibility that it just can't be done."

This is basis of your, ID's and Creationists argument. Boiled down it's the standard "God of the Gaps" argument.

When one gap is explained you abandon that point like rats leaving the sinking ship and move on to the next gap.  You (IDiots/Creationists) never admit that it was you that was wrong in your thinking.

It's disingenuous at best because no matter how much Science proves, there will always be a gap for you and yours to hide in.
---------------------QUOTE-------------------


I've already answered your "god of the gaps" objection once - don't you remember?
Let me just nutshell it for you:
Even though man can explain certain things, it doesn't mean they weren't designed.  I can explain many of the systems at work within my car.  Does that mean they weren't designed?
---------------------QUOTE-------------------


Err. They all were designed? Different example perhaps?
Posted by: JAM on Nov. 26 2007,16:07

Quote (Assassinator @ Nov. 26 2007,13:22)


---------------------QUOTE-------------------
Among unique sequence, most (70-90%). Among repeats, less, and I'd predict that the probability of transcription increases with proximity to genes for both repeats and nonrepeats.
---------------------QUOTE-------------------


At biology class we calculated that about 1.7% of the whole human genome is for coding. Is that correct?
---------------------QUOTE-------------------


Yes, but that would be a minimum.

Note that Daniel is making a mammoth error in assuming that transcription implies function.

I think that he is beginning to realize that, too.
Posted by: Steverino on Nov. 26 2007,16:36

Quote (Daniel Smith @ Nov. 26 2007,13:56)
 
Quote (Steverino @ Nov. 25 2007,14:58)
Daniel,

"...Now maybe that's because we just don't know enough.  But there's also the possibility that it just can't be done."

This is basis of your, ID's and Creationists argument. Boiled down it's the standard "God of the Gaps" argument.

When one gap is explained you abandon that point like rats leaving the sinking ship and move on to the next gap.  You (IDiots/Creationists) never admit that it was you that was wrong in your thinking.

It's disingenuous at best because no matter how much Science proves, there will always be a gap for you and yours to hide in.
---------------------QUOTE-------------------


I've already answered your "god of the gaps" objection once - don't you remember?
Let me just nutshell it for you:
Even though man can explain certain things, it doesn't mean they weren't designed.  I can explain many of the systems at work within my car.  Does that mean they weren't designed?
---------------------QUOTE-------------------


"Let me just nutshell it for you:
Even though man can explain certain things, it doesn't mean they weren't designed...."


Now that argument is called "moving the goal posts".

So, at Dumbfvck U, DI/Creationist Institute of Higher Edumacation, everything is and was designed....until proven otherwise.

"...I can explain many of the systems at work within my car.  Does that mean they weren't designed?"

I'm gonna have to call a non sequitur the play.  Does your car reproduce?

Where is the proof that the appearance of design, proves design?
Posted by: Daniel Smith on Nov. 26 2007,19:15

Quote (JAM @ Nov. 19 2007,00:38)

Sit down and take a deep breath. Think, as a Christian, for a moment about what YOU are accusing me and the other scientists of doing here. YOU are accusing US of gross incompetence, and in direct contradiction of clear Biblical guidance, you have made this accusation on the basis of nothing but hearsay.

Put yourself in my shoes, Dan. I've spent most of my life doing biology, and you come along. Would you describe your claims as humble ones?

What sort of character makes grandiose claims without evidence, and then discounts the evidence?
---------------------QUOTE-------------------


These statements have been the cause of much reflection and trouble for me lately.  Am I really accusing you (and the other real scientists here) of something?  If so - what?  And what are my motives?

I think I've come to a bit of a realization here.  What I've realized is that my interest in biology is purely theological.  I look at the inner workings of life as a way to learn more about God.  I'm not interested in biology for biology's sake.  These are my motivations.

So from a theological perspective, when I look at the inner workings of the genome, I expect to find complexity and function.  It has nothing whatsoever to do with my knowledge of biology.  This is my realization.  I have no right to accuse anyone of anything - especially not someone who has devoted their life to the study of biology.  So for that - for that arrogance - I apologize.  I should have prefaced everything with "From my theological perspective...".  Then perhaps my arrogant points would have been seen in their true context.

I've been reading the ENCODE paper on < pseudogenes >.  This paper, and my reaction to it, clearly illustrate (for me) my motives.  The consensus position on pseudogenes seems to be that they are "dead" copies of once-active genes.  From a theological perspective, I can't believe that God would have "dead wood" in the genome, so I find myself shrugging off their conclusions and latching onto the few statements that hint at pseudogenes being more functional than previously thought.  Again, from a purely theological perspective, I'm expecting that pseudogenes will be found to be functional in some as-of-yet unseen way.  This expectation has nothing whatsoever to do with my knowledge of biology.  Neither do any of my predictions.  My knowledge is of God and his ways - not of science.

With that said, I must say this:  From a theological perspective, I do see much that encourages my beliefs when I look at biology.  I don't see any reason to abandon my core beliefs at all.  The recent discoveries of the inner workings of DNA, RNA, and their chromosomal packaging have me excited to see what scientists will discover next!  I feel encouraged in my beliefs by such things.  I feel in awe of the mind that (I believe) created such things.  I feel I am just that much closer to finding out what actually happened and I am trying to formulate a coherent picture in my mind.

So, my beliefs as to what happened are by no means set in stone.  I study biology as a way to learn what God did - a kind of bio-theology if you will.

So JAM, from the perspective of a life-long biologist, you predict that most of the genome will be found non-functional; and I - from a purely theological perspective - predict that most of the genome will be found to be functional.  We shall see who's right.

I hope this clears things up.
Posted by: Daniel Smith on Nov. 26 2007,19:20

Quote (Steverino @ Nov. 26 2007,16:36)
 
Quote (Daniel Smith @ Nov. 26 2007,13:56)
   
Quote (Steverino @ Nov. 25 2007,14:58)
Daniel,

"...Now maybe that's because we just don't know enough.  But there's also the possibility that it just can't be done."

This is basis of your, ID's and Creationists argument. Boiled down it's the standard "God of the Gaps" argument.

When one gap is explained you abandon that point like rats leaving the sinking ship and move on to the next gap.  You (IDiots/Creationists) never admit that it was you that was wrong in your thinking.

It's disingenuous at best because no matter how much Science proves, there will always be a gap for you and yours to hide in.
---------------------QUOTE-------------------


I've already answered your "god of the gaps" objection once - don't you remember?
Let me just nutshell it for you:
Even though man can explain certain things, it doesn't mean they weren't designed.  I can explain many of the systems at work within my car.  Does that mean they weren't designed?
---------------------QUOTE-------------------


"Let me just nutshell it for you:
Even though man can explain certain things, it doesn't mean they weren't designed...."


Now that argument is called "moving the goal posts".

So, at Dumbfvck U, DI/Creationist Institute of Higher Edumacation, everything is and was designed....until proven otherwise.

"...I can explain many of the systems at work within my car.  Does that mean they weren't designed?"

I'm gonna have to call a non sequitur the play.  Does your car reproduce?

Where is the proof that the appearance of design, proves design?
---------------------QUOTE-------------------


Steverino,

I see everything as designed - even lightning.  It doesn't matter to me if man can explain it.  I don't see that as an issue - for the reasons I specified.  I'm not advocating "god of the gaps", I'm advocating "God over all".

I'm hoping you can see the difference.
Posted by: Steverino on Nov. 26 2007,19:36

I can, and that is not science.

You start with an assumption that skews your research, your interpretation of evidence and your results.  You have identified your goal and cherry pick or distort the evidence that supports your hypothesis. That's not science.

Now, you might wish to argue that evolutionary biologists do the same.  The difference is, their methodology is based on something that has been proven, something that has successful applications in other scientific fields and something that has been validated over and over....and they don't discard evidence that alters their path.

What you are arguing for is not Science.
Posted by: IanBrown_101 on Nov. 26 2007,20:27

Quote (Daniel Smith @ Nov. 27 2007,01:20)
Quote (Steverino @ Nov. 26 2007,16:36)
 
Quote (Daniel Smith @ Nov. 26 2007,13:56)
     
Quote (Steverino @ Nov. 25 2007,14:58)
Daniel,

"...Now maybe that's because we just don't know enough.  But there's also the possibility that it just can't be done."

This is basis of your, ID's and Creationists argument. Boiled down it's the standard "God of the Gaps" argument.

When one gap is explained you abandon that point like rats leaving the sinking ship and move on to the next gap.  You (IDiots/Creationists) never admit that it was you that was wrong in your thinking.

It's disingenuous at best because no matter how much Science proves, there will always be a gap for you and yours to hide in.
---------------------QUOTE-------------------


I've already answered your "god of the gaps" objection once - don't you remember?
Let me just nutshell it for you:
Even though man can explain certain things, it doesn't mean they weren't designed.  I can explain many of the systems at work within my car.  Does that mean they weren't designed?
---------------------QUOTE-------------------


"Let me just nutshell it for you:
Even though man can explain certain things, it doesn't mean they weren't designed...."


Now that argument is called "moving the goal posts".

So, at Dumbfvck U, DI/Creationist Institute of Higher Edumacation, everything is and was designed....until proven otherwise.

"...I can explain many of the systems at work within my car.  Does that mean they weren't designed?"

I'm gonna have to call a non sequitur the play.  Does your car reproduce?

Where is the proof that the appearance of design, proves design?
---------------------QUOTE-------------------


Steverino,

I see everything as designed - even lightning.  It doesn't matter to me if man can explain it.  I don't see that as an issue - for the reasons I specified.  I'm not advocating "god of the gaps", I'm advocating "God over all".

I'm hoping you can see the difference.
---------------------QUOTE-------------------


Point is, i's absolutely fine to say "God, then this"

That is, god is the root cause of everything.

What you cannot do is state anything along the lines of "This was designed, this is a scientific statement."
Just because you believe something to be so doesn't mean it is, and what you believe certainly isn't science.

You can state that god used evolution to create life, by all means fill your boots, but don't start saying "nuh huh evolution!!!!!" because then you look like a tit.
Posted by: W. Kevin Vicklund on Nov. 26 2007,22:03



---------------------QUOTE-------------------
I look at the inner workings of life as a way to learn more about God.
---------------------QUOTE-------------------





---------------------QUOTE-------------------
From a theological perspective, I can't believe that God would have "dead wood" in the genome
---------------------QUOTE-------------------



These are contradictory.  You claim you want to learn more about God, yet when confronted with data that contradicts your preconceptions of God, you refuse to adjust your concept of God.  You don't want to learn about God, you just want science to confirm what you already believe.

I can easily conceive of a God that would have "dead wood" in the genome*.  I know of many people who accept that God might very well do something like that.  Yours is not a theological inquiry, its a blind quest for confirmation of deeply held beliefs.

*my religious beliefs or lack thereof are private and thus any statements I make about religion are made from a scholarly, not personal, perspective - as much as I am able, at least
Posted by: JAM on Nov. 26 2007,23:29

[quote=Daniel Smith,Nov. 26 2007,19:15]
Quote (JAM @ Nov. 19 2007,00:38)

Sit down and take a deep breath. Think, as a Christian, for a moment about what YOU are accusing me and the other scientists of doing here. YOU are accusing US of gross incompetence, and in direct contradiction of clear Biblical guidance, you have made this accusation on the basis of nothing but hearsay.

Put yourself in my shoes, Dan. I've spent most of my life doing biology, and you come along. Would you describe your claims as humble ones?

What sort of character makes grandiose claims without evidence, and then discounts the evidence?
---------------------QUOTE-------------------


These statements have been the cause of much reflection and trouble for me lately.[/quote]
Obviously, you haven't reflected enough.


---------------------QUOTE-------------------
Am I really accusing you (and the other real scientists here) of something?  If so - what?
---------------------QUOTE-------------------


Incompetence and dishonesty.


---------------------QUOTE-------------------
 And what are my motives?
---------------------QUOTE-------------------


Ego.


---------------------QUOTE-------------------
I think I've come to a bit of a realization here.  What I've realized is that my interest in biology is purely theological.
---------------------QUOTE-------------------


You are lying, Dan. Your interest is purely political. If you'll disregard the Ninth Commandment and the Bible's advice to avoid hearsay, you've thrown the baby out with the bathwater.


---------------------QUOTE-------------------
I look at the inner workings of life as a way to learn more about God.
---------------------QUOTE-------------------


But you don't look at any inner workings, Dan, you only look long enough to concoct a lie that supports your political positions.


---------------------QUOTE-------------------
I'm not interested in biology for biology's sake.  These are my motivations.
---------------------QUOTE-------------------


You're simply not interested in biology for any sake at all.


---------------------QUOTE-------------------
So from a theological perspective, when I look at the inner workings of the genome, I expect to find complexity and function.
---------------------QUOTE-------------------


So why do you keep lying and claiming that transcription of a DNA sequence is sufficient to conclude that it is functional?

Why wouldn't you expect elegance in something designed by God?

Why aren't you answering the questions you said you'd answer?


---------------------QUOTE-------------------
It has nothing whatsoever to do with my knowledge of biology.
---------------------QUOTE-------------------


You don't have any significant knowledge of biology, and if any of it threatens your political stance, you'll throw it in the garbage and substitute a lie that pleases you.


---------------------QUOTE-------------------
This is my realization.  I have no right to accuse anyone of anything - especially not someone who has devoted their life to the study of biology.  So for that - for that arrogance - I apologize.
---------------------QUOTE-------------------


Accepted.


---------------------QUOTE-------------------
I should have prefaced everything with "From my theological perspective...".  Then perhaps my arrogant points would have been seen in their true context.
---------------------QUOTE-------------------


Your perspective isn't theological, either. As my minister said, "Creationism and ID aren't merely bad science, they are bad theology."


---------------------QUOTE-------------------
I've been reading the ENCODE paper on < pseudogenes >.  This paper, and my reaction to it, clearly illustrate (for me) my motives.
---------------------QUOTE-------------------


Indeed.


---------------------QUOTE-------------------
The consensus position on pseudogenes seems to be that they are "dead" copies of once-active genes.
---------------------QUOTE-------------------


Which they generally are, EVEN WHEN THEY ARE TRANSCRIBED.


---------------------QUOTE-------------------
From a theological perspective, I can't believe that God would have "dead wood" in the genome, so I find myself shrugging off their conclusions and latching onto the few statements that hint at pseudogenes being more functional than previously thought.
---------------------QUOTE-------------------


Like which statements?


---------------------QUOTE-------------------
Again, from a purely theological perspective, I'm expecting that pseudogenes will be found to be functional in some as-of-yet unseen way.  This expectation has nothing whatsoever to do with my knowledge of biology.  Neither do any of my predictions.  My knowledge is of God and his ways - not of science.
---------------------QUOTE-------------------


I don't see that you have very much knowledge of God, as one of "his ways" is evolution, which you clearly reject completely.


---------------------QUOTE-------------------
With that said, I must say this:  From a theological perspective, I do see much that encourages my beliefs when I look at biology.  I don't see any reason to abandon my core beliefs at all.
---------------------QUOTE-------------------


That's because you're not really looking at biology.


---------------------QUOTE-------------------
The recent discoveries of the inner workings of DNA, RNA, and their chromosomal packaging have me excited to see what scientists will discover next!  I feel encouraged in my beliefs by such things.
---------------------QUOTE-------------------


Why? Because you'll just lie about the data that don't fit your beliefs?


---------------------QUOTE-------------------
I feel in awe of the mind that (I believe) created such things.  I feel I am just that much closer to finding out what actually happened and I am trying to formulate a coherent picture in my mind.
---------------------QUOTE-------------------


I feel that you are afraid of finding out what actually happened and you are desperately trying to formulate a coherent picture in your mind BY IGNORING MOST OF THE DATA.


---------------------QUOTE-------------------
So, my beliefs as to what happened are by no means set in stone.  I study biology as a way to learn what God did - a kind of bio-theology if you will.
---------------------QUOTE-------------------


But you don't study at all, Dan!


---------------------QUOTE-------------------
So JAM, from the perspective of a life-long biologist, you predict that most of the genome will be found non-functional; and I - from a purely theological perspective - predict that most of the genome will be found to be functional.  We shall see who's right.
---------------------QUOTE-------------------


So are we betting our houses, Dan, or do you lack real faith in your "purely theological perspective"?

I say it's a political perspective, and you have no real faith.


---------------------QUOTE-------------------
I hope this clears things up.
---------------------QUOTE-------------------


It does, but you need to quit conflating your political position with an untenable theological one.
Posted by: oldmanintheskydidntdoit on Nov. 27 2007,06:43



---------------------QUOTE-------------------
So JAM, from the perspective of a life-long biologist, you predict that most of the genome will be found non-functional; and I - from a purely theological perspective - predict that most of the genome will be found to be functional.  We shall see who's right.
---------------------QUOTE-------------------



Always with the wriggle room. "most" is not "all". If, Daniel, you are right and god made the all genomes by hand why would there be *any* non-functional parts?

I mean, you can hardly say that over time evolution damaged parts of it to make it non functional as you've alreay stated that god interferes on a regular basis and would therefore have repaired the damage as it happened. Or, even better, as it's god we're talking about, made it so that it was protected in the first place. Or made the thing that "damaged" it not happen in the first place.

And so on and on and on. I wonder is this the sort of pointless circles that are discussed as science in the religious universities?

Daniel, put a figure on "most" please. Is that 99.9999999% 90% 9%? What?
Posted by: swbarnes2 on Nov. 27 2007,12:10

Quote (Daniel Smith @ Nov. 26 2007,19:15)

These statements have been the cause of much reflection and trouble for me lately.
---------------------QUOTE-------------------



Oh please.
If this were true, you would not have to tell us this.  

 

---------------------QUOTE-------------------
I look at the inner workings of life as a way to learn more about God.
---------------------QUOTE-------------------



No, you don't.  This statement of yours is simply a bald-faced lie.  The evidence is below...

 

---------------------QUOTE-------------------
So from a theological perspective, when I look at the inner workings of the genome, I expect to find complexity and function
---------------------QUOTE-------------------



Ah ha.

You told us that you look to nature to tell you about God.  But we all know that that was false, and your lame answers confirmed it.  Now, you have said the honest thing.  You don't look to nature to tell you about God, you already think you know about God, and you look to nature to confirm what you already believe.  And if what you see doesn't match your belief, you simply refuse to believe your eyes.

 

---------------------QUOTE-------------------
a theological perspective, I can't believe that God would have "dead wood" in the genome,
---------------------QUOTE-------------------



See what I mean?  Nature is showing you that there are useless transcription products.  Do you allow this fact to inform you about God?  

Nope.  You refuse to believe it.  You instead "shrug off" the data, and hunt desparately for a shred of an observation that matches what you already believe you know about God.

It shows that you are a liar.  Still.  After all your faux-confessing, you still don't honestly understand yourself.

Aren't you embarassed by the fact that strangers on a message board understand you better than you understand yourself?  Aren't you embarassed to keep showing off our own ignorance and dishonesty time and time again?
Posted by: Daniel Smith on Nov. 27 2007,13:39

Quote (Steverino @ Nov. 26 2007,19:36)
I can, and that is not science.

You start with an assumption that skews your research, your interpretation of evidence and your results.  You have identified your goal and cherry pick or distort the evidence that supports your hypothesis. That's not science.

Now, you might wish to argue that evolutionary biologists do the same.  The difference is, their methodology is based on something that has been proven, something that has successful applications in other scientific fields and something that has been validated over and over....and they don't discard evidence that alters their path.

What you are arguing for is not Science.
---------------------QUOTE-------------------


And I'm not a scientist.  So what's the beef?
Posted by: Daniel Smith on Nov. 27 2007,13:46

Quote (JAM @ Nov. 26 2007,23:29)
You are lying, Dan. Your interest is purely political.

But you don't look at any inner workings, Dan, you only look long enough to concoct a lie that supports your political positions.
---------------------QUOTE-------------------


I'm curious; how do you get "political" out of anything I've said here?
Posted by: JAM on Nov. 27 2007,13:48

Quote (Daniel Smith @ Nov. 27 2007,13:39)
Quote (Steverino @ Nov. 26 2007,19:36)
I can, and that is not science.

You start with an assumption that skews your research, your interpretation of evidence and your results.  You have identified your goal and cherry pick or distort the evidence that supports your hypothesis. That's not science.

Now, you might wish to argue that evolutionary biologists do the same.  The difference is, their methodology is based on something that has been proven, something that has successful applications in other scientific fields and something that has been validated over and over....and they don't discard evidence that alters their path.

What you are arguing for is not Science.
---------------------QUOTE-------------------


And I'm not a scientist.  So what's the beef?
---------------------QUOTE-------------------


The practice of science is not limited to those labeled "scientists:"

< http://www.ucmp.berkeley.edu/fosrec/Lipps.html >

Beyond that red herring, the beef is that you claimed to be interested in biology, and you're not.
Posted by: JAM on Nov. 27 2007,13:50

Quote (Daniel Smith @ Nov. 27 2007,13:46)
Quote (JAM @ Nov. 26 2007,23:29)
You are lying, Dan. Your interest is purely political.

But you don't look at any inner workings, Dan, you only look long enough to concoct a lie that supports your political positions.
---------------------QUOTE-------------------


I'm curious; how do you get "political" out of anything I've said here?
---------------------QUOTE-------------------


Because if you were practicing a Christian theology, you wouldn't disregard the Ninth Commandment and the Biblical warnings about hearsay.

Your position is entirely political; it mocks the fundamental teachings of Jesus Christ.
Posted by: Steverino on Nov. 27 2007,14:32

Quote (Daniel Smith @ Nov. 27 2007,13:39)
Quote (Steverino @ Nov. 26 2007,19:36)
I can, and that is not science.

You start with an assumption that skews your research, your interpretation of evidence and your results.  You have identified your goal and cherry pick or distort the evidence that supports your hypothesis. That's not science.

Now, you might wish to argue that evolutionary biologists do the same.  The difference is, their methodology is based on something that has been proven, something that has successful applications in other scientific fields and something that has been validated over and over....and they don't discard evidence that alters their path.

What you are arguing for is not Science.
---------------------QUOTE-------------------


And I'm not a scientist.  So what's the beef?
---------------------QUOTE-------------------


No, and that's fine.  Then don't get all tweaked when you want to argue your belief scientifically and are told you cannot because your methodology is not scientifically based.

Case closed.
Posted by: Daniel Smith on Nov. 28 2007,13:56

Quote (JAM @ Nov. 27 2007,13:50)
 
Quote (Daniel Smith @ Nov. 27 2007,13:46)
 
Quote (JAM @ Nov. 26 2007,23:29)
You are lying, Dan. Your interest is purely political.

But you don't look at any inner workings, Dan, you only look long enough to concoct a lie that supports your political positions.
---------------------QUOTE-------------------


I'm curious; how do you get "political" out of anything I've said here?
---------------------QUOTE-------------------


Because if you were practicing a Christian theology, you wouldn't disregard the Ninth Commandment and the Biblical warnings about hearsay.

Your position is entirely political; it mocks the fundamental teachings of Jesus Christ.
---------------------QUOTE-------------------


According to... ?
Posted by: JAM on Nov. 28 2007,14:59

Quote (Daniel Smith @ Nov. 28 2007,13:56)
Quote (JAM @ Nov. 27 2007,13:50)
 
Quote (Daniel Smith @ Nov. 27 2007,13:46)
   
Quote (JAM @ Nov. 26 2007,23:29)
You are lying, Dan. Your interest is purely political.

But you don't look at any inner workings, Dan, you only look long enough to concoct a lie that supports your political positions.
---------------------QUOTE-------------------


I'm curious; how do you get "political" out of anything I've said here?
---------------------QUOTE-------------------


Because if you were practicing a Christian theology, you wouldn't disregard the Ninth Commandment and the Biblical warnings about hearsay.

Your position is entirely political; it mocks the fundamental teachings of Jesus Christ.
---------------------QUOTE-------------------


According to... ?
---------------------QUOTE-------------------


Jesus Christ.
Posted by: JAM on Nov. 29 2007,12:36

Quote (JAM @ Nov. 26 2007,13:18)
Quote (Daniel Smith @ Nov. 23 2007,13:47)
 
Quote (JAM @ Nov. 22 2007,18:21)
...

1) Does your hypothesis predict that there will be anything that we humans could reasonably call a "hind-leg gene" based on analogies with our own intelligent designs?

2) Does your hypothesis predict that there will be anything that we humans could reasonably call a "tail gene" based on analogies with our own intelligent designs?

3) What do you mean by "histone activity"?

4) Why would you think that transcription of a particular gene is always happening? WTF do transcription factors do?

5) Wouldn't an intelligent designer design genes so that their transcription was turned on ONLY when (and where) the presence of the gene product is necessary?

6) an you find a single instance of a scientist referring to the design of endocytic (intracellular plumbing) pathways?

7) Explain the intelligence in the design of endocytic pathways, particularly their superiority to more conventional plumbing, as observed from the very same designer in our very own bodies. Be sure to explain the rationale behind the choice of so many similar, closely-related components with partially-overlapping (neither separate nor redundant) pathways.

8) According to your hypothesis, how many human genes won't have a mouse ortholog and vice versa?
---------------------QUOTE-------------------


I'll do my best to answer your questions if you'll do your best to answer this question:
---------------------QUOTE-------------------


I have trouble buying that, as those are questions that I have already asked you, but what the hey:
 

---------------------QUOTE-------------------
In the human genome, what percentage of genomic sequence would you predict is likely to be transcribed as nuclear primary transcripts?
---------------------QUOTE-------------------


Among unique sequence, most (70-90%). Among repeats, less, and I'd predict that the probability of transcription increases with proximity to genes for both repeats and nonrepeats.

Of course, you aren't being upfront about your unsupported belief that transcription implies function. I predict that no function will be found for the vast majority of those transcripts. The next largest class will be those in which the transcript has no function, but the transcription does (can you grasp this important distinction?). Again, the probability that a transcript or transcription serves some function will be highly correlated with proximity to genes.
---------------------QUOTE-------------------


Still waiting...
Posted by: Assassinator on Nov. 29 2007,17:16



---------------------QUOTE-------------------
I see everything as designed - even lightning.
---------------------QUOTE-------------------


And that Daniel, is your whole problem. It's something we called "biased" but not a bit, no you're severly biased because of your faith. This though, life, lightning, is all in the realm of reality. Your faith, you're own personal opinions do not matter there. Lightning doesn't give a damn about what you think, hell the whole universe doesn't give a damn about what you, me, Steve, Arden or anyone thinks! Science is nothing more then a tool to uncover that reality, to know about that reality. It has nothing to do with your emotions, with you as a person. Individuals do not matter in science, they do not matter in the process of uncovering reality.
In your first post in this topic you already admitted, wich was very good, that you're not a scientist and not schooled in this matter. But you are still thinking you can form a decent image about this subject, even though the little things you do know are self-taught and not even neccesarly true because you don't know if you have seen the whole picture.
You can only learn when you let go of that emotional bonding to your personal ideas and thoughts. Myself, I still hope that reïncarnation exists, but that personal thought is not blurring my vision on reality.
Posted by: Assassinator on Nov. 29 2007,17:18

@JAM:
I've asked a little question about that matter myself a while ago, it seems it isn't answerd yet :)
Anyway, a while ago we've calculated in life-science class that only about 1.7% of the whole human genome is for coding. I wonder if that is true.
Posted by: JAM on Nov. 29 2007,18:48

Quote (JAM @ Nov. 26 2007,16:07)
Quote (Assassinator @ Nov. 26 2007,13:22)


---------------------QUOTE-------------------
Among unique sequence, most (70-90%). Among repeats, less, and I'd predict that the probability of transcription increases with proximity to genes for both repeats and nonrepeats.
---------------------QUOTE-------------------


At biology class we calculated that about 1.7% of the whole human genome is for coding. Is that correct?
---------------------QUOTE-------------------


Yes, but that would be a minimum.

Note that Daniel is making a mammoth error in assuming that transcription implies function.

I think that he is beginning to realize that, too.
---------------------QUOTE-------------------


I did answer it.
Posted by: Daniel Smith on Nov. 29 2007,20:47

Quote (Steverino @ Nov. 27 2007,14:32)
 
Quote (Daniel Smith @ Nov. 27 2007,13:39)
   
Quote (Steverino @ Nov. 26 2007,19:36)
I can, and that is not science.

You start with an assumption that skews your research, your interpretation of evidence and your results.  You have identified your goal and cherry pick or distort the evidence that supports your hypothesis. That's not science.

Now, you might wish to argue that evolutionary biologists do the same.  The difference is, their methodology is based on something that has been proven, something that has successful applications in other scientific fields and something that has been validated over and over....and they don't discard evidence that alters their path.

What you are arguing for is not Science.
---------------------QUOTE-------------------


And I'm not a scientist.  So what's the beef?
---------------------QUOTE-------------------


No, and that's fine.  Then don't get all tweaked when you want to argue your belief scientifically and are told you cannot because your methodology is not scientifically based.

Case closed.
---------------------QUOTE-------------------


Maybe my methodology isn't scientifically based, but Schindewolf's, Berg's, and Davison's methodologies are.  The fact that I am co-opting their theories to suit my own needs does not in any way discredit their work.  No one here has taken a serious stab at rebutting those scientists' methodologies or theories.
Posted by: IanBrown_101 on Nov. 29 2007,20:56

Quote (Daniel Smith @ Nov. 30 2007,02:47)
Quote (Steverino @ Nov. 27 2007,14:32)
 
Quote (Daniel Smith @ Nov. 27 2007,13:39)
   
Quote (Steverino @ Nov. 26 2007,19:36)
I can, and that is not science.

You start with an assumption that skews your research, your interpretation of evidence and your results.  You have identified your goal and cherry pick or distort the evidence that supports your hypothesis. That's not science.

Now, you might wish to argue that evolutionary biologists do the same.  The difference is, their methodology is based on something that has been proven, something that has successful applications in other scientific fields and something that has been validated over and over....and they don't discard evidence that alters their path.

What you are arguing for is not Science.
---------------------QUOTE-------------------


And I'm not a scientist.  So what's the beef?
---------------------QUOTE-------------------


No, and that's fine.  Then don't get all tweaked when you want to argue your belief scientifically and are told you cannot because your methodology is not scientifically based.

Case closed.
---------------------QUOTE-------------------


Maybe my methodology isn't scientifically based, but Schindewolf's, Berg's, and Davison's methodologies are.  The fact that I am co-opting their theories to suit my own needs does not in any way discredit their work.  No one here has taken a serious stab at rebutting those scientists' methodologies or theories.
---------------------QUOTE-------------------


Davison states that all things are front loaded to end up how they are now, kind of like how a foetus becomes a baby, right?

How the bloody hell do you test that?
Posted by: Daniel Smith on Nov. 29 2007,21:06

Quote (JAM @ Nov. 26 2007,23:29)

Incompetence and dishonesty.
 
Ego.
 
You are lying, Dan.

Your interest is purely political.

If you'll disregard the Ninth Commandment and the Bible's advice to avoid hearsay, you've thrown the baby out with the bathwater.

...Dan, you only look long enough to concoct a lie that supports your political positions.

You're simply not interested in biology for any sake at all.

So why do you keep lying...?

You don't have any significant knowledge of biology, and if any of it threatens your political stance, you'll throw it in the garbage and substitute a lie that pleases you.

Because you'll just lie about the data that don't fit your beliefs?

But you don't study at all, Dan!

---------------------QUOTE-------------------


   
Quote (swbarnes2 @ Nov. 27 2007,12:10)

This statement of yours is simply a bald-faced lie.

But we all know that that was false, and your lame answers confirmed it.  

It shows that you are a liar.  

Aren't you embarassed to keep showing off our own ignorance and dishonesty time and time again?
---------------------QUOTE-------------------



After awhile, these endless strings of hollow accusations will say more about your character than mine.
Posted by: Daniel Smith on Nov. 29 2007,21:25

[quote=JAM,Nov. 26 2007,23:29]        
Quote (Daniel Smith @ Nov. 26 2007,19:15)

         

---------------------QUOTE-------------------
The consensus position on pseudogenes seems to be that they are "dead" copies of once-active genes.
---------------------QUOTE-------------------


Which they generally are, EVEN WHEN THEY ARE TRANSCRIBED.
         

---------------------QUOTE-------------------
From a theological perspective, I can't believe that God would have "dead wood" in the genome, so I find myself shrugging off their conclusions and latching onto the few statements that hint at pseudogenes being more functional than previously thought.
---------------------QUOTE-------------------


Like which statements?
---------------------QUOTE-------------------


Like these ones:
         

---------------------QUOTE-------------------
However, a few pseudogenes have been indicated to have potential biological roles (Ota and Nei 1995; Korneev et al. 1999; Mighell et al. 2000; Balakirev and Ayala 2003). Whether these are anecdotal cases or pseudogenes do play cellular roles is still a matter of debate at this point, simply because not enough studies have been conducted with pseudogenes as the primary subjects. To be clear, in this study the nonfunctionality of a pseudogene is strictly interpreted as a sequence’s lacking protein coding potential, regardless of whether it can produce a (functional or nonfunctional) RNA transcript.
---------------------QUOTE-------------------



---------------------QUOTE-------------------
We believe that the data obtained by RACE experiments or by sequencing analyses (CAGE, PET, EST, and mRNA) provide unambiguous evidence for pseudogene transcription. Altogether, these data indicate that 38 (19% of 201, 20 nonprocessed and 18 processed) pseudogenes are the sources of novel RNA transcripts. This may well represent a low-bound estimate and does not include the ambiguous and possibly inconclusive cases supported only by transfrags. We should emphasize that most cases of pseudogene transcription were only detected in one or a few experiments (manifested by small overlaps between data from different evidence) (Table 1), and thus the example in Figure 3 is not typical. This indicates that pseudogene transcription is quite tissue-specific, as RACEfrags, CAGE, PET, and transfrags were obtained from different cell lines or tissues (see Methods). On the other hand, such a pattern of tissue- (or cell line)-specific transcription was a common characteristic of novel non-coding transcripts (Cheng et al. 2005).
---------------------QUOTE-------------------



---------------------QUOTE-------------------
Although transcription of a pseudogene is not sufficient to indicate whether it has a meaningful biological function, our data showed that pseudogene transcription often occurred at a low level and with a pattern of tissue or cell line specificity. These are similar to the transcriptional characteristics that have been observed for antisense RNA (Dahary et al. 2005; Katayama et al. 2005) and many intronic and intergenic transcripts whose biochemical functions are yet to be unraveled (Bertone et al. 2004; Cheng et al. 2005; Johnson et al. 2005; Willingham and Gingeras 2006). It would not, therefore, be surprising if pseudogenes proved to be one source of novel, functional non-coding RNAs.
---------------------QUOTE-------------------



---------------------QUOTE-------------------
However, these results do not exclude the possibility that some transcribed pseudogenes play biological roles, since it has been found that many experimentally determined functional elements (e.g., promoters) are not significantly conserved either (The ENCODE Project Consortium 2007).
---------------------QUOTE-------------------


Remember now, I'm not saying that these statements show pseudogenes to be functional.  My statement was that these are "the few statements that hint at pseudogenes being more functional than previously thought."
Posted by: Daniel Smith on Nov. 29 2007,21:38

Quote (IanBrown_101 @ Nov. 29 2007,20:56)

Davison states that all things are front loaded to end up how they are now, kind of like how a foetus becomes a baby, right?

How the bloody hell do you test that?
---------------------QUOTE-------------------


You should be able to test it the same way you test the MET - by looking at fossil, molecular and phylogenetic evidence and seeing if it supports the hypothesis.

It would seem you could make predictions based on his hypothesis and then test them to see if they were valid.

I believe Davison also suggested some experiments that could be done to test the semi-meiotic reproductive mechanism, but I don't know the details.
Posted by: JAM on Nov. 29 2007,21:45

Quote (Daniel Smith @ Nov. 29 2007,21:06)
Quote (JAM @ Nov. 26 2007,23:29)

Incompetence and dishonesty.
 
Ego.
 
You are lying, Dan.

Your interest is purely political.

If you'll disregard the Ninth Commandment and the Bible's advice to avoid hearsay, you've thrown the baby out with the bathwater.

...Dan, you only look long enough to concoct a lie that supports your political positions.

You're simply not interested in biology for any sake at all.

So why do you keep lying...?

You don't have any significant knowledge of biology, and if any of it threatens your political stance, you'll throw it in the garbage and substitute a lie that pleases you.

Because you'll just lie about the data that don't fit your beliefs?

But you don't study at all, Dan!

---------------------QUOTE-------------------


   
Quote (swbarnes2 @ Nov. 27 2007,12:10)

This statement of yours is simply a bald-faced lie.

But we all know that that was false, and your lame answers confirmed it.  

It shows that you are a liar.  

Aren't you embarassed to keep showing off our own ignorance and dishonesty time and time again?
---------------------QUOTE-------------------



After awhile, these endless strings of hollow accusations will say more about your character than mine.
---------------------QUOTE-------------------


What's hollow about them, Dan?
Posted by: IanBrown_101 on Nov. 29 2007,22:07

Quote (Daniel Smith @ Nov. 30 2007,03:38)
Quote (IanBrown_101 @ Nov. 29 2007,20:56)

Davison states that all things are front loaded to end up how they are now, kind of like how a foetus becomes a baby, right?

How the bloody hell do you test that?
---------------------QUOTE-------------------


You should be able to test it the same way you test the MET - by looking at fossil, molecular and phylogenetic evidence and seeing if it supports the hypothesis.

It would seem you could make predictions based on his hypothesis and then test them to see if they were valid.

I believe Davison also suggested some experiments that could be done to test the semi-meiotic reproductive mechanism, but I don't know the details.
---------------------QUOTE-------------------


But you CAN'T do that. How the heck are we supposed to tell from fossils if things were MEANT to turn out how they did?

If you flip a coin 5 times and it comes out heads each time, I could say it was predestined. How the hell can you test that idea?
Posted by: Daniel Smith on Nov. 29 2007,22:14

Quote (JAM @ Nov. 29 2007,12:36)
 
1) Does your hypothesis predict that there will be anything that we humans could reasonably call a "hind-leg gene" based on analogies with our own intelligent designs?

---------------------QUOTE-------------------

Not a single gene.  More likely "hind leg" development would be controlled by a region containing many genes.        

---------------------QUOTE-------------------

2) Does your hypothesis predict that there will be anything that we humans could reasonably call a "tail gene" based on analogies with our own intelligent designs?

---------------------QUOTE-------------------

Same        

---------------------QUOTE-------------------

3) What do you mean by "histone activity"?

---------------------QUOTE-------------------

I mean the affect specific histones have on the transcription, packaging, expression and suppression of DNA sequences.        

---------------------QUOTE-------------------

4) Why would you think that transcription of a particular gene is always happening? WTF do transcription factors do?

---------------------QUOTE-------------------

Well, I'm unsure of this now.  I think transcription is probably very cell specific - so it would depend on the cell type.  I believe (theologically) that the entire genome is used somewhere and sometime, but not "always" - as I stated.        

---------------------QUOTE-------------------

5) Wouldn't an intelligent designer design genes so that their transcription was turned on ONLY when (and where) the presence of the gene product is necessary?

---------------------QUOTE-------------------

Probably.  That makes more sense than what I originally said.        

---------------------QUOTE-------------------

6) an you find a single instance of a scientist referring to the design of endocytic (intracellular plumbing) pathways?

---------------------QUOTE-------------------

Does < this > qualify?        

---------------------QUOTE-------------------

7) Explain the intelligence in the design of endocytic pathways, particularly their superiority to more conventional plumbing, as observed from the very same designer in our very own bodies. Be sure to explain the rationale behind the choice of so many similar, closely-related components with partially-overlapping (neither separate nor redundant) pathways.

---------------------QUOTE-------------------

I don't know enough about endocytic pathways to answer this.        

---------------------QUOTE-------------------

8) According to your hypothesis, how many human genes won't have a mouse ortholog and vice versa?
---------------------QUOTE-------------------


No idea.  Such things seem completely irrelevant to me.  But, just to hazard a guess, I'd say humans and mice have probably 30-50% similar genes        

---------------------QUOTE-------------------

           

---------------------QUOTE-------------------
In the human genome, what percentage of genomic sequence would you predict is likely to be transcribed as nuclear primary transcripts?
---------------------QUOTE-------------------


Among unique sequence, most (70-90%). Among repeats, less, and I'd predict that the probability of transcription increases with proximity to genes for both repeats and nonrepeats.

Of course, you aren't being upfront about your unsupported belief that transcription implies function. I predict that no function will be found for the vast majority of those transcripts. The next largest class will be those in which the transcript has no function, but the transcription does (can you grasp this important distinction?).
---------------------QUOTE-------------------

I'm not sure what the difference is.        

---------------------QUOTE-------------------
Again, the probability that a transcript or transcription serves some function will be highly correlated with proximity to genes.
---------------------QUOTE-------------------

No doubt that's the safest bet.  I'm still expecting scientists to be "surprised" by functional elements found further and further from genes (again based on my theological beliefs - as are all these answers).
Posted by: Daniel Smith on Nov. 29 2007,22:21

Quote (JAM @ Nov. 29 2007,21:45)
   
Quote (Daniel Smith @ Nov. 29 2007,21:06)
   
Quote (JAM @ Nov. 26 2007,23:29)

Incompetence and dishonesty.
 
Ego.
 
You are lying, Dan.

Your interest is purely political.

If you'll disregard the Ninth Commandment and the Bible's advice to avoid hearsay, you've thrown the baby out with the bathwater.

...Dan, you only look long enough to concoct a lie that supports your political positions.

You're simply not interested in biology for any sake at all.

So why do you keep lying...?

You don't have any significant knowledge of biology, and if any of it threatens your political stance, you'll throw it in the garbage and substitute a lie that pleases you.

Because you'll just lie about the data that don't fit your beliefs?

But you don't study at all, Dan!

---------------------QUOTE-------------------


         
Quote (swbarnes2 @ Nov. 27 2007,12:10)

This statement of yours is simply a bald-faced lie.

But we all know that that was false, and your lame answers confirmed it.  

It shows that you are a liar.  

Aren't you embarassed to keep showing off our own ignorance and dishonesty time and time again?
---------------------QUOTE-------------------



After awhile, these endless strings of hollow accusations will say more about your character than mine.
---------------------QUOTE-------------------


What's hollow about them, Dan?
---------------------QUOTE-------------------


They're "hollow" because I've never purposefully lied during this discussion.  I may have said things which I thought to be true at the time, and later found they weren't (in which case I've retracted them), but I've never ever lied.
The fact that you and a few others here seem obsessed with calling me a "liar" says more about you than it does me.
Posted by: Daniel Smith on Nov. 29 2007,22:31

Quote (IanBrown_101 @ Nov. 29 2007,22:07)
   
Quote (Daniel Smith @ Nov. 30 2007,03:38)
   
Quote (IanBrown_101 @ Nov. 29 2007,20:56)

Davison states that all things are front loaded to end up how they are now, kind of like how a foetus becomes a baby, right?

How the bloody hell do you test that?
---------------------QUOTE-------------------


You should be able to test it the same way you test the MET - by looking at fossil, molecular and phylogenetic evidence and seeing if it supports the hypothesis.

It would seem you could make predictions based on his hypothesis and then test them to see if they were valid.

I believe Davison also suggested some experiments that could be done to test the semi-meiotic reproductive mechanism, but I don't know the details.
---------------------QUOTE-------------------


But you CAN'T do that. How the heck are we supposed to tell from fossils if things were MEANT to turn out how they did?

If you flip a coin 5 times and it comes out heads each time, I could say it was predestined. How the hell can you test that idea?
---------------------QUOTE-------------------


What if it comes out heads 1,000,000,000 times?
Posted by: IanBrown_101 on Nov. 29 2007,22:48

Quote (Daniel Smith @ Nov. 30 2007,04:31)
Quote (IanBrown_101 @ Nov. 29 2007,22:07)
   
Quote (Daniel Smith @ Nov. 30 2007,03:38)
     
Quote (IanBrown_101 @ Nov. 29 2007,20:56)

Davison states that all things are front loaded to end up how they are now, kind of like how a foetus becomes a baby, right?

How the bloody hell do you test that?
---------------------QUOTE-------------------


You should be able to test it the same way you test the MET - by looking at fossil, molecular and phylogenetic evidence and seeing if it supports the hypothesis.

It would seem you could make predictions based on his hypothesis and then test them to see if they were valid.

I believe Davison also suggested some experiments that could be done to test the semi-meiotic reproductive mechanism, but I don't know the details.
---------------------QUOTE-------------------


But you CAN'T do that. How the heck are we supposed to tell from fossils if things were MEANT to turn out how they did?

If you flip a coin 5 times and it comes out heads each time, I could say it was predestined. How the hell can you test that idea?
---------------------QUOTE-------------------


What if it comes out heads 1,000,000,000 times?
---------------------QUOTE-------------------


Then that's what happens.

It implies there might be a cause to it, but it might just as easily be a fluke. There would need to be some evidence that it COULDN'T happen by luck aloe, otherwise you could attribute absolutely anything to intelligence.
Posted by: JAM on Nov. 30 2007,00:00

Quote (Daniel Smith @ Nov. 29 2007,22:21)
They're "hollow" because I've never purposefully lied during this discussion.  I may have said things which I thought to be true at the time,
---------------------QUOTE-------------------


No, you've said many, many things that you merely WISHED were true. Those are lies.


---------------------QUOTE-------------------
...and later found they weren't (in which case I've retracted them), but I've never ever lied.
---------------------QUOTE-------------------


ORLY? When did you retract your false claim about introns being coding sequences?


---------------------QUOTE-------------------
The fact that you and a few others here seem obsessed with calling me a "liar"
---------------------QUOTE-------------------


How can I be obsessed with doing something I've never done? I've called some of your statements lies, but I've never gone the ad hominem route and called you a liar.
Posted by: Richard Simons on Nov. 30 2007,00:27

Quote (Daniel Smith @ Nov. 29 2007,20:47)
Maybe my methodology isn't scientifically based, but Schindewolf's, Berg's, and Davison's methodologies are.  The fact that I am co-opting their theories to suit my own needs does not in any way discredit their work.  No one here has taken a serious stab at rebutting those scientists' methodologies or theories.
---------------------QUOTE-------------------


My questions about the 'frontloading' were serious, but you've probably discounted them because they were unanswerable.

 
Quote (Richard Simons @ Nov. 22 2007,16:36)
But you have still not suggested any possible internal mechanism that could constrain evolution or direct it, or any mechanism by which the organism could foresee the future and know what adaptations it will need. As far as I can tell, Schindewolf and Davison are just as barren of ideas for this as you are. The semi-meiotic hypothesis has nothing to do with how the path of evolution is constrained or pre-ordained. Whether evolution procedes by saltation or continuously is a different issue from the mechanism for storing and imposing the constraints.
---------------------QUOTE-------------------


Until these problems are fixed, as far as I am concerned there is no point in attempting a rebuttal.
Posted by: JAM on Nov. 30 2007,00:30

[quote=Daniel Smith,Nov. 29 2007,22:14][quote=JAM,Nov. 29 2007,12:36]  
1) Does your hypothesis predict that there will be anything that we humans could reasonably call a "hind-leg gene" based on analogies with our own intelligent designs?
[/quote]Not a single gene.  More likely "hind leg" development would be controlled by a region containing many genes.         [/quote]
You are completely, utterly wrong; apparently you don't understand God's design at all. That won't change your claim that what you've learned supports your position, though, will it?
[quote]  [quote]2) Does your hypothesis predict that there will be anything that we humans could reasonably call a "tail gene" based on analogies with our own intelligent designs?
[/quote]Same[/quote]
You're wrong again, Ofer.
      [quote]        

---------------------QUOTE-------------------

3) What do you mean by "histone activity"?

---------------------QUOTE-------------------

I mean the affect specific histones have on the transcription, packaging, expression and suppression of DNA sequences. [/quote]
How are any of those four characteristics separate from each other? What do you mean by "specific histones"?       
       

---------------------QUOTE-------------------
       

---------------------QUOTE-------------------
4) Why would you think that transcription of a particular gene is always happening? WTF do transcription factors do?

---------------------QUOTE-------------------

Well, I'm unsure of this now.
---------------------QUOTE-------------------


Yes, and even though you were sure that this was the way that God did it before, you'll still claim to understand Him better than the rest of us do.
     

---------------------QUOTE-------------------
I think transcription is probably very cell specific - so it would depend on the cell type.
---------------------QUOTE-------------------


I, OTOH, KNOW that sometimes it is, but very often it isn't, so your answer is meaningless.
       

---------------------QUOTE-------------------
I believe (theologically) that the entire genome is used somewhere and sometime, but not "always" - as I stated.        
---------------------QUOTE-------------------


That's nice, but both experimentally and ecologically, you're completely wrong.
       

---------------------QUOTE-------------------
       

---------------------QUOTE-------------------
5) Wouldn't an intelligent designer design genes so that their transcription was turned on ONLY when (and where) the presence of the gene product is necessary?

---------------------QUOTE-------------------

Probably.  That makes more sense than what I originally said.        
---------------------QUOTE-------------------


I agree. But in reality, that prediction of ID is laughably false.
   

---------------------QUOTE-------------------
       

---------------------QUOTE-------------------
6) an you find a single instance of a scientist referring to the design of endocytic (intracellular plumbing) pathways?

---------------------QUOTE-------------------

Does < this > qualify?              
---------------------QUOTE-------------------


Not even close, because they aren't talking about endocytosis, they attribute any design to evolution, and they point out the stupidity of the process:
       

---------------------QUOTE-------------------
The resulting terrestrial mammalian kidney is enor-
mously inefficient and energy-consuming, illustrating the tink-
ering premise. Smith (17) famously stated, “What engineer,
wishing to regulate the composition of the internal environ-
ment of the body on which the function of every bone, gland,
muscle, and nerve depends, would devise a scheme that oper-
ated by throwing the whole thing out 16 times a day and rely
on grabbing from it, as it fell to earth, only those precious
elements which he wanted to keep?”
---------------------QUOTE-------------------


So if God designed your kidneys, He is stupid. Who would worship such a god?
       

---------------------QUOTE-------------------
       

---------------------QUOTE-------------------
7) Explain the intelligence in the design of endocytic pathways, particularly their superiority to more conventional plumbing, as observed from the very same designer in our very own bodies. Be sure to explain the rationale behind the choice of so many similar, closely-related components with partially-overlapping (neither separate nor redundant) pathways.

---------------------QUOTE-------------------

I don't know enough about endocytic pathways to answer this.        
---------------------QUOTE-------------------


How convenient. But assume I'm correct about the overlap and explain it in terms of intelligent design.
     

---------------------QUOTE-------------------
 

---------------------QUOTE-------------------
8) According to your hypothesis, how many human genes won't have a mouse ortholog and vice versa?
---------------------QUOTE-------------------


No idea.  Such things seem completely irrelevant to me.  But, just to hazard a guess, I'd say humans and mice have probably 30-50% similar genes
---------------------QUOTE-------------------


Dead wrong. Mice and humans share 100.0% of their genes. The number present in one and lacking in the other is in the single digits. There goes your hypothesis...
       

---------------------QUOTE-------------------
   

---------------------QUOTE-------------------
   

---------------------QUOTE-------------------
In the human genome, what percentage of genomic sequence would you predict is likely to be transcribed as nuclear primary transcripts?
---------------------QUOTE-------------------


Among unique sequence, most (70-90%). Among repeats, less, and I'd predict that the probability of transcription increases with proximity to genes for both repeats and nonrepeats.

Of course, you aren't being upfront about your unsupported belief that transcription implies function. I predict that no function will be found for the vast majority of those transcripts. The next largest class will be those in which the transcript has no function, but the transcription does (can you grasp this important distinction?).
---------------------QUOTE-------------------

I'm not sure what the difference is.
---------------------QUOTE-------------------


You'd have to think about it. Wouldn't it be important if one is testing a design hypothesis?
       

---------------------QUOTE-------------------
       

---------------------QUOTE-------------------
Again, the probability that a transcript or transcription serves some function will be highly correlated with proximity to genes.
---------------------QUOTE-------------------

No doubt that's the safest bet.
---------------------QUOTE-------------------


It's a prediction.
       

---------------------QUOTE-------------------
I'm still expecting scientists to be "surprised" by functional elements found further and further from genes (again based on my theological beliefs - as are all these answers).
---------------------QUOTE-------------------


So far, your theology has been worse than worthless. Why not read from the book of Nature, if you believe that God wrote it?[/quote]
Posted by: Daniel Smith on Nov. 30 2007,18:04

Quote (JAM @ Nov. 30 2007,00:30)
   
Quote (Daniel Smith @ Nov. 29 2007,22:14)

Does < this > qualify?              
---------------------QUOTE-------------------


Not even close, because they aren't talking about endocytosis, they attribute any design to evolution, and they point out the stupidity of the process:
             

---------------------QUOTE-------------------
The resulting terrestrial mammalian kidney is enor-
mously inefficient and energy-consuming, illustrating the tink-
ering premise. Smith (17) famously stated, “What engineer,
wishing to regulate the composition of the internal environ-
ment of the body on which the function of every bone, gland,
muscle, and nerve depends, would devise a scheme that oper-
ated by throwing the whole thing out 16 times a day and rely
on grabbing from it, as it fell to earth, only those precious
elements which he wanted to keep?”
---------------------QUOTE-------------------


So if God designed your kidneys, He is stupid. Who would worship such a god?
---------------------QUOTE-------------------


Interesting then how man cannot improve on such a "flawed" design.  Dialysis is no where near as effective as the natural kidney - in spite of all it's supposed flaws.
Posted by: Assassinator on Nov. 30 2007,18:18

You can't compare biology with human technology in that way. There simply is no solide ground to support that comparison.
We can see and explain why kidney's are inefficient, and well badluck that we don't have the technology to increase that. That doesn't change anything to the fact that kidney's are inefficient. And don't forget, there is simply no way to test if life is designed. It's a worthless hypothesis because it's based on a flawd comparison between nature and man-made technology.
Posted by: Steverino on Nov. 30 2007,18:26

Quote (Daniel Smith @ Nov. 30 2007,18:04)
Quote (JAM @ Nov. 30 2007,00:30)
   
Quote (Daniel Smith @ Nov. 29 2007,22:14)

Does < this > qualify?              
---------------------QUOTE-------------------


Not even close, because they aren't talking about endocytosis, they attribute any design to evolution, and they point out the stupidity of the process:
               

---------------------QUOTE-------------------
The resulting terrestrial mammalian kidney is enor-
mously inefficient and energy-consuming, illustrating the tink-
ering premise. Smith (17) famously stated, “What engineer,
wishing to regulate the composition of the internal environ-
ment of the body on which the function of every bone, gland,
muscle, and nerve depends, would devise a scheme that oper-
ated by throwing the whole thing out 16 times a day and rely
on grabbing from it, as it fell to earth, only those precious
elements which he wanted to keep?”
---------------------QUOTE-------------------


So if God designed your kidneys, He is stupid. Who would worship such a god?
---------------------QUOTE-------------------


Interesting then how man cannot improve on such a "flawed" design.  Dialysis is no where near as effective as the natural kidney - in spite of all it's supposed flaws.
---------------------QUOTE-------------------


Give it time...because it will happen.  Then what will your smart ass answer be

There is no proof Front Loading exists.  It's nothing more than a "catch all" excuse for IDiots because they don't do research.
Posted by: Daniel Smith on Nov. 30 2007,18:50

Quote (Richard Simons @ Nov. 30 2007,00:27)
   
Quote (Daniel Smith @ Nov. 29 2007,20:47)
Maybe my methodology isn't scientifically based, but Schindewolf's, Berg's, and Davison's methodologies are.  The fact that I am co-opting their theories to suit my own needs does not in any way discredit their work.  No one here has taken a serious stab at rebutting those scientists' methodologies or theories.
---------------------QUOTE-------------------


My questions about the 'frontloading' were serious, but you've probably discounted them because they were unanswerable.

       
Quote (Richard Simons @ Nov. 22 2007,16:36)
But you have still not suggested any possible internal mechanism that could constrain evolution or direct it, or any mechanism by which the organism could foresee the future and know what adaptations it will need. As far as I can tell, Schindewolf and Davison are just as barren of ideas for this as you are. The semi-meiotic hypothesis has nothing to do with how the path of evolution is constrained or pre-ordained. Whether evolution procedes by saltation or continuously is a different issue from the mechanism for storing and imposing the constraints.
---------------------QUOTE-------------------


Until these problems are fixed, as far as I am concerned there is no point in attempting a rebuttal.
---------------------QUOTE-------------------


I think your questions are probably answerable.  I'm not sure of the mechanism, but something along the lines of a genetic "switch" - which responds to environmental queues would seem a likely candidate.

It would seem to me that the way to test such a mechanism would be to subject natural organisms to specific conditions and see if their adaptations always follow a certain direction.

Berg cites numerous examples of such adaptations in chapters 6 and 7 of "Nomogenesis".  Among his examples are the coloration, number and size of scales, number of rays in the fins, variation in body length and number of vertebrae of fishes of the same genus living in different regions.
He says:
   

---------------------QUOTE-------------------
It appears that several groups of species, living in approximately identical conditions, are subject to parallel variations. ibid. pg. 269
---------------------QUOTE-------------------


He also cites examples where transplanted species almost immediately (often within a single generation) begin to exhibit variations parallel to other species in that region.  Although he does not propose a specific mechanism, his examples are nonetheless food for thought.
Posted by: swbarnes2 on Nov. 30 2007,19:05

Quote (Daniel Smith @ Nov. 29 2007,21:06)
     
After awhile, these endless strings of hollow accusations will say more about your character than mine.I may have said things which I thought to be true at the time, and later found they weren't (in which case I've retracted them), but I've never ever lied.
---------------------QUOTE-------------------



You made a prediction about the results of a hypothetical bacteria experiment.  Then you lied about what your prediction had been.

You claimed that the VISTA data supported your hypothesis.  Then, you claimed that you didn't understand the VISTA data well enough to draw any conclusions from it.  That makes your first statement a lie.

You claimed that you look to nature to tell you about God.

Then you said that what you already knew about god told you what you should see in nature, and that if the two didn't agree, what you were seeing was wrong.  That makes you a liar too.

Sorry, but everything I listed are lies. So spare us your underlined outrage.  The evidence is plain. 

If you had a reputation for being honest, people would accept an occasional slip up.  But do you think that a person who's done just the few examples I listed above deserves the benefit of the doubt?

If you really want to claim that these are not lies, that what is happening is that you are tripping over your own arguments desperate attempt to appear reasonable, when your postion is anything but, then say so clearly.  Because the only alternative to you being a bald-faced liar is that you are completely ignorant about your own motivations and beliefs, to the point where strangers on a message boards know more about your thinking than you do.
Posted by: Daniel Smith on Nov. 30 2007,19:06

Quote (IanBrown_101 @ Nov. 29 2007,22:48)
           
Quote (Daniel Smith @ Nov. 30 2007,04:31)
             
Quote (IanBrown_101 @ Nov. 29 2007,22:07)
If you flip a coin 5 times and it comes out heads each time, I could say it was predestined. How the hell can you test that idea?
---------------------QUOTE-------------------


What if it comes out heads 1,000,000,000 times?
---------------------QUOTE-------------------

 
Then that's what happens.

It implies there might be a cause to it, but it might just as easily be a fluke. There would need to be some evidence that it COULDN'T happen by luck alone, otherwise you could attribute absolutely anything to intelligence.
---------------------QUOTE-------------------


A coin flip that produces a billion heads in a row makes you think "there might be a cause to it, but it might just as easily be a fluke (my emphasis)"?
Just as easily?  Astounding!  Do you realize what the odds are against such a thing happening?  At some point you have to admit that such a feat is impossible in a fair coin toss.
Pardon me for saying this, but I don't see how any rational person would not conclude that the fix was in.
On the other hand, I think I understand the rationale behind your denial:  If you ascribe a "cut off point" - where something is beyond the realm of chance - you run the risk of negating the mechanism behind the MET.
Maybe I'm wrong - I'm sure pretty much everyone here will say that I am - but that's what I think.
Posted by: Daniel Smith on Nov. 30 2007,19:15

Quote (swbarnes2 @ Nov. 30 2007,19:05)
 
Quote (Daniel Smith @ Nov. 29 2007,21:06)
     
After awhile, these endless strings of hollow accusations will say more about your character than mine.I may have said things which I thought to be true at the time, and later found they weren't (in which case I've retracted them), but I've never ever lied.
---------------------QUOTE-------------------



You made a prediction about the results of a hypothetical bacteria experiment.  Then you lied about what your prediction had been.

You claimed that the VISTA data supported your hypothesis.  Then, you claimed that you didn't understand the VISTA data well enough to draw any conclusions from it.  That makes your first statement a lie.

You claimed that you look to nature to tell you about God.

Then you said that what you already knew about god told you what you should see in nature, and that if the two didn't agree, what you were seeing was wrong.  That makes you a liar too.

Sorry, but everything I listed are lies. So spare us your underlined outrage.  The evidence is plain.

If you had a reputation for being honest, people would accept an occasional slip up.  But do you think that a person who's done just the few examples I listed above deserves the benefit of the doubt?

If you really want to claim that these are not lies, that what is happening is that you are tripping over your own arguments desperate attempt to appear reasonable, when your postion is anything but, then say so clearly.  Because the only alternative to you being a bald-faced liar is that you are completely ignorant about your own motivations and beliefs, to the point where strangers on a message boards know more about your thinking than you do.
---------------------QUOTE-------------------


I have never lied.  I stand by that.  What you perceive as lies are statements made as the result of my own ignorance, and statements where I did not adequately explain my intended meaning  - nothing more - nothing less.
If you want to believe that I'm a liar - go ahead.  I really could care less what you believe.  I will probably just start ignoring your posts - as these endless accusations get old after awhile.  If you want to talk about ideas and issues, that's fine.  If you want to make me the subject - forget it.  I didn't come here for character assassination.
Posted by: Erasmus, FCD on Nov. 30 2007,19:18

Daniel what examples of introduced species with parallel adaptations native species in a single or few generations are there?  i'm skeptical of that claim, but not having read Berg or ever having even seen the book I have no way to address this.
Posted by: Richard Simons on Nov. 30 2007,22:56

Quote (Daniel Smith @ Nov. 30 2007,18:50)
 
Quote (Richard Simons @ Nov. 30 2007,00:27)
     
Quote (Daniel Smith @ Nov. 29 2007,20:47)
Maybe my methodology isn't scientifically based, but Schindewolf's, Berg's, and Davison's methodologies are.  The fact that I am co-opting their theories to suit my own needs does not in any way discredit their work.  No one here has taken a serious stab at rebutting those scientists' methodologies or theories.
---------------------QUOTE-------------------


My questions about the 'frontloading' were serious, but you've probably discounted them because they were unanswerable.

         
Quote (Richard Simons @ Nov. 22 2007,16:36)
But you have still not suggested any possible internal mechanism that could constrain evolution or direct it, or any mechanism by which the organism could foresee the future and know what adaptations it will need. As far as I can tell, Schindewolf and Davison are just as barren of ideas for this as you are. The semi-meiotic hypothesis has nothing to do with how the path of evolution is constrained or pre-ordained. Whether evolution procedes by saltation or continuously is a different issue from the mechanism for storing and imposing the constraints.
---------------------QUOTE-------------------


Until these problems are fixed, as far as I am concerned there is no point in attempting a rebuttal.
---------------------QUOTE-------------------


I think your questions are probably answerable.  I'm not sure of the mechanism, but something along the lines of a genetic "switch" - which responds to environmental queues would seem a likely candidate.
---------------------QUOTE-------------------


They might be answerable although I cannot imagine how. Your hand-waving about a 'genetic switch' says nothing about a means whereby an organism can know what adaptations it will need in the future or how the information can be stored without being corrupted.

Another thing that baffles me is why all of these mythical constrained pathways are needed. Given the existence of natural selection, it is all so unnecessary.

 

---------------------QUOTE-------------------
Berg cites numerous examples of such adaptations in chapters 6 and 7 of "Nomogenesis".  Among his examples are the coloration, number and size of scales, number of rays in the fins, variation in body length and number of vertebrae of fishes of the same genus living in different regions.
He says:
     

---------------------QUOTE-------------------
 
It appears that several groups of species, living in approximately identical conditions, are subject to parallel variations. ibid. pg. 269
---------------------QUOTE-------------------


---------------------QUOTE-------------------


I do not have access to 'Nomogenesis' (my nearest library is a 4 hour drive away) so I am unable to see the context for myself, but how does this differ from the normal predictions of the theory of evolution?

I agree with Erasmus that I would like to see examples where transplanted species often within a single generation begin to exhibit variations parallel to other species in that region. It sounds very unlikely to me.
Posted by: VMartin on Dec. 01 2007,09:12

My latest post has been deleted, so I 'll try it this way:

Jam
   

---------------------QUOTE-------------------

Dead wrong. Mice and humans share 100.0% of their genes. The number present in one and lacking in the other is in the single digits. There goes your hypothesis...

---------------------QUOTE-------------------



If they share 100,0% genes then it back ups frontloading very well I would say. It would mean that also regulatory genes are the same and it was only due to rearrangements of pre-existing genes in DNA that led to the difference between mice and  human in the distant past.

(In that case the possible explanation could be also different composition of cytosole in gametes and zygotes of both species and consequently the difference between man and  mice could be only epigenetical. But is sounds too "German", neglecting the role of DNA in ontogenesis,  doesn't it?)


--------
Hold on, Daniel.
Posted by: Tracy P. Hamilton on Dec. 01 2007,09:40

Quote (VMartin @ Dec. 01 2007,09:12)
My latest post has been deleted, so I 'll try it this way:

Jam
     

---------------------QUOTE-------------------

Dead wrong. Mice and humans share 100.0% of their genes. The number present in one and lacking in the other is in the single digits. There goes your hypothesis...

---------------------QUOTE-------------------



If they share 100,0% genes then it back ups frontloading very well I would say. It would mean that also regulatory genes are the same and it was only due to rearrangements of pre-existing genes in DNA that led to the difference between mice and  human in the distant past.

(In that case the possible explanation could be also different composition of cytosole in gametes and zygotes of both species and consequently the difference between man and  mice could be only epigenetical. But is sounds too "German", neglecting the role of DNA in ontogenesis,  doesn't it?)


--------
Hold on, Daniel.
---------------------QUOTE-------------------


It would appear that VMartin is "mistaken".

Anybody wishing to see how similar the house mouse and human genomes are just need to go to

< http://www.ensembl.org/Mus_musculus/index.html >

and

< http://www.ensembl.org/Homo_sapiens/index.html >

Perhaps VMartin thinks novel genes are those that have fiction books written about them.
Posted by: Lou FCD on Dec. 01 2007,10:09

Quote (VMartin @ Dec. 01 2007,10:12)
My latest post has been deleted, so I 'll try it this way:
---------------------QUOTE-------------------


To the best of my knowledge, that is not true.  You had one post thus far moved to the BW by Steve at my request, and quite frankly I'm leaning toward continuing that practice.

Further discussion can be taken up by PM if you care to make a case for why that shouldn't happen.

Alternatively, you could contribute something more than "This one guy says Darwin sucks".

Either way.  

Again, moderation issues should be taken up via PM per Wesley's policy.  His board, his rules.  Get over it.
Posted by: JAM on Dec. 01 2007,15:10

Quote (Daniel Smith @ Nov. 30 2007,19:06)
A coin flip that produces a billion heads in a row makes you think "there might be a cause to it, but it might just as easily be a fluke (my emphasis)"?
Just as easily?  Astounding!  Do you realize what the odds are against such a thing happening?  At some point you have to admit that such a feat is impossible in a fair coin toss.
Pardon me for saying this, but I don't see how any rational person would not conclude that the fix was in.
On the other hand, I think I understand the rationale behind your denial:  If you ascribe a "cut off point" - where something is beyond the realm of chance - you run the risk of negating the mechanism behind the MET.
---------------------QUOTE-------------------


Your analogy is false, and you're regurgitating the Primary Creationist Lie.

It's easy to get a billion heads in a row if you filter the coin tosses with selection.

Why do you persist with the lie of claiming that because mutation is random only wrt fitness, that therefore all of evolution is random?

Why is defending your political position so much more important than obeying the Ninth Commandment, one of the ones that Jesus Christ reiterated?
Posted by: JAM on Dec. 01 2007,15:13

Quote (Tracy P. Hamilton @ Dec. 01 2007,09:40)
Quote (VMartin @ Dec. 01 2007,09:12)
My latest post has been deleted, so I 'll try it this way:

Jam
     

---------------------QUOTE-------------------

Dead wrong. Mice and humans share 100.0% of their genes. The number present in one and lacking in the other is in the single digits. There goes your hypothesis...

---------------------QUOTE-------------------



If they share 100,0% genes then it back ups frontloading very well I would say. It would mean that also regulatory genes are the same and it was only due to rearrangements of pre-existing genes in DNA that led to the difference between mice and  human in the distant past.

(In that case the possible explanation could be also different composition of cytosole in gametes and zygotes of both species and consequently the difference between man and  mice could be only epigenetical. But is sounds too "German", neglecting the role of DNA in ontogenesis,  doesn't it?)


--------
Hold on, Daniel.
---------------------QUOTE-------------------


It would appear that VMartin is "mistaken".

Anybody wishing to see how similar the house mouse and human genomes are just need to go to

< http://www.ensembl.org/Mus_musculus/index.html >

and

< http://www.ensembl.org/Homo_sapiens/index.html >

Perhaps VMartin thinks novel genes are those that have fiction books written about them.
---------------------QUOTE-------------------


Tracy, your post was unclear. Are you disputing that the number of orthologs present in humans but absent in mice (and vice versa) is tiny? Remember, I'm not talking about sequence identity. The question I'm answering is, "In how many cases do mice lack an ortholog of human gene XXX?"
Posted by: JAM on Dec. 01 2007,15:38

Quote (Daniel Smith @ Nov. 30 2007,19:15)
   
Quote (swbarnes2 @ Nov. 30 2007,19:05)
       
Quote (Daniel Smith @ Nov. 29 2007,21:06)
     
After awhile, these endless strings of hollow accusations will say more about your character than mine.I may have said things which I thought to be true at the time,
---------------------QUOTE-------------------


---------------------QUOTE-------------------


---------------------QUOTE-------------------


That's not what you did, though. You stated things that you merely WISHED were true as fact, and when you learned that they weren't true you didn't admit that you were wrong. That is lying.
 

---------------------QUOTE-------------------
 

---------------------QUOTE-------------------
   

---------------------QUOTE-------------------
and later found they weren't (in which case I've retracted them), but I've never ever lied.
---------------------QUOTE-------------------


---------------------QUOTE-------------------


---------------------QUOTE-------------------


You have not come anywhere close to retracting all of the false claims you've made.
  [quote]    
Quote (swbarnes2 @ Nov. 30 2007,19:05)
...You claimed that the VISTA data supported your hypothesis.  Then, you claimed that you didn't understand the VISTA data well enough to draw any conclusions from it.  That makes your first statement a lie.
---------------------QUOTE-------------------


swbarnes, didn't you miss an additional flipflop on this one? Didn't Dan claim that all the evidence he had seen still confirmed his hypothesis?

Here's another lie:
   
Quote (Daniel Smith @ Nov. 10 2007 @ 11:26)
I am attempting to "open my eyes" to anything and everything.
---------------------QUOTE-------------------


Every time I've tried to get you to open your eyes to the NATURE of biological complexity, you've run away, so that clearly was a lie.


---------------------QUOTE-------------------
I have never lied.  I stand by that.
---------------------QUOTE-------------------


Then explain why you claimed that Atlantic and Pacific humpbacks have been reproductively separated for millions of years.


---------------------QUOTE-------------------
What you perceive as lies are statements made as the result of my own ignorance, and statements where I did not adequately explain my intended meaning  - nothing more - nothing less.
---------------------QUOTE-------------------


Then you should have retracted your false statements. Where did you retract your idiotic claim about the humpback whales, Dan?

BTW, what about your lie that Atlantic and Pacific populations of humpback whales have been separated for millions of years, when in reality, they hang out in Tierra del Fuego?

Do you know where that is?

Where did you retract that incredibly stupid false claim?
Posted by: Henry J on Dec. 01 2007,17:04



---------------------QUOTE-------------------
If they share 100,0% genes then it back ups frontloading very well I would say.
---------------------QUOTE-------------------



Having corresponding genes doesn't mean having the same alleles for those genes.

Henry
Posted by: swbarnes2 on Dec. 01 2007,19:48

Quote (Daniel Smith @ Nov. 30 2007,19:15)
I have never lied.  I stand by that.  What you perceive as lies are statements made as the result of my own ignorance, and statements where I did not adequately explain my intended meaning  - nothing more - nothing less.

---------------------QUOTE-------------------



I don't understand why you think that anyone cares what claims a dishonest person stands by.  Do you not get that that is the essential problem of being dishonest?

Do you also not see that saying "I'm honest, really" isn't going to work?  Because no one will pay attention to that, they are going to look at the posts you actually made.  

Every post you've made is recorded on this board.  Everyone can read what you have written, and knows "inadequate explanations" fail to explain your back-pedeling, and if you expect us to believe that you are ignorant of the contents of your own statements, then you are essentially pleading that you are not of sound mind.

Why do you think that not a soul has stepped forward to defend you?

It because everyone reading this board has come to the same conclusion regarding your posts.  

   

---------------------QUOTE-------------------
If you want to believe that I'm a liar - go ahead.  I really could care less what you believe.
---------------------QUOTE-------------------



Right.  That's why you keep trying in vain to defend your honor.  That's why you decided to portray yourself as too stupid properly assess your understanding of the data presented to you, rather than admit that you just lied about what it meant.

Well, congrats.  Now we all think that you are a liar, and stupid to boot.  Well done.

   

---------------------QUOTE-------------------
If you want to talk about ideas and issues, that's fine.
---------------------QUOTE-------------------



But you posts demonstrate that this will not work.  Your posts prove that you are not prepared, or maybe even able to deal with ideas and issues honestly.

For instance, your prediction about the number of orphan genes between mice and humans.  Your theology told you to expect half the total completment of genes in humans to no have orthologs.  That's about 15,000.  You were wrong by about 4 orders of magnitude.

An honest person would accept that this demonstration was proof that prediction by theology was a crappy method, and that looking at the data first works much, much better.  And that when the data doesn't match one's theological preferences, one ought to suck it up and accept reality.

But you will not do this.  You told us that you would not.  You will take this as a sign that you need to "look deeper".  You will refuse to accept the evidence until you "look deeper".  But you can't look deeper.  You don't know how.  You don't even know where to start.  So until pigs fly and hell freezes over, you will simply ignore that data.  

And in time, you will forget that anyone ever presented data that didn't tally with your precious theological wishes.  You will only remember being right.

No one who posted as you have done is going to behave any differently.

We all understand this about you.  The sad part is that we all understand you better than you understand yourself.
Posted by: IanBrown_101 on Dec. 02 2007,00:00

Quote (Daniel Smith @ Dec. 01 2007,01:06)
Quote (IanBrown_101 @ Nov. 29 2007,22:48)
             
Quote (Daniel Smith @ Nov. 30 2007,04:31)
             
Quote (IanBrown_101 @ Nov. 29 2007,22:07)
If you flip a coin 5 times and it comes out heads each time, I could say it was predestined. How the hell can you test that idea?
---------------------QUOTE-------------------


What if it comes out heads 1,000,000,000 times?
---------------------QUOTE-------------------

 
Then that's what happens.

It implies there might be a cause to it, but it might just as easily be a fluke. There would need to be some evidence that it COULDN'T happen by luck alone, otherwise you could attribute absolutely anything to intelligence.
---------------------QUOTE-------------------


A coin flip that produces a billion heads in a row makes you think "there might be a cause to it, but it might just as easily be a fluke (my emphasis)"?
Just as easily?  Astounding!  Do you realize what the odds are against such a thing happening?  At some point you have to admit that such a feat is impossible in a fair coin toss.
---------------------QUOTE-------------------


Why?



---------------------QUOTE-------------------

Pardon me for saying this, but I don't see how any rational person would not conclude that the fix was in.
On the other hand, I think I understand the rationale behind your denial:  If you ascribe a "cut off point" - where something is beyond the realm of chance - you run the risk of negating the mechanism behind the MET.
Maybe I'm wrong - I'm sure pretty much everyone here will say that I am - but that's what I think.
---------------------QUOTE-------------------



Then you are wrong. Just because something is unlikely doesn't mean it is impossible. It's unlikely to get a hole in one in golf on the same hole a number of times in a row, does that mean god made the ball go in?

You have to provide a theory we can DISPROVE (to within the limits of "proof").
Posted by: Daniel Smith on Dec. 02 2007,19:49

Quote (Erasmus @ FCD,Nov. 30 2007,19:18)
Daniel what examples of introduced species with parallel adaptations native species in a single or few generations are there?  i'm skeptical of that claim, but not having read Berg or ever having even seen the book I have no way to address this.
---------------------QUOTE-------------------


He gives many examples, I'll list a few.

Among cattle:
 

---------------------QUOTE-------------------
Neumayr, (1889, p. 128, note), following Wilckens, relates that Swiss Cattle, on being removed to Hungary, acquire certain features of the local Hungarian cattle, namely, long horns and legs.
Leo S. Berg, Nomogenesis, p. 280
---------------------QUOTE-------------------

 

---------------------QUOTE-------------------
Shorthorns, bred in Uruguay (Artigas), assume the outward appearance of the native cattle, the so-called "criollos."  
Ibid, p.  281
---------------------QUOTE-------------------

 

---------------------QUOTE-------------------
Simmental cows, purely bred in Hesse (Vogelsberg), in three generations became indistinguishable from the native Vogelsberg cattle (Kronacher, l.c., pp. 128, 129).
Ibid, p.  281
---------------------QUOTE-------------------



Among fishes, he cites "the observations of J. Schmidt (1920) on the viviparous fish Zoarces viviparus... caried out in Danish waters", in which transplanted fish varied in the number of vertebrae varied according to location.  He quotes Schmidt as saying:  

---------------------QUOTE-------------------
"It is therefore evident that the external conditions, altered through the transplantation, have decidedly raised the number of vertebrae in the population" (p. 184)
Ibid, p.  282
---------------------QUOTE-------------------



He cites another case of a moth, "Saturnia luna (or Actias Luna)", transplanted from Texas to Switzerland, in 1870 by "J. Boll":  

---------------------QUOTE-------------------
In America, the catepillar of this species feeds on the leaves of the hickory (Carya) and the black walnut tree (Juglans nigra).  In May, 1871, from the cocoons that had hibernated in Switzerland, emerged moths that were indistinguishable from the American typical form.  Some of these moths laid eggs, and the catepillars of this European generation fed on the leaves of the European walnut (Juglans regia).  They became pupae in the end of June, which early in August produced 35 moths.  These latter most unexpectedly exhibited so many points of difference from their maternal American form that they were described as a new species Saturnia bolli.  They differed in form, as well as pattern and coloration: the body and wings were larger and heavier, the antennae narrower, the longitudinal carmine stripe on the abdomen had disappeared, and the moth became lemon-yellow, instead of yellowish-green.  The carmine marginal stripe on the anterior wings had quite disappeared. (M. Wagner, 1889, pp. 307 - 310.)
Ibid, p.  283
---------------------QUOTE-------------------

These are just a few of the examples he cites.  I don't have time to list any more right now.  I'd recommend looking for his book - used - on Amazon.com.  That's where I got my copy.
Posted by: Daniel Smith on Dec. 02 2007,19:56

Quote (IanBrown_101 @ Dec. 02 2007,00:00)
 
Quote (Daniel Smith @ Dec. 01 2007,01:06)
 
Quote (IanBrown_101 @ Nov. 29 2007,22:48)
               
Quote (Daniel Smith @ Nov. 30 2007,04:31)
                 
Quote (IanBrown_101 @ Nov. 29 2007,22:07)
If you flip a coin 5 times and it comes out heads each time, I could say it was predestined. How the hell can you test that idea?
---------------------QUOTE-------------------


What if it comes out heads 1,000,000,000 times?
---------------------QUOTE-------------------

 
Then that's what happens.

It implies there might be a cause to it, but it might just as easily be a fluke. There would need to be some evidence that it COULDN'T happen by luck alone, otherwise you could attribute absolutely anything to intelligence.
---------------------QUOTE-------------------


A coin flip that produces a billion heads in a row makes you think "there might be a cause to it, but it might just as easily be a fluke (my emphasis)"?
Just as easily?  Astounding!  Do you realize what the odds are against such a thing happening?  At some point you have to admit that such a feat is impossible in a fair coin toss.
---------------------QUOTE-------------------


Why?

 

---------------------QUOTE-------------------

Pardon me for saying this, but I don't see how any rational person would not conclude that the fix was in.
On the other hand, I think I understand the rationale behind your denial:  If you ascribe a "cut off point" - where something is beyond the realm of chance - you run the risk of negating the mechanism behind the MET.
Maybe I'm wrong - I'm sure pretty much everyone here will say that I am - but that's what I think.
---------------------QUOTE-------------------



Then you are wrong. Just because something is unlikely doesn't mean it is impossible. It's unlikely to get a hole in one in golf on the same hole a number of times in a row, does that mean god made the ball go in?

You have to provide a theory we can DISPROVE (to within the limits of "proof").
---------------------QUOTE-------------------


Aren't there whole theories of probability designed to determining the "unlikelihood" of something?  It's not like one thing is just as unlikely as another.  I seriously doubt that getting several holes in one on the same hole is just as unlikely as getting a billion heads in a row in a fair coin toss.  I may be wrong though.
Posted by: IanBrown_101 on Dec. 02 2007,22:00

Quote (Daniel Smith @ Dec. 03 2007,01:56)
Quote (IanBrown_101 @ Dec. 02 2007,00:00)
 
Quote (Daniel Smith @ Dec. 01 2007,01:06)
   
Quote (IanBrown_101 @ Nov. 29 2007,22:48)
                 
Quote (Daniel Smith @ Nov. 30 2007,04:31)
                 
Quote (IanBrown_101 @ Nov. 29 2007,22:07)
If you flip a coin 5 times and it comes out heads each time, I could say it was predestined. How the hell can you test that idea?
---------------------QUOTE-------------------


What if it comes out heads 1,000,000,000 times?
---------------------QUOTE-------------------

 
Then that's what happens.

It implies there might be a cause to it, but it might just as easily be a fluke. There would need to be some evidence that it COULDN'T happen by luck alone, otherwise you could attribute absolutely anything to intelligence.
---------------------QUOTE-------------------


A coin flip that produces a billion heads in a row makes you think "there might be a cause to it, but it might just as easily be a fluke (my emphasis)"?
Just as easily?  Astounding!  Do you realize what the odds are against such a thing happening?  At some point you have to admit that such a feat is impossible in a fair coin toss.
---------------------QUOTE-------------------


Why?

   

---------------------QUOTE-------------------

Pardon me for saying this, but I don't see how any rational person would not conclude that the fix was in.
On the other hand, I think I understand the rationale behind your denial:  If you ascribe a "cut off point" - where something is beyond the realm of chance - you run the risk of negating the mechanism behind the MET.
Maybe I'm wrong - I'm sure pretty much everyone here will say that I am - but that's what I think.
---------------------QUOTE-------------------



Then you are wrong. Just because something is unlikely doesn't mean it is impossible. It's unlikely to get a hole in one in golf on the same hole a number of times in a row, does that mean god made the ball go in?

You have to provide a theory we can DISPROVE (to within the limits of "proof").
---------------------QUOTE-------------------


Aren't there whole theories of probability designed to determining the "unlikelihood" of something?  It's not like one thing is just as unlikely as another.  I seriously doubt that getting several holes in one on the same hole is just as unlikely as getting a billion heads in a row in a fair coin toss.  I may be wrong though.
---------------------QUOTE-------------------


The point is it doesn't matter how unlikely it is, but it happened.

Like JAM said, if you filter the coin toss with selection, then it's not even remotely as odd.
Posted by: Daniel Smith on Dec. 02 2007,22:57

Quote (IanBrown_101 @ Dec. 02 2007,22:00)
Quote (Daniel Smith @ Dec. 03 2007,01:56)
 
Quote (IanBrown_101 @ Dec. 02 2007,00:00)
   
Quote (Daniel Smith @ Dec. 01 2007,01:06)
     
Quote (IanBrown_101 @ Nov. 29 2007,22:48)
                   
Quote (Daniel Smith @ Nov. 30 2007,04:31)
                   
Quote (IanBrown_101 @ Nov. 29 2007,22:07)
If you flip a coin 5 times and it comes out heads each time, I could say it was predestined. How the hell can you test that idea?
---------------------QUOTE-------------------


What if it comes out heads 1,000,000,000 times?
---------------------QUOTE-------------------

 
Then that's what happens.

It implies there might be a cause to it, but it might just as easily be a fluke. There would need to be some evidence that it COULDN'T happen by luck alone, otherwise you could attribute absolutely anything to intelligence.
---------------------QUOTE-------------------


A coin flip that produces a billion heads in a row makes you think "there might be a cause to it, but it might just as easily be a fluke (my emphasis)"?
Just as easily?  Astounding!  Do you realize what the odds are against such a thing happening?  At some point you have to admit that such a feat is impossible in a fair coin toss.
---------------------QUOTE-------------------


Why?

     

---------------------QUOTE-------------------

Pardon me for saying this, but I don't see how any rational person would not conclude that the fix was in.
On the other hand, I think I understand the rationale behind your denial:  If you ascribe a "cut off point" - where something is beyond the realm of chance - you run the risk of negating the mechanism behind the MET.
Maybe I'm wrong - I'm sure pretty much everyone here will say that I am - but that's what I think.
---------------------QUOTE-------------------



Then you are wrong. Just because something is unlikely doesn't mean it is impossible. It's unlikely to get a hole in one in golf on the same hole a number of times in a row, does that mean god made the ball go in?

You have to provide a theory we can DISPROVE (to within the limits of "proof").
---------------------QUOTE-------------------


Aren't there whole theories of probability designed to determining the "unlikelihood" of something?  It's not like one thing is just as unlikely as another.  I seriously doubt that getting several holes in one on the same hole is just as unlikely as getting a billion heads in a row in a fair coin toss.  I may be wrong though.
---------------------QUOTE-------------------


The point is it doesn't matter how unlikely it is, but it happened.

Like JAM said, if you filter the coin toss with selection, then it's not even remotely as odd.
---------------------QUOTE-------------------


Ah, but what kind of selection?
Intelligent selection - yes.
Natural selection?  Not so sure about that one.  You'd have to explain how natural selection could cause a billion in a row without intelligent input.
Posted by: JAM on Dec. 03 2007,01:25

Quote (Daniel Smith @ Nov. 30 2007,18:04)
Quote (JAM @ Nov. 30 2007,00:30)
   
Quote (Daniel Smith @ Nov. 29 2007,22:14)

Does < this > qualify?              
---------------------QUOTE-------------------


Not even close, because they aren't talking about endocytosis, they attribute any design to evolution, and they point out the stupidity of the process:
               

---------------------QUOTE-------------------
The resulting terrestrial mammalian kidney is enor-
mously inefficient and energy-consuming, illustrating the tink-
ering premise. Smith (17) famously stated, “What engineer,
wishing to regulate the composition of the internal environ-
ment of the body on which the function of every bone, gland,
muscle, and nerve depends, would devise a scheme that oper-
ated by throwing the whole thing out 16 times a day and rely
on grabbing from it, as it fell to earth, only those precious
elements which he wanted to keep?”
---------------------QUOTE-------------------


So if God designed your kidneys, He is stupid. Who would worship such a god?
---------------------QUOTE-------------------


Interesting then how man cannot improve on such a "flawed" design.  Dialysis is no where near as effective as the natural kidney - in spite of all it's supposed flaws.
---------------------QUOTE-------------------


Really?

Kidneys filter the blood 24/7. How much time does a dialysis patient spend hooked up?

Besides, we're discussing intelligent design, not its implementation. Why are you trying to change the subject?
Posted by: oldmanintheskydidntdoit on Dec. 03 2007,03:10

Quote (Daniel Smith @ Dec. 02 2007,22:57)
Quote (IanBrown_101 @ Dec. 02 2007,22:00)
 
Quote (Daniel Smith @ Dec. 03 2007,01:56)
 
Quote (IanBrown_101 @ Dec. 02 2007,00:00)
     
Quote (Daniel Smith @ Dec. 01 2007,01:06)
     
Quote (IanBrown_101 @ Nov. 29 2007,22:48)
                   
Quote (Daniel Smith @ Nov. 30 2007,04:31)
                     
Quote (IanBrown_101 @ Nov. 29 2007,22:07)
If you flip a coin 5 times and it comes out heads each time, I could say it was predestined. How the hell can you test that idea?
---------------------QUOTE-------------------


What if it comes out heads 1,000,000,000 times?
---------------------QUOTE-------------------

 
Then that's what happens.

It implies there might be a cause to it, but it might just as easily be a fluke. There would need to be some evidence that it COULDN'T happen by luck alone, otherwise you could attribute absolutely anything to intelligence.
---------------------QUOTE-------------------


A coin flip that produces a billion heads in a row makes you think "there might be a cause to it, but it might just as easily be a fluke (my emphasis)"?
Just as easily?  Astounding!  Do you realize what the odds are against such a thing happening?  At some point you have to admit that such a feat is impossible in a fair coin toss.
---------------------QUOTE-------------------


Why?

     

---------------------QUOTE-------------------

Pardon me for saying this, but I don't see how any rational person would not conclude that the fix was in.
On the other hand, I think I understand the rationale behind your denial:  If you ascribe a "cut off point" - where something is beyond the realm of chance - you run the risk of negating the mechanism behind the MET.
Maybe I'm wrong - I'm sure pretty much everyone here will say that I am - but that's what I think.
---------------------QUOTE-------------------



Then you are wrong. Just because something is unlikely doesn't mean it is impossible. It's unlikely to get a hole in one in golf on the same hole a number of times in a row, does that mean god made the ball go in?

You have to provide a theory we can DISPROVE (to within the limits of "proof").
---------------------QUOTE-------------------


Aren't there whole theories of probability designed to determining the "unlikelihood" of something?  It's not like one thing is just as unlikely as another.  I seriously doubt that getting several holes in one on the same hole is just as unlikely as getting a billion heads in a row in a fair coin toss.  I may be wrong though.
---------------------QUOTE-------------------


The point is it doesn't matter how unlikely it is, but it happened.

Like JAM said, if you filter the coin toss with selection, then it's not even remotely as odd.
---------------------QUOTE-------------------


Ah, but what kind of selection?
Intelligent selection - yes.
Natural selection?  Not so sure about that one.  You'd have to explain how natural selection could cause a billion in a row without intelligent input.
---------------------QUOTE-------------------


er, some sort of feedback mechanism perhaps?
Posted by: VMartin on Dec. 03 2007,11:58

Quote (Tracy P. Hamilton @ Dec. 01 2007,09:40)
   
Quote (VMartin @ Dec. 01 2007,09:12)
My latest post has been deleted, so I 'll try it this way:

Jam
           

---------------------QUOTE-------------------

Dead wrong. Mice and humans share 100.0% of their genes. The number present in one and lacking in the other is in the single digits. There goes your hypothesis...

---------------------QUOTE-------------------



If they share 100,0% genes then it back ups frontloading very well I would say. It would mean that also regulatory genes are the same and it was only due to rearrangements of pre-existing genes in DNA that led to the difference between mice and  human in the distant past.

(In that case the possible explanation could be also different composition of cytosole in gametes and zygotes of both species and consequently the difference between man and  mice could be only epigenetical. But is sounds too "German", neglecting the role of DNA in ontogenesis,  doesn't it?)


--------
Hold on, Daniel.
---------------------QUOTE-------------------


It would appear that VMartin is "mistaken".

Anybody wishing to see how similar the house mouse and human genomes are just need to go to

< http://www.ensembl.org/Mus_musculus/index.html >

and

< http://www.ensembl.org/Homo_sapiens/index.html >

Perhaps VMartin thinks novel genes are those that have fiction books written about them.
---------------------QUOTE-------------------


I skimmed the links but I am not wise from them. The misunderestanding rests on my opinion on the concept of gene itself. We should perhaps use alleles instead genes (Dawkins "Selfish gene" is a nonsense, the book should have been titled "Selfish allele").

As Henry noticed:

   

---------------------QUOTE-------------------

Having corresponding genes doesn't mean having the same alleles for those genes.

---------------------QUOTE-------------------



So let say we have a gene for coloration of Iris. Let say human have 5 alleles of this gene and mice also 5 alleles. The average difference between human alleles is let say 15 base pairs and for mice the average difference is also 15 base pairs.

I do't know which alleles of humans and mice are compared on those genes comparisions. Because you can hit on "blue alleles"  in mice and human and such comparision could show a small synonymous difference, or no difference at all.

But you can hit on red allele of mice  having no counterpart in human genome. What will you do? Will you compare this red mice allele with brown human allele?

Obviously difference in pair bases would be much more greater in this case. Consequently it could be inferred that both species diverged sooner as they did.

So I am not expert but I suppose there must exist something like average human allele and average mouse allele or what when we are comparing their genes. Or am I wrong?

The second question (closely connected) is if I give you an allele from mice  would you be able to tell it apart from human alleles because it is more different than are different human alleles of the same gene from each other?
Posted by: Daniel Smith on Dec. 04 2007,18:54

Quote (VMartin @ Dec. 03 2007,11:58)
I skimmed the links but I am not wise from them. The misunderestanding rests on my opinion on the concept of gene itself. We should perhaps use alleles instead genes (Dawkins "Selfish gene" is a nonsense, the book should have been titled "Selfish allele").

As Henry noticed:

         

---------------------QUOTE-------------------

Having corresponding genes doesn't mean having the same alleles for those genes.

---------------------QUOTE-------------------



So let say we have a gene for coloration of Iris. Let say human have 5 alleles of this gene and mice also 5 alleles. The average difference between human alleles is let say 15 base pairs and for mice the average difference is also 15 base pairs.

I do't know which alleles of humans and mice are compared on those genes comparisions. Because you can hit on "blue alleles"  in mice and human and such comparision could show a small synonymous difference, or no difference at all.

But you can hit on red allele of mice  having no counterpart in human genome. What will you do? Will you compare this red mice allele with brown human allele?

Obviously difference in pair bases would be much more greater in this case. Consequently it could be inferred that both species diverged sooner as they did.

So I am not expert but I suppose there must exist something like average human allele and average mouse allele or what when we are comparing their genes. Or am I wrong?

The second question (closely connected) is if I give you an allele from mice  would you be able to tell it apart from human alleles because it is more different than are different human alleles of the same gene from each other?
---------------------QUOTE-------------------


Hi Martin,

I've often wondered the same thing.

How do they settle on a "genome" when there can be much variation within species?

I know of < one example > in mtDNA where a single species was found to have 8% sequence divergence.
Posted by: JAM on Dec. 04 2007,21:12

Quote (Daniel Smith @ Dec. 04 2007,18:54)
How do they settle on a "genome" when there can be much variation within species?

I know of < one example > in mtDNA where a single species was found to have 8% sequence divergence.
---------------------QUOTE-------------------


How much divergence do you think there is between alleles of the genes contained in and haplotypes of the Major Histocompatibility Complex, Dan?

How much divergence among V genes for immunglobulins and T-cell receptors? Hint: "V" is for variable.

Would you mind directing me to your post in which you retracted and apologized for your ridiculously false claim that Atlantic and Pacific humpback whales have been reproductively isolated from each other for millions of years, when Tierra del Fuego is a prime place for watching them?
Posted by: VMartin on Dec. 05 2007,00:07

   

---------------------QUOTE-------------------

Hi Martin,

I've often wondered the same thing.

How do they settle on a "genome" when there can be much variation within species?

I know of one example in mtDNA where a single species was found to have 8% sequence divergence.

---------------------QUOTE-------------------



Hi Daniel,

I have tried to find out on internet something about human heterozygosity or polymorphism. There are surprisingly few articles about the topic. The most articles deal with polymorphism of specific genes.

Yet some articles claim that heterozygosity is about 6%. So I still don't know which genes (having only 1 allele?) are used comparing human vs mice genome.

The whole thing (using coding genes) seems to me be very confusing. Comparing mice vs human genes scientists came to the conclusion that difference is let say 10% and using molecular clocks it means their human/mice ancestors diverged 70 million years ago.

But comparing genome of two people which difference could be 3% no one claims their respective ancestors diverged 25 millions years ago.

I would say the only correct scientific method would be comparing those genes of mice and human having only one allele. But I am afraid no one knows which they are, so we are comparing everything with everything and the results consequently vary sometimes (don't scientists change the number of the same genes between human and chimps every two years? But there is much more polymorphism in chimps than in humans, so again maybe the result depend which heterozygotes from both species they are comparing or what).

And last but not at least. Comparing differences between genome of brother and the genome of his sister there are changes let say in 100 genes having (different alleles of it). But those differences are not caused by "random mutation" purified by natural selection but only due "frontloading". Otherwise using molecular clocks we could make absurd conclusions that their respective parents diverged 5,2 millions years ago.
Posted by: oldmanintheskydidntdoit on Dec. 05 2007,02:52

Quote (VMartin @ Dec. 05 2007,00:07)
only due "frontloading". Otherwise using molecular clocks we could make absurd conclusions that their respective parents diverged 5,2 millions years ago.
---------------------QUOTE-------------------


Hi,
What's frontloading? Could you define it please?

Thanks
Posted by: Lou FCD on Dec. 05 2007,06:38

Quote (VMartin @ Dec. 05 2007,01:07)
And last but not at least. Comparing differences between genome of brother and the genome of his sister there are changes let say in 100 genes having (different alleles of it). But those differences are not caused by "random mutation" purified by natural selection but only due "frontloading".
---------------------QUOTE-------------------



So your alternative hypothesis to modern evolutionary theory is "In the beginning, God did it"?  Please ask whoever is feeding you your lines to explain what sort of predictions you would make from that, and how you would go about testing those predictions.

Also, when next you speak to your "Intelligent" Designer guy, let him know I'd like a refund or exchange on my spinal column, it seems to be defective and I'm frequently in some serious pain.  And it's deteriorating.  While we're on the subject of piss-poor coding, designing, and manufacturing, I'd also like to get refunds and exchanges for the following:

My wife's gall bladder, appendix, large (I think it was the large - whichever one anchors the appendix) intestine, and the whole of her internal girly parts.  They've all had to be removed (well the intestine was a partial) due to manufacturing defects at the frontloading factory.

My son's ankle.  It's a wreck and really should have held up more than 13 years.  You'd think the All Powerful Frontloader would have done a better job with that.  Fortunately, it's still under warranty (although aren't major manufacturing defects an exception to the warranty laws here in the U.S.?).

Also, I'd like to see the code for my Pop.  Is that open-source?  He's having issues of dizziness and fainting, etc., and the doctors don't seem to be able to pin it down.  If they could see the actual code, perhaps they could find the bug and fix it.

Just leave me a message here (or just post the code, I'm sure he won't mind), I have to go back to the hospital to visit my Pop and will be in and out all day.

Thanks.

Lou

P.S. If your "Intelligent" Frontloader needs to make a little extra Christmas money, let him know that I heard that Microsoft was hiring half-assed code writers as temps to work on Vista.  He could look into that.
Posted by: VMartin on Dec. 05 2007,12:50

You didn't answer my previuos questions. Or using another point of view:

1) how great is an average difference between coding regions of  two different  human haplotypes choosen by random

2) how great is an average difference between the coding regions of two different mice haplotypes choosen by random
 
3) how great is an average difference between coding regions of a mouse and human haplotypes choosen by random.

I suppose the questions are very simple, aren't they?
Posted by: JAM on Dec. 05 2007,12:54

Quote (VMartin @ Dec. 05 2007,12:50)
You didn't answer my previuos questions. Or using another point of view:

1) how great is an average difference between coding regions of  two different  human haplotypes choosen by random

2) how great is an average difference between the coding regions of two different mice haplotypes choosen by random
 
3) how great is an average difference between coding regions of a mouse and human haplotypes choosen by random.

I suppose the questions are very simple, aren't they?
---------------------QUOTE-------------------


No, they aren't. Do you know what the term "haplotype" means? If not, why are you using it?
Posted by: Arden Chatfield on Dec. 05 2007,12:57

Quote (VMartin @ Dec. 05 2007,12:50)
You didn't answer my previuos questions. Or using another point of view:

1) how great is an average difference between coding regions of  two different  human haplotypes choosen by random

2) how great is an average difference between the coding regions of two different mice haplotypes choosen by random
 
3) how great is an average difference between coding regions of a mouse and human haplotypes choosen by random.

I suppose the questions are very simple, aren't they?
---------------------QUOTE-------------------


So is the question of what's responsible for variation in nature, but you never answered that one either.
Posted by: VMartin on Dec. 05 2007,14:12

Jam



---------------------QUOTE-------------------

No, they aren't. Do you know what the term "haplotype" means? If not, why are you using it?

---------------------QUOTE-------------------



I mean all alleles in a haploid cell. In human it is sex cell.

Can you answer my questions or no?
Posted by: Arden Chatfield on Dec. 05 2007,14:15

Quote (VMartin @ Dec. 05 2007,14:12)
Jam



---------------------QUOTE-------------------

No, they aren't. Do you know what the term "haplotype" means? If not, why are you using it?

---------------------QUOTE-------------------



I mean all alleles in a haploid cell. In human it is sex cell.

Can you answer my questions or no?
---------------------QUOTE-------------------


Martin, don't you think it's just awful when people here refuse to answer questions?
Posted by: swbarnes2 on Dec. 05 2007,14:33

Quote (VMartin @ Dec. 05 2007,14:12)

I mean all alleles in a haploid cell. In human it is sex cell.
---------------------QUOTE-------------------



That's not what the haplotype is.  You have no idea what you are talking about.  You just picked a technical word that sounded nice, you believed that you know so much about genetics that there can't possibly a use for the word that you didn't already know, and you used it in an attempt to sound like you know what you are talking about.

You can't compare humans and mice like that.  There's been almost no genomic work done on mice breeding ordinarily in the wild.  What we have is tons of sequence data between dozens of different inbred lab strains.  Within a strain, there are virtually no genetic differences.  There are a lot of differences between strains, based on the history of each particular strain, and the genetic make-up of the founder animals.

If you think that this in any way resembles the evolutionary history of humans, I'd like to see you demonstrate it.  Otherwise, the honest thing to do is admit that your question is dumb.

We all anticipate that the honest thing is beyond you.
Posted by: JAM on Dec. 05 2007,14:50

Quote (VMartin @ Dec. 05 2007,14:12)
Jam



---------------------QUOTE-------------------

No, they aren't. Do you know what the term "haplotype" means? If not, why are you using it?

---------------------QUOTE-------------------



I mean all alleles in a haploid cell. In human it is sex cell.
---------------------QUOTE-------------------


That's not even close to what the term means.

If you want people to answer your questions, you have to speak their language--even if you disagree with their conclusions.
Posted by: VMartin on Dec. 05 2007,15:17

Quote (JAM @ Dec. 05 2007,14:50)
 
Quote (VMartin @ Dec. 05 2007,14:12)
Jam

   

---------------------QUOTE-------------------

No, they aren't. Do you know what the term "haplotype" means? If not, why are you using it?

---------------------QUOTE-------------------



I mean all alleles in a haploid cell. In human it is sex cell.
---------------------QUOTE-------------------


That's not even close to what the term means.

If you want people to answer your questions, you have to speak their language--even if you disagree with their conclusions.
---------------------QUOTE-------------------


There are more approaches how a haplotype could be defined. Obviously you have never heard yet about this definition:

"Another way to think about it is that a haplotype is half of a genotype."

< http://www.everythingbio.com/glos/definition.php?word=haplotype >


or wikipedia

"The term haplotype is a portmanteau of "haploid genotype."

In the book "Evolutionary biology" by Flegr there are more definition of haplotype and one of them is "combination of all alleles in a genome of a haploid cell".
Posted by: VMartin on Dec. 05 2007,15:22

swbarnes2



---------------------QUOTE-------------------

Within a strain, there are virtually no genetic differences.

---------------------QUOTE-------------------



Do you mean their genomes are like those of one-egg twins? It would mean that all individuals of the strain are almost homozygous for every gene in their genome. Am I wrong? It seems to me unbelievable.
Posted by: Richard Simons on Dec. 05 2007,18:32

Quote (VMartin @ Dec. 05 2007,15:22)
swbarnes2



---------------------QUOTE-------------------

Within a strain, there are virtually no genetic differences.

---------------------QUOTE-------------------



Do you mean their genomes are like those of one-egg twins? It would mean that all individuals of the strain are almost homozygous for every gene in their genome. Am I wrong? It seems to me unbelievable.
---------------------QUOTE-------------------


That is the intent of doing the inbreeding.
Posted by: JAM on Dec. 05 2007,19:04

Quote (VMartin @ Dec. 05 2007,15:17)
 
Quote (JAM @ Dec. 05 2007,14:50)
   
Quote (VMartin @ Dec. 05 2007,14:12)
Jam

     

---------------------QUOTE-------------------

No, they aren't. Do you know what the term "haplotype" means? If not, why are you using it?

---------------------QUOTE-------------------



I mean all alleles in a haploid cell. In human it is sex cell.
---------------------QUOTE-------------------


That's not even close to what the term means.

If you want people to answer your questions, you have to speak their language--even if you disagree with their conclusions.
---------------------QUOTE-------------------


There are more approaches how a haplotype could be defined. Obviously you have never heard yet about this definition:

"Another way to think about it is that a haplotype is half of a genotype."

< http://www.everythingbio.com/glos/definition.php?word=haplotype >


---------------------QUOTE-------------------



That page provides the proper definition I'm using:
"A haplotype, a contraction of the phrase "haploid genotype", is a set of closely linked genetic markers present on one chromosome which tend to be inherited together (not easily separable by recombination)."

Can't you read? That definition does not even suggest "...all alleles in a haploid cell. In human it is sex cell."
Posted by: IanBrown_101 on Dec. 05 2007,20:29

Quote (Lou FCD @ Dec. 05 2007,12:38)
Quote (VMartin @ Dec. 05 2007,01:07)
And last but not at least. Comparing differences between genome of brother and the genome of his sister there are changes let say in 100 genes having (different alleles of it). But those differences are not caused by "random mutation" purified by natural selection but only due "frontloading".
---------------------QUOTE-------------------



So your alternative hypothesis to modern evolutionary theory is "In the beginning, God did it"?  Please ask whoever is feeding you your lines to explain what sort of predictions you would make from that, and how you would go about testing those predictions.

Also, when next you speak to your "Intelligent" Designer guy, let him know I'd like a refund or exchange on my spinal column, it seems to be defective and I'm frequently in some serious pain.  And it's deteriorating.  While we're on the subject of piss-poor coding, designing, and manufacturing, I'd also like to get refunds and exchanges for the following:

My wife's gall bladder, appendix, large (I think it was the large - whichever one anchors the appendix) intestine, and the whole of her internal girly parts.  They've all had to be removed (well the intestine was a partial) due to manufacturing defects at the frontloading factory.

My son's ankle.  It's a wreck and really should have held up more than 13 years.  You'd think the All Powerful Frontloader would have done a better job with that.  Fortunately, it's still under warranty (although aren't major manufacturing defects an exception to the warranty laws here in the U.S.?).

Also, I'd like to see the code for my Pop.  Is that open-source?  He's having issues of dizziness and fainting, etc., and the doctors don't seem to be able to pin it down.  If they could see the actual code, perhaps they could find the bug and fix it.

Just leave me a message here (or just post the code, I'm sure he won't mind), I have to go back to the hospital to visit my Pop and will be in and out all day.

Thanks.

Lou

P.S. If your "Intelligent" Frontloader needs to make a little extra Christmas money, let him know that I heard that Microsoft was hiring half-assed code writers as temps to work on Vista.  He could look into that.
---------------------QUOTE-------------------


I would also like a refund for my heart please.

You know, needing multiple major surgeries, and effectively having to live out my life on the slow lane kinda puts a cramp on my life. The nearly dying at birth and having to be transported around half the length of the country kinda sucked too. although making the Liverpool Echo was kinda cool.
Posted by: Lou FCD on Dec. 05 2007,20:38

Quote (IanBrown_101 @ Dec. 05 2007,21:29)
I would also like a refund for my heart please.

You know, needing multiple major surgeries, and effectively having to live out my life on the slow lane kinda puts a cramp on my life. The nearly dying at birth and having to be transported around half the length of the country kinda sucked too. although making the Liverpool Echo was kinda cool.
---------------------QUOTE-------------------


I'm with ya' Ian.

Look, I won't deny it's kinda cool to show people X-Rays of the cervical area of my spine and watch their skin crawl, but that whole large titanium plate screwed inside my neck holding my head on thing is kinda creepy at the end of the day.

I'd really like to swap out my spine for a new, better designed model.
Posted by: Erasmus, FCD on Dec. 05 2007,20:46

Sounds-a Like-a You-Guys-a need-a Jeeeeeeeeeeeee-sus-ah!!!  Brother he's the one-ah that's gonn-ah Heeeeeeeeeeeeeeeeal Ya!

try here:


Not trivializing, I'm just saying.  jesus is on the mainline, tell him what you want.
Posted by: Arden Chatfield on Dec. 05 2007,22:46

Quote (Lou FCD @ Dec. 05 2007,20:38)
 
Quote (IanBrown_101 @ Dec. 05 2007,21:29)
I would also like a refund for my heart please.

You know, needing multiple major surgeries, and effectively having to live out my life on the slow lane kinda puts a cramp on my life. The nearly dying at birth and having to be transported around half the length of the country kinda sucked too. although making the Liverpool Echo was kinda cool.
---------------------QUOTE-------------------


I'm with ya' Ian.

Look, I won't deny it's kinda cool to show people X-Rays of the cervical area of my spine and watch their skin crawl, but that whole large titanium plate screwed inside my neck holding my head on thing is kinda creepy at the end of the day.

I'd really like to swap out my spine for a new, better designed model.
---------------------QUOTE-------------------


Guys, guys, guys. You're missing the point. Ian's bum ticker and Lou's bum back are due to the Fall. You see, that naked guy with the leaf screwed up, so because of that we have lower back pain, heart disease, impacted wisdom teeth, appendicitis, osteoperosis, all that.

So you see, it's really our fault cause we're bad.

So this shouldn't interfere with VM's pantloading theory, whatever it is.
Posted by: VMartin on Dec. 06 2007,03:12

Richard Simons



---------------------QUOTE-------------------

That is the intent of doing the inbreeding.

---------------------QUOTE-------------------



You are right. After 20 or 40 inbred generations mice strains are almost homozygous.  Mice are supposed to be polymorphic in 35% of their genes.

So I suppose that if we compare mice genome between two different mice strains we will obtain difference in 10.500 loci. It is a great difference and using molecular clocks here I would say we would obtain the result of divergence more than several million years which is much more  greater than 20 (or 40) generations.


In how many loci we obtain difference comparing human vs mice genome in average? Is it much more than 35%?
Any link?

(I suppose mice and human have 30.000 loci and heterozygosity of human is 6%).
Posted by: VMartin on Dec. 06 2007,03:34

JAM

   

---------------------QUOTE-------------------

Can't you read? That definition does not even suggest "...all alleles in a haploid cell. In human it is sex cell."

---------------------QUOTE-------------------



I can read. I can read also this:


In the case of diploid organisms such as humans, a genome-wide haplotype comprises one member of the pair of alleles for each locus (that is, half of a diploid genome).


But I don't want to dispute with you which definition is correct. I have no problem accept yours as better for scientists and formulate my questions without using "haplotype".I would like to know your opinion about average genetic difference between  mice and human.

First you have written that 100% genes are same.  I have found this:


This is what was actually determined: 99% of mouse genes have homologues in man (the actual protein similarity is much less than 99%....

80% of mouse genes that have a match on the same syntenic region in man are also the best match for that human gene.


< http://www.evolutionpages.com/Mouse%20genome%20genes.htm >


What do they mean using "the best match"? Exactly or synonymous mutation or what?

If scientists speak about genes I am not very wise from it. I would like to know how many different alleles there are between mice and human actually and how great that difference is in let say in  base-pairs.

I suppose mice and human have also same alleles. How many?

(Heterozygosity of mice 35%, humans 6%, 20.000-30.000
genes. Maybe 35% is overesimated number for 10,500  polymorphic loci in mice genome due my incapacity to compute it more exactly).
Posted by: IanBrown_101 on Dec. 07 2007,00:03

Come on Martin, I want to know where I file my complaint to the moron designer who nearly killed me right after I was born and has put limitations on my life since the doctors saved me.
Posted by: VMartin on Dec. 07 2007,12:42

Lou, IanBrown

I feel sorry for both of you.
If you are looking for God I think you are doing well.

Anyway I am not a missionary and I would prefer some answers to my questions.
Posted by: Arden Chatfield on Dec. 07 2007,12:47

Quote (VMartin @ Dec. 07 2007,12:42)
Anyway I am not a missionary and I would prefer some answers to my questions.
---------------------QUOTE-------------------


Our friend Martin seems not to have a grasp of irony.
Posted by: JAM on Dec. 07 2007,18:22

Quote (VMartin @ Dec. 06 2007,03:34)
JAM

         

---------------------QUOTE-------------------

Can't you read? That definition does not even suggest "...all alleles in a haploid cell. In human it is sex cell."

---------------------QUOTE-------------------


I can read. I can read also this:

In the case of diploid organisms such as humans, a genome-wide haplotype comprises one member of the pair of alleles for each locus (that is, half of a diploid genome).

---------------------QUOTE-------------------


But I didn't use the adjective "genome-wide," so it should be obvious to anyone who can read that I didn't mean that.


---------------------QUOTE-------------------
But I don't want to dispute with you which definition is correct. I have no problem accept yours as better for scientists and formulate my questions without using "haplotype".I would like to know your opinion about average genetic difference between  mice and human.

First you have written that 100% genes are same.
---------------------QUOTE-------------------


That's not what I wrote.
 

---------------------QUOTE-------------------
I have found this:


This is what was actually determined: 99% of mouse genes have homologues in man (the actual protein similarity is much less than 99%....

---------------------QUOTE-------------------


That's not supported by the numbers on that page. 118/30000 = ~100%, not 99%. The author also uses "homologues" when he means "orthologs." There's a big difference, but there's little hope for you being able to understand it.


< http://www.evolutionpages.com/Mouse%20genome%20genes.htm >
 

---------------------QUOTE-------------------
What do they mean using "the best match"? Exactly or synonymous mutation or what?
---------------------QUOTE-------------------


Orthologs.
 

---------------------QUOTE-------------------
If scientists speak about genes I am not very wise from it. I would like to know how many different alleles there are between mice and human actually and how great that difference is in let say in  base-pairs.
---------------------QUOTE-------------------


Your question makes no sense. We only use the term "alleles" WITHIN a species.
Posted by: Richard Simons on Dec. 07 2007,19:20

Quote (VMartin @ Dec. 07 2007,12:42)
I would prefer some answers to my questions.
---------------------QUOTE-------------------


We're still waiting for your theory.
Posted by: Arden Chatfield on Dec. 07 2007,21:03

Quote (VMartin @ Dec. 07 2007,12:42)
Lou, IanBrown

I feel sorry for both of you.
If you are looking for God I think you are doing well.
---------------------QUOTE-------------------


And if they're not?
Posted by: Lou FCD on Dec. 07 2007,22:28

The only thing I'm looking for from VMartin is his alternative scientific theory to Evolution.

It's likely that I'll find sunshine in a horse's ass first however, so I'm not watching the clock.


Posted by: VMartin on Dec. 08 2007,08:56

JAM



---------------------QUOTE-------------------

But I didn't use the adjective "genome-wide," so it should be obvious to anyone who can read that I didn't mean that.

---------------------QUOTE-------------------



But it was not you who started the discussion about comparing "genome-wide" haplotypes. It was me. And I have used this definition. So it doesn't matter what did you mean or didn't mean speaking about another definition of haplotype.

         

---------------------QUOTE-------------------

That's not what I wrote.

---------------------QUOTE-------------------



OK. You didn't write that "100% genes are same". You wrote they "share 100.0% of their genes".


         

---------------------QUOTE-------------------

That's not supported by the numbers on that page. 118/30000 = ~100%, not 99%. The author also uses "homologues" when he means "orthologs." There's a big difference, but there's little hope for you being able to understand it.

---------------------QUOTE-------------------



Alec MacAndrew writes evolutionary articles. Perhaps he don't know what's the difference between "homologues" and "orthologs" and "paralogs", I don't know. But believe me I know what orthologs mean. You are not the only person in the world who knows it.



         

---------------------QUOTE-------------------

Your question makes no sense. We only use the term "alleles" WITHIN a species.

---------------------QUOTE-------------------



So we are comparing genes and no alleles? Perhaps you could briefly explain me how we compare genes without comparing their respective alleles.
Because obviously also Alec MacAndrew is as wrong as me:

         

---------------------QUOTE-------------------

The researchers compared human alleles with mouse and found that the mouse gene is identical to the major (most common) human allele in 67% of cases (similar to the 70% amino acids which are identical between mouse and man proteins).

---------------------QUOTE-------------------



< http://www.evolutionpages.com/Mouse%20genome%20proteins.htm >


These words nitpicking is interesting but my questions remain unanswered. Comparing alleles of two genomes of different mouse strains after 20 generation of imbreeding what would be the result as to their last common ancestor using molecular clocks? If the polymorphism of mouse genes is 35% wouldn't be the result several million years?
Posted by: JAM on Dec. 08 2007,20:49

Quote (VMartin @ Dec. 08 2007,08:56)
   

---------------------QUOTE-------------------

That's not supported by the numbers on that page. 118/30000 = ~100%, not 99%. The author also uses "homologues" when he means "orthologs." There's a big difference, but there's little hope for you being able to understand it.

---------------------QUOTE-------------------


Alec MacAndrew writes evolutionary articles.
---------------------QUOTE-------------------


Never heard of him. Clearly, he can't do percentages.
 

---------------------QUOTE-------------------
Perhaps he don't know what's the difference between "homologues" and "orthologs" and "paralogs", I don't know. But believe me I know what orthologs mean.
---------------------QUOTE-------------------


If you really did, you would realize that MacAndrew does not know.


---------------------QUOTE-------------------
 You are not the only person in the world who knows it.
---------------------QUOTE-------------------


I never made such a claim.
 

---------------------QUOTE-------------------
 
The researchers compared human alleles with mouse and found that the mouse gene is identical to the major (most common) human allele in 67% of cases (similar to the 70% amino acids which are identical between mouse and man proteins).

---------------------QUOTE-------------------

You omitted the context, VM. That was preceded by this sentence:
"Further evidence for common ancestry comes SNPs (Single Nucleotide Polymorphisms) – differences in genomes that exist in different humans where the variation is a single base pair substitution and the alleles co-exist in the population."

SNPs aren't genes. You're hopeless.

< http://www.evolutionpages.com/Mouse%20genome%20proteins.htm >

 

---------------------QUOTE-------------------
These words nitpicking is interesting but my questions remain unanswered. Comparing alleles of two genomes of different mouse strains after 20 generation of imbreeding what would be the result as to their last common ancestor using molecular clocks?
---------------------QUOTE-------------------


Molecular clocks are based on sequences that are not under selection. Inbreeding is the most intense artificial selection around, so your question is meaningless. We know where the strains came from:

< http://www.informatics.jax.org/morsebook/figures/figure16-1.shtml >
 

---------------------QUOTE-------------------
If the polymorphism of mouse genes is 35% wouldn't be the result several million years?=
---------------------QUOTE-------------------


No. Inbreeding reduces and eventually eliminates polymorphisms within a strain, so that the only ones one observes are caused by new mutations. Since the lab strains are closely related to each other to begin with, they are not representative of wild populations.

Again, you're hopeless.
Posted by: Daniel Smith on Dec. 09 2007,13:19

Quote (JAM @ Dec. 04 2007,21:12)
 
Quote (Daniel Smith @ Dec. 04 2007,18:54)
How do they settle on a "genome" when there can be much variation within species?

I know of < one example > in mtDNA where a single species was found to have 8% sequence divergence.
---------------------QUOTE-------------------


How much divergence do you think there is between alleles of the genes contained in and haplotypes of the Major Histocompatibility Complex, Dan?

How much divergence among V genes for immunglobulins and T-cell receptors? Hint: "V" is for variable.
---------------------QUOTE-------------------

I don't know.  I'm not knowledgeable enough about such matters to answer your endless barrage of technical questions - and you know that.  

---------------------QUOTE-------------------


Would you mind directing me to your post in which you retracted and apologized for your ridiculously false claim that Atlantic and Pacific humpback whales have been reproductively isolated from each other for millions of years, when Tierra del Fuego is a prime place for watching them?
---------------------QUOTE-------------------


Consider it retracted.  That claim was based on my misunderstanding of a sentence I'd read.  When I went back to check my source, I realized my mistake.
Posted by: IanBrown_101 on Dec. 09 2007,13:23



---------------------QUOTE-------------------
I don't know.  I'm not knowledgeable enough about such matters to answer your endless barrage of technical questions - and you know that.
---------------------QUOTE-------------------



So why do you think you can make claims or predictions about this kind of thing?
Posted by: Daniel Smith on Dec. 09 2007,13:29

Quote (JAM @ Dec. 08 2007,20:49)
Molecular clocks are based on sequences that are not under selection. Inbreeding is the most intense artificial selection around, so your question is meaningless. We know where the strains came from:


No. Inbreeding reduces and eventually eliminates polymorphisms within a strain, so that the only ones one observes are caused by new mutations. Since the lab strains are closely related to each other to begin with, they are not representative of wild populations.
---------------------QUOTE-------------------


I'm confused.

Are the mouse genomes used for comparison to other genomes artificially "purified", (eliminating polymorphisms), by inbreeding?
Posted by: JAM on Dec. 09 2007,14:54

Quote (Daniel Smith @ Dec. 09 2007,13:29)
 
Quote (JAM @ Dec. 08 2007,20:49)
Molecular clocks are based on sequences that are not under selection. Inbreeding is the most intense artificial selection around, so your question is meaningless. We know where the strains came from:


No. Inbreeding reduces and eventually eliminates polymorphisms within a strain, so that the only ones one observes are caused by new mutations. Since the lab strains are closely related to each other to begin with, they are not representative of wild populations.
---------------------QUOTE-------------------


I'm confused.
---------------------QUOTE-------------------


I'll say! I'll second Ian's question: what makes you think that you can make sweeping claims when you can't answer simple questions? If you're going to babble on about 8% sequence divergence as having some significance, you have no business claiming ignorance.

Do you realize that natural selection can INCREASE polymorphism?



---------------------QUOTE-------------------
Are the mouse genomes used for comparison to other genomes artificially "purified", (eliminating polymorphisms), by inbreeding?
---------------------QUOTE-------------------


We have all kinds. The initial genomes have been from inbred lab strains, but we have loads of sequence (AFAIK not whole genomes yet) from quasi-different species like Mus spretus and Mus castaneus. I say "quasi-" because both species will interbreed with the house and lab mouse, Mus domesticus.

If you think the inbreeding will justify ignoring the data, what do you predict will be seen in alignments between the mouse species?

I predict a dodge.
Posted by: Daniel Smith on Dec. 09 2007,15:02

Quote (IanBrown_101 @ Dec. 09 2007,13:23)
                 

---------------------QUOTE-------------------
I don't know.  I'm not knowledgeable enough about such matters to answer your endless barrage of technical questions - and you know that.
---------------------QUOTE-------------------



So why do you think you can make claims or predictions about this kind of thing?
---------------------QUOTE-------------------


In hindsight, I probably should have stated that I wasn't knowledgeable enough in the beginning and kept the discussion on Schindewolf, and Berg rather than attempt to delve into the molecular aspect.

But I can't undo what I've done.

My predictions were based on my expectations of God, not on my knowledge of biology.  Some of them were way off base, but some of them have not been.  Since I in no way claim to fully understand God or his mechanisms, this does not surprise me.

The main contention I have with the currently held theory is that of it's mechanism - Variation + Natural Selection - specifically Natural Selection.

We all know that variation happens.  But what does Natural Selection do with that variation?  That's the BIG question. Does it really build better machines out of it?  Or does it maintain the status quo?

I believe the power of Natural Selection is taken for granted - without any real experimental verification.  It is made out to be almost "godlike" in its creativity - but what is really known about it?  

Most evolutionary experiments use artificial selection - so they do not actually test the proposed mechanism.  The true test of Natural Selection is whether a variant can survive in the wild - not in a lab.

This is the crux of the arguments Schindewolf and Berg made.  Based on their observations, Natural Selection had nothing to do with creative evolution.  

Berg cites an almost endless list of examples in chapters with such titles as: "Facts from comparative morphology", "Facts from palaeontology", "Ontogeny", "Convergence and homology", "Phylogenetic atavism", "Parallelism in heterogeneous variations (mutations) and anomalies", "The geographical landscape as an agency in the production of organic forms", "Mimicry and convergence", and "Polyphyletic origin of similar forms".

Schindewolf also makes a solid case based on his extensive study of some of the most abundant fossils known to man.  His arguments are extensively documented in such chapters as: "Discontinuities between structural designs", "Gaps in the material studied by paleontology and neontology", "Patterns in evolution", "The unfolding of the cephalopods", "The unfolding of the stony corals", "The absence of gradual transitions", "The dovetailing of some types", The irreversibility of evolution", "The phases of evolution", "Examples of major cycles", "The origin of the types", "Proterogenic evolution", "Orthogenesis", "Parallel evolution", and "An imaginary picture of an organic world shaped by mutation and selection".

Their observations of real world examples led both of these scientists to the conclusion that evolution is not a matter of random variations filtered through natural selection, but is rather a result of evolution according to law.  Both of them reject Natural Selection as a creative agent.  As a believer in God, I'm much more inclined to embrace their conclusions.

Now, I came here at the invitation of Alan Fox for the express purpose of debating the works of these scientists and their challenges to the theory of evolution.  To date, no one has shown that their claims do not have scientific merit.  In fact there seems to be a reluctance here to talk about them.  Now what conclusion am I supposed to draw from that?
Posted by: Daniel Smith on Dec. 09 2007,15:23

Quote (JAM @ Dec. 09 2007,14:54)
     
Quote (Daniel Smith @ Dec. 09 2007,13:29)
         
Quote (JAM @ Dec. 08 2007,20:49)
Molecular clocks are based on sequences that are not under selection. Inbreeding is the most intense artificial selection around, so your question is meaningless. We know where the strains came from:


No. Inbreeding reduces and eventually eliminates polymorphisms within a strain, so that the only ones one observes are caused by new mutations. Since the lab strains are closely related to each other to begin with, they are not representative of wild populations.
---------------------QUOTE-------------------


I'm confused.
---------------------QUOTE-------------------


I'll say! I'll second Ian's question: what makes you think that you can make sweeping claims when you can't answer simple questions? If you're going to babble on about 8% sequence divergence as having some significance, you have no business claiming ignorance.

Do you realize that natural selection can INCREASE polymorphism?
---------------------QUOTE-------------------


I know I shouldn't do this but...
Apparently natural selection can also decrease polymorphism - since one of the species in the same study had a sequence divergence of 0.1% - also due to natural selection.  So what does that prove?

       

---------------------QUOTE-------------------
     

---------------------QUOTE-------------------
Are the mouse genomes used for comparison to other genomes artificially "purified", (eliminating polymorphisms), by inbreeding?
---------------------QUOTE-------------------


We have all kinds. The initial genomes have been from inbred lab strains, but we have loads of sequence (AFAIK not whole genomes yet) from quasi-different species like Mus spretus and Mus castaneus. I say "quasi-" because both species will interbreed with the house and lab mouse, Mus domesticus.
---------------------QUOTE-------------------

As will all mice I assume.      

---------------------QUOTE-------------------


If you think the inbreeding will justify ignoring the data, what do you predict will be seen in alignments between the mouse species?
---------------------QUOTE-------------------


Well, since they can all interbreed, they are all the same species (just like all the inbred variations of dogs).  So what we have here is variation within a species.  The differences and similarities within this one species shows us the amount of variation that exists (or can exist) within that species.  I predict therefore that there will be equal evolutionary constraint among all sequences - coding and non-coding - within the mouse species.  But then again, I have no knowledge whatsoever to back up this claim - it's based entirely on my preconceived idea of God.  I therefore welcome correction.
Posted by: oldmanintheskydidntdoit on Dec. 09 2007,15:46

Quote (Daniel Smith @ Dec. 09 2007,15:23)
Well, since they can all interbreed, they are all the same species (just like all the inbred variations of dogs).  So what we have here is variation within a species.  The differences and similarities within this one species shows us the amount of variation that exists (or can exist) within that species.  I predict therefore that there will be equal evolutionary constraint among all sequences - coding and non-coding - within the mouse species.  But then again, I have no knowledge whatsoever to back up this claim - it's based entirely on my preconceived idea of God.  I therefore welcome correction.
---------------------QUOTE-------------------


< Ring species >
From Wikipedia, the free encyclopedia
   

---------------------QUOTE-------------------
The coloured bar to the right shows a number of natural populations, each population represented by a different colour, varying along a cline (a gradual change in conditions which gives rise to slightly different characteristics predominating in the organisms that live along it). Such variation may occur in a straight line (for example, up a mountain slope) as is shown in A, or may bend right around (for example, around the shores of a lake), as is shown in B.

In the case where the cline bends around, populations next to each other on the cline can interbreed, but at the point that the beginning meets the end again, as is shown in C, the genetic differences that have accumulated along the cline are great enough to prevent interbreeding (represented by the gap between pink and green on the diagram). The interbreeding populations in this circular breeding group are then collectively referred to as a ring species.
---------------------QUOTE-------------------



Problem of definition
   

---------------------QUOTE-------------------

The problem, then, is whether to quantify the whole ring as a single species (despite the fact that not all individuals can interbreed) or to classify each population as a distinct species (despite the fact that it can interbreed with its near neighbours). Ring species illustrate that the species concept is not as clear-cut as it is often understood to be.
---------------------QUOTE-------------------


Fasinating stuff. And it's not so simple as "since they can all interbreed, they are all the same species"
< http://en.wikipedia.org/wiki/Ring_species >
Posted by: Daniel Smith on Dec. 09 2007,15:53

Quote (Lou FCD @ Dec. 05 2007,06:38)
 
Quote (VMartin @ Dec. 05 2007,01:07)
And last but not at least. Comparing differences between genome of brother and the genome of his sister there are changes let say in 100 genes having (different alleles of it). But those differences are not caused by "random mutation" purified by natural selection but only due "frontloading".
---------------------QUOTE-------------------



So your alternative hypothesis to modern evolutionary theory is "In the beginning, God did it"?  Please ask whoever is feeding you your lines to explain what sort of predictions you would make from that, and how you would go about testing those predictions.

Also, when next you speak to your "Intelligent" Designer guy, let him know I'd like a refund or exchange on my spinal column, it seems to be defective and I'm frequently in some serious pain.  And it's deteriorating.  While we're on the subject of piss-poor coding, designing, and manufacturing, I'd also like to get refunds and exchanges for the following:

My wife's gall bladder, appendix, large (I think it was the large - whichever one anchors the appendix) intestine, and the whole of her internal girly parts.  They've all had to be removed (well the intestine was a partial) due to manufacturing defects at the frontloading factory.

My son's ankle.  It's a wreck and really should have held up more than 13 years.  You'd think the All Powerful Frontloader would have done a better job with that.  Fortunately, it's still under warranty (although aren't major manufacturing defects an exception to the warranty laws here in the U.S.?).

Also, I'd like to see the code for my Pop.  Is that open-source?  He's having issues of dizziness and fainting, etc., and the doctors don't seem to be able to pin it down.  If they could see the actual code, perhaps they could find the bug and fix it.

Just leave me a message here (or just post the code, I'm sure he won't mind), I have to go back to the hospital to visit my Pop and will be in and out all day.

Thanks.

Lou

P.S. If your "Intelligent" Frontloader needs to make a little extra Christmas money, let him know that I heard that Microsoft was hiring half-assed code writers as temps to work on Vista.  He could look into that.
---------------------QUOTE-------------------


So you only accept Perfection as evidence for intelligent design?

Show me something then that meets your criteria for an intelligently designed object.
Posted by: Assassinator on Dec. 09 2007,16:18

I won't call it perfection, but it's pretty damn wierd that designer would constantly re-design his original, constantly adding new stuff or removing stuff and still certain things won't work as good as they can work. Can't he make up his mind? Ofcourse, we humans do that, but the difference is that we discover new materials, new methodes, new manufacturing methodes. Is that evident in nature too?
Posted by: JAM on Dec. 09 2007,16:43

Quote (Daniel Smith @ Dec. 09 2007,15:02)
 
Quote (IanBrown_101 @ Dec. 09 2007,13:23)
                   

---------------------QUOTE-------------------
I don't know.  I'm not knowledgeable enough about such matters to answer your endless barrage of technical questions - and you know that.
---------------------QUOTE-------------------



So why do you think you can make claims or predictions about this kind of thing?
---------------------QUOTE-------------------


In hindsight, I probably should have stated that I wasn't knowledgeable enough in the beginning and kept the discussion on Schindewolf, and Berg rather than attempt to delve into the molecular aspect.
---------------------QUOTE-------------------


There's so much more molecular evidence, and as you've learned, it's much harder to spin when you haven't been preprogrammed by propaganda.


---------------------QUOTE-------------------
But I can't undo what I've done.

My predictions were based on my expectations of God, not on my knowledge of biology.  Some of them were way off base, but some of them have not been.  Since I in no way claim to fully understand God or his mechanisms, this does not surprise me.
---------------------QUOTE-------------------


Then why make predictions based on your expectations of Him? Why not read His book of nature with an open mind instead of a closed one?


---------------------QUOTE-------------------
The main contention I have with the currently held theory is that of it's mechanism - Variation + Natural Selection - specifically Natural Selection.
---------------------QUOTE-------------------


There are many more mechanisms. How can you be so contentious about something you aren't willing to understand?


---------------------QUOTE-------------------
We all know that variation happens.  But what does Natural Selection do with that variation?
---------------------QUOTE-------------------


It has to do something, as living things generally don't live to ripe old ages.


---------------------QUOTE-------------------
That's the BIG question.
---------------------QUOTE-------------------


So why avoid it?


---------------------QUOTE-------------------
Does it really build better machines out of it?
---------------------QUOTE-------------------


Metaphorically, yes. The biggest clue is the relationships between radically different "machines"--it is in no way consistent with intelligent design.


---------------------QUOTE-------------------
Or does it maintain the status quo?
---------------------QUOTE-------------------


It does that too.


---------------------QUOTE-------------------
I believe the power of Natural Selection is taken for granted - without any real experimental verification.
---------------------QUOTE-------------------


That is simply a lie. When we tested your hypothesis against the data, NONE of what you took for granted turned out to be true.


---------------------QUOTE-------------------
It is made out to be almost "godlike" in its creativity - but what is really known about it?
---------------------QUOTE-------------------


The passive voice is weaselly, Dan--the point is that when you look at the relationships between the components of life, it clearly is NOT "godlike in its creativity." It modifies existing parts, which is anything but creative. The complexity comes from the long spans of time and the cumulative properties of evolution.  


---------------------QUOTE-------------------
Most evolutionary experiments use artificial selection - so they do not actually test the proposed mechanism.
---------------------QUOTE-------------------


False. You haven't even looked. There are plenty of experiments that use artificial variation with natural selection.


---------------------QUOTE-------------------
The true test of Natural Selection is whether a variant can survive in the wild - not in a lab.
---------------------QUOTE-------------------


We find new variants in the wild all the time.


---------------------QUOTE-------------------
...Berg cites an almost endless list of examples...
---------------------QUOTE-------------------


But Dan, how would someone as ignorant as you know whether they are examples or not? Examples are representative.


---------------------QUOTE-------------------
...in chapters with such titles as: "Facts from comparative morphology", "Facts from palaeontology", "Ontogeny", "Convergence and homology", "Phylogenetic atavism", "Parallelism in heterogeneous variations (mutations) and anomalies", "The geographical landscape as an agency in the production of organic forms", "Mimicry and convergence", and "Polyphyletic origin of similar forms".
---------------------QUOTE-------------------


The fact that you prefer to quote titles instead of making predictions about evidence you haven't seen yet proves your dishonest approach to the matter.


---------------------QUOTE-------------------
Schindewolf also makes a solid case based on his extensive study of some of the most abundant fossils known to man.  His arguments are extensively documented in such chapters as: "Discontinuities between structural designs", "Gaps in the material studied by paleontology and neontology", "Patterns in evolution", "The unfolding of the cephalopods", "The unfolding of the stony corals", "The absence of gradual transitions", "The dovetailing of some types", The irreversibility of evolution", "The phases of evolution", "Examples of major cycles", "The origin of the types", "Proterogenic evolution", "Orthogenesis", "Parallel evolution", and "An imaginary picture of an organic world shaped by mutation and selection".
---------------------QUOTE-------------------


Titles aren't evidence. You're afraid of evidence.


---------------------QUOTE-------------------
Their observations of real world examples
---------------------QUOTE-------------------


Again, you have insufficient expertise to know whether they are examples or not. For example, is ID's favorite structure--the eubacterial flagellum (any IDer who omits the adjective is being dishonest)--an example of what appears to be design in biology, or is it an outlier?


---------------------QUOTE-------------------
...As a believer in God, I'm much more inclined to embrace their conclusions.
---------------------QUOTE-------------------


I don't see how the second clause follows the first.


---------------------QUOTE-------------------
Now, I came here at the invitation of Alan Fox for the express purpose of debating the works of these scientists and their challenges to the theory of evolution.
---------------------QUOTE-------------------


So where are the new data they produced?


---------------------QUOTE-------------------
To date, no one has shown that their claims do not have scientific merit.  In fact there seems to be a reluctance here to talk about them.  Now what conclusion am I supposed to draw from that?
---------------------QUOTE-------------------


IIRC, I asked you to direct me to the new data they had produced by testing their hypotheses. You couldn't find any. That means that you can't credibly claim that their hypotheses have any scientific merit at all.

Where are the predictions? Where are the new data produced by testing them?
Posted by: IanBrown_101 on Dec. 09 2007,16:45

Quote (Daniel Smith @ Dec. 09 2007,21:53)
Quote (Lou FCD @ Dec. 05 2007,06:38)
 
Quote (VMartin @ Dec. 05 2007,01:07)
And last but not at least. Comparing differences between genome of brother and the genome of his sister there are changes let say in 100 genes having (different alleles of it). But those differences are not caused by "random mutation" purified by natural selection but only due "frontloading".
---------------------QUOTE-------------------



So your alternative hypothesis to modern evolutionary theory is "In the beginning, God did it"?  Please ask whoever is feeding you your lines to explain what sort of predictions you would make from that, and how you would go about testing those predictions.

Also, when next you speak to your "Intelligent" Designer guy, let him know I'd like a refund or exchange on my spinal column, it seems to be defective and I'm frequently in some serious pain.  And it's deteriorating.  While we're on the subject of piss-poor coding, designing, and manufacturing, I'd also like to get refunds and exchanges for the following:

My wife's gall bladder, appendix, large (I think it was the large - whichever one anchors the appendix) intestine, and the whole of her internal girly parts.  They've all had to be removed (well the intestine was a partial) due to manufacturing defects at the frontloading factory.

My son's ankle.  It's a wreck and really should have held up more than 13 years.  You'd think the All Powerful Frontloader would have done a better job with that.  Fortunately, it's still under warranty (although aren't major manufacturing defects an exception to the warranty laws here in the U.S.?).

Also, I'd like to see the code for my Pop.  Is that open-source?  He's having issues of dizziness and fainting, etc., and the doctors don't seem to be able to pin it down.  If they could see the actual code, perhaps they could find the bug and fix it.

Just leave me a message here (or just post the code, I'm sure he won't mind), I have to go back to the hospital to visit my Pop and will be in and out all day.

Thanks.

Lou

P.S. If your "Intelligent" Frontloader needs to make a little extra Christmas money, let him know that I heard that Microsoft was hiring half-assed code writers as temps to work on Vista.  He could look into that.
---------------------QUOTE-------------------


So you only accept Perfection as evidence for intelligent design?

Show me something then that meets your criteria for an intelligently designed object.
---------------------QUOTE-------------------


Surely if the intelligent designer in life is god, and since god is perfect, then all his creations must be so, right?

Even without this qualifier, intelligent design would be a bad definition for the ridiculously stupid examples, such as my heart. 3 separate problems with the same system in ONE organism? Please, if the designer is that intelligent, this shouldn't happen, surely?
Posted by: JAM on Dec. 09 2007,16:46

Quote (Daniel Smith @ Dec. 09 2007,15:53)
So you only accept Perfection as evidence for intelligent design?
---------------------QUOTE-------------------


Straw man. He accepts intelligence as evidence for intelligent design.

Does having a separate codon(s) for stopping translation (that don't encode an amino acid residue) represent an intelligent design? This allows proteins to have any of the 20 residues at the carboxy terminus.

I predict that you will avoid the question.
Posted by: JAM on Dec. 09 2007,16:56

Quote (Daniel Smith @ Oct. 22 2007,19:26)
Another example is a study done by Scott Baker (from the abstracts on Google Scholar, I was unsure which one corresponds to this study) between Atlantic and Pacific humpback whales - which have been geographically isolated for 3 million years (since the isthmus of Panama separated the two oceans).
---------------------QUOTE-------------------



 
Quote (JAM @ Dec. 04 2007,21:12)
 
Would you mind directing me to your post in which you retracted and apologized for your ridiculously false claim that Atlantic and Pacific humpback whales have been reproductively isolated from each other for millions of years, when Tierra del Fuego is a prime place for watching them?
---------------------QUOTE-------------------


   
Quote (Daniel Smith @ Dec. 04 2007,18:54)

Consider it retracted.  That claim was based on my misunderstanding of a sentence I'd read.  When I went back to check my source, I realized my mistake.
---------------------QUOTE-------------------



Hallelujah! You finally got around to retracting a spectacularly stupid statement that you made SIX WEEKS AGO.

Where do you think that pegs your credibility on our meters, Dan? BTW, what sentence did you misunderstand? I'm fascinated by the way your mind works.

And since you made a false assumption, shouldn't you be retracting the conclusion you derived from it as well?
Posted by: IanBrown_101 on Dec. 09 2007,16:59

Quote (JAM @ Dec. 09 2007,22:56)
And since you made a false assumption, shouldn't you be retracting the conclusion you derived from it as well?
---------------------QUOTE-------------------


This of course assumes that the conclusion came AFTERWARDS.
Posted by: JAM on Dec. 09 2007,17:13

Quote (Daniel Smith @ Dec. 09 2007,15:23)
 
Quote (JAM @ Dec. 09 2007,14:54)
         
Quote (Daniel Smith @ Dec. 09 2007,13:29)
             
Quote (JAM @ Dec. 08 2007,20:49)
Molecular clocks are based on sequences that are not under selection. Inbreeding is the most intense artificial selection around, so your question is meaningless. We know where the strains came from:

No. Inbreeding reduces and eventually eliminates polymorphisms within a strain, so that the only ones one observes are caused by new mutations. Since the lab strains are closely related to each other to begin with, they are not representative of wild populations.
---------------------QUOTE-------------------


I'm confused.
---------------------QUOTE-------------------


I'll say! I'll second Ian's question: what makes you think that you can make sweeping claims when you can't answer simple questions? If you're going to babble on about 8% sequence divergence as having some significance, you have no business claiming ignorance.

Do you realize that natural selection can INCREASE polymorphism?
---------------------QUOTE-------------------


I know I shouldn't do this but...
Apparently natural selection can also decrease polymorphism - since one of the species in the same study had a sequence divergence of 0.1% - also due to natural selection.  So what does that prove?
---------------------QUOTE-------------------


Nothing is considered to be proven in science. What it shows is the nature of the selection pressure(s). That makes testable predictions.

           

---------------------QUOTE-------------------
   

---------------------QUOTE-------------------
         

---------------------QUOTE-------------------
Are the mouse genomes used for comparison to other genomes artificially "purified", (eliminating polymorphisms), by inbreeding?
---------------------QUOTE-------------------


We have all kinds. The initial genomes have been from inbred lab strains, but we have loads of sequence (AFAIK not whole genomes yet) from quasi-different species like Mus spretus and Mus castaneus. I say "quasi-" because both species will interbreed with the house and lab mouse, Mus domesticus.
---------------------QUOTE-------------------

As will all mice I assume.  
---------------------QUOTE-------------------


You assume incorrectly. For example, deer mice don't interbreed with house mice.

       

---------------------QUOTE-------------------


If you think the inbreeding will justify ignoring the data, what do you predict will be seen in alignments between the mouse species?
---------------------QUOTE-------------------


 

---------------------QUOTE-------------------
 Well, since they can all interbreed, they are all the same species (just like all the inbred variations of dogs).
---------------------QUOTE-------------------


Not quite. They CAN interbreed in the lab, but they DON'T interbreed in the wild AFAIK. Inconsistent with your hypothesis, "species" doesn't represent a bright white line. These are members of the same genus.  
 

---------------------QUOTE-------------------
 So what we have here is variation within a species.  The differences and similarities within this one species shows us the amount of variation that exists (or can exist) within that species.  I predict therefore that there will be equal evolutionary constraint among all sequences - coding and non-coding - within the mouse species.
---------------------QUOTE-------------------


You are utterly wrong.
< http://www.jstor.org/view/00222372/ap050331/05a00030/0 >
Note that in this case, the PCR primers used to amplify the introns were in the highly-conserved exons.

< http://genomebiology.com/2007/8/5/R80 >

< http://www.springerlink.com/content/ur1r657751t80262/ >


---------------------QUOTE-------------------
But then again, I have no knowledge whatsoever to back up this claim - it's based entirely on my preconceived idea of God.  I therefore welcome correction.
---------------------QUOTE-------------------


You're wrong. I predict that this will have no effect on your view of God.
Posted by: Richard Simons on Dec. 09 2007,18:03

Quote (Daniel Smith @ Dec. 09 2007,15:02)
Now, I came here at the invitation of Alan Fox for the express purpose of debating the works of these scientists [Schindewolf and Berg] and their challenges to the theory of evolution.  To date, no one has shown that their claims do not have scientific merit.  In fact there seems to be a reluctance here to talk about them.  Now what conclusion am I supposed to draw from that?
---------------------QUOTE-------------------


You keep saying this.

Firstly, their 'theory' is completely unnecessary.
Secondly, there is no suggested, never mind plausible, mechanism whereby the organism knows what conditions it will need to adapt to in the future and what form the organism 'should' take.
Thirdly, there is no suggested means of storing the information free from corruption for millions of years.
Fourthly, there is no suggested means whereby this information could be invoked at a specific time to produce the 'correct' organism in the 'correct' era.
Fifthly, because no means of anticipating the requirement, storing the information or scheduling the changes has been proposed, there is no knowing what evidence to examine or to seek. All the evidence so far seems to consist of 'By heck, it looks like it was planned!"

In short, there is absolutely no reason to take these notions seriously.

I have mentioned these problems before but you don't seem to realize, each one of these points, in itself, is enough to show that the ideas are not sufficiently developed to warrant much serious attention.
Posted by: Lou FCD on Dec. 10 2007,05:25

Quote (JAM @ Dec. 09 2007,17:46)
Quote (Daniel Smith @ Dec. 09 2007,15:53)
So you only accept Perfection as evidence for intelligent design?
---------------------QUOTE-------------------


Straw man. He accepts intelligence as evidence for intelligent design.
---------------------QUOTE-------------------


Well said, thank you.

The end product is a bug ridden, defective hack-job of spare parts and afterthoughts that worked at the time of implementation.

It ain't pretty, it ain't elegant, it ain't intelligent, it just works or it doesn't.
Posted by: Assassinator on Dec. 10 2007,07:01

And don't forget it's re-designed a gazzilion times, seems the designer can't make up his mind.
Posted by: oldmanintheskydidntdoit on Dec. 10 2007,07:36

Quote (Assassinator @ Dec. 10 2007,07:01)
And don't forget it's re-designed a gazzilion times, seems the designer can't make up his mind.
---------------------QUOTE-------------------


Daniel, if we keep to a "design" framework the fact that there is iteration upon iteration, variation upon variation, appears to indicate multiple designers.

Are multiple designers allowed under your theory?
Posted by: VMartin on Dec. 10 2007,11:42

JAM
 

---------------------QUOTE-------------------

118/30000 = ~100%, not 99%.
.
.
.
Never heard of him. Clearly, he can't do percentages.

---------------------QUOTE-------------------



Your result 118/30000 = ~100% is not correct either. I  would say it is 0,39%.

Even if you have meant 99.61% the author you criticized is more correct than you. He claims "This is what was actually determined: 99% of mouse genes have homologues in man". It is true. Even if he had claimed "This is what was actually determined: 98% (or 97%) of mouse genes have homologues in man" he would have been right from the logical point of view.  98% (97%) have homologues. Every number less 99,61% is strictly speaking correct. 100% is simply not true.

I know JAM, that the most important thing for you is  that everybody is wrong except you. So you can attack me again that I confused homologues and orthologs or what.

 
 

 

---------------------QUOTE-------------------

You omitted the context, VM. That was preceded by this sentence:
"Further evidence for common ancestry comes SNPs (Single Nucleotide Polymorphisms) – differences in genomes that exist in different humans where the variation is a single base pair substitution and the alleles co-exist in the population."

SNPs aren't genes. You're hopeless.

---------------------QUOTE-------------------


Straw man. I didn´t adress SNPs as genes. I claimed that comparing genes we compare their alleles actually. You keep on talking off-topic. So keep the track:  how do you compare genes without comparing existing alleles of those genes?

(And how would you explain the sentence from wikipedia: "Almost all common SNPs have only two alleles"? Just if you have enough time for nitpicking in wikipedia sentences.

You should also write to cat.inist why they used  "...and single nucleotide polymorphic (SNP) genes..." if SNPs are not genes on your opinion.

< http://cat.inist.fr/?aModele=afficheN&cpsidt=14418886 >
)
 
   

---------------------QUOTE-------------------

Molecular clocks are based on sequences that are not under selection.

---------------------QUOTE-------------------



What do you mean by "are based"? Because they are calibrated against material evidence such as fossils. And how do you know which sequences are not under selection? According Ka/Ks ratio? Ayala wrote:


....I review the evolution of two genes, Gpdh and Sod. In fruit flies, the encoded glycerol-3-phosphate dehydrogenase (GPDH) protein evolves at a rate of 1.1 x 1010 amino acid replacements per site per year when Drosophila species are compared that diverged within the last 55 million years (My), ...

...If we assume a molecular clock and use the Drosophila rate for estimating the divergence of remote organisms, GPDH yields estimates of 2,500 My for the divergence between the animal phyla


< http://www.cs.unc.edu/~plaisted/ce/clock.html >

Do you mean that GPDH is not under selection? Or - Ayala don´t know how to use molecular clocks? Or - I misunderestood the sentences Ayala wrote?

Maybe you are somehow right. Yet our article compares all genes of human and mice regardless of the fact if they are under selection or not.



 

---------------------QUOTE-------------------

No. Inbreeding reduces and eventually eliminates polymorphisms within a strain, so that the only ones one observes are caused by new mutations. Since the lab strains are closely related to each other to begin with, they are not representative of wild populations.

Again, you're hopeless.

---------------------QUOTE-------------------



But I believe there is some hope for you at least.
I am only a layman but you are an expert on off-topic misleading answers. If polymorphism of wild mice population is 35% and we inbred two strains of them ( 40 generation of inbreeding), how many different alleles there would  be in average between the two strains (in those 30.000 genes)? Or better: how many of those 30.000 loci would be occupied by different alleles comparing that strains? 5.000?  

Why this difference do not serve for you as evidence of divergence from common ancestor but difference on those loci between human vs. mice are used this way? As an evidence of divergence from common ancestor?
Posted by: oldmanintheskydidntdoit on Dec. 10 2007,11:54

Quote (VMartin @ Dec. 10 2007,11:42)
JAM
 

---------------------QUOTE-------------------

118/30000 = ~100%, not 99%.
.
.
.
Never heard of him. Clearly, he can't do percentages.

---------------------QUOTE-------------------



Your result 118/30000 = ~100% is not correct either. I  would say it is 0,39%.

Even if you have meant 99.61% the author you criticized is more correct than you. He claims "This is what was actually determined: 99% of mouse genes have homologues in man". It is true. Even if he had claimed "This is what was actually determined: 98% (or 97%) of mouse genes have homologues in man" he would have been right from the logical point of view.  98% (97%) have homologues. Every number less 99,61% is strictly speaking correct. 100% is simply not true.

I know JAM, that the most important thing for you is  that everybody is wrong except you. So you can attack me again that I confused homologues and orthologs or what.

 
 

 

---------------------QUOTE-------------------

You omitted the context, VM. That was preceded by this sentence:
"Further evidence for common ancestry comes SNPs (Single Nucleotide Polymorphisms) – differences in genomes that exist in different humans where the variation is a single base pair substitution and the alleles co-exist in the population."

SNPs aren't genes. You're hopeless.

---------------------QUOTE-------------------


Straw man. I didn´t adress SNPs as genes. I claimed that comparing genes we compare their alleles actually. You keep on talking off-topic. So keep the track:  how do you compare genes without comparing existing alleles of those genes?

(And how would you explain the sentence from wikipedia: "Almost all common SNPs have only two alleles"? Just if you have enough time for nitpicking in wikipedia sentences.

You should also write to cat.inist why they used  "...and single nucleotide polymorphic (SNP) genes..." if SNPs are not genes on your opinion.

< http://cat.inist.fr/?aModele=afficheN&cpsidt=14418886 >
)
 
   

---------------------QUOTE-------------------

Molecular clocks are based on sequences that are not under selection.

---------------------QUOTE-------------------



What do you mean by "are based"? Because they are calibrated against material evidence such as fossils. And how do you know which sequences are not under selection? According Ka/Ks ratio? Ayala wrote:


....I review the evolution of two genes, Gpdh and Sod. In fruit flies, the encoded glycerol-3-phosphate dehydrogenase (GPDH) protein evolves at a rate of 1.1 x 1010 amino acid replacements per site per year when Drosophila species are compared that diverged within the last 55 million years (My), ...

...If we assume a molecular clock and use the Drosophila rate for estimating the divergence of remote organisms, GPDH yields estimates of 2,500 My for the divergence between the animal phyla


< http://www.cs.unc.edu/~plaisted/ce/clock.html >

Do you mean that GPDH is not under selection? Or - Ayala don´t know how to use molecular clocks? Or - I misunderestood the sentences Ayala wrote?

Maybe strictly speaking you are right. Yet our article compares all genes of human and mice regardless of the fact if they are under selection or not.



 

---------------------QUOTE-------------------

No. Inbreeding reduces and eventually eliminates polymorphisms within a strain, so that the only ones one observes are caused by new mutations. Since the lab strains are closely related to each other to begin with, they are not representative of wild populations.

Again, you're hopeless.

---------------------QUOTE-------------------



But I believe there is some hope for you at least.
I am only a layman but you are an expert on off-topic misleading answers. If polymorphism of wild mice population is 35% and we inbred two strains of them ( 40 generation of inbreeding), how many different alleles there would  be in average between the two strains (in those 30.000 genes)? Or better: how many of those 30.000 loci would be occupied by different alleles comparing that strains? 5.000?  

Why this difference do not serve for you as evidence of divergence from common ancestor but difference on those loci between human vs. mice are used this way? As an evidence of divergence from common ancestor?
---------------------QUOTE-------------------


god did it. that's why.
Posted by: Daniel Smith on Dec. 11 2007,19:46

Quote (Lou FCD @ Dec. 10 2007,05:25)
             
Quote (JAM @ Dec. 09 2007,17:46)
             
Quote (Daniel Smith @ Dec. 09 2007,15:53)
So you only accept Perfection as evidence for intelligent design?
---------------------QUOTE-------------------


Straw man. He accepts intelligence as evidence for intelligent design.
---------------------QUOTE-------------------


Well said, thank you.

The end product is a bug ridden, defective hack-job of spare parts and afterthoughts that worked at the time of implementation.

It ain't pretty, it ain't elegant, it ain't intelligent, it just works or it doesn't.
---------------------QUOTE-------------------


Hogwash.  Pure and simple hogwash.  The "end product" is the most complex, elegant, sophisticated machinery known to man.  

"It ain't pretty"?  Those of us with a preference for the female of the species will beg to differ.  

"it ain't elegant"?  Tell me the human hand is not one of the most elegant structures imaginable.  

"it ain't intelligent"?  The human brain puts our banks of computers to shame with it's processing power.

What is it that blinds you to all this?  Is it your distaste for God?  Do you do this because it's his creation?

I don't understand it; I don't understand how intelligent people can look at such mind-boggling sophistication and deny it even exists!  Within our bodies there are literally billions of working systems - intertwined in complex networks - working together to allow us to do things like laughing and crying, reading and speaking.  All these systems work together so we can cradle a baby, smell a flower, enjoy a sunset, or compose or enjoy music.  They allow us to do the very things we are doing right now.  You can't explain that with "variation and selection".  There's just no way.  There is an "elephant in the room" and I think you know who it is.
Posted by: Daniel Smith on Dec. 11 2007,19:53

Quote (oldmanintheskydidntdoit @ Dec. 09 2007,15:46)
 
Quote (Daniel Smith @ Dec. 09 2007,15:23)
Well, since they can all interbreed, they are all the same species (just like all the inbred variations of dogs).  So what we have here is variation within a species.  The differences and similarities within this one species shows us the amount of variation that exists (or can exist) within that species.  I predict therefore that there will be equal evolutionary constraint among all sequences - coding and non-coding - within the mouse species.  But then again, I have no knowledge whatsoever to back up this claim - it's based entirely on my preconceived idea of God.  I therefore welcome correction.
---------------------QUOTE-------------------


< Ring species >
From Wikipedia, the free encyclopedia
       

---------------------QUOTE-------------------
The coloured bar to the right shows a number of natural populations, each population represented by a different colour, varying along a cline (a gradual change in conditions which gives rise to slightly different characteristics predominating in the organisms that live along it). Such variation may occur in a straight line (for example, up a mountain slope) as is shown in A, or may bend right around (for example, around the shores of a lake), as is shown in B.

In the case where the cline bends around, populations next to each other on the cline can interbreed, but at the point that the beginning meets the end again, as is shown in C, the genetic differences that have accumulated along the cline are great enough to prevent interbreeding (represented by the gap between pink and green on the diagram). The interbreeding populations in this circular breeding group are then collectively referred to as a ring species.
---------------------QUOTE-------------------



Problem of definition
       

---------------------QUOTE-------------------

The problem, then, is whether to quantify the whole ring as a single species (despite the fact that not all individuals can interbreed) or to classify each population as a distinct species (despite the fact that it can interbreed with its near neighbours). Ring species illustrate that the species concept is not as clear-cut as it is often understood to be.
---------------------QUOTE-------------------


Fasinating stuff. And it's not so simple as "since they can all interbreed, they are all the same species"
< http://en.wikipedia.org/wiki/Ring_species >
---------------------QUOTE-------------------


From the page you quoted:  

---------------------QUOTE-------------------
A classic example of ring species is the Larus gulls circumpolar species "ring". The range of these gulls forms a ring around the North Pole. The Herring Gull, which lives primarily in Great Britain, can hybridize with the American Herring Gull (living in North America), which can also interbreed with the Vega or East Siberian Herring Gull, the western subspecies of which, Birula's Gull, can hybridize with Heuglin's gull, which in turn can interbreed with the Siberian Lesser Black-backed Gull (all four of these live across the north of Siberia). The last is the eastern representative of the Lesser Black-backed Gulls back in north-western Europe, including Great Britain. However, the Lesser Black-backed Gulls and Herring Gull are sufficiently different that they do not normally interbreed; thus the group of gulls forms a continuum except in Europe where the two lineages meet. A recent genetic study has shown that this example is far more complicated than presented here (Liebers et al, 2004). This example only speaks of classical Herring Gull - Lesser Black-Backed Gull complex and does not include several other taxonomically unclear examples which belong in the same superspecies complex, such as Yellow-Legged Gull, Glaucous Gull and Caspian Gull.
(My emphasis)
---------------------QUOTE-------------------



The terms "do not normally interbreed" and "cannot interbreed" are not equivalent terms.
Posted by: Lou FCD on Dec. 11 2007,20:25

Quote (Daniel Smith @ Dec. 11 2007,20:46)
Hogwash.  Pure and simple hogwash.  The "end product" is the most complex, elegant, sophisticated machinery known to man.  

"It ain't pretty"?  Those of us with a preference for the female of the species will beg to differ.  

"it ain't elegant"?  Tell me the human hand is not one of the most elegant structures imaginable.  

"it ain't intelligent"?  The human brain puts our banks of computers to shame with it's processing power.

What is it that blinds you to all this?  Is it your distaste for God?  Do you do this because it's his creation?

I don't understand it; I don't understand how intelligent people can look at such mind-boggling sophistication and deny it even exists!  Within our bodies there are literally billions of working systems - intertwined in complex networks - working together to allow us to do things like laughing and crying, reading and speaking.  All these systems work together so we can cradle a baby, smell a flower, enjoy a sunset, or compose or enjoy music.  They allow us to do the very things we are doing right now.  You can't explain that with "variation and selection".  There's just no way.  There is an "elephant in the room" and I think you know who it is.
---------------------QUOTE-------------------


Your personal incredulity does not in any way alter reality.

Just so y'know.
Posted by: Arden Chatfield on Dec. 11 2007,20:45

Quote (Daniel Smith @ Dec. 11 2007,19:53)
Quote (oldmanintheskydidntdoit @ Dec. 09 2007,15:46)
   
Quote (Daniel Smith @ Dec. 09 2007,15:23)
Well, since they can all interbreed, they are all the same species (just like all the inbred variations of dogs).  So what we have here is variation within a species.  The differences and similarities within this one species shows us the amount of variation that exists (or can exist) within that species.  I predict therefore that there will be equal evolutionary constraint among all sequences - coding and non-coding - within the mouse species.  But then again, I have no knowledge whatsoever to back up this claim - it's based entirely on my preconceived idea of God.  I therefore welcome correction.
---------------------QUOTE-------------------


< Ring species >
From Wikipedia, the free encyclopedia
         

---------------------QUOTE-------------------
The coloured bar to the right shows a number of natural populations, each population represented by a different colour, varying along a cline (a gradual change in conditions which gives rise to slightly different characteristics predominating in the organisms that live along it). Such variation may occur in a straight line (for example, up a mountain slope) as is shown in A, or may bend right around (for example, around the shores of a lake), as is shown in B.

In the case where the cline bends around, populations next to each other on the cline can interbreed, but at the point that the beginning meets the end again, as is shown in C, the genetic differences that have accumulated along the cline are great enough to prevent interbreeding (represented by the gap between pink and green on the diagram). The interbreeding populations in this circular breeding group are then collectively referred to as a ring species.
---------------------QUOTE-------------------



Problem of definition
         

---------------------QUOTE-------------------

The problem, then, is whether to quantify the whole ring as a single species (despite the fact that not all individuals can interbreed) or to classify each population as a distinct species (despite the fact that it can interbreed with its near neighbours). Ring species illustrate that the species concept is not as clear-cut as it is often understood to be.
---------------------QUOTE-------------------


Fasinating stuff. And it's not so simple as "since they can all interbreed, they are all the same species"
< http://en.wikipedia.org/wiki/Ring_species >
---------------------QUOTE-------------------


From the page you quoted:    

---------------------QUOTE-------------------
A classic example of ring species is the Larus gulls circumpolar species "ring". The range of these gulls forms a ring around the North Pole. The Herring Gull, which lives primarily in Great Britain, can hybridize with the American Herring Gull (living in North America), which can also interbreed with the Vega or East Siberian Herring Gull, the western subspecies of which, Birula's Gull, can hybridize with Heuglin's gull, which in turn can interbreed with the Siberian Lesser Black-backed Gull (all four of these live across the north of Siberia). The last is the eastern representative of the Lesser Black-backed Gulls back in north-western Europe, including Great Britain. However, the Lesser Black-backed Gulls and Herring Gull are sufficiently different that they do not normally interbreed; thus the group of gulls forms a continuum except in Europe where the two lineages meet. A recent genetic study has shown that this example is far more complicated than presented here (Liebers et al, 2004). This example only speaks of classical Herring Gull - Lesser Black-Backed Gull complex and does not include several other taxonomically unclear examples which belong in the same superspecies complex, such as Yellow-Legged Gull, Glaucous Gull and Caspian Gull.
(My emphasis)
---------------------QUOTE-------------------



The terms "do not normally interbreed" and "cannot interbreed" are not equivalent terms.
---------------------QUOTE-------------------


Therefore evolution is false and goddidit.

USA! USA! USA!
Posted by: IanBrown_101 on Dec. 12 2007,07:38

Quote (Daniel Smith @ Dec. 12 2007,01:46)
Quote (Lou FCD @ Dec. 10 2007,05:25)
             
Quote (JAM @ Dec. 09 2007,17:46)
               
Quote (Daniel Smith @ Dec. 09 2007,15:53)
So you only accept Perfection as evidence for intelligent design?
---------------------QUOTE-------------------


Straw man. He accepts intelligence as evidence for intelligent design.
---------------------QUOTE-------------------


Well said, thank you.

The end product is a bug ridden, defective hack-job of spare parts and afterthoughts that worked at the time of implementation.

It ain't pretty, it ain't elegant, it ain't intelligent, it just works or it doesn't.
---------------------QUOTE-------------------


Hogwash.  Pure and simple hogwash.  The "end product" is the most complex, elegant, sophisticated machinery known to man.  

"It ain't pretty"?  Those of us with a preference for the female of the species will beg to differ.  

"it ain't elegant"?  Tell me the human hand is not one of the most elegant structures imaginable.  

"it ain't intelligent"?  The human brain puts our banks of computers to shame with it's processing power.

What is it that blinds you to all this?  Is it your distaste for God?  Do you do this because it's his creation?

I don't understand it; I don't understand how intelligent people can look at such mind-boggling sophistication and deny it even exists!  Within our bodies there are literally billions of working systems - intertwined in complex networks - working together to allow us to do things like laughing and crying, reading and speaking.  All these systems work together so we can cradle a baby, smell a flower, enjoy a sunset, or compose or enjoy music.  They allow us to do the very things we are doing right now.  You can't explain that with "variation and selection".  There's just no way.  There is an "elephant in the room" and I think you know who it is.
---------------------QUOTE-------------------


Oh for...I thought progress was being made. Evidently it isn't.

First, evolution does not deny god, cannot deny god and should not deny god. PEOPLE deny god, like myself, or PZ, or Dawkins. People.

Second, equating the beauty of certain women to beauty in the internal structures is ridiculous, and equally ridiculous is your apparent assertion that beauty is 1. Only for the hetros and 2. somehow all arching, and  always the same. Do you find a female pig beautiful? So why do pigs?

Thirdly, just because the brain is more complex than current computers means zilch. Nada. Nothing. Comparing a clearly designed object with the human brain is really rather foolish. You are supposing that both are designedin order to show design. Whoops.

Finally, you ACTUALLY came out with "Ever looked at your hand? I mean REALLY looked?". Seriously?
Posted by: stevestory on Dec. 12 2007,08:15

When I saw Daniel's "they can interbreed so they're the same species" the first thing I thought of was ring species. So kudos to Arden.
Posted by: oldmanintheskydidntdoit on Dec. 12 2007,09:23



---------------------QUOTE-------------------
"It ain't pretty"?  Those of us with a preference for the female of the species will beg to differ.  

---------------------QUOTE-------------------


Are lesbians allowed too? Are they "sinners" Daniel? Just wondering...
   

---------------------QUOTE-------------------
"it ain't elegant"?  Tell me the human hand is not one of the most elegant structures imaginable.  
---------------------QUOTE-------------------


The human hand is not one of the most elegant structures imaginable.
 

---------------------QUOTE-------------------
"it ain't intelligent"?  The human brain puts our banks of computers to shame with it's processing power.  
---------------------QUOTE-------------------


Does it? Or, in fact, are the two things not really comparable at all? Perhaps the "software" has more to do with it then raw processing power.
 

---------------------QUOTE-------------------
What is it that blinds you to all this?  Is it your distaste for God?  Do you do this because it's his creation?    
---------------------QUOTE-------------------


Evidently logic blinds me to it. You proclaim it's his creation. Big whoop. So did < Ted Haggard >, every single day. And we know how that ended up.


---------------------QUOTE-------------------
I don't understand it; I don't understand how intelligent people can look at such mind-boggling sophistication and deny it even exists!      
---------------------QUOTE-------------------


mind-boggling sophistication? It seems that scientists are doing a real fine job understanding the structures that evolution has created. Much is yet to be done. Nobody's mind is boggled so much that they have found it necessary to consider this "sophistication" the work of a telic force. Those that do find it necessary to invoke supernatural beings invarably are not contribing to the cutting edge, just writing books for lay people. There is a reason for that, or just prove me wrong and show me some productive scientists using ID (or whatever label you want to use) to generate results that standard reality based science is failing to.
Could I suggest you start here
< A Practical Medical Application of ID Theory (or, Darwinism as a Science-Stopper) > and then < here. >


---------------------QUOTE-------------------
Within our bodies there are literally billions of working systems - intertwined in complex networks - working together to allow us to do things like laughing and crying, reading and speaking.      
---------------------QUOTE-------------------


Got a list?


---------------------QUOTE-------------------
All these systems work together so we can cradle a baby, smell a flower, enjoy a sunset, or compose or enjoy music.      
---------------------QUOTE-------------------


Or die from malaria or HIV or any number of other things that the designer presumably made. Or have any one of thousands of different things go wrong with their body. Or have an unknown aneurysm pop.
 

---------------------QUOTE-------------------
They allow us to do the very things we are doing right now.      
---------------------QUOTE-------------------


Do they? Perhaps our minds are really like radar recievers and the signal of our minds are being transmitted to our bodies. Perhaps the body is nothing to do with it after all. I mean, body is made of material stuff and that has to follow known laws, so it must be deterministic so it must be predictable and so our minds are not really anything to do with our bodies, apart from moving them? If there's no free will how can we choose to be saved eh?


---------------------QUOTE-------------------
They allow us to do the very things we are doing right now.      
---------------------QUOTE-------------------


Well, go on then. Explain how.


---------------------QUOTE-------------------
 You can't explain that with "variation and selection".  There's just no way.      
---------------------QUOTE-------------------


No, you can't. Those are just two words. Quite right. You need millions of words to just make a start. All bound together by people doing actual real work who discarded the need to invoke supernatural beings decades ago.


---------------------QUOTE-------------------
There is an "elephant in the room" and I think you know who it is.
---------------------QUOTE-------------------


Who? Presumably you have a Christian god and from what I remember from school he was in three parts. Father, son, holy ghost. Which part do you think is designing all this cool stuff for us Daniel? Are there really three elephants in the room? Don't you see how silly this all sounds?

Just accept the fact there is nothing in the books that provides evidence for your belief in your particular god. No matter how far back you go and how obscure, modern genetics is not going to turn around and say "by golly, it was designed after all". There are too many evidences for evilution, it's indisputable. Except by you, Vmartin, the loons at UD and a few hundred other misguided folks some of whom are unfortunatly in positions to decide what children will learn about eviluition.

When your position provides a better explanation for observed facts then people will adopt it. It's that simple. It might take time and people fighting and reputations getting destroyed but it happens nonetheless.

Like Dr Dembski. His reputation has been destroyed (E.G Name another professor who makes points with animations that overdub farting noises). Yet his position does not provide a better explanation for observed facts and lo! Nobody is adopting it except lay people who want to get god iinto the classroom. His position = not productive for science.
Posted by: Arden Chatfield on Dec. 12 2007,09:25

Quote (stevestory @ Dec. 12 2007,08:15)
When I saw Daniel's "they can interbreed so they're the same species" the first thing I thought of was ring species. So kudos to Arden.
---------------------QUOTE-------------------


Credit where it's due, oldmanintheskydidntdoit is the one who posted the info on ring species. I just posted the smartassy rejoinder to Daniel's "no forest here, just trees" response.

So maybe I deserve one kudo at most, or perhaps half a kudo.
Posted by: oldmanintheskydidntdoit on Dec. 12 2007,09:27

Quote (Arden Chatfield @ Dec. 12 2007,09:25)
Quote (stevestory @ Dec. 12 2007,08:15)
When I saw Daniel's "they can interbreed so they're the same species" the first thing I thought of was ring species. So kudos to Arden.
---------------------QUOTE-------------------


Credit where it's due, oldmanintheskydidntdoit is the one who posted the info on ring species. I just posted the smartassy rejoinder to Daniel's "no forest here, just trees" response.

So maybe I deserve one kudo at most, or perhaps half a kudo.
---------------------QUOTE-------------------


Triple kudos all round!
Posted by: oldmanintheskydidntdoit on Dec. 12 2007,09:30

Quote (Daniel Smith @ Dec. 11 2007,19:46)
What is it that blinds you to all this?  Is it your distaste for God?  Do you do this because it's his creation?
---------------------QUOTE-------------------


Is it just me or is Daniel implying we're Satanists here?  :p
Posted by: Henry J on Dec. 12 2007,10:17

Half a kudo? isn't that a little like half an eye or half a wing? :p
Posted by: Arden Chatfield on Dec. 12 2007,10:19

Quote (Henry J @ Dec. 12 2007,10:17)
Half a kudo? isn't that a little like half an eye or half a wing? :p
---------------------QUOTE-------------------


What good is half a kudo?
Posted by: Lou FCD on Dec. 12 2007,11:05



< Image credits found here. >


Posted by: JAM on Dec. 12 2007,11:25

Quote (Daniel Smith @ Dec. 11 2007,19:46)
 
Quote (Lou FCD @ Dec. 10 2007,05:25)
               
Quote (JAM @ Dec. 09 2007,17:46)
                 
Quote (Daniel Smith @ Dec. 09 2007,15:53)
So you only accept Perfection as evidence for intelligent design?
---------------------QUOTE-------------------


Straw man. He accepts intelligence as evidence for intelligent design.
---------------------QUOTE-------------------


Well said, thank you.

The end product is a bug ridden, defective hack-job of spare parts and afterthoughts that worked at the time of implementation.

It ain't pretty, it ain't elegant, it ain't intelligent, it just works or it doesn't.
---------------------QUOTE-------------------


Hogwash.  Pure and simple hogwash.  The "end product"
---------------------QUOTE-------------------


What's the "end product," Dan? Humans? If so, there are plenty of aspects of nonhumans that are far more complex, elegant, and/or sophisticated than the homologous aspect of human biology.


---------------------QUOTE-------------------
... is the most complex,
---------------------QUOTE-------------------


Complexity does not imply design.


---------------------QUOTE-------------------
elegant,
---------------------QUOTE-------------------


Now you're lying again. You haven't looked, and you haven't offered a single example of elegance. In fact, the nature of biological complexity is usually profoundly and utterly inelegant. "Elegantly simple" is not an oxymoron.


---------------------QUOTE-------------------
sophisticated machinery known to man. 

"It ain't pretty"?  Those of us with a preference for the female of the species will beg to differ.
---------------------QUOTE-------------------


Why are some females more pretty than others? Experimental psychology tells us that we choose on the basis of symmetry and averageness.


---------------------QUOTE-------------------
"it ain't elegant"?  Tell me the human hand is not one of the most elegant structures imaginable.
---------------------QUOTE-------------------


I can imagine an infinite number of more elegant structures, beginning with obvious improvements on the existing design.  


---------------------QUOTE-------------------
"it ain't intelligent"?  The human brain puts our banks of computers to shame with it's processing power.
---------------------QUOTE-------------------


Your ignorance makes you look foolish. The problem with this claim is that the connections that provide our brains' processing power are acquired, not designed. The "design" is one of reiteration, the common theme of biology.


---------------------QUOTE-------------------
What is it that blinds you to all this?  Is it your distaste for God?  Do you do this because it's his creation?
---------------------QUOTE-------------------


We're the ones who study His creation, Dan, you're the one who avoids studying life itself and resorts to quote mining. You are intentionally blind to the realities of biology. What are you afraid of?


---------------------QUOTE-------------------
I don't understand it; I don't understand how intelligent people can look at such mind-boggling sophistication and deny it even exists!  Within our bodies there are literally billions of working systems -
---------------------QUOTE-------------------


Yes, as are nonworking ones. Time and iteration produce both the working and nonworking ones, while the existence of the latter class is inconsistent with not only design, but intelligent design.


---------------------QUOTE-------------------
intertwined in complex networks - working together to allow us to do things like laughing and crying, reading and speaking.
---------------------QUOTE-------------------


But not all of us can do those things. You can't explain that.


---------------------QUOTE-------------------
All these systems work together so we can cradle a baby, smell a flower, enjoy a sunset, or compose or enjoy music.
---------------------QUOTE-------------------


But not all of us can do those things. This is why you are a deeply dishonest man, Dan.


---------------------QUOTE-------------------
They allow us to do the very things we are doing right now.
---------------------QUOTE-------------------


Why did God design you to remain in denial about your incuriosity, Dan?


---------------------QUOTE-------------------
You can't explain that with "variation and selection".  There's just no way.
---------------------QUOTE-------------------


Sure we can, just as we can explain why those systems break.


---------------------QUOTE-------------------
There is an "elephant in the room" and I think you know who it is.
---------------------QUOTE-------------------


The elephant in the room is your fear of reality.
Posted by: Arden Chatfield on Dec. 12 2007,11:43

Quote (Lou FCD @ Dec. 12 2007,11:05)

---------------------QUOTE-------------------


Lou, despite what your wife says, you rock. :p

I mean -- Steve never made little cartoons describing what it's like to be a moderator here.  :angry:

Tell you what, let's make our goal for 2008 that you will communicate here using nothing but cartoons, and I will communicate using nothing but Lolcats.
Posted by: Lou FCD on Dec. 12 2007,14:06

Quote (Arden Chatfield @ Dec. 12 2007,12:43)
Lou, despite what your wife says, you rock. :p
---------------------QUOTE-------------------



Thanks Arden.  It was fun to do, but a bit of work.  It took a while to find just the right image of a guy at a desk.  The image of the girl in the closet popped right up, and had Daniel's name written all over it.  The Bobby Clarke poster and the "I'm with the banned" poster were easy to put in.  The hardest things to get in there half-way decently were the girls in the right hand monitor and the screenshot of AtBC in the other one. (That's an actual screenshot from my computer.)

Quote (Arden Chatfield @ Dec. 12 2007,12:43)
I mean -- Steve never made little cartoons describing what it's like to be a moderator here.  :angry:
---------------------QUOTE-------------------



Yeah well, I was feeling a little creative, and Danny Boy's slinging the gay insinuation around like it was an insult was in itself offensive enough to merit comment.

Quote (Arden Chatfield @ Dec. 12 2007,12:43)
Tell you what, let's make our goal for 2008 that you will communicate here using nothing but cartoons, and I will communicate using nothing but Lolcats.
---------------------QUOTE-------------------



It's got serial potential just using the same image (maybe just changing the chick pic around for each episode?), but a whole year with nothing else?  

That seems like quite a challenge.

(I'll have to find the original pic again though, just to give proper credit.  I had to finish and get to some errands, and forgot to note the image author.)
Posted by: Henry J on Dec. 12 2007,14:46

Even if some "elegant" features are there, evolution theory doesn't imply the complete absence of such; it just implies that there will also be lots of kludges and inefficiencies along with it.

Henry
Posted by: Lou FCD on Dec. 12 2007,17:20

How funny is this?

< Evolution keeps pregnant women upright >



---------------------QUOTE-------------------
Evolution provided slight differences from men in women's lower backs and hip joints, allowing them to adjust their center of gravity, new research shows.

This elegant engineering is seen only in female humans and our immediate ancestors who walked on two feet, but not in chimps and apes, according to a study published in Thursday's journal Nature.

"That's a big load that's pulling you forward," said Liza Shapiro, an anthropology professor at the University of Texas and the only one of the study's three authors who has actually been pregnant. "You experience discomfort. Maybe it would be a lot worse if (the design changes) were not there."

Harvard anthropology researcher Katherine Whitcomb found two physical differences in male and female backs that until now had gone unnoticed: One lower lumbar vertebra is wedged-shaped in women and more square in men; and a key hip joint is 14 percent larger in women than men when body size is taken into account.
Don't Miss

   * Nature:  How pregnant women bend over backwards for baby

The researchers did engineering tests that show how those slight changes allow women to carry the additional and growing load without toppling over -- and typically without disabling back pain.
---------------------QUOTE-------------------



(emphasis mine)

Well, who am I to argue with CNN?

I concede, Godmustadunit.
Posted by: Richardthughes on Dec. 13 2007,13:22

Quote (Lou FCD @ Dec. 12 2007,11:05)

---------------------QUOTE-------------------


Quality.
Posted by: Lou FCD on Dec. 14 2007,12:15

Pardon the VMartin interruption.  I'm taking care of that.


Posted by: Daniel Smith on Dec. 15 2007,12:24

Quote (oldmanintheskydidntdoit @ Dec. 12 2007,09:27)
 
Quote (Arden Chatfield @ Dec. 12 2007,09:25)
   
Quote (stevestory @ Dec. 12 2007,08:15)
When I saw Daniel's "they can interbreed so they're the same species" the first thing I thought of was ring species. So kudos to Arden.
---------------------QUOTE-------------------


Credit where it's due, oldmanintheskydidntdoit is the one who posted the info on ring species. I just posted the smartassy rejoinder to Daniel's "no forest here, just trees" response.

So maybe I deserve one kudo at most, or perhaps half a kudo.
---------------------QUOTE-------------------


Triple kudos all round!
---------------------QUOTE-------------------


I guess amidst all the kudos and congratulatory back-slapping, you guys missed < my response > to the ring species argument.
Posted by: Daniel Smith on Dec. 15 2007,12:59

Quote (JAM @ Dec. 12 2007,11:25)
     
Quote (Daniel Smith @ Dec. 11 2007,19:46)
elegant,
---------------------QUOTE-------------------


Now you're lying again. You haven't looked, and you haven't offered a single example of elegance. In fact, the nature of biological complexity is usually profoundly and utterly inelegant. "Elegantly simple" is not an oxymoron.

---------------------QUOTE-------------------

Now you're just lying.  I can look at virtually any biological system and immediately see its elegance and sophistication of design.  Take < protein synthesis > for example.  Not only is this an incredibly efficient machine - made up of an intricate web of cooperating smaller molecular machines - but it also self-replicates.  You can't explain the origin of even this most basic foundational element of life via the mechanisms of your theory.  You can't improve upon it either.  Why don't you tell me exactly what's "profoundly and utterly inelegant" about protein synthesis?  Your constant bloviating on these points is just hollow bravado that masks your inabilities to comprehend even the simplest of God's works.
       

---------------------QUOTE-------------------
   

---------------------QUOTE-------------------
"it ain't elegant"?  Tell me the human hand is not one of the most elegant structures imaginable.
---------------------QUOTE-------------------


I can imagine an infinite number of more elegant structures, beginning with obvious improvements on the existing design.
---------------------QUOTE-------------------


How about a list?
Posted by: oldmanintheskydidntdoit on Dec. 15 2007,14:25

Quote (Daniel Smith @ Dec. 15 2007,12:24)
Quote (oldmanintheskydidntdoit @ Dec. 12 2007,09:27)
   
Quote (Arden Chatfield @ Dec. 12 2007,09:25)
   
Quote (stevestory @ Dec. 12 2007,08:15)
When I saw Daniel's "they can interbreed so they're the same species" the first thing I thought of was ring species. So kudos to Arden.
---------------------QUOTE-------------------


Credit where it's due, oldmanintheskydidntdoit is the one who posted the info on ring species. I just posted the smartassy rejoinder to Daniel's "no forest here, just trees" response.

So maybe I deserve one kudo at most, or perhaps half a kudo.
---------------------QUOTE-------------------


Triple kudos all round!
---------------------QUOTE-------------------


I guess amidst all the kudos and congratulatory back-slapping, you guys missed < my response > to the ring species argument.
---------------------QUOTE-------------------


You said


---------------------QUOTE-------------------
The terms "do not normally interbreed" and "cannot interbreed" are not equivalent terms.
---------------------QUOTE-------------------


Perhaps you could elaborate?
Posted by: oldmanintheskydidntdoit on Dec. 15 2007,14:26

Quote (Daniel Smith @ Dec. 15 2007,12:59)
You can't explain the origin of even this most basic foundational element of life via the mechanisms of your theory.
---------------------QUOTE-------------------


Neither can you. Prove me wrong.

goddidt?
Posted by: Assassinator on Dec. 15 2007,14:32



---------------------QUOTE-------------------
Now you're just lying.  I can look at virtually any biological system and immediately see its elegance and sophistication of design.
---------------------QUOTE-------------------


That's an emotional opinion not backed up by anything else then your opinion and emotions. It's not a scientific conclusion, you're not even really educated on these parts.
See this one for this argument:


---------------------QUOTE-------------------
Design is self-evident. You just need to open your eyes and see it.
---------------------QUOTE-------------------


< http://www.talkorigins.org/indexcc/CI/CI100_1.html >
Posted by: oldmanintheskydidntdoit on Dec. 15 2007,17:02

Quote (Daniel Smith @ Dec. 15 2007,12:59)
Now you're just lying.  I can look at virtually any biological system and immediately see its elegance and sophistication of design.
---------------------QUOTE-------------------


 

---------------------QUOTE-------------------
the recurrent pharyngeal nerve, which in all mammals (if
I'm not mistaken) loops around the aorta in order to get from the
brain to the larynx.  In the giraffe, this nerve is thus ~15 feet
long, whereas the larynx is ~1 foot from the brain.  
---------------------QUOTE-------------------



A quote from < TO > there, I also found a great site while searching for info.
< http://darwinstories.blogspot.com/2007....ck.html >
Funny!
Daniel, whats elegant about the pharyngeal nerve in the giraffe then?
Posted by: JAM on Dec. 15 2007,17:42

Quote (Daniel Smith @ Dec. 15 2007,12:24)
I guess amidst all the kudos and congratulatory back-slapping, you guys missed < my response > to the ring species argument.
---------------------QUOTE-------------------


That wasn't a response.
Posted by: IanBrown_101 on Dec. 15 2007,17:47

Quote (oldmanintheskydidntdoit @ Dec. 15 2007,23:02)
Quote (Daniel Smith @ Dec. 15 2007,12:59)
Now you're just lying.  I can look at virtually any biological system and immediately see its elegance and sophistication of design.
---------------------QUOTE-------------------


 

---------------------QUOTE-------------------
the recurrent pharyngeal nerve, which in all mammals (if
I'm not mistaken) loops around the aorta in order to get from the
brain to the larynx.  In the giraffe, this nerve is thus ~15 feet
long, whereas the larynx is ~1 foot from the brain.  
---------------------QUOTE-------------------



A quote from < TO > there, I also found a great site while searching for info.
< http://darwinstories.blogspot.com/2007....ck.html >
Funny!
Daniel, whats elegant about the pharyngeal nerve in the giraffe then?
---------------------QUOTE-------------------


Or the human prostate.

Or the human eyeball.

Or the coccyx.

Or...
Posted by: Arden Chatfield on Dec. 15 2007,17:52

Quote (Daniel Smith @ Dec. 15 2007,12:24)
Quote (oldmanintheskydidntdoit @ Dec. 12 2007,09:27)
   
Quote (Arden Chatfield @ Dec. 12 2007,09:25)
     
Quote (stevestory @ Dec. 12 2007,08:15)
When I saw Daniel's "they can interbreed so they're the same species" the first thing I thought of was ring species. So kudos to Arden.
---------------------QUOTE-------------------


Credit where it's due, oldmanintheskydidntdoit is the one who posted the info on ring species. I just posted the smartassy rejoinder to Daniel's "no forest here, just trees" response.

So maybe I deserve one kudo at most, or perhaps half a kudo.
---------------------QUOTE-------------------


Triple kudos all round!
---------------------QUOTE-------------------


I guess amidst all the kudos and congratulatory back-slapping, you guys missed < my response > to the ring species argument.
---------------------QUOTE-------------------


Was this your whole 'response'?



---------------------QUOTE-------------------
The terms "do not normally interbreed" and "cannot interbreed" are not equivalent terms.
---------------------QUOTE-------------------



Yes, we saw that. We were totally blown away, trust me.

You've convinced us all of creationism, we just don't want to admit it.
Posted by: JAM on Dec. 15 2007,17:52

Quote (Daniel Smith @ Dec. 15 2007,12:59)

Now you're just lying.
---------------------QUOTE-------------------


No, I'm not, and you support my claim to boot:
 

---------------------QUOTE-------------------
 I can look at virtually any biological system and immediately see its elegance and sophistication of design.
---------------------QUOTE-------------------


"I can look at" does not falsify "have not looked at." You haven't really looked; you run away at the slightest challenge.
 

---------------------QUOTE-------------------
 Take < protein synthesis > for example.
---------------------QUOTE-------------------


Since I already did and you ran away from my question, which one of us is lying, Dan?
 

---------------------QUOTE-------------------
Not only is this an incredibly efficient machine - made up of an intricate web of cooperating smaller molecular machines
---------------------QUOTE-------------------


You are incoherent. Intricacy is not a measure of efficiency. You haven't looked at efficiency, have you?
 

---------------------QUOTE-------------------
- but it also self-replicates.
---------------------QUOTE-------------------


Really? How does the protein synthetic machinery self-replicate? What substance makes up the enzymatic core of the ribosome, Dan? Is it synthesized by the protein synthetic machinery?

I predict that you don't know, and you will evade my attempts to get you to look, supporting my claim that you haven't looked.
 

---------------------QUOTE-------------------
You can't explain the origin of even this most basic foundational element of life via the mechanisms of your theory.
---------------------QUOTE-------------------


Can you explain it?
 

---------------------QUOTE-------------------
You can't improve upon it either.
---------------------QUOTE-------------------


You're lying again. It is trivially easy to improve upon it. That's the very point I was making when I asked you this question, from which you ran away, because in your soul, you know that your arguments are fraudulent (i.e., you have no real faith):

 
Quote (JAM @ Dec. 09 2007,16:46)
   
Quote (Daniel Smith @ Dec. 09 2007,15:53)
So you only accept Perfection as evidence for intelligent design?
---------------------QUOTE-------------------


Straw man. He accepts intelligence as evidence for intelligent design.

Does having a separate codon(s) for stopping translation (that don't encode an amino acid residue) represent an intelligent design? This allows proteins to have any of the 20 residues at the carboxy terminus.

I predict that you will avoid the question.
---------------------QUOTE-------------------



Why didn't you answer, Dan? Are you deluded, dishonest, or (my choice) both?

Does this feature of protein synthesis demonstrate intelligent design, elegant design, or both?

 

---------------------QUOTE-------------------
Why don't you tell me exactly what's "profoundly and utterly inelegant" about protein synthesis?
---------------------QUOTE-------------------


I will--exactly--when you answer my question. Otherwise, you'll move the goal posts.
 

---------------------QUOTE-------------------
Your constant bloviating on these points is just hollow bravado that masks your inabilities to comprehend even the simplest of God's works.
---------------------QUOTE-------------------


I ask questions, you run away from them while bloviating, and you accuse me of bloviating? What did Jesus say about hypocrisy?
Posted by: Lou FCD on Dec. 15 2007,17:53

Quote (IanBrown_101 @ Dec. 15 2007,18:47)
Quote (oldmanintheskydidntdoit @ Dec. 15 2007,23:02)
Quote (Daniel Smith @ Dec. 15 2007,12:59)
Now you're just lying.  I can look at virtually any biological system and immediately see its elegance and sophistication of design.
---------------------QUOTE-------------------


   

---------------------QUOTE-------------------
the recurrent pharyngeal nerve, which in all mammals (if
I'm not mistaken) loops around the aorta in order to get from the
brain to the larynx.  In the giraffe, this nerve is thus ~15 feet
long, whereas the larynx is ~1 foot from the brain.  
---------------------QUOTE-------------------



A quote from < TO > there, I also found a great site while searching for info.
< http://darwinstories.blogspot.com/2007....ck.html >
Funny!
Daniel, whats elegant about the pharyngeal nerve in the giraffe then?
---------------------QUOTE-------------------


Or the human prostate.

Or the human eyeball.

Or the coccyx.

Or...
---------------------QUOTE-------------------


And should we even go into the playpen/sewage disposal thing?
Posted by: JAM on Dec. 15 2007,17:56

Quote (Lou FCD @ Dec. 15 2007,17:53)
And should we even go into the playpen/sewage disposal thing?
---------------------QUOTE-------------------


The funny thing is that it's even worse on the intracellular level. Dan ran away from explaining the elegance of that too.
Posted by: Steverino on Dec. 16 2007,07:40

Denial,

Where is your proof that apperance of design, proves design?

Leap of faith is not proof.
Posted by: Daniel Smith on Dec. 16 2007,15:15

Quote (oldmanintheskydidntdoit @ Dec. 15 2007,14:25)
 
Quote (Daniel Smith @ Dec. 15 2007,12:24)
 
Quote (oldmanintheskydidntdoit @ Dec. 12 2007,09:27)
     
Quote (Arden Chatfield @ Dec. 12 2007,09:25)
       
Quote (stevestory @ Dec. 12 2007,08:15)
When I saw Daniel's "they can interbreed so they're the same species" the first thing I thought of was ring species. So kudos to Arden.
---------------------QUOTE-------------------


Credit where it's due, oldmanintheskydidntdoit is the one who posted the info on ring species. I just posted the smartassy rejoinder to Daniel's "no forest here, just trees" response.

So maybe I deserve one kudo at most, or perhaps half a kudo.
---------------------QUOTE-------------------


Triple kudos all round!
---------------------QUOTE-------------------


I guess amidst all the kudos and congratulatory back-slapping, you guys missed < my response > to the ring species argument.
---------------------QUOTE-------------------


You said
 

---------------------QUOTE-------------------
The terms "do not normally interbreed" and "cannot interbreed" are not equivalent terms.
---------------------QUOTE-------------------


Perhaps you could elaborate?
---------------------QUOTE-------------------


Sure.  Your contention that the sub-species at the ends of these "ring-species" are not the same species is only valid if the hybrid is infertile.  If the sub-species hybrid is fertile, they're still the same species - in spite of their inhibition to mate with each other.
Therefore the terms "do not normally interbreed" and "cannot interbreed" are not equivalent terms.
Posted by: Daniel Smith on Dec. 16 2007,15:44

Quote (oldmanintheskydidntdoit @ Dec. 15 2007,17:02)
   
Quote (Daniel Smith @ Dec. 15 2007,12:59)
Now you're just lying.  I can look at virtually any biological system and immediately see its elegance and sophistication of design.
---------------------QUOTE-------------------


     

---------------------QUOTE-------------------
the recurrent pharyngeal nerve, which in all mammals (if
I'm not mistaken) loops around the aorta in order to get from the
brain to the larynx.  In the giraffe, this nerve is thus ~15 feet
long, whereas the larynx is ~1 foot from the brain.  
---------------------QUOTE-------------------



A quote from < TO > there, I also found a great site while searching for info.
< http://darwinstories.blogspot.com/2007....ck.html >
Funny!
Daniel, whats elegant about the pharyngeal nerve in the giraffe then?
---------------------QUOTE-------------------


The reason the nerve passes between the internal and external carotid arteries is because the giraffe evolved from a short-necked ancestor.  The giraffe most likely represents the over-specialized typolysis phase of Schindewolf's theory.

My guess is that the giraffe will exhibit low genetic variability when compared with other mammals also.

You have to remember that creation took place a long time ago, and lots of evolution and variation has happened since then.  The fact that so much of what remains is still functional is a testament to the brilliance of the Creator.
Posted by: mitschlag on Dec. 16 2007,15:57

Quote (Daniel Smith @ Dec. 16 2007,15:44)
You have to remember that creation took place a long time ago, and lots of evolution and variation has happened since then.  The fact that so much of what remains is still functional is a testament to the brilliance of the Creator.
---------------------QUOTE-------------------


One expects no less from an omniscient, omnipotent being.  So I'm not terribly impressed.

But when did that being stop tinkering?
Posted by: Richard Simons on Dec. 16 2007,16:40

Quote (Daniel Smith @ Dec. 16 2007,15:44)
The reason the nerve passes between the internal and external carotid arteries is because the giraffe evolved from a short-necked ancestor.  The giraffe most likely represents the over-specialized typolysis phase of Schindewolf's theory.
---------------------QUOTE-------------------


I just don't understand what causes this facination with what was a passing fad amongst some biologists 70 years ago, and that lasted for even shorter than the streamlined steam locomotives of the same era. It is pure fancy, with no evidence to support it and not even a postulated mechanism.
Posted by: oldmanintheskydidntdoit on Dec. 16 2007,17:02

Quote (Daniel Smith @ Dec. 16 2007,15:44)
The giraffe most likely represents the over-specialized typolysis phase of Schindewolf's theory.
---------------------QUOTE-------------------


Why?
Posted by: Daniel Smith on Dec. 16 2007,21:15

Quote (Richard Simons @ Dec. 16 2007,16:40)
   
Quote (Daniel Smith @ Dec. 16 2007,15:44)
The reason the nerve passes between the internal and external carotid arteries is because the giraffe evolved from a short-necked ancestor.  The giraffe most likely represents the over-specialized typolysis phase of Schindewolf's theory.
---------------------QUOTE-------------------


I just don't understand what causes this facination with what was a passing fad amongst some biologists 70 years ago, and that lasted for even shorter than the streamlined steam locomotives of the same era. It is pure fancy, with no evidence to support it and not even a postulated mechanism.
---------------------QUOTE-------------------


I'm assuming you have not read Schindewolf's Basic Questions in Paleontology.  If you had, you'd know that Schindewolf endorsed Richard Goldschmidt's theory of Systemmutation, or the "repatterning" of the chromosomes, as a mechanism:    

---------------------QUOTE-------------------
This repatterning or Systemmutation, is attributed to cytologically provable breaks in the chromosomes, which evoke inversions, duplications, and translocations.  A single modification of an embryonic character produced in this way would then regulate a whole series of related ontogenetic processes, leading to a completely new developmental type.
Basic Questions in Paleontology, pg. 352, footnote (emphasis his)
---------------------QUOTE-------------------


That this mechanism has merit has been spelled out in this discussion by the contention that mice and men share "100%" of their genes, yet their chromosomes show complete restructuring in relation to each other.
Posted by: Daniel Smith on Dec. 16 2007,21:25

Quote (oldmanintheskydidntdoit @ Dec. 16 2007,17:02)
 
Quote (Daniel Smith @ Dec. 16 2007,15:44)
The giraffe most likely represents the over-specialized typolysis phase of Schindewolf's theory.
---------------------QUOTE-------------------


Why?
---------------------QUOTE-------------------


Mainly because he uses it as an example of over-specialization on pg. 287 of his book:


---------------------QUOTE-------------------
The Recent giraffe is overspecialized in the extreme lengthening of the neck and forelimbs, which is usually assumed to be a special adaptation for browsing on the leaves and twigs of tall trees.  The excessive length of the legs is compensated for only very incompletely by the neck, upsetting normal proportions; the giraffe can no longer reach the ground or the surface of a water hole with its mouth when standing in a normal position but must instead spread its forelegs wide apart (fig. 3.126).  In addition, the long slender neck makes impossible the development of extensive weapons on the forehead, as are seen, for example, in the related, relatively short-necked Pliocene Sivatherium.  For reasons of weight, only short ossicones could develop.
Basic Questions in Paleontology, pg. 287 (his italics)
---------------------QUOTE-------------------


Posted by: Daniel Smith on Dec. 16 2007,21:27

Quote (Steverino @ Dec. 16 2007,07:40)
Denial,

Where is your proof that apperance of design, proves design?

Leap of faith is not proof.
---------------------QUOTE-------------------


Are you admitting life shows the appearance of design?
Or is this a trick question?
Posted by: Daniel Smith on Dec. 16 2007,21:37

Quote (JAM @ Dec. 15 2007,17:52)
     
Quote (Daniel Smith @ Dec. 15 2007,12:59)
Take < protein synthesis > for example.
---------------------QUOTE-------------------


Since I already did and you ran away from my question, which one of us is lying, Dan?
       

---------------------QUOTE-------------------
Not only is this an incredibly efficient machine - made up of an intricate web of cooperating smaller molecular machines
---------------------QUOTE-------------------


You are incoherent. Intricacy is not a measure of efficiency. You haven't looked at efficiency, have you?
       

---------------------QUOTE-------------------
- but it also self-replicates.
---------------------QUOTE-------------------


Really? How does the protein synthetic machinery self-replicate? What substance makes up the enzymatic core of the ribosome, Dan? Is it synthesized by the protein synthetic machinery?

I predict that you don't know, and you will evade my attempts to get you to look, supporting my claim that you haven't looked.
       

---------------------QUOTE-------------------
You can't explain the origin of even this most basic foundational element of life via the mechanisms of your theory.
---------------------QUOTE-------------------


Can you explain it?
       

---------------------QUOTE-------------------
You can't improve upon it either.
---------------------QUOTE-------------------


You're lying again. It is trivially easy to improve upon it. That's the very point I was making when I asked you this question, from which you ran away, because in your soul, you know that your arguments are fraudulent (i.e., you have no real faith):

         
Quote (JAM @ Dec. 09 2007,16:46)
         
Quote (Daniel Smith @ Dec. 09 2007,15:53)
So you only accept Perfection as evidence for intelligent design?
---------------------QUOTE-------------------


Straw man. He accepts intelligence as evidence for intelligent design.

Does having a separate codon(s) for stopping translation (that don't encode an amino acid residue) represent an intelligent design? This allows proteins to have any of the 20 residues at the carboxy terminus.

I predict that you will avoid the question.
---------------------QUOTE-------------------



Why didn't you answer, Dan? Are you deluded, dishonest, or (my choice) both?

Does this feature of protein synthesis demonstrate intelligent design, elegant design, or both?

       

---------------------QUOTE-------------------
Why don't you tell me exactly what's "profoundly and utterly inelegant" about protein synthesis?
---------------------QUOTE-------------------


I will--exactly--when you answer my question. Otherwise, you'll move the goal posts.
       

---------------------QUOTE-------------------
Your constant bloviating on these points is just hollow bravado that masks your inabilities to comprehend even the simplest of God's works.
---------------------QUOTE-------------------


I ask questions, you run away from them while bloviating, and you accuse me of bloviating? What did Jesus say about hypocrisy?
---------------------QUOTE-------------------


I take these non-answers as admission that your theory cannot explain the origin of even the most basic building blocks of life.  

Also, your contention that you could improve upon the process of protein synthesis is just posturing, IMO.  If you really can, there's a Nobel prize with your name on it, just waiting for you to come pick it up.
Posted by: Lou FCD on Dec. 16 2007,22:50

Quote (Daniel Smith @ Dec. 16 2007,16:44)
You have to remember that creation took place a long time ago, and lots of evolution and variation has happened since then.  The fact that so much of what remains is still functional is a testament to the brilliance of the Creator.
---------------------QUOTE-------------------


The key phrase in that final sentence would seem to be "of what remains".

The vast majority of the "Intelligent" Designer's work failed miserably and went ignobly extinct.

That ain't so very brilliant.  Even baseball players are expected to get a hit about 10% of the time when they're in a slump.  

A hockey team with a 10% success rate on the power play is likely to get its coach fired.

If you go to work and 10% of your assignments from your boss are successful, you'll be in the unemployment line.

A first grade student with a 10% success rate of answering exam questions will most certainly be remanded to remedial course work, and surely will not be promoted to second grade.

That's 10%.  Your "Brilliant Creator" has a batting average significantly below that.

Just sayin'.
Posted by: Arden Chatfield on Dec. 16 2007,23:00

Quote (Daniel Smith @ Dec. 16 2007,21:27)
Quote (Steverino @ Dec. 16 2007,07:40)
Denial,

Where is your proof that apperance of design, proves design?

Leap of faith is not proof.
---------------------QUOTE-------------------


Are you admitting life shows the appearance of design?
Or is this a trick question?
---------------------QUOTE-------------------


And this year's award for Missing the Point goes to...
Posted by: Erasmus, FCD on Dec. 17 2007,00:01

Daniel your argument relies upon the empirical content of the proposition that 'Living things are just like non-living things'.  In other words, if we knew enough about physics and chemistry, saith the reductive absurdist who is attempting a muppet mimicry of modern biology, we could derive the rules that govern the origin and maintenance of biological diversity.  Since we can't, Jesus did it.  

The problem lies in the fact that you have been unable to give a first principle defense of why your teleological view should even be considered.  parsimony is a bitch.  

No biologist who is seriously thinking about the issue is willing to go to the plate for that proposition 'living things are reducible to non-living things' (note that this position is an absurd strawman derived from a hard-line formulation of what you call 'materialism'), namely an atomistic determined best of all possible worlds nonsensical hypothesis.  I imagine you will find a wide common ground with modern biology if you express skepticism that living things are reducible to non-living things, but you must do more than say "un-unhhh".  Case studies and examples do nothing to support your thesis, which must ultimately derive some testable first principles of it's own instead of merely denying other theories.  Ask Bob O'Hare why the notion of 'laws' governing biology or ecology has been an unfruitful concept.  It has a lot to do with the fact that no distillable generalizations are available at the level of your analysis, only many examples and counter examples.

I'll add this again, a wise redneck indian once told me something that I consider as hard and fast a biological law that ever could be:

Shit varies.  It matters.  Sometimes.

The teleological view could provide some testable predictions.  relying on schindewolf and goldschmidt means that you are relying on the simple assertions of those who never derived any test of their hypotheses.  Simpson showed that Schindewolf's view of telic horse evolution was at odds with empirical evidence (you should read Tempo and
Mode, there is a chapter devoted to deconstructing Schindewolf that is particularly salient to this discussion).  you should think about some predictions that would distinguish your telic view from an atelic view.  I doubt that this is possible, since we have no a priori notion of what such a teleology would involve (unless of course you are just looking at nature to confirm theological beliefs that you have already held, per your previous comments).  

So here we go:  Life is not reducible to non-living elements (I'll buy this for the sake of discussion, and this has no bearing on whether I personally accept this hypothesis).  If this is true, you have no data from which to evaluate teleology.  If you can tell me 'What is the purpose of living things' then we will have a place to start here.  Otherwise you are just mumbling in the dark.  The sad part about that is I believe you are interested in empiricism.  Your approach, however, is at odds with it.

Edited to add:  Michelob may have something to do with the length of this post.
Posted by: JAM on Dec. 17 2007,00:54

Quote (Daniel Smith @ Dec. 16 2007,21:37)
Quote (JAM @ Dec. 15 2007,17:52)
       
Quote (Daniel Smith @ Dec. 15 2007,12:59)
Take < protein synthesis > for example.
---------------------QUOTE-------------------


Since I already did and you ran away from my question, which one of us is lying, Dan?
         

---------------------QUOTE-------------------
Not only is this an incredibly efficient machine - made up of an intricate web of cooperating smaller molecular machines
---------------------QUOTE-------------------


You are incoherent. Intricacy is not a measure of efficiency. You haven't looked at efficiency, have you?
         

---------------------QUOTE-------------------
- but it also self-replicates.
---------------------QUOTE-------------------


Really? How does the protein synthetic machinery self-replicate? What substance makes up the enzymatic core of the ribosome, Dan? Is it synthesized by the protein synthetic machinery?

I predict that you don't know, and you will evade my attempts to get you to look, supporting my claim that you haven't looked.
         

---------------------QUOTE-------------------
You can't explain the origin of even this most basic foundational element of life via the mechanisms of your theory.
---------------------QUOTE-------------------


Can you explain it?
         

---------------------QUOTE-------------------
You can't improve upon it either.
---------------------QUOTE-------------------


You're lying again. It is trivially easy to improve upon it. That's the very point I was making when I asked you this question, from which you ran away, because in your soul, you know that your arguments are fraudulent (i.e., you have no real faith):

           
Quote (JAM @ Dec. 09 2007,16:46)
           
Quote (Daniel Smith @ Dec. 09 2007,15:53)
So you only accept Perfection as evidence for intelligent design?
---------------------QUOTE-------------------


Straw man. He accepts intelligence as evidence for intelligent design.

Does having a separate codon(s) for stopping translation (that don't encode an amino acid residue) represent an intelligent design? This allows proteins to have any of the 20 residues at the carboxy terminus.

I predict that you will avoid the question.
---------------------QUOTE-------------------



Why didn't you answer, Dan? Are you deluded, dishonest, or (my choice) both?

Does this feature of protein synthesis demonstrate intelligent design, elegant design, or both?

         

---------------------QUOTE-------------------
Why don't you tell me exactly what's "profoundly and utterly inelegant" about protein synthesis?
---------------------QUOTE-------------------


I will--exactly--when you answer my question. Otherwise, you'll move the goal posts.
         

---------------------QUOTE-------------------
Your constant bloviating on these points is just hollow bravado that masks your inabilities to comprehend even the simplest of God's works.
---------------------QUOTE-------------------


I ask questions, you run away from them while bloviating, and you accuse me of bloviating? What did Jesus say about hypocrisy?
---------------------QUOTE-------------------


I take these non-answers as admission that your theory cannot explain the origin of even the most basic building blocks of life.  

Also, your contention that you could improve upon the process of protein synthesis is just posturing, IMO.  If you really can, there's a Nobel prize with your name on it, just waiting for you to come pick it up.
---------------------QUOTE-------------------


Does having a separate codon(s) for stopping translation (that don't encode an amino acid residue) represent an intelligent design? This allows proteins to have any of the 20 residues at the carboxy terminus.

It's a simple question, and you'd have the integrity to answer it if you really thought that I was just posturing.

You need to answer it beforehand because we both know that you are dishonest when it comes to critically evaluating your own position, and you'll move the goal posts.

You define intelligent design operationally in this case, and I'll show an unequivocal improvement on the "design" USING YOUR CRITERIA. Any knowledgeable biologist can propose reams of obvious improvements.

You don't have any real faith in your position, Dan.
Posted by: JAM on Dec. 17 2007,00:59

Quote (Daniel Smith @ Dec. 16 2007,21:15)
Quote (Richard Simons @ Dec. 16 2007,16:40)
     
Quote (Daniel Smith @ Dec. 16 2007,15:44)
The reason the nerve passes between the internal and external carotid arteries is because the giraffe evolved from a short-necked ancestor.  The giraffe most likely represents the over-specialized typolysis phase of Schindewolf's theory.
---------------------QUOTE-------------------


I just don't understand what causes this facination with what was a passing fad amongst some biologists 70 years ago, and that lasted for even shorter than the streamlined steam locomotives of the same era. It is pure fancy, with no evidence to support it and not even a postulated mechanism.
---------------------QUOTE-------------------


I'm assuming you have not read Schindewolf's Basic Questions in Paleontology.  If you had, you'd know that Schindewolf endorsed Richard Goldschmidt's theory of Systemmutation, or the "repatterning" of the chromosomes, as a mechanism:      

---------------------QUOTE-------------------
This repatterning or Systemmutation, is attributed to cytologically provable breaks in the chromosomes, which evoke inversions, duplications, and translocations.  A single modification of an embryonic character produced in this way would then regulate a whole series of related ontogenetic processes, leading to a completely new developmental type.
Basic Questions in Paleontology, pg. 352, footnote (emphasis his)
---------------------QUOTE-------------------


That this mechanism has merit has been spelled out in this discussion by the contention that mice and men share "100%" of their genes, yet their chromosomes show complete restructuring in relation to each other.
---------------------QUOTE-------------------


You're lying again, or perhaps profoundly stupid.

Their chromosomes do NOT show "complete restructuring in relation to each other." There are vast regions in which gene order has been perfectly preserved (synteny), falsifying your desperate claim.

Or are you being so idiotically ignorant that you are implicitly claiming that the chromosomes were numbered on the basis of homology, instead of the single, simple criterion of length?
Posted by: oldmanintheskydidntdoit on Dec. 17 2007,06:12

Daniel, you said
 

---------------------QUOTE-------------------
I can look at virtually any biological system and immediately see its elegance and sophistication of design.
---------------------QUOTE-------------------


I then posted a quote    

---------------------QUOTE-------------------
the recurrent pharyngeal nerve, which in all mammals (if
I'm not mistaken) loops around the aorta in order to get from the
brain to the larynx.  In the giraffe, this nerve is thus ~15 feet
long, whereas the larynx is ~1 foot from the brain.  
---------------------QUOTE-------------------

and I then asked you "Daniel, whats elegant about the pharyngeal nerve in the giraffe then? " To which you < responded >
     

---------------------QUOTE-------------------
The reason the nerve passes between the internal and external carotid arteries is because the giraffe evolved from a short-necked ancestor.  The giraffe most likely represents the over-specialized typolysis phase of Schindewolf's theory.
My guess is that the giraffe will exhibit low genetic variability when compared with other mammals also.

You have to remember that creation took place a long time ago, and lots of evolution and variation has happened since then.  The fact that so much of what remains is still functional is a testament to the brilliance of the Creator.
---------------------QUOTE-------------------


So what you appear to be saying really is "I can look at virtually any biological system and immediately see its elegance and sophistication of design unless lots of evolution and variation has happened since the "kind" was originally created"
So, if there is elegance and sophistication it's because it was designed in, and if there is not it's because lots of evolution and variation has destroyed what elegance and sophistication was originally designed in.

What a pathetic cop-out. I doubt you even believe this tripe youself.

In addition you said
 

---------------------QUOTE-------------------
I take these non-answers as admission that your theory cannot explain the origin of even the most basic building blocks of life.  
---------------------QUOTE-------------------



Why not show us how much better your theory is and please describe for us all the origin of even the most basic building blocks of life under your theory. Can you do it without using the world "miracle"? I doubt it.
Posted by: oldmanintheskydidntdoit on Dec. 17 2007,06:31

And in any case Daniel,  

---------------------QUOTE-------------------
The reason the nerve passes between the internal and external carotid arteries is because the giraffe evolved from a short-necked ancestor.  
---------------------QUOTE-------------------


Would it not have been more "elegant" to avoid all this looping and make a direct connection in the first place? Even in the short-necked ancestor? Why did the designer do it that way Daniel?

No doubt you'll have some reason that the "designer" (god) did it that way that'll make perfect sense.

Or you'll say that we can't know the designers intentions, or some such total cop-out. Yet you are willing to say


---------------------QUOTE-------------------
I can look at virtually any biological system and immediately see its elegance and sophistication of design.
---------------------QUOTE-------------------


And somehow you still don't see the irony there.

Please describe for me the elegance and sophistication of the malaria parasite.
Posted by: Steverino on Dec. 17 2007,07:03

Quote (Daniel Smith @ Dec. 16 2007,21:27)
Quote (Steverino @ Dec. 16 2007,07:40)
Denial,

Where is your proof that apperance of design, proves design?

Leap of faith is not proof.
---------------------QUOTE-------------------


Are you admitting life shows the appearance of design?
Or is this a trick question?
---------------------QUOTE-------------------


ID proponents are big of spouting "this was designed and this looks designed...blah...blah...blah...."

What I'm asking is, if you believe something has the appearance of design, where is the proof that the appearance of design, proves design.
Posted by: Richard Simons on Dec. 17 2007,10:00

Quote (Daniel Smith @ Dec. 16 2007,21:15)
I'm assuming you have not read Schindewolf's Basic Questions in Paleontology.  If you had, you'd know that Schindewolf endorsed Richard Goldschmidt's theory of Systemmutation, or the "repatterning" of the chromosomes, as a mechanism:        

---------------------QUOTE-------------------
This repatterning or Systemmutation, is attributed to cytologically provable breaks in the chromosomes, which evoke inversions, duplications, and translocations.  A single modification of an embryonic character produced in this way would then regulate a whole series of related ontogenetic processes, leading to a completely new developmental type.
Basic Questions in Paleontology, pg. 352, footnote (emphasis his)
---------------------QUOTE-------------------


That this mechanism has merit has been spelled out in this discussion by the contention that mice and men share "100%" of their genes, yet their chromosomes show complete restructuring in relation to each other.
---------------------QUOTE-------------------


Even if this were correct, it does not answer the problems of how organisms know what information they will need for the future, how this information is stored without being corrupted and how it is turned on at the 'correct' time. You have previously admitted you can't answer these questions and you must have known this is what I was asking about, so in future try to be more honest in your responses.

It still does not answer the question 'Why the fascination with a defunct theory?'
Posted by: Steverino on Dec. 17 2007,17:53

Quote (Richard Simons @ Dec. 17 2007,10:00)
   
Quote (Daniel Smith @ Dec. 16 2007,21:15)
I'm assuming you have not read Schindewolf's Basic Questions in Paleontology.  If you had, you'd know that Schindewolf endorsed Richard Goldschmidt's theory of Systemmutation, or the "repatterning" of the chromosomes, as a mechanism:            

---------------------QUOTE-------------------
This repatterning or Systemmutation, is attributed to cytologically provable breaks in the chromosomes, which evoke inversions, duplications, and translocations.  A single modification of an embryonic character produced in this way would then regulate a whole series of related ontogenetic processes, leading to a completely new developmental type.
Basic Questions in Paleontology, pg. 352, footnote (emphasis his)
---------------------QUOTE-------------------


That this mechanism has merit has been spelled out in this discussion by the contention that mice and men share "100%" of their genes, yet their chromosomes show complete restructuring in relation to each other.
---------------------QUOTE-------------------


Even if this were correct, it does not answer the problems of how organisms know what information they will need for the future, how this information is stored without being corrupted and how it is turned on at the 'correct' time. You have previously admitted you can't answer these questions and you must have known this is what I was asking about, so in future try to be more honest in your responses.

It still does not answer the question 'Why the fascination with a defunct theory?'
---------------------QUOTE-------------------


Richard....Richard.....Richard......(big sigh)......

You miss the point, they don't need to know because.....


Everyone Now.........!!!!



"GODDIDIT!!!!!....GODDIDIT!!!!!.....GODDIDIT!!!!!

Damn!....I love those group chants...Don't we all feel better now!!!???....God!....I do!!!!
Posted by: Daniel Smith on Dec. 17 2007,18:04

Quote (Richard Simons @ Dec. 17 2007,10:00)
   
Quote (Daniel Smith @ Dec. 16 2007,21:15)
I'm assuming you have not read Schindewolf's Basic Questions in Paleontology.  If you had, you'd know that Schindewolf endorsed Richard Goldschmidt's theory of Systemmutation, or the "repatterning" of the chromosomes, as a mechanism:            

---------------------QUOTE-------------------
This repatterning or Systemmutation, is attributed to cytologically provable breaks in the chromosomes, which evoke inversions, duplications, and translocations.  A single modification of an embryonic character produced in this way would then regulate a whole series of related ontogenetic processes, leading to a completely new developmental type.
Basic Questions in Paleontology, pg. 352, footnote (emphasis his)
---------------------QUOTE-------------------


That this mechanism has merit has been spelled out in this discussion by the contention that mice and men share "100%" of their genes, yet their chromosomes show complete restructuring in relation to each other.
---------------------QUOTE-------------------


Even if this were correct, it does not answer the problems of how organisms know what information they will need for the future, how this information is stored without being corrupted and how it is turned on at the 'correct' time.
---------------------QUOTE-------------------


How do organisms or organs "know" anything?
How does the eye "know" to rotate in it's socket when you tilt your head?
How do the ears "know" how to hear?
How do the sex cells "know" they have to cut their number of chromosomes in half?
How do cells "know" during ontogeny what types of cells to differentiate into?

The fact that Life is still here after all these eons is testament to the ingenuity of the designer.  Think about it:  The "god" of the atheist - Natural Selection - has no stake in the matter.  It could care less if genomes get corrupted and unravel.  What does Natural Selection care if life ceases to exist?  Why does every epoch throughout history show an incredible balance of lifeforms - in spite of all variations of environmental conditions? Natural Selection could care less about this.  Again, it has no stake in the matter.  If the earth were to become a dead, uninhabitable planet, Natural Selection would not know the difference.  No, there's something else in play here.  Something is keeping this balance we see.  Something much greater than you and me.

So, to answer both our questions:  It's not that organisms "know" anything, it's that there was someone behind them that knows everything.  God programmed life to live and die, to flourish and become extinct, to evolve and devolve.  It is God who keeps all these things going - for whatever his unknown purposes are.
Posted by: Steverino on Dec. 17 2007,18:11

Ding....Ding...Ding!!!!

"So, to answer both our questions:  It's not that organisms "know" anything, it's that there was someone behind them that knows everything.  God programmed life to live and die, to flourish and become extinct, to evolve and devolve.  It is God who keeps all these things going - for whatever his unknown purposes are."


Did I call it or what!!!

"Backed into a corner.....with no valid supporting information, evidence or data....crayons running low....our God Warrior, young Denial Smith whips out the God Card!"

It's all about the science folks!!!  Check please!
Posted by: oldmanintheskydidntdoit on Dec. 17 2007,18:46

Quote (Daniel Smith @ Dec. 17 2007,18:04)
 
Quote (Richard Simons @ Dec. 17 2007,10:00)
       
Quote (Daniel Smith @ Dec. 16 2007,21:15)
I'm assuming you have not read Schindewolf's Basic Questions in Paleontology.  If you had, you'd know that Schindewolf endorsed Richard Goldschmidt's theory of Systemmutation, or the "repatterning" of the chromosomes, as a mechanism:                

---------------------QUOTE-------------------
This repatterning or Systemmutation, is attributed to cytologically provable breaks in the chromosomes, which evoke inversions, duplications, and translocations.  A single modification of an embryonic character produced in this way would then regulate a whole series of related ontogenetic processes, leading to a completely new developmental type.
Basic Questions in Paleontology, pg. 352, footnote (emphasis his)
---------------------QUOTE-------------------


That this mechanism has merit has been spelled out in this discussion by the contention that mice and men share "100%" of their genes, yet their chromosomes show complete restructuring in relation to each other.
---------------------QUOTE-------------------


Even if this were correct, it does not answer the problems of how organisms know what information they will need for the future, how this information is stored without being corrupted and how it is turned on at the 'correct' time.
---------------------QUOTE-------------------


How do organisms or organs "know" anything?
How does the eye "know" to rotate in it's socket when you tilt your head?
How do the ears "know" how to hear?
How do the sex cells "know" they have to cut their number of chromosomes in half?
How do cells "know" during ontogeny what types of cells to differentiate into?

The fact that Life is still here after all these eons is testament to the ingenuity of the designer.  Think about it:  The "god" of the atheist - Natural Selection - has no stake in the matter.  It could care less if genomes get corrupted and unravel.  What does Natural Selection care if life ceases to exist?  Why does every epoch throughout history show an incredible balance of lifeforms - in spite of all variations of environmental conditions? Natural Selection could care less about this.  Again, it has no stake in the matter.  If the earth were to become a dead, uninhabitable planet, Natural Selection would not know the difference.  No, there's something else in play here.  Something is keeping this balance we see.  Something much greater than you and me.

So, to answer both our questions:  It's not that organisms "know" anything, it's that there was someone behind them that knows everything.  God programmed life to live and die, to flourish and become extinct, to evolve and devolve.  It is God who keeps all these things going - for whatever his unknown purposes are.
---------------------QUOTE-------------------


Can I post the recursive hoff now then?  :D

This thread is toast!
Posted by: Daniel Smith on Dec. 17 2007,18:52

Quote (Erasmus @ FCD,Dec. 17 2007,00:01)
Daniel your argument relies upon the empirical content of the proposition that 'Living things are just like non-living things'.  In other words, if we knew enough about physics and chemistry, saith the reductive absurdist who is attempting a muppet mimicry of modern biology, we could derive the rules that govern the origin and maintenance of biological diversity.  Since we can't, Jesus did it.  

The problem lies in the fact that you have been unable to give a first principle defense of why your teleological view should even be considered.  parsimony is a bitch.  

No biologist who is seriously thinking about the issue is willing to go to the plate for that proposition 'living things are reducible to non-living things' (note that this position is an absurd strawman derived from a hard-line formulation of what you call 'materialism'), namely an atomistic determined best of all possible worlds nonsensical hypothesis.  I imagine you will find a wide common ground with modern biology if you express skepticism that living things are reducible to non-living things, but you must do more than say "un-unhhh".  Case studies and examples do nothing to support your thesis, which must ultimately derive some testable first principles of it's own instead of merely denying other theories.  Ask Bob O'Hare why the notion of 'laws' governing biology or ecology has been an unfruitful concept.  It has a lot to do with the fact that no distillable generalizations are available at the level of your analysis, only many examples and counter examples.

I'll add this again, a wise redneck indian once told me something that I consider as hard and fast a biological law that ever could be:

Shit varies.  It matters.  Sometimes.

The teleological view could provide some testable predictions.  relying on schindewolf and goldschmidt means that you are relying on the simple assertions of those who never derived any test of their hypotheses.  Simpson showed that Schindewolf's view of telic horse evolution was at odds with empirical evidence (you should read Tempo and
Mode, there is a chapter devoted to deconstructing Schindewolf that is particularly salient to this discussion).  you should think about some predictions that would distinguish your telic view from an atelic view.  I doubt that this is possible, since we have no a priori notion of what such a teleology would involve (unless of course you are just looking at nature to confirm theological beliefs that you have already held, per your previous comments).  

So here we go:  Life is not reducible to non-living elements (I'll buy this for the sake of discussion, and this has no bearing on whether I personally accept this hypothesis).  If this is true, you have no data from which to evaluate teleology.  If you can tell me 'What is the purpose of living things' then we will have a place to start here.  Otherwise you are just mumbling in the dark.  The sad part about that is I believe you are interested in empiricism.  Your approach, however, is at odds with it.

Edited to add:  Michelob may have something to do with the length of this post.
---------------------QUOTE-------------------


Michael Denton, in his book Nature's Destiny makes the case for teleological origins much better than I ever could.  While he doesn't really get into empirical tests for design, he does explore its falsification:        

---------------------QUOTE-------------------
The strength of any teleological argument is basically accumulative.  It does not lie with any one individual piece of evidence alone but with a whole series of coincidences, all of which point irresistibly to one conclusion.  It is the same here.  Neither the thermal properties of water, nor the chemical properties of carbon dioxide, nor the exceptional complexity of living things, nor the difficu;ties this leads to when attempting to give plausible explanations in Darwinian terms--none of these individually counts for much.  Rather it lies in the summation of all the evidence, in the whole long chain of coincidences which leads so convincingly toward the unique end of life, in the fact that all the independent lines of evidence fit together into a beautiful self-consistent teleological whole...

But the design hypothesis can, of course, be refuted by far less dramatic evidence...  For example, the discovery of an alternative liquid as fit as water for carbon based life, or of a superior means of constructing a genetic tape, better than the double helix, of alternatives superior to oxidation, superior to proteins, superior to the bilayer lipid membrane, to the cell system, to bicarbonate, to phosphates, and so on...  Just one clear case where a constituent of life or a law of nature is evidently not unique or ideally adapted for life, and the design hypothesis collapses.

Nature's Destiny, pp. 384, 386
---------------------QUOTE-------------------



I should add that Denton's view is that the ultimate purpose of life on this earth was to bring about homo sapiens.  I'd add to that -- "so that mankind can ultimately find God".  Denton cites the unique properties of fire, and man's unique ability to harness it that led to our ability to explore and learn about not only this planet, but the cosmos.  I'd say that the more man learns about life, the more God will become a necessary explanation - as opposed to the commonly held belief that the more we learn, the less God is required.

That's the test I guess.  If the farther we delve into it, the more complicated and amazing it gets, the more likely it's a product of supreme intelligence.  If, on the other hand, the deeper we delve, the simpler it becomes, we can safely assume random causes.

Personally, with what I've learned about the properties of DNA; with all the different transcriptional methods which allow for the transcription of multiple types of RNA from opposing strands, in opposing directions, while often overlapping protein coding DNA; I'd say we're past that point.  But I already believe in God.  You might have a much higher threshold.
Posted by: Daniel Smith on Dec. 17 2007,18:57

Quote (oldmanintheskydidntdoit @ Dec. 17 2007,06:12)
 

---------------------QUOTE-------------------
I take these non-answers as admission that your theory cannot explain the origin of even the most basic building blocks of life.  
---------------------QUOTE-------------------



Why not show us how much better your theory is and please describe for us all the origin of even the most basic building blocks of life under your theory. Can you do it without using the world "miracle"? I doubt it.
---------------------QUOTE-------------------


It was built out of atomic components by a being capable of building such things.  It was intelligently designed to read the programming tape of life and construct proteins from it.
Mankind has done similar things with his limited technology and abilities, so it's not what you'd call a miracle - although to our puny minds it seems so.
Posted by: Lou FCD on Dec. 17 2007,19:06

Daniel you've gone from illustrating that your god is inconceivably incompetent to shading him as supremely superfluous.

I guess that's upward progress, but...
Posted by: Erasmus, FCD on Dec. 17 2007,19:16

God is the Life Farce?

Fascinating.  I wish you had a blog.  I would read it.  So would a dozen or so other people.  We should come up with a good name.
Posted by: Lou FCD on Dec. 17 2007,19:23

Quote (Erasmus @ FCD,Dec. 17 2007,20:16)
Fascinating.  I wish you had a blog.  I would read it.  So would a dozen or so other people.  We should come up with a good name.
---------------------QUOTE-------------------


"Schindewolf's God"
"Recursive Hoff" (just kiddin')
"Daniel's Horse"
"Of Giraffes and Men"
"Elegant Design"

Edited to add:

Daniel, I once started a blog with the perfect title for what I wanted to do with it.  Problem is, I've lost interest in doing it.  If I just delete it, no one can ever use that address at WP again.  (It's a private, invisible blog at the moment.)

If you're interested, I'd be willing to hand you the keys to it, just so it doesn't go down the drain, and the title would work well for you.

missingthepoint.wordpress.com

(For that matter, if anyone at all is interested, PM me.)


Posted by: Erasmus, FCD on Dec. 17 2007,19:30

Added that before that I saw that you responded to my last post.



---------------------QUOTE-------------------
If the farther we delve into it, the more complicated and amazing it gets, the more likely it's a product of supreme intelligence.  If, on the other hand, the deeper we delve, the simpler it becomes, we can safely assume random causes.
---------------------QUOTE-------------------



But you have no a priori reason to assign complicated and amazing things to the products of unobserved supreme intelligences.  In other words, you can't parse 'it is supposed to be this way' and 'it is this way'.  Since the operationally preferable null is 'it is this way', and being conveniently agnostic (per instance) about teleology is a much more productive mode of inquiry (see the history of modern science, for instance), it seems that you'd have to compile ALL of the examples that biology has provided in order to provide a first order approximation of how relevant this teleological notion is to biology.  

And since of course no one has done this (ID is all about cherrypicking particularly undeveloped areas of research for minutiae examples), I'd say that you'll be hard pressed to find any sort of first principle explanations about what exactly the purpose of living things is (other than to live and reproduce and die, and that is difficult to disentangle from supposed to and just does, see above).  

But you must realize that if there is a teleology it must not only explain the pathetic detail of intercellular biochemistry but also the phyletic evolution of life in time as well as extant patterns of biodiversity and the trophic structure of ecosystems, for starters.  If it doesn't, then it doesn't have that much to offer.  

cheers

serious about the blog.  do it.
Posted by: Albatrossity2 on Dec. 17 2007,20:21

Quote (Erasmus @ FCD,Dec. 17 2007,19:16)
God is the Life Farce?

Fascinating.  I wish you had a blog.  I would read it.  So would a dozen or so other people.  We should come up with a good name.
---------------------QUOTE-------------------


Well, I've been reading this thread (religiously) and I have to say that I probably won't read Daniel's blog if he goes that route. While the defense of long-dead biologists like Schindewolf might be interesting for a while, it won't pay the rent. Most of this thread has been classic goal-post moving, nit-picking, and a general misunderstanding of where science has progressed since the Art Deco era.

"God did it that way" is not an answer I need to see over and over and over again. Tain't interesting, and tain't science.
Posted by: Erasmus, FCD on Dec. 17 2007,20:35

Albie, you're right.  I suppose I would be interested in a capable, coherent and intentionally empirical defense of orthogenesis as a challenge to focus my thoughts.  Not God Did It That Way (that's what UD is for).  I think JAD fails the first two prongs of that test, but AFAIK he is a candidate.  Most instruction at my university ignores that supposed controversy, but the more I read Gould the more respect I have for the view (IN PRINCIPLE).  I have yet to see anyone make a convincing principled argument however (Martin that especially means you buddyismus).
Posted by: Lou FCD on Dec. 17 2007,20:45

But UD is getting sooooo boring.  Even Dr. Dr. is bailing on his Friday meltdowns.  Tardicus isn't inserting his homophobic wisdom in comments, and Denyse was never terribly interesting in the first place.  Barry's been a little fun lately, but he can't carry the whole team over there.

We need some fresh meat.
Posted by: JAM on Dec. 17 2007,22:26

Quote (Daniel Smith @ Dec. 17 2007,18:52)
Personally, with what I've learned about the properties of DNA; with all the different transcriptional methods which allow for the transcription of multiple types of RNA from opposing strands, in opposing directions,...
---------------------QUOTE-------------------


Dan, this is just absurd. You haven't learned much about the properties of DNA if you don't even realize that its strands are antiparallel. Therefore, transcription on opposing strands can only occur in opposite directions.

High-school students know this, while you're so arrogant that you claim to understand complexity better than practicing scientists while lacking the knowledge of a ninth-grader.

Most of the things you claimed to have learned turned out to be fabrications, like your false claim that introns are coding sequences.

You're afraid to confront and discuss the NATURE of biological complexity.
Posted by: Alan Fox on Dec. 18 2007,03:36



---------------------QUOTE-------------------
I suppose I would be interested in a capable, coherent and intentionally empirical defense of orthogenesis as a challenge to focus my thoughts.  Not God Did It That Way (that's what UD is for).  I think JAD fails the first two prongs of that test, but AFAIK he is a candidate.
---------------------QUOTE-------------------



There may be something to interest you shortly.

Edit: (I know, Don't call me Shortly!)
Posted by: Assassinator on Dec. 18 2007,03:46



---------------------QUOTE-------------------
Are you admitting life shows the appearance of design?
---------------------QUOTE-------------------


The fact that life looks designed in your eyes has nothing to do with science and it's also 0.00 evidence for design. You're overrating your own emotional opinion.


---------------------QUOTE-------------------
But I already believe in God.
---------------------QUOTE-------------------


Wich is the main problem, you're so emotionally attached to your beleifs that you're only looking for things wich confirm your own beleifs.
Posted by: oldmanintheskydidntdoit on Dec. 18 2007,05:58

Quote (Daniel Smith @ Dec. 17 2007,18:57)
Quote (oldmanintheskydidntdoit @ Dec. 17 2007,06:12)
   

---------------------QUOTE-------------------
I take these non-answers as admission that your theory cannot explain the origin of even the most basic building blocks of life.  
---------------------QUOTE-------------------



Why not show us how much better your theory is and please describe for us all the origin of even the most basic building blocks of life under your theory. Can you do it without using the world "miracle"? I doubt it.
---------------------QUOTE-------------------


It was built out of atomic components by a being capable of building such things.  It was intelligently designed to read the programming tape of life and construct proteins from it.
Mankind has done similar things with his limited technology and abilities, so it's not what you'd call a miracle - although to our puny minds it seems so.
---------------------QUOTE-------------------


Atomic components eh? What would they be then? Atoms?


---------------------QUOTE-------------------
It was built out of atomic components by a being capable of building such things.
---------------------QUOTE-------------------


That's really just another way of saying "I don't know".


---------------------QUOTE-------------------
It was intelligently designed to read the programming tape of life and construct proteins from it.
---------------------QUOTE-------------------


That's really just another way of saying "I don't know".


---------------------QUOTE-------------------
Mankind has done similar things with his limited technology and abilities,
---------------------QUOTE-------------------


Has he really? In that case, If ManKind can do it why do we need to invoke a supernatural being in this case?


---------------------QUOTE-------------------
so it's not what you'd call a miracle - although to our puny minds it seems so.
---------------------QUOTE-------------------


Speak for yourself.

So Daniel. Simple question. Who designed the designer? If we're now approaching the level of technology and understanding you claim is required for the "intelligent designer"  

---------------------QUOTE-------------------
Mankind has done similar things with his limited technology and abilities
---------------------QUOTE-------------------

then it seems much more likely that the "intelligent designer" is simply another race of beings about as advanced as we are now. So hardly proof for your gods existence? I simply don't see how you can see it that way.

If mankind can "intelligently design" in a similar way to the "designer" you claim invented life then why does it automatically have to be supernatural? If we can do it..

Daniel, who designed the designer?
Posted by: oldmanintheskydidntdoit on Dec. 18 2007,06:24

Quote (Daniel Smith @ Dec. 17 2007,18:52)
I should add that Denton's view is that the ultimate purpose of life on this earth was to bring about homo sapiens.  I'd add to that -- "so that mankind can ultimately find God".
---------------------QUOTE-------------------


So if the ultimate purpose of the 99.9999999999% of all living beings that have gone extinct was lead up to homo sapiens that seems kind of wasteful.

Daniel, so let me get this straight. The purpose of life for millions of now extinct animals was to lay the ground work for human beings? Right?

Presumably therefore the "designer" can see into the future? Otherwise how could it be sure that the "design decisions" made back then would produce humans? It was a very long time ago remember. And if the "purpose" was so mankind can find god then I guess it would be a bad idea to, for example, allow a dinosaur to munch on the ancestor of humans right? Like a kind of "back to the future" situation?

So, we've got a designer who wants to make sure that humans exist at some point. So they go back billions of years, create life that has nothing to do with humans as we know it because this designer knows that over millions of years out will pop humans at the other end. In the meanwhile the vast majority of life created goes extinct, but never ancestors of modern humanity.

Daniel, what's the point of all that? Why would the designer not just make humans a few thousand years ago (6000 years sounds like a good round number) whole? Why go through the process of

a) Going back millions of years to do something that may or may not result in humanity
b) Waste millions of species in the process
c) Make it look exactly like "eviluiton" did it all all along anyway

when this designer could have just made man whole and not bothered with all the "ohh, I hope i've designed the right design for humans to appear in millions of years".

Seems like a bit of a bastard to me, to make it appear as if in fact it was nature all along and hope that "humans" look past the facade. Seems like your designer is in fact the DEVIL! heh. And seems like the only evidence you have for your position is "look at the molecular machines in the cell they are sooo complex". Did the enlightenment happen where you live?
Posted by: Steverino on Dec. 18 2007,06:58

I'm no scientist, but even I can see the logical flaw in his position.

Why are we even engaging this twit:

"So, to answer both our questions:  It's not that organisms "know" anything, it's that there was someone behind them that knows everything.  God programmed life to live and die, to flourish and become extinct, to evolve and devolve.  It is God who keeps all these things going - for whatever his unknown purposes are."

There is no proof to back that statement up and he knows it.  It’s an argument that cannot be proven on way or the other, so he clings to it because is leaves the door open for God.

You cannot argue/debate science once someone invokes the God card like this because it’s jut another form of moving the goal posts and at that point it becomes useless.
Posted by: oldmanintheskydidntdoit on Dec. 18 2007,07:17

Quote (Steverino @ Dec. 18 2007,06:58)
I'm no scientist, but even I can see the logical flaw in his position.

Why are we even engaging this twit:

"So, to answer both our questions:  It's not that organisms "know" anything, it's that there was someone behind them that knows everything.  God programmed life to live and die, to flourish and become extinct, to evolve and devolve.  It is God who keeps all these things going - for whatever his unknown purposes are."

There is no proof to back that statement up and he knows it.  It’s an argument that cannot be proven on way or the other, so he clings to it because is leaves the door open for God.

You cannot argue/debate science once someone invokes the God card like this because it’s jut another form of moving the goal posts and at that point it becomes useless.
---------------------QUOTE-------------------


Aye. I've nothing more to say on this thread I tink...
Posted by: George on Dec. 18 2007,08:09

I've not posted on this thread since near the beginning as I'm no gene jockey and not as patient as others.  But I found this an interesting argument:



---------------------QUOTE-------------------
The fact that Life is still here after all these eons is testament to the ingenuity of the designer.  Think about it:  The "god" of the atheist - Natural Selection - has no stake in the matter.  It could care less if genomes get corrupted and unravel.  What does Natural Selection care if life ceases to exist?  Why does every epoch throughout history show an incredible balance of lifeforms - in spite of all variations of environmental conditions? Natural Selection could care less about this.  Again, it has no stake in the matter.  If the earth were to become a dead, uninhabitable planet, Natural Selection would not know the difference.  No, there's something else in play here.  Something is keeping this balance we see.  Something much greater than you and me.
---------------------QUOTE-------------------



This is exactly the argument that bolsters climate change deniers - the feeling that someone trustworthy is in charge and that everything will be ok.  But this argument is entirely unfounded.

Daniel:  I've news.  There is no Balance of Nature.  The only people who believe in it anymore are those who write really bad dialogue for nature documentaries.  There is a flux of nature.  Everything changes, nothing stays the same.  Populations of organisms increase, decrease and move around the place.  In the northern hemisphere we're still recovering from the last glaciation.  Sometimes there's variation around a mean population size, but often not.  Many years of ecological research have shown that.

All those variations in environmental conditions you refer to resulted in extinctions.  Lots of them.  Who was looking out for those plants and animals?  Three mass extinctions in geological history, and Homo sapiens are causing the fourth.  These should suggest to you that Natural Selection is in charge of life on this planet and that if a really big, friendly comet comes along or if we banjax the climate, no one is coming to our rescue.

A "balance of nature" is not an argument for teleology, because it doesn't exist.

And by the way, I'm also a Christian and I do science just fine without needing a Designer tugging the strings.  It's bad religion, too.

</rant>
Posted by: Daniel Smith on Dec. 18 2007,18:00

Quote (oldmanintheskydidntdoit @ Dec. 18 2007,05:58)
So Daniel. Simple question. Who designed the designer? If we're now approaching the level of technology and understanding you claim is required for the "intelligent designer"          

---------------------QUOTE-------------------
Mankind has done similar things with his limited technology and abilities
---------------------QUOTE-------------------

then it seems much more likely that the "intelligent designer" is simply another race of beings about as advanced as we are now. So hardly proof for your gods existence? I simply don't see how you can see it that way.

If mankind can "intelligently design" in a similar way to the "designer" you claim invented life then why does it automatically have to be supernatural? If we can do it..

Daniel, who designed the designer?
---------------------QUOTE-------------------

I think your view of man is inflated.  We are not even close to being intelligent enough to design life - especially the act of designing self-replicating, evolving systems that can adapt to a multitude of environments - all the while keeping their "programming" intact enough through countless cell divisions and generations to continue giving life to still more generations.

We're nowhere near that level.  When I say man has designed "similar" systems, I'm talking about his tape readers, computers and CD/DVD players which use read-heads and associated circuitry to transfer/translate data from one form to another.

But, if you want to get into first causes, you really only have two choices:  Either the first cause is nothing, or the first cause is eternal.
If you vote for nothing, then you must accept that you can get something from nothing.
Therefore the only logical answer is that the first cause is eternal.
Posted by: Daniel Smith on Dec. 18 2007,18:04

Quote (Steverino @ Dec. 18 2007,06:58)
I'm no scientist, but even I can see the logical flaw in his position.

Why are we even engaging this twit:

"So, to answer both our questions:  It's not that organisms "know" anything, it's that there was someone behind them that knows everything.  God programmed life to live and die, to flourish and become extinct, to evolve and devolve.  It is God who keeps all these things going - for whatever his unknown purposes are."

There is no proof to back that statement up and he knows it.  It’s an argument that cannot be proven on way or the other, so he clings to it because is leaves the door open for God.

You cannot argue/debate science once someone invokes the God card like this because it’s jut another form of moving the goal posts and at that point it becomes useless.
---------------------QUOTE-------------------


Do you just trot out the standard "anti-creationist bag of arguments" - no matter who you're debating?  Because you obviously haven't been paying very close attention to what I've been saying.  I've been claiming "God did it" from the beginning.  Where have you been?
Posted by: Daniel Smith on Dec. 18 2007,18:14

Quote (JAM @ Dec. 17 2007,00:54)
Does having a separate codon(s) for stopping translation (that don't encode an amino acid residue) represent an intelligent design? This allows proteins to have any of the 20 residues at the carboxy terminus.

It's a simple question, and you'd have the integrity to answer it if you really thought that I was just posturing.

You need to answer it beforehand because we both know that you are dishonest when it comes to critically evaluating your own position, and you'll move the goal posts.

You define intelligent design operationally in this case, and I'll show an unequivocal improvement on the "design" USING YOUR CRITERIA. Any knowledgeable biologist can propose reams of obvious improvements.

You don't have any real faith in your position, Dan.
---------------------QUOTE-------------------


To be honest JAM, I do ignore most of your questions because they seem intentionally deflective - as if you're trying to steer me down a hundred rabbit trails.

This one I don't even understand:  

---------------------QUOTE-------------------
Does having a separate codon(s) for stopping translation (that don't encode an amino acid residue) represent an intelligent design? This allows proteins to have any of the 20 residues at the carboxy terminus.
---------------------QUOTE-------------------


How can a stop codon "[not] encode an amino acid residue" and "allow proteins to have any of the 20 residues" at the same time?
You'll have to make the question less cryptic for me to be able to answer it.
Posted by: Daniel Smith on Dec. 18 2007,18:27

Quote (JAM @ Dec. 12 2007,11:25)
We're the ones who study His creation, Dan,
---------------------QUOTE-------------------


Do you really consider it "His creation"?
   
Quote (JAM @ Dec. 09 2007,16:43)
Why not read His book of nature with an open mind instead of a closed one?
---------------------QUOTE-------------------


I am willing.  What exactly is it that God is trying to teach me?  Give me lesson #1.  Tell me what you've learned about God through "His book of nature".
Posted by: swbarnes2 on Dec. 18 2007,18:40

Quote (Daniel Smith @ Dec. 18 2007,18:04)
Because you obviously haven't been paying very close attention to what I've been saying.  I've been claiming "God did it" from the beginning.  Where have you been?
---------------------QUOTE-------------------



So your point was not to demonstrate that your conclusion is justified by the facts, your point was to keep making the the same unjustified claim over and over again?

And you think that we will find this an intelligent rebuttal?
Posted by: Daniel Smith on Dec. 18 2007,18:40

Quote (George @ Dec. 18 2007,08:09)
I've not posted on this thread since near the beginning as I'm no gene jockey and not as patient as others.  But I found this an interesting argument:

     

---------------------QUOTE-------------------
The fact that Life is still here after all these eons is testament to the ingenuity of the designer.  Think about it:  The "god" of the atheist - Natural Selection - has no stake in the matter.  It could care less if genomes get corrupted and unravel.  What does Natural Selection care if life ceases to exist?  Why does every epoch throughout history show an incredible balance of lifeforms - in spite of all variations of environmental conditions? Natural Selection could care less about this.  Again, it has no stake in the matter.  If the earth were to become a dead, uninhabitable planet, Natural Selection would not know the difference.  No, there's something else in play here.  Something is keeping this balance we see.  Something much greater than you and me.
---------------------QUOTE-------------------



This is exactly the argument that bolsters climate change deniers - the feeling that someone trustworthy is in charge and that everything will be ok.  But this argument is entirely unfounded.

Daniel:  I've news.  There is no Balance of Nature.  The only people who believe in it anymore are those who write really bad dialogue for nature documentaries.  There is a flux of nature.  Everything changes, nothing stays the same.  Populations of organisms increase, decrease and move around the place.  In the northern hemisphere we're still recovering from the last glaciation.  Sometimes there's variation around a mean population size, but often not.  Many years of ecological research have shown that.

All those variations in environmental conditions you refer to resulted in extinctions.  Lots of them.  Who was looking out for those plants and animals?  Three mass extinctions in geological history, and Homo sapiens are causing the fourth.  These should suggest to you that Natural Selection is in charge of life on this planet and that if a really big, friendly comet comes along or if we banjax the climate, no one is coming to our rescue.

A "balance of nature" is not an argument for teleology, because it doesn't exist.

And by the way, I'm also a Christian and I do science just fine without needing a Designer tugging the strings.  It's bad religion, too.

</rant>
---------------------QUOTE-------------------


There's a difference between balance and stasis.  It's true that there is no stasis in nature.  There is balance however.  If there weren't we'd be overrun by cockroaches by now.  Extinctions are a part of that balance.  When climate conditions change radically, species that once thrived die out and new ones take their place - all the while maintaining the balance that sustains this planet for life.
Posted by: Daniel Smith on Dec. 18 2007,18:42

Quote (swbarnes2 @ Dec. 18 2007,18:40)
So your point was not to demonstrate that your conclusion is justified by the facts, your point was to keep making the the same unjustified claim over and over again?

And you think that we will find this an intelligent rebuttal?
---------------------QUOTE-------------------


Point me to "the facts" that don't justify my conclusion.
Posted by: swbarnes2 on Dec. 18 2007,18:44

Quote (Daniel Smith @ Dec. 18 2007,18:14)
How can a stop codon "[not] encode an amino acid residue" and "allow proteins to have any of the 20 residues" at the same time?
You'll have to make the question less cryptic for me to be able to answer it.
---------------------QUOTE-------------------



You think the question is cryptic?

A question that 14 year old freshman can eaaily understand is too cryptic for you?
Posted by: George on Dec. 18 2007,18:47

Quote (Daniel Smith @ Dec. 18 2007,18:40)
[/quote]
There's a difference between balance and stasis.  It's true that there is no stasis in nature.  There is balance however.  If there weren't we'd be overrun by cockroaches by now.  Extinctions are a part of that balance.  When climate conditions change radically, species that once thrived die out and new ones take their place - all the while maintaining the balance that sustains this planet for life.
---------------------QUOTE-------------------


Then please explain to me what you mean by "balance".  And how it relates to cockroaches.  I don't know what you're getting at.
Posted by: Steverino on Dec. 18 2007,18:48

Quote (Daniel Smith @ Dec. 18 2007,18:04)
Quote (Steverino @ Dec. 18 2007,06:58)
I'm no scientist, but even I can see the logical flaw in his position.

Why are we even engaging this twit:

"So, to answer both our questions:  It's not that organisms "know" anything, it's that there was someone behind them that knows everything.  God programmed life to live and die, to flourish and become extinct, to evolve and devolve.  It is God who keeps all these things going - for whatever his unknown purposes are."

There is no proof to back that statement up and he knows it.  It’s an argument that cannot be proven on way or the other, so he clings to it because is leaves the door open for God.

You cannot argue/debate science once someone invokes the God card like this because it’s jut another form of moving the goal posts and at that point it becomes useless.
---------------------QUOTE-------------------


Do you just trot out the standard "anti-creationist bag of arguments" - no matter who you're debating?  Because you obviously haven't been paying very close attention to what I've been saying.  I've been claiming "God did it" from the beginning.  Where have you been?
---------------------QUOTE-------------------


Denial,

""So, to answer both our questions:  It's not that organisms "know" anything, it's that there was someone behind them that knows everything.  God programmed life to live and die, to flourish and become extinct, to evolve and devolve.  It is God who keeps all these things going - for whatever his unknown purposes are."

This is you throwing in the towel because you have nothing.  You bullshit a good game getting all sciency....until you cannot argue your point with valid science...and then you just toss in what you have been dying to say all along.  Why debate science at all?

Piss off and go over to UD with the other shills.  The only thing ID has proven without a doubt is that you can fool some of the people some of the time and jerk the rest off.

Which one are you?
Posted by: JAM on Dec. 18 2007,18:49

Quote (Daniel Smith @ Dec. 18 2007,18:14)
Quote (JAM @ Dec. 17 2007,00:54)
Does having a separate codon(s) for stopping translation (that don't encode an amino acid residue) represent an intelligent design? This allows proteins to have any of the 20 residues at the carboxy terminus.

It's a simple question, and you'd have the integrity to answer it if you really thought that I was just posturing.

You need to answer it beforehand because we both know that you are dishonest when it comes to critically evaluating your own position, and you'll move the goal posts.

You define intelligent design operationally in this case, and I'll show an unequivocal improvement on the "design" USING YOUR CRITERIA. Any knowledgeable biologist can propose reams of obvious improvements.

You don't have any real faith in your position, Dan.
---------------------QUOTE-------------------


To be honest JAM, I do ignore most of your questions because they seem intentionally deflective - as if you're trying to steer me down a hundred rabbit trails.
---------------------QUOTE-------------------


I'm trying to steer you into the light of reality. Do you realize that you just completely contradicted your claim that I was "posturing"?


---------------------QUOTE-------------------
This one I don't even understand:    

---------------------QUOTE-------------------
Does having a separate codon(s) for stopping translation (that don't encode an amino acid residue) represent an intelligent design? This allows proteins to have any of the 20 residues at the carboxy terminus.
---------------------QUOTE-------------------


How can a stop codon "[not] encode an amino acid residue" and "allow proteins to have any of the 20 residues" at the same time?
---------------------QUOTE-------------------


The stop codons are TAA, TAG, and TGA. They do not code for aa residues. I didn't write that it allowed them to HAVE any of the residues, I wrote that this allowed them to END in any one of them (i.e., carboxy terminus). Does that make more sense now? Is that an intelligent and/or elegant design?
Posted by: swbarnes2 on Dec. 18 2007,18:58

Quote (Daniel Smith @ Dec. 18 2007,18:40)
There is balance however.
---------------------QUOTE-------------------



Yes, yes.  We all learned about equilbrium constants in chemistry.  You put acetic acid in water, and ([H3O+][A-])/[HA] will always be constant.  Add more acid, the  numbers will change, but that ratio won't.

So now you think that the ordianry rules of chemistry are insufficient to explain this behavior?  You think that god stps in and nudges the ions back together?  You think that high schoolers ought to be taught that this is what happens, because blind chemicals couldn't do this otherwise?

You asked how the cells of the eye "know" how to grow into an eye.  The answer is, they do what they do because of the rules of chemistry.  Those laws of chemsitry say that when you have translation proteins and RNA and amino acids and what not, a protein with a certain configuration will be formed.  The laws of chemistry say that a certain protein will bind well to this sequence of DNA, and not at all to that sequence.  

Life is chemistry.  It's not some magical special non-chemical process, that was figured out with the synthesis of urea, what, a hundred years ago?

Chemistry is not totally blind, but proceeds by rules, and like it or not, those rules do lead to an extremely diverse set of phenomena, like life.  No intelligence required.
Posted by: swbarnes2 on Dec. 18 2007,19:13

Quote (Daniel Smith @ Dec. 18 2007,18:42)

Point me to "the facts" that don't justify my conclusion.
---------------------QUOTE-------------------


All the facts support the notion that evolution is a purely natural process.  No intelligence required.

Almost every single time you used your theology to predict what biology would look like, you were totally wrong.  Conservation of DNA.  Mouse/human orthologs.  Results of bacterial selection experiments.  I'm sure everyone on this board can name more.  Everywhere we used evolution to predict what we would see, we were right.

Those are the facts.
Posted by: BWE on Dec. 18 2007,23:46

Quote (Daniel Smith @ Dec. 18 2007,18:00)
But, if you want to get into first causes, you really only have two choices:  Either the first cause is nothing, or the first cause is eternal.
If you vote for nothing, then you must accept that you can get something from nothing.
Therefore the only logical answer is that the first cause is eternal.
---------------------QUOTE-------------------


Sure, fine. How do you get from there (eternal) to over there-----> where you are talking about this guy with angels licking his feet and demanding servitude of people who have no reliable way to even detect his existence? People who have to believe other people just to find out what he has done?

I mean, hello... Doesn't this strike you as rather... um... like suckering a mark?
Posted by: Steverino on Dec. 19 2007,06:37

Denial,

Please provide proof or existance of something "eternal".

Can be anything.  I'm not picky.
Posted by: oldmanintheskydidntdoit on Dec. 19 2007,07:12

Quote (BWE @ Dec. 18 2007,23:46)
Sure, fine. How do you get from there (eternal) to over there-----> where you are talking about this guy with angels licking his feet and demanding servitude of people who have no reliable way to even detect his existence? People who have to believe other people just to find out what he has done?

I mean, hello... Doesn't this strike you as rather... um... like suckering a mark?
---------------------QUOTE-------------------


Exactly so. This is the thing that amuses me most of all.

Get ten people in a room, and one claims to have a vision from god. Perhaps the other 9 will believe him and lo! We've got a hotline from god.

Usually the first "instruction" from god, via his chosen one, is to get on your f*cking knees and worship (via the chosen one) god, and follow all his instructions.  Don't think, just worship. Then, empty your pockets out and give it all to the "chosen one". You'll just have to take the chosen ones word for the fact that god is really speaking to them. The fact that all his instructions appear to entrench the power and wealth of the "chosen one" from that point on is because that's what god wants. Really. Can't honour the old man upstairsu unless his representatives on earth are covered in gold and silk

Is it any wonder the Vatican is gold plated?
In the modern world, a sexless old man controls the reproductive abilities of millions of people. It would not be possible but for religion.

god talks to alot of people. So they say. Often he tells them to "kill".
Posted by: oldmanintheskydidntdoit on Dec. 19 2007,07:21

Quote (Daniel Smith @ Dec. 18 2007,18:00)
Quote (oldmanintheskydidntdoit @ Dec. 18 2007,05:58)
So Daniel. Simple question. Who designed the designer? If we're now approaching the level of technology and understanding you claim is required for the "intelligent designer"            

---------------------QUOTE-------------------
Mankind has done similar things with his limited technology and abilities
---------------------QUOTE-------------------

then it seems much more likely that the "intelligent designer" is simply another race of beings about as advanced as we are now. So hardly proof for your gods existence? I simply don't see how you can see it that way.

If mankind can "intelligently design" in a similar way to the "designer" you claim invented life then why does it automatically have to be supernatural? If we can do it..

Daniel, who designed the designer?
---------------------QUOTE-------------------

I think your view of man is inflated.  We are not even close to being intelligent enough to design life - especially the act of designing self-replicating, evolving systems that can adapt to a multitude of environments - all the while keeping their "programming" intact enough through countless cell divisions and generations to continue giving life to still more generations.

We're nowhere near that level.  When I say man has designed "similar" systems, I'm talking about his tape readers, computers and CD/DVD players which use read-heads and associated circuitry to transfer/translate data from one form to another.

But, if you want to get into first causes, you really only have two choices:  Either the first cause is nothing, or the first cause is eternal.
If you vote for nothing, then you must accept that you can get something from nothing.
Therefore the only logical answer is that the first cause is eternal.
---------------------QUOTE-------------------


Ok, last time.



---------------------QUOTE-------------------

We're nowhere near that level.
---------------------QUOTE-------------------


No? It's just a matter of time.


---------------------QUOTE-------------------
When I say man has designed "similar" systems, I'm talking about his tape readers, computers and CD/DVD players which use read-heads and associated circuitry to transfer/translate data from one form to another.
---------------------QUOTE-------------------


So not "similar" at all then? For your information you could say  that these "systems" have existed for thousands of years. For example, write something down, read it out. Lo! Data has been transfered from "one form to another". See what happens when you use language?


---------------------QUOTE-------------------
But, if you want to get into first causes, you really only have two choices:  Either the first cause is nothing, or the first cause is eternal.
If you vote for nothing, then you must accept that you can get something from nothing.
---------------------QUOTE-------------------


As you have been shown to be a complete non-expert about everything else you have posted here then forgive me if I ignore totally what you think are the only "two possible" options. What do you know about it? What you've read in the bible presumably.



---------------------QUOTE-------------------
Therefore the only logical answer is that the first cause is eternal.
---------------------QUOTE-------------------



Daniel. Go to the north pole. When you are there, it looks just the same as any other spot on the globe. Nothing different at all. Look around. Every direction from that point is south. Now, imagine that the north pole is T=0, the big bang moment. Every moment from that point is T>0. Yet there is nothing "special" about that time/place.

There are lots of theorys about the big bang. Apparently you are ignorant of them all, prefering to go with "god did it or god did not do it". I find that odd, as presumably you think that god did in fact do it, yet you've no proof for that at all.

Daniel, accept the fact that your faith will not be able to hang on physical evidence. That's why they call it faith. Belief. If there was proof then all but the most stubborn would accept it. Just like this situation, but in reverse. You have no evidence, therefore your faith is in peril. Accept that, move on, and grow up.
Posted by: Daniel Smith on Dec. 20 2007,18:26

Quote (George @ Dec. 18 2007,18:47)
   
Quote (Daniel Smith @ Dec. 18 2007,18:40)

There's a difference between balance and stasis.  It's true that there is no stasis in nature.  There is balance however.  If there weren't we'd be overrun by cockroaches by now.  Extinctions are a part of that balance.  When climate conditions change radically, species that once thrived die out and new ones take their place - all the while maintaining the balance that sustains this planet for life.
---------------------QUOTE-------------------


Then please explain to me what you mean by "balance".  And how it relates to cockroaches.  I don't know what you're getting at.
---------------------QUOTE-------------------


I mean that the world always has exactly the right mixture of species to keep life going (even though the players are in a constant state of flux).  

There's no reason - from an unthinking, uncaring natural selection standpoint - for it to be thus.  If it truly is "the survival of the fittest", cockroaches would win out, take over the world, then die out too when their food sources ran out.  The planet would then be dead - like every other planet we know of.  (Of course, this is just an imaginary scenario where cockroaches just happen to win - you can substitute any "fit", rapidly reproducing species - it doesn't matter, one species should overtake all the others if there's no balance in nature).

That's what I mean by balance.
Posted by: Steverino on Dec. 20 2007,18:40

Quote (Daniel Smith @ Dec. 20 2007,18:26)
Quote (George @ Dec. 18 2007,18:47)
     
Quote (Daniel Smith @ Dec. 18 2007,18:40)

There's a difference between balance and stasis.  It's true that there is no stasis in nature.  There is balance however.  If there weren't we'd be overrun by cockroaches by now.  Extinctions are a part of that balance.  When climate conditions change radically, species that once thrived die out and new ones take their place - all the while maintaining the balance that sustains this planet for life.
---------------------QUOTE-------------------


Then please explain to me what you mean by "balance".  And how it relates to cockroaches.  I don't know what you're getting at.
---------------------QUOTE-------------------


I mean that the world always has exactly the right mixture of species to keep life going (even though the players are in a constant state of flux).  

There's no reason - from an unthinking, uncaring natural selection standpoint - for it to be thus.  If it truly is "the survival of the fittest", cockroaches would win out, take over the world, then die out too when their food sources ran out.  The planet would then be dead - like every other planet we know of.  (Of course, this is just an imaginary scenario where cockroaches just happen to win - you can substitute any "fit", rapidly reproducing species - it doesn't matter, one species should overtake all the others if there's no balance in nature).

That's what I mean by balance.
---------------------QUOTE-------------------


....from that you make your leap of faith to a "Designer".

Argument from Incredulity, nuff said.  Leave.
Posted by: Daniel Smith on Dec. 20 2007,18:46

Quote (swbarnes2 @ Dec. 18 2007,19:13)
   
Quote (Daniel Smith @ Dec. 18 2007,18:42)

Point me to "the facts" that don't justify my conclusion.
---------------------QUOTE-------------------


All the facts support the notion that evolution is a purely natural process.  No intelligence required.

Almost every single time you used your theology to predict what biology would look like, you were totally wrong.  Conservation of DNA.  Mouse/human orthologs.  Results of bacterial selection experiments.  I'm sure everyone on this board can name more.  Everywhere we used evolution to predict what we would see, we were right.

Those are the facts.
---------------------QUOTE-------------------



On the issue of mouse/human orthologs I was way off - yes.  

On the issue of the conservation of DNA, I'm still in the running - since even members of the same species have widely different DNA conservation percentages - anywhere from 0.1% to 8%.

On the results of bacterial selection experiments - none have been done that actually test my prediction (to my knowledge).

So there's actually only one out of the three you listed that would qualify as "totally wrong".
Posted by: Daniel Smith on Dec. 20 2007,19:07

Quote (JAM @ Dec. 18 2007,18:49)
     
Quote (Daniel Smith @ Dec. 18 2007,18:14)
This one I don't even understand:          

---------------------QUOTE-------------------
Does having a separate codon(s) for stopping translation (that don't encode an amino acid residue) represent an intelligent design? This allows proteins to have any of the 20 residues at the carboxy terminus.
---------------------QUOTE-------------------


How can a stop codon "[not] encode an amino acid residue" and "allow proteins to have any of the 20 residues" at the same time?
---------------------QUOTE-------------------


The stop codons are TAA, TAG, and TGA. They do not code for aa residues. I didn't write that it allowed them to HAVE any of the residues, I wrote that this allowed them to END in any one of them (i.e., carboxy terminus). Does that make more sense now? Is that an intelligent and/or elegant design?
---------------------QUOTE-------------------


I'm still a bit unclear because I don't know what's wrong with having stop codons the way they are.  Are you saying it would be better if they did code for amino acids?  

It might help if you could give me an analogy to better illustrate what's going on.

Let me try a language analogy on you and you can correct it where it's wrong:
In my analogy, amino acids would be like the letters of the alphabet and stop codons like sentence ending punctuation ( . ? and !).  So proteins in my analogy would be like sentences.

Is this anywhere near close?

If so, could you use my analogy (or yours - if you have a better one) to show me what's wrong with stop codons?
Posted by: JAM on Dec. 20 2007,19:14

Quote (Daniel Smith @ Dec. 20 2007,19:07)
Quote (JAM @ Dec. 18 2007,18:49)
       
Quote (Daniel Smith @ Dec. 18 2007,18:14)
This one I don't even understand:            

---------------------QUOTE-------------------
Does having a separate codon(s) for stopping translation (that don't encode an amino acid residue) represent an intelligent design? This allows proteins to have any of the 20 residues at the carboxy terminus.
---------------------QUOTE-------------------


How can a stop codon "[not] encode an amino acid residue" and "allow proteins to have any of the 20 residues" at the same time?
---------------------QUOTE-------------------


The stop codons are TAA, TAG, and TGA. They do not code for aa residues. I didn't write that it allowed them to HAVE any of the residues, I wrote that this allowed them to END in any one of them (i.e., carboxy terminus). Does that make more sense now? Is that an intelligent and/or elegant design?
---------------------QUOTE-------------------


I'm still a bit unclear because I don't know what's wrong with having stop codons the way they are.  Are you saying it would be better if they did code for amino acids?
---------------------QUOTE-------------------


No, I'm asking for your characterization. Was it an intelligent design decision to use separate codons for stop, instead of combining one or more of those "signals" with a signal to add an amino acid? 


---------------------QUOTE-------------------
It might help if you could give me an analogy to better illustrate what's going on.
---------------------QUOTE-------------------


I don't think so.


---------------------QUOTE-------------------
Let me try a language analogy on you and you can correct it where it's wrong:
In my analogy, amino acids would be like the letters of the alphabet and stop codons like sentence ending punctuation ( . ? and !).  So proteins in my analogy would be like sentences.

Is this anywhere near close?
---------------------QUOTE-------------------


Yes. Is it more intelligent to have separate letters and punctuation marks, or is it more intelligent to always end each sentence with the same letter?


---------------------QUOTE-------------------
If so, could you use my analogy (or yours - if you have a better one) to show me what's wrong with stop codons?
---------------------QUOTE-------------------


I'm not saying that there's anything wrong with them. I'm asking for your judgment.
Posted by: JAM on Dec. 20 2007,19:15

Quote (Daniel Smith @ Dec. 20 2007,18:46)
On the issue of the conservation of DNA, I'm still in the running - since even members of the same species have widely different DNA conservation percentages - anywhere from 0.1% to 8%.
---------------------QUOTE-------------------


No, you were wrong in every case. You are using fallacies of equivocation to pretend that you're still in the running.
Posted by: Daniel Smith on Dec. 20 2007,19:25

Quote (BWE @ Dec. 18 2007,23:46)
       
Quote (Daniel Smith @ Dec. 18 2007,18:00)
But, if you want to get into first causes, you really only have two choices:  Either the first cause is nothing, or the first cause is eternal.
If you vote for nothing, then you must accept that you can get something from nothing.
Therefore the only logical answer is that the first cause is eternal.
---------------------QUOTE-------------------


Sure, fine. How do you get from there (eternal) to over there-----> where you are talking about this guy with angels licking his feet and demanding servitude of people who have no reliable way to even detect his existence? People who have to believe other people just to find out what he has done?

I mean, hello... Doesn't this strike you as rather... um... like suckering a mark?
---------------------QUOTE-------------------


The question is not how did I get from here to there, but how did you get, "this guy with angels licking his feet and demanding servitude of people who have no reliable way to even detect his existence", from anything I've said?

When have I ever characterized God in that way?  That sounds more like bitterness talking.  

I've often wondered why some who profess not to believe in God seem to actively hate him.

How can you hate something you believe doesn't exist?
Posted by: Daniel Smith on Dec. 20 2007,19:31

Quote (JAM @ Dec. 20 2007,19:14)
 
Quote (Daniel Smith @ Dec. 20 2007,19:07)
   
Quote (JAM @ Dec. 18 2007,18:49)
         
Quote (Daniel Smith @ Dec. 18 2007,18:14)
This one I don't even understand:                

---------------------QUOTE-------------------
Does having a separate codon(s) for stopping translation (that don't encode an amino acid residue) represent an intelligent design? This allows proteins to have any of the 20 residues at the carboxy terminus.
---------------------QUOTE-------------------


How can a stop codon "[not] encode an amino acid residue" and "allow proteins to have any of the 20 residues" at the same time?
---------------------QUOTE-------------------


The stop codons are TAA, TAG, and TGA. They do not code for aa residues. I didn't write that it allowed them to HAVE any of the residues, I wrote that this allowed them to END in any one of them (i.e., carboxy terminus). Does that make more sense now? Is that an intelligent and/or elegant design?
---------------------QUOTE-------------------


I'm still a bit unclear because I don't know what's wrong with having stop codons the way they are.  Are you saying it would be better if they did code for amino acids?
---------------------QUOTE-------------------


No, I'm asking for your characterization. Was it an intelligent design decision to use separate codons for stop, instead of combining one or more of those "signals" with a signal to add an amino acid?
 

---------------------QUOTE-------------------
It might help if you could give me an analogy to better illustrate what's going on.
---------------------QUOTE-------------------


I don't think so.
 

---------------------QUOTE-------------------
Let me try a language analogy on you and you can correct it where it's wrong:
In my analogy, amino acids would be like the letters of the alphabet and stop codons like sentence ending punctuation ( . ? and !).  So proteins in my analogy would be like sentences.

Is this anywhere near close?
---------------------QUOTE-------------------


Yes. Is it more intelligent to have separate letters and punctuation marks, or is it more intelligent to always end each sentence with the same letter?
---------------------QUOTE-------------------

I'd say it's better to differentiate the letters from the punctuation marks.

---------------------QUOTE-------------------

 

---------------------QUOTE-------------------
If so, could you use my analogy (or yours - if you have a better one) to show me what's wrong with stop codons?
---------------------QUOTE-------------------


I'm not saying that there's anything wrong with them. I'm asking for your judgment.
---------------------QUOTE-------------------


If my analogy is correct, then I'd say stop codons should be separate from coding codons (if that's the correct term).
Posted by: Daniel Smith on Dec. 20 2007,19:44

Quote (JAM @ Dec. 20 2007,19:15)
     
Quote (Daniel Smith @ Dec. 20 2007,18:46)
On the issue of the conservation of DNA, I'm still in the running - since even members of the same species have widely different DNA conservation percentages - anywhere from 0.1% to 8%.
---------------------QUOTE-------------------


No, you were wrong in every case. You are using fallacies of equivocation to pretend that you're still in the running.
---------------------QUOTE-------------------


You know that I'm wrong - fine - but I'm not sure how you arrived at that conclusion.  You've pointed me to VISTA and said that the white areas prove me wrong - with very little in the way of explanation.  I'm still not sure I understand exactly how this proves me wrong - since there would be (I'm guessing) white areas if you were to compare your genome to mine.  Maybe I'm wrong about that as well.

I don't have any problem with being wrong.  I only have a problem when someone declares me wrong without showing me, in a way I can understand, exactly how I am wrong.
Posted by: Daniel Smith on Dec. 20 2007,19:45

Quote (JAM @ Dec. 20 2007,19:15)
       
Quote (Daniel Smith @ Dec. 20 2007,18:46)
On the issue of the conservation of DNA, I'm still in the running - since even members of the same species have widely different DNA conservation percentages - anywhere from 0.1% to 8%.
---------------------QUOTE-------------------


No, you were wrong in every case. You are using fallacies of equivocation to pretend that you're still in the running.
---------------------QUOTE-------------------


You know that I'm wrong - fine - but I'm not sure how you arrived at that conclusion.  You've pointed me to VISTA and said that the white areas prove me wrong - with very little in the way of explanation.  I'm still not sure I understand exactly how this proves me wrong - since there would be (I'm guessing) white areas if you were to compare your genome to mine.  Maybe I'm wrong about that as well.

I don't have any problem with being wrong.  I only have a problem when someone declares me wrong without showing me, in a way I can understand, exactly how I am wrong.
Posted by: Daniel Smith on Dec. 20 2007,19:46

Oops!  Sorry about the double post.
Posted by: Richard Simons on Dec. 20 2007,21:15

Quote (Daniel Smith @ Dec. 20 2007,18:26)
There's no reason - from an unthinking, uncaring natural selection standpoint - for it to be thus.  If it truly is "the survival of the fittest", cockroaches would win out, take over the world, then die out too when their food sources ran out.  The planet would then be dead - like every other planet we know of.  (Of course, this is just an imaginary scenario where cockroaches just happen to win - you can substitute any "fit", rapidly reproducing species - it doesn't matter, one species should overtake all the others if there's no balance in nature).

That's what I mean by balance.
---------------------QUOTE-------------------


This is not going to happen on a global scale because of the vast number of different habitats, but it takes place on a local scale all the time. An organism becomes more plentiful it changes the local environment (it provides more food for its own diseases and things that feed on it, it reduces its own food source or whatever) with the result that fewer reproduce or even survive and there is a drop in the population, with the more fortunate ones, or the better adapted ones, surviving. Some of the basic processes in ecology driving a basic process in evolution.
Posted by: JAM on Dec. 20 2007,23:47

Quote (Daniel Smith @ Dec. 20 2007,19:31)
Quote (JAM @ Dec. 20 2007,19:14)
 
Quote (Daniel Smith @ Dec. 20 2007,19:07)
   
Quote (JAM @ Dec. 18 2007,18:49)
           
Quote (Daniel Smith @ Dec. 18 2007,18:14)
This one I don't even understand:                

---------------------QUOTE-------------------
Does having a separate codon(s) for stopping translation (that don't encode an amino acid residue) represent an intelligent design? This allows proteins to have any of the 20 residues at the carboxy terminus.
---------------------QUOTE-------------------


How can a stop codon "[not] encode an amino acid residue" and "allow proteins to have any of the 20 residues" at the same time?
---------------------QUOTE-------------------


The stop codons are TAA, TAG, and TGA. They do not code for aa residues. I didn't write that it allowed them to HAVE any of the residues, I wrote that this allowed them to END in any one of them (i.e., carboxy terminus). Does that make more sense now? Is that an intelligent and/or elegant design?
---------------------QUOTE-------------------


I'm still a bit unclear because I don't know what's wrong with having stop codons the way they are.  Are you saying it would be better if they did code for amino acids?
---------------------QUOTE-------------------


No, I'm asking for your characterization. Was it an intelligent design decision to use separate codons for stop, instead of combining one or more of those "signals" with a signal to add an amino acid?
   

---------------------QUOTE-------------------
It might help if you could give me an analogy to better illustrate what's going on.
---------------------QUOTE-------------------


I don't think so.
   

---------------------QUOTE-------------------
Let me try a language analogy on you and you can correct it where it's wrong:
In my analogy, amino acids would be like the letters of the alphabet and stop codons like sentence ending punctuation ( . ? and !).  So proteins in my analogy would be like sentences.

Is this anywhere near close?
---------------------QUOTE-------------------


Yes. Is it more intelligent to have separate letters and punctuation marks, or is it more intelligent to always end each sentence with the same letter?
---------------------QUOTE-------------------

I'd say it's better to differentiate the letters from the punctuation marks.  

---------------------QUOTE-------------------

   

---------------------QUOTE-------------------
If so, could you use my analogy (or yours - if you have a better one) to show me what's wrong with stop codons?
---------------------QUOTE-------------------


I'm not saying that there's anything wrong with them. I'm asking for your judgment.
---------------------QUOTE-------------------


If my analogy is correct, then I'd say stop codons should be separate from coding codons (if that's the correct term).
---------------------QUOTE-------------------


And the same goes for start codons, right?
Posted by: George on Dec. 21 2007,01:25

Quote (Daniel Smith @ Dec. 20 2007,18:26)
Quote (George @ Dec. 18 2007,18:47)
   
Quote (Daniel Smith @ Dec. 18 2007,18:40)

There's a difference between balance and stasis.  It's true that there is no stasis in nature.  There is balance however.  If there weren't we'd be overrun by cockroaches by now.  Extinctions are a part of that balance.  When climate conditions change radically, species that once thrived die out and new ones take their place - all the while maintaining the balance that sustains this planet for life.
---------------------QUOTE-------------------


Then please explain to me what you mean by "balance".  And how it relates to cockroaches.  I don't know what you're getting at.
---------------------QUOTE-------------------


I mean that the world always has exactly the right mixture of species to keep life going (even though the players are in a constant state of flux).  

There's no reason - from an unthinking, uncaring natural selection standpoint - for it to be thus.  If it truly is "the survival of the fittest", cockroaches would win out, take over the world, then die out too when their food sources ran out.  The planet would then be dead - like every other planet we know of.  (Of course, this is just an imaginary scenario where cockroaches just happen to win - you can substitute any "fit", rapidly reproducing species - it doesn't matter, one species should overtake all the others if there's no balance in nature).

That's what I mean by balance.
---------------------QUOTE-------------------


Ok.  Now I've three more questions for you, if you'll be so kind, to make sure I know where you're coming from:

Do you think God actively tweaks or toggles the various ecological mechanisms that keep population sizes in check?  Or is it more of a case that the mechanisms have been set up ahead of time to ensure that no one species can outcompete all others?

What do you mean by "fit" species?  Could you explain what characteristics they have?  Or maybe give some examples of fit species that perhaps should take over the world but don't?

Have you ever thought that we are the cockroaches in your example above, and that since we've taken over the world and are now making a huge mess of it, our downfall is at hand?  Didn't think so.
Posted by: oldmanintheskydidntdoit on Dec. 21 2007,05:07

This information may dispel some of your ignorance Daniel.
< >

Have a good read
< http://comptlsci.anu.edu.au/Module-ODEs/ode-overview-notes.html >
And let us know if god is still required to maintain population levels.
Posted by: oldmanintheskydidntdoit on Dec. 21 2007,05:31

Quote (Daniel Smith @ Dec. 20 2007,19:25)
 
Quote (BWE @ Dec. 18 2007,23:46)
         
Quote (Daniel Smith @ Dec. 18 2007,18:00)
But, if you want to get into first causes, you really only have two choices:  Either the first cause is nothing, or the first cause is eternal.
If you vote for nothing, then you must accept that you can get something from nothing.
Therefore the only logical answer is that the first cause is eternal.
---------------------QUOTE-------------------


Sure, fine. How do you get from there (eternal) to over there-----> where you are talking about this guy with angels licking his feet and demanding servitude of people who have no reliable way to even detect his existence? People who have to believe other people just to find out what he has done?

I mean, hello... Doesn't this strike you as rather... um... like suckering a mark?
---------------------QUOTE-------------------


The question is not how did I get from here to there, but how did you get, "this guy with angels licking his feet and demanding servitude of people who have no reliable way to even detect his existence", from anything I've said?

When have I ever characterized God in that way?  That sounds more like bitterness talking.  

I've often wondered why some who profess not to believe in God seem to actively hate him.

How can you hate something you believe doesn't exist?
---------------------QUOTE-------------------


It's not god that deserves the hate. As you say, it's illogical to  hate something you don't believe exists.

It's the people that claim that god is whispering in their ear and telling them how other people should live their lives that's the problem. They deserve the hate. Believe whatever you want Daniel, I've no problem with that. There are plenty of theists on this board FYI.

It's when you try and tell me that
a) Action X is a sin because "god said so" and hold up a holy book as proof.
b) Item Y was designed because "I said so" and therefore that proves god exists and evolution is untrue and therefore lets teach it to children as fact.
c) Person Z is unclean because "god said so".

that problems will occur. Any many other things too.

Anyway, I'm not talking to you anymore!

 

---------------------QUOTE-------------------
The question is not how did I get from here to there, but how did you get, "this guy with angels licking his feet and demanding servitude of people who have no reliable way to even detect his existence", from anything I've said?
---------------------QUOTE-------------------


The point is it's credulous people that will accept facts that on the surface seem "right" without looking into it deeper that enable the sort of behaviour that people who claim to "know the mind of god" indulge in. Without those credulous enablers the worst excesses of religion cannot happen. Without followers you can have no leaders.
Posted by: VMartin on Dec. 21 2007,10:35

Hi Daniel,

somebody at EvC gave the link to the article written by Professor Richard C. Strohman, Uni California : "Epigenesis and Complexity: The Coming Revolution in Biology"

< http://www.thecomplementarynature.com/TCN%20A....ics.pdf >

If you have time check it. It is very interesting. I hope such voices will be more common in the future.


According professor Zdenek Neubauer (Charles Uni Prague) modern biology is under strong influence of "fachidiots". You know, some people don't know how to tell apart tiger and lion  but they study, analyze and compare their DNA making bold predictions of evolution of that species .

You don't have to worry about JAM arguments. His concept of many basic bilological words are wrong.    

Epigenesis, epistatic interactions or pleitropic effects of genes play obviously significant role in development of an organism. According Strohman real, genetic disease acount for less than 2% of total disease load.  

Strohman quoted also Feynman who should have said:
"Mind must be a sort of dynamical pattern,not so much founded in a neurological substrate as floating above it, independent above it". But you know, Feynmann is an expert on quantum mechanics and maybe he should more discuss his opinions with evolutionary biologists (JAM etc...).
Posted by: oldmanintheskydidntdoit on Dec. 21 2007,10:42

Quote (VMartin @ Dec. 21 2007,10:35)
Hi Daniel,

somebody at EvC gave the link to the article written by Professor Richard C. Strohman, Uni California : "Epigenesis and Complexity: The Coming Revolution in Biology"

< http://www.thecomplementarynature.com/TCN%20A....ics.pdf >

If you have time check it. It is very interesting. I hope such voices will be more common in the future.


According professor Zdenek Neubauer (Charles Uni Prague) modern biology is under strong influence of "fachidiots". You know, some people don't know how to tell apart tiger and lion  but they study, analyze and compare their DNA making bold predictions of evolution of that species .

You don't have to worry about JAM arguments. His concept of many basic bilological words are wrong.    

Epigenesis, epistatic interactions or pleitropic effects of genes play obviously significant role in development of an organism. According Strohman real, genetic disease acount for less than 2% of total disease load.  

Strohman quoted also Feynman who should have said:
"Mind must be a sort of dynamical pattern,not so much founded in a neurological substrate as floating above it, independent above it". But you know, Feynmann is an expert on quantum mechanics and maybe he should more discuss his opinions with evolutionary biologists (JAM etc...).
---------------------QUOTE-------------------


Still pretending huh~?

Carry on....
Posted by: Arden Chatfield on Dec. 21 2007,11:06

Quote (VMartin @ Dec. 21 2007,10:35)
You don't have to worry about JAM arguments. His concept of many basic bilological words are wrong.    
---------------------QUOTE-------------------


Where did you get your training in 'bilology', Martin?
Posted by: Occam's Toothbrush on Dec. 21 2007,11:08

Quote (Arden Chatfield @ Dec. 21 2007,12:06)
Quote (VMartin @ Dec. 21 2007,10:35)
You don't have to worry about JAM arguments. His concept of many basic bilological words are wrong.    
---------------------QUOTE-------------------


Where did you get your training in 'bilology', Martin?
---------------------QUOTE-------------------


He's bilious, anyway.
Posted by: Occam's Toothbrush on Dec. 21 2007,11:13

Edit:remove double post
Posted by: Occam's Toothbrush on Dec. 21 2007,11:16



---------------------QUOTE-------------------
But you know, Feynmann is an expert on quantum mechanics and maybe he should more discuss his opinions with evolutionary biologists (JAM etc...).
---------------------QUOTE-------------------


Feynman's dead.  Has been for 19 years.

Judging by the age of the biology research VM likes to cite, he's not that up to date on anything else.  So I guess it's understandable he hasn't heard about Feynman's passing.  

I wonder if he knows about Czechoslovakia breaking up yet.
Posted by: VMartin on Dec. 21 2007,11:37

I've adressed your objection about Feynman at Bathroom wall.

< http://www.antievolution.org/cgi-bin....st=4500 >
Posted by: Steverino on Dec. 21 2007,21:58

Quote (Arden Chatfield @ Dec. 21 2007,11:06)
Quote (VMartin @ Dec. 21 2007,10:35)
You don't have to worry about JAM arguments. His concept of many basic bilological words are wrong.    
---------------------QUOTE-------------------


Where did you get your training in 'bilology', Martin?
---------------------QUOTE-------------------


Marty,

I think this is an honest question.
Posted by: Daniel Smith on Dec. 22 2007,18:13

Quote (JAM @ Dec. 20 2007,23:47)
 
Quote (Daniel Smith @ Dec. 20 2007,19:31)

If my analogy is correct, then I'd say stop codons should be separate from coding codons (if that's the correct term).
---------------------QUOTE-------------------


And the same goes for start codons, right?
---------------------QUOTE-------------------


Most likely - yes.  But then again I have no idea what God was thinking when he designed start and stop codons.  The fact that there even are such things; and that they stop and start the encoding of amino acids; which then somehow "know" to join together and fold into proteins; which then "know" exactly where to go and what to do when they get there, is mind-boggling enough.  Now you want me to critique such a system?  It's way over my head.  My analogy of simple letters and punctuation probably comes nowhere near the actual intricacies involved in God's system. But, yes, if stop and start codons are anything like punctuation marks, they should probably be different from amino acid coding codons.
Posted by: IanBrown_101 on Dec. 22 2007,18:16

Quote (Daniel Smith @ Dec. 23 2007,00:13)
Quote (JAM @ Dec. 20 2007,23:47)
   
Quote (Daniel Smith @ Dec. 20 2007,19:31)

If my analogy is correct, then I'd say stop codons should be separate from coding codons (if that's the correct term).
---------------------QUOTE-------------------


And the same goes for start codons, right?
---------------------QUOTE-------------------


Most likely - yes.  But then again I have no idea what God was thinking when he designed start and stop codons.  The fact that there even are such things; and that they stop and start the encoding of amino acids; which then somehow "know" to join together and fold into proteins; which then "know" exactly where to go and what to do when they get there, is mind-boggling enough.  Now you want me to critique such a system?  It's way over my head.  My analogy of simple letters and punctuation probably comes nowhere near the actual intricacies involved in God's system. But, yes, if stop and start codons are anything like punctuation marks, they should probably be different from amino acid coding codons.
---------------------QUOTE-------------------


My analogy may be wrong (god knows I'm no scientist, but then, neither are you) but I think your claim they "know" to do these things is like saying a light switch "knows" to turn on (or off) a light when pressed.

In fact, a better analogy would be that litmus paper "knows" to turn red when acid is put on it. It doesn't "know" thats just what happens.
Posted by: Assassinator on Dec. 22 2007,18:18



---------------------QUOTE-------------------
Now you want me to critique such a system?  It's way over my head.
---------------------QUOTE-------------------




---------------------QUOTE-------------------
But then again I have no idea what God was thinking when he designed start and stop codons.
---------------------QUOTE-------------------





---------------------QUOTE-------------------
The fact that there even are such things; and that they stop and start the encoding of amino acids; which then somehow "know" to join together and fold into proteins; which then "know" exactly where to go and what to do when they get there, is mind-boggling enough.
---------------------QUOTE-------------------


Get yourself into bio-chemistry. You're really making yourself to important to yourself. And also, but this is a common thing wich happens, is that you're looking wáy to much from a human perspective.
Posted by: Daniel Smith on Dec. 22 2007,18:23

Quote (George @ Dec. 21 2007,01:25)
   
Quote (Daniel Smith @ Dec. 20 2007,18:26)
   
Quote (George @ Dec. 18 2007,18:47)
         
Quote (Daniel Smith @ Dec. 18 2007,18:40)

There's a difference between balance and stasis.  It's true that there is no stasis in nature.  There is balance however.  If there weren't we'd be overrun by cockroaches by now.  Extinctions are a part of that balance.  When climate conditions change radically, species that once thrived die out and new ones take their place - all the while maintaining the balance that sustains this planet for life.
---------------------QUOTE-------------------


Then please explain to me what you mean by "balance".  And how it relates to cockroaches.  I don't know what you're getting at.
---------------------QUOTE-------------------


I mean that the world always has exactly the right mixture of species to keep life going (even though the players are in a constant state of flux).  

There's no reason - from an unthinking, uncaring natural selection standpoint - for it to be thus.  If it truly is "the survival of the fittest", cockroaches would win out, take over the world, then die out too when their food sources ran out.  The planet would then be dead - like every other planet we know of.  (Of course, this is just an imaginary scenario where cockroaches just happen to win - you can substitute any "fit", rapidly reproducing species - it doesn't matter, one species should overtake all the others if there's no balance in nature).

That's what I mean by balance.
---------------------QUOTE-------------------


Ok.  Now I've three more questions for you, if you'll be so kind, to make sure I know where you're coming from:

Do you think God actively tweaks or toggles the various ecological mechanisms that keep population sizes in check?
---------------------QUOTE-------------------

Perhaps.  I don't know.  Maybe there's no such thing as natural selection - maybe God does the selecting.  

---------------------QUOTE-------------------
 Or is it more of a case that the mechanisms have been set up ahead of time to ensure that no one species can outcompete all others?
---------------------QUOTE-------------------

Also a possibility.  Or it could be a combination of both.  

---------------------QUOTE-------------------


What do you mean by "fit" species?  Could you explain what characteristics they have?  Or maybe give some examples of fit species that perhaps should take over the world but don't?
---------------------QUOTE-------------------

I already gave the example of cockroaches.  There are probably several insects that could do it - locusts for example, could strip the worlds vegetation bare and completely knock it's ecosystem for a loop.  A resilient virus could wipe out life as we know it and then die out itself for lack of hosts.  There are lots of possibilities.  

---------------------QUOTE-------------------


Have you ever thought that we are the cockroaches in your example above, and that since we've taken over the world and are now making a huge mess of it, our downfall is at hand?  Didn't think so.
---------------------QUOTE-------------------

Yes, I have - in fact that is entirely consistent with the biblical doctrine of the fall.  If you remove man from the world, nature would be much better off.  We are the one organism that's out of sync on this planet.
Posted by: Daniel Smith on Dec. 22 2007,18:25

Quote (oldmanintheskydidntdoit @ Dec. 21 2007,05:31)
 
Quote (Daniel Smith @ Dec. 20 2007,19:25)

The question is not how did I get from here to there, but how did you get, "this guy with angels licking his feet and demanding servitude of people who have no reliable way to even detect his existence", from anything I've said?

When have I ever characterized God in that way?  That sounds more like bitterness talking.  

I've often wondered why some who profess not to believe in God seem to actively hate him.

How can you hate something you believe doesn't exist?
---------------------QUOTE-------------------


It's not god that deserves the hate. As you say, it's illogical to  hate something you don't believe exists.

It's the people that claim that god is whispering in their ear and telling them how other people should live their lives that's the problem. They deserve the hate. Believe whatever you want Daniel, I've no problem with that. There are plenty of theists on this board FYI.

It's when you try and tell me that
a) Action X is a sin because "god said so" and hold up a holy book as proof.
b) Item Y was designed because "I said so" and therefore that proves god exists and evolution is untrue and therefore lets teach it to children as fact.
c) Person Z is unclean because "god said so".

---------------------QUOTE-------------------


I never told you any of those things.
Posted by: Daniel Smith on Dec. 22 2007,18:27

Quote (IanBrown_101 @ Dec. 22 2007,18:16)
 
Quote (Daniel Smith @ Dec. 23 2007,00:13)
 
Quote (JAM @ Dec. 20 2007,23:47)
     
Quote (Daniel Smith @ Dec. 20 2007,19:31)

If my analogy is correct, then I'd say stop codons should be separate from coding codons (if that's the correct term).
---------------------QUOTE-------------------


And the same goes for start codons, right?
---------------------QUOTE-------------------


Most likely - yes.  But then again I have no idea what God was thinking when he designed start and stop codons.  The fact that there even are such things; and that they stop and start the encoding of amino acids; which then somehow "know" to join together and fold into proteins; which then "know" exactly where to go and what to do when they get there, is mind-boggling enough.  Now you want me to critique such a system?  It's way over my head.  My analogy of simple letters and punctuation probably comes nowhere near the actual intricacies involved in God's system. But, yes, if stop and start codons are anything like punctuation marks, they should probably be different from amino acid coding codons.
---------------------QUOTE-------------------


My analogy may be wrong (god knows I'm no scientist, but then, neither are you) but I think your claim they "know" to do these things is like saying a light switch "knows" to turn on (or off) a light when pressed.

In fact, a better analogy would be that litmus paper "knows" to turn red when acid is put on it. It doesn't "know" thats just what happens.
---------------------QUOTE-------------------


They act like they know what to do - which is why I put "know" in quotes.
Posted by: Assassinator on Dec. 22 2007,18:29

They just act, it happens, that it's. That happening is an action, and is also a reaction from an action that caused that happening. Again, you're think too much in human terms. Trying to fit the normal human perspective onto non-human things.
Posted by: Daniel Smith on Dec. 22 2007,18:33

Quote (VMartin @ Dec. 21 2007,10:35)
Hi Daniel,

somebody at EvC gave the link to the article written by Professor Richard C. Strohman, Uni California : "Epigenesis and Complexity: The Coming Revolution in Biology"

< http://www.thecomplementarynature.com/TCN%20A....ics.pdf >

If you have time check it. It is very interesting. I hope such voices will be more common in the future.


According professor Zdenek Neubauer (Charles Uni Prague) modern biology is under strong influence of "fachidiots". You know, some people don't know how to tell apart tiger and lion  but they study, analyze and compare their DNA making bold predictions of evolution of that species .

You don't have to worry about JAM arguments. His concept of many basic bilological words are wrong.    

Epigenesis, epistatic interactions or pleitropic effects of genes play obviously significant role in development of an organism. According Strohman real, genetic disease acount for less than 2% of total disease load.  

Strohman quoted also Feynman who should have said:
"Mind must be a sort of dynamical pattern,not so much founded in a neurological substrate as floating above it, independent above it". But you know, Feynmann is an expert on quantum mechanics and maybe he should more discuss his opinions with evolutionary biologists (JAM etc...).
---------------------QUOTE-------------------


Thanks for the link Martin.  I'm in the process of reading the article now.  I followed some of the comments made about it over at the bathroom wall.  How much do you want to bet that none of them read the article?  None of their objections reference anything actually stated in the article so I'm guessing that's a safe bet.  But I could be wrong (I often am).
Posted by: IanBrown_101 on Dec. 22 2007,18:37

Quote (Daniel Smith @ Dec. 23 2007,00:27)
Quote (IanBrown_101 @ Dec. 22 2007,18:16)
 
Quote (Daniel Smith @ Dec. 23 2007,00:13)
   
Quote (JAM @ Dec. 20 2007,23:47)
       
Quote (Daniel Smith @ Dec. 20 2007,19:31)

If my analogy is correct, then I'd say stop codons should be separate from coding codons (if that's the correct term).
---------------------QUOTE-------------------


And the same goes for start codons, right?
---------------------QUOTE-------------------


Most likely - yes.  But then again I have no idea what God was thinking when he designed start and stop codons.  The fact that there even are such things; and that they stop and start the encoding of amino acids; which then somehow "know" to join together and fold into proteins; which then "know" exactly where to go and what to do when they get there, is mind-boggling enough.  Now you want me to critique such a system?  It's way over my head.  My analogy of simple letters and punctuation probably comes nowhere near the actual intricacies involved in God's system. But, yes, if stop and start codons are anything like punctuation marks, they should probably be different from amino acid coding codons.
---------------------QUOTE-------------------


My analogy may be wrong (god knows I'm no scientist, but then, neither are you) but I think your claim they "know" to do these things is like saying a light switch "knows" to turn on (or off) a light when pressed.

In fact, a better analogy would be that litmus paper "knows" to turn red when acid is put on it. It doesn't "know" thats just what happens.
---------------------QUOTE-------------------


They act like they know what to do - which is why I put "know" in quotes.
---------------------QUOTE-------------------


So what you're saying is, the fact that chemical reactions occur boggles your mind.

That is in fact, exactly what you are saying, it may not be what you mean, but it's what you said.

And that's terrible (I reckon noone else will get this joke).
Posted by: Daniel Smith on Dec. 22 2007,18:43

Quote (Assassinator @ Dec. 22 2007,18:29)
They just act, it happens, that it's. That happening is an action, and is also a reaction from an action that caused that happening. Again, you're think too much in human terms. Trying to fit the normal human perspective onto non-human things.
---------------------QUOTE-------------------


You're right - it's way beyond human comprehension how "they just act" exactly the way they need to in order to keep an immense, intricate network of embedded systems functioning.

"They just act" explains everything - kind of like "godidit" but in the opposite direction.  It's the kind of explanation that uses the thing that needs explaining as the explanation for the thing that needs explaining.  Makes perfect sense in a kind of blind, mind numbing acceptance of "Nature as Nature's cause" kind of way.
Posted by: IanBrown_101 on Dec. 22 2007,18:46

Quote (Daniel Smith @ Dec. 23 2007,00:43)
Quote (Assassinator @ Dec. 22 2007,18:29)
They just act, it happens, that it's. That happening is an action, and is also a reaction from an action that caused that happening. Again, you're think too much in human terms. Trying to fit the normal human perspective onto non-human things.
---------------------QUOTE-------------------


You're right - it's way beyond human comprehension how "they just act" exactly the way they need to in order to keep an immense, intricate network of embedded systems functioning.
---------------------QUOTE-------------------


I hate to sy it, but you really aren't the world Dan.

I'm sorry I had to break it to you....but well, you really aren't. There are other people. Millions of them (billions if you use the incorrect definition of the word).

Sorry man, but...you don't speak for all of us.
Posted by: Daniel Smith on Dec. 22 2007,18:46

Quote (IanBrown_101 @ Dec. 22 2007,18:37)
   
Quote (Daniel Smith @ Dec. 23 2007,00:27)

They act like they know what to do - which is why I put "know" in quotes.
---------------------QUOTE-------------------


So what you're saying is, the fact that chemical reactions occur boggles your mind.

That is in fact, exactly what you are saying, it may not be what you mean, but it's what you said.

And that's terrible (I reckon noone else will get this joke).
---------------------QUOTE-------------------


No, what I'm saying is that it boggles the mind that exactly the right chemical reactions occur at exactly the right time and exactly the right place.  

Life is not just "chemical reactions".  If it were, you could just measure out all the chemicals in an organism, throw them together in a beaker, and make life.

You're too smart to think that's all that's involved here.
Posted by: Daniel Smith on Dec. 22 2007,18:48

Quote (IanBrown_101 @ Dec. 22 2007,18:46)
 
Quote (Daniel Smith @ Dec. 23 2007,00:43)
 
Quote (Assassinator @ Dec. 22 2007,18:29)
They just act, it happens, that it's. That happening is an action, and is also a reaction from an action that caused that happening. Again, you're think too much in human terms. Trying to fit the normal human perspective onto non-human things.
---------------------QUOTE-------------------


You're right - it's way beyond human comprehension how "they just act" exactly the way they need to in order to keep an immense, intricate network of embedded systems functioning.
---------------------QUOTE-------------------


I hate to sy it, but you really aren't the world Dan.

I'm sorry I had to break it to you....but well, you really aren't. There are other people. Millions of them (billions if you use the incorrect definition of the word).

Sorry man, but...you don't speak for all of us.
---------------------QUOTE-------------------


Hey I was agreeing with him!
(Well kinda anyway).
Posted by: IanBrown_101 on Dec. 22 2007,18:48

Quote (Daniel Smith @ Dec. 23 2007,00:46)
Quote (IanBrown_101 @ Dec. 22 2007,18:37)
   
Quote (Daniel Smith @ Dec. 23 2007,00:27)

They act like they know what to do - which is why I put "know" in quotes.
---------------------QUOTE-------------------


So what you're saying is, the fact that chemical reactions occur boggles your mind.

That is in fact, exactly what you are saying, it may not be what you mean, but it's what you said.

And that's terrible (I reckon noone else will get this joke).
---------------------QUOTE-------------------


No, what I'm saying is that it boggles the mind that exactly the right chemical reactions occur at exactly the right time and exactly the right place.  

Life is not just "chemical reactions".  If it were, you could just measure out all the chemicals in an organism, throw them together in a beaker, and make life.

You're too smart to think that's all that's involved here.
---------------------QUOTE-------------------


No, that IS what you're saying. Just because they occur at certain times doesn't indicate intelligence, it indicates a working system.

Oh, and are you seriously saying that only stupid people think there isn't more to life than what we can see? Chemical reactions and such like?
Posted by: IanBrown_101 on Dec. 22 2007,18:50

Quote (Daniel Smith @ Dec. 23 2007,00:48)
Quote (IanBrown_101 @ Dec. 22 2007,18:46)
 
Quote (Daniel Smith @ Dec. 23 2007,00:43)
   
Quote (Assassinator @ Dec. 22 2007,18:29)
They just act, it happens, that it's. That happening is an action, and is also a reaction from an action that caused that happening. Again, you're think too much in human terms. Trying to fit the normal human perspective onto non-human things.
---------------------QUOTE-------------------


You're right - it's way beyond human comprehension how "they just act" exactly the way they need to in order to keep an immense, intricate network of embedded systems functioning.
---------------------QUOTE-------------------


I hate to sy it, but you really aren't the world Dan.

I'm sorry I had to break it to you....but well, you really aren't. There are other people. Millions of them (billions if you use the incorrect definition of the word).

Sorry man, but...you don't speak for all of us.
---------------------QUOTE-------------------


Hey I was agreeing with him!
(Well kinda anyway).
---------------------QUOTE-------------------


You were also claiming that your limit of knowledge is THE limit of knowledge.

Which it isn't.
Posted by: IanBrown_101 on Dec. 22 2007,18:53

Testing.

EDIT: Just checking something.
Posted by: Assassinator on Dec. 22 2007,18:54



---------------------QUOTE-------------------
No, what I'm saying is that it boggles the mind that exactly the right chemical reactions occur at exactly the right time and exactly the right place.
---------------------QUOTE-------------------


Biochemistry is not chance, so the word "exactly" does not mean anything. It happens, that's it, that's just what it does. Nothing more, just happening.


---------------------QUOTE-------------------
Oh, and are you seriously saying that only stupid people think there isn't more to life than what we can see? Chemical reactions and such like?
---------------------QUOTE-------------------


Yeap, that's earthern life: chemistry. Bad thing is, we don't know what the exact circumstances were when life first arouse on earth, so we can't.
Posted by: Daniel Smith on Dec. 22 2007,19:00

Quote (IanBrown_101 @ Dec. 22 2007,18:48)
   
Quote (Daniel Smith @ Dec. 23 2007,00:46)
     
Quote (IanBrown_101 @ Dec. 22 2007,18:37)
         
Quote (Daniel Smith @ Dec. 23 2007,00:27)

They act like they know what to do - which is why I put "know" in quotes.
---------------------QUOTE-------------------


So what you're saying is, the fact that chemical reactions occur boggles your mind.

That is in fact, exactly what you are saying, it may not be what you mean, but it's what you said.

And that's terrible (I reckon noone else will get this joke).
---------------------QUOTE-------------------


No, what I'm saying is that it boggles the mind that exactly the right chemical reactions occur at exactly the right time and exactly the right place.  

Life is not just "chemical reactions".  If it were, you could just measure out all the chemicals in an organism, throw them together in a beaker, and make life.

You're too smart to think that's all that's involved here.
---------------------QUOTE-------------------


No, that IS what you're saying. Just because they occur at certain times doesn't indicate intelligence, it indicates a working system.
---------------------QUOTE-------------------


Saying chemical reactions, happening at exactly the right time, in exactly the right proportion, "indicates a working system", is a case of using that which needs explaining as an explanation.  It's pure circular reasoning.    

---------------------QUOTE-------------------
Oh, and are you seriously saying that only stupid people think there isn't more to life than what we can see? Chemical reactions and such like?
---------------------QUOTE-------------------


How did you get that from what i said?
Posted by: Daniel Smith on Dec. 22 2007,19:07

Quote (Assassinator @ Dec. 22 2007,18:54)
 

---------------------QUOTE-------------------
No, what I'm saying is that it boggles the mind that exactly the right chemical reactions occur at exactly the right time and exactly the right place.
---------------------QUOTE-------------------


Biochemistry is not chance, so the word "exactly" does not mean anything. It happens, that's it, that's just what it does. Nothing more, just happening.
   

---------------------QUOTE-------------------
Oh, and are you seriously saying that only stupid people think there isn't more to life than what we can see? Chemical reactions and such like?
---------------------QUOTE-------------------


Yeap, that's earthern life: chemistry. Bad thing is, we don't know what the exact circumstances were when life first arouse on earth, so we can't.
---------------------QUOTE-------------------


I agree.  There's not much chance involved.  The question is:  How did we get from "chemicals" to "living, breathing organisms" - if not by chance?
Posted by: IanBrown_101 on Dec. 22 2007,19:23

Quote (Daniel Smith @ Dec. 23 2007,01:07)
Quote (Assassinator @ Dec. 22 2007,18:54)
   

---------------------QUOTE-------------------
No, what I'm saying is that it boggles the mind that exactly the right chemical reactions occur at exactly the right time and exactly the right place.
---------------------QUOTE-------------------


Biochemistry is not chance, so the word "exactly" does not mean anything. It happens, that's it, that's just what it does. Nothing more, just happening.
   

---------------------QUOTE-------------------
Oh, and are you seriously saying that only stupid people think there isn't more to life than what we can see? Chemical reactions and such like?
---------------------QUOTE-------------------


Yeap, that's earthern life: chemistry. Bad thing is, we don't know what the exact circumstances were when life first arouse on earth, so we can't.
---------------------QUOTE-------------------


I agree.  There's not much chance involved.  The question is:  How did we get from "chemicals" to "living, breathing organisms" - if not by chance?
---------------------QUOTE-------------------


A combination of chance and selection is my guess.

Or possibly something else entirely, we don't know for sure, but that's no reason to go "therefore God!!!!!!".

Why is it you seem to suggest we need to be certain of this, and yet accept God without any evidence? (If you have evidence please, PM me and tell me what it is, I'll listen, and tell you what I think.)
Posted by: IanBrown_101 on Dec. 22 2007,19:25

Quote (Daniel Smith @ Dec. 23 2007,01:00)
Quote (IanBrown_101 @ Dec. 22 2007,18:48)
     
Quote (Daniel Smith @ Dec. 23 2007,00:46)
       
Quote (IanBrown_101 @ Dec. 22 2007,18:37)
           
Quote (Daniel Smith @ Dec. 23 2007,00:27)

They act like they know what to do - which is why I put "know" in quotes.
---------------------QUOTE-------------------


So what you're saying is, the fact that chemical reactions occur boggles your mind.

That is in fact, exactly what you are saying, it may not be what you mean, but it's what you said.

And that's terrible (I reckon noone else will get this joke).
---------------------QUOTE-------------------


No, what I'm saying is that it boggles the mind that exactly the right chemical reactions occur at exactly the right time and exactly the right place.  

Life is not just "chemical reactions".  If it were, you could just measure out all the chemicals in an organism, throw them together in a beaker, and make life.

You're too smart to think that's all that's involved here.
---------------------QUOTE-------------------


No, that IS what you're saying. Just because they occur at certain times doesn't indicate intelligence, it indicates a working system.
---------------------QUOTE-------------------


Saying chemical reactions, happening at exactly the right time, in exactly the right proportion, "indicates a working system", is a case of using that which needs explaining as an explanation.  It's pure circular reasoning.
---------------------QUOTE-------------------


Oh, you want to know WHY they work!

Because they do. Certain properties of the chemicals react when they meet other chemicals.



---------------------QUOTE-------------------
Oh, and are you seriously saying that only stupid people think there isn't more to life than what we can see? Chemical reactions and such like?
---------------------QUOTE-------------------


How did you get that from what i said?

Because that is what you said.


---------------------QUOTE-------------------
Life is not just "chemical reactions". ........
You're too smart to think that's all that's involved here.
---------------------QUOTE-------------------


Posted by: Erasmus, FCD on Dec. 22 2007,20:38

Daniel, the null is 'they act that way'.  It is certainly your burden to show that this is worthy of a design inference.  if they didn't 'act that way', but acted 'another way', and we still had life as it is now, then you would still be claiming a design inference.  it's the kind of crap presupposition that you bring to the table with you.  It has no explanatory value, it has no empirical basis, it is completely a Panglossian jesus loves me the world is perfectly crafted kind of eight year old awe and wonder about the universe.

you're not interested in science and you never have been.  this is all about providing you with an apologetic.  

don't get me wrong.  I'm not saying life is 'just' chemicals.  I'm saying, what is it and how do you know?  Because I smell bullshit.
Posted by: oldmanintheskydidntdoit on Dec. 23 2007,05:32

Daniel,
Does god make 2+2=4?
There's your answer then to "why" chemicals behave as they do. 2+2=4.

I sent you a link about populations. No god required. No comment? Coward.
Posted by: Assassinator on Dec. 23 2007,07:55



---------------------QUOTE-------------------
The question is:  How did we get from "chemicals" to "living, breathing organisms" - if not by chance?
---------------------QUOTE-------------------


By certain chemical mechanisms. Another bad misconception about the origin of life, is that lots of people think that abiogenesis says that life spontaniously arised. That's a huge mistake, abiogenesis isn't letting out external sources.
Posted by: Daniel Smith on Dec. 23 2007,10:56

Quote (oldmanintheskydidntdoit @ Dec. 23 2007,05:32)
Daniel,
Does god make 2+2=4?
There's your answer then to "why" chemicals behave as they do. 2+2=4.

I sent you a link about populations. No god required. No comment? Coward.
---------------------QUOTE-------------------


I thought you weren't talking to me.
Posted by: oldmanintheskydidntdoit on Dec. 23 2007,11:52

Quote (Daniel Smith @ Dec. 23 2007,10:56)
Quote (oldmanintheskydidntdoit @ Dec. 23 2007,05:32)
Daniel,
Does god make 2+2=4?
There's your answer then to "why" chemicals behave as they do. 2+2=4.

I sent you a link about populations. No god required. No comment? Coward.
---------------------QUOTE-------------------


I thought you weren't talking to me.
---------------------QUOTE-------------------


True.

Still, foxes and rabbits, I remember learning that as a child at the science museum. Never heard of them?
Posted by: Erasmus, FCD on Dec. 23 2007,18:21

Daniel:

Ecology.  Look it up.  There is a precedent.
Posted by: Daniel Smith on Dec. 26 2007,10:56

Quote (oldmanintheskydidntdoit @ Dec. 23 2007,11:52)
Quote (Daniel Smith @ Dec. 23 2007,10:56)
 
Quote (oldmanintheskydidntdoit @ Dec. 23 2007,05:32)
Daniel,
Does god make 2+2=4?
There's your answer then to "why" chemicals behave as they do. 2+2=4.

I sent you a link about populations. No god required. No comment? Coward.
---------------------QUOTE-------------------


I thought you weren't talking to me.
---------------------QUOTE-------------------


True.

Still, foxes and rabbits, I remember learning that as a child at the science museum. Never heard of them?
---------------------QUOTE-------------------


Yeah, don't they kind of "balance" each other out?
Posted by: oldmanintheskydidntdoit on Dec. 26 2007,11:01

Quote (Daniel Smith @ Dec. 26 2007,10:56)
Quote (oldmanintheskydidntdoit @ Dec. 23 2007,11:52)
 
Quote (Daniel Smith @ Dec. 23 2007,10:56)
 
Quote (oldmanintheskydidntdoit @ Dec. 23 2007,05:32)
Daniel,
Does god make 2+2=4?
There's your answer then to "why" chemicals behave as they do. 2+2=4.

I sent you a link about populations. No god required. No comment? Coward.
---------------------QUOTE-------------------


I thought you weren't talking to me.
---------------------QUOTE-------------------


True.

Still, foxes and rabbits, I remember learning that as a child at the science museum. Never heard of them?
---------------------QUOTE-------------------


Yeah, don't they kind of "balance" each other out?
---------------------QUOTE-------------------


Nah, it's a supernatural force controlling the numbers from behind the scenes, outside of the observable universe. Likely via "quantum" effects. It just looks like a feedback mechanism.
Posted by: Daniel Smith on Dec. 26 2007,11:07

Quote (oldmanintheskydidntdoit @ Dec. 21 2007,05:07)
This information may dispel some of your ignorance Daniel.
< >

Have a good read
< http://comptlsci.anu.edu.au/Module-ODEs/ode-overview-notes.html >
And let us know if god is still required to maintain population levels.
---------------------QUOTE-------------------


You do realize that their equations were entirely based on theoretical populations and behavior don't you?

Still, they do illustrate how multiple variables in nature contribute to its overall balance - which was my point in the first place.
Posted by: Assassinator on Dec. 26 2007,11:11

Daniel, I'll repeat Erasmus:


---------------------QUOTE-------------------
Ecology.  Look it up. There is a precedent.
---------------------QUOTE-------------------


Posted by: Daniel Smith on Dec. 26 2007,11:19

Quote (Erasmus @ FCD,Dec. 22 2007,20:38)
Daniel, the null is 'they act that way'.  It is certainly your burden to show that this is worthy of a design inference.  if they didn't 'act that way', but acted 'another way', and we still had life as it is now, then you would still be claiming a design inference.  it's the kind of crap presupposition that you bring to the table with you.  It has no explanatory value, it has no empirical basis, it is completely a Panglossian jesus loves me the world is perfectly crafted kind of eight year old awe and wonder about the universe.

you're not interested in science and you never have been.  this is all about providing you with an apologetic.  

don't get me wrong.  I'm not saying life is 'just' chemicals.  I'm saying, what is it and how do you know?  Because I smell bullshit.
---------------------QUOTE-------------------


Well, "the null" doesn't explain very much does it?  "They act that way" does not tell us anything about how chemicals become chromosomes.  As far as I know though, that's all you've got.  There are no other explanations but "the null" for you - if you exclude design.
You ask me what life is...  Well it's an array of simple compounds organized in such a matter as to create working, self replicating systems.
I say that that organization cannot be explained via natural causes and therefore requires design.  But that's just me.
Posted by: Erasmus, FCD on Dec. 26 2007,11:28

It is just you (well, and a few other misinformed folks).  

The organization of my little boy has been designed?  I've been present since his conception, and we have no evidence of any designer meddling around with him.  Maybe we can't detect infinite wavelength radiation though.

The null can tell you how chemicals become chromosomes.  Look up biochemistry and cellular biology.  They aren't made of magical powder you know.  They are material.  As unpalatable as that may seem.

What you desire is an ontological explanation.  We've been over this.

Your assertion that this organization requires supernatural intervention is just that.  An assertion.  In particular, a bland assertion that is predicated solely upon what you don't know.  

The more parsimonious route is:  It may be that supernatural intervention is required for, say, my little boy to grow teeth or his balls to drop.  It may be that it is not.

If you phrase it that way, and then are honest with yourself about what 'supernatural' might mean, and how you would determine such a thing, then you'll drop the foolishness about putting gods in every gap.

Again, how would you know?
Posted by: oldmanintheskydidntdoit on Dec. 26 2007,17:09

Quote (Daniel Smith @ Dec. 26 2007,11:19)
I say that that organization cannot be explained via natural causes and therefore requires design.  But that's just me.
---------------------QUOTE-------------------


Well, go on then. Explain it!

Daniel, what is your explanation then?

For example, a snippet from EvoWiki


---------------------CODE SAMPLE-------------------
The modern era of abiogenesis research can be considered to start from Charles Darwin's speculations about life emerging "in some warm little pond, with all sorts of ammonia and phosphoric salts, light, heat, electricity, etc., present." He also speculated that no environments for abiogenesis would exist on the present-day Earth, because such environments would be quickly consumed by various organisms.

But there was no further progress since the 1920's, when Aleksandr Ivanovich Oparin and John Burdon Sanderson Haldane independently worked out scenarios of "chemical evolution". They concluded from various chemical grounds that the Earth had originally had hydrogen, ammonia, carbon dioxide, methane, and other simple compounds in its atmosphere -- but no oxygen molecules. And larger and larger molecules formed by various chemical processes until some of them succeeded in making copies of themselves, forming the first living things.
---------------------CODE SAMPLE-------------------


< http://wiki.cotch.net/index.php/Abiogenesis >

Now you say  

---------------------QUOTE-------------------
I say that that organization cannot be explained via natural causes and therefore requires design.
---------------------QUOTE-------------------



Does "design" have a similar explanation, similar in level of detail that is? I.E specific molecules named? Care to take a stab at proposing a mechanism? Anything at all? No? No warm little pond? Alien Crèche?
Posted by: Assassinator on Dec. 26 2007,18:33



---------------------QUOTE-------------------
I say that that organization cannot be explained via natural causes and therefore requires design.  But that's just me.
---------------------QUOTE-------------------


I don't just want to know your explanation, I also want to know why you think that and wich knowledge (or lack of it) caused you to think that. Because I wonder how you can know such a thing.
Posted by: Daniel Smith on Dec. 26 2007,18:37

Quote (Erasmus @ FCD,Dec. 26 2007,11:28)
It is just you (well, and a few other misinformed folks).  

The organization of my little boy has been designed?  I've been present since his conception, and we have no evidence of any designer meddling around with him.  Maybe we can't detect infinite wavelength radiation though.

The null can tell you how chemicals become chromosomes.  Look up biochemistry and cellular biology.  They aren't made of magical powder you know.  They are material.  As unpalatable as that may seem.

What you desire is an ontological explanation.  We've been over this.
---------------------QUOTE-------------------

No, I do not desire an ontological explanation.  What I desire is an explanation that actually explains something!  "That's the way it is."; or "It just happened"; are no explanations at all.
Sure, you can explain the nuts and bolts of chromosome formation (within a working system that regularly produces chromosomes), but no one has any explanation for the origin of chromosomes.      

---------------------QUOTE-------------------


Your assertion that this organization requires supernatural intervention is just that.  An assertion.  In particular, a bland assertion that is predicated solely upon what you don't know.  

The more parsimonious route is:  It may be that supernatural intervention is required for, say, my little boy to grow teeth or his balls to drop.  It may be that it is not.

If you phrase it that way, and then are honest with yourself about what 'supernatural' might mean, and how you would determine such a thing, then you'll drop the foolishness about putting gods in every gap.

Again, how would you know?
---------------------QUOTE-------------------


I fell the wool being pulled over my eyes here.  You act as if the requirement for explaining the origin of a system is to explain how it works.  These are two separate things.  You can show me how things work all day long, but what you can't show me is how any living system originated.  Now, you take a subtle twist on that line and point to your son.  But that doesn't explain anything.  It just shows me that reproduction happens (again amongst living systems that already reproduce regularly) - it does not explain anything about the origin of even one novel biological system.

This is what frustrates me:  In spite of all the smug answers - no one can explain to me how even the simplest living systems originated via natural causes.  At some point, when no natural explanation is forthcoming, you have to begin looking outside nature for an explanation.
Posted by: Assassinator on Dec. 26 2007,18:57



---------------------QUOTE-------------------
"That's the way it is."; or "It just happened"; are no explanations at all.
---------------------QUOTE-------------------


As Erasmus sad: read up on molecular biology and biochemistry. Besides, is that any different from "It just got designed.", now what does that explain?


---------------------QUOTE-------------------
This is what frustrates me:  In spite of all the smug answers - no one can explain to me how even the simplest living systems originated via natural causes.  At some point, when no natural explanation is forthcoming, you have to begin looking outside nature for an explanation.
---------------------QUOTE-------------------


Gee, maybe that is because we don't know what the simplest living systems were. Life is natural, why the hell should we go looking for an explanation outside nature just because you're tired of looking.
Posted by: Daniel Smith on Dec. 26 2007,19:04

Quote (Richard Simons @ Dec. 17 2007,10:00)
It still does not answer the question 'Why the fascination with a defunct theory?'
---------------------QUOTE-------------------


The "fascination" continues for me because this "defunct theory" (as you call it) actually explains the fossil record better than the currently held theory.

For instance: The fossil record shows clear evidence of smooth, gradual evolution amongst the cephalopods.  This evolution is well documented, consisting of millions of fossils, across multiple continents and ages.  In fact these fossils are so numerous and so universal, they are regularly used as index fossils.  

Which brings me to my point:  It's not the smooth, gradual evolution amongst the cephalopods that are used as demarcation for indexing - it's the breaks between these periods.  You see, these breaks are also well documented, and universal.  They are always followed by new forms and types - for which there is no clear, smooth, gradual link to the past - always.  That's why they can be used for index fossils.

So there are periods of "formation of new types"; there are periods of smooth, gradual variation; and there are periods of extinction.  Then the cycle repeats.

All these things are well documented among the cephalopods.  The currently held theory only explains two of them.  Schindewolf's "defunct" theory explains them all - and I find that fascinating.
Posted by: Daniel Smith on Dec. 26 2007,19:29

Quote (VMartin @ Dec. 21 2007,10:35)
Hi Daniel,

somebody at EvC gave the link to the article written by Professor Richard C. Strohman, Uni California : "Epigenesis and Complexity: The Coming Revolution in Biology"

< http://www.thecomplementarynature.com/TCN%20A....ics.pdf >

If you have time check it. It is very interesting. I hope such voices will be more common in the future.


According professor Zdenek Neubauer (Charles Uni Prague) modern biology is under strong influence of "fachidiots". You know, some people don't know how to tell apart tiger and lion  but they study, analyze and compare their DNA making bold predictions of evolution of that species .

You don't have to worry about JAM arguments. His concept of many basic bilological words are wrong.    

Epigenesis, epistatic interactions or pleitropic effects of genes play obviously significant role in development of an organism. According Strohman real, genetic disease acount for less than 2% of total disease load.  

Strohman quoted also Feynman who should have said:
"Mind must be a sort of dynamical pattern,not so much founded in a neurological substrate as floating above it, independent above it". But you know, Feynmann is an expert on quantum mechanics and maybe he should more discuss his opinions with evolutionary biologists (JAM etc...).
---------------------QUOTE-------------------


Martin,

I finally finished that paper.  I must say, the science of epigenetics is fascinating.  Here's < another article > confirming that there's more to life than genes and DNA.  
Abstract:    

---------------------QUOTE-------------------
Chromatin, the physiological template of all eukaryotic genetic information, is subject to a diverse array of posttranslational modifications that largely impinge on histone amino termini, thereby regulating access to the underlying DNA. Distinct histone amino-terminal modifications can generate synergistic or antagonistic interaction affinities for chromatin-associated proteins, which in turn dictate dynamic transitions between transcriptionally active or transcriptionally silent chromatin states. The combinatorial nature of histone amino-terminal modifications thus reveals a "histone code" that considerably extends the information potential of the genetic code. We propose that this epigenetic marking system represents a fundamental regulatory mechanism that has an impact on most, if not all, chromatin-templated processes, with far-reaching consequences for cell fate decisions and both normal and pathological development.
---------------------QUOTE-------------------



I think it's only obvious that genetic determinism is an incomplete explanation.  Genes are only the beginning.  Cells are where the action is!  It blows my mind how cells act as both feedback and control devices for, and within, a multitude of systems - including DNA - to which they can provide limited or unlimited access, based on many as-yet-unknown factors.

Oh, the mind of God!
Posted by: swbarnes2 on Dec. 26 2007,23:58



---------------------QUOTE-------------------
What I desire is an explanation that actually explains something!
---------------------QUOTE-------------------



Well, we don't know one yet.

But now I get it.

You were expecting us to read you a passage from a Bible of biochemistry.  The Second Epistle of Lodish to Baltimore, third chapter:

"Dealy beloved, know that the first form of life began when catylytic metallic surfaces next to deep-sea vents began catalyzing the catabolism of small molecules into longer ones.  When small chunks of this catalytic material became embedded in leaky phospholipid layered cells, the catabolism continued.  If there are any among you who doubt the wisdom I have received and shared with you here, any who might believe in the primacy of clay pockets,  you shall first speak to him alone, if he does not change his ways, the whole community shall confront him, and if he is still obstinate in the heresy of clay pockets, then you shall cut off his grant, and cast him out of the university."

Is that enough of an explantion for you?  Or shall I make up more speculation, and clothe it in the rhetorical garb which you associate with unquestionable truth?  An honest "We don't know" is simpler, but you don't seem to accept the honest answer, so what's left but the innovative ones?
Posted by: VMartin on Dec. 27 2007,00:14

Daniel



---------------------QUOTE-------------------

Now, you take a subtle twist on that line and point to your son.

---------------------QUOTE-------------------




Erasmus obviously thinks that neodarwinian explanation of descent of testicles is correct. The opposite is the fact. We are observing a process that has nothing to do
with any neodarwinian "function".

I've addressed the problem of descent of testicles here:

< http://www.antievolution.org/cgi-bin....;st=180 >
Posted by: oldmanintheskydidntdoit on Dec. 27 2007,04:15

Quote (VMartin @ Dec. 27 2007,00:14)
Daniel

 

---------------------QUOTE-------------------

Now, you take a subtle twist on that line and point to your son.

---------------------QUOTE-------------------




Erasmus obviously thinks that neodarwinian explanation of descent of testicles is correct. The opposite is the fact. We are observing a process that has nothing to do
with any neodarwinian "function".

I've addressed the problem of descent of testicles here:

< http://www.antievolution.org/cgi-bin....;st=180 >
---------------------QUOTE-------------------


That's really rather ironic VMartin, as the current evidence suggests that yours are yet to make an appearance.

And Daniel, I see no "design explanation" for a single thing yet.  Just admit that's because there is no "design explanation" for a single thing and we'll move on.
Posted by: oldmanintheskydidntdoit on Dec. 27 2007,04:22

Quote (Daniel Smith @ Dec. 26 2007,18:37)
This is what frustrates me:  In spite of all the smug answers - no one can explain to me how even the simplest living systems originated via natural causes.  At some point, when no natural explanation is forthcoming, you have to begin looking outside nature for an explanation.
---------------------QUOTE-------------------


Then it's odd how you are not frustrated with your belief in god then. After all, no explanations of how even the simplest living systems originated via god are available apart from "poof".

It's odd how you addressed other points but avoid this one.

It's not nice to admit you've been misled, I know, but you've no alternative here.

Whatever the shortcomings of natural explanations for biological systems then are better then nothing. And nothing is what you are offering. Nothing, nada, zip.

The funny thing is Daniel, and this is why you are an entertainment rather then a worry, is that the people doing the research (you know, with lab coats and all that) don't agree at all with you when you say:


---------------------QUOTE-------------------
At some point, when no natural explanation is forthcoming, you have to begin looking outside nature for an explanation.
---------------------QUOTE-------------------


No, they don't. They'll keep on working inside of a natural framework. Your frustration  only matters if you are funding a team to look into those issues. Daniel, this is a messageboard, not a lab,  and your opinions are irrelevant in the place it matters, the lab.  

You and your new buddy can back slap all you want but it won't make a whit of difference unless you can put your money where your overlarge mouth is and produce some results

Goddit is the best you've got? They've had that for thousands of years already. I guess your ignorance also extends to history.
Posted by: oldmanintheskydidntdoit on Dec. 27 2007,04:29

Quote (Daniel Smith @ Dec. 26 2007,11:19)
You ask me what life is...  Well it's an array of simple compounds organized in such a matter as to create working, self replicating systems.
I say that that organization cannot be explained via natural causes and therefore requires design.  But that's just me.
---------------------QUOTE-------------------


< http://www.news.cornell.edu/stories/May05/selfrep.ws.html >
Self replicating robots. According to you, they are "alive".


---------------------QUOTE-------------------
Admittedly the machine is just a proof of concept -- it performs no useful function except to self-replicate -- but the basic principle could be extended to create robots that could replicate or at least repair themselves while working in space or in hazardous environments
---------------------QUOTE-------------------



it's ALIVE!

Think again about your definition of "life" Daniel.
Posted by: oldmanintheskydidntdoit on Dec. 27 2007,04:40

Quote (Daniel Smith @ Dec. 26 2007,11:07)
Still, they do illustrate how multiple variables in nature contribute to its overall balance - which was my point in the first place.
---------------------QUOTE-------------------


Liar.
You said
 

---------------------QUOTE-------------------
Maybe there's no such thing as natural selection - maybe God does the selecting.  
---------------------QUOTE-------------------


< Link >

That's quite different from "multiple variables in nature contribute to overall balance". Nobody can disagree with the latter statement - of course multiple variables contribute. Nothing crazy there. Yet you claim that was what you meant all along, and continently forget about maybe there's no such thing as natural selection - maybe God does the selecting.

EDIT: If you look at the post I linked to, Daniel appears to be saying it's god stopping the world being overrun by cockroaches or similar. It's god keeping it "in balance" by not allowing that to happen. Daniel, why did got just not create them in the first place? Problem solved!
Posted by: oldmanintheskydidntdoit on Dec. 27 2007,04:53

Quote (Daniel Smith @ Dec. 26 2007,19:29)
Oh, the mind of God!
---------------------QUOTE-------------------


Your god must love misery, < deformity >, < malaria >,  and < parasites > then. Oh, and beetles. He really likes beetles.
Posted by: VMartin on Dec. 27 2007,10:52

Quote (oldmanintheskydidntdoit @ Dec. 27 2007,04:53)
Quote (Daniel Smith @ Dec. 26 2007,19:29)
Oh, the mind of God!
---------------------QUOTE-------------------


Your god must love misery, < deformity >, < malaria >,  and < parasites > then. Oh, and beetles. He really likes beetles.
---------------------QUOTE-------------------


Yeaah. And all those colors of beetles in which neodarwinian scientists see "function", "survival advantge", "aposematism" or "mimicry".
You have heard about black wasps or yellow ladybirds, haven't you? I can send pictures if you like. And you will give us explanation to it.
Posted by: oldmanintheskydidntdoit on Dec. 27 2007,11:37

Quote (VMartin @ Dec. 27 2007,10:52)
Quote (oldmanintheskydidntdoit @ Dec. 27 2007,04:53)
 
Quote (Daniel Smith @ Dec. 26 2007,19:29)
Oh, the mind of God!
---------------------QUOTE-------------------


Your god must love misery, < deformity >, < malaria >,  and < parasites > then. Oh, and beetles. He really likes beetles.
---------------------QUOTE-------------------


Yeaah. And all those colors of beetles in which neodarwinian scientists see "function", "survival advantge", "aposematism" or "mimicry".
You have heard about black wasps or yellow ladybirds, haven't you? I can send pictures if you like. And you will give us explanation to it.
---------------------QUOTE-------------------


I asked first.

So is this first time you'll say something about your "theory" then VMartin?

He (the designer) really likes lots of coloured beetles. The color has no function, stupido. He just like".

Not a very auspicious start, but a start nonetheless. What's next VMartin? Why he likes beetles?
Posted by: Richard Simons on Dec. 28 2007,22:03

Quote (Daniel Smith @ Dec. 26 2007,19:04)
 
Quote (Richard Simons @ Dec. 17 2007,10:00)
It still does not answer the question 'Why the fascination with a defunct theory?'
---------------------QUOTE-------------------


The "fascination" continues for me because this "defunct theory" (as you call it) actually explains the fossil record better than the currently held theory.

For instance: The fossil record shows clear evidence of smooth, gradual evolution amongst the cephalopods.  This evolution is well documented, consisting of millions of fossils, across multiple continents and ages.  In fact these fossils are so numerous and so universal, they are regularly used as index fossils.  

Which brings me to my point:  It's not the smooth, gradual evolution amongst the cephalopods that are used as demarcation for indexing - it's the breaks between these periods.  You see, these breaks are also well documented, and universal.  They are always followed by new forms and types - for which there is no clear, smooth, gradual link to the past - always.  That's why they can be used for index fossils.

So there are periods of "formation of new types"; there are periods of smooth, gradual variation; and there are periods of extinction.  Then the cycle repeats.

All these things are well documented among the cephalopods.  The currently held theory only explains two of them.  Schindewolf's "defunct" theory explains them all - and I find that fascinating.
---------------------QUOTE-------------------


Schindewolf's musing has holes large enough to drive a truck through. His theory has no plausible (or even implausible) mechanism for anticipating, storing and implementing the required changes. Without those the theory is completely, utterly useless, explaining nothing, which is why the vast majority of biologists have regarded it as having no more than historical interest.
Posted by: Hawk on Dec. 29 2007,21:30

Quote (Daniel Smith @ Dec. 26 2007,19:04)
Quote (Richard Simons @ Dec. 17 2007,10:00)
It still does not answer the question 'Why the fascination with a defunct theory?'
---------------------QUOTE-------------------


The "fascination" continues for me because this "defunct theory" (as you call it) actually explains the fossil record better than the currently held theory.

For instance: The fossil record shows clear evidence of smooth, gradual evolution amongst the cephalopods.  This evolution is well documented, consisting of millions of fossils, across multiple continents and ages.  In fact these fossils are so numerous and so universal, they are regularly used as index fossils.  

Which brings me to my point:  It's not the smooth, gradual evolution amongst the cephalopods that are used as demarcation for indexing - it's the breaks between these periods.  You see, these breaks are also well documented, and universal.  They are always followed by new forms and types - for which there is no clear, smooth, gradual link to the past - always.  That's why they can be used for index fossils.

So there are periods of "formation of new types"; there are periods of smooth, gradual variation; and there are periods of extinction.  Then the cycle repeats.

All these things are well documented among the cephalopods.  The currently held theory only explains two of them.  Schindewolf's "defunct" theory explains them all - and I find that fascinating.
---------------------QUOTE-------------------


It is true, there are breaks between these periods, but if you are using this as evidence that god exists then it implies that there has been more than one creation.
Either that or he/she/it was just unhappy with what he currently had so "poof", he creates an entire new species, and gets rid of the old one. This then implies that the supposedly perfect god is not perfect.
Posted by: Arden Chatfield on Dec. 30 2007,21:03

Quote (VMartin @ Dec. 27 2007,10:52)
 
Quote (oldmanintheskydidntdoit @ Dec. 27 2007,04:53)
 
Quote (Daniel Smith @ Dec. 26 2007,19:29)
Oh, the mind of God!
---------------------QUOTE-------------------


Your god must love misery, < deformity >, < malaria >,  and < parasites > then. Oh, and beetles. He really likes beetles.
---------------------QUOTE-------------------


Yeaah. And all those colors of beetles in which neodarwinian scientists see "function", "survival advantge", "aposematism" or "mimicry".
You have heard about black wasps or yellow ladybirds, haven't you? I can send pictures if you like. And you will give us explanation to it.
---------------------QUOTE-------------------



[my boldfacing]

Speaking of explanations, Marty....
Posted by: Daniel Smith on Dec. 31 2007,13:46

Quote (Richard Simons @ Dec. 28 2007,22:03)
 
Quote (Daniel Smith @ Dec. 26 2007,19:04)
     
Quote (Richard Simons @ Dec. 17 2007,10:00)
It still does not answer the question 'Why the fascination with a defunct theory?'
---------------------QUOTE-------------------


The "fascination" continues for me because this "defunct theory" (as you call it) actually explains the fossil record better than the currently held theory.

For instance: The fossil record shows clear evidence of smooth, gradual evolution amongst the cephalopods.  This evolution is well documented, consisting of millions of fossils, across multiple continents and ages.  In fact these fossils are so numerous and so universal, they are regularly used as index fossils.  

Which brings me to my point:  It's not the smooth, gradual evolution amongst the cephalopods that are used as demarcation for indexing - it's the breaks between these periods.  You see, these breaks are also well documented, and universal.  They are always followed by new forms and types - for which there is no clear, smooth, gradual link to the past - always.  That's why they can be used for index fossils.

So there are periods of "formation of new types"; there are periods of smooth, gradual variation; and there are periods of extinction.  Then the cycle repeats.

All these things are well documented among the cephalopods.  The currently held theory only explains two of them.  Schindewolf's "defunct" theory explains them all - and I find that fascinating.
---------------------QUOTE-------------------


Schindewolf's musing has holes large enough to drive a truck through. His theory has no plausible (or even implausible) mechanism for anticipating, storing and implementing the required changes. Without those the theory is completely, utterly useless, explaining nothing, which is why the vast majority of biologists have regarded it as having no more than historical interest.
---------------------QUOTE-------------------


Have you read Schindewolf's book?  You describe his carefully laid out theory as his "musing" - as if he's just kinda guessing about some vague ideas he has.  In fact, his book is full of evidence for his theory.  I'm guessing that you have not (and probably will not) read it.
Posted by: Daniel Smith on Dec. 31 2007,14:48

Quote (oldmanintheskydidntdoit @ Dec. 27 2007,04:22)
                         
Quote (Daniel Smith @ Dec. 26 2007,18:37)
This is what frustrates me:  In spite of all the smug answers - no one can explain to me how even the simplest living systems originated via natural causes.  At some point, when no natural explanation is forthcoming, you have to begin looking outside nature for an explanation.
---------------------QUOTE-------------------


Then it's odd how you are not frustrated with your belief in god then. After all, no explanations of how even the simplest living systems originated via god are available apart from "poof".

It's odd how you addressed other points but avoid this one.

It's not nice to admit you've been misled, I know, but you've no alternative here.

Whatever the shortcomings of natural explanations for biological systems then are better then nothing. And nothing is what you are offering. Nothing, nada, zip.

The funny thing is Daniel, and this is why you are an entertainment rather then a worry, is that the people doing the research (you know, with lab coats and all that) don't agree at all with you when you say:
                         

---------------------QUOTE-------------------
At some point, when no natural explanation is forthcoming, you have to begin looking outside nature for an explanation.
---------------------QUOTE-------------------


No, they don't. They'll keep on working inside of a natural framework. Your frustration  only matters if you are funding a team to look into those issues. Daniel, this is a messageboard, not a lab,  and your opinions are irrelevant in the place it matters, the lab.  

You and your new buddy can back slap all you want but it won't make a whit of difference unless you can put your money where your overlarge mouth is and produce some results

Goddit is the best you've got? They've had that for thousands of years already. I guess your ignorance also extends to history.
---------------------QUOTE-------------------


I am of the opinion that a careful, honest assessment of the evidence will show that;
A) There are no plausible natural explanations for the origin of any of life's systems;
And
B) These systems are so intricate, so complex and specific, they require a designer with a mind of infinite intelligence as their source.

It is therefore my prediction that the study of genetics and cellular functions will lead scientists down such a dizzying array of complex, intertwined chemical reactions, that they'll be forced to admit (at least privately) that there are no possible natural explanations for the formation of such systems and their mechanisms.

Statements such as this will become more and more common:
                         

---------------------QUOTE-------------------
The mechanisms by which around 2 m of DNA is packaged into the cell nucleus while remaining functional border on the miraculous and are still poorly understood.
Bryan M. Turner, Cellular Memory and the Histone Code, Cell, Vol. 111, 285–291, November 1, 2002, (Emphasis mine)
---------------------QUOTE-------------------


And from the same article:
                       

---------------------QUOTE-------------------
Studies on the rapid transcriptional upregulation of inducible genes provide evidence for a “cascade” of events, each dependent on the one preceding it and each involving specific histone tail modifications (Agalioti et al., 2002; Daujat et al., 2002, and references therein). The final pattern of modifications will represent the end result of this cascade and thus may have no significance in itself.
Ibid, (Emphasis mine)
---------------------QUOTE-------------------


In essence, cellular life and genetics are just like the earth's ecological system where 'everything affects something else' and where 'everything is dependent on something else'.  Such cascading systems don't just happen.  Perhaps a simple system could beat the odds and 'just happen', but it could never sustain itself for a protracted length of time without another system (its perfect complement no less) coming along behind it.  Now multiply such 'just happens' by trillions of times and you can theoretically explain life via natural causes.  Do you see the dilemma?

Systems such as those on the scale we see in life, could never 'just happen', and also 'just happen to sustain themselves', and that for millions of years!  No, for something such as this; on the scale we see; from the most minute particles to the entire universe itself; all supremely tailored for the sustenance of carbon-based life on this planet; it would require an infinite mind as the source.  No other explanation will suffice.

That is how I address your objections.

Now does that mean scientists should give up?  That they should throw up their hands and say "God did it. what more can we learn?"?

Obviously not.

If we were to find an ancient artifact that exhibited a technological knowledge far beyond that of any known civilization, would we refuse to study it?  Of course not.  We would pour over it in an effort to learn that technology and to learn of that civilization.  

Well such is life.  Life is an artifact of supreme technology laid in our lap by God so that we can learn of it and of him.

We should definitely continue its study.
Posted by: JAM on Dec. 31 2007,16:11

Quote (Daniel Smith @ Dec. 31 2007,13:46)
Have you read Schindewolf's book?  You describe his carefully laid out theory as his "musing" - as if he's just kinda guessing about some vague ideas he has.
---------------------QUOTE-------------------


Dan,
Your misrepresentations continue. A hypothesis does not get promoted to a theory unless it has a long record of successful predictions. Schindewolf produced no data from testing his predictions, so there's really no point in considering his musings seriously--he obviously didn't himself, if he couldn't be bothered to test predictions.
 

---------------------QUOTE-------------------
In fact, his book is full of evidence for his theory.  I'm guessing that you have not (and probably will not) read it.
---------------------QUOTE-------------------


But what about the evidence that doesn't support his vague notions? Your incredible ignorance about biology doesn't leave you in a position to make any credible claims.
Posted by: JAM on Dec. 31 2007,16:29

Quote (Daniel Smith @ Dec. 31 2007,14:48)
I am of the opinion that a careful, honest assessment of the evidence
---------------------QUOTE-------------------


You've been neither careful nor honest, so your assessment doesn't count. I'm still waiting for your explanation of how you honestly misread anything that would allow you to conclude that Atlantic and Pacific humpback populations have been isolated from each other for millions of years when in fact, they frolic at the junction between those oceans.


---------------------QUOTE-------------------
will show that;
A) There are no plausible natural explanations for the origin of any of life's systems;
---------------------QUOTE-------------------


We already have them. Your claim that they are implausible is based on aggressive ignorance.

Why are stop codons separate from amino acid codons, but start codons aren't? Give me a plausible reason from a design perspective instead of running away.


---------------------QUOTE-------------------
And
B) These systems are so intricate, so complex and specific,
---------------------QUOTE-------------------


Again, you are simply being dishonest. The complexity comes from the iterative nature of evolution. The specificity is an illusion, which you'd realize if you had the smidgen of integrity required to take me up on my challenge to look at the NATURE of biological complexity.

For example, how do you explain the LACK of specificity in receptors and second-messenger pathways? That lack would be trivially easy to avoid in design.


---------------------QUOTE-------------------
they require a designer with a mind of infinite intelligence as their source.
---------------------QUOTE-------------------


So, why would an infinitely intelligent designer separate stop from aa incorporation, but fail to separate start from aa incorporation?


---------------------QUOTE-------------------
It is therefore my prediction that the study of genetics and cellular functions will lead scientists down such a dizzying array of complex, intertwined chemical reactions, that they'll be forced to admit (at least privately) that there are no possible natural explanations for the formation of such systems and their mechanisms.
---------------------QUOTE-------------------


Evolution explains their complexity and intertwining quite easily. It also explains their lack of specificity, which you don't have a hope in hell of explaining.


---------------------QUOTE-------------------
Statements such as this will become more and more common:
                           

---------------------QUOTE-------------------
The mechanisms by which around 2 m of DNA is packaged into the cell nucleus while remaining functional border on the miraculous and are still poorly understood.
Bryan M. Turner, Cellular Memory and the Histone Code, Cell, Vol. 111, 285–291, November 1, 2002, (Emphasis mine)
---------------------QUOTE-------------------


---------------------QUOTE-------------------


Statements aren't evidence.


---------------------QUOTE-------------------
In essence, cellular life and genetics are just like the earth's ecological system where 'everything affects something else' and where 'everything is dependent on something else'.
---------------------QUOTE-------------------


But intelligent designs tend to prevent such interactions.


---------------------QUOTE-------------------
Such cascading systems don't just happen.  Perhaps a simple system could beat the odds and 'just happen',
---------------------QUOTE-------------------


You're lying, Dan. Evolution doesn't "just happen."


---------------------QUOTE-------------------
but it could never sustain itself for a protracted length of time without another system (its perfect complement no less) coming along behind it.
---------------------QUOTE-------------------


You're lying. Your claim of perfect complementation is a complete fabrication.


---------------------QUOTE-------------------
Now multiply such 'just happens' by trillions of times and you can theoretically explain life via natural causes.  Do you see the dilemma?
---------------------QUOTE-------------------


No, since evolution doesn't work that way.


---------------------QUOTE-------------------
Systems such as those on the scale we see in life, could never 'just happen', and also 'just happen to sustain themselves', and that for millions of years!
---------------------QUOTE-------------------


How would you know? You can't even bring yourself to examine the evidence in any detail without throwing up your hands and lying about it.


---------------------QUOTE-------------------
No, for something such as this; on the scale we see; from the most minute particles to the entire universe itself; all supremely tailored for the sustenance of carbon-based life on this planet; it would require an infinite mind as the source.  No other explanation will suffice.
---------------------QUOTE-------------------


Explain what is "supremely tailored" about endocytosis, when the "sewage" keeps getting mixed up with the "drinking water."



---------------------QUOTE-------------------
That is how I address your objections.
---------------------QUOTE-------------------


You haven't addressed any of them. You've misrepresented them.


---------------------QUOTE-------------------
Now does that mean scientists should give up?  That they should throw up their hands and say "God did it. what more can we learn?"?

Obviously not.
---------------------QUOTE-------------------


So what's YOUR explanation for reality, in which every single ID proponent in the world has done exactly that?


---------------------QUOTE-------------------
Well such is life.  Life is an artifact of supreme technology laid in our lap by God so that we can learn of it and of him.
---------------------QUOTE-------------------


But you don't learn. You run away and pretend that you understand it better than those of us who jump into its study.


---------------------QUOTE-------------------
We should definitely continue its study.
---------------------QUOTE-------------------


But you don't study. You take a preposterously superficial approach and pronounce yourself superior to the people who study life in depth.
Posted by: oldmanintheskydidntdoit on Dec. 31 2007,19:16

Quote (Daniel Smith @ Dec. 31 2007,14:48)
In essence, cellular life and genetics are just like the earth's ecological system where 'everything affects something else' and where 'everything is dependent on something else'.  Such cascading systems don't just happen.  Perhaps a simple system could beat the odds and 'just happen', but it could never sustain itself for a protracted length of time without another system (its perfect complement no less) coming along behind it.  Now multiply such 'just happens' by trillions of times and you can theoretically explain life via natural causes.  Do you see the dilemma?

Systems such as those on the scale we see in life, could never 'just happen', and also 'just happen to sustain themselves', and that for millions of years!  No, for something such as this; on the scale we see; from the most minute particles to the entire universe itself; all supremely tailored for the sustenance of carbon-based life on this planet; it would require an infinite mind as the source.  No other explanation will suffice.

That is how I address your objections.

Now does that mean scientists should give up?  That they should throw up their hands and say "God did it. what more can we learn?"?

Obviously not.

If we were to find an ancient artifact that exhibited a technological knowledge far beyond that of any known civilization, would we refuse to study it?  Of course not.  We would pour over it in an effort to learn that technology and to learn of that civilization.  

Well such is life.  Life is an artifact of supreme technology laid in our lap by God so that we can learn of it and of him.

We should definitely continue its study.
---------------------QUOTE-------------------


There is a slight problem.
For example.



---------------------QUOTE-------------------
Such cascading systems don't just happen.
---------------------QUOTE-------------------


I can ask why?


---------------------QUOTE-------------------
all supremely tailored for the sustenance of carbon-based life on this planet
---------------------QUOTE-------------------


why?


---------------------QUOTE-------------------
it would require an infinite mind as the source
---------------------QUOTE-------------------


why?


---------------------QUOTE-------------------
.  No other explanation will suffice.

---------------------QUOTE-------------------


why?
Daniel


---------------------QUOTE-------------------
from the most minute particles to the entire universe itself; all supremely tailored for the sustenance of carbon-based life on this planet
---------------------QUOTE-------------------


Don't you think that's a bit arrogant, that teh entire universe is as it is just so we exist? That's crazy talk...
After all, a grain of sand half the universe away could alter our reality via gravity, chaos theory and all that. So the entire universe is directed to making sure that...exactly what Daniel?  :p
Is mankind evolving or is it too late?
Posted by: Richard Simons on Dec. 31 2007,23:13

Daniel,

No, I have not read Schindewolf's book. I would probably read it if it were easily available (I do not have ready access to inter-library loan). From what you have presented, it seems to attempt to explain nothing more than can be explained by conventional evolutionary theory, while at the same time using the equivalent of sky hooks for mechanisms, so I have little incentive to make much effort to track down his book.

Is JAM correct in saying that Schindewolf lacked the courage of his convictions and never used his ideas to make testable predictions?
Posted by: VMartin on Jan. 01 2008,04:21

I don't know what you mean by "testable predictions" that you are still talking about. What "testable predictions" did neodarwinism make? Is evolution from fish to human by RM/NS  "testable prediction" or what?

Neodarwinism hasn't made more "testable predicions" about evolution as Schindewolfs has made I would say.

As you can see in "VMartin comsology" scientists admit that explanation of descent of testicles is untestable.

As to human behaviour these neodarwinian predictions changed as often as socks of scientists who conceived them. I reccomend "Sense and nonsense" from Laland and Brown 2002.

< http://www.accampbell.uklinux.net/bookreviews/r/laland-brown.html >

The history of explanation of concealed ovulation is really enchanting.

There is no need to suppose that modern synthesis has made any "testable prediction" that would not change soon to another "testable prediction" contradicting the former one.
Posted by: oldmanintheskydidntdoit on Jan. 01 2008,05:24

Quote (VMartin @ Jan. 01 2008,04:21)
I don't know what you mean by "testable predictions" that you are still talking about. What "testable predictions" did neodarwinism make? Is evolution from fish to human by RM/NS  "testable prediction" or what?

Neodarwinism hasn't made more "testable predicions" about evolution as Schindewolfs has made I would say.

As you can see in "VMartin comsology" scientists admit that explanation of descent of testicles is untestable.

As to human behaviour these neodarwinian predictions changed as often as socks of scientists who conceived them. I reccomend "Sense and nonsense" from Laland and Brown 2002.

< http://www.accampbell.uklinux.net/bookreviews/r/laland-brown.html >

The history of explanation of concealed ovulation is really enchanting.

There is no need to suppose that modern synthesis has made any "testable prediction" that would not change soon to another "testable prediction" contradicting the former one.
---------------------QUOTE-------------------


Yes, we may yet also discover that the sun goes around the earth too.
Posted by: oldmanintheskydidntdoit on Jan. 01 2008,05:36

Quote (VMartin @ Jan. 01 2008,04:21)
I don't know what you mean by "testable predictions" that you are still talking about. What "testable predictions" did neodarwinism make?
---------------------QUOTE-------------------


What "testable predictions" does your theory make VMartin?

None?

ok....
Posted by: Alan Fox on Jan. 01 2008,06:23



---------------------QUOTE-------------------
As you can see in "VMartin comsology" scientists admit that explanation of descent of testicles is untestable.
---------------------QUOTE-------------------



Your assertion led me to google and I came across < this >. It seems someone is testing the idea that undescended testicles result in sterility in the Florida panther. There is lots more on sperm viability and temperature control of the testes.

It seems to me differential temperatures and sperm viability are measurable, and a resultant hypothesis, (sperm survives better at a slightly lower temperature than normal internal body temperature in mammals) is quite testable.
Posted by: oldmanintheskydidntdoit on Jan. 01 2008,06:29

Quote (Daniel Smith @ Dec. 31 2007,13:46)
Have you read Schindewolf's book?  You describe his carefully laid out theory as his "musing" - as if he's just kinda guessing about some vague ideas he has.  In fact, his book is full of evidence for his theory.  I'm guessing that you have not (and probably will not) read it.
---------------------QUOTE-------------------




---------------------QUOTE-------------------
In the American vernacular, "theory" often means "imperfect fact"--part of a hierarchy of confidence running downhill from fact to theory to hypothesis to guess. Thus creationists can (and do) argue: evolution is "only" a theory, and intense debate now rages about many aspects of the theory. If evolution is less than a fact, and scientists can't even make up their minds about the theory, then what confidence can we have in it? Indeed, President Reagan echoed this argument before an evangelical group in Dallas when he said (in what I devoutly hope was campaign rhetoric): "Well, it is a theory. It is a scientific theory only, and it has in recent years been challenged in the world of science--that is, not believed in the scientific community to be as infallible as it once was."

Well, evolution is a theory. It is also a fact. And facts and theories are different things, not rungs in a hierarchy of increasing certainty. Facts are the world's data. Theories are structures of ideas that explain and interpret facts. Facts do not go away when scientists debate rival theories to explain them. Einstein's theory of gravitation replaced Newton's, but apples did not suspend themselves in mid-air, pending the outcome. And humans evolved from apelike ancestors whether they did so by Darwin's proposed mechanism or by some other, yet to be discovered.

Moreover, "fact" does not mean "absolute certainty." The final proofs of logic and mathematics flow deductively from stated premises and achieve certainty only because they are not about the empirical world. Evolutionists make no claim for perpetual truth, though creationists often do (and then attack us for a style of argument that they themselves favor). In science, "fact" can only mean "confirmed to such a degree that it would be perverse to withhold provisional assent." I suppose that apples might start to rise tomorrow, but the possibility does not merit equal time in physics classrooms.
---------------------QUOTE-------------------


Stephen Jay Gould, written for Discover magazine in 1981 via
< http://scienceblogs.com/dispatc....hp#more >
Now, Daniel, care to re-phrase that?
Posted by: Daniel Smith on Jan. 01 2008,18:21

Quote (oldmanintheskydidntdoit @ Jan. 01 2008,06:29)
 
Quote (Daniel Smith @ Dec. 31 2007,13:46)
Have you read Schindewolf's book?  You describe his carefully laid out theory as his "musing" - as if he's just kinda guessing about some vague ideas he has.  In fact, his book is full of evidence for his theory.  I'm guessing that you have not (and probably will not) read it.
---------------------QUOTE-------------------


   

---------------------QUOTE-------------------
In the American vernacular, "theory" often means "imperfect fact"--part of a hierarchy of confidence running downhill from fact to theory to hypothesis to guess. Thus creationists can (and do) argue: evolution is "only" a theory, and intense debate now rages about many aspects of the theory. If evolution is less than a fact, and scientists can't even make up their minds about the theory, then what confidence can we have in it? Indeed, President Reagan echoed this argument before an evangelical group in Dallas when he said (in what I devoutly hope was campaign rhetoric): "Well, it is a theory. It is a scientific theory only, and it has in recent years been challenged in the world of science--that is, not believed in the scientific community to be as infallible as it once was."

Well, evolution is a theory. It is also a fact. And facts and theories are different things, not rungs in a hierarchy of increasing certainty. Facts are the world's data. Theories are structures of ideas that explain and interpret facts. Facts do not go away when scientists debate rival theories to explain them. Einstein's theory of gravitation replaced Newton's, but apples did not suspend themselves in mid-air, pending the outcome. And humans evolved from apelike ancestors whether they did so by Darwin's proposed mechanism or by some other, yet to be discovered.

Moreover, "fact" does not mean "absolute certainty." The final proofs of logic and mathematics flow deductively from stated premises and achieve certainty only because they are not about the empirical world. Evolutionists make no claim for perpetual truth, though creationists often do (and then attack us for a style of argument that they themselves favor). In science, "fact" can only mean "confirmed to such a degree that it would be perverse to withhold provisional assent." I suppose that apples might start to rise tomorrow, but the possibility does not merit equal time in physics classrooms.
---------------------QUOTE-------------------


Stephen Jay Gould, written for Discover magazine in 1981 via
< http://scienceblogs.com/dispatc....hp#more >
Now, Daniel, care to re-phrase that?
---------------------QUOTE-------------------


What, in the passage you quoted, would give me any reason to rephrase my statement?
Posted by: Arden Chatfield on Jan. 01 2008,18:25

Quote (VMartin @ Jan. 01 2008,04:21)
I don't know what you mean by "testable predictions" that you are still talking about. What "testable predictions" did neodarwinism make? Is evolution from fish to human by RM/NS  "testable prediction" or what?
---------------------QUOTE-------------------


Martin:

1) What predictions does YOUR theory make?

2) What IS your theory, BTW?

3) Is your theory Simple and Nice?
Posted by: Daniel Smith on Jan. 01 2008,18:53

Quote (JAM @ Dec. 31 2007,16:11)
     
Quote (Daniel Smith @ Dec. 31 2007,13:46)
Have you read Schindewolf's book?  You describe his carefully laid out theory as his "musing" - as if he's just kinda guessing about some vague ideas he has.
---------------------QUOTE-------------------


Dan,
Your misrepresentations continue. A hypothesis does not get promoted to a theory unless it has a long record of successful predictions. Schindewolf produced no data from testing his predictions, so there's really no point in considering his musings seriously--he obviously didn't himself, if he couldn't be bothered to test predictions.
---------------------QUOTE-------------------


Schindewolf was a paleontologist.  His "data" is the fossil record.  He introduced his theory in a paper in 1943 - 7 years before he published Basic Questions in Paleontology in 1950.  He tested his predictions as any paleontologist would - by excavating and sifting through fossils.  He produced much data himself during this period and continued his pursuit of fossils until his death in 1971.  As of this date, I am not aware of anything found in the fossil record that falsifies his theory.  Are you?      

---------------------QUOTE-------------------

       

---------------------QUOTE-------------------
In fact, his book is full of evidence for his theory.  I'm guessing that you have not (and probably will not) read it.
---------------------QUOTE-------------------


But what about the evidence that doesn't support his vague notions? Your incredible ignorance about biology doesn't leave you in a position to make any credible claims.
---------------------QUOTE-------------------


What "vague notions" are you talking about?  What evidence does not support his theory?  Do you even know what his theory is?  If you're relying on my characterization of it, you're cheating yourself - as I am ill prepared to do it justice.
Posted by: Erasmus, FCD on Jan. 01 2008,19:55

Daniel, Simpson destroys Schindewolf's misunderstanding of horse evolution in the 1944 book Tempo and Mode in Evolution.  I suggest giving it a read.
Posted by: JAM on Jan. 01 2008,20:33

Quote (Daniel Smith @ Jan. 01 2008,18:53)
 
Quote (JAM @ Dec. 31 2007,16:11)
         
Quote (Daniel Smith @ Dec. 31 2007,13:46)
Have you read Schindewolf's book?  You describe his carefully laid out theory as his "musing" - as if he's just kinda guessing about some vague ideas he has.
---------------------QUOTE-------------------


Dan,
Your misrepresentations continue. A hypothesis does not get promoted to a theory unless it has a long record of successful predictions. Schindewolf produced no data from testing his predictions, so there's really no point in considering his musings seriously--he obviously didn't himself, if he couldn't be bothered to test predictions.
---------------------QUOTE-------------------


Schindewolf was a paleontologist.
---------------------QUOTE-------------------


I know, twit. That does not falsify the fact that SCHINDEWOLF PRODUCED NO DATA FROM TESTING THE PREDICTIONS OF HIS HYPOTHESIS. Quit lying, and stop calling it a theory.
 

---------------------QUOTE-------------------
 His "data" is the fossil record.
---------------------QUOTE-------------------


That does not falsify the fact that SCHINDEWOLF PRODUCED NO DATA FROM TESTING THE PREDICTIONS OF HIS HYPOTHESIS.
 

---------------------QUOTE-------------------
He introduced his theory in a paper in 1943 - 7 years before he published Basic Questions in Paleontology in 1950.
---------------------QUOTE-------------------


You continue to lie. It was a mere hypothesis, and SCHINDEWOLF PRODUCED NO DATA FROM TESTING THE PREDICTIONS OF HIS HYPOTHESIS.
 

---------------------QUOTE-------------------
He tested his predictions as any paleontologist would - by excavating and sifting through fossils.
---------------------QUOTE-------------------


Dan, you lie like a rug. The way that paleontologists test predictions of their hypotheses is by predicting the locations, time of deposition, and morphologies of fossils BEFORE THEY FIND THEM, not after. Tiktaalik is a fine example of this sort of prediction.

SCHINDEWOLF PRODUCED NO DATA FROM TESTING THE PREDICTIONS OF HIS HYPOTHESIS. Do the caps help?
 

---------------------QUOTE-------------------
He produced much data himself during this period and continued his pursuit of fossils until his death in 1971.
---------------------QUOTE-------------------


You are a deeply dishonest man, Dan. I didn't claim that Schindewolf produced no data, I pointed out that SCHINDEWOLF PRODUCED NO DATA FROM TESTING THE PREDICTIONS OF THE HYPOTHESIS WITH WHICH YOU ARE ENAMORED.

Can't you read?
 

---------------------QUOTE-------------------
As of this date, I am not aware of anything found in the fossil record that falsifies his theory.  Are you?
---------------------QUOTE-------------------


You are blatantly dishonest, Dan, as Schindewolf's hypothesis makes clear predictions about the molecular evidence, and what we know about molecular and developmental biology falsifies his hypothesis.

For example,

1) What magnitude of genetic change is required to change the number of vertebrae in a vertebrate?
2) What magnitude of genetic change is required to change the IDENTITY of a vertebra in a vertebrate?

         

---------------------QUOTE-------------------

What "vague notions" are you talking about?
---------------------QUOTE-------------------


His hypothesis that you dishonestly describe as a theory!
 

---------------------QUOTE-------------------
What evidence does not support his theory?
---------------------QUOTE-------------------


His hypothesis, you mean. Can you carry on a conversation without using such a blatant lie?
 

---------------------QUOTE-------------------
Do you even know what his theory is?  If you're relying on my characterization of it, you're cheating yourself - as I am ill prepared to do it justice.
---------------------QUOTE-------------------


I know and am not relying on your falsehoods, particularly the one that you pretend that his hypothesis doesn't make predictions about molecular and developmental biology. BTW, there are thousands of fossil discoveries that do not support his hypothesis.
Posted by: oldmanintheskydidntdoit on Jan. 02 2008,08:47

Quote (Daniel Smith @ Jan. 01 2008,18:21)
Quote (oldmanintheskydidntdoit @ Jan. 01 2008,06:29)
 
Quote (Daniel Smith @ Dec. 31 2007,13:46)
Have you read Schindewolf's book?  You describe his carefully laid out theory as his "musing" - as if he's just kinda guessing about some vague ideas he has.  In fact, his book is full of evidence for his theory.  I'm guessing that you have not (and probably will not) read it.
---------------------QUOTE-------------------


   

---------------------QUOTE-------------------
In the American vernacular, "theory" often means "imperfect fact"--part of a hierarchy of confidence running downhill from fact to theory to hypothesis to guess. Thus creationists can (and do) argue: evolution is "only" a theory, and intense debate now rages about many aspects of the theory. If evolution is less than a fact, and scientists can't even make up their minds about the theory, then what confidence can we have in it? Indeed, President Reagan echoed this argument before an evangelical group in Dallas when he said (in what I devoutly hope was campaign rhetoric): "Well, it is a theory. It is a scientific theory only, and it has in recent years been challenged in the world of science--that is, not believed in the scientific community to be as infallible as it once was."

Well, evolution is a theory. It is also a fact. And facts and theories are different things, not rungs in a hierarchy of increasing certainty. Facts are the world's data. Theories are structures of ideas that explain and interpret facts. Facts do not go away when scientists debate rival theories to explain them. Einstein's theory of gravitation replaced Newton's, but apples did not suspend themselves in mid-air, pending the outcome. And humans evolved from apelike ancestors whether they did so by Darwin's proposed mechanism or by some other, yet to be discovered.

Moreover, "fact" does not mean "absolute certainty." The final proofs of logic and mathematics flow deductively from stated premises and achieve certainty only because they are not about the empirical world. Evolutionists make no claim for perpetual truth, though creationists often do (and then attack us for a style of argument that they themselves favor). In science, "fact" can only mean "confirmed to such a degree that it would be perverse to withhold provisional assent." I suppose that apples might start to rise tomorrow, but the possibility does not merit equal time in physics classrooms.
---------------------QUOTE-------------------


Stephen Jay Gould, written for Discover magazine in 1981 via
< http://scienceblogs.com/dispatc....hp#more >
Now, Daniel, care to re-phrase that?
---------------------QUOTE-------------------


What, in the passage you quoted, would give me any reason to rephrase my statement?
---------------------QUOTE-------------------


You appear to not understand what a hypothesis is and what a theory is.
Posted by: VMartin on Jan. 02 2008,12:14



---------------------QUOTE-------------------

SCHINDEWOLF PRODUCED NO DATA FROM TESTING THE PREDICTIONS OF HIS HYPOTHESIS. Do the caps help?

---------------------QUOTE-------------------



Someone seems to be pretty angry that Schindewolf didn't support neodarwinian explanation of the horse evolution. But capital letters and hysteria wouldn't do it.
Posted by: Assassinator on Jan. 02 2008,12:16

You REALLY do miss the point now don't you?
Posted by: oldmanintheskydidntdoit on Jan. 02 2008,12:27

Quote (VMartin @ Jan. 02 2008,12:14)


---------------------QUOTE-------------------

SCHINDEWOLF PRODUCED NO DATA FROM TESTING THE PREDICTIONS OF HIS HYPOTHESIS. Do the caps help?

---------------------QUOTE-------------------



Someone seems to be pretty angry that Schindewolf didn't support neodarwinian explanation of the horse evolution. But capital letters and hysteria wouldn't do it.
---------------------QUOTE-------------------


Why don't you go write a book VMartin?

At least SCHINDEWOLF can claim that, whatever his faults may be.

Go write it down. Got that?
Posted by: Daniel Smith on Jan. 02 2008,18:21

Quote (JAM @ Dec. 31 2007,16:29)
Why are stop codons separate from amino acid codons, but start codons aren't? Give me a plausible reason from a design perspective instead of running away.
...
So, why would an infinitely intelligent designer separate stop from aa incorporation, but fail to separate start from aa incorporation?
---------------------QUOTE-------------------


Well, if we can continue our written language analogy (which < you agreed > was valid), the "start codons" (if you will) of written language are capital letters - which are not separate in meaning from other letters, (being only distinguished by capitalization); whereas the "stop codons" (punctuation marks) are completely separate.  Now, by your  standards, written language should have to either start and stop every sentence with a capital letter, or with punctuation marks.  Any combination of the two (by your standards) would disqualify written language as an intelligent design.
This will of course, come as quite a shock to the thousands of grammarians, linguists and syntacticians who have so diligently shaped our written language rules for centuries.
So, from a design perspective, there seems to be plausible reasons for utilizing different types of start and stop signals in the coding of information.
Posted by: Daniel Smith on Jan. 02 2008,18:44

Quote (JAM @ Jan. 01 2008,20:33)
SCHINDEWOLF PRODUCED NO DATA FROM TESTING THE PREDICTIONS OF HIS HYPOTHESIS...
SCHINDEWOLF PRODUCED NO DATA FROM TESTING THE PREDICTIONS OF HIS HYPOTHESIS...
SCHINDEWOLF PRODUCED NO DATA FROM TESTING THE PREDICTIONS OF HIS HYPOTHESIS...
SCHINDEWOLF PRODUCED NO DATA FROM TESTING THE PREDICTIONS OF HIS HYPOTHESIS...
SCHINDEWOLF PRODUCED NO DATA FROM TESTING THE PREDICTIONS OF THE HYPOTHESIS WITH WHICH YOU ARE ENAMORED...
---------------------QUOTE-------------------


HOW DO YOU KNOW THAT?  
HAVE YOU READ ALL OF SCHINDEWOLF'S PAPERS?  
DO YOU READ GERMAN?

(WHY ARE WE YELLING?)

     

---------------------QUOTE-------------------
I know and am not relying on your falsehoods, particularly the one that you pretend that his hypothesis doesn't make predictions about molecular and developmental biology. BTW, there are thousands of fossil discoveries that do not support his hypothesis.
---------------------QUOTE-------------------


Then you should be able to provide some good examples and explain how they do not support his theory.

BTW, I will continue to call it a "theory" - since Stephen J. Gould has labeled it as such in his forward to Schindewolf's book:
   

---------------------QUOTE-------------------
Schindewolf relied on two major theories: (1) The cyclical theory of typostrophism... [and] (2) The ontogenetic theory of proterogenesis...

Stephen Jay Gould, pg. xiii, Forward, Basic Questions in Paleontology (emphasis mine)
---------------------QUOTE-------------------


Posted by: JAM on Jan. 02 2008,22:30

Quote (Daniel Smith @ Jan. 02 2008,18:21)
Quote (JAM @ Dec. 31 2007,16:29)
Why are stop codons separate from amino acid codons, but start codons aren't? Give me a plausible reason from a design perspective instead of running away.
...
So, why would an infinitely intelligent designer separate stop from aa incorporation, but fail to separate start from aa incorporation?
---------------------QUOTE-------------------


Well, if we can continue our written language analogy (which < you agreed > was valid), the "start codons" (if you will)
---------------------QUOTE-------------------


Oh, but Dan, there is only one start codon.


---------------------QUOTE-------------------
of written language are capital letters
---------------------QUOTE-------------------


Plural. There is only one start codon. Therefore, using the language analogy (or any other), the design of the genetic code is profoundly unintelligent.


---------------------QUOTE-------------------
...- which are not separate in meaning from other letters,
---------------------QUOTE-------------------


There's only one start codon. Therefore, using the language analogy, every sentence must start with the same letter, which would be incredibly stupid.


---------------------QUOTE-------------------
(being only distinguished by capitalization); whereas the "stop codons" (punctuation marks) are completely separate.  Now, by your  standards, written language should have to either start and stop every sentence with a capital letter,
---------------------QUOTE-------------------


You're lying again, Dan. In the analogy, every sentence must start not with "a capital letter," but a SINGLE capital letter, M.


---------------------QUOTE-------------------
... or with punctuation marks.  Any combination of the two (by your standards) would disqualify written language as an intelligent design.
---------------------QUOTE-------------------


You're lying again.


---------------------QUOTE-------------------
This will of course, come as quite a shock to the thousands of grammarians, linguists and syntacticians who have so diligently shaped our written language rules for centuries.
---------------------QUOTE-------------------


I don't see anyone proposing that all sentences should start with the same letter, do you?

BTW, do all functional proteins end up having methionine at their N-termini?


---------------------QUOTE-------------------
So, from a design perspective, there seems to be plausible reasons for utilizing different types of start and stop signals in the coding of information.
---------------------QUOTE-------------------


But there's no plausible reason to use a SINGLE start signal. You lie like a rug.
Posted by: Daniel Smith on Jan. 03 2008,17:56

Quote (JAM @ Jan. 02 2008,22:30)
Oh, but Dan, there is only one start codon.
...
Plural. There is only one start codon. Therefore, using the language analogy (or any other), the design of the genetic code is profoundly unintelligent.
...
There's only one start codon. Therefore, using the language analogy, every sentence must start with the same letter, which would be incredibly stupid.
...
In the analogy, every sentence must start not with "a capital letter," but a SINGLE capital letter, M.
...
I don't see anyone proposing that all sentences should start with the same letter, do you?
...
But there's no plausible reason to use a SINGLE start signal.
---------------------QUOTE-------------------


OK, so we've established that genetic coding is not exactly the same as written language - although both use different start-stop signals.  You seem to be suggesting there's something wrong with the way life is coded for.  It seems to work pretty well to me.
Did you ever stop to ponder the fact that there even is such a thing as a code for life?  It seems profoundly arrogant for a man to call such a thing "stupid".  I guess you'll have to take that up with God when you meet him face to face.

Now, how about all that fossil evidence you promised me?
Posted by: Daniel Smith on Jan. 03 2008,18:17

Quote (Erasmus @ FCD,Jan. 01 2008,19:55)
Daniel, Simpson destroys Schindewolf's misunderstanding of horse evolution in the 1944 book Tempo and Mode in Evolution.  I suggest giving it a read.
---------------------QUOTE-------------------


First, Schindewolf did not base his theory on horse evolution - he cites horse evolution as clear evidence of gradual, continuous evolution.  His theory was based on the fossils of ammonites and corals (he believed fossil evidence of mammalian evolution too sporadic to base a theory on).

Second, Schindewolf's book was written in 1950 (6 years after Simpson's).

Third, Schindewolf cites Simpson extensively in his book - mentioning him a total of 9 times - sometimes favorably, sometimes not.  

In light of this, I highly doubt Schindewolf felt threatened (or destroyed) by Simpson.
Posted by: Daniel Smith on Jan. 03 2008,18:23

Quote (Daniel Smith @ Jan. 02 2008,18:44)
BTW, I will continue to call it a "theory" - since Stephen J. Gould has labeled it as such in his forward to Schindewolf's book:
         

---------------------QUOTE-------------------
Schindewolf relied on two major theories: (1) The cyclical theory of typostrophism... [and] (2) The ontogenetic theory of proterogenesis...

Stephen Jay Gould, pg. xiii, Forward, Basic Questions in Paleontology (emphasis mine)
---------------------QUOTE-------------------


---------------------QUOTE-------------------


Since I am not allowed to edit my own posts, I'll just point out that I should have said "foreword" rather than "forward".
Posted by: Daniel Smith on Jan. 03 2008,18:33

Quote (Richard Simons @ Dec. 31 2007,23:13)
Is JAM correct in saying that Schindewolf lacked the courage of his convictions and never used his ideas to make testable predictions?
---------------------QUOTE-------------------


I've never heard that about Schindewolf anywhere else but here - if that tells you anything.  The main problem is that Schindewolf's writings are all in German, so most of us have no idea what predictions he made.  Certainly though, in the one book that was translated into English, he felt confident enough to lay out a theory that makes some bold predictions about what will be found in the fossil record.  He described definite patterns in evolution that he fully expected to be confirmed with increasing fossil evidence.  I'd say that shows the "courage of his convictions", wouldn't you?
Posted by: IanBrown_101 on Jan. 03 2008,18:47

Quote (Daniel Smith @ Jan. 03 2008,23:56)
It seems to work pretty well to me.
Did you ever stop to ponder the fact that there even is such a thing as a code for life?  It seems profoundly arrogant for a man to call such a thing "stupid".
---------------------QUOTE-------------------


Jesus H Christ man, what is your problem?

Just because something just about works doesn't mean it isn't stupid.

Iron lungs are pretty damn stupid, and boy are they oddly designed, but hell, they still work.
Posted by: JAM on Jan. 04 2008,00:03

Quote (Daniel Smith @ Jan. 03 2008,17:56)
 
Quote (JAM @ Jan. 02 2008,22:30)
Oh, but Dan, there is only one start codon.
...
Plural. There is only one start codon. Therefore, using the language analogy (or any other), the design of the genetic code is profoundly unintelligent.
...
There's only one start codon. Therefore, using the language analogy, every sentence must start with the same letter, which would be incredibly stupid.
...
In the analogy, every sentence must start not with "a capital letter," but a SINGLE capital letter, M.
...
I don't see anyone proposing that all sentences should start with the same letter, do you?
...
But there's no plausible reason to use a SINGLE start signal.
---------------------QUOTE-------------------


OK, so we've established that genetic coding is not exactly the same as written language - although both use different start-stop signals.
---------------------QUOTE-------------------


We've established that we agree that the "design" of translational initiation is profoundly unintelligent.


---------------------QUOTE-------------------
You seem to be suggesting there's something wrong with the way life is coded for.
---------------------QUOTE-------------------


Dan, you're a weasel. I've shown that by YOUR standard, the designer made an obviously unintelligent choice.


---------------------QUOTE-------------------
It seems to work pretty well to me.
---------------------QUOTE-------------------


Selection does that, but how would you possibly know, since you're lying about your fascination with life? However, we weren't discussing whether it "works pretty well," we were discussing whether intelligent design choices were made, and by the criterion YOU stipulated, they weren't. This makes perfect sense as a product of evolution, though.
Since it seems to work pretty well to you, maybe you can comment on the number of different N-terminal modifications that proteins are known to undergo as a result of this unintelligent design.


---------------------QUOTE-------------------
Did you ever stop to ponder the fact that there even is such a thing as a code for life?
---------------------QUOTE-------------------


There isn't a "code for life." It's a figure of speech. Do you realize that there's nothing symbolic about it? It only looks like a code when we organize it into a table for you.


---------------------QUOTE-------------------
It seems profoundly arrogant for a man to call such a thing "stupid".
---------------------QUOTE-------------------


You agreed that the design choice made on the back end was more intelligent than the one made for the front end. Therefore, the design itself could not have come from a perfect being.


---------------------QUOTE-------------------
I guess you'll have to take that up with God when you meet him face to face.
---------------------QUOTE-------------------


Don't you mean Him?


---------------------QUOTE-------------------
Now, how about all that fossil evidence you promised me?
---------------------QUOTE-------------------


So you can tell lies about that, too?



---------------------QUOTE-------------------
Korn, Dieter (2003):
Typostrophism in Palaeozoic Ammonoids?.
Palaeontologische Zeitschrift, Band 77, Heft 2 . p. 445-470, 20 fig.

Die antidarwinistische ,Typostrophentheorie" von O.H. Schindewolf wird mit den Ammonoiden-Beipielen getestet, auf welchen sie begründet worden ist. Es kann gezeigt werden dass keines der drei theoretischen Elemente der Theorie (Saltationismus, Internalismus und Zyklismus) durch empirische Befunde gestützt werden kann. Vermeintliche Saltationen (,Typogenese") werden durch das Fehlen von Zwischenformen vorgetäuscht. Internalistische und orthogenetische Entwicklung (,Typostase") kann nur postuliert werden, wenn mögliche Funktionen abgelehnt werden. Vorprogrammiertes Aussterben von ,degenerierten" Entwicklungslinien (,Typolyse") kann ausgeschlossen werden, wenn Ammonoideen-Morphologien frei von anthropozentrischen Ansichten betrachtet werden. Auf Grund der Studie von paläozoischen Ammonoideen gibt es keinen Grund, die ,Typostrophenlehre" oder einige der sie aufbauenden Elemente, wie das ,Typus-Konzept" und ,Proterogenese", dem darwinistischen Evolutionsmodell vorzuziehen.

The anti-Darwinian ,Typostrophe Theory" of O.H. Schindewolf can be put to the test by revisiting the ammonoid examples on which this macroevolutionary model was founded. It is shown that none of the three theoretical elements saltationism, internalism, and cyclism can be supported by empirical data obtained from ammonoid research. Putative saltations (,Typogenesis") were feigned because of the lack of knowledge of intermediate forms. Internalistic and orthogenetic development (,Typostasis") can only be favoured by neglecting possible functions of morphological characters. Preprogrammed extinction of ,degenerated" clades (,Typolysis") is unlikely when ruling out anthropocentric views regarding ammonoid morphology. In terms of evolution of Palaeozoic ammonoids, there is no basis for the preference of the ,Typostrophe Theory" or some of its composing elements, including the ,Type Concept" and ,Proterogenesis", over the Darwinian evolutionary model and the Modern Synthesis.
---------------------QUOTE-------------------


Posted by: JAM on Jan. 04 2008,12:14

Quote (Daniel Smith @ Jan. 03 2008,18:33)
Quote (Richard Simons @ Dec. 31 2007,23:13)
Is JAM correct in saying that Schindewolf lacked the courage of his convictions and never used his ideas to make testable predictions?
---------------------QUOTE-------------------


I've never heard that about Schindewolf anywhere else but here - if that tells you anything.  The main problem is that Schindewolf's writings are all in German, so most of us have no idea what predictions he made.
---------------------QUOTE-------------------


Stop weaseling, Dan. The issue is not whether he made predictions in his writings, but whether he tested the predictions of his hypothesis(es). If a hypothesis is properly formulated to be useful, there simply is no debate about its predictions.


---------------------QUOTE-------------------
Certainly though, in the one book that was translated into English, he felt confident enough to lay out a theory that makes some bold predictions about what will be found in the fossil record.
---------------------QUOTE-------------------


BS. The measure of confidence and boldness is whether he (or for that matter, you) seeks to test the predictions, particularly those that have the potential to falsify the hypothesis.


---------------------QUOTE-------------------
He described definite patterns in evolution that he fully expected to be confirmed with increasing fossil evidence.
---------------------QUOTE-------------------


"Patterns in evolution" is the hypothesis, not the prediction. Whether he expected them to be confirmed is best measured by the extent of his efforts to confirm AND FALSIFY them. Predictions are about what will be found, not their interpretation. Keeping to that is what makes science so much more honest than religion.


---------------------QUOTE-------------------
I'd say that shows the "courage of his convictions", wouldn't you?
---------------------QUOTE-------------------


Not at all.
Posted by: Daniel Smith on Jan. 04 2008,22:52

Quote (IanBrown_101 @ Jan. 03 2008,18:47)
 
Quote (Daniel Smith @ Jan. 03 2008,23:56)
It seems to work pretty well to me.
Did you ever stop to ponder the fact that there even is such a thing as a code for life?  It seems profoundly arrogant for a man to call such a thing "stupid".
---------------------QUOTE-------------------


Jesus H Christ man, what is your problem?

Just because something just about works doesn't mean it isn't stupid.

Iron lungs are pretty damn stupid, and boy are they oddly designed, but hell, they still work.
---------------------QUOTE-------------------


And they are still designed aren't they?
Posted by: Daniel Smith on Jan. 04 2008,23:13

Quote (JAM @ Jan. 04 2008,00:03)

We've established that we agree that the "design" of translational initiation is profoundly unintelligent.
...
Dan, you're a weasel. I've shown that by YOUR standard, the designer made an obviously unintelligent choice.
---------------------QUOTE-------------------


See, this is why I hate debating with you.  You ask me loaded questions, then twist my answers around to make out like I meant something you know I didn't really mean.  It's a completely dishonest tactic and has nothing to do with the actual debate.  It's all about "winning" (or seeming to) for you isn't it?
       

---------------------QUOTE-------------------
Selection does that,
---------------------QUOTE-------------------

Almighty Selection.  Yes I know, It (capitalized) designed the genetic code.  It's amazing how well this unintelligent, uncaring, unguided, directionless "force" was able to create such complex interleaved systems.  THAT you'll believe, but mention God and it's "liar, liar pants on fire!".
     

---------------------QUOTE-------------------

but how would you possibly know, since you're lying about your fascination with life? However, we weren't discussing whether it "works pretty well," we were discussing whether intelligent design choices were made, and by the criterion YOU stipulated, they weren't. This makes perfect sense as a product of evolution, though.
Since it seems to work pretty well to you, maybe you can comment on the number of different N-terminal modifications that proteins are known to undergo as a result of this unintelligent design.
---------------------QUOTE-------------------

Not again you don't.  Save your "I know more than you do" attitude and your loaded questions for someone else.      

---------------------QUOTE-------------------

       

---------------------QUOTE-------------------
Did you ever stop to ponder the fact that there even is such a thing as a code for life?
---------------------QUOTE-------------------


There isn't a "code for life." It's a figure of speech. Do you realize that there's nothing symbolic about it? It only looks like a code when we organize it into a table for you.
---------------------QUOTE-------------------

Since when does a code have to be symbolic?  Can't I speak to you in a coded language?  All that is necessary is that both of us agree what the code is.  It's the same with the genetic code.    

---------------------QUOTE-------------------

       

---------------------QUOTE-------------------
It seems profoundly arrogant for a man to call such a thing "stupid".
---------------------QUOTE-------------------


You agreed that the design choice made on the back end was more intelligent than the one made for the front end. Therefore, the design itself could not have come from a perfect being.
---------------------QUOTE-------------------

Why not?  Did I ever say the design itself was perfect?  How did you get that from what I said?  That's a complete strawman.      

---------------------QUOTE-------------------

       

---------------------QUOTE-------------------
I guess you'll have to take that up with God when you meet him face to face.
---------------------QUOTE-------------------


Don't you mean Him?
---------------------QUOTE-------------------

Do you?
       

---------------------QUOTE-------------------
   

---------------------QUOTE-------------------
Now, how about all that fossil evidence you promised me?
---------------------QUOTE-------------------


So you can tell lies about that, too?

       

---------------------QUOTE-------------------
Korn, Dieter (2003):
Typostrophism in Palaeozoic Ammonoids?.
Palaeontologische Zeitschrift, Band 77, Heft 2 . p. 445-470, 20 fig.

Die antidarwinistische ,Typostrophentheorie" von O.H. Schindewolf wird mit den Ammonoiden-Beipielen getestet, auf welchen sie begründet worden ist. Es kann gezeigt werden dass keines der drei theoretischen Elemente der Theorie (Saltationismus, Internalismus und Zyklismus) durch empirische Befunde gestützt werden kann. Vermeintliche Saltationen (,Typogenese") werden durch das Fehlen von Zwischenformen vorgetäuscht. Internalistische und orthogenetische Entwicklung (,Typostase") kann nur postuliert werden, wenn mögliche Funktionen abgelehnt werden. Vorprogrammiertes Aussterben von ,degenerierten" Entwicklungslinien (,Typolyse") kann ausgeschlossen werden, wenn Ammonoideen-Morphologien frei von anthropozentrischen Ansichten betrachtet werden. Auf Grund der Studie von paläozoischen Ammonoideen gibt es keinen Grund, die ,Typostrophenlehre" oder einige der sie aufbauenden Elemente, wie das ,Typus-Konzept" und ,Proterogenese", dem darwinistischen Evolutionsmodell vorzuziehen.

The anti-Darwinian ,Typostrophe Theory" of O.H. Schindewolf can be put to the test by revisiting the ammonoid examples on which this macroevolutionary model was founded. It is shown that none of the three theoretical elements saltationism, internalism, and cyclism can be supported by empirical data obtained from ammonoid research. Putative saltations (,Typogenesis") were feigned because of the lack of knowledge of intermediate forms. Internalistic and orthogenetic development (,Typostasis") can only be favoured by neglecting possible functions of morphological characters. Preprogrammed extinction of ,degenerated" clades (,Typolysis") is unlikely when ruling out anthropocentric views regarding ammonoid morphology. In terms of evolution of Palaeozoic ammonoids, there is no basis for the preference of the ,Typostrophe Theory" or some of its composing elements, including the ,Type Concept" and ,Proterogenesis", over the Darwinian evolutionary model and the Modern Synthesis.
---------------------QUOTE-------------------


---------------------QUOTE-------------------


Someone once told me that opinions do not equal evidence.  This is pure opinion.  I asked for fossil evidence and an explanation of exactly how it falsifies Schindewolf's theory.  You provided neither.
Posted by: Daniel Smith on Jan. 04 2008,23:15

Quote (JAM @ Jan. 04 2008,12:14)
Keeping to that is what makes science so much more honest than religion.
---------------------QUOTE-------------------


You must be profoundly religious then.
Posted by: oldmanintheskydidntdoit on Jan. 05 2008,05:28

Quote (Daniel Smith @ Jan. 04 2008,23:13)
Since when does a code have to be symbolic?  Can't I speak to you in a coded language?  All that is necessary is that both of us agree what the code is.  It's the same with the genetic code.
---------------------QUOTE-------------------


Then if it's "the same" with the genetic code who is the "both of us".

If I speak to you in a "coded language" then the "both of us" is you and me.

If genetic code speaks in a "coded language" then who are the "both of us" then?
Posted by: oldmanintheskydidntdoit on Jan. 05 2008,05:31

Quote (Daniel Smith @ Jan. 04 2008,23:15)
Quote (JAM @ Jan. 04 2008,12:14)
Keeping to that is what makes science so much more honest than religion.
---------------------QUOTE-------------------


You must be profoundly religious then.
---------------------QUOTE-------------------


Ah, accusations of dishonesty.

Daniel. The thread title is "Evolution of the Horse; a problem for Darwinism".

I think from what you said above


---------------------QUOTE-------------------
First, Schindewolf did not base his theory on horse evolution - he cites horse evolution as clear evidence of gradual, continuous evolution.
---------------------QUOTE-------------------



I think that you are giving up on that point right? No *god* required for the horsey? Right?
Posted by: oldmanintheskydidntdoit on Jan. 05 2008,06:00

Quote (Daniel Smith @ Jan. 04 2008,22:52)
Quote (IanBrown_101 @ Jan. 03 2008,18:47)
 
Quote (Daniel Smith @ Jan. 03 2008,23:56)
It seems to work pretty well to me.
Did you ever stop to ponder the fact that there even is such a thing as a code for life?  It seems profoundly arrogant for a man to call such a thing "stupid".
---------------------QUOTE-------------------


Jesus H Christ man, what is your problem?

Just because something just about works doesn't mean it isn't stupid.

Iron lungs are pretty damn stupid, and boy are they oddly designed, but hell, they still work.
---------------------QUOTE-------------------


And they are still designed aren't they?
---------------------QUOTE-------------------


Yes, they are designed, yes they are stupid solutions to problems that we've not managed to find better solutions for.

So are you saying your designer is stupid? Your designer makes stupid things? Your designer makes stupid mistakes?
Your designer does things that are so stupid a child can point out the mistakes.

Yet you think that terrible design is a indicator of some supreme intelligence behind it all.

Daniel, what's HIV for?
Posted by: Mark Iosim on Jan. 05 2008,07:37

[QUOTE]Selection does that
Posted by: Mark Iosim on Jan. 05 2008,07:55

Opps! The previous reply was due to “fat fingers” error.

JAM
You mentioned before that "Selection does that...".
You probably realize, that Selection cannot create, but only chouse from what was already created.
So I am going back to the question I asked before. If a chance (mutation) is a creator, do you think that it is a scientist’s obligation to demonstrate that the probability of this chance is in agreement with statistical analysis? Do you know anything about this issue?

I am not the ID supporter, so you don’t have not politicized your answer.
Posted by: Mark Iosim on Jan. 05 2008,08:01

Sorry, error again.

I mean "... you don’t have to politicize your answer".
Posted by: Daniel Smith on Jan. 05 2008,13:11

Quote (JAM @ Jan. 04 2008,12:14)
Whether he expected them to be confirmed is best measured by the extent of his efforts to confirm AND FALSIFY them.
---------------------QUOTE-------------------


How hard have you tried to falsify "Selection" as a mechanism?
You seem perfectly willing to believe "Selection does that", but how do you know that?  Explain how Selection produced protein synthesis, or chromosomes, or sexual reproduction, or cell division, or... any fundamental biological system.
Give me a plausible pathway from the state that existed before to the state that existed after.  Remember, Selection cannot select for potential so you must be able to show an immediate advantage for every intermediate step in the creation of these systems.
Do you have a viable, plausible pathway for even one?
Posted by: Daniel Smith on Jan. 05 2008,13:25

Quote (oldmanintheskydidntdoit @ Jan. 05 2008,06:00)
     
Quote (Daniel Smith @ Jan. 04 2008,22:52)
     
Quote (IanBrown_101 @ Jan. 03 2008,18:47)
         
Quote (Daniel Smith @ Jan. 03 2008,23:56)
It seems to work pretty well to me.
Did you ever stop to ponder the fact that there even is such a thing as a code for life?  It seems profoundly arrogant for a man to call such a thing "stupid".
---------------------QUOTE-------------------


Jesus H Christ man, what is your problem?

Just because something just about works doesn't mean it isn't stupid.

Iron lungs are pretty damn stupid, and boy are they oddly designed, but hell, they still work.
---------------------QUOTE-------------------


And they are still designed aren't they?
---------------------QUOTE-------------------


Yes, they are designed, yes they are stupid solutions to problems that we've not managed to find better solutions for.

So are you saying your designer is stupid? Your designer makes stupid things? Your designer makes stupid mistakes?
Your designer does things that are so stupid a child can point out the mistakes.

Yet you think that terrible design is a indicator of some supreme intelligence behind it all.

Daniel, what's HIV for?
---------------------QUOTE-------------------


First, you are going to have to convince me that any of life's systems qualify as "stupid".
Just because JAM says they're stupid does not make them so.  Does he dictate your opinions on the matter?
Besides "stupid" is a subjective term in this argument.  What's "stupid" to you may be "brilliance" to another.
I've always said, if you think it's stupid, improve upon it--design a better working system, (like we did with the iron lung).
Most arguments seem to fall by the wayside at that point.
At least we both agree now that the property "stupid" does not negate the property "designed".  There are lots of (subjectively) "stupid designs".  They all remain designs however.
Now, why don't you tell me what's really "stupid" about the start and stop codons in life's code?
Oh and HIV is a disease.  God introduced disease as a consequence of the fall.  It's all there in black and white if you want to read about it.  A designer can make things however he wishes.  God chose to allow humans (and everything else) to die.  It's a fact of life.  Are you only willing to accept a God that makes a perfect world for you to live in?
Posted by: Assassinator on Jan. 05 2008,13:54

Daniel, let me ask you a simple question (and thanks for that Kristine): What do you see in life what makes you say it's designed?



---------------------QUOTE-------------------
God introduced disease as a consequence of the fall.
---------------------QUOTE-------------------


You DO know that's completly awfull? It was there first mistake, instead of giving Adam and Eve another chance and talk about what they did (God was so forgiving right?) He gave them the deathpenalty (made them mortal) and forced them into incest (how the hell do you make a population of 2 billion from 2 in 6000 years?) and forced the whole of humanity to suffer horrible from ONE dammed mistake. Sounds good doesn't it? Really sounds like someone I would want to worship...

---------------------QUOTE-------------------
It's all there in black and white if you want to read about it.
---------------------QUOTE-------------------


O really? And who says the writers wanted those texts to be interpreted so literally as you do it? Why are YOU right and for example Hindus not? You have any idea how many creation stories are out there completly different from yours? What's so special and good about yours that makes it right?
Posted by: oldmanintheskydidntdoit on Jan. 05 2008,15:02

Quote (Daniel Smith @ Jan. 05 2008,13:25)
 
Quote (oldmanintheskydidntdoit @ Jan. 05 2008,06:00)
       
Quote (Daniel Smith @ Jan. 04 2008,22:52)
         
Quote (IanBrown_101 @ Jan. 03 2008,18:47)
           
Quote (Daniel Smith @ Jan. 03 2008,23:56)
It seems to work pretty well to me.
Did you ever stop to ponder the fact that there even is such a thing as a code for life?  It seems profoundly arrogant for a man to call such a thing "stupid".
---------------------QUOTE-------------------


Jesus H Christ man, what is your problem?

Just because something just about works doesn't mean it isn't stupid.

Iron lungs are pretty damn stupid, and boy are they oddly designed, but hell, they still work.
---------------------QUOTE-------------------


And they are still designed aren't they?
---------------------QUOTE-------------------


Yes, they are designed, yes they are stupid solutions to problems that we've not managed to find better solutions for.

So are you saying your designer is stupid? Your designer makes stupid things? Your designer makes stupid mistakes?
Your designer does things that are so stupid a child can point out the mistakes.

Yet you think that terrible design is a indicator of some supreme intelligence behind it all.

Daniel, what's HIV for?
---------------------QUOTE-------------------


First, you are going to have to convince me that any of life's systems qualify as "stupid".
Just because JAM says they're stupid does not make them so.  Does he dictate your opinions on the matter?
Besides "stupid" is a subjective term in this argument.  What's "stupid" to you may be "brilliance" to another.
I've always said, if you think it's stupid, improve upon it--design a better working system, (like we did with the iron lung).
Most arguments seem to fall by the wayside at that point.
At least we both agree now that the property "stupid" does not negate the property "designed".  There are lots of (subjectively) "stupid designs".  They all remain designs however.
Now, why don't you tell me what's really "stupid" about the start and stop codons in life's code?
Oh and HIV is a disease.  God introduced disease as a consequence of the fall.  It's all there in black and white if you want to read about it.  A designer can make things however he wishes.  God chose to allow humans (and everything else) to die.  It's a fact of life.  Are you only willing to accept a God that makes a perfect world for you to live in?
---------------------QUOTE-------------------


 

---------------------QUOTE-------------------
First, you are going to have to convince me that any of life's systems qualify as "stupid".
---------------------QUOTE-------------------


I asked you what was not stupid about a giraffe having a nerve that went up and down it's neck needlessly. That time you < said >
 

---------------------QUOTE-------------------
You have to remember that creation took place a long time ago, and lots of evolution and variation has happened since then.
---------------------QUOTE-------------------


Now, it seems to me that get out clause can be used at any time. Therefore it will not be possible to convince you that any of life's systems are stupid. I'll try nonetheless.
 

---------------------QUOTE-------------------
Just because JAM says they're stupid does not make them so.  Does he dictate your opinions on the matter?
---------------------QUOTE-------------------


JAM is arguing a specific point with specific data. No, he does not dictate my options on the matter. The self evident that'll do of evolution is apparent in many everyday biological events.
 

---------------------QUOTE-------------------
Besides "stupid" is a subjective term in this argument.
---------------------QUOTE-------------------


And what is objective is the list of benefits that thinking of biological systems as deliberately designed brings. The tally so far equals zero.
 

---------------------QUOTE-------------------
What's "stupid" to you may be "brilliance" to another.
---------------------QUOTE-------------------


Can you give us a couple of examples then?
 

---------------------QUOTE-------------------
I've always said, if you think it's stupid, improve upon it--design a better working system, (like we did with the iron lung).
---------------------QUOTE-------------------


OK, how about separate holes to eat and breath through?
 

---------------------QUOTE-------------------
Most arguments seem to fall by the wayside at that point.
---------------------QUOTE-------------------


Hum. We'll see. It depends on if by design a better working system you want the DNA sequence to go along with it. An unreasonable amount of detail.
 

---------------------QUOTE-------------------
At least we both agree now that the property "stupid" does not negate the property "designed".  
---------------------QUOTE-------------------


Even if you remain convinced there are no stupid designs in nature?
 

---------------------QUOTE-------------------
There are lots of (subjectively) "stupid designs".  They all remain designs however.
---------------------QUOTE-------------------


Yes, designed by evolution. I'm glad we can agree. They evolved. Their design evolved.
 

---------------------QUOTE-------------------
Now, why don't you tell me what's really "stupid" about the start and stop codons in life's code?
---------------------QUOTE-------------------


I have a better idea. Why don't you tell JAM why it makes more sense for them to be the way they are then any other possible way?
 

---------------------QUOTE-------------------
Oh and HIV is a disease.  God introduced disease as a consequence of the fall.
---------------------QUOTE-------------------


Prove it. Without the bible.
 

---------------------QUOTE-------------------
It's all there in black and white if you want to read about it.
---------------------QUOTE-------------------


Read it. Not there. Nothing about HIV at all in fact.
 

---------------------QUOTE-------------------
A designer can make things however he wishes.
---------------------QUOTE-------------------


How do you know?
 

---------------------QUOTE-------------------
God chose to allow humans (and everything else) to die.
---------------------QUOTE-------------------


Prove it. Without the bible. And I asked you what HIV was for not where HIV came from or anything about god or allowing things to die or not. What is HIV for?
 

---------------------QUOTE-------------------
.  It's a fact of life.  Are you only willing to accept a God that makes a perfect world for you to live in?
---------------------QUOTE-------------------


It's a fact of life? As you said it, so must it be.
Define a perfect world and then I'll let you know.
Posted by: VMartin on Jan. 05 2008,17:12

I've never read anything from Otto Schindewolf but as far as I can judge he pointed something very paradoxical. In one side there was darwinian gradualism and on the other side there was a biostratigraphy (which focuses on correlating and assigning relative ages of rock strata by using the fossil assemblages). The basic rule of the biostratigraphy was in direct contradction with gradual evolution. Biostratographic always knew there were some species in given rock strata that didn't change continually - otherwise he couldn't have work.  
Because biostratigraphy do not often see in fossil records (there are sometimes exceptions) what gradualists insisted they should have see there, some   tensions arose - with outcomes like "punctuated equilibria" etc..
Posted by: Daniel Smith on Jan. 06 2008,13:36

Quote (Assassinator @ Jan. 05 2008,13:54)
Daniel, let me ask you a simple question (and thanks for that Kristine): What do you see in life what makes you say it's designed?
---------------------QUOTE-------------------


I don't know where I got it or who wrote it, but I think this quote fairly sums up my reason for viewing life as designed:  

---------------------QUOTE-------------------
Biology is full of problems that are solved, including the problems of
how to harness the sun's energy and how to obtain nutrients.  The
solutions to numerous problems are present throughout biology, and the
solutions involve extraordinarily-complicated and interdependent
organs, structures, and biochemical processes.  The incredibly-complex
solutions strongly exhibit the appearance of having been established/
put together by a problem-solving being(s).

---------------------QUOTE-------------------


Posted by: oldmanintheskydidntdoit on Jan. 06 2008,13:47

Quote (Daniel Smith @ Jan. 06 2008,13:36)
exhibit the appearance of
---------------------QUOTE-------------------


Play much cards Daniel?
Posted by: Daniel Smith on Jan. 06 2008,13:49

Quote (oldmanintheskydidntdoit @ Jan. 05 2008,05:28)
 
Quote (Daniel Smith @ Jan. 04 2008,23:13)
Since when does a code have to be symbolic?  Can't I speak to you in a coded language?  All that is necessary is that both of us agree what the code is.  It's the same with the genetic code.
---------------------QUOTE-------------------


Then if it's "the same" with the genetic code who is the "both of us".

If I speak to you in a "coded language" then the "both of us" is you and me.

If genetic code speaks in a "coded language" then who are the "both of us" then?
---------------------QUOTE-------------------


There are many actually - else how does the RNA polymerase "know" to separate DNA strands and produce mRNA from it?

How does mRNA "know" what is an exon and what is an intron during the splicing process?

How does the ribosome "know" to bind to the mRNA at the start codon?

How does the tRNA "know" which amino acids to link to during the translation process?

How does the release factor "know" to bind to the stop codon - thus terminating translation and releasing the polypeptide?

And finally, what's "stupid" about any of the above?
Posted by: Daniel Smith on Jan. 06 2008,14:21

Quote (VMartin @ Jan. 05 2008,17:12)
I've never read anything from Otto Schindewolf but as far as I can judge he pointed something very paradoxical. In one side there was darwinian gradualism and on the other side there was a biostratigraphy (which focuses on correlating and assigning relative ages of rock strata by using the fossil assemblages). The basic rule of the biostratigraphy was in direct contradction with gradual evolution. Biostratographic always knew there were some species in given rock strata that didn't change continually - otherwise he couldn't have work.  
Because biostratigraphy do not often see in fossil records (there are sometimes exceptions) what gradualists insisted they should have see there, some   tensions arose - with outcomes like "punctuated equilibria" etc..
---------------------QUOTE-------------------


That's correct Martin.
Schindewolf pointed out "striking contrasts" between biostratigraphic ages.  But it wasn't the species that did not change which formed the boundaries - it was the sudden appearances and rapid evolution of new forms that delineated the boundaries between ages.  This evolution would then slow down and usually (but not always) become the gradual evolution Darwin speculated about, (although Schindewolf attributed it to constrained, internal factors), thus indicating the middle of the age.  This gradual evolution would usually follow a pattern that trended towards overspecialization and mass extinctions - thus delineating the end of that age.  Then the process would repeat - either with new forms bursting upon the scene, or with one lineage from the previous age, that had not overspecialized, then becoming the "root" species for another explosion of forms.

Of course this (as I've presented it), is an oversimplified view of this since there were numerous fossil types upon which these ages were marked.  I'm sure this stuff is all common knowledge amongst paleontologists and geologists.
Posted by: oldmanintheskydidntdoit on Jan. 06 2008,14:44

Quote (Daniel Smith @ Jan. 06 2008,13:49)

And finally, what's "stupid" about any of the above?
---------------------QUOTE-------------------


Well, Daniel, according to you
 

---------------------QUOTE-------------------
All that is necessary is that both of us agree what the code is. It's the same with the genetic code.
---------------------QUOTE-------------------


so
 

---------------------QUOTE-------------------
how does the RNA polymerase "know" to separate DNA strands and produce mRNA from it?
---------------------QUOTE-------------------


They agree what the code is
 

---------------------QUOTE-------------------
How does mRNA "know" what is an exon and what is an intron during the splicing process?

---------------------QUOTE-------------------


They agree what the code is
 

---------------------QUOTE-------------------
How does the ribosome "know" to bind to the mRNA at the start codon?
---------------------QUOTE-------------------


They agree what the code is
 

---------------------QUOTE-------------------
How does the tRNA "know" which amino acids to link to during the translation process?
---------------------QUOTE-------------------


They agree what the code is
 

---------------------QUOTE-------------------
How does the release factor "know" to bind to the stop codon - thus terminating translation and releasing the polypeptide?
---------------------QUOTE-------------------


They agree what the code is
 

---------------------QUOTE-------------------
And finally, what's "stupid" about any of the above?
---------------------QUOTE-------------------


All of it.
Posted by: Assassinator on Jan. 06 2008,14:54

Quote (Daniel Smith @ Jan. 06 2008,13:36)
Quote (Assassinator @ Jan. 05 2008,13:54)
Daniel, let me ask you a simple question (and thanks for that Kristine): What do you see in life what makes you say it's designed?
---------------------QUOTE-------------------


I don't know where I got it or who wrote it, but I think this quote fairly sums up my reason for viewing life as designed:    

---------------------QUOTE-------------------
Biology is full of problems that are solved, including the problems of
how to harness the sun's energy and how to obtain nutrients.  The
solutions to numerous problems are present throughout biology, and the
solutions involve extraordinarily-complicated and interdependent
organs, structures, and biochemical processes.  The incredibly-complex
solutions strongly exhibit the appearance of having been established/
put together by a problem-solving being(s).

---------------------QUOTE-------------------


---------------------QUOTE-------------------


E.a, because it's so complex from your point of view, it must be designed. I can understand that life looks designed, but you have to make a difference between your own point of view and opinion, and reality. The fact that it looks designed in your eyes, says 0.00 about reality. You do understand that, right?
Posted by: JAM on Jan. 06 2008,15:59

Quote (Daniel Smith @ Jan. 04 2008,23:13)
   
Quote (JAM @ Jan. 04 2008,00:03)

We've established that we agree that the "design" of translational initiation is profoundly unintelligent.
...
Dan, you're a weasel. I've shown that by YOUR standard, the designer made an obviously unintelligent choice.
---------------------QUOTE-------------------


See, this is why I hate debating with you.
---------------------QUOTE-------------------


No, you hate debating with me because your predictions are always dead wrong, and you try to deny that with falsehoods.
   

---------------------QUOTE-------------------
You ask me loaded questions, then twist my answers around to make out like I meant something you know I didn't really mean.
---------------------QUOTE-------------------


My questions were not loaded, and I did not twist your answers. You explicitly agreed that separating stop from aa "signals" was an intelligent choice. Therefore, it is inescapable that we also agree that not separating start from aa signals is an unintelligent choice, unless you can explain why there should be different criteria for starting and stopping translation. I can easily explain this huge difference in evolutionary terms.
   

---------------------QUOTE-------------------
It's a completely dishonest tactic and has nothing to do with the actual debate.
---------------------QUOTE-------------------

 There's nothing dishonest at all about what I did. I was merely preventing you from being dishonest and moving the goalposts, which we both know you would have done.
   

---------------------QUOTE-------------------
It's all about "winning" (or seeming to) for you isn't it?
---------------------QUOTE-------------------


No, it's about honesty and your lack of it. I am perfectly willing to admit when I don't understand something.

BTW, the humble path (the one you didn't take) would have been to question your own ability to judge the intelligence of the "design" of a biological mechanism, but I knew that your ego wouldn't let you do that.


           

---------------------QUOTE-------------------
   

---------------------QUOTE-------------------
Selection does that,
---------------------QUOTE-------------------

Almighty Selection.  Yes I know, It (capitalized) designed the genetic code.
---------------------QUOTE-------------------


Not by itself. The explanation for the huge difference between the "design" of starting and that of stopping translation has a lot to do with variation, too.
   

---------------------QUOTE-------------------
It's amazing how well this unintelligent, uncaring, unguided, directionless "force" was able to create such complex interleaved systems.
---------------------QUOTE-------------------


Let's look at the interleaving, shall we? The evidence eliminating design is very prominent there.
   

---------------------QUOTE-------------------
THAT you'll believe, but mention God and it's "liar, liar pants on fire!".
---------------------QUOTE-------------------


Quote an example of me doing that. Your lies have been about the evidence and your feigned interest in it.
           

---------------------QUOTE-------------------
   

---------------------QUOTE-------------------

but how would you possibly know, since you're lying about your fascination with life? However, we weren't discussing whether it "works pretty well," we were discussing whether intelligent design choices were made, and by the criterion YOU stipulated, they weren't. This makes perfect sense as a product of evolution, though.
Since it seems to work pretty well to you, maybe you can comment on the number of different N-terminal modifications that proteins are known to undergo as a result of this unintelligent design.
---------------------QUOTE-------------------

Not again you don't.  Save your "I know more than you do" attitude and your loaded questions for someone else.
---------------------QUOTE-------------------


See, you aren't interested in the NATURE of biological complexity at all. The simple fact is that I know much more about this than you do, because it's my life's work. You're trying to project your massive arrogance onto me, and THAT'S dishonest!
           

---------------------QUOTE-------------------
 

---------------------QUOTE-------------------
 

---------------------QUOTE-------------------
Did you ever stop to ponder the fact that there even is such a thing as a code for life?
---------------------QUOTE-------------------


There isn't a "code for life." It's a figure of speech. Do you realize that there's nothing symbolic about it? It only looks like a code when we organize it into a table for you.
---------------------QUOTE-------------------

Since when does a code have to be symbolic?
---------------------QUOTE-------------------


Every time.
   

---------------------QUOTE-------------------
Can't I speak to you in a coded language?  All that is necessary is that both of us agree what the code is.  It's the same with the genetic code.
---------------------QUOTE-------------------


If we agree what the code is, then it is symbolic. It's nothing like the "genetic code."

         

---------------------QUOTE-------------------


---------------------QUOTE-------------------
   

---------------------QUOTE-------------------
It seems profoundly arrogant for a man to call such a thing "stupid".
---------------------QUOTE-------------------


You agreed that the design choice made on the back end was more intelligent than the one made for the front end. Therefore, the design itself could not have come from a perfect being.
---------------------QUOTE-------------------

Why not?  Did I ever say the design itself was perfect?  How did you get that from what I said?  That's a complete strawman.
---------------------QUOTE-------------------


That's pretty funny, since I wrote that the design could not have come from a perfect being and you misrepresented that as a claim that the design was perfect.[/quote]
   

---------------------QUOTE-------------------
Someone once told me that opinions do not equal evidence.  This is pure opinion.
---------------------QUOTE-------------------


How is pointing out the existence of intermediates "pure opinion," Dan?
Posted by: JAM on Jan. 06 2008,16:02

Quote (Mark Iosim @ Jan. 05 2008,07:55)
Opps! The previous reply was due to “fat fingers” error.

JAM
You mentioned before that "Selection does that...".
You probably realize, that Selection cannot create, but only chouse from what was already created.
---------------------QUOTE-------------------


Yes, I do.


---------------------QUOTE-------------------
So I am going back to the question I asked before. If a chance (mutation) is a creator, do you think that it is a scientist’s obligation to demonstrate that the probability of this chance is in agreement with statistical analysis? Do you know anything about this issue?
---------------------QUOTE-------------------


A lot, given my training in genetics. It's been demonstrated over and over. Have you considered looking at the data?
Posted by: JAM on Jan. 06 2008,16:12

Quote (Daniel Smith @ Jan. 05 2008,13:11)
   
Quote (JAM @ Jan. 04 2008,12:14)
Whether he expected them to be confirmed is best measured by the extent of his efforts to confirm AND FALSIFY them.
---------------------QUOTE-------------------


How hard have you tried to falsify "Selection" as a mechanism?
---------------------QUOTE-------------------


In what context? Are you so blinded by your arrogance that you think that I must be an evolutionary biologist?
 

---------------------QUOTE-------------------
You seem perfectly willing to believe "Selection does that", but how do you know that?
---------------------QUOTE-------------------


Because it's been shown to do similar things in real time.
 

---------------------QUOTE-------------------
Explain how Selection produced protein synthesis, or chromosomes, or sexual reproduction, or cell division, or... any fundamental biological system.
---------------------QUOTE-------------------


Let's go with the immune system. How long does it take to produce a new, unique, incredibly specific protein-protein interaction using nothing but genetic variation (random wrt fitness) and selection?
Note that this is a response to your arrogant, ignorant skepticism about the power of selection.
 

---------------------QUOTE-------------------
Give me a plausible pathway from the state that existed before to the state that existed after.
---------------------QUOTE-------------------


Why? You'll just ignore or misrepresent it, as you do all of the other evidence. It's better to be Socratic and present it in a historical context, so there's a slim chance that you might be able to see how real scientists work. It also shows that you're anything but fascinated by biology.

Why does your immune system react so massively to an allogeneic stimulus?

Does your immune system initially recognize any foreign antigen as an independent entity? If not, how does it initially recognize foreign antigens?

Making an honest effort to answer these questions will make the evolutionary origin of your immune system pretty damn obvious. If I just tell you, you'll blow it off.

Remember, I'm claiming that your claim to be fascinated by the complexity of biology was a lie, so you're boxed in. ;-)


---------------------QUOTE-------------------
Remember, Selection cannot select for potential so you must be able to show an immediate advantage for every intermediate step in the creation of these systems.
---------------------QUOTE-------------------


We don't know what every intermediate step was (nor do you), so your creationist demand is both preposterous and dishonest. We can, however, show how the main intermediates that had to have existed were selected for.


---------------------QUOTE-------------------
Do you have a viable, plausible pathway for even one?
---------------------QUOTE-------------------


Yes. Let's start with the acquired immune system. So do you have a viable, plausible pathway for design of the immune system or anything else?

Do you realize that you're missing the entire mechanism of science here? The way it really works is that if we hypothesize that mammalian system Z evolved from protochordate system X via intermediate Y, we test the hypothesis by making predictions about what mechanisms will exist in other organisms that branched off at critical times.

That's powerful evidence, which is why you completely ignore it in favor of ignorant creationist demands.
Posted by: Mark Iosim on Jan. 06 2008,22:22



---------------------QUOTE-------------------
Mark Iosim:
So I am going back to the question I asked before. If a chance (mutation) is a creator, do you think that it is a scientist’s obligation to demonstrate that the probability of this chance is in agreement with statistical analysis? Do you know anything about this issue?

JAM:
A lot, given my training in genetics. It's been demonstrated over and over. Have you considered looking at the data?
---------------------QUOTE-------------------



JAM,

Looks like your answer is: “There are plenty of evidences go and find for your self.” I am looking, but didn’t find them yet? Looks like you have plenty of these evidences, so can you refer me to any sort of statistical analysis that in your opinion demonstrates that random mutations could be responsible (does'n contradict probability) for adaptive changes in biological systems?
Posted by: Mark Iosim on Jan. 06 2008,22:25

Mark Iosim:


---------------------QUOTE-------------------
So I am going back to the question I asked before. If a chance (mutation) is a creator, do you think that it is a scientist’s obligation to demonstrate that the probability of this chance is in agreement with statistical analysis? Do you know anything about this issue?

JAM:
A lot, given my training in genetics. It's been demonstrated over and over. Have you considered looking at the data?
---------------------QUOTE-------------------



Looks like your answer is: “There are plenty of evidences go and find for your self”
I am looking for the relevant studies, but didn’t find them yet? Apparently, you have plenty of evidences. Can you refer me to any sort of statistical analysis that in your opinion demonstrates that random mutations could be responsible for adaptive changes in biological systems?
Posted by: Mark Iosim on Jan. 06 2008,22:29

Any body knows if the post can be edited after being submitted. I just accidentally post the same respond twice.
Posted by: mitschlag on Jan. 07 2008,07:35

The Jerry Falwell explanation for AIDS:
   
Quote (Daniel Smith @ Jan. 05 2008,13:25)
Oh and HIV is a disease.  God introduced disease as a consequence of the fall.  It's all there in black and white if you want to read about it.  A designer can make things however he wishes.  God chose to allow humans (and everything else) to die.  It's a fact of life.  Are you only willing to accept a God that makes a perfect world for you to live in?
---------------------QUOTE-------------------

Considering that HIV-induced AIDS originated in the 20th century, it's evident that Jesus the angry tinkerer wasn't satisfied with the amount of misery he'd already inflicted upon humanity, so he deliberately designed and created that charming little enhancement to our suffering.  Makes perfect sense.
Posted by: oldmanintheskydidntdoit on Jan. 07 2008,07:50

Quote (Mark Iosim @ Jan. 06 2008,22:25)
Mark Iosim:
 

---------------------QUOTE-------------------
So I am going back to the question I asked before. If a chance (mutation) is a creator, do you think that it is a scientist’s obligation to demonstrate that the probability of this chance is in agreement with statistical analysis? Do you know anything about this issue?

JAM:
A lot, given my training in genetics. It's been demonstrated over and over. Have you considered looking at the data?
---------------------QUOTE-------------------



Looks like your answer is: “There are plenty of evidences go and find for your self”
I am looking for the relevant studies, but didn’t find them yet? Apparently, you have plenty of evidences. Can you refer me to any sort of statistical analysis that in your opinion demonstrates that random mutations could be responsible for adaptive changes in biological systems?
---------------------QUOTE-------------------


I know it's not what you are after but
< http://www.talkorigins.org/faqs/fitness/ >
is the first result for alot of your terms.
Posted by: Daniel Smith on Jan. 07 2008,10:54

Quote (JAM @ Jan. 06 2008,15:59)
BTW, the humble path (the one you didn't take) would have been to question your own ability to judge the intelligence of the "design" of a biological mechanism, but I knew that your ego wouldn't let you do that.
---------------------QUOTE-------------------


You mean like < this >?
Posted by: oldmanintheskydidntdoit on Jan. 07 2008,11:05

Quote (Daniel Smith @ Jan. 07 2008,10:54)
Quote (JAM @ Jan. 06 2008,15:59)
BTW, the humble path (the one you didn't take) would have been to question your own ability to judge the intelligence of the "design" of a biological mechanism, but I knew that your ego wouldn't let you do that.
---------------------QUOTE-------------------


You mean like < this >?
---------------------QUOTE-------------------


Yeah, but you kinda blow it when you say things like


---------------------QUOTE-------------------
First, you are going to have to convince me that any of life's systems qualify as "stupid".
---------------------QUOTE-------------------


y'know!

So you can judge the "design" of a biological mechanism after all, insofar as you simply *know* it's not stupid. So don't come all meek now Daniel.

And Daniel, what's HIV for? Not why does it exist, but for what purpose did god/jesus create it?
Posted by: Daniel Smith on Jan. 07 2008,17:55

Quote (oldmanintheskydidntdoit @ Jan. 07 2008,11:05)
       
Quote (Daniel Smith @ Jan. 07 2008,10:54)
         
Quote (JAM @ Jan. 06 2008,15:59)
BTW, the humble path (the one you didn't take) would have been to question your own ability to judge the intelligence of the "design" of a biological mechanism, but I knew that your ego wouldn't let you do that.
---------------------QUOTE-------------------


You mean like < this >?
---------------------QUOTE-------------------


Yeah, but you kinda blow it when you say things like
         

---------------------QUOTE-------------------
First, you are going to have to convince me that any of life's systems qualify as "stupid".
---------------------QUOTE-------------------


y'know!

So you can judge the "design" of a biological mechanism after all, insofar as you simply *know* it's not stupid. So don't come all meek now Daniel.
---------------------QUOTE-------------------


But you're the one calling it "stupid"!  Shouldn't it be up to you to provide the convincing evidence?

 

---------------------QUOTE-------------------
And Daniel, what's HIV for? Not why does it exist, but for what purpose did god/jesus create it?
---------------------QUOTE-------------------


I don't know.  I can't read God's mind.  I only know what he's spelled out in black and white.
Posted by: oldmanintheskydidntdoit on Jan. 07 2008,18:17

a) it's stupid to have the pipe you suck air down combined with the pipe you suck food down. Care to make a case for the elegance of that?
b) What do *you* think HIV is for then Daniel? Take a guess? Behe seems to think satan sent malaria. You think something similar?

One of the ways you can "detect design" is being able to determine the purpose of something. What it was designed for.
Posted by: Daniel Smith on Jan. 07 2008,18:24

Quote (Assassinator @ Jan. 05 2008,13:54)
Daniel, let me ask you a simple question (and thanks for that Kristine): What do you see in life what makes you say it's designed?

       

---------------------QUOTE-------------------
God introduced disease as a consequence of the fall.
---------------------QUOTE-------------------


You DO know that's completly awfull? It was there first mistake, instead of giving Adam and Eve another chance and talk about what they did (God was so forgiving right?) He gave them the deathpenalty (made them mortal) and forced them into incest (how the hell do you make a population of 2 billion from 2 in 6000 years?) and forced the whole of humanity to suffer horrible from ONE dammed mistake. Sounds good doesn't it? Really sounds like someone I would want to worship...
---------------------QUOTE-------------------


Do you know how long an eternity is? (Hint: it is actually not "long" at all - since time will not be reckoned there).
The crux of Christianity is that this world, and this life, is not the end but is just a "mist" in the light of eternity.  Therefore, whatever the pain and suffering mankind suffers in this life (including death) will be long forgotten in contrast to the eternal life God is willing to give us freely.
So all that you count as "awful", and "horrible", is only a blink.

I'm sure you'll characterize this as awful and escapist as well.  But that's Christianity.  Millions of people take great comfort in that knowledge.        

---------------------QUOTE-------------------
     

---------------------QUOTE-------------------
It's all there in black and white if you want to read about it.
---------------------QUOTE-------------------


O really? And who says the writers wanted those texts to be interpreted so literally as you do it?
---------------------QUOTE-------------------


You're right, many interpretations are possible.  But that does not change the fact of what the text says (in black and white).  Which is what I meant by that.      

---------------------QUOTE-------------------
Why are YOU right and for example Hindus not? You have any idea how many creation stories are out there completly different from yours? What's so special and good about yours that makes it right?
---------------------QUOTE-------------------


The main attraction for me is the man, Jesus.  His words struck a chord within me.  That's all I can say.  Maybe I am wrong (it won't be the first time), but I'll take my chances.
Posted by: oldmanintheskydidntdoit on Jan. 07 2008,18:27

Quote (Daniel Smith @ Jan. 07 2008,18:24)
The main attraction for me is the man, Jesus.  His words struck a chord within me.  That's all I can say.  Maybe I am wrong (it won't be the first time), but I'll take my chances.
---------------------QUOTE-------------------


Fine, witness away, great. Just don't claim life is "designed" or that it can be proved that life was created.
Posted by: Daniel Smith on Jan. 07 2008,18:30

Quote (Assassinator @ Jan. 06 2008,14:54)
 
Quote (Daniel Smith @ Jan. 06 2008,13:36)
   
Quote (Assassinator @ Jan. 05 2008,13:54)
Daniel, let me ask you a simple question (and thanks for that Kristine): What do you see in life what makes you say it's designed?
---------------------QUOTE-------------------


I don't know where I got it or who wrote it, but I think this quote fairly sums up my reason for viewing life as designed:        

---------------------QUOTE-------------------
Biology is full of problems that are solved, including the problems of
how to harness the sun's energy and how to obtain nutrients.  The
solutions to numerous problems are present throughout biology, and the
solutions involve extraordinarily-complicated and interdependent
organs, structures, and biochemical processes.  The incredibly-complex
solutions strongly exhibit the appearance of having been established/
put together by a problem-solving being(s).

---------------------QUOTE-------------------


---------------------QUOTE-------------------


E.a, because it's so complex from your point of view, it must be designed. I can understand that life looks designed, but you have to make a difference between your own point of view and opinion, and reality. The fact that it looks designed in your eyes, says 0.00 about reality. You do understand that, right?
---------------------QUOTE-------------------


Yes, of course I do.  That is why I've said numerous times that science will never find a plausible explanation for the origin of any of life's most basic biological systems.  This is a prediction that anyone can falsify.  So it's not just me, and it's not just opinion.
You understand that don't you?
Posted by: Daniel Smith on Jan. 07 2008,19:34

Quote (JAM @ Jan. 06 2008,16:12)
   
Quote (Daniel Smith @ Jan. 05 2008,13:11)
       
Quote (JAM @ Jan. 04 2008,12:14)
Whether he expected them to be confirmed is best measured by the extent of his efforts to confirm AND FALSIFY them.
---------------------QUOTE-------------------


How hard have you tried to falsify "Selection" as a mechanism?
---------------------QUOTE-------------------


In what context? Are you so blinded by your arrogance that you think that I must be an evolutionary biologist?
       

---------------------QUOTE-------------------
You seem perfectly willing to believe "Selection does that", but how do you know that?
---------------------QUOTE-------------------


Because it's been shown to do similar things in real time.
       

---------------------QUOTE-------------------
Explain how Selection produced protein synthesis, or chromosomes, or sexual reproduction, or cell division, or... any fundamental biological system.
---------------------QUOTE-------------------


Let's go with the immune system. How long does it take to produce a new, unique, incredibly specific protein-protein interaction using nothing but genetic variation (random wrt fitness) and selection?
Note that this is a response to your arrogant, ignorant skepticism about the power of selection.
       

---------------------QUOTE-------------------
Give me a plausible pathway from the state that existed before to the state that existed after.
---------------------QUOTE-------------------


Why? You'll just ignore or misrepresent it, as you do all of the other evidence. It's better to be Socratic and present it in a historical context, so there's a slim chance that you might be able to see how real scientists work. It also shows that you're anything but fascinated by biology.

Why does your immune system react so massively to an allogeneic stimulus?

Does your immune system initially recognize any foreign antigen as an independent entity? If not, how does it initially recognize foreign antigens?

Making an honest effort to answer these questions will make the evolutionary origin of your immune system pretty damn obvious. If I just tell you, you'll blow it off.

Remember, I'm claiming that your claim to be fascinated by the complexity of biology was a lie, so you're boxed in. ;-)
     

---------------------QUOTE-------------------
Remember, Selection cannot select for potential so you must be able to show an immediate advantage for every intermediate step in the creation of these systems.
---------------------QUOTE-------------------


We don't know what every intermediate step was (nor do you), so your creationist demand is both preposterous and dishonest. We can, however, show how the main intermediates that had to have existed were selected for.
   

---------------------QUOTE-------------------
Do you have a viable, plausible pathway for even one?
---------------------QUOTE-------------------


Yes. Let's start with the acquired immune system. So do you have a viable, plausible pathway for design of the immune system or anything else?

Do you realize that you're missing the entire mechanism of science here? The way it really works is that if we hypothesize that mammalian system Z evolved from protochordate system X via intermediate Y, we test the hypothesis by making predictions about what mechanisms will exist in other organisms that branched off at critical times.

That's powerful evidence, which is why you completely ignore it in favor of ignorant creationist demands.
---------------------QUOTE-------------------



No more questions.  Quit dancing around the issues and asking questions in the hope of trapping me with my own words.  If you have a position - just state it.  I'm not playing this game with you anymore.  If you believe you can show me the evolutionary origin of the immune system - step by step - from whatever existed before there were immune systems, then go for it.
Posted by: Daniel Smith on Jan. 07 2008,19:36

Quote (oldmanintheskydidntdoit @ Jan. 07 2008,18:17)
a) it's stupid to have the pipe you suck air down combined with the pipe you suck food down. Care to make a case for the elegance of that?
---------------------QUOTE-------------------


What has that to do with start/stop codons and the genetic code?  Remember, you said that was "all" stupid.
Posted by: Daniel Smith on Jan. 07 2008,19:40

Quote (oldmanintheskydidntdoit @ Jan. 07 2008,18:27)
 
Quote (Daniel Smith @ Jan. 07 2008,18:24)
The main attraction for me is the man, Jesus.  His words struck a chord within me.  That's all I can say.  Maybe I am wrong (it won't be the first time), but I'll take my chances.
---------------------QUOTE-------------------


Fine, witness away, great. Just don't claim life is "designed" or that it can be proved that life was created.
---------------------QUOTE-------------------


I never claimed it can be "proved".  As for claiming life was designed - why not?  You claim it wasn't.
Posted by: Ideaforager on Jan. 07 2008,19:45

Daniel,
I've been holding out way too long!


---------------------QUOTE-------------------
But that does not change the fact of what the text says (in black and white).
---------------------QUOTE-------------------


How do you distinguish the amount of honesty contained in two opposing texts?
Posted by: JAM on Jan. 07 2008,20:01

Quote (Daniel Smith @ Jan. 07 2008,18:30)
Yes, of course I do.  That is why I've said numerous times that science will never find a plausible explanation for the origin of any of life's most basic biological systems.  This is a prediction that anyone can falsify.
---------------------QUOTE-------------------


It's not science, Dan, because scientific predictions are about what will be observed, not one's interpretation of it, not one's explanation.

Scientifically, you're still a total fraud.


---------------------QUOTE-------------------
So it's not just me, and it's not just opinion.
---------------------QUOTE-------------------


You're lying, because you inserted the adjective "plausible." That makes it entirely subjective opinion.


---------------------QUOTE-------------------
You understand that don't you?
---------------------QUOTE-------------------


Yes, I understand that you are a deeply dishonest person.
Posted by: Ideaforager on Jan. 07 2008,20:45

Jam,
You said to Daniel,
 

---------------------QUOTE-------------------
Yes, I understand that you are a deeply dishonest person.
---------------------QUOTE-------------------


I disagree, he is a "deeply" honest person in that he was convinced emotionally by text/words/feelings alone and it is up to educated/enlightened folks like you to make that perfectly clear to him.
Posted by: JAM on Jan. 07 2008,23:52

Quote (Daniel Smith @ Jan. 07 2008,19:34)
Quote (JAM @ Jan. 06 2008,16:12)
   
Quote (Daniel Smith @ Jan. 05 2008,13:11)
         
Quote (JAM @ Jan. 04 2008,12:14)
Whether he expected them to be confirmed is best measured by the extent of his efforts to confirm AND FALSIFY them.
---------------------QUOTE-------------------


How hard have you tried to falsify "Selection" as a mechanism?
---------------------QUOTE-------------------


In what context? Are you so blinded by your arrogance that you think that I must be an evolutionary biologist?
       

---------------------QUOTE-------------------
You seem perfectly willing to believe "Selection does that", but how do you know that?
---------------------QUOTE-------------------


Because it's been shown to do similar things in real time.
       

---------------------QUOTE-------------------
Explain how Selection produced protein synthesis, or chromosomes, or sexual reproduction, or cell division, or... any fundamental biological system.
---------------------QUOTE-------------------


Let's go with the immune system. How long does it take to produce a new, unique, incredibly specific protein-protein interaction using nothing but genetic variation (random wrt fitness) and selection?
Note that this is a response to your arrogant, ignorant skepticism about the power of selection.
       

---------------------QUOTE-------------------
Give me a plausible pathway from the state that existed before to the state that existed after.
---------------------QUOTE-------------------


Why? You'll just ignore or misrepresent it, as you do all of the other evidence. It's better to be Socratic and present it in a historical context, so there's a slim chance that you might be able to see how real scientists work. It also shows that you're anything but fascinated by biology.

Why does your immune system react so massively to an allogeneic stimulus?

Does your immune system initially recognize any foreign antigen as an independent entity? If not, how does it initially recognize foreign antigens?

Making an honest effort to answer these questions will make the evolutionary origin of your immune system pretty damn obvious. If I just tell you, you'll blow it off.

Remember, I'm claiming that your claim to be fascinated by the complexity of biology was a lie, so you're boxed in. ;-)
     

---------------------QUOTE-------------------
Remember, Selection cannot select for potential so you must be able to show an immediate advantage for every intermediate step in the creation of these systems.
---------------------QUOTE-------------------


We don't know what every intermediate step was (nor do you), so your creationist demand is both preposterous and dishonest. We can, however, show how the main intermediates that had to have existed were selected for.
     

---------------------QUOTE-------------------
Do you have a viable, plausible pathway for even one?
---------------------QUOTE-------------------


Yes. Let's start with the acquired immune system. So do you have a viable, plausible pathway for design of the immune system or anything else?

Do you realize that you're missing the entire mechanism of science here? The way it really works is that if we hypothesize that mammalian system Z evolved from protochordate system X via intermediate Y, we test the hypothesis by making predictions about what mechanisms will exist in other organisms that branched off at critical times.

That's powerful evidence, which is why you completely ignore it in favor of ignorant creationist demands.
---------------------QUOTE-------------------



No more questions.  Quit dancing around the issues and asking questions in the hope of trapping me with my own words.  If you have a position - just state it.  I'm not playing this game with you anymore.  If you believe you can show me the evolutionary origin of the immune system - step by step - from whatever existed before there were immune systems, then go for it.
---------------------QUOTE-------------------


Dan,

Science isn't about showing an arrogant twit like Daniel Smith anything because he throws a hissy fit after his blatant lies about being fascinated by biological complexity are exposed.

Science is about making and testing predictions. It's not dancing and it's not trapping.

If you are fascinated by the complexity of biology, go for it yourself.

You won't, because you're afraid of what you might find. Better to make stupid demands.
Posted by: Erasmus, FCD on Jan. 08 2008,00:21

well as much as i have enjoyed this thread (Daniel you have received quite a spanking and also been an absolutely great sport about it) I am tempted to go concern trolling here.

JAM:  Daniel is a creationist.  pure and simple.  no amount of data will change his mind, he brought it with him.

daniel:  we value evidence.  cartesian empirical equivalencies is mental masturbation.  yes we may be brains in vats.  this does not further your argument, which boils down to the awe and wonder that you feel when experiencing 'creation'.  We all feel that, or we wouldn't be biologists or interested in science in general.  You simply fail to discern the appropriate distinction between your emotionally valuable presuppositions and the realities imposed by objective evidence*.

I am sympathetic, on some level, to these orthogenetic notions.  Simply because I think there is something about individual organisms (agency, identity, blah blah imprecise blah) that defies the mereological reductionism that is at least the caricature of evolutionary biology.  Where and what these entities and processes exist and exercise is the question.

the IDC movement conveniently stands on the shoulders of these monumental questions in biology and philosophy in general and proclaims them answered, and you will find those answers in black and white in the ancient handed-down texts of a particular clan of nomadic coprophagic** numerologists.

Pardon the rest of us, me included, if we don't fall for your martyrdom.

*  objective is as objective does.  but i'll be less likely to believe you when you run around yammering about front-loaded this or omphalos that.  you know.

**  see Ezekiel Bread.  True Christians, TM, use cows dung for mans dung.  I have it on as good an authority as you do that the earth was created by yahweh or whatever your sect calls it.
Posted by: JAM on Jan. 08 2008,00:35

Quote (Erasmus @ FCD,Jan. 08 2008,00:21)
JAM:  Daniel is a creationist.  pure and simple.
---------------------QUOTE-------------------


I'm well aware of that, thanks.


---------------------QUOTE-------------------
 no amount of data will change his mind, he brought it with him.
---------------------QUOTE-------------------


I know. The only thing maintaining my interest in this thread has been that Dan didn't know this about himself until we dragged him, kicking and screaming, to look at the data. There was a bit of sincerity wrapped up in all of his arrogance.

Since then, he's become the standard dishonest creationist and I'm losing interest.
Posted by: JAM on Jan. 08 2008,00:38

Quote (Mark Iosim @ Jan. 06 2008,22:25)
I am looking for the relevant studies, but didn’t find them yet? Apparently, you have plenty of evidences. Can you refer me to any sort of statistical analysis that in your opinion demonstrates that random mutations could be responsible for adaptive changes in biological systems?
---------------------QUOTE-------------------


Why would you want a "statistical analysis" instead of the evidence itself?

Do you realize that statistical analysis is something a scientist does WITH the evidence?
Posted by: oldmanintheskydidntdoit on Jan. 08 2008,02:48

Quote (Daniel Smith @ Jan. 07 2008,19:40)
Quote (oldmanintheskydidntdoit @ Jan. 07 2008,18:27)
 
Quote (Daniel Smith @ Jan. 07 2008,18:24)
The main attraction for me is the man, Jesus.  His words struck a chord within me.  That's all I can say.  Maybe I am wrong (it won't be the first time), but I'll take my chances.
---------------------QUOTE-------------------


Fine, witness away, great. Just don't claim life is "designed" or that it can be proved that life was created.
---------------------QUOTE-------------------


I never claimed it can be "proved".  As for claiming life was designed - why not?  You claim it wasn't.
---------------------QUOTE-------------------


Then in the event of a tie the side with the most evidence wins.

Now, care to take a guess at which side you are on?
Posted by: Assassinator on Jan. 08 2008,03:10



---------------------QUOTE-------------------
The main attraction for me is the man, Jesus.
---------------------QUOTE-------------------


Jesus has nothing to do with the origins of life, earth and the universe. If he existed he was a man with a message, a message of love wich has nothing to do with science.


---------------------QUOTE-------------------
Yes, of course I do.  That is why I've said numerous times that science will never find a plausible explanation for the origin of any of life's most basic biological systems.  This is a prediction that anyone can falsify.  So it's not just me, and it's not just opinion.
You understand that don't you?
---------------------QUOTE-------------------


No, I do not. The fact that your opinion is not equal to reality, has nothing to do with science. Explain yourself.
Posted by: VMartin on Jan. 08 2008,13:51

Quote (Daniel Smith @ Jan. 06 2008,14:21)
   
Quote (VMartin @ Jan. 05 2008,17:12)
I've never read anything from Otto Schindewolf but as far as I can judge he pointed something very paradoxical. In one side there was darwinian gradualism and on the other side there was a biostratigraphy (which focuses on correlating and assigning relative ages of rock strata by using the fossil assemblages). The basic rule of the biostratigraphy was in direct contradction with gradual evolution. Biostratographic always knew there were some species in given rock strata that didn't change continually - otherwise he couldn't have work.  
Because biostratigraphy do not often see in fossil records (there are sometimes exceptions) what gradualists insisted they should have see there, some   tensions arose - with outcomes like "punctuated equilibria" etc..
---------------------QUOTE-------------------


That's correct Martin.
Schindewolf pointed out "striking contrasts" between biostratigraphic ages.  But it wasn't the species that did not change which formed the boundaries - it was the sudden appearances and rapid evolution of new forms that delineated the boundaries between ages.  This evolution would then slow down and usually (but not always) become the gradual evolution Darwin speculated about, (although Schindewolf attributed it to constrained, internal factors), thus indicating the middle of the age.  This gradual evolution would usually follow a pattern that trended towards overspecialization and mass extinctions - thus delineating the end of that age.  Then the process would repeat - either with new forms bursting upon the scene, or with one lineage from the previous age, that had not overspecialized, then becoming the "root" species for another explosion of forms.

Of course this (as I've presented it), is an oversimplified view of this since there were numerous fossil types upon which these ages were marked.  I'm sure this stuff is all common knowledge amongst paleontologists and geologists.
---------------------QUOTE-------------------


That's very interesting Daniel. It's a pity you have to waste time here with people who do not care a bit what is the crux of Schindewolf's theory. Discussion about it would be more instructive.

I hit on the problem of biostartgraphy in the following text-book which is unfortunately in Czech. But the author is no way darwinist I dare say.

< http://www.mprinstitute.org/vaclav/Kapitol2.htm >

The autor has written on my opinion extraordinary good essay "British metaphysics as reflected in Robert Broom's evolutionary theory" available in English here:

< http://www.mprinstitute.org/vaclav/Broom.htm >

I was surprised with all that memory capacity of Robert Broom and the mentioned article about autism, it can be found also inet - unbelievable what all is hidden in human brains. One would say Plato was right.
Posted by: oldmanintheskydidntdoit on Jan. 08 2008,14:00

Quote (VMartin @ Jan. 08 2008,13:51)
That's very interesting Daniel. It's a pity you have to waste time here with people who do not care a bit what is the crux of Schindewolf's theory. Discussion about it would be more instructive.
---------------------QUOTE-------------------


So start a thread and have a discussion. We'd all enjoy that so very much.

Or is there no money where that mouth is, the pair of you?
Posted by: oldmanintheskydidntdoit on Jan. 08 2008,14:01

Quote (Daniel Smith @ Jan. 07 2008,19:40)
Quote (oldmanintheskydidntdoit @ Jan. 07 2008,18:27)
 
Quote (Daniel Smith @ Jan. 07 2008,18:24)
The main attraction for me is the man, Jesus.  His words struck a chord within me.  That's all I can say.  Maybe I am wrong (it won't be the first time), but I'll take my chances.
---------------------QUOTE-------------------


Fine, witness away, great. Just don't claim life is "designed" or that it can be proved that life was created.
---------------------QUOTE-------------------


I never claimed it can be "proved".  As for claiming life was designed - why not?  You claim it wasn't.
---------------------QUOTE-------------------


I claim that erk eep noop woop deep.
Posted by: Daniel Smith on Jan. 08 2008,18:27

Quote (Ideaforager @ Jan. 07 2008,19:45)
Daniel,
I've been holding out way too long!
   

---------------------QUOTE-------------------
But that does not change the fact of what the text says (in black and white).
---------------------QUOTE-------------------


How do you distinguish the amount of honesty contained in two opposing texts?
---------------------QUOTE-------------------


I don't hold to the belief that the bible is the literal, inerrant word of God.  I believe it is inspired by God - and that it is the spirit of it, not the letter - that reveals God to us.  So, I don't get hung up on the contradictions in the bible (yes there are many), rather I view it as an historical document written by ancient peoples who all had a relationship with the same God I do.  I want to know the reality of God and of this world he created.  I think the truth is in the bible and in the creation.  I want to know what it is.
Posted by: Daniel Smith on Jan. 08 2008,18:38

Quote (JAM @ Jan. 07 2008,23:52)
Dan,

Science isn't about showing an arrogant twit like Daniel Smith anything because he throws a hissy fit after his blatant lies about being fascinated by biological complexity are exposed.

Science is about making and testing predictions. It's not dancing and it's not trapping.

If you are fascinated by the complexity of biology, go for it yourself.

You won't, because you're afraid of what you might find. Better to make stupid demands.
---------------------QUOTE-------------------


I am 'going for it myself' - thank you.  I was hoping to learn something from you along the way, but there's just too much baggage that goes along with your "lessons" for me to continue.
So, I'll continue to talk to the others here, but not to you anymore.
I wish you well in your pursuit of biology.  I'd appreciate a link to your next published paper - if it's not too much trouble - or to any of your published papers for that matter.
I think that would be a far better way for me to understand where you're coming from than this forum has been.
Posted by: Daniel Smith on Jan. 08 2008,18:44

Quote (Erasmus @ FCD,Jan. 08 2008,00:21)
well as much as i have enjoyed this thread (Daniel you have received quite a spanking and also been an absolutely great sport about it) I am tempted to go concern trolling here.

JAM:  Daniel is a creationist.  pure and simple.  no amount of data will change his mind, he brought it with him.

daniel:  we value evidence.  cartesian empirical equivalencies is mental masturbation.  yes we may be brains in vats.  this does not further your argument, which boils down to the awe and wonder that you feel when experiencing 'creation'.  We all feel that, or we wouldn't be biologists or interested in science in general.  You simply fail to discern the appropriate distinction between your emotionally valuable presuppositions and the realities imposed by objective evidence*.

I am sympathetic, on some level, to these orthogenetic notions.  Simply because I think there is something about individual organisms (agency, identity, blah blah imprecise blah) that defies the mereological reductionism that is at least the caricature of evolutionary biology.  Where and what these entities and processes exist and exercise is the question.

the IDC movement conveniently stands on the shoulders of these monumental questions in biology and philosophy in general and proclaims them answered, and you will find those answers in black and white in the ancient handed-down texts of a particular clan of nomadic coprophagic** numerologists.

Pardon the rest of us, me included, if we don't fall for your martyrdom.

*  objective is as objective does.  but i'll be less likely to believe you when you run around yammering about front-loaded this or omphalos that.  you know.

**  see Ezekiel Bread.  True Christians, TM, use cows dung for mans dung.  I have it on as good an authority as you do that the earth was created by yahweh or whatever your sect calls it.
---------------------QUOTE-------------------


Erasmus,

You say, "we value evidence".  Please define "evidence" for me.  Tell me exactly what kind of evidence you value.
Posted by: Daniel Smith on Jan. 08 2008,18:58

Quote (Assassinator @ Jan. 08 2008,03:10)
     

---------------------QUOTE-------------------
The main attraction for me is the man, Jesus.
---------------------QUOTE-------------------


Jesus has nothing to do with the origins of life, earth and the universe. If he existed he was a man with a message, a message of love wich has nothing to do with science.
---------------------QUOTE-------------------


I'm sorry, I misread your question.  I thought you were asking what made my beliefs (i.e. Christianity) right, I see now that you were asking what makes my creation story right.

Sorry.

As for creation stories, I think they all have an element of truth to them.

(BTW, the bible claims that Jesus did have something to do with "origins of life, earth and the universe", FYI.)
     

---------------------QUOTE-------------------
   

---------------------QUOTE-------------------
Yes, of course I do.  That is why I've said numerous times that science will never find a plausible explanation for the origin of any of life's most basic biological systems.  This is a prediction that anyone can falsify.  So it's not just me, and it's not just opinion.
You understand that don't you?
---------------------QUOTE-------------------


No, I do not. The fact that your opinion is not equal to reality, has nothing to do with science. Explain yourself.
---------------------QUOTE-------------------


Uh, I think your going to have to explain yourself on that one.  I have no idea what you meant by that - nor do I know what you want me to explain.
Posted by: Daniel Smith on Jan. 08 2008,19:36

Quote (VMartin @ Jan. 08 2008,13:51)
   
Quote (Daniel Smith @ Jan. 06 2008,14:21)
         
Quote (VMartin @ Jan. 05 2008,17:12)
I've never read anything from Otto Schindewolf but as far as I can judge he pointed something very paradoxical. In one side there was darwinian gradualism and on the other side there was a biostratigraphy (which focuses on correlating and assigning relative ages of rock strata by using the fossil assemblages). The basic rule of the biostratigraphy was in direct contradction with gradual evolution. Biostratographic always knew there were some species in given rock strata that didn't change continually - otherwise he couldn't have work.  
Because biostratigraphy do not often see in fossil records (there are sometimes exceptions) what gradualists insisted they should have see there, some   tensions arose - with outcomes like "punctuated equilibria" etc..
---------------------QUOTE-------------------


That's correct Martin.
Schindewolf pointed out "striking contrasts" between biostratigraphic ages.  But it wasn't the species that did not change which formed the boundaries - it was the sudden appearances and rapid evolution of new forms that delineated the boundaries between ages.  This evolution would then slow down and usually (but not always) become the gradual evolution Darwin speculated about, (although Schindewolf attributed it to constrained, internal factors), thus indicating the middle of the age.  This gradual evolution would usually follow a pattern that trended towards overspecialization and mass extinctions - thus delineating the end of that age.  Then the process would repeat - either with new forms bursting upon the scene, or with one lineage from the previous age, that had not overspecialized, then becoming the "root" species for another explosion of forms.

Of course this (as I've presented it), is an oversimplified view of this since there were numerous fossil types upon which these ages were marked.  I'm sure this stuff is all common knowledge amongst paleontologists and geologists.
---------------------QUOTE-------------------


That's very interesting Daniel. It's a pity you have to waste time here with people who do not care a bit what is the crux of Schindewolf's theory. Discussion about it would be more instructive.

I hit on the problem of biostartgraphy in the following text-book which is unfortunately in Czech. But the author is no way darwinist I dare say.

< http://www.mprinstitute.org/vaclav/Kapitol2.htm >

The autor has written on my opinion extraordinary good essay "British metaphysics as reflected in Robert Broom's evolutionary theory" available in English here:

< http://www.mprinstitute.org/vaclav/Broom.htm >

I was surprised with all that memory capacity of Robert Broom and the mentioned article about autism, it can be found also inet - unbelievable what all is hidden in human brains. One would say Plato was right.
---------------------QUOTE-------------------


Thanks so much for that Martin.  I'm also interested in the works of Goldschmidt and Grasse.  I found Goldschmidt's A Material Basis for Evolution for about $50 on Amazon, but they want almost $150 for Grasse's Evolution of Living Organisms!  Too much for me right now.

Another modern skeptic of Darwinism you might want to check out is Michael Denton.
 
Here's a couple of his recent papers:

< Physical law not natural selection as the major determinant of biological complexity in the subcellular realm: new support for the pre-Darwinian conception of evolution by natural law >

< The Protein Folds as Platonic Forms: New Support for the Pre-Darwinian Conception of Evolution by Natural Law >

He also wrote the books Evolution: A Theory in Crisis and Nature's Destiny.
Posted by: Ideaforager on Jan. 08 2008,20:57

Daniel,  

---------------------QUOTE-------------------
I don't hold to the belief that the bible is the literal, inerrant word of God.
---------------------QUOTE-------------------

Good, but how do you distinguish    

---------------------QUOTE-------------------
there in black and white
---------------------QUOTE-------------------

from the gray?    

---------------------QUOTE-------------------
I believe it is inspired by God - and that it is the spirit of it, not the letter - that reveals God to us.
---------------------QUOTE-------------------

Again is that spirit        

---------------------QUOTE-------------------
there in black and white
---------------------QUOTE-------------------

or gray?    

---------------------QUOTE-------------------
So, I don't get hung up on the contradictions in the bible (yes there are many), rather I view it as an historical document written by ancient peoples who all had a relationship with the same God I do.
---------------------QUOTE-------------------

How do you know this? Could the writers have had other more immediate/practical motives?
     

---------------------QUOTE-------------------
I want to know the reality of God and of this world he created.
---------------------QUOTE-------------------

That is extremely similar to the sentiments expressed by the greatest scientists. Hopefully, your own foraging efforts are rewarded.      

---------------------QUOTE-------------------
I think the truth is in the bible and in the creation. I want to know what it is.
---------------------QUOTE-------------------


That's good, the key is that you keep on your course and never abandon your individual thinking/analysis.
Welcome to the club.
Posted by: oldmanintheskydidntdoit on Jan. 09 2008,05:15

Hey Daniel,
Seeing as things have taken a turn for the off-topic, perhaps you could answer a few simple questions that'll allow the lurkers to decide if you are sincere?

a) How old is the earth?
b) How old is the solar system?
c) How old is the universe?
d) Did man and dinosaur share the planet at the same time?
e) Did every human but 8 die in a global flood?
f) Does the "designer" actively "interfere" with the day to day running of the universe?
g) If "yes" to f) then how come we've not noticed?

There are plenty more, of course.
Posted by: mitschlag on Jan. 09 2008,07:34

Quote (oldmanintheskydidntdoit @ Jan. 09 2008,05:15)
Hey Daniel,
Seeing as things have taken a turn for the off-topic, perhaps you could answer a few simple questions that'll allow the lurkers to decide if you are sincere?

a) How old is the earth?
b) How old is the solar system?
c) How old is the universe?
d) Did man and dinosaur share the planet at the same time?
e) Did every human but 8 die in a global flood?
f) Does the "designer" actively "interfere" with the day to day running of the universe?
g) If "yes" to f) then how come we've not noticed?

There are plenty more, of course.
---------------------QUOTE-------------------


Please pay attention, Daniel has already answered.

f) Does the "designer" actively "interfere" with the day to day running of the universe?

Answer: he created HIV in the 20th century.

g) If "yes" to f) then how come we've not noticed?

Answer: We've noticed the effect.  Big time.
Posted by: oldmanintheskydidntdoit on Jan. 09 2008,07:52

Quote (mitschlag @ Jan. 09 2008,07:34)
Quote (oldmanintheskydidntdoit @ Jan. 09 2008,05:15)
Hey Daniel,
Seeing as things have taken a turn for the off-topic, perhaps you could answer a few simple questions that'll allow the lurkers to decide if you are sincere?

a) How old is the earth?
b) How old is the solar system?
c) How old is the universe?
d) Did man and dinosaur share the planet at the same time?
e) Did every human but 8 die in a global flood?
f) Does the "designer" actively "interfere" with the day to day running of the universe?
g) If "yes" to f) then how come we've not noticed?

There are plenty more, of course.
---------------------QUOTE-------------------


Please pay attention, Daniel has already answered.

f) Does the "designer" actively "interfere" with the day to day running of the universe?

Answer: he created HIV in the 20th century.

g) If "yes" to f) then how come we've not noticed?

Answer: We've noticed the effect.  Big time.
---------------------QUOTE-------------------


I've asked Daniel *why* HIV was created, but as yet no answer, apart from "I can't read the mind of god".

Funny that, seems when it's convenient people can tell you what god meant when he did all sorts of things in general, but get down to specifics and it all goes quiet.

Daniel, speculate based on your knowledge *why* HIV was created please.

Does the word "punish" come into it at all? As that's where I've been trying to lead you to you see. If you say it, you lose whatever credibility you have left.

Well, now I've said it. Lets see what he says.
Posted by: Assassinator on Jan. 09 2008,11:35



---------------------QUOTE-------------------
Sorry.

As for creation stories, I think they all have an element of truth to them.
---------------------QUOTE-------------------


Because of what? Why would they?


---------------------QUOTE-------------------
(BTW, the bible claims that Jesus did have something to do with "origins of life, earth and the universe", FYI.)
---------------------QUOTE-------------------


What I ment that, even if Jesus existed, it says nothing about the origin of life etc etc.


---------------------QUOTE-------------------
Uh, I think your going to have to explain yourself on that one.  I have no idea what you meant by that - nor do I know what you want me to explain.
---------------------QUOTE-------------------


I've asked if you understood that your view that life looks designed says nothing about if it's actually designed. Then you say that science will never find a plausible explanation, huh?

Besides, what do you know about this subject Daniel? Have you got any education on these subjects whatsoever?
Posted by: Daniel Smith on Jan. 09 2008,18:24

Quote (oldmanintheskydidntdoit @ Jan. 09 2008,05:15)
Hey Daniel,
Seeing as things have taken a turn for the off-topic, perhaps you could answer a few simple questions that'll allow the lurkers to decide if you are sincere?

a) How old is the earth?
b) How old is the solar system?
c) How old is the universe?
---------------------QUOTE-------------------


I don't know.  I haven't really studied both sides of the whole "age of the earth" debate, so I'm not prepared to give an answer on those.
   

---------------------QUOTE-------------------
d) Did man and dinosaur share the planet at the same time?
---------------------QUOTE-------------------


It's possible, but again I don't know.
   

---------------------QUOTE-------------------
e) Did every human but 8 die in a global flood?
---------------------QUOTE-------------------


I believe in the flood, but only because I haven't seen the evidence against it.  My main reason for believing it (other than the bible), is that the landscape looks like the aftermath of massive flood runoff when viewed from the air.  Not very scientific, I know but that's where I'm at.  (insert joke here)
   

---------------------QUOTE-------------------
f) Does the "designer" actively "interfere" with the day to day running of the universe?
g) If "yes" to f) then how come we've not noticed?

---------------------QUOTE-------------------


Again it's possible, although it is equally possible that he planned everything out in advance, and it is just unfolding accordingly.
I definitely don't have all the answers and my opinions are in a constant state of flux.
Posted by: Daniel Smith on Jan. 09 2008,18:35

Quote (Ideaforager @ Jan. 08 2008,20:57)
Daniel,      

---------------------QUOTE-------------------
I don't hold to the belief that the bible is the literal, inerrant word of God.
---------------------QUOTE-------------------

Good, but how do you distinguish        

---------------------QUOTE-------------------
there in black and white
---------------------QUOTE-------------------

from the gray?        

---------------------QUOTE-------------------
I believe it is inspired by God - and that it is the spirit of it, not the letter - that reveals God to us.
---------------------QUOTE-------------------

Again is that spirit            

---------------------QUOTE-------------------
there in black and white
---------------------QUOTE-------------------

or gray?
---------------------QUOTE-------------------


There's a lot more gray than there is black and white.  As to how to distinguish this:  I think it can only come through a sincere desire to know God and the truth.  It is only then that you will let everything go; everything you've ever been taught, everything that is orthodox, and be open to correction from God himself - whether it's through a new understanding of scripture or a new understanding of life, the cosmos, or man's place in it.
 

---------------------QUOTE-------------------
 

---------------------QUOTE-------------------
So, I don't get hung up on the contradictions in the bible (yes there are many), rather I view it as an historical document written by ancient peoples who all had a relationship with the same God I do.
---------------------QUOTE-------------------

How do you know this? Could the writers have had other more immediate/practical motives?
---------------------QUOTE-------------------


Perhaps.  I think God has had a say in the matter however.          

---------------------QUOTE-------------------
 

---------------------QUOTE-------------------
I want to know the reality of God and of this world he created.
---------------------QUOTE-------------------

That is extremely similar to the sentiments expressed by the greatest scientists. Hopefully, your own foraging efforts are rewarded.          

---------------------QUOTE-------------------
I think the truth is in the bible and in the creation. I want to know what it is.
---------------------QUOTE-------------------


That's good, the key is that you keep on your course and never abandon your individual thinking/analysis.
Welcome to the club.
---------------------QUOTE-------------------


Thanks.
Posted by: Erasmus, FCD on Jan. 09 2008,18:36



---------------------QUOTE-------------------
I believe in the flood, but only because I haven't seen the evidence against it.  My main reason for believing it (other than the bible), is that the landscape looks like the aftermath of massive flood runoff when viewed from the air.  Not very scientific, I know but that's where I'm at.  (insert joke here)
 
---------------------QUOTE-------------------



Are you kidding?  Where in the hell does it look like that?

That isn't even worth making a joke about.  You need some help dude.
Posted by: Darth Robo on Jan. 09 2008,18:37



---------------------QUOTE-------------------
I haven't really studied both sides of the whole "age of the earth" debate
---------------------QUOTE-------------------



Wait, there are TWO sides to that?!?

:O



---------------------QUOTE-------------------
It's possible, but again I don't know.
---------------------QUOTE-------------------



Then the Flinstones could be a documentary?



---------------------QUOTE-------------------
I believe in the flood, but only because I haven't seen the evidence against it.  My main reason for believing it (other than the bible), is that the landscape looks like the aftermath of massive flood runoff when viewed from the air.  Not very scientific, I know but that's where I'm at.(insert joke here)
---------------------QUOTE-------------------



BIG FLUD CARVES TEH LANDSCAPE - dinky (but not too dinky) wooden boat SURVIVES.  

Hooray fer humanity.   ???

Where did this massive flud runoff to?  

:O
Posted by: Erasmus, FCD on Jan. 09 2008,18:38

Ummm, that would be Detroit.  And perhaps New Orleans.

Oh yeah and Philly.

that's where all crap floweth.
Posted by: Daniel Smith on Jan. 09 2008,18:43

Quote (oldmanintheskydidntdoit @ Jan. 09 2008,07:52)
I've asked Daniel *why* HIV was created, but as yet no answer, apart from "I can't read the mind of god".

Funny that, seems when it's convenient people can tell you what god meant when he did all sorts of things in general, but get down to specifics and it all goes quiet.

Daniel, speculate based on your knowledge *why* HIV was created please.

Does the word "punish" come into it at all? As that's where I've been trying to lead you to you see. If you say it, you lose whatever credibility you have left.

Well, now I've said it. Lets see what he says.
---------------------QUOTE-------------------


I don't know the "why" for almost anything God created.  I don't know why he made horses, flies, starfish, HIV, or man.
I'm not just avoiding the question when it come to HIV.
I can speculate: he made horses for us to ride, flies for us to swat, starfish for us to look at, HIV to kill us, and man so that we could ask "why?" for all this.  My speculations are just that though - speculations.  They mean nothing and have no basis in reality (and they are not even my real speculations).  So why do you ask?
Posted by: Darth Robo on Jan. 09 2008,18:46



---------------------QUOTE-------------------
It is only then that you will let everything go
---------------------QUOTE-------------------



LET GO, Luke!   ???



---------------------QUOTE-------------------
new understanding of life, the cosmos, or man's place in it.
---------------------QUOTE-------------------



Contrast with:

Age of the Earth/Solar system/Universe



---------------------QUOTE-------------------
I don't know.  I haven't really studied both sides of the whole "age of the earth" debate, so I'm not prepared to give an answer on those.
---------------------QUOTE-------------------



Man (Fred?) and dino:



---------------------QUOTE-------------------
It's possible, but again I don't know.
---------------------QUOTE-------------------



Teh FLUD:



---------------------QUOTE-------------------
I believe in the flood, but only because I haven't seen the evidence against it.
---------------------QUOTE-------------------







---------------------QUOTE-------------------
whether it's through a new understanding of scripture
---------------------QUOTE-------------------



Have you considered trying to understand that if scripture is taken literally, some parts could be complete bollux?
Posted by: Daniel Smith on Jan. 09 2008,18:55

Quote (Assassinator @ Jan. 09 2008,11:35)
 

---------------------QUOTE-------------------
Sorry.

As for creation stories, I think they all have an element of truth to them.
---------------------QUOTE-------------------


Because of what? Why would they?
---------------------QUOTE-------------------


They all (to my knowledge) point to life as being designed/created by an intelligent being of some sort.
   

---------------------QUOTE-------------------
 

---------------------QUOTE-------------------
(BTW, the bible claims that Jesus did have something to do with "origins of life, earth and the universe", FYI.)
---------------------QUOTE-------------------


What I ment that, even if Jesus existed, it says nothing about the origin of life etc etc.
   

---------------------QUOTE-------------------
Uh, I think your going to have to explain yourself on that one.  I have no idea what you meant by that - nor do I know what you want me to explain.
---------------------QUOTE-------------------


I've asked if you understood that your view that life looks designed says nothing about if it's actually designed. Then you say that science will never find a plausible explanation, huh?
---------------------QUOTE-------------------


But that is one of the tests for design.  If there is no plausible chance/random/natural explanation, we can infer that something happened as the result of the actions of intelligent beings.  This is the method coroners use to determine whether a death was the result of natural causes or human intervention.

If man were to discover an ancient artifact that exhibited a technology far superior to that of ancient (or modern) man, could he infer that perhaps an alien race had visited this planet from that artifact?  Of course he could.  In fact, that would be the first inclination in such a discovery.  The only way to falsify that theory would be to provide another plausible explanation.

Biological systems represent just such an advanced technology in my opinion.  Until you provide me with a plausible explanation as to their origin, I'll continue to hold that they were designed by a supreme intelligence.  That's my position.
 

---------------------QUOTE-------------------
Besides, what do you know about this subject Daniel? Have you got any education on these subjects whatsoever?
---------------------QUOTE-------------------


Completely self taught, with gaping holes in my knowledge.
Posted by: Steverino on Jan. 09 2008,19:19

"Biological systems represent just such an advanced technology in my opinion.  Until you provide me with a plausible explanation as to their origin, I'll continue to hold that they were designed by a supreme intelligence.  That's my position."

No proof, failure to accept proof.  Argument from Incredulity.

Does gravity pull things up in your world?
Posted by: swbarnes2 on Jan. 09 2008,19:52

Quote (Daniel Smith @ Jan. 09 2008,18:55)

But that is one of the tests for design.  If there is no plausible chance/random/natural explanation, we can infer that something happened as the result of the actions of intelligent beings.
---------------------QUOTE-------------------



Sigh.  But since you know nothing about biology, physics, or chemistry, you are a lousy at determining what is plausible.

Three days ago, you thought it was plausiable that there were multiple amino acids that could be translator initiators.  And you were crazy wrong.  

A few months ago, you thought it was plausible that half the genes in mice would have no human ortholog.

Well, you were crazy wrong there too.

You also thought it was plausible for there to be a resistant bacteruim in EVERY colony.  

Crazy wrong yet again.

And now you tell us that it's plausible for there to have been a global flood.  

So pretty much whatever YOU think is plausible turns out to not be plausible at all, and all that things that you think are implausible have either been demonstrated to be true, or likely soon will be.

Tell us, why should we value the judgments of someone who has proven that he knows nothing about biology, chemistry, or physics?

Oh wait, let me guess.  We should trust your judgement in matters of which you are appallingly ignorant and flat out mistaken...because you believe in Jesus.
Posted by: SpeedDemon on Jan. 09 2008,20:08

Quote (Daniel Smith @ Jan. 09 2008,18:55)
 

---------------------QUOTE-------------------
Besides, what do you know about this subject Daniel? Have you got any education on these subjects whatsoever?
---------------------QUOTE-------------------


Completely self taught, with gaping holes in my knowledge.
---------------------QUOTE-------------------


It's clear from reading this thread that a lot of those gaps have been filled by kind and patient people that post here.

Why then do you still resist the obvious conclusion when it's crystal clear that you've been wrong so consistently?

SD
Posted by: Erasmus, FCD on Jan. 09 2008,20:48

Well, being wrong ain't that bad.

It's the damn smug attitude, the one that shows that you are ignernt and proud of it, that is the killer.

Coroners are looking for Intelligent Design?

Jesus.

Again, will you tell me what part of the Appalachians look like they were scrubbed by Teh Flud?  Im'a dyin' ta be knowin'.
Posted by: Coyote on Jan. 10 2008,00:03

Quote (Daniel Smith @ Jan. 10 2008,04:24)


---------------------QUOTE-------------------
I believe in the flood, but only because I haven't seen the evidence against it.
---------------------QUOTE-------------------


---------------------QUOTE-------------------


OK, here are a couple of pieces of evidence against the idea of a global flood.

1) In southern Alaska there is a cave, called On Your Knees Cave. A partial skeleton produced a radiocarbon date at 10,300 years ago. The mtDNA of that individual has been traced to 40+ living descendants from California to the tip of South America.

2) From my own work I have a skeleton from the west coast dated to 5,300 years ago. Its mtDNA pattern matched living descendants in the same area.

These cases illustrate continuity, and show that there was no population drop on the west coast ca. 4350 years ago followed by replacement with a Middle Eastern mtDNA pattern.

In addition, we have continuity of Native cultures, soil horizons, fauna and flora, and a lot of other lines of evidence.  All would be different if there was a global flood 4350 years ago.

But there were some smaller floods at the end of the Ice Age. Google "channeled scablands" and see what happened to central and southern Washington when some ice dams let go.

Now, if we can see those small floods, back some 9,000+ years ago, just think how obvious a global flood at half that age would be.

Can you account for this evidence?
Posted by: Wesley R. Elsberry on Jan. 10 2008,02:00



---------------------QUOTE-------------------

If there is no plausible chance/random/natural explanation, we can infer that something happened as the result of the actions of intelligent beings.  This is the method coroners use to determine whether a death was the result of natural causes or human intervention.

---------------------QUOTE-------------------



The first sentence makes a false assertion, and the second is contradicted by reality.

I take it that you haven't got any experience with the subject of your claim, nor do you appear to have read Dr. Gary Hurd's chapter in "< Why Intelligent Design Fails >".
Posted by: oldmanintheskydidntdoit on Jan. 10 2008,02:54

Quote (Daniel Smith @ Jan. 09 2008,18:43)
Quote (oldmanintheskydidntdoit @ Jan. 09 2008,07:52)
I've asked Daniel *why* HIV was created, but as yet no answer, apart from "I can't read the mind of god".

Funny that, seems when it's convenient people can tell you what god meant when he did all sorts of things in general, but get down to specifics and it all goes quiet.

Daniel, speculate based on your knowledge *why* HIV was created please.

Does the word "punish" come into it at all? As that's where I've been trying to lead you to you see. If you say it, you lose whatever credibility you have left.

Well, now I've said it. Lets see what he says.
---------------------QUOTE-------------------


I don't know the "why" for almost anything God created.  I don't know why he made horses, flies, starfish, HIV, or man.
I'm not just avoiding the question when it come to HIV.
I can speculate: he made horses for us to ride, flies for us to swat, starfish for us to look at, HIV to kill us, and man so that we could ask "why?" for all this.  My speculations are just that though - speculations.  They mean nothing and have no basis in reality (and they are not even my real speculations).  So why do you ask?
---------------------QUOTE-------------------


I ask becuase if everything is designed, as you say, then there must be a purpose to those designs.

The main plank of your "it's designed" argument fails if you can't say "what for" IMHO. We're back to "it looks designed to me".
Posted by: Assassinator on Jan. 10 2008,07:06



---------------------QUOTE-------------------
They all (to my knowledge) point to life as being designed/created by an intelligent being of some sort.
---------------------QUOTE-------------------


Yea, so? And why would those contribute to the actual truthness of those stories? The fact that they say life was formed by some sort of design, doesn't mean it's per definition true.


---------------------QUOTE-------------------
But that is one of the tests for design.  If there is no plausible chance/random/natural explanation, we can infer that something happened as the result of the actions of intelligent beings.  This is the method coroners use to determine whether a death was the result of natural causes or human intervention.
---------------------QUOTE-------------------


No, it's nor a test for ID nor the method of coroners. If we would not be able to get a plausible explanation for life, that's not proof for ID, that's not the way science works. Same with a coroner, if there is no explanation for the death of someone that isn't proof for someone being killed by someone else if there isn't direct evidence for that.
And like swbarnes2 sad, you don't have any real background for this subject, just self-taught stuff. And by the looks of it, that means you picked up information from sources confirming the world-view you already had. That's not learning. You admit that you've got gaping (and how!!) holes in your knowledge yet you have your opinion set. That's not learning.
Posted by: Daniel Smith on Jan. 10 2008,10:47

Quote (Erasmus @ FCD,Jan. 09 2008,18:36)
 

---------------------QUOTE-------------------
I believe in the flood, but only because I haven't seen the evidence against it.  My main reason for believing it (other than the bible), is that the landscape looks like the aftermath of massive flood runoff when viewed from the air.  Not very scientific, I know but that's where I'm at.  (insert joke here)
 
---------------------QUOTE-------------------



Are you kidding?  Where in the hell does it look like that?

That isn't even worth making a joke about.  You need some help dude.
---------------------QUOTE-------------------


Next time you're up in an airplane -- look down.
Posted by: Erasmus, FCD on Jan. 10 2008,10:50



There went all pretenses to 'following the evidence wherever it leads'.

So long, thanks for playing.
Posted by: Erasmus, FCD on Jan. 10 2008,11:04

Perhaps you could interpret < this > from Teh Flud perspective.  I've sure always been curious how one might do that.  Walt Brown was no help.
Posted by: Assassinator on Jan. 10 2008,11:23

Daniel, how good is your science education (in general)?
Posted by: EoRaptor013 on Jan. 10 2008,14:16



---------------------QUOTE-------------------

 

---------------------QUOTE-------------------
I believe in the flood, but only because I haven't seen the evidence against it.  My main reason for believing it (other than the bible), is that the landscape looks like the aftermath of massive flood runoff when viewed from the air.  Not very scientific, I know but that's where I'm at.  (insert joke here)

---------------------QUOTE-------------------



Are you kidding?  Where in the hell does it look like that?

That isn't even worth making a joke about.  You need some help dude.
---------------------QUOTE-------------------



The scablands of Idaho and eastern Washington look very much like the result of a giant flood. And, it turns out they are, but note that it was a giant flood (on a human scale), not a worldwide flood. I don't doubt that there are similar landscapes elsewhere in the world. Nevertheless, the morphology of the terranes immediately abutting the scablands, the evidence for several such great floods in this same area, and the complete lack of any evidence for a flood of a non-localized (albeit large) area rather undermines the hypothesis of a world wide flood.
One more point: Isn't it illogical to be saying you believe in something  because there's no evidence against it when there's no physical evidence for it in the first place? Just asking.

$0.02
Posted by: Richard Simons on Jan. 10 2008,18:04

Quote (Daniel Smith @ Jan. 10 2008,10:47)
 
Quote (Erasmus @ FCD,Jan. 09 2008,18:36)
   

---------------------QUOTE-------------------
I believe in the flood, but only because I haven't seen the evidence against it.  My main reason for believing it (other than the bible), is that the landscape looks like the aftermath of massive flood runoff when viewed from the air.  Not very scientific, I know but that's where I'm at.  (insert joke here)
 
---------------------QUOTE-------------------



Are you kidding?  Where in the hell does it look like that?

That isn't even worth making a joke about.  You need some help dude.
---------------------QUOTE-------------------


Next time you're up in an airplane -- look down.
---------------------QUOTE-------------------


Next time you are in your garden, dig down. There are not many places where you could find a jumble of particles of all sizes from silt to boulders plus organic remains that typically results from massive floods.
Posted by: Henry J on Jan. 10 2008,22:41



---------------------QUOTE-------------------
I believe in the flood, but only because I haven't seen the evidence against it.
---------------------QUOTE-------------------



Ice caps, one with more than 100,000 annual layers.

Over a million species presently living (a handful of survivors would take a long time to diversify that much).

Lots of genetic diversity within those living species (i.e., lots of species that don't show signs of recent extreme inbreeding, including our own).

Lots of unique ecosystems on continents and islands and other geographically isolated regions (those don't form overnight).

At least two civilizations that were keeping records through the period in question (unless the usual estimates for the date are way wrong).

Continuity in geological record from before the presumed dates of the event and after (i.e., no sudden world wide change in what lived where).

Absence of identifiable layer of debris in geological record around the estimated time.

Henry
Posted by: oldmanintheskydidntdoit on Jan. 11 2008,02:51

So Daniel, still a believer in "the great fludde" or has anything said here permeated that skull yet?

If you are still a believer, perhaps you can answer these simple questions?

How many people were alive

During the flood
100 years after the flood
1000 years after the flood
During the construction of the great pyramid of Giza (2467 BC approx)

And what would the population growth rate have to be to get from "the fludde" to "the great pyramid of Giza" levels?
Posted by: Darth Robo on Jan. 11 2008,08:47



---------------------QUOTE-------------------
Next time you're up in an airplane -- look down.
---------------------QUOTE-------------------



But, but...  I never get a seat by the window!

:(
Posted by: Daniel Smith on Jan. 12 2008,08:23

Quote (Henry J @ Jan. 10 2008,22:41)
 

---------------------QUOTE-------------------
I believe in the flood, but only because I haven't seen the evidence against it.
---------------------QUOTE-------------------



Ice caps, one with more than 100,000 annual layers.

Over a million species presently living (a handful of survivors would take a long time to diversify that much).

Lots of genetic diversity within those living species (i.e., lots of species that don't show signs of recent extreme inbreeding, including our own).

Lots of unique ecosystems on continents and islands and other geographically isolated regions (those don't form overnight).

At least two civilizations that were keeping records through the period in question (unless the usual estimates for the date are way wrong).

Continuity in geological record from before the presumed dates of the event and after (i.e., no sudden world wide change in what lived where).

Absence of identifiable layer of debris in geological record around the estimated time.

Henry
---------------------QUOTE-------------------


I'm really not interested at all right now in debating the flood issue.  As I said, I really haven't researched it much at all and I don't want to get into another debate where I am unprepared to defend my position.  I have seen the evidence you've listed and it is food for thought.  I will consider it, I won't just ignore it - I promise you.  But right now this is a rabbit trail I'm not prepared to go down.  I hope you all can respect that.

I'd really like to get back to talking about Schindewolf, Berg, and their theories of constrained evolution and evolution by law.
Posted by: oldmanintheskydidntdoit on Jan. 12 2008,08:47

Quote (Daniel Smith @ Jan. 12 2008,08:23)
 
Quote (Henry J @ Jan. 10 2008,22:41)
     

---------------------QUOTE-------------------
I believe in the flood, but only because I haven't seen the evidence against it.
---------------------QUOTE-------------------



Ice caps, one with more than 100,000 annual layers.

Over a million species presently living (a handful of survivors would take a long time to diversify that much).

Lots of genetic diversity within those living species (i.e., lots of species that don't show signs of recent extreme inbreeding, including our own)
Lots of unique ecosystems on continents and islands and other geographically isolated regions (those don't form overnight).

At least two civilizations that were keeping records through the period in question (unless the usual estimates for the date are way wrong).

Continuity in geological record from before the presumed dates of the event and after (i.e., no sudden world wide change in what lived where).

Absence of identifiable layer of debris in geological record around the estimated time.

Henry
---------------------QUOTE-------------------


I'm really not interested at all right now in debating the flood issue.  As I said, I really haven't researched it much at all and I don't want to get into another debate where I am unprepared to defend my position.  I have seen the evidence you've listed and it is food for thought.  I will consider it, I won't just ignore it - I promise you.  But right now this is a rabbit trail I'm not prepared to go down.  I hope you all can respect that.

I'd really like to get back to talking about Schindewolf, Berg, and their theories of constrained evolution and evolution by law.
---------------------QUOTE-------------------


There is nothing to debate. The "debate" happened decades ago.

Daniel, simply put, there is no debate over the age of the earth, only refinements as to exactly how old it is.

By not saying "the earth is not 6000 years old" you simply indicate you are the worst sort of creationist.
 

---------------------QUOTE-------------------

I'd really like to get back to talking about Schindewolf, Berg, and their theories of constrained evolution and evolution by law.
---------------------QUOTE-------------------



What's the point if you don't even understand the status quo? How can you say their theories are better if you don't know what you are comparing them to?

 

---------------------QUOTE-------------------
I haven't really studied both sides of the whole "age of the earth" debate, so I'm not prepared to give an answer on those.
---------------------QUOTE-------------------



Fine. You don't need to study both sides to give your current opinion, whatever it may be. You are putting yourself in the same category as FTK here Daniel, do you really want that?

How old is the earth Daniel, to the best of your current understanding? How did you obtain that understanding?

See, if you can't be convinced of the truth of that matter even though every data point indicates an old earth, what chance of you being convinced of anything regarding subjects where the evidence is less clear cut? Evolution is messy, plenty of gaps for your god to hide in.

OK, to put it another way:

Daniel, in your opinion are  Schindewolf, Berg, and their theories of constrained evolution and evolution by law compatible with a 6000 year old earth and a global flood?
Posted by: Richard Simons on Jan. 12 2008,09:05

It seems to me that for Biblical literalists, everything is piecemeal, held together by 'Godidit'. The result is that a solution to one problem ('there were no rainbows before the Flood because refraction was different then') produces another problem ('then how did people see?')

It is similar with Schindewolf's ideas. 'Here is an explanation for different organisms apparently following the same evolutionary path.' - 'How was it implemented?' - 'Hush. We don't talk about that.'

In science, everything fits into a (generally) coherent whole, the less coherent areas being the ones that tend to get the research attention. A solution to one problem can throw light on another area. For example, the explanation for the banded pattern of magnetic orientation on the sea floor of the Atlantic also explains the distribution of volcanoes and some problems in biogeography. I know of nothing comparable produced by creationists or IDers of any stripe.

Although this thought was prompted by Daniel's reluctance to discuss the Flood, it is not intended as a criticism of that. Even if everything fits together perfectly, it is often reasonable to concentrate on one area.
Posted by: Richard Simons on Jan. 12 2008,09:18

Oldman:
You are right. It did not occur to me that accepting the biblical Flood and accepting Schindewolf requires adopting two contradictory positions.
Posted by: Erasmus, FCD on Jan. 12 2008,09:24

Daniel fair enough we can deal with flood and young earth nonsense at a later date.

If I may be so bold as to offer a summary of Berg Schindewolf Broom etc, the outcome of evolutionary processes are determined by natural law.  In other words, it could not have been any other way.

Post synthesis thought has recognized that there are many constraints imposed on the landscape of what 'could be' (hint, this makes Dembski's NFL a stinky steam-pile), while emphasizing the role of contingency and (for lack of a better word) 'chance'.  

Now, my point is that if there were 'laws' governing evolution, don't you think some of these would have emerged from the millions of statistical analyses performed on biological data since Fisher and Wright?  There is no single distillable biological principle, formulable at any level of detail*, that is held without exception.  There are 'No Laws' (you should chat with Bob O'H about that'un).  

There are some eastern mystical philosophies that have some principles that may on a first order approximation roughly describe evolution, particularly the zen teachings about variation and perception.  There are probably hundreds of other examples of such concepts in other religions and philosophies, but none have enough detail to have any referential value in biology.

* There is an exception, and as far as I can tell this is as much of a coherent and absolute general law that has ever been proposed in biology.  

---------------------QUOTE-------------------
Robinsons Rule:  Shit Varies. It Matters. Sometimes.  
---------------------QUOTE-------------------



Edited to add:  The contradictory positions OM brought up are serious and need to be dealt with by honest creationists who value science first, as you claim to.  The fact that they are routinely ignored by dishonest charlatans frauds and shaman raconteurs is one of the primary reasons that the reality based community has such a strong and intense opposition to the proponents of these ideas.
Posted by: Ideaforager on Jan. 12 2008,13:30



---------------------QUOTE-------------------
You are right. It did not occur to me that accepting the biblical Flood and accepting Schindewolf requires adopting two contradictory positions.
---------------------QUOTE-------------------

and  

---------------------QUOTE-------------------
Edited to add: The contradictory positions OM brought up are serious and need to be dealt with by honest creationists who value science first, as you claim to. The fact that they are routinely ignored by dishonest charlatans frauds and shaman raconteurs is one of the primary reasons that the reality based community has such a strong and intense opposition to the proponents of these ideas.
---------------------QUOTE-------------------


The problem is that reconciling contradictory concepts is very common, e.g. Brotherhood and Patriotism.!
Posted by: oldmanintheskydidntdoit on Jan. 12 2008,13:36

Quote (Ideaforager @ Jan. 12 2008,13:30)


---------------------QUOTE-------------------
You are right. It did not occur to me that accepting the biblical Flood and accepting Schindewolf requires adopting two contradictory positions.
---------------------QUOTE-------------------

and  

---------------------QUOTE-------------------
Edited to add: The contradictory positions OM brought up are serious and need to be dealt with by honest creationists who value science first, as you claim to. The fact that they are routinely ignored by dishonest charlatans frauds and shaman raconteurs is one of the primary reasons that the reality based community has such a strong and intense opposition to the proponents of these ideas.
---------------------QUOTE-------------------


The problem is that reconciling contradictory concepts is very common, e.g. Brotherhood and Patriotism.!
---------------------QUOTE-------------------


perhaps then "mutually exclusive" is a better term.
Posted by: Daniel Smith on Jan. 12 2008,14:16

I'll just say this and be done with it:
I'm perfectly content with a 4.5 billion year old earth, and I wouldn't cry if it turned out to be only 10,000 years old either.  IOW, it's not really an issue for me.

It's not how old things are; it's their chronological order that matters.
Posted by: oldmanintheskydidntdoit on Jan. 12 2008,14:47

Quote (Daniel Smith @ Jan. 12 2008,14:16)
It's not how old things are; it's their chronological order that matters.
---------------------QUOTE-------------------


Rubbish.
Posted by: Assassinator on Jan. 12 2008,14:50

Then what's your problem with the chronological order? We know that life arose step by step, in a certain order (the very first steps of life are unknown, then we've got the theorised RNA-world, DNA-organisms, recognisable microbial life, multi-cellular sea life, multi-cellular land life etc etc). Then what's your problem?
Posted by: Erasmus, FCD on Jan. 12 2008,17:17

Ooooh Oooooh Ooooh Call On Me!!!!

Because it's hard to reconcile the fact that "this is the best of all possible worlds" is a logical fallacy, and also reconcile that with christianist theology that has focused on omnipotence, omnipresence, omniscience, and free will endowed by a creator.
Posted by: Daniel Smith on Jan. 12 2008,19:11

Quote (Assassinator @ Jan. 12 2008,14:50)
Then what's your problem with the chronological order? We know that life arose step by step, in a certain order (the very first steps of life are unknown, then we've got the theorised RNA-world, DNA-organisms, recognisable microbial life, multi-cellular sea life, multi-cellular land life etc etc). Then what's your problem?
---------------------QUOTE-------------------


I think you must've missed the first 30 or so pages of this discussion.  I came here to discuss the theories of  Schindewolf and Berg.  Both of them believe in evolution.  The only difference is that they deny "Selection" as the mechanism by which evolution progresses from type to type.  Both favor nomogenesis (evolution by law) instead.  In fact, that's the title of Berg's book.  While Berg did not propose a mechanism for his theory (other than physical law), Schindewolf proposed Goldschmidt's "systemmutation" of chromosomal re-ordering, which has been refined today by Davison as the semi-meiotic hypothesis.

Recent findings that suggest protein folds are more a product of natural law than selection would seem to vindicate these long neglected scientists:            

---------------------QUOTE-------------------
Consider the case of the protein folds. Although entirely counter intuitive, the complex spatial arrangements of the amino acid chains in the 1000 protein folds are as natural and necessary as the arrangements of subatomic particles in atoms or atoms in molecules (Denton and Marshall, 2001). This is now the inescapable conclusion of the past 30 years of research into protein structure and folding which have shown that the protein folds used by life on earth represent a set of about 1000 natural and immutable forms, which like atoms or crystals arise from the natural intrinsic self-organizing properties of their constituents, in this case—amino acid polymers (Ptitsyn and Finkelstein, 1980; Chothia and Finkelstein, 1990; Banavar and Maritan, 2003). Moreover, a number of organization rules, ‘laws of form,’ which govern the local interactions between the main structural submotifs have been identified, and these restrict the spatial arrangement of amino acid polymers to a tiny set of about 1000 allowable higher-order architectures (Ptitsyn and Finkelstein, 1980; Chothia and Finkelstein, 1990). These rules are analogous to the laws of chemistry or rules of crystallography which determine the form of molecules and crystals or the rules of grammar which determine the form of meaningful letter and word strings in a language. These are nothing more nor less than a set of ‘laws of form’ like those sought after by pre-Darwinian biology to account lawfully for the diversity of form in the organic world. It is not, as is commonly supposed, the amino acid sequences which specify the three-dimensional form of a protein fold, but rather the abstract laws of protein form. Each of the 1000 allowable folds represents a preferred arrangement of matter which corresponds to an energy minimum (Ptitsyn and Finkelstein, 1980; Banavar and Maritan, 2003). This acts as a pre-existing mold or attractor, drawing the amino acid sequence from its initially disordered structure to its final and predetermined native conformation. So the forms of the folds are given by physics and matter is drawn by a process of free energy minimization into the complex form of the native conformation...
...It is now clear that many different amino acid sequences can fold into the same three-dimensional form (Brandon and Tooze, 1999) and sometimes the same sequence can fold into two different folds (Cordes et al., 2000). Evidently, the rules of fold form are highly restrictive at the level of three-dimensional structure, permitting only 1000 atomic patterns, but highly permissive in terms of sequence—a high proportion of sequences can fold into one or another fold. By analogy with language, we might think of the rules of syntax (fold architecture) as being very strict but the rules of spelling (fold sequence) very lax. Consequently, although the folds are immutable and discontinuosly distributed in fold space they can still be easily found (spelt) in sequence space and utilized by the cell.
< Physical law not natural selection as the major determinant of biological complexity in the subcellular realm: new support for the pre-Darwinian conception of evolution by natural law >, BioSystems 71 (2003) pp. 297–303, Michael J. Denton, Peter K. Dearden, Stephen J. Sowerby, Biochemistry Department, University of Otago, P.O. Box 56, Dunedin, New Zealand Global Technologies, Dunedin, New Zealand, Received 26 February 2003; received in revised form 16 May 2003; accepted 22 May 2003
---------------------QUOTE-------------------


And it is not only protein folds that behave this way, it is also RNA folds, the bipolar aster, tensegrity structures in the cell, even cell forms (though less is known about all of these).
So these findings would seem to vindicate both Schindewolf and Berg who knew that evolution must've happened lawfully, but just didn't know how.
Posted by: Daniel Smith on Jan. 12 2008,19:15

Quote (Erasmus @ FCD,Jan. 12 2008,09:24)
Daniel fair enough we can deal with flood and young earth nonsense at a later date.

If I may be so bold as to offer a summary of Berg Schindewolf Broom etc, the outcome of evolutionary processes are determined by natural law.  In other words, it could not have been any other way.

Post synthesis thought has recognized that there are many constraints imposed on the landscape of what 'could be' (hint, this makes Dembski's NFL a stinky steam-pile), while emphasizing the role of contingency and (for lack of a better word) 'chance'.  

Now, my point is that if there were 'laws' governing evolution, don't you think some of these would have emerged from the millions of statistical analyses performed on biological data since Fisher and Wright?  There is no single distillable biological principle, formulable at any level of detail*, that is held without exception.  There are 'No Laws' (you should chat with Bob O'H about that'un).
---------------------QUOTE-------------------


See < here > and < here > please.
Posted by: oldmanintheskydidntdoit on Jan. 12 2008,19:16

Quote (Daniel Smith @ Jan. 12 2008,19:15)
Quote (Erasmus @ FCD,Jan. 12 2008,09:24)
Daniel fair enough we can deal with flood and young earth nonsense at a later date.

If I may be so bold as to offer a summary of Berg Schindewolf Broom etc, the outcome of evolutionary processes are determined by natural law.  In other words, it could not have been any other way.

Post synthesis thought has recognized that there are many constraints imposed on the landscape of what 'could be' (hint, this makes Dembski's NFL a stinky steam-pile), while emphasizing the role of contingency and (for lack of a better word) 'chance'.  

Now, my point is that if there were 'laws' governing evolution, don't you think some of these would have emerged from the millions of statistical analyses performed on biological data since Fisher and Wright?  There is no single distillable biological principle, formulable at any level of detail*, that is held without exception.  There are 'No Laws' (you should chat with Bob O'H about that'un).
---------------------QUOTE-------------------


See < here > and < here > please.
---------------------QUOTE-------------------


No chance of a summary in your own words? Alot of points raised in the post you quoted, what were you responding to in particular?
Posted by: Henry J on Jan. 12 2008,21:58



---------------------QUOTE-------------------
Then what's your problem with the chronological order?
---------------------QUOTE-------------------



There's not enough time to be chronological!!!111!!

:p

Henry
Posted by: Henry J on Jan. 12 2008,21:58



---------------------QUOTE-------------------
Recent findings that suggest protein folds are more a product of natural law than selection would seem to vindicate these long neglected scientists:            
[...]

---------------------QUOTE-------------------



That's quite interesting. But near as I can tell, it's not talking about evolution of the DNA for that protein, it's talking about what the protein does after it's been synthesized.

Henry
Posted by: oldmanintheskydidntdoit on Jan. 13 2008,05:55

Quote (Daniel Smith @ Jan. 09 2008,18:24)
I haven't really studied both sides of the whole "age of the earth" debate, so I'm not prepared to give an answer on those.
---------------------QUOTE-------------------


Daniel,
Does the sun go around the earth, or the earth around the sun?

Or have you not studied that debate either?
Posted by: Assassinator on Jan. 13 2008,07:06

Daniel, what's the difference between that natural law and selection (selection is a natural law).
As far as I can see, you're talking about protein folding, we know why that happens. It's biochemistry. I think you don't think what natural selection is, yes the folding of proteins happen by natural law, but that's not what selection is about. Selection works on a bigger scale and we can view the effect of selection in nature and document it.
Posted by: oldmanintheskydidntdoit on Jan. 13 2008,07:15

Daniel, in your opinion are  Schindewolf, Berg, and their theories of constrained evolution and evolution by law compatible with a 6000 year old earth and a global flood?

If not, what will you rule out?

Either way, progress will have been made.
Posted by: Albatrossity2 on Jan. 13 2008,08:19

Quote (Daniel Smith @ Jan. 12 2008,19:11)
   
Quote (Assassinator @ Jan. 12 2008,14:50)
Then what's your problem with the chronological order? We know that life arose step by step, in a certain order (the very first steps of life are unknown, then we've got the theorised RNA-world, DNA-organisms, recognisable microbial life, multi-cellular sea life, multi-cellular land life etc etc). Then what's your problem?
---------------------QUOTE-------------------


I think you must've missed the first 30 or so pages of this discussion.  I came here to discuss the theories of  Schindewolf and Berg.  Both of them believe in evolution.  The only difference is that they deny "Selection" as the mechanism by which evolution progresses from type to type.  Both favor nomogenesis (evolution by law) instead.  In fact, that's the title of Berg's book.  While Berg did not propose a mechanism for his theory (other than physical law), Schindewolf proposed Goldschmidt's "systemmutation" of chromosomal re-ordering, which has been refined today by Davison as the semi-meiotic hypothesis.

Recent findings that suggest protein folds are more a product of natural law than selection would seem to vindicate these long neglected scientists:  

(---odious tard by another IDiot deleted-------)

So these findings would seem to vindicate both Schindewolf and Berg who knew that evolution must've happened lawfully, but just didn't know how.
---------------------QUOTE-------------------


I was trying to stay out of this conversation, because it is abundantly clear that Daniel has no clues about recent advances in biology or biochemistry. But this post is just way too stupid to ignore.

I'll let JAM handle the gory details, but it needs to be pointed out that the notion that "protein folds are more a product of natural law than selection" is a strawman. If it is not a strawman, Daniel, please document where any reputable scientist claims that natural selection governs the molecular processes involved in protein folding. This sort of argument bespeaks not only a profound misunderstanding of evolutionary theory (which Daniel has already demonstrated abundantly), but a profound ignorance about the molecular processes that occur within cells.

Here's a clue, Daniel. It would be a huge surprise if the laws of chemistry and physics did NOT govern the folding of proteins and other biological macromolecules. To claim that these obvious and experimentally determined facts are vindication of Schindewolf and Berg's half-baked notions is profoundly ignorant.
Posted by: oldmanintheskydidntdoit on Jan. 13 2008,08:26

Quote (Albatrossity2 @ Jan. 13 2008,08:19)
Here's a clue, Daniel. It would be a huge surprise if the laws of chemistry and physics did NOT govern the folding of proteins and other biological macromolecules. To claim that these obvious and experimentally determined facts are vindication of Schindewolf and Berg's half-baked notions is profoundly ignorant.
---------------------QUOTE-------------------


What he said.
Posted by: Assassinator on Jan. 13 2008,08:36

Odd though that a just-beyond-highschool kid like me can note those things, but you Daniel can't.
Posted by: Lou FCD on Jan. 13 2008,09:40

Quote (Assassinator @ Jan. 13 2008,09:36)
Odd though that a just-beyond-highschool kid like me can note those things, but you Daniel can't.
---------------------QUOTE-------------------


Oddly after almost forty pages, I don't find that odd at all.
Posted by: Mark Iosim on Jan. 13 2008,11:48



---------------------QUOTE-------------------
Mark Iosim:
Can you (JAM) refer me to any sort of statistical analysis that in your opinion demonstrates that random mutations could be responsible for adaptive changes in biological systems?

oldmanintheskydidntdoit:
I know it's not what you are after but
< http://www.talkorigins.org/faqs/fitness/ >
is the first result for alot of your terms.
---------------------QUOTE-------------------



oldmanintheskydidntdoit,

Thank you for this link. It is good enough for a start … and for the end also, because the arguments the author used in the favor of random genetic mutations, probably, the best arguments exist (unless JAM knows better ones).

In this article Edward E. Max recognizes the problem of accepting concept of evolution through random genetic mutations and brought examples that in his opinion show how random mutation plus selection can lead to improved "fitness."

He uses an example from book “The Blind Watchmaker” by Richard Dawkins in which a computer was programmed to generate random sequences to see if it would ever generate a line from Hamlet: "Methinks it is a Weasel." using 27 characters. Since choosing all alternatives it would take a million and million years for the correct sequence to be printed, Dawkins argues that the real evolutionist model is that modern amino acid sequences evolved by successive steps in which random mutations of pre-existing sequences were subjected to selection.

To prove this concept the computer was programmed to make multiple copies (progeny) of this sequence, while introducing random "errors" (mutations) into the copies. The computer examined all the mutated progeny AND SELECTED THE ONE THAT HAD MOST SIMILARITY (however slight) to the line from Hamlet. Instead of taking millions of years, the computer generated "Methinks it is a Weasel" in about half an hour.

I am really surprised by this example, because by introduction the selection of the one that HAD MOST SIMILARITY TO THE LINE FROM HAMLET this process is as random as spray-painting using a stencil. I think that this example it better illustrates ID point of view than Neo Darwinism.

Authors’ arguments in the   “Antibody Genes” section, I think, are also very week, because the “template” of antigen plays role of selective (deterministic) agent and therefore a role of chance is diminished. By the way, the chance also play role in the directed processes like developing antibiotics by pharmaceutical industry: a large variety of them exists on market and even higher numbers of them are just prototypes that never left research laboratory.

I could never understood why evolutionists put a wagon in front of horse by claming that they do know how living things were involving (random mutation plus selection) while the rest of the Life Sciences still struggle with the basics questions what is the life and how it operates even for the most primitive organisms.

So can we just admit that we do not know yet what a mechanism of evolution is? This could be a good start in solving this mystery.
Posted by: Wesley R. Elsberry on Jan. 13 2008,11:56

I take it Mark didn't bother to read Dawkins' critique of "weasel"'s "distant ideal target". That puts him in the company of just about every other antievolution advocate.
Posted by: oldmanintheskydidntdoit on Jan. 13 2008,11:59

The watchmaker example is far too simple to draw conclusions regarding what RM+NS can or cannot do.
Posted by: Erasmus, FCD on Jan. 13 2008,12:03

It is however complex enough to sort the wheat from the chaff.

Mark, meet chaff.
Posted by: Wesley R. Elsberry on Jan. 13 2008,12:12

And Mark doesn't appear to have read even the Edward Max page, which includes this response to the criticism leveled:



---------------------QUOTE-------------------

1. The target sequence was specified by an intelligent designer.

The fact that the target sequence in the "weasel" model was chosen in advance is an unavoidable consequence of Dawkins's goal of contrasting the single-step selection model with the model of multiple sequential rounds of mutation and selection. The creationist single-step model also starts with a specific protein sequence and then tries to calculate the odds of ever achieving this target sequence by a single selection step from random sequences; thus, a target sequence is specified in advance for either model. (Incidentally, whether this target sequence originally derived from an intelligent design or an evolutionary process is irrelevant to the question of whether it can be created anew by a procedure involving randomness and selection. In particular, Dawkins's choice of a 28-letter line from Shakespeare rather than a 28-residue amino acid sequence from a known protein is irrelevant in judging the relative efficacies of the two procedures in reproducing the target sequence.) The result of Dawkins's exercise is to show that the single-step procedure is essentially incapable of arriving at the target sequence within a reasonable timeframe, while the sequential-step procedure can readily achieve the same pre-specified target sequence. This difference is all that Dawkins was trying to show. Thus the complaint that "specification of the target sequence in advance weakens Dawkins's result" is not valid, in that this same feature (specifying a target sequence in advance) is applied equally to both models, as it must be to compare their efficacy.

---------------------QUOTE-------------------


Posted by: Daniel Smith on Jan. 13 2008,17:51

Responses such as these...
 
Quote (Richard Simons @ Jan. 12 2008,09:05)
It is similar with Schindewolf's ideas. 'Here is an explanation for different organisms apparently following the same evolutionary path.' - 'How was it implemented?' - 'Hush. We don't talk about that.'
---------------------QUOTE-------------------


   
Quote (Henry J @ Jan. 12 2008,21:58)
That's quite interesting. But near as I can tell, it's not talking about evolution of the DNA for that protein, it's talking about what the protein does after it's been synthesized.
---------------------QUOTE-------------------


   
Quote (Assassinator @ Jan. 13 2008,07:06)
As far as I can see, you're talking about protein folding, we know why that happens. It's biochemistry.
---------------------QUOTE-------------------


   
Quote (Albatrossity2 @ Jan. 13 2008,08:19)
(---odious tard by another IDiot deleted-------)
---------------------QUOTE-------------------


...lead me to believe that none of you have bothered to read any of the material I've presented thus far.

Let me ask this:  Has anyone here read anything by Schindewolf or Berg?  Did any of you read the Denton papers I linked to?  How about any of the ENCODE consortium papers I cited?

And if not, why not?
Posted by: Daniel Smith on Jan. 13 2008,18:11

Quote (Albatrossity2 @ Jan. 13 2008,08:19)
     
Quote (Daniel Smith @ Jan. 12 2008,19:11)
           
Quote (Assassinator @ Jan. 12 2008,14:50)
Then what's your problem with the chronological order? We know that life arose step by step, in a certain order (the very first steps of life are unknown, then we've got the theorised RNA-world, DNA-organisms, recognisable microbial life, multi-cellular sea life, multi-cellular land life etc etc). Then what's your problem?
---------------------QUOTE-------------------


I think you must've missed the first 30 or so pages of this discussion.  I came here to discuss the theories of  Schindewolf and Berg.  Both of them believe in evolution.  The only difference is that they deny "Selection" as the mechanism by which evolution progresses from type to type.  Both favor nomogenesis (evolution by law) instead.  In fact, that's the title of Berg's book.  While Berg did not propose a mechanism for his theory (other than physical law), Schindewolf proposed Goldschmidt's "systemmutation" of chromosomal re-ordering, which has been refined today by Davison as the semi-meiotic hypothesis.

Recent findings that suggest protein folds are more a product of natural law than selection would seem to vindicate these long neglected scientists:  

(---odious tard by another IDiot deleted-------)

So these findings would seem to vindicate both Schindewolf and Berg who knew that evolution must've happened lawfully, but just didn't know how.
---------------------QUOTE-------------------


I was trying to stay out of this conversation, because it is abundantly clear that Daniel has no clues about recent advances in biology or biochemistry. But this post is just way too stupid to ignore.

I'll let JAM handle the gory details, but it needs to be pointed out that the notion that "protein folds are more a product of natural law than selection" is a strawman. If it is not a strawman, Daniel, please document where any reputable scientist claims that natural selection governs the molecular processes involved in protein folding.
---------------------QUOTE-------------------


I've been searching through the various papers that cite the Denton papers for negative comments about his hypothesis but have yet to find any.
This leads me to believe that the reputable scientists that actually work in his field don't hold his views in contempt like the posters on this board do.  If you can point me to a published paper where the authors take a stance against Denton's hypothesis, please do.
     

---------------------QUOTE-------------------
This sort of argument bespeaks not only a profound misunderstanding of evolutionary theory (which Daniel has already demonstrated abundantly), but a profound ignorance about the molecular processes that occur within cells.

Here's a clue, Daniel. It would be a huge surprise if the laws of chemistry and physics did NOT govern the folding of proteins and other biological macromolecules. To claim that these obvious and experimentally determined facts are vindication of Schindewolf and Berg's half-baked notions is profoundly ignorant.
---------------------QUOTE-------------------


So you're saying that a limited number of protein folds, given an infinite number of potential amino acid sequences available for selection, is a prediction of the MET?
Why then do so many of these scientists use words like "surprising", when referring to the discovery that there are only a finite number of protein folds?
Posted by: JAM on Jan. 13 2008,18:24

Quote (Daniel Smith @ Jan. 13 2008,18:11)
I've been searching through the various papers that cite the Denton papers for negative comments about his hypothesis but have yet to find any.
---------------------QUOTE-------------------


You're pathetic. Biology isn't rhetoric.

If you think Denton's hypothesis is so wonderful, why don't you and/or Denton test it and publish data instead of rhetoric?


---------------------QUOTE-------------------
This leads me to believe that the reputable scientists that actually work in his field don't hold his views in contempt like the posters on this board do.
---------------------QUOTE-------------------


Has anyone who actually works in Denton's field tested his hypothesis?

Precisely what IS Denton's field, Dan? Your criterion is blatantly dishonest.


---------------------QUOTE-------------------
If you can point me to a published paper where the authors take a stance against Denton's hypothesis, please do.
---------------------QUOTE-------------------


Biology isn't about taking stances. It's about TESTING hypotheses and publishing the data, not crap like Denton's repetitive musings.


---------------------QUOTE-------------------
So you're saying that a limited number of protein folds, given an infinite number of potential amino acid sequences available for selection, is a prediction of the MET?
---------------------QUOTE-------------------


No, moron, it's a prediction of physical biochemistry.


---------------------QUOTE-------------------
Why then do so many of these scientists use words like "surprising", when referring to the discovery that there are only a finite number of protein folds?
---------------------QUOTE-------------------


"Surprising" doesn't even suggest that "the pseudoscientists who could never be bothered to test their hypotheses were correct."
Posted by: Henry J on Jan. 13 2008,18:54



---------------------QUOTE-------------------
Responses such as these...
---------------------QUOTE-------------------



I based my comment on the section that you quoted, which usually implies that the quoter thinks it supports something he said. It didn't appear to me to even address what you've been saying, hence my comment.

Henry
Posted by: Albatrossity2 on Jan. 13 2008,20:59

Quote (Daniel Smith @ Jan. 13 2008,18:11)
 I've been searching through the various papers that cite the Denton papers for negative comments about his hypothesis but have yet to find any.
This leads me to believe that the reputable scientists that actually work in his field don't hold his views in contempt like the posters on this board do.  If you can point me to a published paper where the authors take a stance against Denton's hypothesis, please do.
                   

---------------------QUOTE-------------------
This sort of argument bespeaks not only a profound misunderstanding of evolutionary theory (which Daniel has already demonstrated abundantly), but a profound ignorance about the molecular processes that occur within cells.

Here's a clue, Daniel. It would be a huge surprise if the laws of chemistry and physics did NOT govern the folding of proteins and other biological macromolecules. To claim that these obvious and experimentally determined facts are vindication of Schindewolf and Berg's half-baked notions is profoundly ignorant.
---------------------QUOTE-------------------


So you're saying that a limited number of protein folds, given an infinite number of potential amino acid sequences available for selection, is a prediction of the MET?
Why then do so many of these scientists use words like "surprising", when referring to the discovery that there are only a finite number of protein folds?
---------------------QUOTE-------------------


Daniel

That Denton paper you cited, published in 2003, has been cited a grand total of 4 (four) times. That is not exactly the hallmark of a seminal paper. Three of those papers have never been cited; one of them has been cited exactly another four times. No biological revolution seems imminent there. Exactly none of these four cite either Berg or Schindewolf. That is not exactly the hallmark of a resurrection of those half-baked notions. But I'll dig out those papers that cited Denton and let you know what I find out.

But that is a red herring. Let's quit talking about citations and talk about ideas, e.g. your original statement about that Denton paper. The point is, as stated before, that nobody in their right mind states "protein folds are more a product of natural law than selection" as if it was in doubt.

Let's break it down. There are various levels in the biological hierarchy, from atoms to biomes. Protein folding (at the subcellular level) is governed by the laws of chemistry and phsyics. Natural selection acts at the level of the organism (several levels up in the hierarchy), and affects populations (another level up).

So no, I'm not saying that "a limited number of protein folds, given an infinite number of potential amino acid sequences available for selection, is a prediction of the MET." Please quit putting words in my mouth. I'm saying that evolutionary theory says, appropriately, exactly NOTHING about protein folding per se. The notion that natural selection acts at the level of protein folding (rather than several levels up in the hierarchy) is, as noted before, a strawman. Furthermore, it is evidence of either profound ignorance or profound deceitfulness. I don't see any other options at this time. But I'd be happy to hear your explanation of this statement.
Posted by: Erasmus, FCD on Jan. 13 2008,21:13

Daniel

Again, with the snippy parts snipped



---------------------QUOTE-------------------
Post synthesis thought has recognized that there are many constraints imposed on the landscape of what 'could be'..., while emphasizing the role of contingency and... 'chance'.  
---------------------QUOTE-------------------



It's a mystery to me how you can argue that there is a burgeoning scientific revolution based on the misguided presumptions of some biologists with physics envy, and indeed it would be hard for me to understand if I did not also know that you have concluded that some sort of biblical creationism is best supported by the facts, without consulting the facts first.

Fact:  To some unknown, yet potentially enormous, degree, evolution of organisms has been directed by physical laws and constants such as gravity, the weak force, the strong force, arbitrary wavelengths and frequencies of available energy in our sector of the universe, etc, AND NOT BY NATURAL SELECTION.

I believe you missed a little book by Voltaire, you should check it out if you think the idea that protein folding is not a function of natural selection is an earthshaking observation.
Posted by: stevestory on Jan. 13 2008,21:18

Dan Smith:



---------------------QUOTE-------------------
This leads me to believe that the reputable scientists that actually work in his field don't hold his views in contempt like the posters on this board do.  If you can point me to a published paper where the authors take a stance against Denton's hypothesis, please do.
---------------------QUOTE-------------------



Albatrossity2:



---------------------QUOTE-------------------
That Denton paper you cited, published in 2003, has been cited a grand total of 4 (four) times. That is not exactly the hallmark of a seminal paper. Three of those papers have never been cited; one of them has been cited exactly another four times. No biological revolution seems imminent there. Exactly none of these four cite either Berg or Schindewolf. That is not exactly the hallmark of a resurrection of those half-baked notions.
---------------------QUOTE-------------------



Looks like the scientific community has basically ignored Denton's stupid ideas.



Ugarte: You despise me, don't you?

Rick: If I gave you any thought I probably would.
Posted by: Richard Simons on Jan. 13 2008,22:08

Daniel, as I mentioned earlier, it is not easy for me to get hold of literature such as Schindewolf's book (I do not have access to interlibrary loan). That is why I have been asking you to provide details of the putative mechanisms for determining the future course required for evolution of an organism, for storing this information and for implementing the scheduling. You replied that you did not know, but have shown no hint of curiosity as to what these mechanisms could be. You have also shown no sign of awareness that this problem alone stops Schindewolf's ideas dead in their tracks.

BTW, thinking of checking up on things, have you dug down in your garden yet to see if you can find evidence of a global flood?
Posted by: Albatrossity2 on Jan. 14 2008,06:50

Quote (stevestory @ Jan. 13 2008,21:18)
Looks like the scientific community has basically ignored Denton's stupid ideas.
---------------------QUOTE-------------------


Well, Denton is saying nothing surprising - physical laws govern subcellular activities like protein folding. So they are not so much stupid as they are irrelevant in the context of evolution. I haven't yet read that Denton paper, but I can also tell you (from the information on Web of Science) that it does not cite either Berg or Schindewolf.

Thus it is not surprising that Denton's stuff is ignored. What Daniel is doing, however, is pretending that evolutionary theory has some predictions about how evolutionary processes govern this subcellular realm. Strawman, pure and simple. Furthermore he is pretending that it supports his vague notions based on Schindewolf and Berg. And that is just plain wrong; statements like that, written by Denton, would be excoriated by reviewers.

So, Daniel, when you answer, please heed the request that I posted earlier. Please cite a reputable scientist or two who say that evolutionary theory has predictions that imply that natural selection can override physical laws governing protein folding.

This seems to be based on the standard creationist confusion of abiogenesis and evolution. Physical laws certainly govern abiogenesis, and we don't know a lot about abiogenesis other than that. There are legitimate hypotheses out there, based on the similarities of intermediary metabolism in all living organisms, postulating that early life was as driven by physical/chemical constraints as it was by the requirements to develop a method of inheritance. This mixed paradigm makes a lot of sense, can generate hypotheses, and lots of speculation (e.g. Smith & Hororwitz, "Universality in intermediary metabolism", PNAS, 101(36):13168, 2004). But none of that is primed to overthrow evolutionary theory; it merely changes how we look at abiogenesis. So Daniel, here's another clue. Abiogenesis is not the same thing as evolution.
Posted by: oldmanintheskydidntdoit on Jan. 14 2008,07:27

Quote (Daniel Smith @ Jan. 13 2008,18:11)
Why then do so many of these scientists use words like "surprising", when referring to the discovery that there are only a finite number of protein folds?
---------------------QUOTE-------------------


Ah, that old one.

Daniel, if people knew what it was they were going to find out before they found it out then it would hardly be research would it? If you knew the answers before you set out, why would you set out in the first place? So is it really surprising that people are "surprised" when they find something new? Something perhaps unexpected?

Are you joining the uncommondescent gang in their love of pointing to "how scientists were surprised" by a finding and somehow thinking this supports Intelligent design? If so, the barrel has been empty for a while...

No doubt the lack of "surprise" in your "research" is because the bible provides all answers from the start. Nothing to be surprised about, the answers are all immutable and timeless for you. Not really getting you anywhere is it though?

And could you tell me what the signs of the global flood are that I should be looking out for when flying next, apart from "all of the world"? Something a bit more specific would help.

Daniel, in your opinion are  Schindewolf, Berg, and their theories of constrained evolution and evolution by law compatible with a 6000 year old earth and a global flood?

If not, what will you rule out?

Either way, progress will have been made and your worldview will be that little more accurate.
Posted by: Daniel Smith on Jan. 14 2008,10:50

Quote (Albatrossity2 @ Jan. 14 2008,06:50)
What Daniel is doing, however, is pretending that evolutionary theory has some predictions about how evolutionary processes govern this subcellular realm. Strawman, pure and simple.
---------------------QUOTE-------------------


If selection does not act at the subcellular level, why then is it said to "constrain" DNA sequences?  The MET surely has a lot to say about DNA sequences - does selection "skip a level" and not act upon protein folds?
Posted by: Daniel Smith on Jan. 14 2008,10:52

Denton (with others) wrote several papers on this subject - each being cited numerous times, none AFAIK, have been cited unfavorably.
Posted by: Daniel Smith on Jan. 14 2008,11:03

Quote (Wesley R. Elsberry @ Jan. 13 2008,11:56)
I take it Mark didn't bother to read Dawkins' critique of "weasel"'s "distant ideal target". That puts him in the company of just about every other antievolution advocate.
---------------------QUOTE-------------------


Dawkins' attempt to illustrate RM+NS with his "Methinks it is a Weasel." example seems more like an example of constrained evolution to me.
The fact that the goal was predetermined, and functional sentences would have to be selected against if they were not on a path towards "Methinks it is a Weasel.", completely destroys the NS part of it IMO.
It is "goal oriented", predetermined selection he illustrates - and which he shows works very well thank you.
Posted by: oldmanintheskydidntdoit on Jan. 14 2008,11:19

Quote (Daniel Smith @ Jan. 14 2008,11:03)
Quote (Wesley R. Elsberry @ Jan. 13 2008,11:56)
I take it Mark didn't bother to read Dawkins' critique of "weasel"'s "distant ideal target". That puts him in the company of just about every other antievolution advocate.
---------------------QUOTE-------------------


Dawkins' attempt to illustrate RM+NS with his "Methinks it is a Weasel." example seems more like an example of constrained evolution to me.
The fact that the goal was predetermined, and functional sentences would have to be selected against if they were not on a path towards "Methinks it is a Weasel.", completely destroys the NS part of it IMO.
It is "goal oriented", predetermined selection he illustrates - and which he shows works very well thank you.
---------------------QUOTE-------------------


Wrong, wrong wrong wrong wrong.

Daniel, what's the goal for evolution?

Your abuse of the Weasel example simply illustrates your ignorance of the real point Dawkins' was trying to make.

Have you read the book?
Posted by: oldmanintheskydidntdoit on Jan. 14 2008,11:20

Quote (Daniel Smith @ Jan. 14 2008,10:52)
Denton (with others) wrote several papers on this subject - each being cited numerous times, none AFAIK, have been cited unfavorably.
---------------------QUOTE-------------------


List them.
Posted by: Albatrossity2 on Jan. 14 2008,11:29

Quote (Daniel Smith @ Jan. 14 2008,10:50)
 
Quote (Albatrossity2 @ Jan. 14 2008,06:50)
What Daniel is doing, however, is pretending that evolutionary theory has some predictions about how evolutionary processes govern this subcellular realm. Strawman, pure and simple.
---------------------QUOTE-------------------


If selection does not act at the subcellular level, why then is it said to "constrain" DNA sequences?  The MET surely has a lot to say about DNA sequences - does selection "skip a level" and not act upon protein folds?
---------------------QUOTE-------------------


This really shouldn't have to be explicitly stated more than once, but since you seem to be so confused, I'll try again.

Selection acts on organisms. Properties of those organisms certainly depend upon the DNA, and certainly depend upon what happens at the subcellular level. The DNA determines the sequence of the proteins; the folding of those proteins is determined by both the primary sequence AND physical chemical laws. If those proteins fold into a conformation that is functional and beneficial to the entire organism, that organism may have a selective advantage. It may leave more offspring, and those DNA sequences will be more widely represented in the population.

So what you want to believe, apparently, is that natural selection mysteriously influences the folding of proteins. That is exactly backward. Protein conformations depend upon physical and chemical laws, and those conformations have some part (along with the environment, other organisms in the population, genetic drift, etc) in determining the survival and fitness of the organism in which those proteins reside. Selection acts on the organism. If there was no selection, those proteins would still fold exactly the same. Both physical laws AND natural selection act on organisms; it is not an either/or situation. What part of that seems mysterious to you, exactly?

So let's review. You wrote "protein folds are more a product of natural law than selection" as if that was somehow a strike against evolutionary theory, or as if it was surprising. It is neither. I asked you to provide some evidence (in the form of citations of published papers) that scientists advocated a role for natural selection as a determinant of protein folding. I asked twice. So far you have not answered that question, but you did move the goalposts to another macromolecule, DNA. Furthermore in true creationist fashion, you merely provided more questions.

I have answered your questions. You need to answer mine. If you cannot, then it is obvious that you have constructed a strawman with your statements and quotes from Denton. As I said before, that statement in bold above implies either a profound ignorance of the nature of biology and chemistry, or a profound deceitfulness. Which is it?

As for your second point (Denton's work has been cited, and not unfavorably), that has also been addressed. It says nothing surprising about evolution. It addresses some questions about abiogenesis. Abiogenesis and evolution are not the same thing, even though it seems important for you to continually conflate them.

Final clue - pointing out gaps in our knowledge of either evolution or abiogenesis is easy. This activity does not, however, give any support to alternative notions such as nomogenesis, creationism, or ID. As JAM has repeatedly pointed out to you, positive support for your hypothesis will require active experimentation and publication of the results so that the scientific world can take a whack at them, just as you are taking a whack at evolutionary theory.
Posted by: Albatrossity2 on Jan. 14 2008,11:43

Quote (oldmanintheskydidntdoit @ Jan. 14 2008,11:20)
   
Quote (Daniel Smith @ Jan. 14 2008,10:52)
Denton (with others) wrote several papers on this subject - each being cited numerous times, none AFAIK, have been cited unfavorably.
---------------------QUOTE-------------------


List them.
---------------------QUOTE-------------------


Daniel is right about this narrow but irrelevant point. For example, a paper by Denton et al. in the Journal of Theoretical Biology was cited in passing in that PNAS paper that I noted in an earlier comment.

BUT here's the rub.

1) Denton is careful to say nothing about ID, nomogenesis, or any other woo in those papers. He is addressing theoretical aspects of abiogenesis (hence the use of the term "pre-Darwinian" rather than "anti-Darwinian).

2) These are all theoretical papers, in journals that accept theoretical papers. AFAIK, he has produced no experimental papers.

3) As pointed out before, he is saying nothing that is surprising or earth-shattering. Physical and chemical laws govern protein folding. Big deal. His papers are merely verbose statements about the flaming obvious, which is perfectly consistent with the low citation rate he enjoys.

If Denton did mention this stuff as support for ID, or did act as if he was overthrowing the strawman of natural selection somehow being a direct determinant of protein folding, I suspect that his citation count would go higher, but none of the citations would be very favorable!

So Daniel is right about this. Unfortunately for him, however, it's completely irrelevant to his points about nomogenesis, etc. Another red herring for the steaming pile that has accumulated on this thread already.
Posted by: Mark Iosim on Jan. 14 2008,15:11

Wesley:        

---------------------QUOTE-------------------
And Mark doesn't appear to have read even the Edward Max page, which includes this response to the criticism leveled:      

---------------------QUOTE-------------------


   1. The target sequence was specified by an intelligent designer.
The fact that the target sequence in the "weasel" model was chosen in advance is an unavoidable consequence of Dawkins's goal of contrasting the single-step selection model with the model of multiple sequential rounds of mutation and selection….
...
…Thus the complaint that "specification of the target sequence in advance weakens Dawkins's result" is not valid, in that this same feature (specifying a target sequence in advance) is applied equally to both models, as it must be to compare their efficacy.

---------------------QUOTE-------------------


---------------------QUOTE-------------------


Wesley,

Regarding the "weasel" model, or any other Genetic Algorithm (GA) I don’t have a problem with target sequence chosen in advance. I have a problem with the inadequacy of this modeling with the biological evolution for another reason.

Within GA the Fitness Function enables reproduction of a candidate that demonstrates even the very remote resemblance to fitness function. In turn, during biological evolution, randomly generated candidates first have to reach the threshold of usefulness to be reproduced. Without this reproduction, we cannot use the "weasel" model of multiple sequential rounds of mutation and selection, but the single-step selection model instead that brings us back to the prohibited long evolution process.

I do not want to be misunderstood, so let me restate my position.
I do not have problem with Darwin’s theory of evolution itself and even with Darwin’s explanation of its mechanism in terms of gradual changes and selection – it was a very clever explanation given how little was known at that time. But I do have a problem with the current state of affairs with very little progress in this area. Instead we are religiously repeating the same mantra about natural selection pretending that this is a sufficient explanation of the MECHANISM of evolution.

I did read Edward E. Max page. I also read Genetic Algorithms and Evolutionary Computation by Adam Marczyk < http://www.talkorigins.org/faqs/genalg/genalg.html# > and explored  some of its links, but I still didn’t find the satisfactory explanation of mechanism of evolution’s changes. In this regard, I think, that Behe and Dembski ask good questions even though I do not accept their answers, the same way as I don’t accept yours.
Posted by: swbarnes2 on Jan. 14 2008,16:03

Quote (Mark Iosim @ Jan. 14 2008,15:11)
Regarding the "weasel" model, or any other Genetic Algorithm (GA)
---------------------QUOTE-------------------



The weasel example is trivial, and only meant to prove a very limited point.  Most GA's are more sophisiticated.  

 

---------------------QUOTE-------------------
In turn, during biological evolution, randomly generated candidates first have to reach the threshold of usefulness to be reproduced.
---------------------QUOTE-------------------



How is this a problem for a GA?  Enough random starts, and you will pass any threshold you like.

The hard fact is that GA's have and do succeed in solving problems that humans don't know the answers too.

 

---------------------QUOTE-------------------
Without this reproduction, we cannot use the "weasel" model of multiple sequential rounds of mutation and selection, but the single-step selection model instead that brings us back to the prohibited long evolution process.
---------------------QUOTE-------------------



Okay, so on that talkorigins page, which of the GAs listed do you claim uses a weasel algorithm?  The one that designed a asymetrical antenna?  The one that made a circuit board using only a fraction of the logic gates that humans would have?

 

---------------------QUOTE-------------------
but I still didn’t find the satisfactory explanation of mechanism of evolution’s changes.
---------------------QUOTE-------------------



Evolutionists can show with math and evidence where ID advocates are wrong.

Can you show with sound math and evidence where evolutionists are wrong?
Posted by: oldmanintheskydidntdoit on Jan. 14 2008,16:16

Quote (Mark Iosim @ Jan. 14 2008,15:11)
I have a problem with the inadequacy of this modeling with the biological evolution for another reason.
---------------------QUOTE-------------------


One day, perhaps in our lifetimes, we'll be able to model biology from the gluon to the electron to the molecule to the cell. Maybe even without any actual "rules" about biology, it'll come from emergent behaviour due to the accuracy of the simulation. No intelligence required.

Perhaps, if the wildest quantum interpretations/speculations are right, one day living things could use the multiverse as a computer and simulate processes that in fact use more then the available number of bits in this single universe. Simulation of improbable events then just becomes a somewhat different proposition. Not in our lifetimes :)

I understand you were making a somewhat different point, but I'm sure everybody would agree better models are desirable. And current models do show evolution as a useful and working process that generates results with no pre programmed target. No Weasel.

What do you make of
< http://ic.arc.nasa.gov/projects/esg/research/antenna.htm >
 

---------------------QUOTE-------------------
The fitness function used to evaluate antennas is a function of the voltage standing wave ratio (VSWR) and gain values on the transmit and receive frequencies. VSWR is a way to quantify reflected-wave interference, and thus the amount of impedance mismatch at the junction. VSWR is the ratio between the highest voltage and the lowest voltage in the signal envelope along a transmission line.

The two best antennas found, one (ST5-3-10) from a GA that allowed branching and one (ST5-4W-03) from a GA that did not, were fabricated and tested. Antenna ST5-3-10 is a requirements-compliant antenna that was built and tested on an antenna test range. While it is slightly difficult to manufacture without the aid of automated wire-forming and soldering machines, it has a number of benefits as compared to the conventionally-designed antenna.
---------------------QUOTE-------------------





Also here
< http://pandasthumb.org/archives/2007/11/dumbest-attack.html >
and the linked posts.
Posted by: Wesley R. Elsberry on Jan. 14 2008,17:08

Quote (Mark Iosim @ Jan. 14 2008,15:11)
Wesley:              

---------------------QUOTE-------------------
And Mark doesn't appear to have read even the Edward Max page, which includes this response to the criticism leveled:            

---------------------QUOTE-------------------


   1. The target sequence was specified by an intelligent designer.
The fact that the target sequence in the "weasel" model was chosen in advance is an unavoidable consequence of Dawkins's goal of contrasting the single-step selection model with the model of multiple sequential rounds of mutation and selection….
...
…Thus the complaint that "specification of the target sequence in advance weakens Dawkins's result" is not valid, in that this same feature (specifying a target sequence in advance) is applied equally to both models, as it must be to compare their efficacy.

---------------------QUOTE-------------------


---------------------QUOTE-------------------


Wesley,

Regarding the "weasel" model, or any other Genetic Algorithm (GA) I don’t have a problem with target sequence chosen in advance. I have a problem with the inadequacy of this modeling with the biological evolution for another reason.

Within GA the Fitness Function enables reproduction of a candidate that demonstrates even the very remote resemblance to fitness function. In turn, during biological evolution, randomly generated candidates first have to reach the threshold of usefulness to be reproduced. Without this reproduction, we cannot use the "weasel" model of multiple sequential rounds of mutation and selection, but the single-step selection model instead that brings us back to the prohibited long evolution process.

I do not want to be misunderstood, so let me restate my position.
I do not have problem with Darwin’s theory of evolution itself and even with Darwin’s explanation of its mechanism in terms of gradual changes and selection – it was a very clever explanation given how little was known at that time. But I do have a problem with the current state of affairs with very little progress in this area. Instead we are religiously repeating the same mantra about natural selection pretending that this is a sufficient explanation of the MECHANISM of evolution.

I did read Edward E. Max page. I also read Genetic Algorithms and Evolutionary Computation by Adam Marczyk < http://www.talkorigins.org/faqs/genalg/genalg.html# > and explored  some of its links, but I still didn’t find the satisfactory explanation of mechanism of evolution’s changes. In this regard, I think, that Behe and Dembski ask good questions even though I do not accept their answers, the same way as I don’t accept yours.
---------------------QUOTE-------------------



What a difference a page makes.

"One Page Ago Mark":



---------------------QUOTE-------------------

Can you (JAM) refer me to any sort of statistical analysis that in your opinion demonstrates that random mutations could be responsible for adaptive changes in biological systems?

---------------------QUOTE-------------------



That noise you hear? Goalposts being moved along.

About "weasel"... a page ago, Mark was saying that he thought that the use of a distant ideal target made it a demonstration of intelligent design or the like.

"One Page Ago Mark":



---------------------QUOTE-------------------

I am really surprised by this example,because by introduction the selection of the one that HAD MOST SIMILARITY TO THE LINE FROM HAMLET this process is as random as spray-painting using a stencil. I think that this example it better illustrates ID point of view than Neo Darwinism.

---------------------QUOTE-------------------



Now he says that he doesn't have a problem with it on the score of the use of the distant ideal target, but on other grounds.

"New Page Mark":



---------------------QUOTE-------------------

Regarding the "weasel" model, or any other Genetic Algorithm (GA) I don’t have a problem with target sequence chosen in advance. I have a problem with the inadequacy of this modeling with the biological evolution for another reason.

Within GA the Fitness Function enables reproduction of a candidate that demonstrates even the very remote resemblance to fitness function. In turn, during biological evolution, randomly generated candidates first have to reach the threshold of usefulness to be reproduced. Without this reproduction, we cannot use the "weasel" model of multiple sequential rounds of mutation and selection, but the single-step selection model instead that brings us back to the prohibited long evolution process.

---------------------QUOTE-------------------



Now, on the new page, Mark says of course he read the Edward Max text... which makes for a new mystery, since there was no indication a page ago that Mark had ever encountered anything to give him the slightest pause in saying what he said then about the "weasel" program and distant ideal targets.

Besides which, "weasel" is a pedagogical toy example, not the sum total of the progress in the field of evolutionary computation.

Artificial life systems, such as Avida, can be configured such that the digital organisms contain -- and make modifiable -- the code that performs the self-replication process, making them an instance of evolution, not a simulation of evolution. Given an ancestral digital organism capable of reproduction and nothing else, Avida provides an experimental platform to do precisely what last page's rant said was the issue: examine the process of adaptive change by means of selection. And they do < adapt >.

Now, about the new goalpost position: it doesn't sound coherent. At least, I'm still not understanding Mark's position, despite the phrasing. Do biologists think that natural selection is sufficient to describe life's history? I think a vanishingly small fraction of biologists would venture to say that only natural selection has been active; where things get more contentious is in determining exactly how much of life's history is described best in terms of genetic drift and other non-selective mechanisms, as opposed to how much is due to natural selection. So Mark's new goalpost appeals to facts not in evidence, to wit, that anyone is claiming that only natural selection causes evolutionary change, or that these non-existent persons are somehow non-existently, but religiously, repeating some mantra. Another fact not in evidence is the claimed "very little progress in the area". What area might that be, Mark? Evolutionary science comprises thousands of research papers published every year, without even an apparent relative  diminishment in recent years to give something for Mark's claim to hang on. What the heck are you trying to say, Mark, and can you be bothered to substantiate any part of it?
Posted by: JAM on Jan. 14 2008,17:12

Quote (Daniel Smith @ Jan. 14 2008,10:50)
 
Quote (Albatrossity2 @ Jan. 14 2008,06:50)
What Daniel is doing, however, is pretending that evolutionary theory has some predictions about how evolutionary processes govern this subcellular realm. Strawman, pure and simple.
---------------------QUOTE-------------------


If selection does not act at the subcellular level, why then is it said to "constrain" DNA sequences?
---------------------QUOTE-------------------


You're delusional. If you recall your false prediction, selection only acts on DNA sequences when they affect fitness at the organismal level.


---------------------QUOTE-------------------
The MET surely has a lot to say about DNA sequences - does selection "skip a level" and not act upon protein folds?
---------------------QUOTE-------------------


Selection doesn't "skip a level." You just don't know enough biology (less than a smart 8th-grader) to understand what informed people are saying, making you vulnerable to making ridiculously hasty generalizations in your desperate attempt to defend your bad theology.
Posted by: Mr_Christopher on Jan. 14 2008,17:26

Danny Boy, if you really want to stump the darwinistas simply ask them if evolution is true why don't we see any half ape half horses.

Ha ha ha they'll NEVER be able to answer that one!

Praise the Mighty Space Alien, brother!
Posted by: Daniel Smith on Jan. 14 2008,18:27

Quote (Albatrossity2 @ Jan. 14 2008,11:43)
     
Quote (oldmanintheskydidntdoit @ Jan. 14 2008,11:20)
           
Quote (Daniel Smith @ Jan. 14 2008,10:52)
Denton (with others) wrote several papers on this subject - each being cited numerous times, none AFAIK, have been cited unfavorably.
---------------------QUOTE-------------------


List them.
---------------------QUOTE-------------------


Daniel is right about this narrow but irrelevant point. For example, a paper by Denton et al. in the Journal of Theoretical Biology was cited in passing in that PNAS paper that I noted in an earlier comment.

BUT here's the rub.

1) Denton is careful to say nothing about ID, nomogenesis, or any other woo in those papers. He is addressing theoretical aspects of abiogenesis (hence the use of the term "pre-Darwinian" rather than "anti-Darwinian).

2) These are all theoretical papers, in journals that accept theoretical papers. AFAIK, he has produced no experimental papers.

3) As pointed out before, he is saying nothing that is surprising or earth-shattering. Physical and chemical laws govern protein folding. Big deal. His papers are merely verbose statements about the flaming obvious, which is perfectly consistent with the low citation rate he enjoys.

If Denton did mention this stuff as support for ID, or did act as if he was overthrowing the strawman of natural selection somehow being a direct determinant of protein folding, I suspect that his citation count would go higher, but none of the citations would be very favorable!

So Daniel is right about this. Unfortunately for him, however, it's completely irrelevant to his points about nomogenesis, etc. Another red herring for the steaming pile that has accumulated on this thread already.
---------------------QUOTE-------------------


I think you are wrong about this.  Denton makes it very clear what "pre-Darwinian biology" means - and it's not abiogenesis:  

---------------------QUOTE-------------------
Before Darwin, the majority of leading biologists adhered to a Platonic model of nature, referred to by Owen (1849) in his classic monograph On the Nature of Limbs as ‘‘the Platonic cosmogony.’’ According to this conception, all the basic recurrent forms of the organic world, such as the pentadactyl design of the vertebrate limb, the body plans of the major phyla, the forms of leaves and so forth, as well as the recurrent forms of the inorganic realm, such as atoms, crystals, etc., represent the material manifestations of a finite set of immutable immaterial archetypes or ‘‘ideas’’ termed by Owen (1849) ‘‘predetermined or primal patterns.’’ These pre-existing abstract types or ideas are materialized, or to cite Owen (1849) again, ‘‘clothed in material garb,’’ by the agency of natural law, or more precisely in the case of organic forms by a special class of natural laws which applied uniquely to the vital realm--the celebrated ‘‘Laws of Form.’’

Denton et al, The Protein Folds as Platonic Forms: New Support for the Pre-Darwinian Conception of Evolution by Natural Law, (emphasis mine)
---------------------QUOTE-------------------


So how exactly does the term "pre-Darwinian biology" come to mean "abiogenesis" in your eyes?  I mean, look at the title of the paper for goodness sake!
Posted by: Daniel Smith on Jan. 14 2008,19:26

Here's my critique of the "GA as support for biological evolution via RM+NS" argument.

From the talk-origins page:
         

---------------------QUOTE-------------------
The GA then evaluates each candidate according to the fitness function. In a pool of randomly generated candidates, of course, most will not work at all, and these will be deleted. However, purely by chance, a few may hold promise - they may show activity, even if only weak and imperfect activity, toward solving the problem.
---------------------QUOTE-------------------


Here's the first problem in my eyes:  Natural selection does not select for "promise".   Also, reproductive fitness is not considered - since all non-eliminated candidates will reproduce equally for the duration of the GA.      

---------------------QUOTE-------------------
These promising candidates are kept and allowed to reproduce. Multiple copies are made of them, but the copies are not perfect; random changes are introduced during the copying process. These digital offspring then go on to the next generation, forming a new pool of candidate solutions, and are subjected to a second round of fitness evaluation. Those candidate solutions which were worsened, or made no better, by the changes to their code are again deleted;
---------------------QUOTE-------------------


OK, another problem: the candidates that were "made no better" are deleted.  They were good enough to be selected before, but now they are selected against.  While this is the correct way to improve a design, it surely doesn't imitate natural selection - which tends to stabilize populations by maintaining the status quo rather than eliminating all organisms that are not making progress toward a goal.          

---------------------QUOTE-------------------
but again, purely by chance, the random variations introduced into the population may have improved some individuals, making them into better, more complete or more efficient solutions to the problem at hand. Again these winning individuals are selected and copied over into the next generation with random changes, and the process repeats. The expectation is that the average fitness of the population will increase each round, and so by repeating this process for hundreds or thousands of rounds, very good solutions to the problem can be discovered.
---------------------QUOTE-------------------


The selection criteria rewards "promise", does not have anything to do with reproductive fitness, is unrealistic in regard to competition and has to do with the goal oriented solving of a problem. I have no doubt that these types of algorithms will work very well, but they don't mimic biological evolution (via RM+NS) IMO.
Posted by: Albatrossity2 on Jan. 14 2008,19:51

Quote (Daniel Smith @ Jan. 14 2008,18:27)
I think you are wrong about this.  Denton makes it very clear what "pre-Darwinian biology" means - and it's not abiogenesis:      

---------------------QUOTE-------------------
Before Darwin, the majority of leading biologists adhered to a Platonic model of nature, referred to by Owen (1849) in his classic monograph On the Nature of Limbs as ‘‘the Platonic cosmogony.’’ According to this conception, all the basic recurrent forms of the organic world, such as the pentadactyl design of the vertebrate limb, the body plans of the major phyla, the forms of leaves and so forth, as well as the recurrent forms of the inorganic realm, such as atoms, crystals, etc., represent the material manifestations of a finite set of immutable immaterial archetypes or ‘‘ideas’’ termed by Owen (1849) ‘‘predetermined or primal patterns.’’ These pre-existing abstract types or ideas are materialized, or to cite Owen (1849) again, ‘‘clothed in material garb,’’ by the agency of natural law, or more precisely in the case of organic forms by a special class of natural laws which applied uniquely to the vital realm--the celebrated ‘‘Laws of Form.’’

Denton et al, The Protein Folds as Platonic Forms: New Support for the Pre-Darwinian Conception of Evolution by Natural Law, (emphasis mine)
---------------------QUOTE-------------------


So how exactly does the term "pre-Darwinian biology" come to mean "abiogenesis" in your eyes?  I mean, look at the title of the paper for goodness sake!
---------------------QUOTE-------------------


Daniel

Are you really this thick naturally, or are you simply stringing this red herring out so that you hope that I will forget that you haven't answered my questions yet? If the latter, don't count on it. I'd appreciate, greatly, an answer, especially since I have answered all of yours so far, and will now answer the latest one. Your debt is building up...

I haven't read that < 2003 Biosystems paper that you originally cited >; interlibrary loan hasn't delivered it yet. But I can tell you what he said in that  2002 J. Theor. Biol. paper (Denton, M.J., Marshall, C.J., Legge, M., 2002. The protein folds as Platonic forms: new support for the pre-Darwinian conception of evolution by natural laws. J. theor. Biol. 219, 325–342.)
   

---------------------QUOTE-------------------
‘‘the lawful nature of the folds together with the intriguing fact that many of the 20 protogenic  amino acids—out of which the folds are constructed—are amongst the most common amino acids found in meteorites and the easiest amino acids to generate in pre-biotic syntheses is surely of considerable significance, consistent with and supporting a deterministic theory of the origin of life
---------------------QUOTE-------------------


FYI, the "origin of life" = abiogenesis.

FYI, "pre-biotic" = prior to the development of biological life.

FYI, pre-Darwinian also means, in this context, metabolic and chemical processes PRIOR to the development of a system of inheritance.

FYI, a system of inheritance is required for the mechanisms of Darwinian evolution to be effective.

So, despite your notion that "pre-Darwinian" might have a solely philosophical meaning, I think it is clear that Denton's focus is abiogenesis. These papers were published in biology journals, not philosophy journals. My interpretation is confirmed by my reading of all four (4) papers that cite this 2003 Biosystems paper; all the citations cite it in a context that is discussing abiogenesis.

I will report back on my reading of the 2003 Biosystems paper when I get my hands on it. In the meantime, I'm sticking with my interpretation of "pre-Darwinian".

And you're still avoiding questions. Please work on that.

thanks
Posted by: Wesley R. Elsberry on Jan. 14 2008,20:10



---------------------QUOTE-------------------

Here's my critique of the "GA as support for biological evolution via RM+NS" argument.

---------------------QUOTE-------------------



Learning something about (1) evolution and (2) evolutionary computation might be considered prerequisites for that sort of thing. Maybe things are different where you are.
Posted by: oldmanintheskydidntdoit on Jan. 15 2008,02:56

Quote (Daniel Smith @ Jan. 14 2008,19:26)
Natural selection does not select for "promise".
---------------------QUOTE-------------------


What does it select for then Daniel?
Posted by: Mark Iosim on Jan. 15 2008,04:13

Wesley:

Please, don’t accuse me in flip flopping and lying. I say what I do and do what I say. And if I make mistakes I admit them.

My previous comment about “weasel” example that create the targeted information same way as “spray-painting using a stencil” I referred not to the final target, but to the fact that in each generation of progeny computer performed artificial selection using the template (stencil) to select one that “HAD MOST SIMILARITY TO THE LINE FROM HAMLET”. The second time I referred to this example I tried to emphasize (and probably should say so) that this example demonstrates the statistical probability not for a natural selection, but for an artificial one because a “selectionist” (template) decides what will be reproduced and what not.

As you and other mentioned that "weasel" is a pedagogical toy example, I will treat it as such and for further analysis I will use more sophisticated GA algorithms. The area of GA is new for me and therefore I have to do my homework before responding to swbarnes2 (threshold of usefulness) and oldmanintheskydidntdoit about GA used to evolve WIRE ANTENNAS and learn about Artificial life systems, such as Avida. I will be back in a few days with my findings.

P.S. "very little progress in the area" I referred to MECHANISM of evolution. I will be back to this statement to conform or dismiss it depending on my further studies.
Posted by: IanBrown_101 on Jan. 15 2008,05:06

Quote (Mark Iosim @ Jan. 15 2008,10:13)
My previous comment about “weasel” example that create the targeted information same way as “spray-painting using a stencil” I referred not to the final target, but to the fact that in each generation of progeny computer performed artificial selection using the template (stencil) to select one that “HAD MOST SIMILARITY TO THE LINE FROM HAMLET”. The second time I referred to this example I tried to emphasize (and probably should say so) that this example demonstrates the statistical probability not for a natural selection, but for an artificial one because a “selectionist” (template) decides what will be reproduced and what not.
---------------------QUOTE-------------------


Swing and a miss.....

The line from Hamlet isn't particularly important as a target, but assume that the changes that are closest to the line are the ones which represent a positive change in the organism for its environment.

The selection is natural, because how close the line is represents how fit the organism is for the environment compared to the previous incarnation.
Posted by: Wesley R. Elsberry on Jan. 15 2008,06:41



---------------------QUOTE-------------------

I will be back in a few days with my findings.

---------------------QUOTE-------------------



Mark's going to become an expert commenter on evolutionary computation and its implications in "a few days"?

I've heard of setting bad schedules, but this takes the cake.
Posted by: Lou FCD on Jan. 15 2008,08:02

I was going to become an astrophysicist this weekend, but with Phreaky Phred Phelps coming to town, I might have to postpone that 'til next weekend.
Posted by: Erasmus, FCD on Jan. 15 2008,08:05

I just switched my car insurance to Geico.
Posted by: Tracy P. Hamilton on Jan. 15 2008,09:16

Quote (Lou FCD @ Jan. 15 2008,08:02)
I was going to become an astrophysicist this weekend, but with Phreaky Phred Phelps coming to town, I might have to postpone that 'til next weekend.
---------------------QUOTE-------------------


I think I will just listen to some Queen albums for my astrophysics training.
Posted by: Albatrossity2 on Jan. 15 2008,09:30

Clever banter aside, Mark's airy reply about "further studies" brings up a critical point that IDCists always fail to appreciate.

It does take time (often years) and effort to become conversant in some of these areas. When you couple that with the fact that many of these folks are barely conversant with biology at the intellectual level that we teach in junior high, it is frankly insulting to read a comment like Mark's last one.

Self-proclaimed, self-educated "experts" making bold categorical assertions (e.g. very little progress in understanding the MECHANISM of evolution, you know) tend to piss off the real experts, for good reasons, but lots of IDCists never seem to figure that out...
Posted by: Mark Iosim on Jan. 15 2008,17:31

IanBrown_101      

---------------------QUOTE-------------------

The line from Hamlet isn't particularly important as a target, but assume that the changes that are closest to the line are the ones which represent a positive change in the organism for its environment.
The selection is natural, because how close the line is represents how fit the organism is for the environment compared to the previous incarnation.
IanBrown_101
---------------------QUOTE-------------------


In this example, for selection to be natural the line must to be recognized by environment as meaningful - has to exceed a threshold of recognition. However the initial random line in this example is beyond recognition.

Lets assume that for line to become naturally recognizable (by human) as the line from Hamlet at least 80% of characters must be correctly identified (that is 22 characters). Therefore untill this critical number of correctly placed carachters will be reached the single-step selection evolutionary model must be used (that still means milions and milions years) and only ofter this treshold is reached the evolutionary model of multiple sequential rounds of mutation and selection could be applied.
Posted by: oldmanintheskydidntdoit on Jan. 15 2008,17:45



---------------------QUOTE-------------------
line must to be recognized by environment as meaningful
---------------------QUOTE-------------------


Which of these two has the most meaning?

a) "Q"
b) " "

Why 80%?
Posted by: Mr_Christopher on Jan. 15 2008,18:00

Quote (Albatrossity2 @ Jan. 15 2008,09:30)
Clever banter aside, Mark's airy reply about "further studies" brings up a critical point that IDCists always fail to appreciate.

It does take time (often years) and effort to become conversant in some of these areas. When you couple that with the fact that many of these folks are barely conversant with biology at the intellectual level that we teach in junior high, it is frankly insulting to read a comment like Mark's last one.

Self-proclaimed, self-educated "experts" making bold categorical assertions (e.g. very little progress in understanding the MECHANISM of evolution, you know) tend to piss off the real experts, for good reasons, but lots of IDCists never seem to figure that out...
---------------------QUOTE-------------------


"Further studies" is a creationist/crank coded message that means "I need to spend more time at the AIG web site so I can use both barrels on you the next time!"

Seriously.  That's the only studying they do.  That's why all their arguements are the same and they all make the same idiotic, ignorant claims.
Posted by: Richard Simons on Jan. 15 2008,18:14

Quote (Albatrossity2 @ Jan. 15 2008,09:30)
It does take time (often years) and effort to become conversant in some of these areas. When you couple that with the fact that many of these folks are barely conversant with biology at the intellectual level that we teach in junior high, it is frankly insulting to read a comment like Mark's last one.
---------------------QUOTE-------------------


I recently pointed out (can't remember where) that the difference in the time and effort spent gaining information and honing their skills between a newly-independent researcher and someone who has high-school biology is comparable with that between a professional hockey player and 6-year-olds playing street-hockey.
Posted by: Daniel Smith on Jan. 15 2008,19:03

Quote (Albatrossity2 @ Jan. 14 2008,19:51)
         
Quote (Daniel Smith @ Jan. 14 2008,18:27)
I think you are wrong about this.  Denton makes it very clear what "pre-Darwinian biology" means - and it's not abiogenesis:                  

---------------------QUOTE-------------------
Before Darwin, the majority of leading biologists adhered to a Platonic model of nature, referred to by Owen (1849) in his classic monograph On the Nature of Limbs as ‘‘the Platonic cosmogony.’’ According to this conception, all the basic recurrent forms of the organic world, such as the pentadactyl design of the vertebrate limb, the body plans of the major phyla, the forms of leaves and so forth, as well as the recurrent forms of the inorganic realm, such as atoms, crystals, etc., represent the material manifestations of a finite set of immutable immaterial archetypes or ‘‘ideas’’ termed by Owen (1849) ‘‘predetermined or primal patterns.’’ These pre-existing abstract types or ideas are materialized, or to cite Owen (1849) again, ‘‘clothed in material garb,’’ by the agency of natural law, or more precisely in the case of organic forms by a special class of natural laws which applied uniquely to the vital realm--the celebrated ‘‘Laws of Form.’’

Denton et al, The Protein Folds as Platonic Forms: New Support for the Pre-Darwinian Conception of Evolution by Natural Law, (emphasis mine)
---------------------QUOTE-------------------


So how exactly does the term "pre-Darwinian biology" come to mean "abiogenesis" in your eyes?  I mean, look at the title of the paper for goodness sake!
---------------------QUOTE-------------------


Daniel

Are you really this thick naturally, or are you simply stringing this red herring out so that you hope that I will forget that you haven't answered my questions yet? If the latter, don't count on it. I'd appreciate, greatly, an answer, especially since I have answered all of yours so far, and will now answer the latest one. Your debt is building up...

I haven't read that < 2003 Biosystems paper that you originally cited >; interlibrary loan hasn't delivered it yet.
---------------------QUOTE-------------------


I linked to a .pdf copy of the paper when I cited it.  (The entire title was the link). < Here it is > again.    

---------------------QUOTE-------------------
But I can tell you what he said in that  2002 J. Theor. Biol. paper (Denton, M.J., Marshall, C.J., Legge, M., 2002. The protein folds as Platonic forms: new support for the pre-Darwinian conception of evolution by natural laws. J. theor. Biol. 219, 325–342.)
               

---------------------QUOTE-------------------
‘‘the lawful nature of the folds together with the intriguing fact that many of the 20 protogenic  amino acids—out of which the folds are constructed—are amongst the most common amino acids found in meteorites and the easiest amino acids to generate in pre-biotic syntheses is surely of considerable significance, consistent with and supporting a deterministic theory of the origin of life
---------------------QUOTE-------------------


FYI, the "origin of life" = abiogenesis.

FYI, "pre-biotic" = prior to the development of biological life.

FYI, pre-Darwinian also means, in this context, metabolic and chemical processes PRIOR to the development of a system of inheritance.

FYI, a system of inheritance is required for the mechanisms of Darwinian evolution to be effective.

So, despite your notion that "pre-Darwinian" might have a solely philosophical meaning, I think it is clear that Denton's focus is abiogenesis. These papers were published in biology journals, not philosophy journals. My interpretation is confirmed by my reading of all four (4) papers that cite this 2003 Biosystems paper; all the citations cite it in a context that is discussing abiogenesis.

I will report back on my reading of the 2003 Biosystems paper when I get my hands on it. In the meantime, I'm sticking with my interpretation of "pre-Darwinian".
---------------------QUOTE-------------------


I'm sorry to say this, but you are just dead wrong in your assessment of what Denton means by "pre-Darwinian".
Here is every passage where he uses the term "pre-Darwinian" in the paper:

---------------------QUOTE-------------------
the Pre-Darwinian Conception of Evolution by Natural Law ...
The folds are evidently determined by natural law, not natural selection, and are ‘‘lawful forms’’ in the Platonic and  pre-Darwinian sense of the word ...
pre-Darwinian biologists hoped to provide a rational and lawful account of the diversity of organic forms via the ‘‘Laws of Biological Form’’ ...
The fundamental goal of biologists in the pre-Darwinian era to seek rational and lawful explanations for biological form is reflected in Goeffroy St Hillaire’s attempt to derive all the
basic body plans of the major biological types from a basic fundamental plan by a system of simple natural transformations ...
The widespread belief that organic forms are lawful ‘‘givens of nature’’ explains why it was that throughout the pre-Darwinian period from the naturphilosophie of the late 18th century, right up to the period just before the publication of the Origin, although it was universally
accepted that organisms exhibited functional adaptations, for Goethe, Carus Goeffroy and Owen, it was always form which was of primary concern. ...
Holding organic forms to be the result of a set of natural laws which applied uniquely to the organic realm, nearly all the leading biologists of the pre-Darwinian era might be described as ‘‘vitalists,’’ ...
the pre-Darwinian conception of organic forms as intrinsic features of the natural order was never completely laid to rest after 1859. It survived well into the 20th century
particularly on the continent of Europe ...
the pre-Darwinian concept of organic forms as ‘‘built-in’’ intrinsic features of nature determined by natural law provides a more powerful explanatory framework than its selectionist successor ...
They self evidently represent a set of ‘‘Laws of Biological Form’’ of precisely the kind sought after by Geoffroy, Carus and many other Platonic biologists of the pre-Darwinian era. ...
Moreover even the extreme Platonic position of some of the pre-Darwinian biologists, such as Goethe--that form directly determines function, without any or only minimal selective modification--may also be true in certain cases. ...
In their book Biochemical Predestination, the authors Kenyon & Steinman (1969) echoing the early 19th
century views of Owen and Schwann, conclude with sentiments consistent with the pre-Darwinian concept of evolution by natural law and the viewpoint defended in this paper ...
On the contrary, they are wonderful exemplars of the pre-Darwinian and Platonic conception of organic forms as abstract, lawful and rational features of the eternal world order, which will occur throughout the cosmos wherever the same 20 protogenic amino acids are used to make proteins. ...
For the folds represent the first case in the history of biology where a set of complex organic forms can be shown to be unambiguously lawful natural forms in the classic pre-Darwinian sense. ...
turned out to be such perfect exemplars of the pre-Darwinian Platonic cosmogony, and the idea of natural law as the major determinant of organic form and evolution ...
Whether or not there are other sets of lawful organic forms, there is no doubt that the universe of protein folds represents a Platonic universe of precisely the kind sought after by pre-Darwinian biology. ....
For it holds out the prospect that the study of organic form, might eventually become as the pre-Darwinian biologists such as Goethe, Goeffroy and Owen had always hoped, a fully rational and predictive science, and that biology may in the end be unified with physics in Plato’s timeless realm of the gods
---------------------QUOTE-------------------

 
From these passages it is quite evident that he is using the term "pre-Darwinian" to describe the scientific philosophy that was the paradigm prior to Darwin's publication of The Origin.  "Pre-Darwinian Conception", "pre-Darwinian sense", "the pre-Darwinian era", etc., etc.. are not synonyms for "metabolic and chemical processes PRIOR to the development of a system of inheritance".

And, what - by your concept of his meaning - are "pre-Darwinian biologists" exactly?

Are "biologists in the pre-Darwinian era", biologists who were around for abiogenesis?

Sorry, but this time, you're just plain wrong.
Posted by: Daniel Smith on Jan. 15 2008,19:17

Quote (Richard Simons @ Jan. 15 2008,18:14)
     
Quote (Albatrossity2 @ Jan. 15 2008,09:30)
It does take time (often years) and effort to become conversant in some of these areas. When you couple that with the fact that many of these folks are barely conversant with biology at the intellectual level that we teach in junior high, it is frankly insulting to read a comment like Mark's last one.
---------------------QUOTE-------------------


I recently pointed out (can't remember where) that the difference in the time and effort spent gaining information and honing their skills between a newly-independent researcher and someone who has high-school biology is comparable with that between a professional hockey player and 6-year-olds playing street-hockey.
---------------------QUOTE-------------------


It seems to me (and I'm not trying to be insulting) that you educated guys have a lot of trouble explaining why you're right.  You seem to be much better at telling us uneducated saps how ignorant we are and leaving it at that.  
If you say you're right, but give--as the only reason--the fact that we are not educated, you didn't really tell us what's right about your position.  All you're doing is the equivalent of name calling.  This is just an observation.
Posted by: JAM on Jan. 15 2008,19:50

Quote (Daniel Smith @ Jan. 15 2008,19:17)
 
Quote (Richard Simons @ Jan. 15 2008,18:14)
         
Quote (Albatrossity2 @ Jan. 15 2008,09:30)
It does take time (often years) and effort to become conversant in some of these areas. When you couple that with the fact that many of these folks are barely conversant with biology at the intellectual level that we teach in junior high, it is frankly insulting to read a comment like Mark's last one.
---------------------QUOTE-------------------


I recently pointed out (can't remember where) that the difference in the time and effort spent gaining information and honing their skills between a newly-independent researcher and someone who has high-school biology is comparable with that between a professional hockey player and 6-year-olds playing street-hockey.
---------------------QUOTE-------------------


It seems to me (and I'm not trying to be insulting) that you educated guys have a lot of trouble explaining why you're right.
---------------------QUOTE-------------------


In science, it's not a matter of explaining things to a dilettante's satisfaction. Science is about making and testing predictions. You are egotistically ignoring the fact that every prediction you made here is false.


---------------------QUOTE-------------------
You seem to be much better at telling us uneducated saps how ignorant we are and leaving it at that.
---------------------QUOTE-------------------


That's a lie, Dan. We got you to make predictions and we showed you that you were wrong. Then you metaphorically closed your eyes and claimed that you haven't seen anything inconsistent with your hypotheses.


---------------------QUOTE-------------------
If you say you're right, but give--as the only reason--the fact that we are not educated, you didn't really tell us what's right about your position.
---------------------QUOTE-------------------


But we did, Dan. We led you by the hand through the process of making and testing predictions. Yours were uniformly wrong.


---------------------QUOTE-------------------
All you're doing is the equivalent of name calling.  This is just an observation.
---------------------QUOTE-------------------


No, it's a self-serving lie. Prodding you into making predictions and showing you that they were wrong is in no way equivalent to name calling.
Posted by: Erasmus, FCD on Jan. 15 2008,19:50

Daniel that is because we have all been indoctrinated on Teh Altar of Darwinism and don't really remember the details.

Or there are some other reasons.  But let's just stick with that one, it's much sexier.
Posted by: Albatrossity2 on Jan. 15 2008,20:32

Quote (Daniel Smith @ Jan. 15 2008,19:03)
Sorry, but this time, you're just plain wrong.
---------------------QUOTE-------------------


Maybe, but that doesn't explain why EVERY paper that cites that article cites it in a context of abiogenesis. If I'm wrong, I have company, at least.

But even if we agree to disagree on this diversion, let's get back to the original reason why you cited this article. You stated, as if it was surprising, that "protein folds are more a product of natural law than selection". I pointed out  < then > that this is a strawman. I asked you  

---------------------QUOTE-------------------
If it is not a strawman, Daniel, please document where any reputable scientist claims that natural selection governs the molecular processes involved in protein folding. This sort of argument bespeaks not only a profound misunderstanding of evolutionary theory (which Daniel has already demonstrated abundantly), but a profound ignorance about the molecular processes that occur within cells.
---------------------QUOTE-------------------


To date, you have provided no answer.

Is this a strawman, Daniel?  If not, what point is proven by citing that Denton article? I'd really appreciate an answer this time; you've stalled long enough.

As for this assertion

---------------------QUOTE-------------------
It seems to me (and I'm not trying to be insulting) that you educated guys have a lot of trouble explaining why you're right.  You seem to be much better at telling us uneducated saps how ignorant we are and leaving it at that.  
If you say you're right, but give--as the only reason--the fact that we are not educated, you didn't really tell us what's right about your position.  All you're doing is the equivalent of name calling.  This is just an observation.
---------------------QUOTE-------------------


I have not yet ONCE claimed to be right based on education. I have engaged your arguments with logic and evidence from the literature. I have asked you to prove your assertion (above) at least 4 or 5 times, and you have not engaged that argument. So this revisionist crap is just plain wrong in this instance.

Quit stalling. Tell us why, exactly, this paper from Denton is support for any of your assertions. Tell us why, exactly, your statement in bold above is not a strawman.

Thanks in advance for not addressing these points again.
Posted by: Wesley R. Elsberry on Jan. 15 2008,20:35



---------------------QUOTE-------------------

at least 80% of characters must be correctly identified

---------------------QUOTE-------------------



Never heard of Shannon, eh?
Posted by: Mark Iosim on Jan. 15 2008,20:43



---------------------QUOTE-------------------
Mark Iosim:
 
...line must to be recognized by environment as meaningful...

oldmanintheskydidntdoit:

Which of these two has the most meaning?
a) "Q"
b) " "

---------------------QUOTE-------------------

None, in the reference to given “weasel” model, but we could define a model for which it could be on a treshold of some meaning. In the "weisel" model, for selection to be natural the line must to be recognized by environment as meaningful, i.e line has to exceed a threshold of recognition. However the initial random line in this model is beyond recognition.
   

---------------------QUOTE-------------------
oldmanintheskydidntdoit:

Why 80%?

---------------------QUOTE-------------------

Feel free to chose different % as follows:
Misspell every word in the line "METHINKS IT IS LIKE A WEASEL" starting with one error per word and continue until every word in the line  became completely unrecognizable. This is a treshold in recognition of an emerging “positive change”. Now count number of mispelled letters and express it in % in reference to number 27.
Posted by: Richard Simons on Jan. 15 2008,22:01

Quote (Daniel Smith @ Jan. 15 2008,19:17)
 
Quote (Richard Simons @ Jan. 15 2008,18:14)
         
Quote (Albatrossity2 @ Jan. 15 2008,09:30)
It does take time (often years) and effort to become conversant in some of these areas. When you couple that with the fact that many of these folks are barely conversant with biology at the intellectual level that we teach in junior high, it is frankly insulting to read a comment like Mark's last one.
---------------------QUOTE-------------------


I recently pointed out (can't remember where) that the difference in the time and effort spent gaining information and honing their skills between a newly-independent researcher and someone who has high-school biology is comparable with that between a professional hockey player and 6-year-olds playing street-hockey.
---------------------QUOTE-------------------


It seems to me (and I'm not trying to be insulting) that you educated guys have a lot of trouble explaining why you're right.  You seem to be much better at telling us uneducated saps how ignorant we are and leaving it at that.  
If you say you're right, but give--as the only reason--the fact that we are not educated, you didn't really tell us what's right about your position.  All you're doing is the equivalent of name calling.  This is just an observation.
---------------------QUOTE-------------------


First, I was not thinking of you when I wrote this, but of opponents of the theory of evolution in general.

Secondly, I would not expect a mathematician to be able to give me a quick run-down on Diophantine conditions in the well-posedness theory of a coupled KdV-type system, a physicist to give me a defence of their views on Lorentzian wormholes and their relationship to spacetime foam or even a linguist to tell me why the minimum scope of an operator cannot exceed its c-command domain at s-structure (to quote from a book review). I realize I fall far short of the minimum knowledge required to understand these topics.

However, at times it seems that anyone who has taken a single high-school course in biology (or not, in many cases) feels perfectly well-qualified to pour scorn on virtually every biologist in the world for accepting the theory of evolution. Do these people never have just the tiniest glimmer of a notion that perhaps they need to gain a little more knowledge before they start? For me, this is one of life's more enduring mysteries.
Posted by: Erasmus, FCD on Jan. 15 2008,22:22

Richard that is exactly true.  I recall reading on UD just recently that 'most of the commenters here have as an expert a command of the field of biology as any university' or something very similar.  

it's not that this is ludicrous.  of course it is.  the amazing thing is that it is said with all earnest seriousness, THEY BELIEVE IT TO BE SO.

just like the situation here.  any jackass that has ever seen Marty Stauffer and Omaha Wild Kingdom is an f-ing biologist, and should be taken seriously.

so don't get your panties in a wad, Daniel.  it's just the same old dishonest honorary degree type behavior we've seen a million times before.  Perhaps you are different, but surely you understand posterior probabilities and why the null is set where it is.
Posted by: Darth Robo on Jan. 16 2008,09:55



---------------------QUOTE-------------------
Misspell every word in the line "METHINKS IT IS LIKE A WEASEL" starting with one error per word and continue until every word in the line  became completely unrecognizable.
---------------------QUOTE-------------------



Seen this years ago, in fact someone made a whole website out of it.  Simple program, click the button once and a number of characters randomly change into different symbols, it's not even  restricted to alphanumeric characters - speechmarks, commas, anything can show up.  

The problem is that it's an argument by analogy, and a poor one too, conflating english language with biology.  

Another thing is, that pressing the button over and over for millions of years, it is easily possible that "Weasel" would appear.  In the "real world", weasels would stick around for a while (major catastrophes not withstanding).  Mutations may occur that may affect some weasels, but in the program, click the button once and the "Weasel" will disappear, replaced by gibberish.  That's analogous to the entire species dying off due to detrimental mutations in one click.  Which I would have thought would not happen very often in the "real world".  

I'm not a scientist of course, so if I've made any errors, point 'em out.
Posted by: oldmanintheskydidntdoit on Jan. 17 2008,03:12

Quote (Mark Iosim @ Jan. 15 2008,20:43)
Feel free to chose different %
---------------------QUOTE-------------------


No, I asked *you* why *you* chose the figure of 80%? Or did you just *poof* 80% into thin air?

Why did you choose 80%?
Posted by: Mark Iosim on Jan. 17 2008,03:55

oldmanintheskydidntdoit:

---------------------QUOTE-------------------
No, I asked *you* why *you* chose the figure of 80%? Or did you just *poof* 80% into thin air?

Why did you choose 80%?
---------------------QUOTE-------------------


I performed the same steps described in my previous post and come up with approximately 80%. This threshold of recognition depends on the system’s, (environment) recognition ability. Because you and me are representing deferent “environments” we should come up with different threshold of recognition (%).
Posted by: IanBrown_101 on Jan. 17 2008,04:02

Quote (Mark Iosim @ Jan. 17 2008,09:55)
oldmanintheskydidntdoit:  

---------------------QUOTE-------------------
No, I asked *you* why *you* chose the figure of 80%? Or did you just *poof* 80% into thin air?

Why did you choose 80%?
---------------------QUOTE-------------------


I performed the same steps described in my previous post and come up with approximately 80%. This threshold of recognition depends on the system’s, (environment) recognition ability. Because you and me are representing deferent “environments” we should come up with different threshold of recognition (%).
---------------------QUOTE-------------------


What the hell are you on about?

In the Hamlet line, in the particular environment that this "takes place" in the line represents fitness due to what each letter of the line means in terms of the animal.

Therefore the first letter being an "M" means nothing as an M, but when taken as a specific morphological (I think that's the word I want) feature, M is a bonus in this environment over Q. There's nothing at all about the environment "recognising" anything. What the hell does that even MEAN?
Posted by: oldmanintheskydidntdoit on Jan. 17 2008,04:07

Methinks 'tis like a weasel.

M******s '*** l**e * wea***l.

80%? Hardly.

See this link
< http://www.bignell.demon.co.uk/weasel.htm >


---------------------QUOTE-------------------
the chances of getting any string of n characters right by random generation of characters is (1/256)n. n is known as the exponent, and as n increases, the probability diminishes very rapidly indeed. For our target phrase, 27 characters long, the probability of getting it right by chance are (1/256)27, or about 9.5 * 10-66. That's 65 zeroes after the decimal point before you start hitting numbers with any magnitude.

0.00000000000000000000000000000000000000000000000000000000000000000095
---------------------QUOTE-------------------


Posted by: Mark Iosim on Jan. 17 2008,05:01

oldmanintheskydidntdoit,

This is the line I used to illustrate 80%. (?) – means misspelled word.
We?hin?s it is li?e a w?a?el
(?) – means misspelled word.
It was beyond my ability to recognize this line.
You should come up with a different %. Actually if randomly misspelled words in this line the thresholds of recognition (%) will vary.
What is you’re the most optimistic (lowest) thresholds of recognition (%) to prove your point.

P.S.
I am leaving to work now and I am not sure when I may respond.
Posted by: oldmanintheskydidntdoit on Jan. 17 2008,06:18

Quote (Mark Iosim @ Jan. 17 2008,05:01)
What is you’re the most optimistic (lowest) thresholds of recognition (%) to prove your point.
---------------------QUOTE-------------------


>0
Posted by: Wesley R. Elsberry on Jan. 17 2008,07:51

I suspect Mark said "80%" because, IIRC, that's the number Bill Dembski pulled out of his butt for the same purpose in "No Free Lunch" in his argument concerning the Gettysburg Address.

There is actually peer-reviewed literature about the subject of predictability of messages in English. Dembski certainly did not cite it (it wouldn't support the high value he apparently wanted), and I doubt Mark is familiar with the work.

Of course, I think the whole notion Mark is hinging his argument upon is silly. It depends critically upon arguing over what analogy supposedly applies to evolutionary computation that manipulates character strings. When I posed the problem of evolutionary computation for Dembski's arguments to Dembski back in 1997, I certainly didn't put my example in terms of changes in characters in strings to match arbitrary targets; I posed the problem in terms of a genetic algorithm to provide a near-optimal solution to the "traveling salesman problem". Here, the issue is simply how long a tour a candidate solution represents and there is no question about thresholds. The TSP is biologically relevant because movement costs metabolic energy, and organisms that minimize movement in a closed path thus have an advantage.

Dembski has, so far as I can tell, *never* since even had a try at a response that addresses evolutionary computation's successful approach to finding near-optimal solutions to TSP type problems. He has gone on at length about toy evolutionary computation examples, such as Dawkins' "weasel".
Posted by: Daniel Smith on Jan. 17 2008,19:11

Quote (Albatrossity2 @ Jan. 15 2008,20:32)
     
Quote (Daniel Smith @ Jan. 15 2008,19:03)
Sorry, but this time, you're just plain wrong.
---------------------QUOTE-------------------


Maybe, but that doesn't explain why EVERY paper that cites that article cites it in a context of abiogenesis. If I'm wrong, I have company, at least.

But even if we agree to disagree on this diversion, let's get back to the original reason why you cited this article. You stated, as if it was surprising, that "protein folds are more a product of natural law than selection". I pointed out  < then > that this is a strawman. I asked you          

---------------------QUOTE-------------------
If it is not a strawman, Daniel, please document where any reputable scientist claims that natural selection governs the molecular processes involved in protein folding. This sort of argument bespeaks not only a profound misunderstanding of evolutionary theory (which Daniel has already demonstrated abundantly), but a profound ignorance about the molecular processes that occur within cells.
---------------------QUOTE-------------------



---------------------QUOTE-------------------


They don't (to my knowledge) claim that selection governs the molecular processes that specifically control protein folding.  They do claim however, that selection governs the amino acid sequences that make up these proteins.
Denton (if my reading of him is correct) is arguing that the sequences are not governed by selection because the same folds can be arrived at by several routes (sequences) and the same sequence can yield different folds.
That's what I get out of it anyway.

Also, in regard to whether or not this supports Schindewolf and Berg:  While Denton does not mention them by name, he does say this:      

---------------------QUOTE-------------------
However the pre-Darwinian conception of organic forms as intrinsic features of the natural order was never completely laid to rest after 1859. It survived well into the 20th century particularly on the continent of Europe (Gould & Lewontin, 1979).
(Emphasis mine)
---------------------QUOTE-------------------


So -- A) Denton is making a case for evolution by natural law.  B) He describes that philosophy as "pre-Darwinian" science.  C) He then mentions that this pre-Darwinian concept "survived" the Darwinian revolution in Europe.

That, to me, would include Schindewolf, Berg, Grasse, Bateson and even Goldschmidt -- who all advocated evolution by some sort of natural law.

So - maybe you disagree with that - fine, that's OK, I just think we'll have to disagree on that.
Posted by: Daniel Smith on Jan. 17 2008,19:56

Quote (Wesley R. Elsberry @ Jan. 17 2008,07:51)
I suspect Mark said "80%" because, IIRC, that's the number Bill Dembski pulled out of his butt for the same purpose in "No Free Lunch" in his argument concerning the Gettysburg Address.

There is actually peer-reviewed literature about the subject of predictability of messages in English. Dembski certainly did not cite it (it wouldn't support the high value he apparently wanted), and I doubt Mark is familiar with the work.

Of course, I think the whole notion Mark is hinging his argument upon is silly. It depends critically upon arguing over what analogy supposedly applies to evolutionary computation that manipulates character strings. When I posed the problem of evolutionary computation for Dembski's arguments to Dembski back in 1997, I certainly didn't put my example in terms of changes in characters in strings to match arbitrary targets; I posed the problem in terms of a genetic algorithm to provide a near-optimal solution to the "traveling salesman problem". Here, the issue is simply how long a tour a candidate solution represents and there is no question about thresholds. The TSP is biologically relevant because movement costs metabolic energy, and organisms that minimize movement in a closed path thus have an advantage.

Dembski has, so far as I can tell, *never* since even had a try at a response that addresses evolutionary computation's successful approach to finding near-optimal solutions to TSP type problems. He has gone on at length about toy evolutionary computation examples, such as Dawkins' "weasel".
---------------------QUOTE-------------------


If I might.

I think you're all missing one thing.

No matter what, natural selection is not perfect.  

If an unborn bird has a genetic mutation that will turn it into a super-bird -- impervious to all predators -- yet, while still in the egg, gets eaten by a fox, that "solution" is gone.  It was selected against because it did not confer an advantage that was relevant to that particular stage of the bird's development.

If the same bird makes it through to adulthood, yet is killed in an oil spill before it can breed, again that solution is lost -- not because it didn't have the solution to the predator problem -- but because it didn't have the correct solution to another problem (oil).

What if the super-bird is sterile?  What if it is shunned and cannot mate?  What if its 'super-allele' is recessive and its progeny are all wiped out without passing it on?  Etc.

Real life requires multiple solutions to multiple problems (and a lot of times just dumb luck) for survival (selection).  Genetic algorithms are (I'm guessing) much more narrowly fixated than that.

So, unless a genetic algorithm periodically wipes out promising solutions randomly, or throws other unrelated problems into the mix suddenly and removes the bad solutions to those problems as well, it is not a realistic model for natural selection.

Artificial selection, on the other hand, works differently.  It narrows the focus, and essentially (attempts to at least) shield organisms from natural selection.  Dog breeders selectively breed only those dogs with the specific traits they want.  In this way, they can narrow the path genetically and arrive at the correct solution for the much simplified problem.

This is what (I would think) good genetic algorithms, (those that are being actively used to look for solutions), should do as well.

That's my uneducated opinion.
Posted by: Mark Iosim on Jan. 17 2008,20:31



---------------------QUOTE-------------------
Mark Iosim:
What is you’re the most optimistic (lowest) thresholds of recognition (%) to prove your point.

oldmanintheskydidntdoit:
>0
---------------------QUOTE-------------------


It means that you can recognize "METHINKS IT IS LIKE A WEASEL"  from this line “MAAAAAAAAAAAAAAAAAAAA”

Wow!
Posted by: IanBrown_101 on Jan. 17 2008,20:35

Quote (Daniel Smith @ Jan. 18 2008,01:56)
Quote (Wesley R. Elsberry @ Jan. 17 2008,07:51)
I suspect Mark said "80%" because, IIRC, that's the number Bill Dembski pulled out of his butt for the same purpose in "No Free Lunch" in his argument concerning the Gettysburg Address.

There is actually peer-reviewed literature about the subject of predictability of messages in English. Dembski certainly did not cite it (it wouldn't support the high value he apparently wanted), and I doubt Mark is familiar with the work.

Of course, I think the whole notion Mark is hinging his argument upon is silly. It depends critically upon arguing over what analogy supposedly applies to evolutionary computation that manipulates character strings. When I posed the problem of evolutionary computation for Dembski's arguments to Dembski back in 1997, I certainly didn't put my example in terms of changes in characters in strings to match arbitrary targets; I posed the problem in terms of a genetic algorithm to provide a near-optimal solution to the "traveling salesman problem". Here, the issue is simply how long a tour a candidate solution represents and there is no question about thresholds. The TSP is biologically relevant because movement costs metabolic energy, and organisms that minimize movement in a closed path thus have an advantage.

Dembski has, so far as I can tell, *never* since even had a try at a response that addresses evolutionary computation's successful approach to finding near-optimal solutions to TSP type problems. He has gone on at length about toy evolutionary computation examples, such as Dawkins' "weasel".
---------------------QUOTE-------------------


If I might.

I think you're all missing one thing.

No matter what, natural selection is not perfect.  

If an unborn bird has a genetic mutation that will turn it into a super-bird -- impervious to all predators -- yet, while still in the egg, gets eaten by a fox, that "solution" is gone.  It was selected against because it did not confer an advantage that was relevant to that particular stage of the bird's development.

If the same bird makes it through to adulthood, yet is killed in an oil spill before it can breed, again that solution is lost -- not because it didn't have the solution to the predator problem -- but because it didn't have the correct solution to another problem (oil).

What if the super-bird is sterile?  What if it is shunned and cannot mate?  What if its 'super-allele' is recessive and its progeny are all wiped out without passing it on?  Etc.

Real life requires multiple solutions to multiple problems (and a lot of times just dumb luck) for survival (selection).  Genetic algorithms are (I'm guessing) much more narrowly fixated than that.

So, unless a genetic algorithm periodically wipes out promising solutions randomly, or throws other unrelated problems into the mix suddenly and removes the bad solutions to those problems as well, it is not a realistic model for natural selection.

Artificial selection, on the other hand, works differently.  It narrows the focus, and essentially (attempts to at least) shield organisms from natural selection.  Dog breeders selectively breed only those dogs with the specific traits they want.  In this way, they can narrow the path genetically and arrive at the correct solution for the much simplified problem.

This is what (I would think) good genetic algorithms, (those that are being actively used to look for solutions), should do as well.

That's my uneducated opinion.
---------------------QUOTE-------------------


Well firstly your mention of a super gene is complete science fiction that even Jean Luc Picard would take exception to.

Secondly, so what?

Just because something doesn't make it to adulthood doesn't mean the gene was any less useful for its environment. So some "super genes" don't make it. Your point is? there are errors in the gene copying (as far as I understand it) all the sodding time. Are you an EXACT mix of your parents? No.
Posted by: Mark Iosim on Jan. 17 2008,20:45

IanBrown_101:  

---------------------QUOTE-------------------
What the hell are you on about?

In the Hamlet line, in the particular environment that this "takes place" in the line represents fitness due to what each letter of the line means in terms of the animal.

Therefore the first letter being an "M" means nothing as an M, but when taken as a specific morphological (I think that's the word I want) feature, M is a bonus in this environment over Q. There's nothing at all about the environment "recognizing" anything. What the hell does that even MEAN?
---------------------QUOTE-------------------



Ok. Lets assume that this is not about biological evolution, but just about "weasel" pedagogical toy example only. But let me finish my homework and we can start talking about real stuff.

P.S.
IanBrown_101, what the hell is wrong with you? Why you are getting so upset?
I also get upset when some member of this fine community has rude or humiliation remarks, but I have remedy how to cope with this. When I am responding to a bully, first I am writing everything what I think about him and his dull arguments, have a good laugh, and then I edit my post by deleting the comments that would pissed off my opponent (who, fully deserve to be pissing off). As a result I have full satisfaction and in the same time well-mannered respond.

Have a fun too.
Posted by: Mark Iosim on Jan. 17 2008,20:55

Richard Simons:    

---------------------QUOTE-------------------
However, at times it seems that anyone who has taken a single high-school course in biology (or not, in many cases) feels perfectly well-qualified to pour scorn on virtually every biologist in the world for accepting the theory of evolution.
---------------------QUOTE-------------------


Richard, if you are talking about me, I didn’t know that I was “pouring scorn” on respected biologists. I thought that I spoke my mind in front of a bunch of bullies who were using language of garbage collectors were terrorizing the victims who disagrees with them. Did you speak out against that behavior? If not, I have no sympathy for your hurt feeling. If those bullies were pissed off by my comments I have no regret for that also.
Posted by: IanBrown_101 on Jan. 17 2008,21:00

Quote (Mark Iosim @ Jan. 18 2008,02:45)
IanBrown_101:    

---------------------QUOTE-------------------
What the hell are you on about?

In the Hamlet line, in the particular environment that this "takes place" in the line represents fitness due to what each letter of the line means in terms of the animal.

Therefore the first letter being an "M" means nothing as an M, but when taken as a specific morphological (I think that's the word I want) feature, M is a bonus in this environment over Q. There's nothing at all about the environment "recognizing" anything. What the hell does that even MEAN?
---------------------QUOTE-------------------



Ok. Lets assume that this is not about biological evolution, but just about "weasel" pedagogical toy example only. But let me finish my homework and we can start talking about real stuff.

P.S.
IanBrown_101, what the hell is wrong with you? Why you are getting so upset?
I also get upset when some member of this fine community has rude or humiliation remarks, but I have remedy how to cope with this. When I am responding to a bully, first I am writing everything what I think about him and his dull arguments, have a good laugh, and then I edit my post by deleting the comments that would pissed off my opponent (who, fully deserve to be pissing off). As a result I have full satisfaction and in the same time well-mannered respond.

Have a fun too.
---------------------QUOTE-------------------


Err, lets NOT ignore the fact it's supposed to represent biological evolution, since that was the whole point of it being brought up. If you use something as an (ARGH! My mind has gone blank, what word am I searching for?) you can't just drop that and say "take it literally". It represents biological evolution.


Oh, and I'm not upset.

"What the hell...." is, to my mind, mild to moderate emphasis on a point. It isn't a display of anger (although it can be surprise) nor is it an insult.

"What the hell are you on about?" is my way of conveing genuine confusion about what you were saying. I understood each of the words, but strung together they made no sense.
Posted by: IanBrown_101 on Jan. 17 2008,21:01

Quote (Mark Iosim @ Jan. 18 2008,02:55)
Richard Simons:    

---------------------QUOTE-------------------
However, at times it seems that anyone who has taken a single high-school course in biology (or not, in many cases) feels perfectly well-qualified to pour scorn on virtually every biologist in the world for accepting the theory of evolution.
---------------------QUOTE-------------------


Richard, if you are talking about me, I didn’t know that I was “pouring scorn” on respected biologists. I thought that I spoke my mind in front of a bunch of bullies who were using language of garbage collectors were terrorizing the victims who disagrees with them. Did you speak out against that behavior? If not, I have no sympathy for your hurt feeling. If those bullies were pissed off by my comments I have no regret for that also.
---------------------QUOTE-------------------


Pointing out that someone who fails to understand the basics of an idea shouldn't really talk about it with any pretence of knowledge is, in your world, bullying?
Posted by: Mark Iosim on Jan. 17 2008,21:38

Wesley R. Elsberry:
 

---------------------QUOTE-------------------
I suspect Mark said "80%" because, IIRC, that's the number Bill Dembski pulled out of his butt for the same purpose in "No Free Lunch" in his argument concerning the Gettysburg Address.

---------------------QUOTE-------------------



I would like to insure you that I am not undercover agent of Bill Dembski, never read his papers or book and know about him only from guys like you who criticize him. I have to admit that I do not know much about Evolution Biology, I am as clean, as a white sheet of paper, my mind is wide open to accept any reasonable idea from your guys, but do not expect much room for wiggling.

When you mentioned Bill Dembski, I Googled “Dembski + weasel”, and the first item from the search result list was Weasel Program from Wikipedia: < http://en.wikipedia.org/wiki/Weasel_program. >
Look, what I found there:

“ Implications for biology
The human eye has an active role to play in the story. It is the selecting agent. It surveys the litter of progeny and chooses one for breeding. ...Our model, in other words, is strictly a model of artificial selection, not natural selection. The criterion for 'success' is not the direct criterion of survival, as it is in true natural selection. In true natural selection, if a body has what it takes to survive, its genes automatically survive because they are inside it. So the genes that survive tend to be, automatically, those genes that confer on bodies the qualities that assist them to survive.”

That pretty much what I said - this is the model of artificial selection and not natural selection.
I think the case is closed and the face of Neo-Darvinism is saved, of cause if Genetic Algoritms weren’t based on misunderstading of the Weasel Program. I hope, we are going to find it out soon.
Posted by: Wesley R. Elsberry on Jan. 17 2008,22:09

If you knew something about this topic and Dawkins, you'd also know that the quote is talking not about "weasel", but rather about "biomorphs". I've tried to explain this to the rather possessive editor of that Wikipedia page, but he seems not to be able to take the point.
Posted by: Richard Simons on Jan. 17 2008,22:13



---------------------QUOTE-------------------
Richard, if you are talking about me, I didn’t know that I was “pouring scorn” on respected biologists.
---------------------QUOTE-------------------


Mark, No, I was not thinking of you, nor indeed anyone in particular. My original comment was prompted by Albatrossity's comment which was less than favourable to you, but I was thinking in much more general terms. For example, there is always someone posting here or at PT complaining about the theory of evolution yet at the same time demonstrating that they do not even know how the word 'theory' is used in science. Most of these people either fail to respond or become increasingly abusive before leaving in a huff (Jesse Hoots, IIRC, last week called us the angels of Satan).


---------------------QUOTE-------------------
I spoke my mind in front of a bunch of bullies who were using language of garbage collectors were terrorizing the victims who disagrees with them.
---------------------QUOTE-------------------


I have had a quick look back over recent posts and failed to see anything remotely fitting this accusation. All I have seen is some people getting frustrated over covering the same ground. Can you give a link to the passage you have in mind?
Posted by: Wesley R. Elsberry on Jan. 17 2008,22:15



---------------------QUOTE-------------------

I would like to insure you that I am not undercover agent of Bill Dembski, never read his papers or book and know about him only from guys like you who criticize him. I have to admit that I do not know much about Evolution Biology, I am as clean, as a white sheet of paper, my mind is wide open to accept any reasonable idea from your guys, but do not expect much room for wiggling.

---------------------QUOTE-------------------



The Lord High Executioner states his will. Elsewhere, he speaks of taking "bullies" to task.

Anybody else getting a distinctly "h"-flavored vibe?


Posted by: IanBrown_101 on Jan. 17 2008,22:22

Quote (Wesley R. Elsberry @ Jan. 18 2008,04:15)


---------------------QUOTE-------------------

I would like to insure you that I am not undercover agent of Bill Dembski, never read his papers or book and know about him only from guys like you who criticize him. I have to admit that I do not know much about Evolution Biology, I am as clean, as a white sheet of paper, my mind is wide open to accept any reasonable idea from your guys, but do not expect much room for wiggling.

---------------------QUOTE-------------------



The Lord High Executioner states his will. Elsewhere, he speaks of taking "bullies" to task.

Anybody else getting a distinctly "h"-flavored vibe?
---------------------QUOTE-------------------


I'm getting the impression that FtK's cross is about to be reused.

I'll get the martyr-removal-kit so we can use the wood....
Posted by: Wesley R. Elsberry on Jan. 17 2008,22:49

I do find it amusing that two people would pull the same bogus number out of their posteriors when speaking to the same topic, and both of them show no sign of having an acquaintance with the actual research that does provide numbers on the topic of interest.

It also is not surprising that we get a digression based upon talking about personalities rather than the technical points I raised. It's almost as if there was an instant recognition that if one actually discusses evolutionary computation and the TSP, one isn't going to actually end up with a win for antievolution, so there's also an instant, "Hey, look over there, isn't that shiny?" reaction.

The bit about judging "wiggling" is a master-stroke of obfuscatory rhetoric, I have to admit. At once, it puts the speaker in the position of authority: he's going to be the arbiter of the discussion. It also simultaneously implies that the burden of proof lies with his interlocutors, such that he has no responsibility to substantiate his previous claims and assertions, which one assumes will simply be taken as brute facts in the absence of further scrutiny. And, as a special bonus, it even implies that bad behavior is expected from his interlocutors, so it even delivers an insult on top of everything else. The fact that I'm not buying any of those for a second doesn't detract from my appreciation of truly excellent weaseling in progress.
Posted by: Richard Simons on Jan. 17 2008,23:05

Quote (Mark Iosim @ Jan. 17 2008,21:38)
I have to admit that I do not know much about Evolution Biology, I am as clean, as a white sheet of paper
---------------------QUOTE-------------------


Three days ago . . .
Quote (Mark Iosim @ Jan. 14 2008,15:11)
I do not have problem with Darwin’s theory of evolution itself and even with Darwin’s explanation of its mechanism in terms of gradual changes and selection – it was a very clever explanation given how little was known at that time. But I do have a problem with the current state of affairs with very little progress in this area. Instead we are religiously repeating the same mantra about natural selection pretending that this is a sufficient explanation of the MECHANISM of evolution.
---------------------QUOTE-------------------


So tell me, did you have just the tiniest glimmer of a notion that perhaps you needed to gain a little more knowledge before writing this?
Posted by: oldmanintheskydidntdoit on Jan. 18 2008,02:57

Quote (Mark Iosim @ Jan. 17 2008,21:38)
I would like to insure you that I am not undercover agent of Bill Dembski, never read his papers or book and know about him only from guys like you who criticize him. I have to admit that I do not know much about Evolution Biology, I am as clean, as a white sheet of paper, my mind is wide open to accept any reasonable idea from your guys, but do not expect much room for wiggling.
---------------------QUOTE-------------------


Must be a different Mark Iosim then.
< http://www.iscid.org/papers/Iosim_ComplexSystemSimplicity.pdf >
< http://www.evcforum.net/cgi-bin....814&m=1 >  


---------------------QUOTE-------------------
Abstract:
In this essay, the widely accepted paradigm that "The whole is more than the sum of its parts" is chalenged. It is also argued that no system properties emerge, but a cumulative effect and interaction in the system just reveals the part’s hidden properties that cause a perception of Emergence phenomena. A system acts as a “litmus paper” and a “magnifying glass” that just reveal the element’s properties not observable otherwise.
To explain the living system phenomenon, it is proposed that Consciousness is a fundamental property of MATTER. According to this hypothesis, Consciousness property is not observable in the non-living equilibrium systems. However if a system steered far enough from an equilibrium and passed the critical point, a non-equilibrium system will emerge that may reveal the property that wasn’t recognized in their elements. This property we call - LIFE.
---------------------QUOTE-------------------


< http://lists.vcu.edu/cgi-bin....A&P=166 >
   

---------------------QUOTE-------------------
My interest in Theoretical Biology started about 25 years ago, while working
in the Neurophysiology Institute, as a lab engineer. I got fascinated by the
complexity of the problem this science is facing. Soon I decided to switch
from Engineering to Biology, got support from my peers and my boss and
started intensive reading in the area of the cell neurobiology. While
reading, I found the striking contrast between how much it is known (facts,
data, observations etc.) and how little is understood in this field.
---------------------QUOTE-------------------


Posted by: Wesley R. Elsberry on Jan. 18 2008,06:12

< Open-minded? >



---------------------QUOTE-------------------

I. WE.    …The engineer sciences are good example of how mathematics was used effectively in a vide range of application. One could argue that many biologists found them self in similar situation ... when they faced with the need to analyze and to control the complex dynamics systems…

Biology occupies a very different place in Science. It doesn’t have foundation, like other mature disciplines have. We do not know what the Life is, how it emerged and even a single cell organism is still a mystery. It may take more than advance modeling to solve these problems. The wild imagination could be needed instead.

Attempting to model the system that is fundamentally not understood would lead to even more misunderstanding.

Mathematical formalism is finding the applications in Biology, but the particular mathematical tool should be chosen not because it was effective in other disciplines. The microscope, regardless how useful it is for the Sciences isn’t useful to build a house. The regular hammer would serve better in this case.

---------------------QUOTE-------------------


Posted by: Mark Iosim on Jan. 18 2008,07:28



---------------------QUOTE-------------------
I have had a quick look back over recent posts and failed to see anything remotely fitting this accusation. All I have seen is some people getting frustrated over covering the same ground. Can you give a link to the passage you have in mind?
---------------------QUOTE-------------------



I also looked back over resent posts, but couldn’t find the post where JAM calling, Daniel moron. However you can find plenty (every other) of JAM’s posts are filled with accusation that Daniel is “deeply dishonest person”, lier, and that his arguments are stupid. Daniel is a very bright person and if his arguments some time get fuzzy it is because he tried to defend his convictions and we all have the same problem, as was demonstrated in the recent discussion.

My whole reason to follow up this forum was to see how Daniel withstanding a heat and I was impressed with his intelligence, ability to learn quickly and with his dignity. In the same time I was irritated by some folks and especially by JAM who was trashing Daniel in manner not acceptable for scientifically inclined discussion (at least not in my book) and by bragging his knowledge. Eventually, I decided to participate just to have an opportunity to tell JAM that having Curriculum Vita instead of Resume doesn’t make him a scientist yet. Unfortunately, I exploded prematurely and I apologize for “collateral damages”
Posted by: Mark Iosim on Jan. 18 2008,07:32

oldmanintheskydidntdoit,

I indeed do not know much knowledge about Evolution Biology, and I indeed open to accept any reasonable idea. My interest in Biology never extended to Evolution Biology and I routinely skip reading this section from Biology text book, because I didn’t expect learn much from it. I just happen to have reasons to belief that Darwinism is a great theory, but Neo-Darwinism is a religion.
Posted by: Mark Iosim on Jan. 18 2008,07:40

Wesley,

Your are running this show like a political campaign, trying to discredit person instead to refute him on an actual issue.
I am not feeling ashamed with what you found. I was telling a truth, but I would prefer to not discuss my controversial ideas now. I would be thrilled to give you this opportunity later, but should I frespond to the Logic Algorithms challengeirst ? Let’s do one step in a time.

You were right, my schedule wasn’t realistic and I have to reschedule it to include also Dawkins’ book “The Blind Watchmaker” and Behe’s book "Darwin's Black Box". I need at least a couple a weeks; it would be my new unrealistic target schedule.
Posted by: oldmanintheskydidntdoit on Jan. 18 2008,07:50

Quote (Mark Iosim @ Jan. 18 2008,07:32)
oldmanintheskydidntdoit,

I indeed do not know much knowledge about Evolution Biology, and I indeed open to accept any reasonable idea.
---------------------QUOTE-------------------


I don't see how you can say
 

---------------------QUOTE-------------------
I routinely skip reading this section from Biology text book
---------------------QUOTE-------------------


and
 

---------------------QUOTE-------------------
I just happen to have reasons to belief that Darwinism is a great theory, but Neo-Darwinism is a religion.
---------------------QUOTE-------------------


and keep a straight face.

You are obviously not open to any reasonable idea or you'd not have "skipped those pages".
Posted by: oldmanintheskydidntdoit on Jan. 18 2008,08:07

Quote (Mark Iosim @ Jan. 18 2008,07:40)
You were right, my schedule wasn’t realistic and I have to reschedule it to include also Dawkins’ book “The Blind Watchmaker” and Behe’s book "Darwin's Black Box". I need at least a couple a weeks; it would be my new unrealistic target schedule.
---------------------QUOTE-------------------


Don't just swallow what you read wholesale either and come back with the same old tired arguments that have been refuted over and over.

< http://www.talkorigins.org/faqs/behe/review.html >
Behe's response to the above
< http://www.arn.org/docs/behe/mb_toresp.htm >
Why a mousetrap is not IC
< http://udel.edu/~mcdonald/mousetrap.html >
And for balance
< http://www.origins.org/articles/disilvestro_rebuttalsdarwinsblack.html >
< http://www.answersingenesis.org/docs/264.asp >

Now, what side has the most convincing arguments?
Posted by: Wesley R. Elsberry on Jan. 18 2008,08:16

Mark Iosim:



---------------------QUOTE-------------------

Your are running this show like a political campaign, trying to discredit person instead to refute him on an actual issue.

---------------------QUOTE-------------------



Mark is mistaken. I have refuted him on the actual issues. I also choose to point out the various inconsistencies between what Mark says at various times. So "instead" is precisely the wrong word to describe my approach.
Posted by: Albatrossity2 on Jan. 18 2008,09:24

Quote (Daniel Smith @ Jan. 17 2008,19:11)
   
Quote (Albatrossity2 @ Jan. 15 2008,20:32)
         
Quote (Daniel Smith @ Jan. 15 2008,19:03)
Sorry, but this time, you're just plain wrong.
---------------------QUOTE-------------------


Maybe, but that doesn't explain why EVERY paper that cites that article cites it in a context of abiogenesis. If I'm wrong, I have company, at least.

But even if we agree to disagree on this diversion, let's get back to the original reason why you cited this article. You stated, as if it was surprising, that "protein folds are more a product of natural law than selection". I pointed out  < then > that this is a strawman. I asked you              

---------------------QUOTE-------------------
If it is not a strawman, Daniel, please document where any reputable scientist claims that natural selection governs the molecular processes involved in protein folding. This sort of argument bespeaks not only a profound misunderstanding of evolutionary theory (which Daniel has already demonstrated abundantly), but a profound ignorance about the molecular processes that occur within cells.
---------------------QUOTE-------------------



---------------------QUOTE-------------------


They don't (to my knowledge) claim that selection governs the molecular processes that specifically control protein folding.  They do claim however, that selection governs the amino acid sequences that make up these proteins.
Denton (if my reading of him is correct) is arguing that the sequences are not governed by selection because the same folds can be arrived at by several routes (sequences) and the same sequence can yield different folds.
That's what I get out of it anyway.
---------------------QUOTE-------------------


Sigh.

Selection operates on biological FUNCTIONS, carried out by macromolecules within organisms, but it acts at the level of the organism. Moving the goalposts to say that scientists claim that "selection governs the amino acid sequences that make up these proteins" is still wrong. Indeed, once you have a new amino acid sequence that generates a new function, selection can operate to favor or disfavor that FUNCTION. But if another amino acid sequence generates the same 3-d structure that also gives rise to the same function, selection had no hand in the molecular processes governing any of that. Selection operates AFTER all of that. It is still a strawman to pretend that reputable scientists ascribe these properties to natural selection.

Daniel, do you understand that different sequences giving rise to the same 3-d structure is exactly what you would expect if selection for the FUNCTION of the sequence, rather than the sequence itself, is operating?

As noted before, Denton is saying nothing surprising from a biochemical or evolutionary point of view. Why you see this as support for your notions is a mystery to me as well.
Posted by: Steverino on Jan. 18 2008,17:29

Quote (Mark Iosim @ Jan. 18 2008,07:28)


---------------------QUOTE-------------------
I have had a quick look back over recent posts and failed to see anything remotely fitting this accusation. All I have seen is some people getting frustrated over covering the same ground. Can you give a link to the passage you have in mind?
---------------------QUOTE-------------------



I also looked back over resent posts, but couldn’t find the post where JAM calling, Daniel moron. However you can find plenty (every other) of JAM’s posts are filled with accusation that Daniel is “deeply dishonest person”, lier, and that his arguments are stupid. Daniel is a very bright person and if his arguments some time get fuzzy it is because he tried to defend his convictions and we all have the same problem, as was demonstrated in the recent discussion.

My whole reason to follow up this forum was to see how Daniel withstanding a heat and I was impressed with his intelligence, ability to learn quickly and with his dignity. In the same time I was irritated by some folks and especially by JAM who was trashing Daniel in manner not acceptable for scientifically inclined discussion (at least not in my book) and by bragging his knowledge. Eventually, I decided to participate just to have an opportunity to tell JAM that having Curriculum Vita instead of Resume doesn’t make him a scientist yet. Unfortunately, I exploded prematurely and I apologize for “collateral damages”
---------------------QUOTE-------------------


I think you left out "ass hat".  I'm pretty sure I called him that more than once.  But, that is more of a label of observation rather than your ordinary run-of-the-mill name calling.

Cheers!
Posted by: JAM on Jan. 18 2008,18:26

Quote (Mark Iosim @ Jan. 18 2008,07:28)
I also looked back over resent posts, but couldn’t find the post where JAM calling, Daniel moron. However you can find plenty (every other) of JAM’s posts are filled with accusation that Daniel is “deeply dishonest person”, lier,...
---------------------QUOTE-------------------


He sure is, at least in the realm of biology. How would you describe someone who made patently false predictions, but revises that in his mind to claim that we have offered nothing but arguments from authority?

Honest?


---------------------QUOTE-------------------
and that his arguments are stupid.
---------------------QUOTE-------------------


Would you mind pointing me to that one? Dan's hypotheses are wrong because the predictions they make have no basis in reality.


---------------------QUOTE-------------------
Daniel is a very bright person...
---------------------QUOTE-------------------


I don't see any evidence for that.


---------------------QUOTE-------------------
...and if his arguments some time get fuzzy it is because he tried to defend his convictions...
---------------------QUOTE-------------------


But if we're to approach this scientifically, we're supposed to attack our own convictions. If I had racist convictions, would you admire me for defending them?


---------------------QUOTE-------------------
... and we all have the same problem, as was demonstrated in the recent discussion.
---------------------QUOTE-------------------


I don't see how we all have the same problem. I see that you're not credible when you claim to have an open mind.


---------------------QUOTE-------------------
My whole reason to follow up this forum was to see how Daniel withstanding a heat and I was impressed with his intelligence, ability to learn quickly and with his dignity.
---------------------QUOTE-------------------


How is it dignified to pretend that God is killing children with malaria to teach a lesson to white-bread folks in the US? That's theologically obscene.


---------------------QUOTE-------------------
In the same time I was irritated by some folks and especially by JAM who was trashing Daniel in manner not acceptable for scientifically inclined discussion (at least not in my book)
---------------------QUOTE-------------------


Daniel rejects the scientific method. What book have you written?


---------------------QUOTE-------------------
and by bragging his knowledge.
---------------------QUOTE-------------------


More than Dan was discounting my knowledge?


---------------------QUOTE-------------------
Eventually, I decided to participate just to have an opportunity to tell JAM that having Curriculum Vita instead of Resume doesn’t make him a scientist yet.
---------------------QUOTE-------------------


Haha, funny. What makes me a scientist is that I publish papers with new data that come from testing my own hypotheses, something no creationist or ID proponent has ever done. How do you explain that massive deficiency?
Posted by: Mark Iosim on Jan. 19 2008,07:31

oldmanintheskydidntdoit,

Thank you for the links.
I just spent one hour in the bookstore looking over Behe’s new book “The Edge of Evolution: The Search for the Limits of Darwinism” and I agree with your characterization that this is a “wholesale”. I just want to make sure that Behe’s critics didn’t distort his arguments. I done with Behe’s.

I am taking a two weeks off from this forum to focus on my homeworks. I will be back.
Posted by: Daniel Smith on Jan. 19 2008,09:56

Quote (Albatrossity2 @ Jan. 18 2008,07:24)
           
Quote (Daniel Smith @ Jan. 17 2008,19:11)
               
Quote (Albatrossity2 @ Jan. 15 2008,20:32)
                       
Quote (Daniel Smith @ Jan. 15 2008,19:03)
Sorry, but this time, you're just plain wrong.
---------------------QUOTE-------------------


Maybe, but that doesn't explain why EVERY paper that cites that article cites it in a context of abiogenesis. If I'm wrong, I have company, at least.

But even if we agree to disagree on this diversion, let's get back to the original reason why you cited this article. You stated, as if it was surprising, that "protein folds are more a product of natural law than selection". I pointed out  < then > that this is a strawman. I asked you                            

---------------------QUOTE-------------------
If it is not a strawman, Daniel, please document where any reputable scientist claims that natural selection governs the molecular processes involved in protein folding. This sort of argument bespeaks not only a profound misunderstanding of evolutionary theory (which Daniel has already demonstrated abundantly), but a profound ignorance about the molecular processes that occur within cells.
---------------------QUOTE-------------------



---------------------QUOTE-------------------


They don't (to my knowledge) claim that selection governs the molecular processes that specifically control protein folding.  They do claim however, that selection governs the amino acid sequences that make up these proteins.
Denton (if my reading of him is correct) is arguing that the sequences are not governed by selection because the same folds can be arrived at by several routes (sequences) and the same sequence can yield different folds.
That's what I get out of it anyway.
---------------------QUOTE-------------------


Sigh.

Selection operates on biological FUNCTIONS, carried out by macromolecules within organisms, but it acts at the level of the organism. Moving the goalposts to say that scientists claim that "selection governs the amino acid sequences that make up these proteins" is still wrong. Indeed, once you have a new amino acid sequence that generates a new function, selection can operate to favor or disfavor that FUNCTION. But if another amino acid sequence generates the same 3-d structure that also gives rise to the same function, selection had no hand in the molecular processes governing any of that. Selection operates AFTER all of that. It is still a strawman to pretend that reputable scientists ascribe these properties to natural selection.

Daniel, do you understand that different sequences giving rise to the same 3-d structure is exactly what you would expect if selection for the FUNCTION of the sequence, rather than the sequence itself, is operating?

As noted before, Denton is saying nothing surprising from a biochemical or evolutionary point of view. Why you see this as support for your notions is a mystery to me as well.
---------------------QUOTE-------------------


I'm not as dumb as I may appear.  I actually do realize how selection is supposed to work.  I know it cannot work at any other level below the level of the organism.  In a way, you're making my point for me.  In order to produce a function at the organism level, mutations are filtered through the bottleneck of protein folding - which we agree is constrained by natural law.  Therefore, evolution is constrained by natural law (at least in this one basic area).  Denton's hypothesis (which is spelled out in the two papers we've discussed, as well as a third which appeared in Nature), is that there may be other areas in which evolution is also constrained.  Did you read any of these papers?  Because he very meticulously lays out his case; beginning with a history of the theory of evolution by natural law:      

---------------------QUOTE-------------------
that the whole pattern of evolution was itself in a sense already pre-determined or pre-specified by natural law---being the material manifestation of a pre-existing and eternal plan.
pg 327 of the J. Theor. Biol. paper
---------------------QUOTE-------------------

continuing with an overview of how protein folding is governed by said law; and concluding that this is the first vindication for the theory of evolution by natural law:      

---------------------QUOTE-------------------
The subcellular world is thus the first important realm of biology in which the early 19th century idea of evolution by natural law discarded as archaic by most biologists since Darwin, is being finally vindicated.
pg. 302 of the Biosystems paper
---------------------QUOTE-------------------

 
If he is "saying nothing surprising... from a[n] ... evolutionary point of view", then you must be in agreement with his assessment?
Posted by: Albatrossity2 on Jan. 19 2008,10:30

Quote (Daniel Smith @ Jan. 19 2008,09:56)

I'm not as dumb as I may appear.  I actually do realize how selection is supposed to work.  I know it cannot work at any other level below the level of the organism.  In a way, you're making my point for me.  In order to produce a function at the organism level, mutations are filtered through the bottleneck of protein folding - which we agree is constrained by natural law.  Therefore, evolution is constrained by natural law (at least in this one basic area).  Denton's hypothesis (which is spelled out in the two papers we've discussed, as well as a third which appeared in Nature), is that there may be other areas in which evolution is also constrained.  Did you read any of these papers?  Because he very meticulously lays out his case; beginning with a history of the theory of evolution by natural law:              

---------------------QUOTE-------------------
that the whole pattern of evolution was itself in a sense already pre-determined or pre-specified by natural law---being the material manifestation of a pre-existing and eternal plan.
pg 327 of the J. Theor. Biol. paper
---------------------QUOTE-------------------

continuing with an overview of how protein folding is governed by said law; and concluding that this is the first vindication for the theory of evolution by natural law:              

---------------------QUOTE-------------------
The subcellular world is thus the first important realm of biology in which the early 19th century idea of evolution by natural law discarded as archaic by most biologists since Darwin, is being finally vindicated.
pg. 302 of the Biosystems paper
---------------------QUOTE-------------------

 
If he is "saying nothing surprising... from a[n] ... evolutionary point of view", then you must be in agreement with his assessment?
---------------------QUOTE-------------------


Daniel

You may not be as dumb as you appear, but you show a remarkable knack for missing the point, and moving the goalposts.

It is NOT surprising that living things are constrained by physical and chemical laws; I'll avoid using Denton's term "natural law" because I don't really think he and I mean the same thing by it. Therefore it is NOT surprising that forces which act on living things are affected by the action of physical and chemical laws. But you continually put the cart before the horse when you pretend (without ever providing evidence for this assertion) that science proceeds on the assumption that natural selection affects protein folding.

As pointed out numerous times before, that is backward and also off by multiple levels. Protein folding (governed by physical and chemical laws) directly affects protein function. Protein function directly affects cellular function. Cellular function directly affects organism function. Organism function is the level at which natural selection acts.

Thus, natural selection SELECTS for proteins with particular folds, but it does not directly influence that folding. If another protein sequence can fold that way and mimic that function (at all levels from molecule to organism) natural selection could SELECT for that protein conformation as well. But it does not influence the folding itself; that conformation is independent of selection at the time when it happens. Folding happens first, selection happens later and at multiple levels UP in the biological hierarchy.

If you don't understand that, and if you don't understand why your notion that scientists are saying that selection governs protein folding is a strawman, I have exhausted my abilities to explain, and will conclude that either you are being purposefully obtuse, or you are indeed as dumb as you seem to be.

Yes, evolution (and all of biology) is constrained by chemical and physical laws. Living things get no special dispensation from chemical and physical laws, and processes which affect living things (e.g. natural selection) are thus also influenced by chemical and physical laws. But it is manifestly not the case that this can be extrapolated to the teleological conclusion that you quote from the J. Theor. Biol paper. When Denton says    

---------------------QUOTE-------------------
that the whole pattern of evolution was itself in a sense already pre-determined or pre-specified by natural law---being the material manifestation of a pre-existing and eternal plan.
---------------------QUOTE-------------------


it is a non sequitur. A "pre-existing and eternal plan" does not logically follow from the statement that physical and chemical laws govern biology. A plan necessarily invokes a planner. There is no evidence for a planner, and physical and chemical laws are no support for that teleological conclusion.
Posted by: Daniel Smith on Jan. 19 2008,10:31

Quote (Wesley R. Elsberry @ Jan. 17 2008,05:51)
When I posed the problem of evolutionary computation for Dembski's arguments to Dembski back in 1997, I certainly didn't put my example in terms of changes in characters in strings to match arbitrary targets; I posed the problem in terms of a genetic algorithm to provide a near-optimal solution to the "traveling salesman problem". Here, the issue is simply how long a tour a candidate solution represents and there is no question about thresholds. The TSP is biologically relevant because movement costs metabolic energy, and organisms that minimize movement in a closed path thus have an advantage.
---------------------QUOTE-------------------


So I am no longer accused of avoiding the issue...

My problem with the TSP -- and indeed any GA -- is that the selection mechanism always selects the best solution.  This is not a realistic simulation of how natural selection works in real life (for the reasons I've already stated).  

GAs, at best, simulate artificial selection -- and even then unrealistically -- since even artificial selection (in real life), cannot negate such things as natural disasters, diseases, sterility, chance and coincidence.

To illustrate:  Recently a local breeder of prize dogs had nearly her entire kennel wiped out in a flash flood.  Neither natural selection nor artificial selection could stop that.  These dogs were selected against because they were not ducks!

Show me a GA that can realistically simulate that and you'll have something.
Posted by: Assassinator on Jan. 19 2008,10:39

You don't know what natural selection is, wich you prove in that post. Please learn what natural selection is, thank you. I hope I don't have to explain why.
Posted by: Wesley R. Elsberry on Jan. 19 2008,10:45

Daniel Smith:

 

---------------------QUOTE-------------------

So I am no longer accused of avoiding the issue...

My problem with the TSP -- and indeed any GA -- is that the selection mechanism always selects the best solution.

---------------------QUOTE-------------------



IIRC, the Lenski et al. 2003 paper in Nature on Avida specifically analyzes a number of instances in lineages leading to successful evolution of the EQU logic function where overall fitness of organisms declined for a period. This is not an isolated finding in the evolutionary computation literature.

Of course, I suppose it is way out of line to ask Daniel that he learn something about the stuff he feels compelled to criticize.
Posted by: Albatrossity2 on Jan. 19 2008,11:11

Quote (Daniel Smith @ Jan. 19 2008,10:31)
To illustrate:  Recently a local breeder of prize dogs had nearly her entire kennel wiped out in a flash flood.  Neither natural selection nor artificial selection could stop that.  These dogs were selected against because they were not ducks!

Show me a GA that can realistically simulate that and you'll have something.
---------------------QUOTE-------------------


Daniel

The evidence seems to be mounting that you may indeed be as dumb as you appear. This comment implies that you think that natural selection based on fitness is the only mechanism that evolutionary theory predicts for the removal of organisms from the gene pool.

Is my inference, based on the evidence in your comment, correct?
Posted by: Daniel Smith on Jan. 19 2008,11:37

Quote (Albatrossity2 @ Jan. 19 2008,08:30)
if you don't understand why your notion that scientists are saying that selection governs protein folding is a strawman, I have exhausted my abilities to explain, and will conclude that either you are being purposefully obtuse, or you are indeed as dumb as you seem to be.
---------------------QUOTE-------------------


I didn't mean to imply that scientists were still saying that.  Scientists are not saying "selection governs protein folding", because the discoveries of recent years have proven otherwise.  I don't know whether they used to think that or not, but from the gist of Denton's papers, I get the impression that they did at one time expect protein folding to be the product of selection from an infinite number of possibilities as opposed to a finite set of about 1000 folds:
           

---------------------QUOTE-------------------
By the late 1960s several other proteins had been determined including hemoglobin and lysozyme. Despite these early successes the lack of any apparent regularity in protein structures, and the great dissimilarity among those that had been determined, provided no basis for a rational classification (Ptitsyn & Finkelstein, 1980; Richardson, 1981). The picture was still in those early days compatible with the Lego model---that the folds in living organisms on earth might be individual members of a near infinite set of contingent material assemblages put together by natural selection over millions of years of evolution.
It was only during the 1970s, as the number of 3D structures began to grow significantly, that it first became apparent that there might not be an unlimited number of protein folds---that the folds might not belong to a potentially infinite set of artifactual Lego-like constructs.
pg 330, J. Theor. Biol. paper (my emphasis)
---------------------QUOTE-------------------



I've also often seen scientists refer to amino acid sequences as "evolutionarily constrained", implying that these sequences are so important for function, they do not tolerate mutations.  Denton takes a different view:
         

---------------------QUOTE-------------------
It is not, as is commonly supposed, the amino acid sequences which specify the three-dimensional form of a protein fold, but rather the abstract laws of protein form...
The biological fitness of the folds is greatly enhanced by their accessibility in sequence space. It is now clear that many different amino acid sequences can fold into the same three-dimensional form (Brandon and Tooze, 1999) and sometimes the same sequence can fold into two different folds (Cordes et al., 2000). Evidently, the rules of fold form are highly restrictive at the level of three-dimensional structure, permitting only 1000 atomic patterns, but highly permissive in terms of sequence—a high proportion of sequences can fold into one or another fold. By analogy with language, we might think of the rules of syntax (fold architecture) as being very strict but the rules of spelling (fold sequence) very lax. Consequently, although the folds are immutable and discontinuosly distributed in fold space they can still be easily found (spelt) in sequence space and utilized by the cell.
pg 299, BioSystems paper (my emphasis)
---------------------QUOTE-------------------


Denton is building a case here.  He's laying the groundwork for a revitalized theory of evolution by natural law and he's striking at the genetic foundations of the MET.  I don't know why you wouldn't expect me to appreciate that!
Posted by: oldmanintheskydidntdoit on Jan. 19 2008,11:39

Quote (Daniel Smith @ Jan. 19 2008,10:31)
To illustrate:  Recently a local breeder of prize dogs had nearly her entire kennel wiped out in a flash flood.  Neither natural selection nor artificial selection could stop that.  These dogs were selected against because they were not ducks!

Show me a GA that can realistically simulate that and you'll have something.
---------------------QUOTE-------------------


The sad thing is you are serious.

I pity you.
Posted by: oldmanintheskydidntdoit on Jan. 19 2008,11:43

Quote (Daniel Smith @ Jan. 19 2008,10:31)
My problem with the TSP -- and indeed any GA -- is that the selection mechanism always selects the best solution.
---------------------QUOTE-------------------


This is simply wrong.
Posted by: Daniel Smith on Jan. 19 2008,11:45

Quote (Albatrossity2 @ Jan. 19 2008,09:11)
 
Quote (Daniel Smith @ Jan. 19 2008,10:31)
To illustrate:  Recently a local breeder of prize dogs had nearly her entire kennel wiped out in a flash flood.  Neither natural selection nor artificial selection could stop that.  These dogs were selected against because they were not ducks!

Show me a GA that can realistically simulate that and you'll have something.
---------------------QUOTE-------------------


Daniel

The evidence seems to be mounting that you may indeed be as dumb as you appear. This comment implies that you think that natural selection based on fitness is the only mechanism that evolutionary theory predicts for the removal of organisms from the gene pool.

Is my inference, based on the evidence in your comment, correct?
---------------------QUOTE-------------------


From what I've seen, natural selection is given an almost god-like quality amongst many believers in the currently held theory.  It is talked about as if it is all-knowing, all-powerful, and able to predict the future and select the optimal solution for any and all potential problems.

So, to answer your question: I wouldn't be surprised by any "power" ascribed to NS by the currently held theory of evolution.
Posted by: blipey on Jan. 19 2008,13:03

So, I take it you had trouble distinguishing the question, Daniel?  I'll do it in bold so that you can find it:

Do you think that natural selection is the only mechanism that ToE predicts will remove organisms from the gene pool?

This can be easily answered with a "yes" or a "no".
Posted by: oldmanintheskydidntdoit on Jan. 19 2008,13:15

Quote (Daniel Smith @ Jan. 19 2008,11:45)
It is talked about as if it is all-knowing, all-powerful, and able to predict the future and select the optimal solution for any and all potential problems.
---------------------QUOTE-------------------


Got an example or is that just more empty talk?

predict the future?

What bullshit.
Posted by: Henry J on Jan. 19 2008,13:47



---------------------QUOTE-------------------
My problem with the TSP -- and indeed any GA -- is that the selection mechanism always selects the best solution.  
---------------------QUOTE-------------------



Who claimed that GA's always hit the best solution? That's not consistent with my understanding of how GA's work.



---------------------QUOTE-------------------
GAs, at best, simulate artificial selection -- and even then unrealistically -- since even artificial selection (in real life),
---------------------QUOTE-------------------



Meaning that simulations are simpler than the thing being simulated, and always leave out some details.

Yeah, artificial selection tends to focus on one (or maybe a few) specific traits, whereas I'd expect natural selection to be less constrained in what traits get selected.

Henry
Posted by: Albatrossity2 on Jan. 19 2008,13:48

Quote (Daniel Smith @ Jan. 19 2008,11:37)
I didn't mean to imply that scientists were still saying that.  Scientists are not saying "selection governs protein folding", because the discoveries of recent years have proven otherwise.  I don't know whether they used to think that or not, but from the gist of Denton's papers, I get the impression that they did at one time expect protein folding to be the product of selection from an infinite number of possibilities as opposed to a finite set of about 1000 folds:
---------------------QUOTE-------------------


Well, either you or Denton (or both) are absolutely wrong about that. Or, more likely, one or both of you are confused, perhaps purposefully so, about the use of certain words in the scientific literature. If you recall, when you first broached this topic, I asked you for some citations that would support your assertion. To date you have been unable to come up with any. What have you found?
 

---------------------QUOTE-------------------
I've also often seen scientists refer to amino acid sequences as "evolutionarily constrained", implying that these sequences are so important for function, they do not tolerate mutations.
---------------------QUOTE-------------------


This is an example of the confusion. "Constrained" in this context does not mean what you said you thought it meant in previous comments. In those comments it was apparent that you were saying that scientists asserted that natural selection "controlled" protein folding. Natural selection, as pointed out previously a number of times, merely chooses which protein conformations work best. It selects from among the options offered, and the options offered are all the result of physical and chemical laws. The ones that work are the ones that we find, and indeed, once they have been selected for, if their function is critical to the life or reproduction of the organism, very little change in the sequence is tolerated. There is a temporal aspect to this that I am pretty sure you are ignoring. Physical and chemical laws control the folding of proteins, and natural selection THEN controls which particular conformations we find, based on the functionality of that conformation.

Your strawman, that scientists were asserting that natural selection controlled protein folding at both levels, remains unsupported by any evidence. So if Denton is "building a case" based on the destruction of a strawman, color me unimpressed.

And I really hate to point this out to you, but I cannot figure out what testable hypotheses arise from Denton's "case" that would help us distinguish his teleological scheme from scenarios that are explicable using known mechanisms based on evolutionary theory. Even if we allow him to build on a strawman, he hasn't built anything until he generates AND TESTS hypotheses with predictions that are distinguishable from current evolutionary theory.

Does he offer any testable hypotheses that fit that description?  We know he hasn't tested any hypotheses, since all of these papers are theoretical in nature, but if he has even offered up a testable hypothesis, it would be the first in the history of ID.
Posted by: clamboy on Jan. 20 2008,01:03

Quote (Daniel Smith @ Jan. 19 2008,11:45)
Quote (Albatrossity2 @ Jan. 19 2008,09:11)
   
Quote (Daniel Smith @ Jan. 19 2008,10:31)
To illustrate:  Recently a local breeder of prize dogs had nearly her entire kennel wiped out in a flash flood.  Neither natural selection nor artificial selection could stop that.  These dogs were selected against because they were not ducks!

Show me a GA that can realistically simulate that and you'll have something.
---------------------QUOTE-------------------


Daniel

The evidence seems to be mounting that you may indeed be as dumb as you appear. This comment implies that you think that natural selection based on fitness is the only mechanism that evolutionary theory predicts for the removal of organisms from the gene pool.

Is my inference, based on the evidence in your comment, correct?
---------------------QUOTE-------------------


From what I've seen, natural selection is given an almost god-like quality amongst many believers in the currently held theory.  It is talked about as if it is all-knowing, all-powerful, and able to predict the future and select the optimal solution for any and all potential problems.

So, to answer your question: I wouldn't be surprised by any "power" ascribed to NS by the currently held theory of evolution.
---------------------QUOTE-------------------


Now I understand, having quietly held back and read the thread during its progression, why Daniel Smith has such a problem with "Darwinism." Daniel, I am no more a biologist than you, but even I understand that your post shows that you have no grasp of the idea of natural selection, much less a grasp of the theory of evolution. You really think natural selection is about finding "the optimal solution for any and all potential problems"? You really think natural selection is seen by actual biologists as "able to predict the future"? You say "From what I've seen...", but of course you have no evidence beyond those words. I will not call you stupid, just grossly misinformed and willfully ignorant.

It disgusts me that our educational system churns out millions of "Daniel Smith"s per year. He is not just pointed the wrong direction, he's like an aircraft carrier going that way at full steam. Just to turn to face the right way will require miles and miles and hours and hours of effort.

You poor, pathetic kid, Daniel Smith. On the one hand I'm sorry for you, but on the other I'm repulsed at your determination never to learn about what it is you have chosen to criticize.
Posted by: oldmanintheskydidntdoit on Jan. 20 2008,04:45

Yeah, I got one word for you Daniel!

Knees

Either your designer is a tard or evolution has selected a sub-optimal solution.
Posted by: mitschlag on Jan. 20 2008,05:18

Quote (clamboy @ Jan. 20 2008,01:03)
It disgusts me that our educational system churns out millions of "Daniel Smith"s per year. He is not just pointed the wrong direction, he's like an aircraft carrier going that way at full steam. Just to turn to face the right way will require miles and miles and hours and hours of effort.
---------------------QUOTE-------------------


Don't blame the system.  Daniel and his compatriots have issues that interfere with learning.
Posted by: Richard Simons on Jan. 20 2008,10:41

Quote (Daniel Smith @ Jan. 19 2008,11:45)
From what I've seen, natural selection is given an almost god-like quality amongst many believers in the currently held theory.  It is talked about as if it is all-knowing, all-powerful, and able to predict the future and select the optimal solution for any and all potential problems.
---------------------QUOTE-------------------


This explains why he considers that the requirement of Schindewolf's ideas, that organisms can adapt to future events, is no big deal. He thinks that biologists assume evolution and natural selection operate the same way. (Shakes head in bemusement)
Posted by: Daniel Smith on Jan. 20 2008,12:25

Quote (Albatrossity2 @ Jan. 19 2008,11:48)
"Constrained" in this context does not mean what you said you thought it meant in previous comments. In those comments it was apparent that you were saying that scientists asserted that natural selection "controlled" protein folding.
---------------------QUOTE-------------------


I've never meant that natural selection controlled protein folding.  If you got that impression from what I said, I apologize.  Personally, I don't know how you could get that impression, but maybe I worded things weirdly.  I don't know.  It would appear then, that the root of our disagreement is a misunderstanding.
Posted by: Albatrossity2 on Jan. 20 2008,13:05

Quote (Daniel Smith @ Jan. 20 2008,12:25)
 
Quote (Albatrossity2 @ Jan. 19 2008,11:48)
"Constrained" in this context does not mean what you said you thought it meant in previous comments. In those comments it was apparent that you were saying that scientists asserted that natural selection "controlled" protein folding.
---------------------QUOTE-------------------


I've never meant that natural selection controlled protein folding.  If you got that impression from what I said, I apologize.  Personally, I don't know how you could get that impression, but maybe I worded things weirdly.  I don't know.  It would appear then, that the root of our disagreement is a misunderstanding.
---------------------QUOTE-------------------


Gee, I have no idea how one could get that impression from what you wrote.  

---------------------QUOTE-------------------
Recent findings that suggest protein folds are more a product of natural law than selection would seem to vindicate these long neglected scientists.

and

So these findings would seem to vindicate both Schindewolf and Berg who knew that evolution must've happened lawfully, but just didn't know how.
---------------------QUOTE-------------------


Additionally, when I asked you to "please document where any reputable scientist claims that natural selection governs the molecular processes involved in protein folding," you ignored it for a bit, and then came up with this.  

---------------------QUOTE-------------------
They don't (to my knowledge) claim that selection governs the molecular processes that specifically control protein folding.  They do claim however, that selection governs the amino acid sequences that make up these proteins.
Denton (if my reading of him is correct) is arguing that the sequences are not governed by selection because the same folds can be arrived at by several routes (sequences) and the same sequence can yield different folds.
---------------------QUOTE-------------------


The use of the word "govern" tends to be similar to the use of the word "control".

Daniel, the fact that similar conformations can be achieved with different sequences surely cannot be surprising to anyone. The archetypal protein conformation, the alpha-helix, arises from a huge variety of different sequences. This has been known since 1948. The fact that sequences can give rise to different conformations was a bit surprising until scientists gained a better understanding of the role of chaperonins and post-translational processing in the generation of protein conformations. So that observation was based on faulty assumptions that proteins folded into their final conformation immediately upon being translated. They don't; the story is a lot more complicated than that. Get a good biochemistry book and read up on this stuff, please.

Finally, speaking of faulty assumptions, here's a question about your assumptions that you skirted around earlier. Maybe you can try again.

Do you think that natural selection is the only mechanism that ToE predicts will remove organisms from the gene pool?
Posted by: Daniel Smith on Jan. 20 2008,13:32

Quote (Wesley R. Elsberry @ Jan. 19 2008,08:45)
Daniel Smith:

                       

---------------------QUOTE-------------------

So I am no longer accused of avoiding the issue...

My problem with the TSP -- and indeed any GA -- is that the selection mechanism always selects the best solution.

---------------------QUOTE-------------------



IIRC, the Lenski et al. 2003 paper in Nature on Avida specifically analyzes a number of instances in lineages leading to successful evolution of the EQU logic function where overall fitness of organisms declined for a period. This is not an isolated finding in the evolutionary computation literature.

Of course, I suppose it is way out of line to ask Daniel that he learn something about the stuff he feels compelled to criticize.
---------------------QUOTE-------------------


I don't pretend to be an expert on this subject by any means Wesley.  I'm sure your knowledge on this subject exceeds mine by light years.  I barely know the basics and thus am only able to critique these things at there most basic and fundamental level.  So that said...

My objection was that selection algorithms always select the best solution.  By this I mean, of course, the best available solution.  If all the solutions degrade at some point during the process---which seems likely since bad solutions will always outnumber good ones when the mechanism for generation is random---then that still does not address my objection, since the best available solutions are still always selected for.  In fact, it would be better for the GAs overall result if the selection criteria had a low threshold for fitness -- as this would allow more potential solutions to survive.  

Selection in real life cannot afford such low fitness levels however.  In fact, selection in real life is often arbitrary and many times selects for completely unrelated solutions to completely unrelated problems, so unless the best solutions were sometimes selected against, the selection algorithm still does not reflect the way NS works in the real world.  In the EQU logic function or the TSP algorithm, were any of the best solutions selected against Wesley?

Another objection I will raise here concerns the pool of potential solutions from which GAs can select.  Are these pools infinite?  Or are they constrained?  Real life selection does not have an infinite pool of solutions to select from -- as we have been discussing with protein folding -- the pool is limited for real life selection.  This is also evidenced by the many, many known instances of convergent and parallel evolution where the same solution is arrived at via different pathways.  This phenomenon can be interpreted to represent a limited number of lawful solutions for life's problems from which nature has to select.  As Leo S. Berg said in his book Nomogenesis:          

---------------------QUOTE-------------------
Had infinite variations prevailed in nature, and had every organ varied in all directions, deformed beings and monstrosities would have become the rule, while normal beings well adapted to their surroundings would form the exception.
An organism is a stable system, in which a tendency towards variation is confined within certain limits by inheritance.  This truth is self-evident.
pg. 27
---------------------QUOTE-------------------


Perhaps some GAs reflect this, I don't know, but if they don't, it's another instance where their algorithms don't accurately reflect real life.  If all the solutions in the pool from which the GA selects are not viable solutions for at least some problem, (representing a stable system), then they would have to be eliminated in the very beginning to realistically mimic the process of evolution via RM+NS - don't you think?
Posted by: Daniel Smith on Jan. 20 2008,13:59

Quote (Albatrossity2 @ Jan. 20 2008,11:05)
         
Quote (Daniel Smith @ Jan. 20 2008,12:25)
             
Quote (Albatrossity2 @ Jan. 19 2008,11:48)
"Constrained" in this context does not mean what you said you thought it meant in previous comments. In those comments it was apparent that you were saying that scientists asserted that natural selection "controlled" protein folding.
---------------------QUOTE-------------------


I've never meant that natural selection controlled protein folding.  If you got that impression from what I said, I apologize.  Personally, I don't know how you could get that impression, but maybe I worded things weirdly.  I don't know.  It would appear then, that the root of our disagreement is a misunderstanding.
---------------------QUOTE-------------------


Gee, I have no idea how one could get that impression from what you wrote.              

---------------------QUOTE-------------------
Recent findings that suggest protein folds are more a product of natural law than selection would seem to vindicate these long neglected scientists.

and

So these findings would seem to vindicate both Schindewolf and Berg who knew that evolution must've happened lawfully, but just didn't know how.
---------------------QUOTE-------------------


---------------------QUOTE-------------------


When I said "protein folds are more a product of natural law than selection", I meant selection in the traditional sense (top down, via function).  I assumed you'd know that.
       

---------------------QUOTE-------------------
Additionally, when I asked you to "please document where any reputable scientist claims that natural selection governs the molecular processes involved in protein folding," you ignored it for a bit, and then came up with this.              

---------------------QUOTE-------------------
They don't (to my knowledge) claim that selection governs the molecular processes that specifically control protein folding.  They do claim however, that selection governs the amino acid sequences that make up these proteins.
Denton (if my reading of him is correct) is arguing that the sequences are not governed by selection because the same folds can be arrived at by several routes (sequences) and the same sequence can yield different folds.
---------------------QUOTE-------------------


The use of the word "govern" tends to be similar to the use of the word "control".
---------------------QUOTE-------------------


When I said "They do claim however, that selection governs the amino acid sequences that make up these proteins.", I meant (when are you going to learn to read my mind?) that these sequences are (said to be) arrived at via the mechanism of RM+NS.  I didn't mean that scientists meant natural selection was in there moving amino acids around in order to get the sequence it wanted.
Do I really come across as that dumb?
       

---------------------QUOTE-------------------
Daniel, the fact that similar conformations can be achieved with different sequences surely cannot be surprising to anyone. The archetypal protein conformation, the alpha-helix, arises from a huge variety of different sequences. This has been known since 1948. The fact that sequences can give rise to different conformations was a bit surprising until scientists gained a better understanding of the role of chaperonins and post-translational processing in the generation of protein conformations. So that observation was based on faulty assumptions that proteins folded into their final conformation immediately upon being translated. They don't; the story is a lot more complicated than that. Get a good biochemistry book and read up on this stuff, please.

Finally, speaking of faulty assumptions, here's a question about your assumptions that you skirted around earlier. Maybe you can try again.

Do you think that natural selection is the only mechanism that ToE predicts will remove organisms from the gene pool?
---------------------QUOTE-------------------


Define what you mean by "natural selection".  When I think of natural selection, I think of anything that keeps an individual from reproducing.  If you have a narrower definition, then I can see how there'd be a difference of opinion.
I guess there's also reproductive isolation -- so long as it remains permanent.  This would separate the gene pool.  Of course it could possibly come back together at some point.  So I don't know if that technically qualifies as "removal" from the gene pool.
I do know this: "SELECTION" (whether alone or coupled with something else) is always credited with being the force behind evolution.  I cannot think of a single instance where "selection" is not credited with being the final arbitrator for the evolution of some organ or feature.  Can you?
Posted by: Daniel Smith on Jan. 20 2008,14:02

Quote (Henry J @ Jan. 19 2008,11:47)
 

---------------------QUOTE-------------------
My problem with the TSP -- and indeed any GA -- is that the selection mechanism always selects the best solution.  
---------------------QUOTE-------------------



Who claimed that GA's always hit the best solution? That's not consistent with my understanding of how GA's work.
---------------------QUOTE-------------------


I said "select", you said "hit".  Do we mean the same thing?


---------------------QUOTE-------------------
 

---------------------QUOTE-------------------
GAs, at best, simulate artificial selection -- and even then unrealistically -- since even artificial selection (in real life),
---------------------QUOTE-------------------



Meaning that simulations are simpler than the thing being simulated, and always leave out some details.

Yeah, artificial selection tends to focus on one (or maybe a few) specific traits, whereas I'd expect natural selection to be less constrained in what traits get selected.

Henry
---------------------QUOTE-------------------


So we agree on something!
Posted by: JAM on Jan. 20 2008,14:06

Quote (Daniel Smith @ Jan. 20 2008,13:32)
Quote (Wesley R. Elsberry @ Jan. 19 2008,08:45)
...Of course, I suppose it is way out of line to ask Daniel that he learn something about the stuff he feels compelled to criticize.
---------------------QUOTE-------------------


I don't pretend to be an expert on this subject by any means Wesley.
---------------------QUOTE-------------------


You claim to understand it better than the experts, which is an implicit claim of expertise. The reality is that you are avoiding learning about it. God is screaming at you with evidence. Why do you cover your ears?


---------------------QUOTE-------------------
I'm sure your knowledge on this subject exceeds mine by light years.  I barely know the basics and thus am only able to critique these things at there most basic and fundamental level.
---------------------QUOTE-------------------


No, Dan, you don't even barely know the basics. You repeatedly bear false witness, demonstrating your contempt for one of the central rules of Christianity. Therefore, you shouldn't be critiquing anything that you can't describe accurately.


---------------------QUOTE-------------------
So that said...

My objection was that selection algorithms always select the best solution.  By this I mean, of course, the best available solution.
---------------------QUOTE-------------------


I don't see how you got that "of course," because of course, "the best solution" doesn't mean "the best available solution."


---------------------QUOTE-------------------
If all the solutions degrade at some point during the process---which seems likely since bad solutions will always outnumber good ones when the mechanism for generation is random---then that still does not address my objection, since the best available solutions are still always selected for.
---------------------QUOTE-------------------


That's not true at all.


---------------------QUOTE-------------------
Selection in real life cannot afford such low fitness levels however.
---------------------QUOTE-------------------


How would you know?


---------------------QUOTE-------------------
Another objection I will raise here concerns the pool of potential solutions from which GAs can select.  Are these pools infinite?  Or are they constrained?
---------------------QUOTE-------------------


They are incredibly constrained, which is why it is both stupid and arrogant to claim that life's "solutions" were intelligently designed by an omnipotent God.


---------------------QUOTE-------------------
Real life selection does not have an infinite pool of solutions to select from -- as we have been discussing with protein folding
---------------------QUOTE-------------------


You haven't been discussing selection wrt protein folding. We've been trying to explain to you that you are using a straw man fallacy.


---------------------QUOTE-------------------
-- the pool is limited for real life selection.  This is also evidenced by the many, many known instances of convergent and parallel evolution where the same solution is arrived at via different pathways.
---------------------QUOTE-------------------


The pool is limited, but that's not the evidence. The evidence is common descent of both organisms and their components, a phenomenon for which every one of your predictions has been WRONG.


---------------------QUOTE-------------------
This phenomenon can be interpreted to represent a limited number of lawful solutions for life's problems from which nature has to select.
---------------------QUOTE-------------------


Your insertion of the unnecessary qualifier "lawful" is pure sophistry, and you know it.


---------------------QUOTE-------------------
As Leo S. Berg said...
---------------------QUOTE-------------------


If you were a seeker of God's handiwork, you would look at the handiwork (the data) instead of what lowly humans write about it.

Intellectually, you are a fraud, Dan. God has put the evidence on display for you, and all you do is run to politically-motivated misrepresentations of it to defend your ego and your political motivations.
Posted by: Daniel Smith on Jan. 20 2008,14:21

Quote (clamboy @ Jan. 19 2008,23:03)
You really think natural selection is about finding "the optimal solution for any and all potential problems"?
---------------------QUOTE-------------------


No.
Posted by: oldmanintheskydidntdoit on Jan. 20 2008,14:31

Quote (Daniel Smith @ Jan. 20 2008,13:32)
Another objection I will raise here concerns the pool of potential solutions from which GAs can select.  Are these pools infinite?  Or are they constrained?
---------------------QUOTE-------------------


Recently I purchased my infinite memory USB drive. I can now run simulations as they are meant to be run.

< >
Obviously such an advanced storage system requires a top-of-the-line interface module.
< >
Posted by: oldmanintheskydidntdoit on Jan. 20 2008,14:37

Quote (Daniel Smith @ Jan. 20 2008,14:21)
 
Quote (clamboy @ Jan. 19 2008,23:03)
You really think natural selection is about finding "the optimal solution for any and all potential problems"?
---------------------QUOTE-------------------


No.
---------------------QUOTE-------------------


So how come you say
 

---------------------QUOTE-------------------
My problem with the TSP -- and indeed any GA -- is that the selection mechanism always selects the best solution.  
---------------------QUOTE-------------------


Have you now learnt new stuff and changed your mind?

I mean, I know you are saying that the "optimal" solution could be selected against by, say, a meteor hitting the earth and killing the thing in question, but......equally, it might not!

Bit of a thin "what if" objection?

EDIT: And I suspect it could be incorporated into any GA by a simple kill one at random routine. Big deal. How would it affect the end result? Answer that one please Daniel.
Posted by: Albatrossity2 on Jan. 20 2008,15:05

Quote (Daniel Smith @ Jan. 20 2008,13:59)
Define what you mean by "natural selection".  When I think of natural selection, I think of anything that keeps an individual from reproducing.  If you have a narrower definition, then I can see how there'd be a difference of opinion.
I guess there's also reproductive isolation -- so long as it remains permanent.  This would separate the gene pool.  Of course it could possibly come back together at some point.  So I don't know if that technically qualifies as "removal" from the gene pool.
I do know this: "SELECTION" (whether alone or coupled with something else) is always credited with being the force behind evolution.
---------------------QUOTE-------------------


Daniel

I think the wikipedia definition works just fine  

---------------------QUOTE-------------------
Natural selection is the process by which favorable traits that are heritable become more common in successive generations of a population of reproducing organisms, and unfavorable traits that are heritable become less common.
---------------------QUOTE-------------------


Now let's look at what is wrong with your definition, which I am merely guessing at, since you haven't provided it..

This discussion started when you criticized the study of evolution via genetic algorithms as being unable to model an event in which dogs were drowned in a flood "because they weren't ducks."

A natural disaster certainly can keep "an individual from reproducing". Is that an instance of natural selection? Apparently you think so. But that not the case; any individual with any combination of genes would be unfit in that situation. There was no selection; no individuals had the right combination of genes that would allow them to survive and reproduce. Note that a key parameter is survival and reproduction. There can be no natural selection without survival and reproduction. Natural selection does not mean death; it is the process by which even marginally more fit phenotypes become more common in successive generations. In order to become more common, there must be survival and reproduction.

You need to learn a bit more about other mechanisms of evolution (e.g. genetic drift) rather than ascribe all power to your idiosyncratic definition of natural selection.
Posted by: swbarnes2 on Jan. 20 2008,16:17

Quote (Daniel Smith @ Jan. 20 2008,13:32)
I don't pretend to be an expert on this subject by any means Wesley.
---------------------QUOTE-------------------



Yes, you do.  When you claim that you understand the evolutionary implications of GA's better than the people who write them, you are indeed claiming to be an expert.

Chalk up another lie for Danny boy.

 

---------------------QUOTE-------------------
I barely know the basics and thus am only able to critique these things at there most basic and fundamental level.
---------------------QUOTE-------------------



No.

You can't criticize something "on the basics" if you do not know what the basics are.

Somoene who thinks that a whole population dying in a freak flood is an example of natural selection is not in posession of the basics.

 

---------------------QUOTE-------------------
My objection was that selection algorithms always select the best solution.  By this I mean, of course, the best available solution.
---------------------QUOTE-------------------



Oh no.  We're not going to let you get away with lying about what you wrote again.  You wrote "the best solution".  Then everyone pointed out to you how stupid that was, so you are trying to fix your mistake by lying to us, and pretending that you meant the best available solution.

 

---------------------QUOTE-------------------
If all the solutions degrade at some point during the process---which seems likely since bad solutions will always outnumber good ones when the mechanism for generation is random
---------------------QUOTE-------------------



Good grief, you are stupid.

All the solutions are under selection.  That keeps them from degrading.  

If you think I'm wrong, and you are right, prove it.

Find data on the output of a GA, and show us how the solutions degrade.

Just show us the evidence that you are right.  I'll look like a loud mouthed idiot, and you'll be vindicated.  What do you have to lose?  

Just in the past few months, someone on Panda's Thumb wrote a GA to solve a problem involving the shortest path between a set of points.  Why don't you contact the person who wrote that GA, ask to see all the output, and then you can show us how the solutions degrade over time?

It's what an honest, intelligent peron would do: look at the real data, then draw their conclusions.

I'm sure that the span of a few days will once again confirm that you have absolutely no intention of behaving like an intelligent, honest person in this regard.
Posted by: Henry J on Jan. 20 2008,16:51

Daniel,


---------------------QUOTE-------------------
I said "select", you said "hit".  Do we mean the same thing?
---------------------QUOTE-------------------



Yeah. Select/hit the variety that outproduces the other variety. That's on average, of course, and in the absence of major disasters taking out some fraction of the population all at once. A disaster that would kill the individual regardless of its DNA isn't really a factor in natural selection, since such doesn't give any advantage to one variety over another.

Henry
Posted by: clamboy on Jan. 20 2008,17:54

Quote (Daniel Smith @ Jan. 20 2008,14:21)
Quote (clamboy @ Jan. 19 2008,23:03)
You really think natural selection is about finding "the optimal solution for any and all potential problems"?
---------------------QUOTE-------------------


No.
---------------------QUOTE-------------------


Well done, Daniel. You've quoted me out of context and so distorted the obvious intent of my question. You've learned your creationist tactics well. From what I wrote, it was clear that I meant your portrayal of the prevailing view of actual scientists who study evolution, not your opinion.

But it can't hurt to try again, I guess. *ahem* You really think that natural selection is viewed by evolutionary biologists as a process intent on finding "the optimal solution for any and all potential problems" encountered by organisms? From what you wrote above, your answer must be

"Yes."
Posted by: Wesley R. Elsberry on Jan. 21 2008,07:21

Daniel Smith:



---------------------QUOTE-------------------

I'm sure your knowledge on this subject exceeds mine by light years.

[...]

In fact, it would be better for the GAs overall result if the selection criteria had a low threshold for fitness -- as this would allow more potential solutions to survive.

---------------------QUOTE-------------------



I only need to be a few regular seconds ahead of Daniel to find and read Wikipedia's < article on fitness proportionate selection >, which states:



---------------------QUOTE-------------------

While candidate solutions with a higher fitness will be less likely to be eliminated, there is still a chance that they may be. Contrast this with a less sophisticated selection algorithm, such as truncation selection, which will eliminate a fixed percentage of the weakest candidates. With fitness proportionate selection there is a chance some weaker solutions may survive the selection process; this is an advantage, as though a solution may be weak, it may include some component which could prove useful following the recombination process.

---------------------QUOTE-------------------



I have to echo what others have already noted, that Daniel's "criticisms" are too ill-informed to be considered a substantive contribution to discussion. One finds that one has to guess at what might even be an applicable way to map Daniel's blitherings to what actually exists in the literature.
Posted by: blipey on Jan. 21 2008,08:07

The problem may stem from Daniel not realizing that there is anything that constitutes "the literature".  It may be that he believes that no one has ever studied this "field of biology".  He "may" be breaking "new" ground.

edited to "add" some more Ftk "importance" pointers
Posted by: oldmanintheskydidntdoit on Jan. 21 2008,14:45

ere, Daniel, you know what would really progress your case imho.

Some, like, maths, or a computer program designed to show how your ideas work in practice.

Programming is fun.

Honestly. You too Mr Iosim.

Anybody can learn. More importantly, anybody can teach themselves. I did. The tools are free. Tell me what OS you have and I will post some links. Java and (for example, not necessarily the best to combine with Java) OpenGL are platform independent.

You just gotta stick at it. Hour a day for a month and you'll be away. What was impenetrable symbols becomes meaningful. You should try it.


---------------------CODE SAMPLE-------------------
funkGroove
       = let p1 = perc LowTom qn
             p2 = perc AcousticSnare en
         in Tempo 3 (Instr Percussion (cut 8 (repeatM
                 ((p1 :+: qnr :+: p2 :+: qnr :+: p2 :+:
                   p1 :+: p1 :+: qnr :+: p2 :+: enr)
                  :=: roll en (perc ClosedHiHat 2))
            )))
---------------------CODE SAMPLE-------------------


< http://beautifulcode.oreillynet.com/ >
Not that I do perl, but you get the idea.
Posted by: Daniel Smith on Jan. 21 2008,18:02

Quote (Albatrossity2 @ Jan. 20 2008,13:05)
     
Quote (Daniel Smith @ Jan. 20 2008,13:59)
Define what you mean by "natural selection".  When I think of natural selection, I think of anything that keeps an individual from reproducing.  If you have a narrower definition, then I can see how there'd be a difference of opinion.
I guess there's also reproductive isolation -- so long as it remains permanent.  This would separate the gene pool.  Of course it could possibly come back together at some point.  So I don't know if that technically qualifies as "removal" from the gene pool.
I do know this: "SELECTION" (whether alone or coupled with something else) is always credited with being the force behind evolution.
---------------------QUOTE-------------------


Daniel

I think the wikipedia definition works just fine          

---------------------QUOTE-------------------
Natural selection is the process by which favorable traits that are heritable become more common in successive generations of a population of reproducing organisms, and unfavorable traits that are heritable become less common.
---------------------QUOTE-------------------


Now let's look at what is wrong with your definition, which I am merely guessing at, since you haven't provided it..

This discussion started when you criticized the study of evolution via genetic algorithms as being unable to model an event in which dogs were drowned in a flood "because they weren't ducks."

A natural disaster certainly can keep "an individual from reproducing". Is that an instance of natural selection? Apparently you think so. But that not the case; any individual with any combination of genes would be unfit in that situation. There was no selection; no individuals had the right combination of genes that would allow them to survive and reproduce. Note that a key parameter is survival and reproduction. There can be no natural selection without survival and reproduction. Natural selection does not mean death; it is the process by which even marginally more fit phenotypes become more common in successive generations. In order to become more common, there must be survival and reproduction.

You need to learn a bit more about other mechanisms of evolution (e.g. genetic drift) rather than ascribe all power to your idiosyncratic definition of natural selection.
---------------------QUOTE-------------------


If we can reduce it to basics; your definition of natural selection applies only to positive selection:  Only that which survives to reproduce is said to be selected.  
My definition includes both the positive and the negative:  If something survives to reproduce, it was selected for, if it doesn't survive to reproduce, it was selected against.

As far as I can tell, that's the only difference between our two positions.
I might not be using the word correctly.  If not, I need to find another way of expressing the thought.
Posted by: Ideaforager on Jan. 21 2008,18:15

Daniel,

---------------------QUOTE-------------------
My definition includes both the positive and the negative:  If something survives to reproduce, it was selected for, if it doesn't survive to reproduce, it was selected against.
---------------------QUOTE-------------------


Are you implying that that "everything" happens according to a plan?
Posted by: Assassinator on Jan. 21 2008,18:21

You don't completly grasp the idea of natural selection Daniel. But it's pretty easy (that's why I wonder why you've got so much trouble with it...). First of all, it's relative, because natural selection matters between other groups of animals. Imagine a population of butterflies living in a dark forest, you've got red one's and you've got brown one's. The red one's will be a much easier prey for birds for example, because they're much easier spotted by a fast flying bird then brown one's. The red one's will be the number one on the bird's menu, and will get eaten much more then the brown butterflies. The brown one's can preduce much more offspring then the red one's, and after a while a dominatly brown population of butterflies will populate the forest. You can turn it around ofcourse, and set them in a brightly collored field of flowers, where the red butterflies will have a survival advantage. Thus you can get a red population in the field, and a brown population in the forest. If certain separations occure, you ultimatly end up with 2 different species of butterflies.
If anyone can correct me on errors, I'm not perfect afterall, please do.
Posted by: Albatrossity2 on Jan. 21 2008,18:35

Quote (Daniel Smith @ Jan. 21 2008,18:02)
If we can reduce it to basics; your definition of natural selection applies only to positive selection:  Only that which survives to reproduce is said to be selected.  
My definition includes both the positive and the negative:  If something survives to reproduce, it was selected for, if it doesn't survive to reproduce, it was selected against.

As far as I can tell, that's the only difference between our two positions.
I might not be using the word correctly.  If not, I need to find another way of expressing the thought.
---------------------QUOTE-------------------


Yes. My definition (which is generally accepted in the biological science community) includes the concept of the next generations. Those next generations are rather critical in considering how natural selection works to generate diversity, don't you think?

Your "definition" (again, I am fishing for it, because you haven't stated it explicitly) is almost certainly wrong. It will make it easier if you can get that notion out of your head.

Furthermore, your concept seems to be that natural selection is horrendously and uniformly negative, which is pretty much the standard creationist perspective. "Darwinism" is nothing more than death and pain, suffering and and horror. The FACT that there must be subsequent generations in order for natural selection to have an effect on shaping the diversity of living things seems to be ignored.

So please understand that natural selection is not just death and suffering. Natural selection is a process that occurs over GENERATIONS, and catastrophes that wipe out every organism in a population (floods, asteroids, volcanic eruptions) are not included in the definition of natural selection. It certainly makes it easier to oppose something when you misunderstand it in such a negative way. Hopefully it will make it easier now for you to understand why GAs which model natural selection per se don't include the catastrophic events that you find so compelling.
Posted by: swbarnes2 on Jan. 21 2008,18:43

Quote (Daniel Smith @ Jan. 21 2008,18:02)
If we can reduce it to basics; your definition of natural selection applies only to positive selection:  Only that which survives to reproduce is said to be selected.
---------------------QUOTE-------------------



No, the definition quoted doesn't imply that at all.  Comparatively beneficial traits become more common, are selected for, comparatively detrimental traits become less common, are selected against.  Didn't you read it?

 

---------------------QUOTE-------------------
My definition includes both the positive and the negative:  If something survives to reproduce, it was selected for, if it doesn't survive to reproduce, it was selected against.

---------------------QUOTE-------------------



Good grief, you still don't understand.  Why are you incapable of reading the things you are responding to?

The Wiki defintion is about how nature works on heritable differences within a population.  It says so right there!  When a freak flood kills a group of organisms, such that none of them posess a heritbale bit of DNA to help them reproduce better than their fellow organisms, it's not what intelligent people call natural selection.  That's just a freak accident.

Only you think that is natural selection.  But you are wrong.  Perhaps if you listened and read what people were telling you, instead of patting them on the head and telling them that your defintions are better than theirs, you would be wrong a little less often.

Perhaps if you actually looked at a few facts, (like what the output of a GA actually looks like) you could start saying intelligent things on these subjects, instead of your usual made-up nonsense.  Then, you wouldn't have to lie about your claims in order to attempt to defend your nonsense claims.

 

---------------------QUOTE-------------------
I might not be using the word correctly.  If not, I need to find another way of expressing the thought.
---------------------QUOTE-------------------



Have you even considered the possibility that your problem isn't that you aren't eloquent enough, but that you are peddling dumb arguments?  

And that we are rejecting them, not because they are put forth with too little rhetorical skill, but because we know the facts, and you do not, and your claims don't stand up to the facts?

No, of course you haven't considered that.  Jesus told you that everything was designed, therefore, any argument that supports that eternal truth has to be right.  Details like, conserved regions in genomes, or the numbers of bacteria that can survive a selection, those details confuse.  But "Jesus loves me, and designed me", that's simple.
Posted by: Daniel Smith on Jan. 21 2008,19:05

Quote (Wesley R. Elsberry @ Jan. 21 2008,05:21)
Daniel Smith:

             

---------------------QUOTE-------------------

I'm sure your knowledge on this subject exceeds mine by light years.

[...]

In fact, it would be better for the GAs overall result if the selection criteria had a low threshold for fitness -- as this would allow more potential solutions to survive.

---------------------QUOTE-------------------



I only need to be a few regular seconds ahead of Daniel to find and read Wikipedia's < article on fitness proportionate selection >, which states:

             

---------------------QUOTE-------------------

While candidate solutions with a higher fitness will be less likely to be eliminated, there is still a chance that they may be. Contrast this with a less sophisticated selection algorithm, such as truncation selection, which will eliminate a fixed percentage of the weakest candidates. With fitness proportionate selection there is a chance some weaker solutions may survive the selection process; this is an advantage, as though a solution may be weak, it may include some component which could prove useful following the recombination process.

---------------------QUOTE-------------------



I have to echo what others have already noted, that Daniel's "criticisms" are too ill-informed to be considered a substantive contribution to discussion. One finds that one has to guess at what might even be an applicable way to map Daniel's blitherings to what actually exists in the literature.
---------------------QUOTE-------------------


Wesley,

I apologize for my "blitherings".
I keep it simple because that's all I can do.
My only question is how well genetic algorithms actually simulate real-life biological evolution via natural selection.
My focus has been on selection algorithms - and whether or not they accurately simulate real-life selection.
I take it you feel they do, (at least some of them anyway).
You mention 'fitness proportionate selection', but don't say if that was the method used by the two algorithms you mentioned.  
Was 'fitness proportionate selection' the selection algorithm used in the EQU logic function or the TSP algorithm?
If not, were any of the best solutions selected against in those GAs?
Could you at least answer that for me?
Thank you.

I've been reading up on the basics of GAs over at wikipedia -- starting with the link you provided.
For instance, I found this:          

---------------------QUOTE-------------------
The fitness function is defined over the genetic representation and measures the quality of the represented solution. The fitness function is always problem dependent. ...
In some problems, it is hard or even impossible to define the fitness expression; in these cases, interactive genetic algorithms are used.
< link > (my emphasis)
---------------------QUOTE-------------------


It would seem to me that real-world biological evolution has so many variables, it would have to be in the "impossible to define" category.  Is that your opinion also?

Then there's this from the same page:        

---------------------QUOTE-------------------
Most functions are stochastic and designed so that a small proportion of less fit solutions are selected. This helps keep the diversity of the population large, preventing premature convergence on poor solutions.
---------------------QUOTE-------------------


This implies that successful evolution requires large, diverse populations.  Is that an accurate reflection of the MET?

Well, I may have found the answer myself (farther down the page):        

---------------------QUOTE-------------------
Diversity is important in genetic algorithms (and genetic programming) because crossing over a homogeneous population does not yield new solutions. In evolution strategies and evolutionary programming, diversity is not essential because of a greater reliance on mutation.
---------------------QUOTE-------------------


So, from this it would seem that genetic algorithms are not an accurate representation of real-world evolution.  For that we need to look at evolution strategies and evolutionary programming.
Were you aware of this important distinction Wesley?  (I'm sure you were.)  Am I missing something?  (I'm sure I am.)
Following this < link > for Evolution Strategies at scholarpedia:
       

---------------------QUOTE-------------------
The performance of an ES on a specific problem class depends crucially on the design of the ES-operators (mutation, recombination, selection) used and on the manner in which the ES-operators are adapted during the evolution process (adaptation schemes, e.g., \sigma-self-adaptation, covariance matrix adaptation, etc.). Ideally they should be designed in such a manner that they guarantee the evolvability of the system throughout the whole evolution process. Here are some principles and general guide lines:

   * Selection is done by population truncation similar to that what breeders are doing when breeding animals or plants.
---------------------QUOTE-------------------


So, at least according to this author, even evolution strategies are using selection algorithms that more closely resemble artificial, as opposed to natural, selection.

Again, I'm sure I'm missing something and will happily follow any links you can provide which will shine a light on my ignorance.
Posted by: Daniel Smith on Jan. 21 2008,19:17

Quote (Assassinator @ Jan. 21 2008,16:21)
You don't completly grasp the idea of natural selection Daniel. But it's pretty easy (that's why I wonder why you've got so much trouble with it...). First of all, it's relative, because natural selection matters between other groups of animals. Imagine a population of butterflies living in a dark forest, you've got red one's and you've got brown one's. The red one's will be a much easier prey for birds for example, because they're much easier spotted by a fast flying bird then brown one's. The red one's will be the number one on the bird's menu, and will get eaten much more then the brown butterflies. The brown one's can preduce much more offspring then the red one's, and after a while a dominatly brown population of butterflies will populate the forest. You can turn it around ofcourse, and set them in a brightly collored field of flowers, where the red butterflies will have a survival advantage. Thus you can get a red population in the field, and a brown population in the forest. If certain separations occure, you ultimatly end up with 2 different species of butterflies.
If anyone can correct me on errors, I'm not perfect afterall, please do.
---------------------QUOTE-------------------


I don't see the difference between what you said and what I said.  

The red butterflies die as a result of predators and are thus selected against.  

The brown ones don't die, (because of predators anyway), and are thus selected for.  

The population slowly moves from 50/50 red/brown to more brown that red.

You guys are making this out like it's terribly complicated when it seems pretty simple to me.
Posted by: Daniel Smith on Jan. 21 2008,19:31

Quote (Albatrossity2 @ Jan. 21 2008,16:35)
   
Quote (Daniel Smith @ Jan. 21 2008,18:02)
If we can reduce it to basics; your definition of natural selection applies only to positive selection:  Only that which survives to reproduce is said to be selected.  
My definition includes both the positive and the negative:  If something survives to reproduce, it was selected for, if it doesn't survive to reproduce, it was selected against.

As far as I can tell, that's the only difference between our two positions.
I might not be using the word correctly.  If not, I need to find another way of expressing the thought.
---------------------QUOTE-------------------


Yes. My definition (which is generally accepted in the biological science community) includes the concept of the next generations. Those next generations are rather critical in considering how natural selection works to generate diversity, don't you think?

Your "definition" (again, I am fishing for it, because you haven't stated it explicitly) is almost certainly wrong. It will make it easier if you can get that notion out of your head.

Furthermore, your concept seems to be that natural selection is horrendously and uniformly negative, which is pretty much the standard creationist perspective. "Darwinism" is nothing more than death and pain, suffering and and horror. The FACT that there must be subsequent generations in order for natural selection to have an effect on shaping the diversity of living things seems to be ignored.

So please understand that natural selection is not just death and suffering. Natural selection is a process that occurs over GENERATIONS, and catastrophes that wipe out every organism in a population (floods, asteroids, volcanic eruptions) are not included in the definition of natural selection. It certainly makes it easier to oppose something when you misunderstand it in such a negative way.
---------------------QUOTE-------------------


I think you and I are just talking past each other.  My definition (which I gave you) is not complicated.  Acting like I've completely missed the point and talking about 'generations' -- as if my definition will somehow not apply to succeeding generations -- is pointless.
Accusing me of negativism because I dare to mention negative selection is pointless as well.  

---------------------QUOTE-------------------
Hopefully it will make it easier now for you to understand why GAs which model natural selection per se don't include the catastrophic events that you find so compelling.
---------------------QUOTE-------------------



First, point me to one of these "GAs which model natural selection".

Second, it's not just "catastrophic events" which I find so compelling, it's all the forces of nature which conspire against the survival of organisms, (and they are legion), thereby severely hampering the success of evolution by natural selection.  

And third, if these GAs don't include these factors, then they don't model real-life biological evolution.
Posted by: Wesley R. Elsberry on Jan. 21 2008,20:17

Daniel Smith:



---------------------QUOTE-------------------

My only question is how well genetic algorithms actually simulate real-life biological evolution via natural selection.

---------------------QUOTE-------------------



Genetic algorithms don't "simulate real-life biological evolution". If that's really Daniel's only question, then we can shorten things up nicely.

Genetic algorithms, though, do serve as models of natural selection.



---------------------QUOTE-------------------

There are any number of optimization techniques that share nothing in common with NS, and for which I would not advance the notion that they "model" NS in any significant sense.  However, this is not the basis upon which I state that GAs model NS.  GAs model NS because GAs use the *same* theoretical framework as NS.  The mismatches occur in the genetics used and the mode by which the environment is established.

---------------------QUOTE-------------------



So far, Daniel has advanced to the fourth of the common antievolution dismissals of evolutionary computation that I wrote about in 1999.
Posted by: Albatrossity2 on Jan. 21 2008,21:05

Quote (Daniel Smith @ Jan. 21 2008,19:31)
I think you and I are just talking past each other.  My definition (which I gave you) is not complicated.  Acting like I've completely missed the point and talking about 'generations' -- as if my definition will somehow not apply to succeeding generations -- is pointless.
Accusing me of negativism because I dare to mention negative selection is pointless as well.          

---------------------QUOTE-------------------
Hopefully it will make it easier now for you to understand why GAs which model natural selection per se don't include the catastrophic events that you find so compelling.
---------------------QUOTE-------------------



First, point me to one of these "GAs which model natural selection".

Second, it's not just "catastrophic events" which I find so compelling, it's all the forces of nature which conspire against the survival of organisms, (and they are legion), thereby severely hampering the success of evolution by natural selection.  

And third, if these GAs don't include these factors, then they don't model real-life biological evolution.
---------------------QUOTE-------------------


Daniel

Let's keep it simple.

In the first place, when you talk about natural selection wiping out entire populations, and I point out that natural selection doesn't work that way because you need subsequent generations to visualize the effects of natural selection, it is hardly "pointless". Rather it is pointless for you to pretend that catastrophes that wipe out entire populations are examples of natural selection, because they simply are not.

In the second place, natural selection (precisely because it invokes the concept of subsequent generations!) involves not just survival, but survival and reproduction. An organism that survives 100 years but leaves no offspring is less fit in a given environment than an organism that dies early but manages to leave some offspring. Please purge your mind of the notion that survival is the only important parameter in natural selection. It is simply wrong.

Finally, try to wrap your head around the fact that natural selection does not usually involve complete elimination of one genotype and complete success of another genotype in one generation. Natural selection does involve differential reproductive success, and that differential can be very small and still have a large effect on the gene frequency in a population.

For example, consider a population with equal numbers (50% each) of organisms with two genotypes, A and B. If the average number of offspring for genotype A is 2.0, and the average number for genotype B is just 2.2, genotype B will be over 99% of the population after just 50 generations. Fitness is not all-or-none. Selection is not all-or none. Please try to integrate this reality into your simplistic notions about natural selection and other mechanisms of evolutionary change.

As for genetic algorithms, I know little or nothing about them. But, unlike you, I know enough not to pontificate about what they can do, or what they should do. I'll leave your education about genetic algorithms to those who work with them.
Posted by: Coyote on Jan. 21 2008,21:56

Quote (Albatrossity2 @ Jan. 22 2008,07:05)
For example, consider a population with equal numbers (50% each) of organisms with two genotypes, A and B. If the average number of offspring for genotype A is 2.0, and the average number for genotype B is just 2.2, genotype B will be over 99% of the population after just 50 generations. Fitness is not all-or-none. Selection is not all-or none. Please try to integrate this reality into your simplistic notions about natural selection and other mechanisms of evolutionary change.
---------------------QUOTE-------------------


It is even worse than your example describes. Change is going on in hundreds or thousands of traits in a population at the same time. And sometimes change works in two directions at once!

That is why, for example, sickle cell anemia can be detrimental on one hand and can confer some malaria immunity on the other hand. Somehow the adaptations came as a package and were 1) useful enough to convey some survival advantage while 2) not being too detrimental.

It is too easy to think of evolution in terms of single, isolated traits, but many traits are changing all at the same time.
Posted by: swbarnes2 on Jan. 22 2008,00:46

Quote (Daniel Smith @ Jan. 21 2008,19:31)
I think you and I are just talking past each other.
---------------------QUOTE-------------------



No, not really.  People are giving you the facts, and you are refusing to listen, because you think you know better.

 

---------------------QUOTE-------------------
My definition (which I gave you) is not complicated.
---------------------QUOTE-------------------



But it's wrong.  Given the choice, honest and intelligent people will choose to believe the complex, right thing, instead of the simple, wrong thing.

Well, it didn't take you long to prove that once again, you reject the ways of intelligent, honest people.

Real natural selection requires different heritable elements that cause differential reproductive success.

You think that natural selection is just about organisms dying.  You said so plainly.

 

---------------------QUOTE-------------------
Accusing me of negativism because I dare to mention negative selection is pointless as well.
---------------------QUOTE-------------------



You, the person who thinks he invented the notion that selection can work against...whatever you think selection works against, is accusing others of being on a high horse?

You plainly said that you think that solutions to GAs will degrade over time.  Of course, you can't demonstrate this, because it's not true.  But that's why people are accusing you of thinking that evolution is all negative, because you keep saying that evolutionary processes lead to degradation.

You also thought that evolutionary forces would degrade all types of DNA sequences equally, and you were plainly shown to be wrong there as well.  

See, the way people on this board operate is, they collect the data (in this case, the words you post about genomes and GAs and the like), and then they draw conclusions about the data (namely, that you think that evolution is a totally negative, degrading, destructive process).

We understand that this is a long way from your "Make up how (insert: GAs, mouse orthologs, bacterial selections experiments, the list goes on) works, and then pontificate about how it proves that Jesus designed you.  

I know that pointing this out to you is a waste of time, since you don't intend on looking at any data (like GA output) or paying attention to data that you don't like (like the percentage of non-orthologous genes between humans and mice) but this way, it can't be said that no one tried to teach you how to think and reason like an intellignet, honest person.

 

---------------------QUOTE-------------------
Second, it's not just "catastrophic events" which I find so compelling, it's all the forces of nature which conspire against the survival of organisms, (and they are legion), thereby severely hampering the success of evolution by natural selection.
---------------------QUOTE-------------------



Right.  Nature is soooo hard on life that the planet is saturated with it from top to bottom.  That's a really compelling argument.  

Yes, by all means, hammer on this angle.  Use the fact that that those strains of malaria that kill other people's children would never be so deadly if God weren't helping them to evade the medicines that desperate parents and doctors throw at them.  It's what you believe, isn't it?  That God helps those parasites rip apart the blood cells of children in order to teach you a lesson?  

Or are you going to lie and say that you didn't mean that at all?
Posted by: oldmanintheskydidntdoit on Jan. 22 2008,02:54



---------------------QUOTE-------------------

My only question is how well genetic algorithms actually simulate real-life biological evolution via natural selection.

---------------------QUOTE-------------------


Daniel,
Do you think weather modelling includes a real mini-thunderstorm inside the computer?

If not, it's hardly an accurate simulation is it?

EDIT: Your compadres have been here before Daniel.
< gil-has-never-grasped-the-nature-of-a-simulation-model/ >
And they were badly embarrassed. Of course, it was "all a joke".....
Posted by: Albatrossity2 on Jan. 22 2008,06:01

Quote (Coyote @ Jan. 21 2008,21:56)
It is even worse than your example describes. Change is going on in hundreds or thousands of traits in a population at the same time. And sometimes change works in two directions at once!

That is why, for example, sickle cell anemia can be detrimental on one hand and can confer some malaria immunity on the other hand. Somehow the adaptations came as a package and were 1) useful enough to convey some survival advantage while 2) not being too detrimental.

It is too easy to think of evolution in terms of single, isolated traits, but many traits are changing all at the same time.
---------------------QUOTE-------------------


Absolutely.

But I was trying to keep it simple, because Daniel seems to have trouble with complexity...
Posted by: George on Jan. 22 2008,07:44

Daniel,

There's a difference between a "simulation" and a "model".  A simulation tries to be a more or less faithful mathematical copy of a system or a part of a system.  A model is a simplified representation of one or a limited number of features of a system.  It doesn't try to be an exact replicate of the system it models.  Rather it is a tool to help us understand certain aspects of a system.  

For example, you can come up with a hypothesis that natural selection will work in a certain way in a given situation.  You can then make a model of your hypothesis and compare its results with reality.  If they don't match, your hypothesis is wrong; if they do match, then the model supports your hypothesis.

Because of the complexity of ecology, there has never been a good simulation of ecological processes, including natural selection, in a real-world ecosystem (except maybe some extremely simplified ones I'm not aware of).  I'm not aware that anyone's really tried.  The closest ones I'm aware of are some spatially explicit single-tree models of forest dynamics.  However, there have been all sorts of very useful models that have provided insights into ecological and evolutionary processes.  You don't need to see the whole picture at once to begin to understand large parts of it.
Posted by: Daniel Smith on Jan. 22 2008,11:09

Quote (Albatrossity2 @ Jan. 21 2008,19:05)
Quote (Daniel Smith @ Jan. 21 2008,19:31)
I think you and I are just talking past each other.  My definition (which I gave you) is not complicated.  Acting like I've completely missed the point and talking about 'generations' -- as if my definition will somehow not apply to succeeding generations -- is pointless.
Accusing me of negativism because I dare to mention negative selection is pointless as well.            

---------------------QUOTE-------------------
Hopefully it will make it easier now for you to understand why GAs which model natural selection per se don't include the catastrophic events that you find so compelling.
---------------------QUOTE-------------------



First, point me to one of these "GAs which model natural selection".

Second, it's not just "catastrophic events" which I find so compelling, it's all the forces of nature which conspire against the survival of organisms, (and they are legion), thereby severely hampering the success of evolution by natural selection.  

And third, if these GAs don't include these factors, then they don't model real-life biological evolution.
---------------------QUOTE-------------------


Daniel

Let's keep it simple.

In the first place, when you talk about natural selection wiping out entire populations, and I point out that natural selection doesn't work that way because you need subsequent generations to visualize the effects of natural selection, it is hardly "pointless". Rather it is pointless for you to pretend that catastrophes that wipe out entire populations are examples of natural selection, because they simply are not.

In the second place, natural selection (precisely because it invokes the concept of subsequent generations!) involves not just survival, but survival and reproduction. An organism that survives 100 years but leaves no offspring is less fit in a given environment than an organism that dies early but manages to leave some offspring. Please purge your mind of the notion that survival is the only important parameter in natural selection. It is simply wrong.

Finally, try to wrap your head around the fact that natural selection does not usually involve complete elimination of one genotype and complete success of another genotype in one generation. Natural selection does involve differential reproductive success, and that differential can be very small and still have a large effect on the gene frequency in a population.

For example, consider a population with equal numbers (50% each) of organisms with two genotypes, A and B. If the average number of offspring for genotype A is 2.0, and the average number for genotype B is just 2.2, genotype B will be over 99% of the population after just 50 generations. Fitness is not all-or-none. Selection is not all-or none. Please try to integrate this reality into your simplistic notions about natural selection and other mechanisms of evolutionary change.

As for genetic algorithms, I know little or nothing about them. But, unlike you, I know enough not to pontificate about what they can do, or what they should do. I'll leave your education about genetic algorithms to those who work with them.
---------------------QUOTE-------------------


Everything you're saying about NS, I already know and understand.  I also have not said anything that should give you the impression that I don't understand these basics.  Like I said, we're talking past each other.  You're acting as if I'm saying things I'm not really saying and believing things I don't really believe, and if you continue, it will be fruitless for us to continue this exchange.
Posted by: Henry J on Jan. 22 2008,11:10



---------------------QUOTE-------------------
It is too easy to think of evolution in terms of single, isolated traits, but many traits are changing all at the same time.
---------------------QUOTE-------------------



And so's the environment in which those traits act.
Posted by: Albatrossity2 on Jan. 22 2008,11:39

Quote (Daniel Smith @ Jan. 22 2008,11:09)
Everything you're saying about NS, I already know and understand.  I also have not said anything that should give you the impression that I don't understand these basics.  Like I said, we're talking past each other.  You're acting as if I'm saying things I'm not really saying and believing things I don't really believe, and if you continue, it will be fruitless for us to continue this exchange.
---------------------QUOTE-------------------


Hmmmm.

Did you write < this? >    

---------------------QUOTE-------------------
From what I've seen, natural selection is given an almost god-like quality amongst many believers in the currently held theory.  It is talked about as if it is all-knowing, all-powerful, and able to predict the future and select the optimal solution for any and all potential problems.
---------------------QUOTE-------------------


If so, that certainly implies that either you A) don't understand natural selection, or you B) have a bizarre interpretation of how it is understood by most biological scientists. Your choice - which is the real explanation? A or B?

Did you write < this? >    

---------------------QUOTE-------------------
When I think of natural selection, I think of anything that keeps an individual from reproducing.
---------------------QUOTE-------------------


If so, that certainly implies that you needed a primer about relative fitness. In the example I gave you, what was keeping the organisms with genotype A from reproducing? Since they were having 2 offspring per generation, they were clearly reproducing quite well. But not quite as well as those with genotype B. Nevertheless, by the process of natural selection, in 50 generations genotype A would drop from 50% of the population to less than 1% of the population. Nothing was going on that would "keep them from reproducing". So by your definition this is not, therefore, an instance of natural selection. By any accepted definition, it is an instance of natural selection. Can you accept that A) your definition was wrong, or can you B) defend it? Again, it's your choice. A or B?

Hopefully you can now comprehend why, exactly, one or the other of us might be confused about what it is, exactly, that you understand.
Posted by: oldmanintheskydidntdoit on Jan. 22 2008,12:53


Posted by: Daniel Smith on Jan. 22 2008,17:46

Quote (Wesley R. Elsberry @ Jan. 21 2008,18:17)
Daniel Smith:

   

---------------------QUOTE-------------------

My only question is how well genetic algorithms actually simulate real-life biological evolution via natural selection.

---------------------QUOTE-------------------



Genetic algorithms don't "simulate real-life biological evolution". If that's really Daniel's only question, then we can shorten things up nicely.

Genetic algorithms, though, do serve as models of natural selection.

   

---------------------QUOTE-------------------

There are any number of optimization techniques that share nothing in common with NS, and for which I would not advance the notion that they "model" NS in any significant sense.  However, this is not the basis upon which I state that GAs model NS.  GAs model NS because GAs use the *same* theoretical framework as NS.  The mismatches occur in the genetics used and the mode by which the environment is established.

---------------------QUOTE-------------------



---------------------QUOTE-------------------


In your opinion then Wesley, does artificial selection model NS in a similar fashion, (to the way GAs model it)?

After all, artificial selection uses the same theoretical framework as NS as well.
Posted by: Wesley R. Elsberry on Jan. 22 2008,18:12

Artificial selection is analogous to evolutionary computation in the same way that artificial selection is analogous to natural selection.
Posted by: Daniel Smith on Jan. 22 2008,18:18

Quote (Albatrossity2 @ Jan. 22 2008,09:39)
         
Quote (Daniel Smith @ Jan. 22 2008,11:09)
Everything you're saying about NS, I already know and understand.  I also have not said anything that should give you the impression that I don't understand these basics.  Like I said, we're talking past each other.  You're acting as if I'm saying things I'm not really saying and believing things I don't really believe, and if you continue, it will be fruitless for us to continue this exchange.
---------------------QUOTE-------------------


Hmmmm.

Did you write < this? >                

---------------------QUOTE-------------------
From what I've seen, natural selection is given an almost god-like quality amongst many believers in the currently held theory.  It is talked about as if it is all-knowing, all-powerful, and able to predict the future and select the optimal solution for any and all potential problems.
---------------------QUOTE-------------------


If so, that certainly implies that either you A) don't understand natural selection, or you B) have a bizarre interpretation of how it is understood by most biological scientists. Your choice - which is the real explanation? A or B?
---------------------QUOTE-------------------


This was in reference to the way "selection-did-it" is sometimes used as a kind of catch-all explanation for the evolution of some organ or organism.  It has more to do with the usage here and on other boards and newsgroups that with real scientists and their published papers.

       

---------------------QUOTE-------------------
Did you write < this? >                

---------------------QUOTE-------------------
When I think of natural selection, I think of anything that keeps an individual from reproducing.
---------------------QUOTE-------------------


If so, that certainly implies that you needed a primer about relative fitness. In the example I gave you, what was keeping the organisms with genotype A from reproducing? Since they were having 2 offspring per generation, they were clearly reproducing quite well. But not quite as well as those with genotype B. Nevertheless, by the process of natural selection, in 50 generations genotype A would drop from 50% of the population to less than 1% of the population. Nothing was going on that would "keep them from reproducing". So by your definition this is not, therefore, an instance of natural selection. By any accepted definition, it is an instance of natural selection. Can you accept that A) your definition was wrong, or can you B) defend it? Again, it's your choice. A or B?

Hopefully you can now comprehend why, exactly, one or the other of us might be confused about what it is, exactly, that you understand.
---------------------QUOTE-------------------


OK, I see what you're saying there.  NS also includes reproductive rates.  I knew that, but just did not express that in my example - mainly because I was talking about things that would keep an organism from reproducing and passing on its advantageous mutation.  But, yes, you're right, I should have also said that as well.

My point though, (which I feel you've avoided) is that NS is no guarantee that something beneficial will be passed on.  

I'm sure you know that infant mortality rates are incredibly high in the wild - no matter the species.  The mortality rate is very high between infancy and adulthood as well.  Reproduction is also not guaranteed.  Individuals may reach adulthood but never mate.  Or they may be sterile - or infertile.  

My main objection is that NS is so often talked about as if none of these things were an issue; as if anytime mutation produces an advantage, it will automatically be selected.  Such is often not the case in real life.

In real life, NS tends to keep species "centered".  This was evidenced by the extensive drosophila experiments where all manner of mutational features were produced.  However, most of these mutated flies could only survive in the lab.  When subjected to wild conditions, the wild-type fly re-emerged as dominant and these mutated forms died out.

I guess then the point of all this is that NS works much better in theory than it does in real life.

(IMO)
Posted by: Wesley R. Elsberry on Jan. 22 2008,18:28

Daniel Smith:



---------------------QUOTE-------------------

My point though, (which I feel you've avoided) is that NS is no guarantee that something beneficial will be passed on.  

---------------------QUOTE-------------------



I think it was Fisher sometime around 1930 who calculated that a beneficial mutation stood about an 85% chance of being lost in the first 15 generations or so following its introduction in a single member of a population. Or maybe it was Haldane not too long thereafter, I'm not sure. So, thanks, but those of us who had  bothered to read up on evolutionary science already knew that.


Posted by: C.J.O'Brien on Jan. 22 2008,18:30

Artificial selection is just a subset of natural selection in which the selecting environment's most salient feature is the preferences of an intelligent agent. It's a special case of co-evolution. Certainly, in most cases, it is easy to say when artificial selection is going on. But it really is no different in principle from ordinary mutualism, which occurs all the time in natural selection.

And GA's are not "simulations" of anything. Used as engineering solutions, they are an example of actual, real-life Darwinian processes, not models of them. (If we can allow what we'll call a "Darwinian process" to be substrate-neutral, which should be unproblematic. All that is required is that we have reproducing entities that vary arbitrarily, and that said variation non-trivially affects reproductive sucess.) That is why they're so frightening to creationists, and why jokers like Gil Dogen have to play dumb when they make claims about them. Blind, undirected processes can solve problems. And that's the facts.
Posted by: blipey on Jan. 22 2008,18:42

Wes:

Are you saying that somebody has bothered to look into the situation of beneficial traits AND DONE A CALCULATION?  No way that could happen.

I'm sure you are aware that science (in any meaningful usage of the word) is done by SAYING something.  If people don't quite believe you or think there is some flaw with your argument (such as they'd like to see some calculations or detailed descriptions of observations), you merely say it again--LOUDER.

And engage a somewhat above mediocre graphic artist to design a poster of you saying it.

Then you make public appearance with the poster while making farty noises.

Now THAT'S science!  Right, Daniel?
Posted by: Daniel Smith on Jan. 22 2008,18:44

Quote (Wesley R. Elsberry @ Jan. 22 2008,16:12)
Artificial selection is analogous to evolutionary computation in the same way that artificial selection is analogous to natural selection.
---------------------QUOTE-------------------


Would that be favorably or unfavorably?
Posted by: Daniel Smith on Jan. 22 2008,18:45

Quote (blipey @ Jan. 22 2008,16:42)
Wes:

Are you saying that somebody has bothered to look into the situation of beneficial traits AND DONE A CALCULATION?  No way that could happen.

I'm sure you are aware that science (in any meaningful usage of the word) is done by SAYING something.  If people don't quite believe you or think there is some flaw with your argument (such as they'd like to see some calculations or detailed descriptions of observations), you merely say it again--LOUDER.

And engage a somewhat above mediocre graphic artist to design a poster of you saying it.

Then you make public appearance with the poster while making farty noises.

Now THAT'S science!  Right, Daniel?
---------------------QUOTE-------------------


Wrong.

But I can see how you'd think that!
Posted by: blipey on Jan. 22 2008,18:48

On a somewhat more serious (though I'd be truly interested if any part of my above description sounds like science to you, Daniel) note, could you answer the following question?  I think it will start us down the road of whether or not you truly understand NS:

1.  Do you personally believe that NS is a mechanism that can ever bring about an increase in beneficial traits?

Yes or no, to begin with please.  I want to keep this very simple.  We'll leave the explanations for after "yes" or "no".
Posted by: Daniel Smith on Jan. 22 2008,18:50

Quote (C.J.O'Brien @ Jan. 22 2008,16:30)
Certainly, in most cases, it is easy to say when artificial selection is going on. But it really is no different in principle from ordinary mutualism, which occurs all the time in natural selection.
---------------------QUOTE-------------------


So how is it "easy to say when artificial selection is going on" then, if "it really is no different in principle" from something "which occurs all the time in natural selection"?
Posted by: Daniel Smith on Jan. 22 2008,18:52

Quote (blipey @ Jan. 22 2008,16:48)
On a somewhat more serious (though I'd be truly interested if any part of my above description sounds like science to you, Daniel) note, could you answer the following question?  I think it will start us down the road of whether or not you truly understand NS:

1.  Do you personally believe that NS is a mechanism that can ever bring about an increase in beneficial traits?

Yes or no, to begin with please.  I want to keep this very simple.  We'll leave the explanations for after "yes" or "no".
---------------------QUOTE-------------------


Yes.
Posted by: Wesley R. Elsberry on Jan. 22 2008,18:53

Daniel Smith:



---------------------QUOTE-------------------

Would that be favorably or unfavorably?

---------------------QUOTE-------------------



In the way that makes clear that evolution denialists are looking for proof beyond unreasonable doubt. I have no idea what Humpty-Dumpty means by "unfavorably".
Posted by: Daniel Smith on Jan. 22 2008,19:00

Quote (Wesley R. Elsberry @ Jan. 22 2008,16:28)
Daniel Smith:

   

---------------------QUOTE-------------------

My point though, (which I feel you've avoided) is that NS is no guarantee that something beneficial will be passed on.  

---------------------QUOTE-------------------



I think it was Fisher sometime around 1930 who calculated that a beneficial mutation stood about an 85% chance of being lost in the first 15 generations or so following its introduction in a single member of a population. Or maybe it was Haldane not too long thereafter, I'm not sure. So, thanks, but those of us who had  bothered to read up on evolutionary science already knew that.
---------------------QUOTE-------------------


So Wesley, which selection algorithm most closely models that percentage?
Posted by: blipey on Jan. 22 2008,20:15

Alright, now we agree that NS can bring about beneficial (in a specific environment) traits and propagate them through a population.

Can we agree that NS is a mechanism?  It is not any one specific thing, but rather more of a situation?
Posted by: Albatrossity2 on Jan. 22 2008,20:16

Quote (Daniel Smith @ Jan. 22 2008,18:18)
OK, I see what you're saying there.  NS also includes reproductive rates.  I knew that, but just did not express that in my example - mainly because I was talking about things that would keep an organism from reproducing and passing on its advantageous mutation.  But, yes, you're right, I should have also said that as well.
---------------------QUOTE-------------------


If that is indeed your point, then it would perhaps be helpful to all of us if you explicitly stated it. If you read my sig, you might understand where I'm coming from. You can't just say stuff, particularly if you are using terms that have very specific meanings, and expect all of us to track your thoughts accurately.

And I see that others have already taken the time to correct you re your assumptions about what selection can do, the odds of a favorable mutation making it into a population, etc. So I'll let that sink in. But I do caution you about statements that might make us think that you are ignoring facts that have been known for many decades. Frankly, you do that quite a lot. It doesn't help your case, y'know.
Posted by: Wesley R. Elsberry on Jan. 23 2008,00:13

Quote (Daniel Smith @ Jan. 22 2008,19:00)
 
Quote (Wesley R. Elsberry @ Jan. 22 2008,16:28)
Daniel Smith:

     

---------------------QUOTE-------------------

My point though, (which I feel you've avoided) is that NS is no guarantee that something beneficial will be passed on.  

---------------------QUOTE-------------------



I think it was Fisher sometime around 1930 who calculated that a beneficial mutation stood about an 85% chance of being lost in the first 15 generations or so following its introduction in a single member of a population. Or maybe it was Haldane not too long thereafter, I'm not sure. So, thanks, but those of us who had  bothered to read up on evolutionary science already knew that.
---------------------QUOTE-------------------


So Wesley, which selection algorithm most closely models that percentage?
---------------------QUOTE-------------------


That doesn't seem to have any clear relation to Daniel's "point".

Once Daniel figures out what Daniel's "point" really, truly is, maybe there will be some point to discussion. So far as I can tell, though,
Daniel is simply stringing people along and posing scattershot questions to give the false impression that he is actually a participant in an exchange of ideas. I think I'll spend my time working up some papers.
Posted by: oldmanintheskydidntdoit on Jan. 23 2008,03:07

Quote (Daniel Smith @ Jan. 22 2008,18:52)
 
Quote (blipey @ Jan. 22 2008,16:48)
On a somewhat more serious (though I'd be truly interested if any part of my above description sounds like science to you, Daniel) note, could you answer the following question?  I think it will start us down the road of whether or not you truly understand NS:

1.  Do you personally believe that NS is a mechanism that can ever bring about an increase in beneficial traits?

Yes or no, to begin with please.  I want to keep this very simple.  We'll leave the explanations for after "yes" or "no".
---------------------QUOTE-------------------


Yes.
---------------------QUOTE-------------------


So, what is your point Danny boy?

If NS is a mechanism that can being about an increase in beneficial traits then small changes (micro) can add up (macro) and we get goo to you!

Whatever your terrible misunderstandings about GA's are you've just said that NS can bring about and spread useful traits.

Game over man, game over.

I guess your only "out" is to claim that as the world is only 6000 years old that's not enougth time for "darwinism" to do it's thing?

Right?

Daniel, do what I suggested earlier. Learn to program. Write some GA's. Do something, anything, rather then leech off other peoples work and claim it supports your case when you don't even understand it in the first place.
Posted by: JAM on Jan. 23 2008,11:07

Quote (oldmanintheskydidntdoit @ Jan. 23 2008,03:07)
Daniel, do what I suggested earlier. Learn to program. Write some GA's. Do something, anything, rather then leech off other peoples work and claim it supports your case when you don't even understand it in the first place.
---------------------QUOTE-------------------


Or, look directly at (according to you) God's designs for yourself.

If you had any real faith, you wouldn't need to resort to decades-old hearsay from people who lacked the courage/faith to put their own hypotheses to the test.

Dontcha just love the irony?
Posted by: blipey on Jan. 23 2008,15:05

Quote (oldmanintheskydidntdoit @ Jan. 23 2008,03:07)
Quote (Daniel Smith @ Jan. 22 2008,18:52)
 
Quote (blipey @ Jan. 22 2008,16:48)
On a somewhat more serious (though I'd be truly interested if any part of my above description sounds like science to you, Daniel) note, could you answer the following question?  I think it will start us down the road of whether or not you truly understand NS:

1.  Do you personally believe that NS is a mechanism that can ever bring about an increase in beneficial traits?

Yes or no, to begin with please.  I want to keep this very simple.  We'll leave the explanations for after "yes" or "no".
---------------------QUOTE-------------------


Yes.
---------------------QUOTE-------------------


So, what is your point Danny boy?

If NS is a mechanism that can being about an increase in beneficial traits then small changes (micro) can add up (macro) and we get goo to you!

Whatever your terrible misunderstandings about GA's are you've just said that NS can bring about and spread useful traits.

Game over man, game over.

I guess your only "out" is to claim that as the world is only 6000 years old that's not enougth time for "darwinism" to do it's thing?

Right?

Daniel, do what I suggested earlier. Learn to program. Write some GA's. Do something, anything, rather then leech off other peoples work and claim it supports your case when you don't even understand it in the first place.
---------------------QUOTE-------------------


The seminal case study of why creationists don't answer questions.  This very short exchange finishes the argument.  It's neat.  It's concise.  It doesn't work out too well for creationists.

Daniel, do you have any explanation for how you can believe that NS is an effective mechanism for advancing beneficial traits while simultaneously believing that NS cannot be a mechanism for change in the ToE?
Posted by: Daniel Smith on Jan. 23 2008,18:32

Quote (blipey @ Jan. 23 2008,13:05)

The seminal case study of why creationists don't answer questions.  This very short exchange finishes the argument.  It's neat.  It's concise.  It doesn't work out too well for creationists.

Daniel, do you have any explanation for how you can believe that NS is an effective mechanism for advancing beneficial traits while simultaneously believing that NS cannot be a mechanism for change in the ToE?
---------------------QUOTE-------------------


Sure.  It's the same as the explanation given by Leo S. Berg, Otto H. Schindewolf, Richard B. Goldschmidt, John A. Davison, Michael J. Denton and a whole host of evolutionists -- which all these men are (or were) you know.  

That explanation is this: Natural selection can refine and benefit species and sub-species by producing varieties and adaptations within a limited range.  IOW, given a good, working platform to start with, NS can build upon it with limited variations - useful for adaptation to environmental changes.
When environmental changes become too great however, NS simply results in extinction.  This is evidenced by the vast number of extinctions chronicled in the fossil record.

All the men I mentioned expressed serious reservations about the power of NS.  They all felt basically the same.  Berg wrote a book in which he chronicles example after example, from his own observations and the observations of others, which gave him tremendous pause in his assessment of NS.  Schindewolf chronicled obvious patterns in the fossil record in support of his view for the limited power of selection.  Goldschmidt came to the same conclusion from his study of genetics.  These men were not creationists, they were evolutionists.  They all held to common descent.  They just rejected NS as a viable mechanism for macro-evolutionary change.

I get the distinct impression that no one here has read anything these men have published.  I also get the impression no one here wants to.
Posted by: blipey on Jan. 23 2008,18:45



---------------------QUOTE-------------------
When environmental changes become too great however, NS simply results in extinction.
---------------------QUOTE-------------------



Wow.  Tell me you're being deliberately stupid.  Please.  As has been explained to you several times now, NS does not cause extinction.  In fact, NS does not cause anything per se.  Extinction is caused by things like asteroids, acid rain, bullets....

NS can only be talked about in light of SURVIVING.  You said above that you understood and agreed with this.  So, do you retract that?

Do you agree with the following? (Yes or No)

Natural Selection is a mechanism that can conserve beneficial traits.

That's ALL it is.  NS is not something that kills, it is not something that breathes life into anything, it is not something that lowers your mortgage, it is ONLY that little sentence above.

Do you get it?
Posted by: Daniel Smith on Jan. 23 2008,19:03

Quote (Wesley R. Elsberry @ Jan. 22 2008,22:13)
       
Quote (Daniel Smith @ Jan. 22 2008,19:00)
           
Quote (Wesley R. Elsberry @ Jan. 22 2008,16:28)
Daniel Smith:

               

---------------------QUOTE-------------------

My point though, (which I feel you've avoided) is that NS is no guarantee that something beneficial will be passed on.  

---------------------QUOTE-------------------



I think it was Fisher sometime around 1930 who calculated that a beneficial mutation stood about an 85% chance of being lost in the first 15 generations or so following its introduction in a single member of a population. Or maybe it was Haldane not too long thereafter, I'm not sure. So, thanks, but those of us who had  bothered to read up on evolutionary science already knew that.
---------------------QUOTE-------------------


So Wesley, which selection algorithm most closely models that percentage?
---------------------QUOTE-------------------


That doesn't seem to have any clear relation to Daniel's "point".

Once Daniel figures out what Daniel's "point" really, truly is, maybe there will be some point to discussion. So far as I can tell, though,
Daniel is simply stringing people along and posing scattershot questions to give the false impression that he is actually a participant in an exchange of ideas. I think I'll spend my time working up some papers.
---------------------QUOTE-------------------


I'll try to explain myself better Wesley (if you're still there):

I said:        

---------------------QUOTE-------------------
My only question is how well genetic algorithms actually simulate real-life biological evolution via natural selection.
My focus has been on selection algorithms - and whether or not they accurately simulate real-life selection.
---------------------QUOTE-------------------


You replied:        

---------------------QUOTE-------------------
Genetic algorithms don't "simulate real-life biological evolution". If that's really Daniel's only question, then we can shorten things up nicely.

Genetic algorithms, though, do serve as models of natural selection.     (My emphasis)
---------------------QUOTE-------------------


Making it clear we are talking about models not simulations.

So when you stated that; "a beneficial mutation stood about an 85% chance of being lost in the first 15 generations or so following its introduction in a single member of a population", I simply asked; "which selection algorithm most closely models that percentage?".

Does that make my point any clearer Wesley?
Posted by: Daniel Smith on Jan. 23 2008,19:19

Quote (blipey @ Jan. 23 2008,16:45)
           

---------------------QUOTE-------------------
When environmental changes become too great however, NS simply results in extinction.
---------------------QUOTE-------------------



Wow.  Tell me you're being deliberately stupid.  Please.  As has been explained to you several times now, NS does not cause extinction.  In fact, NS does not cause anything per se.  Extinction is caused by things like asteroids, acid rain, bullets....

NS can only be talked about in light of SURVIVING.  You said above that you understood and agreed with this.  So, do you retract that?

Do you agree with the following? (Yes or No)

Natural Selection is a mechanism that can conserve beneficial traits.
---------------------QUOTE-------------------


Yes, I agree with that.  NS can conserve beneficial traits.  It may also fail to.
It is after all...  SELECTION!
Are you saying natural selection can never choose "None of the above"?

Perhaps you'd be happier if I worded my statement this way:
"When environmental changes become too great however, NS fails - resulting in extinction."

Is that better?
     

---------------------QUOTE-------------------
That's ALL it is.  NS is not something that kills, it is not something that breathes life into anything, it is not something that lowers your mortgage, it is ONLY that little sentence above.

Do you get it?
---------------------QUOTE-------------------


Natural Selection lowered my monthly payments and it can lower yours too!  Just call 1-800-NS-MONEY right now to start benefiting from this terrific offer!  Operators are standing by.
Posted by: Jim_Wynne on Jan. 23 2008,19:39

Quote (Daniel Smith @ Jan. 23 2008,19:19)
Perhaps you'd be happier if I worded my statement this way:
"When environmental changes become too great however, NS fails - resulting in extinction."

Is that better?
---------------------QUOTE-------------------


Yes, but only in the sense that it provides more confirmation--as if it were needed--that you can't grasp the most simple evolution principles even after they've been plainly explained to you.
Posted by: blipey on Jan. 23 2008,22:41

Okay, let's start out as if we were in Kindergarten.

NS does not DO anything.  Nothing at all.  NS is not a force.  There is no active verb tense to NS.  NS does not DO or FAIL TO DO anything at all.


---------------------QUOTE-------------------
Are you saying natural selection can never choose "None of the above"?
---------------------QUOTE-------------------


Yes I am saying that.  Because NS never choose anything.  NS is merely something that happens.  Rocks fall toward the Earth not away from it.  This is merely something that happens.  Gravity does not choose to throw rocks at the Earth, it is merely the mechanism that explains why rocks fall to the Earth.

Do you get it?

Along the same lines, NS does not FAIL AT ANYTHING.  To fail at something implies that there was a goal.  There is no goal to being.  Being just is.  NS explains how that being behaves.
Posted by: oldmanintheskydidntdoit on Jan. 24 2008,03:09

Quote (Daniel Smith @ Jan. 23 2008,19:03)
So when you stated that; "a beneficial mutation stood about an 85% chance of being lost in the first 15 generations or so following its introduction in a single member of a population", I simply asked; "which selection algorithm most closely models that percentage?".

Does that make my point any clearer Wesley?
---------------------QUOTE-------------------


IF MUTATION = BENEFICIAL
then { CHANCE_OF_DELETION = 85%; FOR_GENERATIONS = 15}
IF FOR_GENERATIONS > 15
then {CHANCE_OF_DELETION=NORMAL_CHANCE_OF_DELETION}

Or something like that. It's too early to even write pseudocode.
 

---------------------QUOTE-------------------
I simply asked; "which selection algorithm most closely models that percentage?".
---------------------QUOTE-------------------


So the answer to that question is
"the one that you write that models that percentage"
Posted by: oldmanintheskydidntdoit on Jan. 24 2008,03:11

Quote (Daniel Smith @ Jan. 23 2008,18:32)
That explanation is this: Natural selection can refine and benefit species and sub-species by producing varieties and adaptations within a limited range.
---------------------QUOTE-------------------


What is this limited range?

Give us an example.

What's stopping micro adding up to macro?

Did all species fit on the ARK? Is that what you are getting at?
Posted by: oldmanintheskydidntdoit on Jan. 24 2008,03:14

Quote (Daniel Smith @ Jan. 23 2008,19:19)
Perhaps you'd be happier if I worded my statement this way:
"When environmental changes become too great however, NS fails - resulting in extinction."
---------------------QUOTE-------------------


Prove it!

Or no trousers too? Just all mouth?

It's easy to say such things.

Fact is you've no proof at all.

PROVE YOUR POINT DANIEL WITH *EVIDENCE*.

Or quotes from 50 year old books. I guess I already know what you'll pick.

Here, look I can play too


---------------------QUOTE-------------------
"When environmental changes become too great however, NS fails - resulting in extinction via the mechanism of invisible unicorns"
---------------------QUOTE-------------------




---------------------QUOTE-------------------
"When invisible unicorns cry the changes become too great however, NS fails - resulting in unicorn extinction."
---------------------QUOTE-------------------


Posted by: mitschlag on Jan. 24 2008,04:46

Quote (Daniel Smith @ Jan. 23 2008,18:32)
All the men I mentioned expressed serious reservations about the power of NS.  They all felt basically the same.  Berg wrote a book in which he chronicles example after example, from his own observations and the observations of others, which gave him tremendous pause in his assessment of NS.  Schindewolf chronicled obvious patterns in the fossil record in support of his view for the limited power of selection.  Goldschmidt came to the same conclusion from his study of genetics.  These men were not creationists, they were evolutionists.  They all held to common descent.  They just rejected NS as a viable mechanism for macro-evolutionary change.

I get the distinct impression that no one here has read anything these men have published.  I also get the impression no one here wants to.
---------------------QUOTE-------------------


Those mutants did not confer reproductive advantages and left no progeny.  They are fossils in the boneyard of intellectual history.
Posted by: mitschlag on Jan. 24 2008,04:53

Quote (Daniel Smith @ Jan. 23 2008,18:32)
I get the distinct impression that no one here has read anything these men have published.  I also get the impression no one here wants to.
---------------------QUOTE-------------------


Please give citations to PEER-REVIEWED papers.
Posted by: JAM on Jan. 24 2008,10:59

Quote (mitschlag @ Jan. 24 2008,04:53)
Quote (Daniel Smith @ Jan. 23 2008,18:32)
I get the distinct impression that no one here has read anything these men have published.  I also get the impression no one here wants to.
---------------------QUOTE-------------------


Please give citations to PEER-REVIEWED papers.
---------------------QUOTE-------------------


Not just "peer-reviewed," but PRIMARY literature--that is, papers that contain new data from testing the hypotheses you have decided must be true, Dan.

For example, Denton actually publishes in the primary literature, albeit descriptive, relatively minor clinical genetics papers. Ask yourself why he lacks the faith to:

1) Make an unequivocal prediction about future data
2) Go looking for such data himself.

Don't you see the irony in your obvious lack of faith? Why do you have more faith in unsupported musings than you do in the actual evidence (according to you, the very stuff designed by God Himself)?

Why do you need filtration?
Posted by: Daniel Smith on Jan. 24 2008,11:05

Quote (mitschlag @ Jan. 24 2008,02:53)
 
Quote (Daniel Smith @ Jan. 23 2008,18:32)
I get the distinct impression that no one here has read anything these men have published.  I also get the impression no one here wants to.
---------------------QUOTE-------------------


Please give citations to PEER-REVIEWED papers.
---------------------QUOTE-------------------


Like Darwin's?

Please....
Posted by: JAM on Jan. 24 2008,11:10

Quote (Daniel Smith @ Jan. 24 2008,11:05)
Quote (mitschlag @ Jan. 24 2008,02:53)
 
Quote (Daniel Smith @ Jan. 23 2008,18:32)
I get the distinct impression that no one here has read anything these men have published.  I also get the impression no one here wants to.
---------------------QUOTE-------------------


Please give citations to PEER-REVIEWED papers.
---------------------QUOTE-------------------


Like Darwin's?

Please....
---------------------QUOTE-------------------


Darwin's books are primary literature, because they contained new data, unlike the musings you desperately want to believe.

Science is about predicting, not spinning the existing data.

Schindewolf's gaps have been filled, falsifying his hypothesis, even for his speciality, ammonites.
Posted by: oldmanintheskydidntdoit on Jan. 24 2008,11:29

Quote (Daniel Smith @ Jan. 24 2008,11:05)
Quote (mitschlag @ Jan. 24 2008,02:53)
 
Quote (Daniel Smith @ Jan. 23 2008,18:32)
I get the distinct impression that no one here has read anything these men have published.  I also get the impression no one here wants to.
---------------------QUOTE-------------------


Please give citations to PEER-REVIEWED papers.
---------------------QUOTE-------------------


Like Darwin's?

Please....
---------------------QUOTE-------------------


So, that'll be a no then?

Then why not just say that?
Posted by: mitschlag on Jan. 24 2008,13:43

Quote (Daniel Smith @ Jan. 24 2008,11:05)
 
Quote (mitschlag @ Jan. 24 2008,02:53)
   
Quote (Daniel Smith @ Jan. 23 2008,18:32)
I get the distinct impression that no one here has read anything these men have published.  I also get the impression no one here wants to.
---------------------QUOTE-------------------


Please give citations to PEER-REVIEWED papers.
---------------------QUOTE-------------------


Like Darwin's?

Please....
---------------------QUOTE-------------------


If Darwin's ideas had not been useful, they would have been discarded.

The ideas of your icons have not been useful, apparently.

Your job is to correct that impression and establish the utility of those ideas by citing relevant empirical data - as published in the PEER-REVIEWED literature.

Can you do it?
Posted by: Ftk on Jan. 24 2008,14:21

Daniel,

I certainly hope there are lurkers reading this thread who are interested in getting at the truth with regard to what the mechanisms of evolution can actually accomplish, because you are doing a marvelous job of asking the right questions and pointing out the Darwinian fallacies.  Keep up the good work.

BTW, I envy your gift of patience.  It won't pay off with these folks, but like I said, hopefully there are open minded lurkers following this discussion.
Posted by: Mister DNA on Jan. 24 2008,14:29

Quote (Ftk @ Jan. 24 2008,14:21)
Daniel,

I certainly hope there are lurkers reading this thread who are interested in getting at the truth with regard to what the mechanisms of evolution can actually accomplish, because you are doing a marvelous job of asking the right questions and pointing out the Darwinian fallacies.  Keep up the good work.

BTW, I envy your gift of patience.  It won't pay off with these folks, but like I said, hopefully there are open minded lurkers following this discussion.
---------------------QUOTE-------------------


This is what is known in the mafia as "The Kiss of Death".
Posted by: Ftk on Jan. 24 2008,14:33


Posted by: Erasmus, FCD on Jan. 24 2008,15:17

Quote (Ftk @ Jan. 24 2008,14:21)
Daniel,

I certainly hope there are lurkers reading this thread who are interested in getting at the truth with regard to what the mechanisms of evolution can actually accomplish, because you are doing a marvelous job of asking the right questions and pointing out the Darwinian fallacies.  Keep up the good work.

BTW, I envy your gift of patience.  It won't pay off with these folks, but like I said, hopefully there are open minded lurkers following this discussion.
---------------------QUOTE-------------------


Because since evolution either never happened anyway or it like totally did and God did it and also cause the earth is like 10,000 - 4,500,000,000 years old and no one knows for sure, and because the flood was like at least global or maybe even local and Walt Brown once imagined how like all the water could have come from inside the earth or maybe from outside the earth and it could have taken miracles but maybe not because how can you tell God what to do and stuff, Daniel, you are doing a good job pointing out the holes and stuff or at least the places where the holes could be if you wanted to interpret it that way, and definitely the places where we would see holes if weren't predisposed to see things that are really there and could instead just trust God and use the eyes that our faith gives and whatnot.

And I've already discussed all this on my blog anyway.

/FTK

yawn.  don't you have some clothes to wash or some floors to scrub my helpmeet friend?
Posted by: J-Dog on Jan. 24 2008,15:41

Quote (Erasmus, FCD @ Jan. 24 2008,15:17)
Quote (Ftk @ Jan. 24 2008,14:21)
Daniel,

I certainly hope there are lurkers reading this thread who are interested in getting at the truth with regard to what the mechanisms of evolution can actually accomplish, because you are doing a marvelous job of asking the right questions and pointing out the Darwinian fallacies.  Keep up the good work.

BTW, I envy your gift of patience.  It won't pay off with these folks, but like I said, hopefully there are open minded lurkers following this discussion.
---------------------QUOTE-------------------


Because since evolution either never happened anyway or it like totally did and God did it and also cause the earth is like 10,000 - 4,500,000,000 years old and no one knows for sure, and because the flood was like at least global or maybe even local and Walt Brown once imagined how like all the water could have come from inside the earth or maybe from outside the earth and it could have taken miracles but maybe not because how can you tell God what to do and stuff, Daniel, you are doing a good job pointing out the holes and stuff or at least the places where the holes could be if you wanted to interpret it that way, and definitely the places where we would see holes if weren't predisposed to see things that are really there and could instead just trust God and use the eyes that our faith gives and whatnot.

And I've already discussed all this on my blog anyway.

/FTK

yawn.  don't you have some clothes to wash or some floors to scrub my helpmeet friend?
---------------------QUOTE-------------------


Erasamus - Ha!  Good on You!

But... Don't let Kristine and ERV see you posting like that!  Abbie is 7 feet tall and studies kick boxing, and Kristine will shimmy you to death.  

Although they might make an exception for you since your post IS about FTK.

The judges will have to make a ruling.
Posted by: JAM on Jan. 24 2008,15:42

Quote (Ftk @ Jan. 24 2008,14:21)
Daniel,

I certainly hope there are lurkers reading this thread who are interested in getting at the truth with regard to what the mechanisms of evolution can actually accomplish, because you are doing a marvelous job of asking the right questions and pointing out the Darwinian fallacies...
---------------------QUOTE-------------------


What "Darwinian fallacies" has he pointed out, FTK?
Posted by: mitschlag on Jan. 24 2008,15:54

Quote (Ftk @ Jan. 24 2008,14:21)
Daniel,

I certainly hope there are lurkers reading this thread who are interested in getting at the truth with regard to what the mechanisms of evolution can actually accomplish, because you are doing a marvelous job of asking the right questions and pointing out the Darwinian fallacies.  Keep up the good work.

BTW, I envy your gift of patience.  It won't pay off with these folks, but like I said, hopefully there are open minded lurkers following this discussion.
---------------------QUOTE-------------------


Hey, FTK, what's your take on Davison, Schindewolf, Berg, and Goldschmidt?

Have YOU read those books that Daniel is touting?

What's your position on Stammengeschichte, Stammesentwicklung and Gesetzmäßigkeiten?

Have you checked your Baupläne lately?
Posted by: blipey on Jan. 24 2008,17:00

Good on you, Daniel!  You've got the support of Ftk!  There's no one on interwebbies that has answered more questions than Ftk.  She's ALL ABOUT THE ANSWERS.

Why, just look at all of the things she's answered:


---------------------QUOTE-------------------
1.  Is it okay for ID proponents to post personal information of the internet?

2.  Do you think that Wes and/or steve would not remove your personal information from the board if someone posted it?

3.  Do you think that the Baylor curators and other officials post their home addresses and phone numbers to the internet?

4.  Why re you back posting here at AtBC?

5.  How does Behe know what is in a group of books without ever having read the books?


6.  What is the point of the Behe/unread books discussion?

7.  According to ID Theory, how did the immune system develop?

8.  What is gained by jettisoning ToE and saying God did it?

9.  In the light of a science teacher teaching that the study of beetles is not a scientific effort and possibly that spiders evolved from insects (if evolution were true), how is ID theory driving kids toward science?

10. Why don't IDers pursue RESEARCH GRANTS, from the Templeton Foundation, for example?

11. Are you afraid to examine the sequence evidence for ToE?

11A.  Added.  Do you understand what sequence evidence is?

12. Where did Albatrossity2 claim that his students were religious freaks?

12A.  Added.  Where did blipey claim that his nephew's teacher was "a source of evil"?

13. Why don't IDers publish in PCID?

14. Why hasn't PCID been published in over two years?

15. Do you believe that Darwinists have kept PCID from being published?

16. How?

17. Can ID be called a theory when it hasn't made even one prediction?

18. Yes or no: ID wouldn't benefit from publishing any articles, anywhere.

19. Yes or no: Your children should be taught the historical insights of the Bhagavad Gita?

20. What sort of Waterloo can we look forward to on February 8, 2008?

Interesting side note. Just came across this comment back on page 102 where you berate people for not having read the pertinent books.  Which begs several more questions I'll put here.  Why is reading material important?  Do you think it might have been important for Behe to read some books before commenting on them?  Have you read the textbook that Albatrossity2 sent you?  Have you got that list of peer reviewed articles you've read ready to go?  Are you seriously arguing that we should read books and that IDers don't have to?

21. What are IDers doing to garner respect?

22. Given that you believe ID is science because of "design inference", why is ToE not science because all it has is inference?

23. Can any human being know what is contained in a book without having read the book?

24. If everyone died in the Flood, who wrote all the different stories down?

25. What year was the Flood over? 2300 BC

26. What year was the height of the Egyptian Empire? 2030 BC

27. What was the population of the world in that year? 30,000,000

28. How did 8 people (6 really) make that many people?


29. Is Dembski a creationist?

30. How would monogamous gays destroy heterosexual marriage?

31. How did Koalas get from Ararat to Australia?

32. Do you believe that the FLOOD is a scientifically tenable idea?

33. Are the people who run Baylor Darwin Police?

34. Are those same people Baptist?

35. What does this mean?

36. Given that HIV cannot have evolved (Behe), which of the 8 (6 really) people on the ark were carrying HIV?

---------------------QUOTE-------------------


Well, actually she sort of half answered the first 5, but we let her go on it.  And I answered 25 through 28 for her, but you can see how well she's doing!  I mean, it's only been 2 months or so since she said she'd try to answer some of them.

Maybe you should participate at her blog, where she never answer questions, and fails to ask any as well.
Posted by: Daniel Smith on Jan. 24 2008,17:50

Quote (JAM @ Jan. 24 2008,09:10)
Darwin's books are primary literature, because they contained new data, unlike the musings you desperately want to believe.

Science is about predicting, not spinning the existing data.

Schindewolf's gaps have been filled, falsifying his hypothesis, even for his speciality, ammonites.
---------------------QUOTE-------------------


I'm breaking my silence towards you this one time because this cannot go ignored.  

You know nothing of Schindewolf, you've never read his books - so how can you possibly know if his book contains new data or existing data?  Are you just guessing?  (I think you are.)

As for his "gaps" being filled, I'm calling you on that.  Show me from the primary literature where the specific gaps he pointed to (of which you're blissfully unaware) have been filled.
Posted by: Daniel Smith on Jan. 24 2008,17:53

Quote (oldmanintheskydidntdoit @ Jan. 24 2008,09:29)
 
Quote (Daniel Smith @ Jan. 24 2008,11:05)
 
Quote (mitschlag @ Jan. 24 2008,02:53)

Please give citations to PEER-REVIEWED papers.
---------------------QUOTE-------------------


Like Darwin's?

Please....
---------------------QUOTE-------------------


So, that'll be a no then?

Then why not just say that?
---------------------QUOTE-------------------


I've cited peer-reviewed papers plenty of times in this thread.  I can't help the fact that you won't click on the links.
Posted by: Daniel Smith on Jan. 24 2008,17:56

Quote (Ftk @ Jan. 24 2008,12:21)
Daniel,

I certainly hope there are lurkers reading this thread who are interested in getting at the truth with regard to what the mechanisms of evolution can actually accomplish, because you are doing a marvelous job of asking the right questions and pointing out the Darwinian fallacies.  Keep up the good work.

BTW, I envy your gift of patience.  It won't pay off with these folks, but like I said, hopefully there are open minded lurkers following this discussion.
---------------------QUOTE-------------------


Thank you for that.
Posted by: Lou FCD on Jan. 24 2008,18:13

Oh, the drama.
Posted by: Albatrossity2 on Jan. 24 2008,18:18

Quote (Daniel Smith @ Jan. 24 2008,17:53)
I've cited peer-reviewed papers plenty of times in this thread.  I can't help the fact that you won't click on the links.
---------------------QUOTE-------------------


And, as pointed out previously by someone who DID read the links, none of those papers cite Schindewolf or Berg. So their contributions, like Becher's phlogiston and Lamarck's inheritance of acquired characteristics, can be assumed to have been consigned to the dustbin of science, until Daniel can prove otherwise.

PNA
Posted by: Wesley R. Elsberry on Jan. 24 2008,18:36

Schindewolf:

 

---------------------QUOTE-------------------

As we all know, Darwin's theory of evolutionary descent asserts that organisms evolve slowly and very gradually through the smallest of individual steps, through the accumulation of an infinite number of small transformations. Consequently, the fossil organic world would have to consist of an uninterrupted, undivided continuum of forms; as Darwin himself said, geological strata must be filled with the remains of every conceivable transitional form between taxonomic groups, between types of organizations and structural designs of differing magnitudes.

---------------------QUOTE-------------------



The basic problem here is that Darwin did *not* say that. Or, if you think Schindewolf is right, then do the work Schindewolf did not do, and show us where Darwin said just that thing.

Here, have a < link > to help you out in your search.


Posted by: Erasmus, FCD on Jan. 24 2008,23:31

Remember, Danny-Boy (you too FtK, tell yourself that Oprah said it)

invoking Goldschmidt means nonononono Old Earth and nononononono Grate Big Flud.

FtK if we are going to be all 'Goldschmidt-y' then we have to stop pretending to be all 'Walt-Brown-y'.  I don't think our good friend Walt "The Gambler" Brown is going to be very happy with the idea that Noah didn't carry a bunch of VD with him from before the rainbow, and stuff.
Posted by: IanBrown_101 on Jan. 25 2008,00:00

Quote (Erasmus, FCD @ Jan. 25 2008,05:31)
Remember, Danny-Boy (you too FtK, tell yourself that Oprah said it)

invoking Goldschmidt means nonononono Old Earth and nononononono Grate Big Flud.

FtK if we are going to be all 'Goldschmidt-y' then we have to stop pretending to be all 'Walt-Brown-y'.  I don't think our good friend Walt "The Gambler" Brown is going to be very happy with the idea that Noah didn't carry a bunch of VD with him from before the rainbow, and stuff.
---------------------QUOTE-------------------


It's stuff like this that makes me think FtK has been reading a LITTLE too much Orwell. (Have you read any Orwell FtK? Honest, non-leading question, I'm actually curious as to your opinion, if you have read it, of 1984 in particular.)

She seems to absolutely leap from the pages of 1984. Newspeak, doublethink and the Ministry of Truth accusations spring forth from her like water from a spring.
Posted by: JAM on Jan. 25 2008,00:40

Quote (Daniel Smith @ Jan. 24 2008,17:50)
Quote (JAM @ Jan. 24 2008,09:10)
Darwin's books are primary literature, because they contained new data, unlike the musings you desperately want to believe.

Science is about predicting, not spinning the existing data.

Schindewolf's gaps have been filled, falsifying his hypothesis, even for his speciality, ammonites.
---------------------QUOTE-------------------


I'm breaking my silence towards you this one time because this cannot go ignored.  

You know nothing of Schindewolf, you've never read his books - so how can you possibly know if his book contains new data or existing data?  Are you just guessing?  (I think you are.)

As for his "gaps" being filled, I'm calling you on that.  Show me from the primary literature where the specific gaps he pointed to (of which you're blissfully unaware) have been filled.
---------------------QUOTE-------------------


CALLOMON, J. H.  1985.
The evolution of the  Jurassic  ammonite family Cardioceratidae.
Special Papers in Palaeontology. 33, 49-90.

DONOVAN,  D.  T. et al.  1981.
Classification of the Jurassic Ammonitina.
In: HOUSE. M. R. & SENIOR, J. R. (eds)
The Ammonoidea. Systematics Association Special Volumes. 18, Academic Press,  London, 101-155.

Oh, and while you're gagging on those, would you mind summarizing the modern evidence supporting Schindewolf's assertion that ammonites, ichthyosaurs, and terrestrial dinosaurs went synchronously extinct at the very end of the cretaceous?

The most hypocritical thing about you is that you are afraid to look at the designs (according to you) of God himself, frantically hand-waving about what people say.

What does your Bible say about the reliability of hearsay as evidence, Dan?

And why didn't you answer my earlier questions: how many bases must change in the human genome to cause an extra vertebra? How many to change the identity of a vertebra?

Have you found a "hind leg gene" yet, or was that just a lie?
Posted by: JAM on Jan. 25 2008,00:41

Quote (Daniel Smith @ Jan. 24 2008,17:53)
I've cited peer-reviewed papers plenty of times in this thread.
---------------------QUOTE-------------------


Are you claiming that the Denton papers you cited were peer-reviewed, Dan?
Posted by: oldmanintheskydidntdoit on Jan. 25 2008,02:25

Quote (Daniel Smith @ Jan. 24 2008,17:53)
 
Quote (oldmanintheskydidntdoit @ Jan. 24 2008,09:29)
   
Quote (Daniel Smith @ Jan. 24 2008,11:05)
     
Quote (mitschlag @ Jan. 24 2008,02:53)

Please give citations to PEER-REVIEWED papers.
---------------------QUOTE-------------------


Like Darwin's?

Please....
---------------------QUOTE-------------------


So, that'll be a no then?

Then why not just say that?
---------------------QUOTE-------------------


I've cited peer-reviewed papers plenty of times in this thread.  I can't help the fact that you won't click on the links.
---------------------QUOTE-------------------


Call yourself religious do you?

I imagine your preist/whatever would be ashamed of the person they see here on this board.

Are you telling me that your comment was not suppose to be disdainful of Darwin's classic work? Like somehow you've had a better idea? Like you *know* it's simply wrong. Have *you* even read it Danny boy?

So, Danny boy, I'm calling you out.

So in light of the fact that none of those papers you mention cite Schindewolf or Berg what relevance do any of the papers you've cited have to your position?

For each paper you linked to summarise how it supports your case. Or stop claiming that "peer reviewed papers" support your case.

Have a look at my signature.
Posted by: mitschlag on Jan. 25 2008,07:17

Quote (Daniel Smith @ Jan. 24 2008,17:53)
     
Quote (oldmanintheskydidntdoit @ Jan. 24 2008,09:29)
         
Quote (Daniel Smith @ Jan. 24 2008,11:05)
         
Quote (mitschlag @ Jan. 24 2008,02:53)

Please give citations to PEER-REVIEWED papers.
---------------------QUOTE-------------------


Like Darwin's?

Please....
---------------------QUOTE-------------------


So, that'll be a no then?

Then why not just say that?
---------------------QUOTE-------------------


I've cited peer-reviewed papers plenty of times in this thread.  I can't help the fact that you won't click on the links.
---------------------QUOTE-------------------


You seem to think that you have already provided enough documentation to make your case.

If that is so, it would be a kindness and a properly scholarly contribution to this discussion if you would bring together in a single post your list of relevant PEER-REVIEWED PRIMARY* publications.  It would be especially helpful if you would comment on each citation to make clear the point or points that you consider to have been made.

*As noted by < JAM >.

Edited to add: Sorry oldman, I see that you made a similar point already.
Posted by: oldmanintheskydidntdoit on Jan. 25 2008,07:43

Quote (mitschlag @ Jan. 25 2008,07:17)
Edited to add: Sorry oldman, I see that you made a similar point already.
---------------------QUOTE-------------------


The more that ask, the better.

It seems that Daniel thinks he can do a FTK and say

"I've proved my point earlier in this thread, so no need to go back over it".

When of course the point was never even supported, never mind proven.

This reminds me of AFDave and his "I dealt with that earlier in the thread" moments. When it was then re-quoted it was almost always found to be purest handwaving. But it's so simple to say, a la FTK, that a point is proven, harder to back it up with the evidence.

Daniel, nobody here seems to think you've supported your case via citations to primary literature.

Prove them wrong, or stop making the claim! Or do you want to provide more signature worthy handwaving and claim that as evidence?

If you go to the main site page here, and select "ALL" for this thread, you'll get a handy single page containing all posts that can be searched. Use it to collect your citations and put them in a single post.

No doubt it'll be handy for your own reference, as well as our amusement.
Posted by: JAM on Jan. 25 2008,09:02

One more for you not to read, Daniel:

Cladistic analysis of the Middle Jurassic ammonite radiation
S. MOYNE and P. NEIGE
Geological Magazine, Volume 141, Issue 02, Mar 2004, pp 115-123
Posted by: VMartin on Jan. 25 2008,12:10

Quote (Wesley R. Elsberry @ Jan. 24 2008,18:36)
Schindewolf:

       

---------------------QUOTE-------------------

As we all know, Darwin's theory of evolutionary descent asserts that organisms evolve slowly and very gradually through the smallest of individual steps, through the accumulation of an infinite number of small transformations. Consequently, the fossil organic world would have to consist of an uninterrupted, undivided continuum of forms; as Darwin himself said, geological strata must be filled with the remains of every conceivable transitional form between taxonomic groups, between types of organizations and structural designs of differing magnitudes.

---------------------QUOTE-------------------



The basic problem here is that Darwin did *not* say that. Or, if you think Schindewolf is right, then do the work Schindewolf did not do, and show us where Darwin said just that thing.

Here, have a < link > to help you out in your search.
---------------------QUOTE-------------------


I didn't use the link Wesley R. Elsberry had given. I have tried talkorigins instead where the whole Darwin's "The origin of species" is available on-line. I would say Darwin said it unambiguously:


But just in proportion as this process of extermination has acted on an enormous scale, so must the number of intermediate varieties, which have formerly existed on the earth, be truly enormous. Why then is not every geological formation and every stratum full of such intermediate links? Geology assuredly does not reveal any such finely graduated organic chain; and this, perhaps, is the most obvious and gravest objection which can be urged against my theory. The explanation lies, as I believe, in the extreme imperfection of the geological record.


< http://www.talkorigins.org/faqs/origin/chapter9.html >  

Because the problem is the same even after 150 years after Darwin, paleontolgists like Schindewolf tried to solve it many years ago. According paleontologist Vaclav Petr Charles Uni Prague there was a curious situation  when gradual neodarwinian evolution coexisted with biostratigraphy which worked with unchangeable species. Author has also made an interesting observation why Gould hypothesis of "punctuated equilibria" has been somehow accepted, but Schindewolf theory has been totally neglected by neodarwinists. Yet according his opinion Schindewolf "typostrophic theory" has not been invalidated by fossil record yet and so it is possible to consider about it's ressurection as soon as the neodarwinian paradigma falls.


The link is in Czech:

< http://www.mprinstitute.org/vaclav/Slovnik.htm >
Posted by: oldmanintheskydidntdoit on Jan. 25 2008,12:13



---------------------QUOTE-------------------
The explanation lies, as I believe, in the extreme imperfection of the geological record.
---------------------QUOTE-------------------



The answer is in the question VMartin.

So I guess VMartin your position is that the fossil record is in fact perfect?
Posted by: mitschlag on Jan. 25 2008,15:50

Quote (oldmanintheskydidntdoit @ Jan. 25 2008,12:13)
 

---------------------QUOTE-------------------
The explanation lies, as I believe, in the extreme imperfection of the geological record.
---------------------QUOTE-------------------



The answer is in the question VMartin.

So I guess VMartin your position is that the fossil record is in fact perfect?
---------------------QUOTE-------------------


Of course it is.

Stop digging.
Posted by: Daniel Smith on Jan. 25 2008,19:56

Quote (Wesley R. Elsberry @ Jan. 24 2008,16:36)
Schindewolf:

                     

---------------------QUOTE-------------------

As we all know, Darwin's theory of evolutionary descent asserts that organisms evolve slowly and very gradually through the smallest of individual steps, through the accumulation of an infinite number of small transformations. Consequently, the fossil organic world would have to consist of an uninterrupted, undivided continuum of forms; as Darwin himself said, geological strata must be filled with the remains of every conceivable transitional form between taxonomic groups, between types of organizations and structural designs of differing magnitudes.

---------------------QUOTE-------------------



The basic problem here is that Darwin did *not* say that. Or, if you think Schindewolf is right, then do the work Schindewolf did not do, and show us where Darwin said just that thing.

Here, have a < link > to help you out in your search.
---------------------QUOTE-------------------


Darwin did say this:
                 

---------------------QUOTE-------------------
But just in proportion as this process of extermination has acted on an enormous scale, so must the number of intermediate varieties, which have formerly existed on the earth, be truly enormous. Why then is not every geological formation and every stratum full of such intermediate links? Geology assuredly does not reveal any such finely graduated organic chain; and this, perhaps, is the most obvious and gravest objection which can be urged against my theory.
Origin of the Species, pg.280
---------------------QUOTE-------------------

     

---------------------QUOTE-------------------
From the foregoing considerations it cannot be doubted that the geological record, viewed as a whole, is extremely imperfect; but if we confine our attention to any one formation, it becomes more difficult to understand, why we do not therein find closely graduated varieties between the allied species which lived at its commencement and at its close.
Ibid., pp 292-293
---------------------QUOTE-------------------

     

---------------------QUOTE-------------------
Geological research, though it has added numerous species to existing and extinct genera, and has made the intervals between some few groups less wide than they otherwise would have been, yet has done scarcely anything in breaking down the distinction between species, by connecting them together by numerous, fine, intermediate varieties; and this not having been effected, is probably the gravest and most obvious of all the many objections which may be urged against my views.
Ibid., pg 299
---------------------QUOTE-------------------

     

---------------------QUOTE-------------------
But I do not pretend that I should ever have suspected how poor a record of the mutations of life, the best preserved geological section presented, had not the difficulty of our not discovering innumerable transitional links between the species which appeared at the commencement and close of each formation, pressed so hardly on my theory.
Ibid., pg 302
---------------------QUOTE-------------------

     

---------------------QUOTE-------------------
The several difficulties here discussed, namely our not finding in the successive formations infinitely numerous transitional links between the many species which now exist or have existed; the sudden manner in which whole groups of species appear in our European formations; the almost entire absence, as at present known, of fossiliferous formations beneath the Silurian strata, are all undoubtedly of the gravest nature.
Ibid., pg 298
---------------------QUOTE-------------------


Darwin's explanation for all this is:
       

---------------------QUOTE-------------------
The explanation lies, as I believe, in the extreme imperfection of the geological record.
Ibid., pg 280
---------------------QUOTE-------------------


He goes on to say this:        

---------------------QUOTE-------------------
As the accumulation of each formation has often been interrupted, and as long blank intervals have intervened between successive formations, we ought not to expect to find, as I attempted to show in the last chapter, in any one or two formations all the intermediate varieties between the species which appeared at the commencement and close of these periods; but we ought to find after intervals, very long as measured by years, but only moderately long as measured geologically, closely allied forms, or, as they have been called by some authors, representative species; and these we assuredly do find.
Ibid., pg 336
---------------------QUOTE-------------------


So, while technically you're right that Darwin did not expect to find evidence of smooth transitions in a spotty fossil record, Schindewolf was viewing the fossil record quite differently.  He said this:

---------------------QUOTE-------------------
Obviously, there are gaps, even considerable gaps, in the preservation of fossil creatures; it would be silly to deny that.  The criticism applies primarily to groups of soft-bodied animals that had no hard parts susceptible to fossilization.
...
On the other hand, we can naturally study the evolutionary process only on forms that we have and that are suitable for the purpose; we cannot use those we do not have, or do not have enough of.  And we have at our disposal, thanks to mass collecting along the profile of a great many groups, such an abundant, consistent, chronologically well-ordered material that we are entirely capable of arriving at binding evolutionary assertions, even by stringently critical standards.  This is the case with shelled cephalopods, stony corals, and so on...
Investigations of this kind, therefore, are by no means based only on completely isolated, chance finds, as is sometimes assumed by those who do not understand the strict paleontological methodology.
Basic Questions in Paleontology, pp. 103-104  (emphasis mine)
---------------------QUOTE-------------------


I believe this was a direct answer to this statement by Darwin:      

---------------------QUOTE-------------------
According to this view, the chance of discovering in a formation in any one country all the early stages of transition between any two forms, is small, for the successive changes are supposed to have been local or confined to some one spot. Most marine animals have a wide range; and we have seen that with plants it is those which have the widest range, that oftenest present varieties; so that with shells and other marine animals, it is probably those which have had the widest range, far exceeding the limits of the known geological formations of Europe, which have oftenest given rise, first to local varieties and ultimately to new species; and this again would greatly lessen the chance of our being able to trace the stages of transition in any one geological formation.
Ibid., pg 298
---------------------QUOTE-------------------


Schindewolf had the benefit of 100 years of paleontological findings since Darwin's time, and the marine animals which Darwin spoke of had yielded a treasure trove of fossilized forms that followed the same patterns throughout the world.  So, although Darwin didn't expect to find smooth transitionals in a spotty fossil record, Schindewolf had every reason to believe Darwin would have expected to find such evidence amongst the millions of fossilized forms found worldwide amongst the most preserved animals.
Posted by: Wesley R. Elsberry on Jan. 25 2008,20:31

Daniel, you are missing something very basic. Please read the claim that Schindewolf made; nothing you've quoted from Darwin approaches it.

You managed to quote Darwin saying something that absolutely contradicts Schindewolf, though its import apparently eludes you:

"which have oftenest given rise, first to local varieties and ultimately to new species"

There's another component of Darwin's thought that contradicts Schindewolf's misrepresentation, which you don't seem to have come across yet. I'll wait to see if you try to quote it, too, as if it were support for your position. That would continue the amusement.

A reminder of Schindewolf's claim:



---------------------QUOTE-------------------

As we all know, Darwin's theory of evolutionary descent asserts that organisms evolve slowly and very gradually through the smallest of individual steps, through the accumulation of an infinite number of small transformations. Consequently, the fossil organic world would have to consist of an uninterrupted, undivided continuum of forms; as Darwin himself said, geological strata must be filled with the remains of every conceivable transitional form between taxonomic groups, between types of organizations and structural designs of differing magnitudes.

---------------------QUOTE-------------------



This claim is about what Darwin's expectation of the fossil record was. Did Darwin claim that "geological strata must be filled with the remains of every conceivable transitional form"? No, he did not, and what you've quoted thus far demonstrates precisely that Darwin did not do as Schindewolf claimed.

Daniel:



---------------------QUOTE-------------------

Schindewolf had the benefit of 100 years of paleontological findings since Darwin's time, and the marine animals which Darwin spoke of had yielded a treasure trove of fossilized forms that followed the same patterns throughout the world.  So, although Darwin didn't expect to find smooth transitionals in a spotty fossil record, Schindewolf had every reason to believe Darwin would have expected to find such evidence amongst the millions of fossilized forms found worldwide amongst the most preserved animals.

---------------------QUOTE-------------------



It looks here like you are stipulating that Schindewolf was wrong about what Darwin stated. Then you try to change what Schindewolf said to move the goalpost from "every conceivable transitional form" to something that you think can be supported. Sorry, I'm not buying your revisionist drivel. Your position appears to have been that Schindewolf is a more reliable authority than those who have followed after him, yet here we see that he got some pretty basic stuff about previous work *wrong*, and you've even deployed the claim that 'subsequent work counts against the prior arguments', though you've strenuously objected that such should not count against Schindewolf.
Posted by: Daniel Smith on Jan. 26 2008,10:25

Quote (JAM @ Jan. 24 2008,22:40)
       
Quote (Daniel Smith @ Jan. 24 2008,17:50)
       
Quote (JAM @ Jan. 24 2008,09:10)
Darwin's books are primary literature, because they contained new data, unlike the musings you desperately want to believe.

Science is about predicting, not spinning the existing data.

Schindewolf's gaps have been filled, falsifying his hypothesis, even for his speciality, ammonites.
---------------------QUOTE-------------------


I'm breaking my silence towards you this one time because this cannot go ignored.  

You know nothing of Schindewolf, you've never read his books - so how can you possibly know if his book contains new data or existing data?  Are you just guessing?  (I think you are.)

As for his "gaps" being filled, I'm calling you on that.  Show me from the primary literature where the specific gaps he pointed to (of which you're blissfully unaware) have been filled.
---------------------QUOTE-------------------


CALLOMON, J. H.  1985.
The evolution of the  Jurassic  ammonite family Cardioceratidae.
Special Papers in Palaeontology. 33, 49-90.

DONOVAN,  D.  T. et al.  1981.
Classification of the Jurassic Ammonitina.
In: HOUSE. M. R. & SENIOR, J. R. (eds)
The Ammonoidea. Systematics Association Special Volumes. 18, Academic Press,  London, 101-155.
---------------------QUOTE-------------------

 
These two papers only show up as citations in Google Scholar.  That doesn't help me much.    
 
Quote (JAM @ Jan. 25 2008,07:02)
One more for you not to read, Daniel:

Cladistic analysis of the Middle Jurassic ammonite radiation
S. MOYNE and P. NEIGE
Geological Magazine, Volume 141, Issue 02, Mar 2004, pp 115-123
---------------------QUOTE-------------------


I actually found this paper.  I find nothing is this paper which falsifies Schindewolf's theory in any way.  They do mention him once:      

---------------------QUOTE-------------------
The hammatoceratins are thought to be a superfamily, as suggested by Schindewolf (1964, 1965) and Tintant & Mouterde (1981), however, the main difference with the preceding classification is that the hammatoceratins may be divided into two separate lineages, following Westermann (1993). For Rulleau, Elmi & Thevenard (2001), these two lineages are the Hammatoceratidae Buckman, 1887 and the Erycitidae Spath, 1927, each of them with its own descendants: Sonniniidae, Strigoceratidae and Haplocerataceae for the former and Stephanocerataceae for the latter (Fig. 1b).
---------------------QUOTE-------------------


I fail to see how this would lead anyone to conclude that "Schindewolf's gaps have been filled, falsifying his hypothesis".  They mention two hypotheses for the Phylogenetic relationships between the hammatoceratins and their descendants, the single lineage hypothesis and the two-lineage hypothesis.  Schindewolf (along with others), is cited as holding to the former.  If you somehow misconstrue this as falsifying his entire theory, I fail to see it.  In fact, the opposite is true.  The authors also say:      

---------------------QUOTE-------------------
Transitions between Aalenian members of the hammatoceratins and their presumed descendants are very difficult to trace. There are various reasons for this: (1) relationships within the hammatoceratins root stock are still not clearly established; (2) members of the radiation display diverse morphologies featuring a complex mosaic of characters; and (3) the late Aalenian radiation occurred very rapidly with many new forms emerging in a brief span of time.
---------------------QUOTE-------------------


Let's take those one at a time:

"(1) relationships within the hammatoceratins root stock are still not clearly established".  
This is precisely what Schindewolf said.  The relationship with the "root stock" is one of his "gaps".  He theorized that such a gap could only be filled saltationally.  The authors make no claim otherwise.

"(2) members of the radiation display diverse morphologies featuring a complex mosaic of characters".  
This corresponds exactly with Schindewolf's "typogenesis" phase - where evolution of diverse morphological characters occurs very rapidly in the beginning stages of lineages.  The authors make no claim otherwise.

"(3) the late Aalenian radiation occurred very rapidly with many new forms emerging in a brief span of time."  
This also confirms Schindewolf's rapid typogenesis phase.  The authors make no claim otherwise.


---------------------QUOTE-------------------
Oh, and while you're gagging on those, would you mind summarizing the modern evidence supporting Schindewolf's assertion that ammonites, ichthyosaurs, and terrestrial dinosaurs went synchronously extinct at the very end of the cretaceous?

---------------------QUOTE-------------------

That view is not expressed in his book.  You'll have to provide the direct quotation.
Posted by: Wesley R. Elsberry on Jan. 26 2008,10:40

Daniel Smith:



---------------------QUOTE-------------------

That doesn't help me much.

---------------------QUOTE-------------------



This is only a concern if Daniel is being *tutored*.

It is of no relevance if the aim is *rebuttal*.
Posted by: Daniel Smith on Jan. 26 2008,10:52

Quote (Wesley R. Elsberry @ Jan. 25 2008,18:31)
Daniel, you are missing something very basic. Please read the claim that Schindewolf made; nothing you've quoted from Darwin approaches it.

You managed to quote Darwin saying something that absolutely contradicts Schindewolf, though its import apparently eludes you:

"which have oftenest given rise, first to local varieties and ultimately to new species"

There's another component of Darwin's thought that contradicts Schindewolf's misrepresentation, which you don't seem to have come across yet. I'll wait to see if you try to quote it, too, as if it were support for your position. That would continue the amusement.

A reminder of Schindewolf's claim:

     

---------------------QUOTE-------------------

As we all know, Darwin's theory of evolutionary descent asserts that organisms evolve slowly and very gradually through the smallest of individual steps, through the accumulation of an infinite number of small transformations. Consequently, the fossil organic world would have to consist of an uninterrupted, undivided continuum of forms; as Darwin himself said, geological strata must be filled with the remains of every conceivable transitional form between taxonomic groups, between types of organizations and structural designs of differing magnitudes.

---------------------QUOTE-------------------



This claim is about what Darwin's expectation of the fossil record was. Did Darwin claim that "geological strata must be filled with the remains of every conceivable transitional form"? No, he did not, and what you've quoted thus far demonstrates precisely that Darwin did not do as Schindewolf claimed.

Daniel:

     

---------------------QUOTE-------------------

Schindewolf had the benefit of 100 years of paleontological findings since Darwin's time, and the marine animals which Darwin spoke of had yielded a treasure trove of fossilized forms that followed the same patterns throughout the world.  So, although Darwin didn't expect to find smooth transitionals in a spotty fossil record, Schindewolf had every reason to believe Darwin would have expected to find such evidence amongst the millions of fossilized forms found worldwide amongst the most preserved animals.

---------------------QUOTE-------------------



It looks here like you are stipulating that Schindewolf was wrong about what Darwin stated. Then you try to change what Schindewolf said to move the goalpost from "every conceivable transitional form" to something that you think can be supported. Sorry, I'm not buying your revisionist drivel. Your position appears to have been that Schindewolf is a more reliable authority than those who have followed after him, yet here we see that he got some pretty basic stuff about previous work *wrong*, and you've even deployed the claim that 'subsequent work counts against the prior arguments', though you've strenuously objected that such should not count against Schindewolf.
---------------------QUOTE-------------------


Wesley,

You are correct.  As far as I can tell, Darwin never said that and he did not expect to find such.  I do not know where Schindewolf got that info about what "Darwin himself said".  Perhaps it was due to the language barrier?  Also, there's the (slight) possibility that "as Darwin himself said" is a mistranslation of the German to English.  He could also be interjecting what he would expect to find if Darwin's claims of slow, gradual evolution by minute changes were true.  Or maybe Schindewolf is guilty of just being wrong about what he thought Darwin said?  I don't know.

I don't think it addresses the larger point though - that of the completeness of the fossil record in certain areas.  You snipped the quote I provided about that.  Here it is again:
   

---------------------QUOTE-------------------
Obviously, there are gaps, even considerable gaps, in the preservation of fossil creatures; it would be silly to deny that.  The criticism applies primarily to groups of soft-bodied animals that had no hard parts susceptible to fossilization.
...
On the other hand, we can naturally study the evolutionary process only on forms that we have and that are suitable for the purpose; we cannot use those we do not have, or do not have enough of.  And we have at our disposal, thanks to mass collecting along the profile of a great many groups, such an abundant, consistent, chronologically well-ordered material that we are entirely capable of arriving at binding evolutionary assertions, even by stringently critical standards.  This is the case with shelled cephalopods, stony corals, and so on...
Investigations of this kind, therefore, are by no means based only on completely isolated, chance finds, as is sometimes assumed by those who do not understand the strict paleontological methodology.
Basic Questions in Paleontology, pp. 103-104
---------------------QUOTE-------------------


Schindewolf is claiming that--although incomplete in many areas--the fossil record is complete enough in certain areas "that we are entirely capable of arriving at binding evolutionary assertions, even by stringently critical standards".  He believed that the fossils that did speak, spoke volumes against Darwin's theory.

His assertion about exactly what Darwin said aside, Schindewolf's claims about widespread evolutionary patterns of rapid radiation, stasis, and over-specialization are still valid today.  Do you dispute that?
Posted by: Daniel Smith on Jan. 26 2008,10:55

Quote (Wesley R. Elsberry @ Jan. 26 2008,08:40)
Daniel Smith:

 

---------------------QUOTE-------------------

That doesn't help me much.

---------------------QUOTE-------------------



This is only a concern if Daniel is being *tutored*.

It is of no relevance if the aim is *rebuttal*.
---------------------QUOTE-------------------


If I provide two dead links and then ask you to rebut them, how exactly do you do that?
Posted by: Jim_Wynne on Jan. 26 2008,11:14

Quote (Daniel Smith @ Jan. 26 2008,10:55)
 
Quote (Wesley R. Elsberry @ Jan. 26 2008,08:40)
Daniel Smith:

     

---------------------QUOTE-------------------

That doesn't help me much.

---------------------QUOTE-------------------



This is only a concern if Daniel is being *tutored*.

It is of no relevance if the aim is *rebuttal*.
---------------------QUOTE-------------------


If I provide two dead links information that indicates that I have no idea what I'm talking about and then ask you to rebut them it, how exactly do you do that?
---------------------QUOTE-------------------


I fixed that to make it more to the point.
Posted by: Timothy McDougald on Jan. 26 2008,11:18

Quote (Wesley R. Elsberry @ Jan. 24 2008,18:36)
Schindewolf:

 

---------------------QUOTE-------------------

As we all know, Darwin's theory of evolutionary descent asserts that organisms evolve slowly and very gradually through the smallest of individual steps, through the accumulation of an infinite number of small transformations. Consequently, the fossil organic world would have to consist of an uninterrupted, undivided continuum of forms; as Darwin himself said, geological strata must be filled with the remains of every conceivable transitional form between taxonomic groups, between types of organizations and structural designs of differing magnitudes.

---------------------QUOTE-------------------



The basic problem here is that Darwin did *not* say that. Or, if you think Schindewolf is right, then do the work Schindewolf did not do, and show us where Darwin said just that thing.

Here, have a < link > to help you out in your search.
---------------------QUOTE-------------------


Here is a quote from Darwin that might help:



---------------------QUOTE-------------------
To sum up, I believe that species come to be tolerably well-defined objects, and do not at any one period present an inextricable chaos of varying and intermediate links (bold mine - afarensis): firstly, because new varieties are very slowly formed, for variation is a very slow process, and natural selection can do nothing until favourable variations chance to occur, and until a place in the natural polity of the country can be better filled by some modification of some one or more of its inhabitants. And such new places will depend on slow changes of climate, or on the occasional immigration of new inhabitants, and, probably, in a still more important degree, on some of the old inhabitants becoming slowly modified, with the new forms thus produced and the old ones acting and reacting on each other. So that, in any one region and at any one time, we ought only to see a few species presenting slight modifications of structure in some degree permanent; and this assuredly we do see.
---------------------QUOTE-------------------



Darwin, in point of fact, did not think that

---------------------QUOTE-------------------
Consequently, the fossil organic world would have to consist of an uninterrupted, undivided continuum of forms...
---------------------QUOTE-------------------

as the bolded part of the above quote (which comes from pg 177, 1st ed of the Origin of Species) clearly shows.
Posted by: Daniel Smith on Jan. 26 2008,11:36

Quote (Jim_Wynne @ Jan. 26 2008,09:14)
 
Quote (Daniel Smith @ Jan. 26 2008,10:55)
   
Quote (Wesley R. Elsberry @ Jan. 26 2008,08:40)
Daniel Smith:

       

---------------------QUOTE-------------------

That doesn't help me much.

---------------------QUOTE-------------------



This is only a concern if Daniel is being *tutored*.

It is of no relevance if the aim is *rebuttal*.
---------------------QUOTE-------------------


If I provide two dead links information that indicates that I have no idea what I'm talking about and then ask you to rebut them it, how exactly do you do that?
---------------------QUOTE-------------------


I fixed that to make it more to the point.
---------------------QUOTE-------------------


You realize we were speaking of JAMs dead links don't you?
I'm sure he appreciates your assessment of the information he provided.
Posted by: Jim_Wynne on Jan. 26 2008,11:54

Quote (Daniel Smith @ Jan. 26 2008,11:36)
Quote (Jim_Wynne @ Jan. 26 2008,09:14)
 
Quote (Daniel Smith @ Jan. 26 2008,10:55)
     
Quote (Wesley R. Elsberry @ Jan. 26 2008,08:40)
Daniel Smith:

         

---------------------QUOTE-------------------

That doesn't help me much.

---------------------QUOTE-------------------



This is only a concern if Daniel is being *tutored*.

It is of no relevance if the aim is *rebuttal*.
---------------------QUOTE-------------------


If I provide two dead links information that indicates that I have no idea what I'm talking about and then ask you to rebut them it, how exactly do you do that?
---------------------QUOTE-------------------


I fixed that to make it more to the point.
---------------------QUOTE-------------------


You realize we were speaking of JAMs dead links don't you?
I'm sure he appreciates your assessment of the information he provided.
---------------------QUOTE-------------------


You do realize that I sarcastically reframed the question so that it makes more sense in terms of your own blathering, don't you?
Posted by: blipey on Jan. 26 2008,11:58

Quote (Daniel Smith @ Jan. 26 2008,11:36)
Quote (Jim_Wynne @ Jan. 26 2008,09:14)
 
Quote (Daniel Smith @ Jan. 26 2008,10:55)
     
Quote (Wesley R. Elsberry @ Jan. 26 2008,08:40)
Daniel Smith:

         

---------------------QUOTE-------------------

That doesn't help me much.

---------------------QUOTE-------------------



This is only a concern if Daniel is being *tutored*.

It is of no relevance if the aim is *rebuttal*.
---------------------QUOTE-------------------


If I provide two dead links information that indicates that I have no idea what I'm talking about and then ask you to rebut them it, how exactly do you do that?
---------------------QUOTE-------------------


I fixed that to make it more to the point.
---------------------QUOTE-------------------


You realize we were speaking of JAMs dead links don't you?
I'm sure he appreciates your assessment of the information he provided.
---------------------QUOTE-------------------


Except JAM really didn't provide dead links, did he?
Posted by: mitschlag on Jan. 26 2008,12:58

Quote (Daniel Smith @ Jan. 26 2008,10:52)
Schindewolf is claiming that--although incomplete in many areas--the fossil record is complete enough in certain areas "that we are entirely capable of arriving at binding evolutionary assertions, even by stringently critical standards".  He believed that the fossils that did speak, spoke volumes against Darwin's theory.
---------------------QUOTE-------------------


To quote the scholar, "That doesn't help me much."

What exactly did Schindewolf say that the fossils said and where* did he say they said it?

*Page citations in Basic Questions in Paleontology.
Posted by: Wesley R. Elsberry on Jan. 26 2008,13:31

Quote (Daniel Smith @ Jan. 26 2008,10:55)
 
Quote (Wesley R. Elsberry @ Jan. 26 2008,08:40)
Daniel Smith:

     

---------------------QUOTE-------------------

That doesn't help me much.

---------------------QUOTE-------------------



This is only a concern if Daniel is being *tutored*.

It is of no relevance if the aim is *rebuttal*.
---------------------QUOTE-------------------


If I provide two dead links and then ask you to rebut them, how exactly do you do that?
---------------------QUOTE-------------------


There are these buildings on university campuses called libraries. There are people called librarians in them, during the day usually, who understand these strings called references. If asked, they'll tell you whether the library has got a copy onhand of the journal containing the pages of the paper referred to in the reference that you provide. They'll even tell you approximately where in the library you may find the actual volume in question.

Usually, though, they will stop short of requests to read it to you out loud and then explain it.
Posted by: Wesley R. Elsberry on Jan. 26 2008,13:59



---------------------QUOTE-------------------

He believed that the fossils that did speak, spoke volumes against Darwin's theory.

---------------------QUOTE-------------------



Kinda big talk, given that we just established that it is by no means demonstrated that Schindewolf even understood Darwin. At best, Schindewolf can be said to have believed that he was on to something that countered the strawman he erected -- but that is what strawmen are for.
Posted by: JAM on Jan. 26 2008,14:25

Quote (Daniel Smith @ Jan. 26 2008,10:25)
   
Quote (JAM @ Jan. 24 2008,22:40)
             
Quote (Daniel Smith @ Jan. 24 2008,17:50)
             
Quote (JAM @ Jan. 24 2008,09:10)
Darwin's books are primary literature, because they contained new data, unlike the musings you desperately want to believe.

Science is about predicting, not spinning the existing data.

Schindewolf's gaps have been filled, falsifying his hypothesis, even for his speciality, ammonites.
---------------------QUOTE-------------------


I'm breaking my silence towards you this one time because this cannot go ignored.
---------------------QUOTE-------------------


---------------------QUOTE-------------------


---------------------QUOTE-------------------


But you are ignoring the evidence, proving unequivocally that you lied when you claimed to be interested in evidence.
 

---------------------QUOTE-------------------
 

---------------------QUOTE-------------------
 

---------------------QUOTE-------------------
You know nothing of Schindewolf,
---------------------QUOTE-------------------


---------------------QUOTE-------------------


---------------------QUOTE-------------------


This is yet another lie from you, Dan. You are a reflexive, pathological liar when it comes to evolution and evidence.
 

---------------------QUOTE-------------------
 

---------------------QUOTE-------------------
   

---------------------QUOTE-------------------
... you've never read his books - so how can you possibly know if his book contains new data or existing data?  Are you just guessing?  (I think you are.)

As for his "gaps" being filled, I'm calling you on that.  Show me from the primary literature where the specific gaps he pointed to (of which you're blissfully unaware) have been filled.
---------------------QUOTE-------------------


CALLOMON, J. H.  1985.
The evolution of the  Jurassic  ammonite family Cardioceratidae.
Special Papers in Palaeontology. 33, 49-90.

DONOVAN,  D.  T. et al.  1981.
Classification of the Jurassic Ammonitina.
In: HOUSE. M. R. & SENIOR, J. R. (eds)
The Ammonoidea. Systematics Association Special Volumes. 18, Academic Press,  London, 101-155.
---------------------QUOTE-------------------

 
These two papers only show up as citations in Google Scholar.  That doesn't help me much.
---------------------QUOTE-------------------


I long since gave up trying to help you. You demanded that I show you "from the primary literature where the specific gaps he pointed to (of which you're blissfully unaware) have been filled."

Leaving aside your bald-faced lie about my being blissfully unaware, that's precisely what I did. You didn't ask me to help you, you demanded that I show you where the evidence is.

Then, of course, you lied and claimed that I provided "dead links," when what I provided was citations from the primary literature that rebut Schindewolf's claims.

Why can't you keep yourself from lying, Dan?

   

---------------------QUOTE-------------------
       
Quote (JAM @ Jan. 25 2008,07:02)
One more for you not to read, Daniel:

Cladistic analysis of the Middle Jurassic ammonite radiation
S. MOYNE and P. NEIGE
Geological Magazine, Volume 141, Issue 02, Mar 2004, pp 115-123
---------------------QUOTE-------------------


I actually found this paper.  I find nothing is this paper which falsifies Schindewolf's theory in any way.
---------------------QUOTE-------------------


That's not surprising, since you found nothing in the sequence evidence that falsified your patently false prediction about noncoding sequences. Have you considered looking at the evidence? Not what ANYONE writes about the evidence, but the ACTUAL EVIDENCE?  
   

---------------------QUOTE-------------------
 They do mention him once:...
---------------------QUOTE-------------------


My God, you are breathtakingly dishonest. No one has to bother with explicitly stating that Schindewolf was wrong any more, because everyone who looks at the evidence knows that he was.

My claim was about evidence, not rhetoric. Yet again, you prove that you were deliberately lying when you showed up here and claimed to be interested in evidence.
   

---------------------QUOTE-------------------
I fail to see how this would lead anyone to conclude that "Schindewolf's gaps have been filled, falsifying his hypothesis".
---------------------QUOTE-------------------


That's because you are a reflexive liar who places rhetoric above evidence while claiming the polar opposite.
   

---------------------QUOTE-------------------
They mention two hypotheses...
---------------------QUOTE-------------------


What they mention is irrelevant. I'm citing their evidence. Can't you get that simple point through your lying, pseudo-Christian skull?
   

---------------------QUOTE-------------------
If you somehow misconstrue this as falsifying his entire theory, I fail to see it.
---------------------QUOTE-------------------


Quit lying. Their evidence falsifies his CLAIM ABOUT THE EVIDENCE: "The gaps that exist in the continuity of forms, which we always encounter at those very points, are not to be blamed on the fossil record; they are not illusions, but the expression of a natural, primary absence of transitional forms. [italics in the translation]
   

---------------------QUOTE-------------------
The authors make no claim otherwise.
---------------------QUOTE-------------------


It's about evidence, not claims. Does their evidence fill a gap that Schindewolf claimed would not be filled?
   

---------------------QUOTE-------------------
The authors make no claim otherwise.
---------------------QUOTE-------------------


Again, our dispute is about evidence, and again, you prove that you were lying when you claimed to be interested in evidence.
     

---------------------QUOTE-------------------
   

---------------------QUOTE-------------------
Oh, and while you're gagging on those, would you mind summarizing the modern evidence supporting Schindewolf's assertion that ammonites, ichthyosaurs, and terrestrial dinosaurs went synchronously extinct at the very end of the cretaceous?

---------------------QUOTE-------------------

That view is not expressed in his book.
---------------------QUOTE-------------------


I didn't claim that it was, liar.
   

---------------------QUOTE-------------------
You'll have to provide the direct quotation.
---------------------QUOTE-------------------


Why? You haven't bothered to name a single "hind leg gene," even though you clearly claimed that more than one such gene exists.
Posted by: Daniel Smith on Jan. 27 2008,13:41

<Snip of typical JAM accusations>
     
Quote (JAM @ Jan. 26 2008,12:25)
It's about evidence, not claims. Does their evidence fill a gap that Schindewolf claimed would not be filled?
---------------------QUOTE-------------------


No it does not.  
Explain to me specifically, a) which "gap" Schindewolf claimed would never be filled, and b) how their evidence fills it.

<Snip of more typical JAM accusations>
Posted by: oldmanintheskydidntdoit on Jan. 27 2008,14:06

Quote (Daniel Smith @ Jan. 27 2008,13:41)
<Snip of typical JAM accusations>
       
Quote (JAM @ Jan. 26 2008,12:25)
It's about evidence, not claims. Does their evidence fill a gap that Schindewolf claimed would not be filled?
---------------------QUOTE-------------------


No it does not.  

---------------------QUOTE-------------------


How do you know, if it was a "dead link", what it may or may not "fill"?
Posted by: Daniel Smith on Jan. 27 2008,14:15

Quote (Wesley R. Elsberry @ Jan. 26 2008,11:59)
           

---------------------QUOTE-------------------

He believed that the fossils that did speak, spoke volumes against Darwin's theory.

---------------------QUOTE-------------------



Kinda big talk, given that we just established that it is by no means demonstrated that Schindewolf even understood Darwin. At best, Schindewolf can be said to have believed that he was on to something that countered the strawman he erected -- but that is what strawmen are for.
---------------------QUOTE-------------------


It would seem Wesley, that you have erected your own strawman to use against Schindewolf.  You've provided one quote - from a lifetime of work - and concluded (from that one quote) that Schindewolf did not understand Darwin (and by implication - Darwin's theory).  In order to scientifically conclude that Schindewolf did not understand Darwin's theory, it would be necessary to search through his life's work, find every instance where he makes a claim about Darwin's theory, and show that a significant amount of them render that conclusion.

However, as it stands now, it is not Darwin's theory that Schindewolf could be accused of not understanding, but only Darwin's expectations as to the evidence that would be found in support of his theory.

Which brings me back to the point I've been forced to repeat over and over (because you snipped (again) the part of my post which has the most relevance to this conversation -- Schindewolf's claim as to the completeness of the fossil record in certain areas):          

---------------------QUOTE-------------------
Obviously, there are gaps, even considerable gaps, in the preservation of fossil creatures; it would be silly to deny that.  The criticism applies primarily to groups of soft-bodied animals that had no hard parts susceptible to fossilization.
...
On the other hand, we can naturally study the evolutionary process only on forms that we have and that are suitable for the purpose; we cannot use those we do not have, or do not have enough of.  And we have at our disposal, thanks to mass collecting along the profile of a great many groups, such an abundant, consistent, chronologically well-ordered material that we are entirely capable of arriving at binding evolutionary assertions, even by stringently critical standards.  This is the case with shelled cephalopods, stony corals, and so on...
Investigations of this kind, therefore, are by no means based only on completely isolated, chance finds, as is sometimes assumed by those who do not understand the strict paleontological methodology.
Basic Questions in Paleontology, pp. 103-104 (my emphasis)
---------------------QUOTE-------------------


So Wesley, do you dispute Schindewolf's claim that the fossil record is complete enough in certain areas that "we are entirely capable of arriving at binding evolutionary assertions, even by stringently critical standards"?
Do you dispute that?

I'll also ask you this again:

---------------------QUOTE-------------------
His assertion about exactly what Darwin said aside, Schindewolf's claims about widespread evolutionary patterns of rapid radiation, stasis, and over-specialization are still valid today.  Do you dispute that?
---------------------QUOTE-------------------


Do you Wesley?
Posted by: Daniel Smith on Jan. 27 2008,14:17

Quote (oldmanintheskydidntdoit @ Jan. 27 2008,12:06)
 
Quote (Daniel Smith @ Jan. 27 2008,13:41)
<Snip of typical JAM accusations>
         
Quote (JAM @ Jan. 26 2008,12:25)
It's about evidence, not claims. Does their evidence fill a gap that Schindewolf claimed would not be filled?
---------------------QUOTE-------------------


No it does not.  

---------------------QUOTE-------------------


How do you know, if it was a "dead link", what it may or may not "fill"?
---------------------QUOTE-------------------


You're going to have to try to follow along old man.  

The quote I answered was in regard to the one paper I was able to find on the net - not to the two I was unable to find.
Posted by: oldmanintheskydidntdoit on Jan. 27 2008,14:20

Yeah, for once it's me not paying attention.
Posted by: Wesley R. Elsberry on Jan. 27 2008,15:14

Daniel Smith:

 

---------------------QUOTE-------------------

It would seem Wesley, that you have erected your own strawman to use against Schindewolf.

---------------------QUOTE-------------------



I am taking Schindewolf's words as expressing his opinion and holding him responsible for those because, as even Daniel has had to stipulate, they are demonstrably false. It is Daniel who has been engaging in revisionism in the exchange, seeking some exculpatory out for Schindewolf, and is now reduced to making wild and false accusations of bad behavior on the part of his correspondents.

 

---------------------QUOTE-------------------

You've provided one quote - from a lifetime of work - and concluded (from that one quote) that Schindewolf did not understand Darwin (and by implication - Darwin's theory).

---------------------QUOTE-------------------



My point, in case Daniel missed it, is that Schindewolf misrepresented Darwin. Unable to get around that clear demonstration that Schindewolf is an unreliable guide to prior work, Daniel is having a good go at shifting goalposts again. I think I have been pretty clear concerning the limits I was placing on my discussion; I can't help it if Daniel can't parse that.

 

---------------------QUOTE-------------------

In order to scientifically conclude that Schindewolf did not understand Darwin's theory, it would be necessary to search through his life's work, find every instance where he makes a claim about Darwin's theory, and show that a significant amount of them render that conclusion.

---------------------QUOTE-------------------



Hypocrite. Daniel isn't willing to apply that standard to all the other people whose life's work he is willing to denigrate, sight unseen.

And I haven't said anything about the current validity of Schindewolf's ideas on their own because I haven't thoroughly studied Schindewolf's ideas. Unlike Daniel, I don't care to dismiss stuff on the basis of personal ignorance. As to the completeness of the fossil record, I think that studies by Raup and Foote are more quantitatively based, and far more recent. That said, it sounds like the first two points of "rapid radiation, stasis, and over-specialization" are things that even Darwin discussed, and the third sounds like orthogenesis, which is thoroughly discredited.

On "rapid radiation", Darwin said the following:

 

---------------------QUOTE-------------------

I may here recall a remark formerly made, namely that it might require a long succession of ages to adapt an organism to some new and peculiar line of life, for instance to fly through the air; but that when this had been effected, and a few species had thus acquired a great advantage over other organisms, a comparatively short time would be necessary to produce many divergent forms, which would be able to spread rapidly and widely throughout the world.

---------------------QUOTE-------------------



So that one Schindewolf might have cribbed from Darwin, and so much the worse for Schindewolf if he didn't credit Darwin for it.

On long periods of no change, Darwin said the following:

 

---------------------QUOTE-------------------

Nothing can be effected, unless favourable variations occur, and variation itself is apparently always a very slow process. The process will often be greatly retarded by free intercrossing. Many will exclaim that these several causes are amply sufficient wholly to stop the action of natural selection. I do not believe so. On the other hand, I do believe that natural selection will always act very slowly, often only at long intervals of time, and generally on only a very few of the inhabitants of the same region at the same time. I further believe, that this very slow, intermittent action of natural selection accords perfectly well with what geology tells us of the rate and manner at which the inhabitants of this world have changed. [Charles Darwin, Origin of Species 1st Edition 1859, p.153]

---------------------QUOTE-------------------



So that one Schindewolf might have cribbed from Darwin, and so much the worse for Schindewolf if he didn't credit Darwin for it.

Darwin didn't go any way toward the dead-end of orthogenesis, which is a point to him. If Schindewolf did go that way, so much the worse for him (and according to the Afterword by Wolf Reif, that is exactly the way Schindewolf went).

Another interesting bit comes from the Foreword to Schindewolf's book by Stephen Jay Gould, where he notes that Schindewolf's forcefulness of character inhibited expression of critical views in Germany for many years:  

 

---------------------QUOTE-------------------

Reif ends: "Finally, as late as the 1970s young authors risked censure by their superiors if they discussed typostrophism [Schindewolf's main concept] critically. Under the influence of Schindewolf's authority, evolution was no topic for the would-be paleontologist." I believe I sense some legitimate bitterness in Reif's words.

---------------------QUOTE-------------------



So it seems that when he was at his prime, Schindewolf encouraged stifling dissent from typostrophism and failed to be a role model for any sort of "strengths and weaknesses" blather.


Posted by: Wesley R. Elsberry on Jan. 27 2008,15:16

Vmartin:



---------------------QUOTE-------------------

I would say Darwin said it unambiguously:

---------------------QUOTE-------------------



It pays to read the answer, as well as the question.
Posted by: JAM on Jan. 28 2008,01:23

Quote (Daniel Smith @ Jan. 27 2008,13:41)
<Snip of typical JAM accusations>
---------------------QUOTE-------------------


Why? They're all true. You're afraid of evidence.
 

---------------------QUOTE-------------------
       
Quote (JAM @ Jan. 26 2008,12:25)
It's about evidence, not claims. Does their evidence fill a gap that Schindewolf claimed would not be filled?
---------------------QUOTE-------------------


No it does not.
---------------------QUOTE-------------------


You're lying. Read what that arrogant ass Schindewolf wrote on p. 105-106.  


---------------------QUOTE-------------------
Explain to me specifically, a) which "gap" Schindewolf claimed would never be filled, and b) how their evidence fills it.
---------------------QUOTE-------------------


Schindewolf's arrogant, false claim was GLOBAL, fool, so no specific explanation is needed.

You are an intellectual (and theological) fraud, Dan. You asked for evidence, I pointed you to it, and you moved the goalposts. You never even looked at any of the evidence in that paper. You simply searched for the word "Schindewolf," and made a complete ass of yourself yet again.

I just submitted a manuscript describing multiple tests of a competitor's hypothesis, smashing it to smithereens. His name is not anywhere to be found in the text (I did cite his lab's data, so his papers are cited) so your test (and your utterly dishonest, yet predictable, avoidance of actual evidence) is bogus.



---------------------QUOTE-------------------
<Snip of more typical JAM accusations>
---------------------QUOTE-------------------


They're all true. You started lying in your first post here when you claimed to be interested in evidence, and you've continued to lie at a frantic pace. This is all about your ego, because your fear of evidence shows that you have no faith.
Posted by: clamboy on Jan. 28 2008,01:36

Hey, did anyone else but me note that when the poster known as Daniel Smith provided his quotes from (first name omitted) Darwin, the book he quoted was "Origin of the Species"? Does anyone here know when any particular person with the surname Darwin (Daniel Smith failed to give a first name) wrote a book with that title? He also failed to provide edition number, publisher, ISBN, etc.

Daniel Smith, on the off chance that you have read the book you are quoting ("Origin of the Species"), could you provide this information so that curious readers such as myself could find it and make sure your quotes are accurate? I enjoy reading books on evolution, but I have never seen one by someone with last name Darwin titled "Origin of the Species." It sounds fascinating.
Posted by: VMartin on Jan. 28 2008,15:21

Quote (Wesley R. Elsberry @ Jan. 27 2008,15:16)
Vmartin:

   

---------------------QUOTE-------------------

I would say Darwin said it unambiguously:

---------------------QUOTE-------------------



It pays to read the answer, as well as the question.
---------------------QUOTE-------------------


No problem: I might be wrong. Anyway I don't see the point of the discussion. It is of no importance what Darwin exactly said or didn't say. I would say the point is summarized in the last sentences of his chapter IX:  

 

---------------------QUOTE-------------------

For my part, following out Lyell's metaphor, I look at the natural geological record, as a history of the world imperfectly kept, and written in a changing dialect; of this history we possess the last volume alone, relating only to two or three countries. Of this volume, only here and there a short chapter has been preserved; and of each page, only here and there a few lines. Each word of the slowly-changing language, in which the history is supposed to be written, being more or less different in the interrupted succession of chapters, may represent the apparently abruptly changed forms of life, entombed in our consecutive, but widely separated formations. On this view, the difficulties above discussed are greatly diminished, or even disappear.

---------------------QUOTE-------------------



These words are 150 years old and I don't know they are still correct. Do we really know only short chapters and few lines of the book in 2008?

This is the point I would say Daniel addressed talking about Schindewolf. As far as I can judge Schindewolf was of opinion that some chapters of book we know very well today. And he based his theory on it. This is of interest, not if Schindewolf quoted Darwin correctly or not. Btw I would need to see his exactly words in German.
Posted by: Daniel Smith on Jan. 28 2008,19:10

Quote (Wesley R. Elsberry @ Jan. 27 2008,13:14)
Daniel Smith:

     

---------------------QUOTE-------------------

It would seem Wesley, that you have erected your own strawman to use against Schindewolf.

---------------------QUOTE-------------------



I am taking Schindewolf's words as expressing his opinion and holding him responsible for those because, as even Daniel has had to stipulate, they are demonstrably false. It is Daniel who has been engaging in revisionism in the exchange, seeking some exculpatory out for Schindewolf, and is now reduced to making wild and false accusations of bad behavior on the part of his correspondents.  

---------------------QUOTE-------------------

You've provided one quote - from a lifetime of work - and concluded (from that one quote) that Schindewolf did not understand Darwin (and by implication - Darwin's theory).

---------------------QUOTE-------------------



My point, in case Daniel missed it, is that Schindewolf misrepresented Darwin. Unable to get around that clear demonstration that Schindewolf is an unreliable guide to prior work, Daniel is having a good go at shifting goalposts again. I think I have been pretty clear concerning the limits I was placing on my discussion; I can't help it if Daniel can't parse that.
---------------------QUOTE-------------------


Wesley,

I will give you that Schindewolf made one false claim as to what he believed Darwin's expectations were.  I'll give you that.  Even though I could think of (as you say) exculpatory outs for him, for the sake of argument, I'll concede that point.  

The question now is: Is that it then?  Is there no further discussion of Schindewolf allowed?
     

---------------------QUOTE-------------------
 

---------------------QUOTE-------------------

In order to scientifically conclude that Schindewolf did not understand Darwin's theory, it would be necessary to search through his life's work, find every instance where he makes a claim about Darwin's theory, and show that a significant amount of them render that conclusion.

---------------------QUOTE-------------------



Hypocrite. Daniel isn't willing to apply that standard to all the other people whose life's work he is willing to denigrate, sight unseen.

And I haven't said anything about the current validity of Schindewolf's ideas on their own because I haven't thoroughly studied Schindewolf's ideas. Unlike Daniel, I don't care to dismiss stuff on the basis of personal ignorance.
---------------------QUOTE-------------------


You know what, you're right. I do do that.  I have a tendency to dismiss other people's arguments before I hear them because (of course) I'm right.  I know I'm not right most of the time though and, although it probably doesn't look much like it, I am working on it.
 

---------------------QUOTE-------------------
As to the completeness of the fossil record, I think that studies by Raup and Foote are more quantitatively based, and far more recent. That said, it sounds like the first two points of "rapid radiation, stasis, and over-specialization" are things that even Darwin discussed, and the third sounds like orthogenesis, which is thoroughly discredited.
---------------------QUOTE-------------------


Schindewolf's views on orthogenesis are complicated.  He said that it applies to the typostatic phase of his theory but not to the typogenesis phase.  He discusses this in some detail beginning on page 268 of his book.  Basically he puts forth that the rapid radiation phase can go anywhere, but once it arrives there, it is self-limiting.

 

---------------------QUOTE-------------------
On "rapid radiation", Darwin said the following:

     

---------------------QUOTE-------------------

I may here recall a remark formerly made, namely that it might require a long succession of ages to adapt an organism to some new and peculiar line of life, for instance to fly through the air; but that when this had been effected, and a few species had thus acquired a great advantage over other organisms, a comparatively short time would be necessary to produce many divergent forms, which would be able to spread rapidly and widely throughout the world.

---------------------QUOTE-------------------



So that one Schindewolf might have cribbed from Darwin, and so much the worse for Schindewolf if he didn't credit Darwin for it.
---------------------QUOTE-------------------


Schindewolf held the opposite view.  It was the big changes, i.e. the ability to fly, that came rapidly.  The small changes began after that.

 

---------------------QUOTE-------------------
On long periods of no change, Darwin said the following:

     

---------------------QUOTE-------------------

Nothing can be effected, unless favourable variations occur, and variation itself is apparently always a very slow process. The process will often be greatly retarded by free intercrossing. Many will exclaim that these several causes are amply sufficient wholly to stop the action of natural selection. I do not believe so. On the other hand, I do believe that natural selection will always act very slowly, often only at long intervals of time, and generally on only a very few of the inhabitants of the same region at the same time. I further believe, that this very slow, intermittent action of natural selection accords perfectly well with what geology tells us of the rate and manner at which the inhabitants of this world have changed. [Charles Darwin, Origin of Species 1st Edition 1859, p.153]

---------------------QUOTE-------------------



So that one Schindewolf might have cribbed from Darwin, and so much the worse for Schindewolf if he didn't credit Darwin for it.

---------------------QUOTE-------------------


He expresses agreement with Darwin when it comes to the typostatic phase of evolution.  However, he doesn't seem to hold that the fossil record supports Darwin's claim that "this very slow, intermittent action of natural selection accords perfectly well with what geology tells us of the rate and manner at which the inhabitants of this world have changed."

 

---------------------QUOTE-------------------

Darwin didn't go any way toward the dead-end of orthogenesis, which is a point to him. If Schindewolf did go that way, so much the worse for him (and according to the Afterword by Wolf Reif, that is exactly the way Schindewolf went).

Another interesting bit comes from the Foreword to Schindewolf's book by Stephen Jay Gould, where he notes that Schindewolf's forcefulness of character inhibited expression of critical views in Germany for many years:  

     

---------------------QUOTE-------------------

Reif ends: "Finally, as late as the 1970s young authors risked censure by their superiors if they discussed typostrophism [Schindewolf's main concept] critically. Under the influence of Schindewolf's authority, evolution was no topic for the would-be paleontologist." I believe I sense some legitimate bitterness in Reif's words.

---------------------QUOTE-------------------



So it seems that when he was at his prime, Schindewolf encouraged stifling dissent from typostrophism and failed to be a role model for any sort of "strengths and weaknesses" blather.
---------------------QUOTE-------------------



I'm sure many scientists won't win personality contests.  I also don't see where that's an issue except only peripherally - since Schindewolf's 'reign of terror' could only extend as far as his university in Germany.
Posted by: Daniel Smith on Jan. 28 2008,19:29

Quote (JAM @ Jan. 27 2008,23:23)
   

---------------------QUOTE-------------------
             
Quote (JAM @ Jan. 26 2008,12:25)
It's about evidence, not claims. Does their evidence fill a gap that Schindewolf claimed would not be filled?
---------------------QUOTE-------------------


No it does not.
---------------------QUOTE-------------------


You're lying. Read what that arrogant ass Schindewolf wrote on p. 105-106.  
       

---------------------QUOTE-------------------
Explain to me specifically, a) which "gap" Schindewolf claimed would never be filled, and b) how their evidence fills it.
---------------------QUOTE-------------------


Schindewolf's arrogant, false claim was GLOBAL, fool, so no specific explanation is needed.
---------------------QUOTE-------------------


Schindewolf's claim was global, but it wasn't universal.  It doesn't apply to every phase of every lineage.  It only applies to the very beginnings of types - his typogenesis phase.  I hope you can appreciate the difference.
   

---------------------QUOTE-------------------
You asked for evidence, I pointed you to it, and you moved the goalposts. You never even looked at any of the evidence in that paper. You simply searched for the word "Schindewolf," and made a complete ass of yourself yet again.
---------------------QUOTE-------------------


You're wrong about that.  I looked through the entire paper for the evidence you spoke of.  I did not find it.  The crux of the paper was that the authors believed the evidence supported the "two-lineage" hypothesis over the "one lineage".

Schindewolf sided with the "one-lineage" hypothesis, but made no claim that this represented one of the unbridgeable gaps of his theory.  I thought I already explained that to you?

I think, if you're going to critique Schindewolf, you should maybe follow the advice you gave me a while back and read what he actually said first - instead of quote-mining.
Posted by: Wesley R. Elsberry on Jan. 28 2008,19:36

Daniel Smith, today:



---------------------QUOTE-------------------

I'm sure many scientists won't win personality contests.  I also don't see where that's an issue except only peripherally - since Schindewolf's 'reign of terror' could only extend as far as his university in Germany.

---------------------QUOTE-------------------



Daniel Smith, earlier:



---------------------QUOTE-------------------

This is the reason I have sought out authors such as Berg, Schindewolf, Denton, Davison and others.  First, they are true scientists - there are no religious views expressed in their books.  Second, they hold to no preconceived paradigm and they have (or had) nothing to gain by publishing their views.  Most were either ridiculed or shunned, or just put on a shelf and forgotten, but their works stand the test of time (at least so far).  These are the type of people I want to get my information from.

---------------------QUOTE-------------------



Daniel can scratch Schindewolf off the "ridiculed or shunned" list. Schindewolf was apparently someone who determined whether others were ridiculed or shunned.
Posted by: Wesley R. Elsberry on Jan. 28 2008,19:54

Daniel Smith earlier:



---------------------QUOTE-------------------

You might be in a position to show that he made a false claim, but you must base that on evidence from that time period.

---------------------QUOTE-------------------



Daniel Smith today:



---------------------QUOTE-------------------

I will give you that Schindewolf made one false claim as to what he believed Darwin's expectations were.  I'll give you that.  Even though I could think of (as you say) exculpatory outs for him, for the sake of argument, I'll concede that point.  

The question now is: Is that it then?  Is there no further discussion of Schindewolf allowed?

---------------------QUOTE-------------------



Schindewolf made a false claim. That doesn't stop discussion, but it is certainly something to keep in mind when weighing his reliability.
Posted by: Wesley R. Elsberry on Jan. 28 2008,20:28

Daniel Smith, recently:



---------------------QUOTE-------------------

You've provided one quote - from a lifetime of work - and concluded (from that one quote) that Schindewolf did not understand Darwin (and by implication - Darwin's theory).

---------------------QUOTE-------------------



I just noticed that the quote I critiqued was entered much earlier in the conversation, and Daniel did not excoriate the quoter at the time. Of course, he would have needed a < mirror >...
Posted by: JAM on Jan. 28 2008,22:14

Quote (Daniel Smith @ Jan. 28 2008,19:29)
 
Quote (JAM @ Jan. 27 2008,23:23)
       

---------------------QUOTE-------------------
                 
Quote (JAM @ Jan. 26 2008,12:25)
It's about evidence, not claims. Does their evidence fill a gap that Schindewolf claimed would not be filled?
---------------------QUOTE-------------------


No it does not.
---------------------QUOTE-------------------


You're lying. Read what that arrogant ass Schindewolf wrote on p. 105-106.  
         

---------------------QUOTE-------------------
Explain to me specifically, a) which "gap" Schindewolf claimed would never be filled, and b) how their evidence fills it.
---------------------QUOTE-------------------


Schindewolf's arrogant, false claim was GLOBAL, fool, so no specific explanation is needed.
---------------------QUOTE-------------------


Schindewolf's claim was global, but it wasn't universal.  It doesn't apply to every phase of every lineage.  It only applies to the very beginnings of types - his typogenesis phase.
---------------------QUOTE-------------------


You're lying again. His claim applies to gaps. He does not limit his claim.


---------------------QUOTE-------------------
I hope you can appreciate the difference.
---------------------QUOTE-------------------


I appreciate your predictable dishonesty.


---------------------QUOTE-------------------


---------------------QUOTE-------------------
You asked for evidence, I pointed you to it, and you moved the goalposts. You never even looked at any of the evidence in that paper. You simply searched for the word "Schindewolf," and made a complete ass of yourself yet again.
---------------------QUOTE-------------------


You're wrong about that.  I looked through the entire paper for the evidence you spoke of.  I did not find it.
---------------------QUOTE-------------------


That's not what you wrote. Your argument was that the authors didn't MENTION Schindewolf in such a context. You didn't look at the evidence.


---------------------QUOTE-------------------
The crux of the paper was that the authors believed the evidence supported the "two-lineage" hypothesis over the "one lineage".
---------------------QUOTE-------------------


No, this is not lit crit. The crux of the paper was that the authors SHOWED that the evidence supported two lineages. The salient point in our little disagreement is that they had much more evidence to work with--IOW, they had evidence that Schindewolf claimed would never be obtained.

Schindewolf's dependence on suture morphology is another matter that makes his conclusion even more suspect.


---------------------QUOTE-------------------
Schindewolf sided with the "one-lineage" hypothesis,
---------------------QUOTE-------------------


You're doing lit crit again. Schindewolf claimed that the evidence supported one lineage rather than two. That's not what we're disagreeing about. My point is that Schindewolf claimed that the evidence in his possession was complete. He was wrong.


---------------------QUOTE-------------------
... but made no claim that this represented one of the unbridgeable gaps of his theory.
---------------------QUOTE-------------------


The gaps aren't really part of his theory. He claimed that the gaps in continuity of the fossils he had in hand represented gaps in evolution. His hypothesis utterly depended on his assumption that the evidence was complete, BUT HIS ASSUMPTION WAS WRONG.


---------------------QUOTE-------------------
I thought I already explained that to you?
---------------------QUOTE-------------------


No, you didn't. You can't even distinguish between predictions and hypotheses or between evidence and opinion.

When are you going to test your inadvertent prediction that "hind limb genes" exist, Dan? If they don't exist, doesn't that completely trash your hypothesis about the hierarchical nature of God's design of limb development?


---------------------QUOTE-------------------
I think, if you're going to critique Schindewolf, you should maybe follow the advice you gave me a while back and read what he actually said first - instead of quote-mining.
---------------------QUOTE-------------------


I'm not quote mining anything. I'm pointing out that his fundamental assumption about the evidence is spectacularly false. His hypothesis depends on that assumption.
Posted by: JAM on Jan. 28 2008,22:23

Quote (Daniel Smith @ Jan. 28 2008,19:10)
 
Quote (Wesley R. Elsberry @ Jan. 27 2008,13:14)
Another interesting bit comes from the Foreword to Schindewolf's book by Stephen Jay Gould, where he notes that Schindewolf's forcefulness of character inhibited expression of critical views in Germany for many years:  

       

---------------------QUOTE-------------------

Reif ends: "Finally, as late as the 1970s young authors risked censure by their superiors if they discussed typostrophism [Schindewolf's main concept] critically. Under the influence of Schindewolf's authority, evolution was no topic for the would-be paleontologist." I believe I sense some legitimate bitterness in Reif's words.

---------------------QUOTE-------------------



So it seems that when he was at his prime, Schindewolf encouraged stifling dissent from typostrophism and failed to be a role model for any sort of "strengths and weaknesses" blather.
---------------------QUOTE-------------------



I'm sure many scientists won't win personality contests.  I also don't see where that's an issue except only peripherally - since Schindewolf's 'reign of terror' could only extend as far as his university in Germany.
---------------------QUOTE-------------------


Your reflexive mendacity is amazing. So, if Schindewolf's influence was confined entirely to his own university as you claim, you must have evidence that he:

1) Never reviewed any manuscripts from authors at other universities.
2) Never was asked for a tenure recommendation letter from tenure committees at any other universities.
3) Never wrote a letter of recommendation for a student or colleague to any university but his own.

Since all of those are negatives, you must have done an exhaustive search before (ethically) making such a grand claim.

Do you have any evidence that any of the above conditions existed, or were you simply talking out of your pompous hind end again?
Posted by: oldmanintheskydidntdoit on Jan. 29 2008,03:09

Daniel,
lets pretend for the sake of argument you've "won".

You've "proved" your point, whatever it is. As far as I can tell, your point is that some author you've fixated upon was not 100% totally wrong about everything ever.

Now what? What changes? What have you achieved?

Perhaps we could go back to the initial subject?

To wit: the evolution of the horse, a problem for the Darwismius?

Do you think you've now shown horse evolution is impossible?
Posted by: mitschlag on Jan. 29 2008,07:10

Quote (JAM @ Jan. 28 2008,22:23)
Your reflexive mendacity is amazing. So, if Schindewolf's influence was confined entirely to his own university as you claim, you must have evidence that he:

1) Never reviewed any manuscripts from authors at other universities.
2) Never was asked for a tenure recommendation letter from tenure committees at any other universities.
3) Never wrote a letter of recommendation for a student or colleague to any university but his own.

Since all of those are negatives, you must have done an exhaustive search before (ethically) making such a grand claim.

Do you have any evidence that any of the above conditions existed, or were you simply talking out of your pompous hind end again?
---------------------QUOTE-------------------


Not necessarily pompous.

Inexperienced and uninformed, more likely.
Posted by: JAM on Jan. 29 2008,15:01

Quote (mitschlag @ Jan. 29 2008,07:10)
Quote (JAM @ Jan. 28 2008,22:23)
Your reflexive mendacity is amazing. So, if Schindewolf's influence was confined entirely to his own university as you claim, you must have evidence that he:

1) Never reviewed any manuscripts from authors at other universities.
2) Never was asked for a tenure recommendation letter from tenure committees at any other universities.
3) Never wrote a letter of recommendation for a student or colleague to any university but his own.

Since all of those are negatives, you must have done an exhaustive search before (ethically) making such a grand claim.

Do you have any evidence that any of the above conditions existed, or were you simply talking out of your pompous hind end again?
---------------------QUOTE-------------------


Not necessarily pompous.
---------------------QUOTE-------------------


All the evidence points to it, though.

As Wes pointed out, Daniel is perfectly willing to denigrate the life's work of thousands of people, while rationalizing Schindewolf's misrepresentation of Darwin, only because Schindewolf's hypothesis appeals to his particularly offensive twisting of Christian theology.


---------------------QUOTE-------------------
Inexperienced and uninformed, more likely.
---------------------QUOTE-------------------


Absolutely, but I've found that those two qualities tend to be highly associated with pomposity.
Posted by: Daniel Smith on Jan. 29 2008,18:06

Quote (Wesley R. Elsberry @ Jan. 28 2008,18:28)
Daniel Smith, recently:

 

---------------------QUOTE-------------------

You've provided one quote - from a lifetime of work - and concluded (from that one quote) that Schindewolf did not understand Darwin (and by implication - Darwin's theory).

---------------------QUOTE-------------------



I just noticed that the quote I critiqued was entered much earlier in the conversation, and Daniel did not excoriate the quoter at the time. Of course, he would have needed a < mirror >...
---------------------QUOTE-------------------


Or I would have had to know that Darwin never said that.
Posted by: Daniel Smith on Jan. 29 2008,18:53

Wesley,

Here is how Schindewolf counters Darwin's claim that we can't expect to find many transitionals because the fossil record is incomplete:      

---------------------QUOTE-------------------
Investigations of this kind, therefore, are by no means based only on completely isolated, chance finds...
when the fossil contents of two successive massive beds are compared, we are confronted with three different kinds of situations with regard to individual forms:

1. We observe species that have not undergone transformation; they pass from the older to the younger strata unchanged.

2. Other forms from younger horizons differ from those of the older ones, but the modifications are insignificant in nature.  The forms link up with the preceding species so closely that they can be interpreted as being direct descendants that have undergone transformation in small individual steps.  This transformation usually continues in subsequent strata, and what we have, then, is a closed, uninterrupted series showing gradual, smooth transformation.

3. In addition, but much less frequently, we come across forms here and there that are quite different from any other form previously present, forms that are not connected in an unbroken line with previous ones but rather appear suddenly as new designs.

And these are by no means just isolated occurrences; these strange new forms are usually also represented by large numbers of individuals.  Nonetheless, there is no connecting link with the stock from which they derived.  The continuity of the other species gives us no reason to suspect interruptions in the deposition of the layers, or subsequent destruction of layers already deposited, which, furthermore, would be revealed by other geological criteria.  Nothing is missing here, and even drastic changes in living conditions are excluded, for the facies remain the same.

Further, when we see this situation repeated in all stratigraphic sequences of the same time period all over the world... we cannot resort to attributing this phenomenon to immigration of the new type from areas not yet investigated, where perhaps a gradual, slowly progressing evolution had taken place. What we have here must be primary discontinuities, natural evolutionary leaps, and not circumstantial accidents of discovery and gaps in the fossil record
Otto H. Schindewolf, "Basic Questions in Paleontology" pp 104-105 (emphasis his)
---------------------QUOTE-------------------



I'd like to draw your attention especially to item 2 in his list - the abundant evidence for smooth, gradual transitional evolution - which actually runs in parallel to these infrequent appearances of new forms; acting as a kind of control (if I'm using that term correctly) for the data.

And for you JAM:
       

---------------------QUOTE-------------------
It is true that we know of countless lineages with continuous transformation, in as uninterrupted a sequence as could be desired.  However, each time we go back to the beginning of these consistent, abundantly documented series, we stand before an unbridgeable gulf.  The series break off and do not lead beyond the boundaries of their own particular structural type.  The link connecting them is not discernible; the individual structural designs stand apart, beside one another or in sequence, without true transitional forms"
ibid, pp 102-103
---------------------QUOTE-------------------


The only "gaps" Schindewolf was concerned with were at the beginning of a "structural type".  He makes that abundantly clear throughout the book.  Furthermore, since Schindewolf had already mapped out a line of descent for the hammatoceratins, this cannot constitute one of his "gaps".
Posted by: Daniel Smith on Jan. 29 2008,19:09

Quote (oldmanintheskydidntdoit @ Jan. 29 2008,01:09)
Daniel,
lets pretend for the sake of argument you've "won".

You've "proved" your point, whatever it is. As far as I can tell, your point is that some author you've fixated upon was not 100% totally wrong about everything ever.

Now what? What changes? What have you achieved?

Perhaps we could go back to the initial subject?

To wit: the evolution of the horse, a problem for the Darwismius?

Do you think you've now shown horse evolution is impossible?
---------------------QUOTE-------------------


The evolution of the horse was never said to be impossible.  (Again old man, please try to follow along)
Schindewolf believed the horse to be one of the best evidenced examples of smooth, gradual, transitional, mammalian evolution of the type Darwin theorized - with just one minor exception; he felt the development of the horse's toes showed a definite direction.
IOW, the 'toes fit for running on the plains' came first, the 'plains to run on' came later.

Unfortunately, that was the example I was using over at Brainstorms when Alan Fox invited me here, and he decided to make that the subject of this thread - though it is definitely not the focus of Schindewolf's book.
This was all discussed earlier in this thread.

But to answer your question: If I've "won", what I've done is introduced you to the works of Otto Schindewolf and Leo Berg, shown you that Darwin's is not the only theory out there with the word "evolution" in it, and hopefully expanded your horizons a bit.
Posted by: blipey on Jan. 29 2008,19:59

Alright, let me see if I have the argument correct:

1.  Schindewolf only proposes gaps at the "beginning of types".

Q.  Does this mean he believed in special creation of these types?  Are you arguing for special creation of types? That's the kind of reasoning it seems to be.  presumably the horse is a type.  At the beginning, you're saying that there is a gap.  For surely the horse had an ancestor, right?  If the horse did have an ancestor, then there is a gap--and it is not in the beginning.  If the horse did not have an ancestor, you must be arguing for special creation.

2.  The fossil record is a complete record of all life on earth-ever.  There are no gaps in the fossil record, because everything that ever lived fossilized.

Q.  If this is indeed the argument, do you have evidence that everything that ever lived fossilized?  If not, how can you say what once lived and what did not?  If so, could you please present the data for rate of fossilization.

edited: punctuation
Posted by: Henry J on Jan. 29 2008,20:32

That sounds like sometimes a type will develop in relatively small numbers, or in areas in which fossilization is less likely than elsewhere, and then become successful and spread. But then I'm no expert, so my guess could be wrong.

Henry
Posted by: oldmanintheskydidntdoit on Jan. 30 2008,03:17

Quote (Daniel Smith @ Jan. 29 2008,19:09)
But to answer your question: If I've "won", what I've done is introduced you to the works of Otto Schindewolf and Leo Berg, shown you that Darwin's is not the only theory out there with the word "evolution" in it, and hopefully expanded your horizons a bit.
---------------------QUOTE-------------------


Round of applause.

Clap

Clap

Clap

See, I can be condescending too. Not that it's worth it with you.

So, Daniel, is it your understanding that the fossil record has a record of every thing that ever lived?



---------------------QUOTE-------------------
I'd like to draw your attention especially to item 2 in his list - the abundant evidence for smooth, gradual transitional evolution - which actually runs in parallel to these infrequent appearances of new forms; acting as a kind of control (if I'm using that term correctly) for the data.
---------------------QUOTE-------------------



So, item A, a smooth, gradual transitional set of fossils.
Item B,  infrequent appearances of new fossil forms.

Both items have the same chance of being preserved (100%?) and as item B shows "jumps" that's proof of intervention by an external force (your god)? As Item A does not show the same "jumps" you conclude that god interfered with the development of item B but not A? Why? Why not interfere with both? Does logic even stand a chance here?

Is that it? Is that your understanding?
Posted by: oldmanintheskydidntdoit on Jan. 30 2008,04:26

Quote (Daniel Smith @ Jan. 29 2008,19:09)
IOW, the 'toes fit for running on the plains' came first, the 'plains to run on' came later.
---------------------QUOTE-------------------


Just to clarify, which of the following options best represents your position here?

a) god knew that horses might need "toes for running on the plains" before there were plains, and LO! It was so.

b) Another explanation that does not require supernatural intervention in any way shape or form?

Seems to me you are eager to posit divine intervention at the slightest opportunity.

Daniel, do you believe that there *can* be a explanation for the toes that does not require supernatural intervention?
Posted by: mitschlag on Jan. 30 2008,05:40

Quote (Daniel Smith @ Jan. 29 2008,19:09)
Schindewolf believed the horse to be one of the best evidenced examples of smooth, gradual, transitional, mammalian evolution of the type Darwin theorized - with just one minor exception; he felt the development of the horse's toes showed a definite direction.
IOW, the 'toes fit for running on the plains' came first, the 'plains to run on' came later.
---------------------QUOTE-------------------


Surely that is one of the stupidest things that Schindewolf might have said.

I find it hard to believe that he made such an insane claim.

Exact quotation, please, with literature citation.

(The backlog of unsupported claims by Daniel is enormous and keeps growing.)
Posted by: oldmanintheskydidntdoit on Jan. 30 2008,06:33

Daniel, presumably you've read
< Hen's Teeth and Horses' Toes >
?
Posted by: mitschlag on Jan. 30 2008,15:54

Quote (Daniel Smith @ Jan. 29 2008,19:09)
But to answer your question: If I've "won", what I've done is introduced you to the works of Otto Schindewolf and Leo Berg, shown you that Darwin's is not the only theory out there with the word "evolution" in it, and hopefully expanded your horizons a bit.
---------------------QUOTE-------------------


Condescension also noted from this quarter.

What's been accomplished so far is a display of the irrelevance of the archaic, muddled ideas of a few individuals whose predictions have been unconfirmed and whose theories have been discredited.

Of historical and forensic interest, to be sure.  I'm enjoying the autopsy, thanks.
Posted by: Daniel Smith on Jan. 30 2008,18:54

Quote (blipey @ Jan. 29 2008,17:59)
Alright, let me see if I have the argument correct:

1.  Schindewolf only proposes gaps at the "beginning of types".
---------------------QUOTE-------------------


True.


---------------------QUOTE-------------------
Q.  Does this mean he believed in special creation of these types?
---------------------QUOTE-------------------


No,  he most explicitly did not.  


---------------------QUOTE-------------------
Are you arguing for special creation of types? That's the kind of reasoning it seems to be.
---------------------QUOTE-------------------


I have not argued for that on this thread.  

---------------------QUOTE-------------------
presumably the horse is a type.  At the beginning, you're saying that there is a gap.  For surely the horse had an ancestor, right?  If the horse did have an ancestor, then there is a gap--and it is not in the beginning.  If the horse did not have an ancestor, you must be arguing for special creation.
---------------------QUOTE-------------------


The horse had an ancestor - it's just that the evolution of the 'horse type' from this ancestor cannot be explained in terms of Darwinian evolution.  It required a leap of the kind both Schindewolf and Goldschmidt proposed independently of one another.


---------------------QUOTE-------------------
2.  The fossil record is a complete record of all life on earth-ever.  There are no gaps in the fossil record, because everything that ever lived fossilized.
---------------------QUOTE-------------------


Totally wrong.  Apparently you haven't read any of the Schindewolf quotes I've posted here.



---------------------QUOTE-------------------
Q.  If this is indeed the argument, do you have evidence that everything that ever lived fossilized?  If not, how can you say what once lived and what did not?  If so, could you please present the data for rate of fossilization.

edited: punctuation
---------------------QUOTE-------------------


Go back and read what I've already posted please.
Posted by: Daniel Smith on Jan. 30 2008,18:56

Quote (oldmanintheskydidntdoit @ Jan. 30 2008,01:17)
 
Quote (Daniel Smith @ Jan. 29 2008,19:09)
But to answer your question: If I've "won", what I've done is introduced you to the works of Otto Schindewolf and Leo Berg, shown you that Darwin's is not the only theory out there with the word "evolution" in it, and hopefully expanded your horizons a bit.
---------------------QUOTE-------------------


Round of applause.

Clap

Clap

Clap

See, I can be condescending too. Not that it's worth it with you.

So, Daniel, is it your understanding that the fossil record has a record of every thing that ever lived?

   

---------------------QUOTE-------------------
I'd like to draw your attention especially to item 2 in his list - the abundant evidence for smooth, gradual transitional evolution - which actually runs in parallel to these infrequent appearances of new forms; acting as a kind of control (if I'm using that term correctly) for the data.
---------------------QUOTE-------------------



So, item A, a smooth, gradual transitional set of fossils.
Item B,  infrequent appearances of new fossil forms.

Both items have the same chance of being preserved (100%?) and as item B shows "jumps" that's proof of intervention by an external force (your god)? As Item A does not show the same "jumps" you conclude that god interfered with the development of item B but not A? Why? Why not interfere with both? Does logic even stand a chance here?

Is that it? Is that your understanding?
---------------------QUOTE-------------------


Not even close.
Posted by: Daniel Smith on Jan. 30 2008,19:06

Quote (mitschlag @ Jan. 30 2008,03:40)
   
Quote (Daniel Smith @ Jan. 29 2008,19:09)
Schindewolf believed the horse to be one of the best evidenced examples of smooth, gradual, transitional, mammalian evolution of the type Darwin theorized - with just one minor exception; he felt the development of the horse's toes showed a definite direction.
IOW, the 'toes fit for running on the plains' came first, the 'plains to run on' came later.
---------------------QUOTE-------------------


Surely that is one of the stupidest things that Schindewolf might have said.

I find it hard to believe that he made such an insane claim.

Exact quotation, please, with literature citation.
---------------------QUOTE-------------------


It's already been discussed in this thread - beginning < here >.
The quote is there too.
 

---------------------QUOTE-------------------
(The backlog of unsupported claims by Daniel is enormous and keeps growing.)
---------------------QUOTE-------------------


Such as?
Posted by: blipey on Jan. 30 2008,22:37

I have read a great deal of this thread and specifically I certainly read the quote of Schindewolf from 104-105.  It seems that this entire argument rests on a comparison:

that of a fossil progression with very many attributable steps vs. that of a fossil progression with not so many steps.

The only way this works is if we are very sure that everything that ever lived fossilized or that we know specifically what lived and the percentage of each thing that fossilized.  That sort of begs the question though.

So, how do you know that the fossil record is a complete record of everything that lived in both fossil progressions?
Posted by: oldmanintheskydidntdoit on Jan. 31 2008,02:54

Quote (oldmanintheskydidntdoit @ Jan. 30 2008,04:26)
 
Quote (Daniel Smith @ Jan. 29 2008,19:09)
IOW, the 'toes fit for running on the plains' came first, the 'plains to run on' came later.
---------------------QUOTE-------------------


Just to clarify, which of the following options best represents your position here?

a) god knew that horses might need "toes for running on the plains" before there were plains, and LO! It was so.

b) Another explanation that does not require supernatural intervention in any way shape or form?

Seems to me you are eager to posit divine intervention at the slightest opportunity.

Daniel, do you believe that there *can* be a explanation for the toes that does not require supernatural intervention?
---------------------QUOTE-------------------


So, you've chosen option A)

ok, least we know where you stand.

EDIT: The quote in question that shows Daniel has chosen option A.



---------------------QUOTE-------------------
To this extent,the one toed horse must be regarded as the ideal running animal of the plains. It's early Tertiary ancestors had four digits on the front feet and three on the hind feet, and low crowned cheek teeth. Since in the later Tertiary, an expansion of plains at the expense of forests has been observed, this change in environmental conditions and the consequent change in the mode of life has been represented as the cause of linear, progressive selection leading up to the modern horse.
However, in the formulation of this view, not enough consideration has been given to the fact that the evolutionary trend of reduction in the number of toes had already been introduced long before the plains were occupied in the early Tertiary by the precursors of the horse; these inhabited dense scrub, meaning that they lived in an environment where the reduction of the primitive five-toed protoungulate foot was not an advantage at all. In the descendants, then, the rest of the lateral toes degenerated and the teeth grew longer step by step... regardless of the mode of life, which... fluctuated repeatedly, with habitats switching around among forests, savannas, shrubby plains, tundra, and so on.
If selection alone were decisive in this specialization trend, we would have to ascribe to it a completely incomprehensible purposefulness...
---------------------QUOTE-------------------



EDIT EDIT: So, Daniel, where is this time machine that was used to go back and determine all of this? If it's not available could you point us towards the physical evidence for the proposition above? The actual evidence, if it exists, should still exist today in the fossil record. Please tell me where I can view it for myself.
Posted by: mitschlag on Jan. 31 2008,09:53

Quote (Daniel Smith @ Jan. 30 2008,19:06)
             
Quote (mitschlag @ Jan. 30 2008,03:40)
                   
Quote (Daniel Smith @ Jan. 29 2008,19:09)
Schindewolf believed the horse to be one of the best evidenced examples of smooth, gradual, transitional, mammalian evolution of the type Darwin theorized - with just one minor exception; he felt the development of the horse's toes showed a definite direction.
IOW, the 'toes fit for running on the plains' came first, the 'plains to run on' came later.
---------------------QUOTE-------------------


Surely that is one of the stupidest things that Schindewolf might have said.

I find it hard to believe that he made such an insane claim.

Exact quotation, please, with literature citation.
---------------------QUOTE-------------------


It's already been discussed in this thread - beginning < here >.
The quote is there too.
---------------------QUOTE-------------------


Beautiful.

Schindewolf in his own words:      

---------------------QUOTE-------------------
However, in the formulation of this view, not enough consideration has been given to the fact that the evolutionary trend of reduction in the number of toes had already been introduced long before the plains were occupied in the early Tertiary by the precursors of the horse;
---------------------QUOTE-------------------


As honestly construed by Daniel:      

---------------------QUOTE-------------------
IOW, the 'toes fit for running on the plains' came first, the 'plains to run on' came later.
---------------------QUOTE-------------------


So, Schindewolf saw a trend, and Daniel sees a fait accompli.

It's all moot, anyway, being unsupported by the < evidence >:

   

---------------------QUOTE-------------------
Adaptive radiation of a beloved icon. Phylogeny, geographic distribution, diet, and body sizes of the Family Equidae over the past 55 My. The vertical lines represent the actual time ranges of equid genera or clades. The first ~35 My (Eocene to early Miocene) of horse phylogeny are characterized by browsing species of relatively small body size. The remaining ~20 My (middle Miocene until the present day) are characterized by genera that are either primarily browsing/grazing or are mixed feeders, exhibiting a large diversification in body size. Horses became extinct in North America about 10,000 years ago, and were subsequently reintroduced by humans during the 16th century. Yet the principal diversification of this family occurred in North America. Although the phylogenetic tree of the Equidae has retained its "bushy" form since the 19th century [for example, see (2, 3)], advances in knowledge from fossils have refined the taxonomy, phylogenetic interrelationships, chronology, and interpretations of the ancient ecology of fossil horses.
---------------------QUOTE-------------------


Note especially the symbols representing feeding patterns in relation to the geologic time-scale.
Posted by: mitschlag on Jan. 31 2008,10:06

Quote (Daniel Smith @ Jan. 30 2008,19:06)
     

---------------------QUOTE-------------------
(The backlog of unsupported claims by Daniel is enormous and keeps growing.)
---------------------QUOTE-------------------


Such as?
---------------------QUOTE-------------------


Of recent memory, see < here >, < here > and < here >.
Posted by: JAM on Jan. 31 2008,11:21

Quote (mitschlag @ Jan. 31 2008,09:53)
It's all moot, anyway, being unsupported by the < evidence >:
---------------------QUOTE-------------------


Daniel doesn't do evidence, despite his claim on arrival that he was interested in evidence.

Only opinions that support his prejudices are elevated in his narrow mind.
Posted by: Wesley R. Elsberry on Jan. 31 2008,13:35

Schindewolf:



---------------------QUOTE-------------------

Further, when we see this situation repeated in all stratigraphic sequences of the same time period all over the world... we cannot resort to attributing this phenomenon to immigration of the new type from areas not yet investigated, where perhaps a gradual, slowly progressing evolution had taken place. What we have here must be primary discontinuities, natural evolutionary leaps, and not circumstantial accidents of discovery and gaps in the fossil record

---------------------QUOTE-------------------



The bolded part is exactly what punctuated equilibria says most transitions are like. And Eldredge and Gould presented two such examples of transitions found in highly localized spots, taking about ten pages of their 1972 essay on the topic. They said there that the geographic component is of more significance than the stratigraphic component. It looks like Schindewolf was wrong there, too.

I think that we've already established that the simplistic rendition of Darwin's arguments concerning fossils is erroneous. There's no reason, other than mental handicap, for people to keep repeating it as if it were accurate.
Posted by: Daniel Smith on Jan. 31 2008,18:52

Quote (blipey @ Jan. 30 2008,20:37)
I have read a great deal of this thread and specifically I certainly read the quote of Schindewolf from 104-105.  It seems that this entire argument rests on a comparison:

that of a fossil progression with very many attributable steps vs. that of a fossil progression with not so many steps.

The only way this works is if we are very sure that everything that ever lived fossilized or that we know specifically what lived and the percentage of each thing that fossilized.  That sort of begs the question though.

So, how do you know that the fossil record is a complete record of everything that lived in both fossil progressions?
---------------------QUOTE-------------------


Maybe a picture will help:

------------------------------------------------------------------

First let me specify that this is not from Schindewolf.  This image was used on this thread by creeky belly < here >.
Notice first, the thickness of the vertical lines - which represent the number of families.  These vertical lines are the graphical representation of the slow, gradual evolution similar to what Darwin theorized.  The evidence for these small gradual changes are so abundant that Schindewolf was able to document such things as the evolution of shell suture lines - even to the early stages of ontogeny.

Now let me draw your attention to the horizontal lines.  These are labeled by the authors "Suggested lines of descent".  And why are they "suggested"?  Because there are still no known transitionals.  It is these horizontal lines that represent Schindewolf's "gaps".  Notice also that the dotted lines appear only at the beginnings of new types - just as Schindewolf said.

Now as to your contention that every creature must be fossilized to know what happened:
When Schindewolf said this:    

---------------------QUOTE-------------------
Investigations of this kind, therefore, are by no means based only on completely isolated, chance finds...
when the fossil contents of two successive massive beds are compared, we are confronted with three different kinds of situations with regard to individual forms:

1. We observe species that have not undergone transformation; they pass from the older to the younger strata unchanged.

2. Other forms from younger horizons differ from those of the older ones, but the modifications are insignificant in nature.  The forms link up with the preceding species so closely that they can be interpreted as being direct descendants that have undergone transformation in small individual steps.  This transformation usually continues in subsequent strata, and what we have, then, is a closed, uninterrupted series showing gradual, smooth transformation.

3. In addition, but much less frequently, we come across forms here and there that are quite different from any other form previously present, forms that are not connected in an unbroken line with previous ones but rather appear suddenly as new designs.

And these are by no means just isolated occurrences; these strange new forms are usually also represented by large numbers of individuals.  Nonetheless, there is no connecting link with the stock from which they derived.  The continuity of the other species gives us no reason to suspect interruptions in the deposition of the layers, or subsequent destruction of layers already deposited, which, furthermore, would be revealed by other geological criteria.  Nothing is missing here, and even drastic changes in living conditions are excluded, for the facies remain the same.


Further, when we see this situation repeated in all stratigraphic sequences of the same time period all over the world... we cannot resort to attributing this phenomenon to immigration of the new type from areas not yet investigated, where perhaps a gradual, slowly progressing evolution had taken place. What we have here must be primary discontinuities, natural evolutionary leaps, and not circumstantial accidents of discovery and gaps in the fossil record
Otto H. Schindewolf, "Basic Questions in Paleontology" pp 104-105 (italics his - bold and underlines mine)
---------------------QUOTE-------------------



The first two situations he describes are represented by the vertical lines in the graph, the third by the beginnings of a new type - connected by the horizontal lines.

Notice also that the horizontal lines sometimes come out of the middle of a vertical line?  See how the Belemnoids and Nautilida begin from the middle of the Nautiloids?  What this means is that the fossil record shows clearly the gradual evolution in small increments that was going on in the middle of the Nautiloid's "run", but fails to show the rapid evolution or large steps required to evolve the Belemnoids and Nautilida from the Nautiloids.

Why is this?  Why does the fossil record show clear, uninterrupted, gradual evolution once a new type appears, yet fail to record the beginnings of any of these types?   Can you answer this?  Especially since "these strange new forms are usually also represented by large numbers of individuals".  So, it's not like there's a spattering here and there and eventually an increase.  Types begin in large numbers.

This is why Schindewolf - a paleontologist - came up with his theory of saltational evolution for the beginnings of types.
Posted by: Daniel Smith on Jan. 31 2008,19:06

Quote (mitschlag @ Jan. 31 2008,07:53)
Schindewolf in his own words:          

---------------------QUOTE-------------------
However, in the formulation of this view, not enough consideration has been given to the fact that the evolutionary trend of reduction in the number of toes had already been introduced long before the plains were occupied in the early Tertiary by the precursors of the horse;
---------------------QUOTE-------------------


As honestly construed by Daniel:          

---------------------QUOTE-------------------
IOW, the 'toes fit for running on the plains' came first, the 'plains to run on' came later.
---------------------QUOTE-------------------


So, Schindewolf saw a trend, and Daniel sees a fait accompli.

It's all moot, anyway, being unsupported by the < evidence >:

       

---------------------QUOTE-------------------
Adaptive radiation of a beloved icon. Phylogeny, geographic distribution, diet, and body sizes of the Family Equidae over the past 55 My. The vertical lines represent the actual time ranges of equid genera or clades. The first ~35 My (Eocene to early Miocene) of horse phylogeny are characterized by browsing species of relatively small body size. The remaining ~20 My (middle Miocene until the present day) are characterized by genera that are either primarily browsing/grazing or are mixed feeders, exhibiting a large diversification in body size. Horses became extinct in North America about 10,000 years ago, and were subsequently reintroduced by humans during the 16th century. Yet the principal diversification of this family occurred in North America. Although the phylogenetic tree of the Equidae has retained its "bushy" form since the 19th century [for example, see (2, 3)], advances in knowledge from fossils have refined the taxonomy, phylogenetic interrelationships, chronology, and interpretations of the ancient ecology of fossil horses.
---------------------QUOTE-------------------


Note especially the symbols representing feeding patterns in relation to the geologic time-scale.
---------------------QUOTE-------------------


I don't see anything in this graph or in its description that contradicts Schindewolf.  In fact, all the older species (until 25MY ago) were "mostly browsers" - just like Schindewolf said.  And, since the reduction in toes began then, Schindewolf is again proved correct by modern evidence.
Posted by: JAM on Jan. 31 2008,21:48

Quote (Daniel Smith @ Jan. 29 2008,18:53)

And for you JAM:
         

---------------------QUOTE-------------------
It is true that we know of countless lineages with continuous transformation, in as uninterrupted a sequence as could be desired.  However, each time we go back to the beginning of these consistent, abundantly documented series, we stand before an unbridgeable gulf.  The series break off and do not lead beyond the boundaries of their own particular structural type.  The link connecting them is not discernible; the individual structural designs stand apart, beside one another or in sequence, without true transitional forms"
ibid, pp 102-103
---------------------QUOTE-------------------


The only "gaps" Schindewolf was concerned with were at the beginning of a "structural type".  He makes that abundantly clear throughout the book.  Furthermore, since Schindewolf had already mapped out a line of descent for the hammatoceratins, this cannot constitute one of his "gaps".
---------------------QUOTE-------------------


Sure it does. The additional evidence (which, remember, Schindewolf claimed would never be found because it did not exist) supporting two lineages over one eliminates at least two of his vaunted gaps.
Posted by: JAM on Jan. 31 2008,22:11

Quote (Daniel Smith @ Jan. 31 2008,19:06)

I don't see anything in this graph or in its description that contradicts Schindewolf.
---------------------QUOTE-------------------


Yeah, just like you saw introns as coding sequences for no valid reason, and when you were corrected, you retreated to the lie of not seeing anything that contradicted your perverted theological views, which are so important to you that you will justify violating the Commandment against bearing false witness.


---------------------QUOTE-------------------
In fact, all the older species (until 25MY ago) were "mostly browsers" - just like Schindewolf said.  And, since the reduction in toes began then, Schindewolf is again proved correct by modern evidence.
---------------------QUOTE-------------------


Um, Dan, Schindewolf's claim was about the EARLY Tertiary. 25MY ago was not in the early Tertiary. < The early Tertiary was 65MY ago. >

You'll fudge anything, won't you?
Posted by: Albatrossity2 on Feb. 01 2008,07:03

Quote (Daniel Smith @ Jan. 31 2008,18:52)
Why is this?  Why does the fossil record show clear, uninterrupted, gradual evolution once a new type appears, yet fail to record the beginnings of any of these types?   Can you answer this?  Especially since "these strange new forms are usually also represented by large numbers of individuals".  So, it's not like there's a spattering here and there and eventually an increase.  Types begin in large numbers.
---------------------QUOTE-------------------


Oh, I don't know, Daniel. But I'll take a guess, based on the framework of the theory of evolution.

Maybe specimens of "new types", which are generated by mutations, are incredibly rare, just like the mutations that generate them. Maybe the few organisms that constitute a "new type" by your definition, never got fossilized, or maybe we haven't found the fossils. Maybe this happened in a region of the oceans where fossilization was not optimal. Maybe there were fossils of these "new types" but they were destroyed by later geological processes. Or maybe a real paleontologist who is still reading your wretched notions can come up with even more explanations than I can, since I am just a biochemist/cell biologist.

As asked earlier on this thread, do you think everything gets fossilized, or that paleontologists have found ALL of the fossils? Are you really so determined to buttress your faith that you have convinced yourself of those laughable notions?
Posted by: Wesley R. Elsberry on Feb. 01 2008,07:26

As to the completeness of the fossil record, let us consider the passenger pigeon. < Reports exist > of the sky being darkened for days by flocks of these birds during their migrations, so they existed in large numbers, and in areas where people have looked for fossils.

And now consider the number of fossilized passenger pigeons accessioned in the collections of paleontologists.



---------------------QUOTE-------------------

  Abundance and distribution of fossil Passenger Pigeons is at best speculative because of the paucity of the data. Only with additional fossil records, such as this one, can a more realistic interpretation of data be made.

---------------------QUOTE-------------------



That from a report of the third partial fossil of a passenger pigeon from the western United States.
Posted by: oldmanintheskydidntdoit on Feb. 01 2008,07:32

Quote (Daniel Smith @ Jan. 31 2008,19:06)
I don't see anything in this graph or in its description that contradicts Schindewolf.
---------------------QUOTE-------------------


Why don't you tell us, in your own words, what this graph represents and what conclusions can be drawn from it?

It's not that I don't believe you know what you are talking about, it's just that I don't believe you know what you are talking about.

Daniel, why did god make horses have toes that were suitable for plains when he could have just adjusted the landscape to fit with the toes as they initially were created? That would appear to make more "sense". Otherwise why not create them in the first place with the right sort of toe for the environment they were in? Or does your god not know what he's going to be doing next week?
Posted by: mitschlag on Feb. 01 2008,08:15

Quote (Daniel Smith @ Jan. 31 2008,19:06)
I don't see anything in this graph or in its description that contradicts Schindewolf.  In fact, all the older species (until 25MY ago) were "mostly browsers" - just like Schindewolf said.  And, since the reduction in toes began then, Schindewolf is again proved correct by modern evidence.
---------------------QUOTE-------------------


Once again, Daniel faces away from the target, takes careful aim, and misses.

No one is disputing the observation that < Hyracotherium > (early Eocene, about 55 mya) displayed a reduction in the sizes of some digits.

At issue is Schindewolf's claim:            

---------------------QUOTE-------------------
In the descendants, then, the rest of the lateral toes degenerated and the teeth grew longer step by step... regardless of the mode of life, which... fluctuated repeatedly, with habitats switching around among forests, savannas, shrubby plains, tundra, and so on.
If selection alone were decisive in this specialization trend, we would have to ascribe to it a completely incomprehensible purposefulness...
---------------------QUOTE-------------------


as honestly construed by Daniel:        

---------------------QUOTE-------------------
IOW, the 'toes fit for running on the plains' came first, the 'plains to run on' came later.
---------------------QUOTE-------------------


Consider that by the late Eocene and early Oligocene (32–24 mya), grasslands were becoming abundant, yet Mesohippus still had three-toed feet.
 So, "mode of life" was already changing long before the reduction of digits to Schindewolf's one-toed horse:            

---------------------QUOTE-------------------
To this extent, the one toed horse must be regarded as the ideal running animal of the plains.
---------------------QUOTE-------------------


Schindewolf is artificially selective about "giving enough consideration" to facts that don't favor his criticism of the evolutionary power of natural selection.
Posted by: Daniel Smith on Feb. 01 2008,19:02

Quote (JAM @ Jan. 31 2008,19:48)
             
Quote (Daniel Smith @ Jan. 29 2008,18:53)

And for you JAM:
                         

---------------------QUOTE-------------------
It is true that we know of countless lineages with continuous transformation, in as uninterrupted a sequence as could be desired.  However, each time we go back to the beginning of these consistent, abundantly documented series, we stand before an unbridgeable gulf.  The series break off and do not lead beyond the boundaries of their own particular structural type.  The link connecting them is not discernible; the individual structural designs stand apart, beside one another or in sequence, without true transitional forms"
ibid, pp 102-103
---------------------QUOTE-------------------


The only "gaps" Schindewolf was concerned with were at the beginning of a "structural type".  He makes that abundantly clear throughout the book.  Furthermore, since Schindewolf had already mapped out a line of descent for the hammatoceratins, this cannot constitute one of his "gaps".
---------------------QUOTE-------------------


Sure it does. The additional evidence (which, remember, Schindewolf claimed would never be found because it did not exist) supporting two lineages over one eliminates at least two of his vaunted gaps.
---------------------QUOTE-------------------


I'm sorry to have to do this to you JAM, but it appears I was wrong when I said Schindewolf held to the 'one lineage' hypothesis.  A more careful reading reveals that Schindewolf believed the hammatoceratins to be a superfamily that could be divided into two separate lineages.  It's a little hard to follow the author's descriptions of the two hypotheses unless you break them up.  Here's the 'single lineage' hypothesis:
             

---------------------QUOTE-------------------
There are essentially two interpretations. The latest and most complete classification of the Jurassic Ammonitina, (Donovan, Callomon & Howarth, 1981), followed in some recent works such as Wiedmann & Kullmann (1996), considers the hammatoceratins as a subfamily within the Phymatoceratidae Hyatt, 1867, which is itself included in the Hildocerataceae. For those authors, the hammatoceratins are a single lineage giving rise to all groups of post-Aalenian Ammonitina: Sonniniidae, Strigoceratidae, Haplocerataceae and Stephanocerataceae (Fig. 1a). Most authors agree with these relationships, albeit with some slight refinements; Sandoval (1986), for example, suggests the Haplocerataceae derived rather from the Graphoceratidae Buckman, 1905.
---------------------QUOTE-------------------

 
And here is the two lineage hypothesis:
   

---------------------QUOTE-------------------
The alternative interpretation has been proposed by several authors (e.g. G´eczy, 1966;Westermann, 1993; Rulleau, Elmi & Thevenard, 2001) based on different taxonomic conceptions.  The hammatoceratins are thought to be a superfamily, as suggested by Schindewolf (1964, 1965) and Tintant & Mouterde (1981), however, the main difference with the preceding classification is that the hammatoceratins may be divided into two separate lineages, following Westermann (1993). For Rulleau, Elmi & Thevenard (2001), these two lineages are the Hammatoceratidae Buckman, 1887 and the Erycitidae Spath, 1927, each of them with its own descendants: Sonniniidae, Strigoceratidae and Haplocerataceae for the former and Stephanocerataceae for the latter (Fig. 1b).
---------------------QUOTE-------------------


They summarize thus:


---------------------QUOTE-------------------
It would be wrong to see the disagreement over these two phylogenetic hypotheses as evidence of a nomenclatural morass. Both interpretations lead to the conclusion that the hammatoceratins are not a clade (that is, not a monophyletic group), and the second hypothesis holds that the late Aalenian radiation proceeded from two different clades.
---------------------QUOTE-------------------

 

So what did the authors conclude?

     

---------------------QUOTE-------------------
The principal result of the cladistic analysis presented here is that the ammonites under study form two groups, each including members of the hammatoceratins root group and their late Aalenian descendants. This confirms that the hammatoceratins group is in fact an association of two lineages (‘Hammatoceras group’ and ‘Erycites group’) that diverged early on, during the Toarcian stage, in the history of the emerging clade as suggested by Rulleau, Elmi & Thevenard (2001). Late Aalenian and Bajocian genera are distributed between these two lineages, confirming that the Stephanocerataceae derived from the ‘Erycites group’ and that the ‘Hammatoceras group’ gave rise to all the other Bajocian groups. The consequence is that the late Aalenian ammonite radiation progressed from two separate clades rather than one.
---------------------QUOTE-------------------


Thus, much to your chagrin I'd suppose, the paper you cited to undermine Schindewolf actually ends up supporting him!  

Ya gotta love science!
Posted by: Daniel Smith on Feb. 01 2008,19:08

Quote (Wesley R. Elsberry @ Feb. 01 2008,05:26)
As to the completeness of the fossil record, let us consider the passenger pigeon. < Reports exist > of the sky being darkened for days by flocks of these birds during their migrations, so they existed in large numbers, and in areas where people have looked for fossils.

And now consider the number of fossilized passenger pigeons accessioned in the collections of paleontologists.

   

---------------------QUOTE-------------------

  Abundance and distribution of fossil Passenger Pigeons is at best speculative because of the paucity of the data. Only with additional fossil records, such as this one, can a more realistic interpretation of data be made.

---------------------QUOTE-------------------



That from a report of the third partial fossil of a passenger pigeon from the western United States.
---------------------QUOTE-------------------


This is why Schindewolf based his theory on cephalopods and stony corals - as opposed to mammals, reptiles and the like.  He (as far as I can tell) only looked to the latter to see if the patterns he saw in the former abundantly fossilized lineages could be seen in the spotty evidence that existed for those less fossilized creatures.  He found nothing that contradicted those patterns.
Posted by: Daniel Smith on Feb. 01 2008,19:18

Quote (mitschlag @ Feb. 01 2008,06:15)
   
Quote (Daniel Smith @ Jan. 31 2008,19:06)
I don't see anything in this graph or in its description that contradicts Schindewolf.  In fact, all the older species (until 25MY ago) were "mostly browsers" - just like Schindewolf said.  And, since the reduction in toes began then, Schindewolf is again proved correct by modern evidence.
---------------------QUOTE-------------------


Once again, Daniel faces away from the target, takes careful aim, and misses.

No one is disputing the observation that < Hyracotherium > (early Eocene, about 55 mya) displayed a reduction in the sizes of some digits.

At issue is Schindewolf's claim:                  

---------------------QUOTE-------------------
In the descendants, then, the rest of the lateral toes degenerated and the teeth grew longer step by step... regardless of the mode of life, which... fluctuated repeatedly, with habitats switching around among forests, savannas, shrubby plains, tundra, and so on.
If selection alone were decisive in this specialization trend, we would have to ascribe to it a completely incomprehensible purposefulness...
---------------------QUOTE-------------------


as honestly construed by Daniel:            

---------------------QUOTE-------------------
IOW, the 'toes fit for running on the plains' came first, the 'plains to run on' came later.
---------------------QUOTE-------------------


Consider that by the late Eocene and early Oligocene (32–24 mya), grasslands were becoming abundant, yet Mesohippus still had three-toed feet.
So, "mode of life" was already changing long before the reduction of digits to Schindewolf's one-toed horse:                

---------------------QUOTE-------------------
To this extent, the one toed horse must be regarded as the ideal running animal of the plains.
---------------------QUOTE-------------------


Schindewolf is artificially selective about "giving enough consideration" to facts that don't favor his criticism of the evolutionary power of natural selection.
---------------------QUOTE-------------------


Schindewolf did not claim that the one toed foot came about before the plains, he claimed that the reduction of digits began before there was any advantage for it.

You have confirmed his words by pointing out that by the time grasslands were becoming abundant, the horse's ancestors were already down to three toes!

My statement, on the other hand, was my own and probably does a great disservice to Schindewolf.  You'd be much better off to read his book for yourself (if you're interested) than to rely on me for a summary of his views.
Posted by: Erasmus, FCD on Feb. 01 2008,20:01

Daniel you'd be better off reading Simpson's discussion of why this anticipatory radiation and saltational business is not supported by the facts that were available even then.

It's been a while since I have read that, but if I remember correctly there were lots of phyletic changes that occurred before the saltations.  

Have you read this criticism in Tempo and Mode of Evolution?  If necessary I'll dig it out, but it seems to me that if you are going to argue for Schindewolf's ideas (a bizarre fellow traveler for a young earth fluddite) then you might do well to read contemporary (at the time) criticism.
Posted by: JAM on Feb. 01 2008,23:41

Quote (Daniel Smith @ Feb. 01 2008,19:02)

I'm sorry to have to do this to you JAM, but it appears I was wrong when I said Schindewolf held to the 'one lineage' hypothesis.
---------------------QUOTE-------------------


You've been wrong about virtually everything so far, so that's not surprising.

What you can't seem to get through your thick head is that we are trying to point out to you that Schindewolf's claim about the EVIDENCE (that the gaps would not be filled) is wrong, so you can't win by arguing one vs. two lineages.

The point is that the papers I cited contain evidence (not words) that Schindewolf claimed did not exist.
 

---------------------QUOTE-------------------
A more careful reading reveals that Schindewolf believed the hammatoceratins to be a superfamily that could be divided into two separate lineages.
---------------------QUOTE-------------------


Are they the same lineages indicated by the newer evidence? You'd have to examine the evidence to tell, and we both know that you categorically reject examining evidence in favor of lit crit.
 

---------------------QUOTE-------------------
It's a little hard to follow the author's descriptions...
---------------------QUOTE-------------------


The descriptions don't matter. The evidence is what matters, and you ignore evidence.
 

---------------------QUOTE-------------------
So what did the authors conclude?
---------------------QUOTE-------------------


It's not really relevant, because my point is about evidence. Can you grasp the simple fact that opinion is not evidence, Dan?


---------------------QUOTE-------------------
 

---------------------QUOTE-------------------
The principal result of the cladistic analysis presented here is that the ammonites under study form two groups, each including members of the hammatoceratins root group and their late Aalenian descendants. This confirms that the hammatoceratins group is in fact an association of two lineages (‘Hammatoceras group’ and ‘Erycites group’) that diverged early on, during the Toarcian stage, in the history of the emerging clade as suggested by Rulleau, Elmi & Thevenard (2001).
---------------------QUOTE-------------------


---------------------QUOTE-------------------


Do you notice that they aren't citing Schindewolf's evidence here? Why would more recent evidence be more informative than your master's?
 

---------------------QUOTE-------------------
Thus, much to your chagrin I'd suppose, the paper you cited to undermine Schindewolf actually ends up supporting him!
---------------------QUOTE-------------------


No, Dan, it doesn't, because it contains evidence (you ignore evidence) that Schindewolf claimed didn't exist. It's that simple.
 

---------------------QUOTE-------------------
Ya gotta love science!
---------------------QUOTE-------------------


But science is about evidence, not your frantic quote mining.
Posted by: JAM on Feb. 01 2008,23:45

Quote (Daniel Smith @ Feb. 01 2008,19:08)

This is why Schindewolf based his theory on cephalopods and stony corals - as opposed to mammals, reptiles and the like.
---------------------QUOTE-------------------


Hmmm...let's see...octopi have no bones, while birds do. I don't see your point.


---------------------QUOTE-------------------
He (as far as I can tell) only looked to the latter to see if the patterns he saw in the former abundantly fossilized lineages
---------------------QUOTE-------------------


I hate to break it to you, Dan, but not all cephalopods are abundantly fossilized, and italicizing your lie only makes you look silly.


---------------------QUOTE-------------------
...He found nothing that contradicted those patterns.
---------------------QUOTE-------------------


But plenty of others have found the evidence he claimed didn't exist in the decades since.
Posted by: JAM on Feb. 01 2008,23:51

[quote=Daniel Smith,Feb. 01 2008,19:18]  
Quote (mitschlag @ Feb. 01 2008,06:15)

At issue is Schindewolf's claim:                    

---------------------QUOTE-------------------
In the descendants, then, the rest of the lateral toes degenerated and the teeth grew longer step by step... regardless of the mode of life, which... fluctuated repeatedly, with habitats switching around among forests, savannas, shrubby plains, tundra, and so on.
If selection alone were decisive in this specialization trend, we would have to ascribe to it a completely incomprehensible purposefulness...
---------------------QUOTE-------------------


Schindewolf did not claim that the one toed foot came about before the plains,
---------------------QUOTE-------------------


Yes, he did.


---------------------QUOTE-------------------
he claimed that the reduction of digits began before there was any advantage for it.
---------------------QUOTE-------------------


You should reread the text you are so desperately trying to promote.


---------------------QUOTE-------------------
You have confirmed his words by pointing out that by the time grasslands were becoming abundant, the horse's ancestors were already down to three toes!
---------------------QUOTE-------------------


You're lying, Dan. You left out one of Schindewolf's words. The "rest of the lateral toes" refers to the transition from 3 to 1 toe, not from 5 to 3.

Once again, you bold or italicize your dishonesty, as though emphasizing it somehow magically compensates for its falsehood.
Posted by: mitschlag on Feb. 02 2008,06:45

Quote (Daniel Smith @ Feb. 01 2008,19:18)
My statement, on the other hand, was my own and probably does a great disservice to Schindewolf.  You'd be much better off to read his book for yourself (if you're interested) than to rely on me for a summary of his views.
---------------------QUOTE-------------------


No, thanks.

Your misrepresentations are entertaining enough.  :D
Posted by: Daniel Smith on Feb. 02 2008,12:16

Quote (JAM @ Feb. 01 2008,21:41)
Quote (Daniel Smith @ Feb. 01 2008,19:02)

I'm sorry to have to do this to you JAM, but it appears I was wrong when I said Schindewolf held to the 'one lineage' hypothesis.
---------------------QUOTE-------------------


You've been wrong about virtually everything so far, so that's not surprising.

What you can't seem to get through your thick head is that we are trying to point out to you that Schindewolf's claim about the EVIDENCE (that the gaps would not be filled) is wrong, so you can't win by arguing one vs. two lineages.

The point is that the papers I cited contain evidence (not words) that Schindewolf claimed did not exist.
 

---------------------QUOTE-------------------
A more careful reading reveals that Schindewolf believed the hammatoceratins to be a superfamily that could be divided into two separate lineages.
---------------------QUOTE-------------------


Are they the same lineages indicated by the newer evidence? You'd have to examine the evidence to tell, and we both know that you categorically reject examining evidence in favor of lit crit.
 

---------------------QUOTE-------------------
It's a little hard to follow the author's descriptions...
---------------------QUOTE-------------------


The descriptions don't matter. The evidence is what matters, and you ignore evidence.
 

---------------------QUOTE-------------------
So what did the authors conclude?
---------------------QUOTE-------------------


It's not really relevant, because my point is about evidence. Can you grasp the simple fact that opinion is not evidence, Dan?
 

---------------------QUOTE-------------------
 

---------------------QUOTE-------------------
The principal result of the cladistic analysis presented here is that the ammonites under study form two groups, each including members of the hammatoceratins root group and their late Aalenian descendants. This confirms that the hammatoceratins group is in fact an association of two lineages (‘Hammatoceras group’ and ‘Erycites group’) that diverged early on, during the Toarcian stage, in the history of the emerging clade as suggested by Rulleau, Elmi & Thevenard (2001).
---------------------QUOTE-------------------


---------------------QUOTE-------------------


Do you notice that they aren't citing Schindewolf's evidence here? Why would more recent evidence be more informative than your master's?
 

---------------------QUOTE-------------------
Thus, much to your chagrin I'd suppose, the paper you cited to undermine Schindewolf actually ends up supporting him!
---------------------QUOTE-------------------


No, Dan, it doesn't, because it contains evidence (you ignore evidence) that Schindewolf claimed didn't exist. It's that simple.
 

---------------------QUOTE-------------------
Ya gotta love science!
---------------------QUOTE-------------------


But science is about evidence, not your frantic quote mining.
---------------------QUOTE-------------------


Amazing.
Simply amazing.
Posted by: oldmanintheskydidntdoit on Feb. 02 2008,12:29

Is that "amazing" as in "elegant" ?
Posted by: mitschlag on Feb. 02 2008,16:03

Quote (mitschlag @ Jan. 31 2008,10:06)
   
Quote (Daniel Smith @ Jan. 30 2008,19:06)
           

---------------------QUOTE-------------------
(The backlog of unsupported claims by Daniel is enormous and keeps growing.)
---------------------QUOTE-------------------


Such as?
---------------------QUOTE-------------------


Of recent memory, see < here >, < here > and < here >.
---------------------QUOTE-------------------


So, Daniel Smith, what gives?   ???

Edited to add: I'm having so much fun with these emoticons now that I know how to make them work!
Posted by: mitschlag on Feb. 02 2008,16:13



---------------------QUOTE-------------------
The essence of democracy is that you can lie about who you voted for.  Charles Krauthammer
---------------------QUOTE-------------------


What the hell is that supposed to mean?

Edited to add:   ???
Posted by: Daniel Smith on Feb. 04 2008,11:01

Quote (mitschlag @ Feb. 02 2008,14:13)
 

---------------------QUOTE-------------------
The essence of democracy is that you can lie about who you voted for.  Charles Krauthammer
---------------------QUOTE-------------------


What the hell is that supposed to mean?

Edited to add:   ???
---------------------QUOTE-------------------


It means he thinks caucuses are undemocratic.
Posted by: oldmanintheskydidntdoit on Feb. 04 2008,11:35

Hey Daniel,
Welcome back.


Soooooo....

What now?
Posted by: mitschlag on Feb. 04 2008,15:44

Quote (Daniel Smith @ Feb. 04 2008,11:01)
 
Quote (mitschlag @ Feb. 02 2008,14:13)
   

---------------------QUOTE-------------------
The essence of democracy is that you can lie about who you voted for.  Charles Krauthammer
---------------------QUOTE-------------------


What the hell is that supposed to mean?

Edited to add:   ???
---------------------QUOTE-------------------


It means he thinks caucuses are undemocratic.
---------------------QUOTE-------------------


Thanks.  :)
Posted by: Daniel Smith on Feb. 04 2008,19:04

Quote (JAM @ Feb. 01 2008,21:45)
             
Quote (Daniel Smith @ Feb. 01 2008,19:08)
...He found nothing that contradicted those patterns.
---------------------QUOTE-------------------


But plenty of others have found the evidence he claimed didn't exist in the decades since.
---------------------QUOTE-------------------


JAM,

It didn't take long for me, from the time you first entered this discussion, to lose my respect for you as a human being.  Anyone with common courtesy or decency can read back through and immediately see why.

I still, though, maintained a grudging respect for you as a scientist.

Now that's gone too.

In fact, I'm beginning to have doubts that you really are a scientist.  

Nevertheless, I think I'll go back to ignoring you now.  You obviously have nothing of substance to contribute to this conversation.
Posted by: Daniel Smith on Feb. 04 2008,19:16

Quote (oldmanintheskydidntdoit @ Feb. 04 2008,09:35)
Hey Daniel,
Welcome back.


Soooooo....

What now?
---------------------QUOTE-------------------


Good question.  I don't know.  

There's a lot more that can be said about Schindewolf, that's for sure, and we didn't really even get into Berg's Nomogenesis much at all!

But I honestly don't feel that people here are much interested.   I know none of you ran out to buy Schindewolf's or Berg's books!  I guess that's understandable though.  If you're confident in your position, why would you seek evidence against it?

In that light, I think this subject has pretty much exhausted itself.  I'm beginning to tire of this place a little as well.  There's a LOT of negativity here!
Posted by: Wesley R. Elsberry on Feb. 04 2008,22:29

Daniel Smith:



---------------------QUOTE-------------------

It didn't take long for me, from the time you first entered this discussion, to lose my respect for you as a human being.  Anyone with common courtesy or decency can read back through and immediately see why.

---------------------QUOTE-------------------



Daniel Smith, the very next comment:



---------------------QUOTE-------------------

There's a LOT of negativity here!

---------------------QUOTE-------------------



Golly.
Posted by: oldmanintheskydidntdoit on Feb. 05 2008,03:18

Quote (Daniel Smith @ Feb. 04 2008,19:16)
But I honestly don't feel that people here are much interested.   I know none of you ran out to buy Schindewolf's or Berg's books!  I guess that's understandable though.  If you're confident in your position, why would you seek evidence against it?
---------------------QUOTE-------------------


Perhaps it's the same reason that you didn't rush out and buy any contemporary biology textbooks?

I simply don't see how you can criticize the current positions when you don't understand them, as JAM has taken pains to point out. I'm sure you'd agree (sequence data etc) that there are significant gaps in your understanding.

If you are confident in your position then what harm can learning about the other side do?

Don't you think that once you have a full understanding of current positions you can then attempt to criticise them?

Trying to run before you can walk is sheer folly in this forum!

And Daniel, I'm sure that scientists like nothing more then finding evidence that contradicts their position. It simply means that a more accurate description is available and who will argue against progress? Sure, some hold outs may never be convinced, but on the whole progress marches on.

It's people like you, Daniel, that refuse to believe what the evidence is showing. Not the people you have been arguing with.

I know it's hard to believe, but it's true.

If you really want to take on this fight and win, well, go get a degree or two and then try again. FIght them on their own ground.

If you do go that route, well, I'm 99% we will never hear from you again. Why? Well, I'm sure the arguments will convince under strict study. And you'll be turned in no time!
Posted by: mitschlag on Feb. 05 2008,05:10

Quote (Daniel Smith @ Feb. 04 2008,19:16)
There's a lot more that can be said about Schindewolf, that's for sure, and we didn't really even get into Berg's Nomogenesis much at all!

But I honestly don't feel that people here are much interested.   I know none of you ran out to buy Schindewolf's or Berg's books!  I guess that's understandable though.  If you're confident in your position, why would you seek evidence against it?
---------------------QUOTE-------------------


Actually, I bought a copy of Basic Questions and have dipped into it.  What I've seen is a vigorous rejection of selection as a driving force in evolution and the substitution of orthogenesis.

As I've mentioned before, Schindewolf's ideas are of historical interest, but they have not survived the rough and tumble of scientific practice.  Ideas that are not usefully heuristic are doomed.

If Daniel has not read < The Structure of Scientific Revolutions >, he is missing an opportunity to learn how science has worked through history and how it is likely to continue to work.  It will give him insight into how we operate.  (And it's a lot shorter than Grundfragen.)
Posted by: Daniel Smith on Feb. 05 2008,10:55

Quote (Wesley R. Elsberry @ Feb. 04 2008,20:29)
Daniel Smith:



---------------------QUOTE-------------------

It didn't take long for me, from the time you first entered this discussion, to lose my respect for you as a human being.  Anyone with common courtesy or decency can read back through and immediately see why.

---------------------QUOTE-------------------



Daniel Smith, the very next comment:



---------------------QUOTE-------------------

There's a LOT of negativity here!

---------------------QUOTE-------------------



Golly.
---------------------QUOTE-------------------


"Golly" is right.
Posted by: oldmanintheskydidntdoit on Feb. 05 2008,11:11

Quote (Daniel Smith @ Feb. 05 2008,10:55)
Quote (Wesley R. Elsberry @ Feb. 04 2008,20:29)
Daniel Smith:

 

---------------------QUOTE-------------------

It didn't take long for me, from the time you first entered this discussion, to lose my respect for you as a human being.  Anyone with common courtesy or decency can read back through and immediately see why.

---------------------QUOTE-------------------



Daniel Smith, the very next comment:

 

---------------------QUOTE-------------------

There's a LOT of negativity here!

---------------------QUOTE-------------------



Golly.
---------------------QUOTE-------------------


"Golly" is right.
---------------------QUOTE-------------------


Another substance free post consisting of a word or two appended to somebody else's post.

The informational content of your posts here seems to be declining Daniel.

No doubt this is why JAD says "you've won" over at ISCID.

If you like I can go back and find a few unanswered questions for you? There are *plenty* to choose from!
Posted by: Daniel Smith on Feb. 05 2008,18:00

Quote (oldmanintheskydidntdoit @ Feb. 05 2008,01:18)
     
Quote (Daniel Smith @ Feb. 04 2008,19:16)
But I honestly don't feel that people here are much interested.   I know none of you ran out to buy Schindewolf's or Berg's books!  I guess that's understandable though.  If you're confident in your position, why would you seek evidence against it?
---------------------QUOTE-------------------


Perhaps it's the same reason that you didn't rush out and buy any contemporary biology textbooks?

I simply don't see how you can criticize the current positions when you don't understand them, as JAM has taken pains to point out. I'm sure you'd agree (sequence data etc) that there are significant gaps in your understanding.

If you are confident in your position then what harm can learning about the other side do?

Don't you think that once you have a full understanding of current positions you can then attempt to criticise them?

Trying to run before you can walk is sheer folly in this forum!

And Daniel, I'm sure that scientists like nothing more then finding evidence that contradicts their position. It simply means that a more accurate description is available and who will argue against progress? Sure, some hold outs may never be convinced, but on the whole progress marches on.

It's people like you, Daniel, that refuse to believe what the evidence is showing. Not the people you have been arguing with.

I know it's hard to believe, but it's true.
---------------------QUOTE-------------------


Old man, old man, old man...
If only you knew whereof you speak.
During my time here I've bought and read (cover to cover) a book on molecular biology and a book on heredity.  Neither were written by creationists or IDists. I've also read every online paper I was referred to and have read several more on my own.  These papers include most of the ENCODE consortium papers, several on the "histone code" and epigenetics, one on human chromosome 2, one on transposable elements of the Drosophila, plus several other papers I don't have in front of me right now and several wikipedia pages on topics discussed here as well.  None of these were written by creationists, and aside from the Denton papers, none were written by ID supporters either.
The most recent paper I've read was written by Stephen Jay Gould and Niles Eldredge; entitled "Punctuated equilibrium comes of age".  I read that because Wesley mention punctuated equilibrium and I wanted to know a little more about it.
I've gone a long way towards learning what the evidence is against my positions.
How far have you gone?
     

---------------------QUOTE-------------------
If you really want to take on this fight and win, well, go get a degree or two and then try again. FIght them on their own ground.

If you do go that route, well, I'm 99% we will never hear from you again. Why? Well, I'm sure the arguments will convince under strict study. And you'll be turned in no time!
---------------------QUOTE-------------------


There are plenty of people with degrees who don't believe the currently held theory.
Heck, Gould and Eldredge seem more dead set against "gradualism" than Schindewolf was (though their tone is much more conciliatory than his).  So I sincerely doubt that "getting a degree" will cause me to turn my brain off and fall in line.
Posted by: Steverino on Feb. 05 2008,18:09

No, but it might cause you to turn your brain on!
Posted by: swbarnes2 on Feb. 05 2008,18:32



---------------------QUOTE-------------------
Neither were written by creationists or IDists. I've also read every online paper I was referred to and have read several more on my own.  These papers include most of the ENCODE consortium papers, several on the "histone code" and epigenetics, one on human chromosome 2, one on transposable elements of the Drosophila, plus several other papers I don't have in front of me right now and several wikipedia pages on topics discussed here as well.  None of these were written by creationists, and aside from the Denton papers, none were written by ID supporters either.
The most recent paper I've read was written by Stephen Jay Gould and Niles Eldredge; entitled "Punctuated equilibrium comes of age".  I read that because Wesley mention punctuated equilibrium and I wanted to know a little more about it.
---------------------QUOTE-------------------


One could pick apart the ridiculousness of your post piece by piece, but I think a few overall points are more wirth making.

First, by managing to fit all your new-found expertice into one paragraph, you just highlight the fact that the posters who refute you have learned a  hell of a lot more than you have.  You're "I've read two! books, and a few papers all the way through" is laughable compared to the time and effort spent by the professional biologists who post on these boards.

And do you woner why they don't bother touting themselves as you have to?

It's because when you really are knowledgable, it comes through in the content of one's posts.  They don't have to list their publications, their schooling, the papers and boosk they've read, because anyone can see that their posts contain accurate facts which belie their good knowledge and understanding.

Likewise, your posts belie the fact that you have no facts to support you, only 50 year old quotes, paper abstracts that you desperately quote without understanding, and things that you make up.

Why you would want to draw attention to this glaring fact with your lame excuses for study is beyond me.
Posted by: blipey on Feb. 05 2008,19:53

swbarnes2:

Surely you are aware that true knowledge comes from name-dropping?  And that true understanding comes from reading complicated source material without a comprehension of the basics?  That's Creationism 101.
Posted by: Mark Iosim on Feb. 05 2008,23:24

I am back to this lovely discussion forum to report the results of my homework regarding Genetic Algorithm (GA). A few weeks ago I asked to refer me the statistical analysis demonstrating that random mutations are sufficient to cause adaptive changes in biological systems. Respond came from oldmanintheskydidntdoit who suggested to start with
< http://www.talkorigins.org/faqs/fitness/. >
In my following skeptical assessment of “Weasel program” I stated that it cannot be a model for a Natural selection, but for an artificial selection only. Later in Wikipedia (“Weasel program”) I found the same assessment made by Dawkins
“…Shakespeare model is useful for explaining the distinction between single-step selection and cumulative selection, it is misleading in important ways. One of these is that, in each generation of selective 'breeding', the mutant 'progeny' phrases were judged according to the criterion of resemblance to a distant ideal target…”.
I agree with Dawkins’ assestment of “Weasel program”, but I would defend the role of “distant ideal target” in the natural evolution process. I will return to this point later in this post.

Responding to my skeptical assessment I was told that the “weasel program” is just a tutorial example that demonstrates a difference between random changes and accumulative selection, but to understand mechanism of RM+NS I should make myself more familiar with Genetic Algorithm (GA). I followed this advice and spent some time learning about GA. Below is a couple definitions that in my opinion accurately define GA:

[qoute]< http://en.wikipedia.org/wiki/Genetic_algorithm >
“A genetic algorithm (GA) is a search technique used in computing to find exact or approximate solutions to optimization and search problems.
…GAs cannot effectively solve problems in which the only fitness measure is RIGHT/WRONG, as there is no way to converge on the solution. (No hill to climb.) In these cases, a random search may find a solution as quickly as a GA.”

< http://www.talkorigins.org/faqs/genalg/genalg.html# >
… a genetic algorithm (or GA for short) is a programming technique that mimics biological evolution as a problem-solving strategy. Given a specific problem to solve, the input to the GA is a SET OF POTENTIAL SOLUTIONS to that problem, encoded in some fashion…[/qoute]
By reading and thinking about GA over two weeks I think I got enough basic understanding to appreciate a power and limitation of GA to respond to the following challenges addressed to me in the past:

swbarnes2    

---------------------QUOTE-------------------
How is this is a problem (threshold of usefulness) for a GA?  Enough random starts and you will pass any threshold you like.
---------------------QUOTE-------------------


By “threshold of usefulness” I mean a minimum performance of evolved “digital organism” that is recognized by the fitness function as a potential solution. The small mutation in the evolving “digital organism” into direction to solution need to be detected and promoted by Fitness Function, otherwise prohibited amount of simultaneous mutation must occur in order to produce a “jump” to a better solution.
If this explanation still doesn’t make sense to you try this:    

---------------------QUOTE-------------------

< http://www.inf.ed.ac.uk/publications/thesis/online/IM050329.pdf >
“… What we do not always take into account, however, is whether evolution
can provide a logical means of finding that peak (solution) through the gradual process required by an EA. If there is no “incentive” to evolve through the earlier stages required, as in the case of 2% of a wing, our evolution will get nowhere.
---------------------QUOTE-------------------


swbarnes2    

---------------------QUOTE-------------------
The hard fact is that GA's have and do succeed in solving problems that humans don't know the answers too.
---------------------QUOTE-------------------


GA succeeds in solving problems the same way as hand held calculator does. They are both just a tools in our hands. You probably don't know the answers for x = 23.7E20, but a calculator “does”.

oldmanintheskydidntdoit    

---------------------QUOTE-------------------

“What do you make of
< http://ic.arc.nasa.gov/projects/esg/research/antenna.htm >
The fitness function used to evaluate antennas is a function of the voltage standing wave ratio (VSWR) and gain values on the transmit and receive frequencies. VSWR is a way to quantify reflected-wave interference, and thus the amount of impedance mismatch at the junction. VSWR is the ratio between the highest voltage and the lowest voltage in the signal envelope along a transmission line.

The two best antennas found, one (ST5-3-10) from a GA that allowed branching and one (ST5-4W-03) from a GA that did not, were fabricated and tested. Antenna ST5-3-10 is a requirements-compliant antenna that was built and tested on an antenna test range. While it is slightly difficult to manufacture without the aid of automated wire-forming and soldering machines, it has a number of benefits as compared to the conventionally-designed antenna.
---------------------QUOTE-------------------


This is a typical application for GA, as an optimization TOOL by which potential solutions (changing geometry of wires) were RECOGNIZED as less or more effective by fitness function. Following landscape of more effective solutions the program eventually determines one of the optimum geometry of wire antenna.
See a visual illustration for a similar process:
< http://www.obitko.com/tutorials/genetic-algorithms/search-space.php >
Wesley R. Elsberry    

---------------------QUOTE-------------------

Artificial life systems, such as Avida, can be configured such that the digital organisms contain -- and make modifiable -- the code that performs the self-replication process, making them an instance of evolution, not a simulation of evolution. Given an ancestral digital organism capable of reproduction and nothing else, Avida provides an experimental platform to do precisely what last page's rant said was the issue: examine the process of adaptive change by means of selection. And they do adapt.
---------------------QUOTE-------------------


Wesley provided me with the link to the article “The Evolutionary Origin of Complex Features” published in NATURE in 2003. This topic also featured in the Discovery (and probably other) magazine. It took for me a while to understand what this work about, but eventually I learned a few important things I would like to share with the rest of the folks.
   

---------------------QUOTE-------------------
http://myxo.css.msu.edu/lenski/pdf/2003,%20Nature,%20Lenski%20et%20al.pdf
Abstract
A long-standing challenge to evolutionary theory has been whether it can explain the origin of complex organismal features. We examined this issue using digital organisms—computer programs that self-replicate, mutate, compete and evolve. …These findings show how complex functions can originate by random mutation and natural selection.
---------------------QUOTE-------------------


It is indeed a long-standing challenge to evolutionary theory, what Behe refers as Irreducible Complexity. My first impression was that this article addressed and solved this challenge using rigorous scientific method, but it was a wrong impression. Instead the article is flooded with phenomenological details that in my opinion do not help to justify its title.

By using digital organisms of Avida program, the authors traced the genealogy from an ancestor that could replicate only to descendants able to perform multiple logic functions requiring the coordinated execution of many genomic instructions. To demonstrate that complex systems evolve from simpler precursors authors set up small rewards for simpler operations and bigger rewards for more complex ones and this way provide an “incentive” to evolve through the gradual process. However when the researchers took away rewards for simpler operations, “digital organisms” never found a final solution. However to come to this conclusion we do not need the sophistication of artificial intelligence”, because the “Weasel program” demonstrates the same result: if the small improvements in the “Hamlet line” would not be rewarded the final line from Hamlet never evolve.

Conclusion of this article:  

---------------------QUOTE-------------------
Our experiments demonstrate the validity of the hypothesis, first articulated by Darwin and supported today by comparative and experimental evidences that complex features generally evolve by modifying existing structures and functions. Some readers might suggest that we ‘stacked the deck’ by studying the evolution of
a complex feature that could be built on simpler functions that were also useful. However, that is precisely what evolutionary theory requires, and indeed, our experiments showed that the complex feature never evolved when simpler functions were not rewarded.
---------------------QUOTE-------------------


How does this conclusion addresses the biggest challenge of Darwinism – the phenomenon of Irreducible Complexity, by which a “simpler function” is useless? Apparently this article ignores not Irreducible Complexity only, but any analysis of complexity at all. This article, pretending to explane the emergence of complexity from simplicity, avoids defining which of the dozens different and often mutually exclusive definitions of complexity authors have in mind. This is very unusual, especially for scientists from Department of Computer Science and Department of Philosophy where scientific concept of Complexity is the “bread and butter.
The conclusion is also a classical example for the circular logic between RC+NS incorporated into Avida program that bechave like RC+NS and this way this proves the validity of RC+NS.

Another pearl from Discovery magazine:      

---------------------QUOTE-------------------
< http://discovermagazine.com/2005....t:int=1 >
“…When the Avida team published their first results on the evolution of complexity in 2003, they were inundated with e-mails from creationists. Their work hit a nerve in the antievolution movement and hit it hard. A popular claim of creationists is that life shows signs of intelligent design, especially in its complexity. They argue that complex things could have never evolved, because they don’t work unless all their parts are in place. But as Adami points out, if creationists were right, then Avida wouldn’t be able to produce complex digital organisms. … “What we show is that there are irreducibly complex things and they can evolve, says Adami…
---------------------QUOTE-------------------


Holly Molly!!! So the article in Nature indeed addressed and solved the problem of Irreducible Complexity, I just missed it. Try to read this article for you self and may be you will be more successful reconciling the mutually exclusive statements from Nature and Discovery.  

I have been wondering if Neo-Darwinism is theory, hypothesis, paradigm or religion. But this article makes me think that Darwinism is an ideology of Darwinian political party. I am not ID supporter, but after comparing the statements from Nature and Discovery,  
I want to join an opposition party to expose the foolishness, blindness and dishonesty of some “Darwinians”. Unfortunately ID party wouldn’t tolerate me either. If anybody knows about existence of Independent party in Evolution Biology, please let me know.

After being disillusioned with the sophisticated GA, I came back to “Weasel program” that in my opinion is not a tutorial example, but one of the simplest and the most transparent tool that could demonstrate the power of accumulative selection and limitation of random mutation as good as any of its more sophisticated GA cousins. The “Weasel program” was criticized by ID supporters (and this critic was accepted by Dawkins) because of the “final target sequence chosen in advance” (the exact line from Hamlet) is seen as a weakness because it could be interpreted in favor to ID. I think that the “target sequence” isn’t a weakness of this model, but one of the “incarnations” of the real fitness function. The phenomenon of mimicry or camouflage could be an example of living system that matches the target “existing in advance”. The complexity of the “natural targets” is often exceeding the complexity of “line from Hamlet”. The evolution driven by “warfare” with other organisms presents example of this sophisticated “fitness function”. I am defending the practical usefulness of the “Weasel program” and against tutorial example only, because I plan to put it to work helping me solve one problem.

The gradual, step-by-step changes are the most important concepts without each Darwinism wouldn’t be able to explain evolution. The main argument of Behe against gradualism is that it is impossible to define existence of the “appropriate fitness function” that would provide gradual evolution of the so called “Irreducible complex” systems. Dawkins’s counterargument is that regardless that we can’t reproduce these conditions now, it doesn’t mean they couldn’t exist millions or billions years ago. Dawkins expects that sooner or later the “appropriate fitness function” will be found and he has tried to demonstrate that this is not an impossible proposition.

I don’t share Dawkins’ optimism, but I wouldn’t waste time attempting to prove the nonexistence of these conditions billions years ago. How one can prove a non-existence of any thing at all, including the non-existence of God? We may prove a non-existence only in the absolutely defined area of knowledge. For example I may prove to my self the non-existence of a wallet in my empty packet, but only after thorough searching it and even then I may have some reservations.

Therefore I wish Dr. Dawkins a lot of lock in the reproducing of what may happen on Earth million a million years ago, but until these evidences are not discovered, the Neo-Darwinism, in its current form, do not deserve to be called Theory, but a controversial Hypothesis instead.

While evolutionists are working hard stretching their imagination about what may happen millions years ago, I would like to try a different approach by looking in what is happening now, before our eyes. The “Weasel program” (or any other GA tool) that already helped us to rule out the single step selection as unrealistic scenario and shown that an accumulative multi-step model is a much promised one, could help us again. I would like to use “Weasel program” to evaluate RM+NS mechanism in the development of drug resistance in bacteria. For example, in the process of developing drug resistance the particular segment of bacteria’s’ (or virus’) DNA mutates from form A to form B during N generation per mutation rate X etc. Using “Weasel program” (by replacing letters with nucleotides) we can modeling the DNA evolution from form A to form B and see if the model able to reproduce a “target line of nucleotides” within reasonable time frame. I expected to find plenty of published experiments that spell out the changes in bacteria (virus) DNA segment during drug resistance development. However I am having problem to locate these publications. Can anybody help me in this search?
Posted by: oldmanintheskydidntdoit on Feb. 06 2008,03:10

Quote (Daniel Smith @ Feb. 05 2008,18:00)
There are plenty of people with degrees who don't believe the currently held theory.
---------------------QUOTE-------------------


Name them then.

Note, only degrees in relevant fields count.

I'll expect the list never then.

Will "plenty" turn out to be

a) JAD
b) People who have legitimate problems with neo-darwinism but nonetheless do not support your position but you think you can use them to prop up your position?

?
Posted by: oldmanintheskydidntdoit on Feb. 06 2008,03:16

Quote (Mark Iosim @ Feb. 05 2008,23:24)
This is a typical application for GA, as an optimization TOOL by which potential solutions (changing geometry of wires) were RECOGNIZED as less or more effective by fitness function. Following landscape of more effective solutions the program eventually determines one of the optimum geometry of wire antenna.
---------------------QUOTE-------------------


Yes. That's right.

And your point is what, exactly?

You've shown that this TOOL can find solutions not usually available via standard design methods.

And so you've proven the point you were presumably trying to disprove. Is your problem that there is a "target" (optimum signal reception)?

When you say


---------------------QUOTE-------------------
I would like to use “Weasel program” to evaluate RM+NS mechanism in the development of drug resistance in bacteria.
---------------------QUOTE-------------------


It simply means you've learnt nothing from your period of study.
Posted by: mitschlag on Feb. 06 2008,04:51

Daniel Smith, why have the ideas of Schindewolf, Berg, Goldschmidt, and Davison failed to gain scientific traction and have become footnotes in the history of biological thought?

My answer: They have not generated fruitful, testable hypotheses.

Your answer: ?
Posted by: JAM on Feb. 06 2008,11:30

Quote (Daniel Smith @ Feb. 04 2008,19:04)
 
Quote (JAM @ Feb. 01 2008,21:45)
                 
Quote (Daniel Smith @ Feb. 01 2008,19:08)
...He found nothing that contradicted those patterns.
---------------------QUOTE-------------------


But plenty of others have found the evidence he claimed didn't exist in the decades since.
---------------------QUOTE-------------------


JAM,

It didn't take long for me, from the time you first entered this discussion, to lose my respect for you as a human being.
---------------------QUOTE-------------------


Why? Because by making you look at the sequence evidence, your initial proclamation of interest in evidence was shown to be a bald-faced lie?

Look above. I'm arguing evidence, you're ignoring evidence and going for the ad hominem attack.

How many times do you have to hear "opinions aren't evidence" before this essential distinction gets through your head?

Do you realize that a real scientist (or anyone else interested in actual evidence) looks at the tables and figures long before she/he consults the text?



---------------------QUOTE-------------------
Anyone with common courtesy or decency can read back through and immediately see why.
---------------------QUOTE-------------------


I don't see why. I see us calling you on your initial lies:
Quote (Daniel Smith @ Sep. 22 2007,04:48)
My main problem is that I want to see unbiased and unadulterated evidence; not evidence that is made-to-fit the observers viewpoint....I decided what I needed was just to see the evidence for myself.
---------------------QUOTE-------------------


You're scared to death of actual evidence.


---------------------QUOTE-------------------
I still, though, maintained a grudging respect for you as a scientist.
---------------------QUOTE-------------------


Why, given your utter contempt for the scientific method?


---------------------QUOTE-------------------
In fact, I'm beginning to have doubts that you really are a scientist.
---------------------QUOTE-------------------


Cool. How many $K do you wanna bet? 


---------------------QUOTE-------------------
Nevertheless, I think I'll go back to ignoring you now.  You obviously have nothing of substance to contribute to this conversation.
---------------------QUOTE-------------------


Evidence is the substance of science, not opinion. Thanks for demonstrating again that you were lying when you claimed to be interested in evidence.
Posted by: Daniel Smith on Feb. 06 2008,13:48

Quote (mitschlag @ Feb. 06 2008,02:51)
Daniel Smith, why have the ideas of Schindewolf, Berg, Goldschmidt, and Davison failed to gain scientific traction and have become footnotes in the history of biological thought?

My answer: They have not generated fruitful, testable hypotheses.

Your answer: ?
---------------------QUOTE-------------------


I think it's because their proposed mechanisms are saltational - and that seems to be a dirty word in scientific circles.
Posted by: blipey on Feb. 06 2008,13:54

Quote (Daniel Smith @ Feb. 06 2008,13:48)
Quote (mitschlag @ Feb. 06 2008,02:51)
Daniel Smith, why have the ideas of Schindewolf, Berg, Goldschmidt, and Davison failed to gain scientific traction and have become footnotes in the history of biological thought?

My answer: They have not generated fruitful, testable hypotheses.

Your answer: ?
---------------------QUOTE-------------------


I think it's because their proposed mechanisms are saltational - and that seems to be a dirty word in scientific circles.
---------------------QUOTE-------------------


So you think it's a conspiracy?
Posted by: Daniel Smith on Feb. 06 2008,13:54

Quote (swbarnes2 @ Feb. 05 2008,16:32)
 

---------------------QUOTE-------------------
Neither were written by creationists or IDists. I've also read every online paper I was referred to and have read several more on my own.  These papers include most of the ENCODE consortium papers, several on the "histone code" and epigenetics, one on human chromosome 2, one on transposable elements of the Drosophila, plus several other papers I don't have in front of me right now and several wikipedia pages on topics discussed here as well.  None of these were written by creationists, and aside from the Denton papers, none were written by ID supporters either.
The most recent paper I've read was written by Stephen Jay Gould and Niles Eldredge; entitled "Punctuated equilibrium comes of age".  I read that because Wesley mention punctuated equilibrium and I wanted to know a little more about it.
---------------------QUOTE-------------------


One could pick apart the ridiculousness of your post piece by piece, but I think a few overall points are more wirth making.

First, by managing to fit all your new-found expertice into one paragraph, you just highlight the fact that the posters who refute you have learned a  hell of a lot more than you have.  You're "I've read two! books, and a few papers all the way through" is laughable compared to the time and effort spent by the professional biologists who post on these boards.

And do you woner why they don't bother touting themselves as you have to?

It's because when you really are knowledgable, it comes through in the content of one's posts.  They don't have to list their publications, their schooling, the papers and boosk they've read, because anyone can see that their posts contain accurate facts which belie their good knowledge and understanding.

Likewise, your posts belie the fact that you have no facts to support you, only 50 year old quotes, paper abstracts that you desperately quote without understanding, and things that you make up.

Why you would want to draw attention to this glaring fact with your lame excuses for study is beyond me.
---------------------QUOTE-------------------


My post was never meant to be a defense of my level of knowledge.  It was a defense of my level of effort in learning about ideas that don't jibe with my current views.  It was in the context of comparison with the amount of effort spent by others on this board in learning more about Schindewolf and Berg.  That's all it was.  Your post is a strawman.
Posted by: Daniel Smith on Feb. 06 2008,13:58

Quote (JAM @ Feb. 06 2008,09:30)
Evidence is the substance of science, not opinion. Thanks for demonstrating again that you were lying when you claimed to be interested in evidence.
---------------------QUOTE-------------------


Where, specifically, is the evidence [you thought was] in that paper [you never read] that [supposedly] destroys Schindewolf's theory?
Posted by: mitschlag on Feb. 06 2008,14:00

Quote (Daniel Smith @ Feb. 06 2008,13:48)
     
Quote (mitschlag @ Feb. 06 2008,02:51)
Daniel Smith, why have the ideas of Schindewolf, Berg, Goldschmidt, and Davison failed to gain scientific traction and have become footnotes in the history of biological thought?

My answer: They have not generated fruitful, testable hypotheses.

Your answer: ?
---------------------QUOTE-------------------


I think it's because their proposed mechanisms are saltational - and that seems to be a dirty word in scientific circles.
---------------------QUOTE-------------------


Thank you for responding, Daniel, but you didn't really answer, did you?

So, we'll work with what we've got:  Why do you think that "saltational" is a "dirty word" in scientific circles?

Could it be the case that saltational theories of evolution are neither fruitful nor testable?

You realize, don't you, that if a scientific idea is fruitful and testable, its attraction to scientists is irresistible?
Posted by: Daniel Smith on Feb. 06 2008,14:03

Quote (blipey @ Feb. 06 2008,11:54)
 
Quote (Daniel Smith @ Feb. 06 2008,13:48)
 
Quote (mitschlag @ Feb. 06 2008,02:51)
Daniel Smith, why have the ideas of Schindewolf, Berg, Goldschmidt, and Davison failed to gain scientific traction and have become footnotes in the history of biological thought?

My answer: They have not generated fruitful, testable hypotheses.

Your answer: ?
---------------------QUOTE-------------------


I think it's because their proposed mechanisms are saltational - and that seems to be a dirty word in scientific circles.
---------------------QUOTE-------------------


So you think it's a conspiracy?
---------------------QUOTE-------------------


No, I think that people are afraid of being ridiculed for wanting to test a saltational theory - so they dismiss it out of hand.  I base this on the great lengths Gould and Eldredge went to in order to show that their theory was not saltational.
Posted by: mitschlag on Feb. 06 2008,14:22

Quote (Daniel Smith @ Feb. 06 2008,14:03)
 
Quote (blipey @ Feb. 06 2008,11:54)
     
Quote (Daniel Smith @ Feb. 06 2008,13:48)
     
Quote (mitschlag @ Feb. 06 2008,02:51)
Daniel Smith, why have the ideas of Schindewolf, Berg, Goldschmidt, and Davison failed to gain scientific traction and have become footnotes in the history of biological thought?

My answer: They have not generated fruitful, testable hypotheses.

Your answer: ?
---------------------QUOTE-------------------


I think it's because their proposed mechanisms are saltational - and that seems to be a dirty word in scientific circles.
---------------------QUOTE-------------------


So you think it's a conspiracy?
---------------------QUOTE-------------------


No, I think that people are afraid of being ridiculed for wanting to test a saltational theory - so they dismiss it out of hand.  I base this on the great lengths Gould and Eldredge went to in order to show that their theory was not saltational.
---------------------QUOTE-------------------


Here's how it actually works, Daniel:

In the privacy of his/her own laboratory, the scientist can test a saltational hypothesis to his/her heart's content.  And if the tests advance understanding, the scientist can tell the world about it. The scientific literature is full of examples of papers that made extravagant claims, challenging the prevailing wisdom. In some cases, these claims were not confirmed by subsequent work or were otherwise refuted.  In other cases, the findings were seminal and earned the publishing scientists great renown.

A smart person who knows he's on to something does not fear ridicule.  And that's what separates the women from the girls.
Posted by: blipey on Feb. 06 2008,14:28

Quote (Daniel Smith @ Feb. 06 2008,14:03)
Quote (blipey @ Feb. 06 2008,11:54)
   
Quote (Daniel Smith @ Feb. 06 2008,13:48)
   
Quote (mitschlag @ Feb. 06 2008,02:51)
Daniel Smith, why have the ideas of Schindewolf, Berg, Goldschmidt, and Davison failed to gain scientific traction and have become footnotes in the history of biological thought?

My answer: They have not generated fruitful, testable hypotheses.

Your answer: ?
---------------------QUOTE-------------------


I think it's because their proposed mechanisms are saltational - and that seems to be a dirty word in scientific circles.
---------------------QUOTE-------------------


So you think it's a conspiracy?
---------------------QUOTE-------------------


No, I think that people are afraid of being ridiculed for wanting to test a saltational theory - so they dismiss it out of hand.  I base this on the great lengths Gould and Eldredge went to in order to show that their theory was not saltational.
---------------------QUOTE-------------------


So, it's not a conspiracy.  ID researchers are just cowardly?

edit: damn typos
Posted by: oldmanintheskydidntdoit on Feb. 06 2008,14:58

Quote (Daniel Smith @ Feb. 06 2008,14:03)
No, I think that people are afraid of being ridiculed for wanting to test a saltational theory - so they dismiss it out of hand.
---------------------QUOTE-------------------


And you think that applies to every single scientist in every country in the world?

OK.

So, Wikipedia notes  :p
 

---------------------QUOTE-------------------
In biology, saltation (from Latin, saltus, "leap") is a sudden change from one generation to the next, that is large, or very large, in comparison with the usual variation of an organism. The term is used for occasionally hypothesized, nongradual changes (especially single-step speciation) that are atypical of, or violate, standard concepts involved in neo-Darwinian evolution. The unorthodox emphasis on saltation as a means of evolutionary change is called saltationism.

Saltation defies the orthodoxy of evolutionary theory, but there are some prominent proponents, including Carl Woese. Polyploidy (most common in plants but not unknown in animals) can be seen as a type of saltation. Polyploidy meets the basic criterea of saltation in that a significant change (in gene numbers) results in speciation in just one generation.
---------------------QUOTE-------------------


And as you appear to have a stake in this matter I'd be interested in your option, Daniel, as to how this saltational theory you are promoting can be tested?

Speculate away. Educate me. I'm genuinely interested.

And Daniel, earlier you said
 

---------------------QUOTE-------------------
I've gone a long way towards learning what the evidence is against my positions.
---------------------QUOTE-------------------


Remind me, did you ever post the evidence for your positions?
And does it not worry you that you reached your conclusions (and have stuck to them it appears) without considering this new evidence against your position? Have you changed your mind about nothing? I mean, perhaps you should now start over again now that you have a balanced view?

You might come to a different conclusion?

And anyway, any new idea worth it's salt survives the "ridicule" stage if it has any worth. Usually. You can't lock an idea away once it's been released!
Posted by: JAM on Feb. 06 2008,16:27

Quote (Daniel Smith @ Feb. 06 2008,13:58)
 
Quote (JAM @ Feb. 06 2008,09:30)
Evidence is the substance of science, not opinion. Thanks for demonstrating again that you were lying when you claimed to be interested in evidence.
---------------------QUOTE-------------------


Where, specifically, is the evidence...
---------------------QUOTE-------------------


In the figures and tables, Dan.

Why did you search for "Schindewolf" in the text instead of looking at the evidence presented in those papers?


---------------------QUOTE-------------------
[you thought was] in that paper [you never read]
---------------------QUOTE-------------------


There were three papers, remember? You got caught lying when you claimed that two of them were "dead links," when I provided citations, not links.


---------------------QUOTE-------------------
... that [supposedly] destroys Schindewolf's theory?
---------------------QUOTE-------------------


Wow. Your mendacity is astounding. I was very, very specific about what these papers showed:
Quote (JAM @ Jan. 24 2008,11:10)
Schindewolf's gaps have been filled, falsifying his hypothesis, even for his speciality, ammonites.
---------------------QUOTE-------------------


Dan, can you ever muster sufficient integrity to simply portray your opponents' positions accurately?

Aren't you bearing false witness every time you misrepresent anyone's position?

How can anyone claiming to follow the teachings of Jesus Christ (who said nothing about evolution, but a lot about the evils of hypocrisy) do what you do with impunity?
Posted by: JAM on Feb. 06 2008,16:32

Quote (Daniel Smith @ Feb. 06 2008,13:54)
My post was never meant to be a defense of my level of knowledge.  It was a defense of my level of effort in learning about ideas that don't jibe with my current views.
---------------------QUOTE-------------------


Ah, but on your arrival here, you claimed to be interested in EVIDENCE. That was a lie. You have frantically evaded the consideration of evidence in favor of quoting opinions. That's pseudoscience in a nutshell.


---------------------QUOTE-------------------
It was in the context of comparison with the amount of effort spent by others on this board in learning more about Schindewolf and Berg.
---------------------QUOTE-------------------


Why should we learn more about PEOPLE'S OPINIONS when you claimed to be interested in EVIDENCE?

Why weren't you interested in the evidence that's been acquired since Schindewolf offered his hypothesis, which depends utterly on the veracity of his assumption that gaps would not be filled?
Posted by: JAM on Feb. 06 2008,16:36

Quote (Daniel Smith @ Feb. 06 2008,14:03)
No, I think that people are afraid of being ridiculed for wanting to test a saltational theory - so they dismiss it out of hand.
---------------------QUOTE-------------------


But you don't dismiss it, so why are you afraid of offering predictions and testing them? If you're so sure you're right, you have nothing but fame ahead of you. I can only conclude that you are lying about your faith in your position.

Also, aren't IDers and creationists ridiculed because they REFUSE to test any of their own hypotheses?

Isn't that refusal the very reason why they (and you) are pseudoscientific frauds?
Posted by: Daniel Smith on Feb. 06 2008,17:42

Quote (JAM @ Feb. 06 2008,14:27)
       
Quote (Daniel Smith @ Feb. 06 2008,13:58)
 
Where, specifically, is the evidence...
---------------------QUOTE-------------------


In the figures and tables, Dan.
---------------------QUOTE-------------------



Which figure, and which table, and what exactly do they show that falsifies (but apparently doesn't destroy) Schindewolf's theory?  Try to be specific about how the data in "the figures and tables" falsifies Schindewolf.  If you say "it fills his gaps" - explain which gaps you are talking about and cite the quotation where Schindewolf made the claim that those specific gaps would never be filled.   Remember JAM, you're all about the evidence!

       

---------------------QUOTE-------------------
Why did you search for "Schindewolf" in the text instead of looking at the evidence presented in those papers?
---------------------QUOTE-------------------




I searched for Schindewolf's name before I read the paper just to see if they mentioned him, then I read the paper.  I did this before I responded to you the first time.  You accused me of searching for his name without reading the paper.  That was an untrue accusation on your part JAM.  You do understand that an accusation doesn't make something true -- don't you JAM?

Then, after responding to you, I read it again.  So I've read it twice (so far).  

Have you read it once yet?
Posted by: blipey on Feb. 06 2008,19:00

With the caveat that I am an actor, not a scientist, let's see if I can give it a whack.

Schindewolf claims that there must have been a number of saltational events in the history of the species of Earth.  He bases this, in part, on the fossil record.  He says that the fossil record is missing a great number transitional fossils.  He claims that this is so because no one has found them, and his take on this is that enough has been found to conclude that there will be no transitionals found (at least for a great many species).

These areas of "no-transitionals" could be considered gaps.  This is because the ToE posits that Universal Common Descent would lead to a more or less steady diversification of life.  Schindewolf claims that this more or less steady action didn't occur.  Graphically:

ToE (Common Descent)
----------------------------
             A
             /\
           B   C
          / \    \
        D    E   F
       / \    /   /\ \
     G   H  I   J K L


Schindewolf's Idea?
----------------------------
           A
          /
        B       C
                   \
    D              F
   /               / \
 G   H     I    J    K          L


Notice there are gaps, Like "E" never existed, but "I" got her somehow anyway.  "H" is around, but has no lineage, etc....

These are gaps.

the claim is that some of these gaps have been filled.  They could be filled with fossil finds.  They could be filled with genetic data.  They could be filled with the stuff in those papers.

Is that about right?  Come on, Dan!  I'm an actor and I can put together your biology argument for you, I think.  Please tell me if I got anything wrong or misrepresented your argument in any way.
Posted by: Albatrossity2 on Feb. 06 2008,19:23

Quote (Daniel Smith @ Feb. 06 2008,17:42)
Which figure, and which table, and what exactly do they show that falsifies (but apparently doesn't destroy) Schindewolf's theory?  Try to be specific about how the data in "the figures and tables" falsifies Schindewolf.  If you say "it fills his gaps" - explain which gaps you are talking about and cite the quotation where Schindewolf made the claim that those specific gaps would never be filled.   Remember JAM, you're all about the evidence!
---------------------QUOTE-------------------


This is just too hilarious.

Recall that Daniel said, on the very first page of this thread  

---------------------QUOTE-------------------
I decided what I needed was just to see the evidence for myself.
---------------------QUOTE-------------------


But now he can't see it, he needs a guide dog...
Posted by: JAM on Feb. 06 2008,20:58

Quote (Daniel Smith @ Feb. 06 2008,17:42)
 
Quote (JAM @ Feb. 06 2008,14:27)
           
Quote (Daniel Smith @ Feb. 06 2008,13:58)
 
Where, specifically, is the evidence...
---------------------QUOTE-------------------


In the figures and tables, Dan.
---------------------QUOTE-------------------



Which figure, and which table, and what exactly do they show that falsifies (but apparently doesn't destroy) Schindewolf's theory?
---------------------QUOTE-------------------



I was not referring to what you call "Schindewolf's theory." I was referring to the hypothesis (more of an assumption) on which it utterly depends:

"The gaps that exist in the continuity of forms, which we always encounter at those very points, are not to be blamed on the fossil record; they are not illusions, but the expression of a natural, primary absence of transitional forms."

I've already explained this to you. Why are you lying and pretending that the evidence is about anything but this assumption/hypothesis?


---------------------QUOTE-------------------
Try to be specific about how the data in "the figures and tables" falsifies Schindewolf.
---------------------QUOTE-------------------


Why should I bother with someone as mendacious as you?


---------------------QUOTE-------------------
If you say "it fills his gaps" - explain which gaps you are talking about and cite the quotation where Schindewolf made the claim that those specific gaps would never be filled.
---------------------QUOTE-------------------


I already did. You have dishonestly tried to pretend that I did not. Moreover, Schindewolf made a general, not a specific, claim.


---------------------QUOTE-------------------
Remember JAM, you're all about the evidence!
---------------------QUOTE-------------------


And you lied when you claimed that you were!
 

---------------------QUOTE-------------------
         

---------------------QUOTE-------------------
Why did you search for "Schindewolf" in the text instead of looking at the evidence presented in those papers?
---------------------QUOTE-------------------


I searched for Schindewolf's name before I read the paper just to see if they mentioned him, then I read the paper.
---------------------QUOTE-------------------


Did everyone see that goalpost move? I asked why he didn't look at the evidence, then Dan dodges my question completely, pretending I was asking whether he had read the paper or not.


---------------------QUOTE-------------------
I did this before I responded to you the first time.
---------------------QUOTE-------------------


But you didn't look at the evidence--in fact, you still haven't.


---------------------QUOTE-------------------
You accused me of searching for his name without reading the paper.
---------------------QUOTE-------------------


No, Dan, I accused you of searching for his name INSTEAD OF LOOKING AT THE EVIDENCE.


---------------------QUOTE-------------------
That was an untrue accusation on your part JAM.
---------------------QUOTE-------------------


It is an untrue accusation, which is why you deliberately and dishonestly decided to falsely attribute it to me.


---------------------QUOTE-------------------
You do understand that an accusation doesn't make something true -- don't you JAM?
---------------------QUOTE-------------------


I do. Do you realize that falsely attributing an accusation to someone doesn't mean that he made the accusation, Dan? Do you realize that it's a blatant violation of a Commandment?


---------------------QUOTE-------------------
Then, after responding to you, I read it again.  So I've read it twice (so far).
---------------------QUOTE-------------------


But you have yet to look at the evidence. That's the big difference between the primary scientific literature and what you choose to quote-mine.


---------------------QUOTE-------------------
Have you read it once yet?
---------------------QUOTE-------------------


Yes. More importantly, primarily I examined the evidence presented in the papers, which exists independently of my, your, Schindewolf's, or the authors' opinions, which is all you read and quoted.

Have you grasped the essential distinction between evidence and opinion, and do you have the integrity to admit that you lack both the desire and curiosity to examine the evidence for yourself, which means that you opened up here with a laughably bald-faced lie?
Posted by: Mark Iosim on Feb. 07 2008,04:50



---------------------QUOTE-------------------
(Mark Iosim @ Feb. 05 2008,23:24)
This is a typical application for GA, as an optimization TOOL by which potential solutions (changing geometry of wires) were RECOGNIZED as less or more effective by fitness function. Following landscape of more effective solutions the program eventually determines one of the optimum geometry of wire antenna.

oldmanintheskydidntdoit
And your point is what, exactly?
---------------------QUOTE-------------------


My point is that GA is misleading respond to my question about existence of statistical analysis that able demonstrating random mutations able to support Evolutionary changes in biological systems. Instead GA is just a software application (like a bunch of other software tools science couldn’t be possible today). As a software application for engineering problem GA is nothing else but optimization tool that among other banal things can “brainstorms” a predefined SET OF POTENTIAL SOLUTIONS.
Almost forget! GA is also is used as propagandistic and deceiving tool to cause impression that Neo-Darwinism is standing on the solid scientific methodology. The fact that you couldn’t find any better than GA argument in favor of random mutations as an engine of evolution, tells me about a lot about Neo-Darwinism theory.


[quote]Mark Iosim I would like to use “Weasel program” to evaluate RM+NS mechanism in the development of drug resistance in bacteria.

   

---------------------QUOTE-------------------
oldmanintheskydidntdoit
It simply means you've learnt nothing from your period of study.
---------------------QUOTE-------------------



To make “Weasel program” to evaluate RM+NS mechanism in the development of drug resistance I need to eliminates just the target that chooses “any line which, however slightly, most resembles the final target”. I expected to find a version of “Weasel program” that let me do this. But I didn’t find what I was looking for.

However this shouldn’t stop me testing RM+NS mechanism in the development of drug resistance using other tool. Peace of paper and calculator should work.

The idea of experiment I would like to propose is very simple:

According to Neo-Darwinism the mechanism of drug resistance development in Bacteria and Viruses is an example of evolutionary change where random mutations transform the virus DNA into new form that enable resisting a drug. I am proposing to trace this transformations using existing experimental data for viruses that developed drug resistance and calculate the probability of the transformational steps, assuming that they caused by random mutations. It is critical for this experiment to choose initial form of virus that doesn’t have any precursor to drug resistance.

My god-feeling is that a calculated probability of these events will be way too low to support observation. But I could be wrong and instead we may have an example of rigorous scientific method that proves beyond reasonable doubt that RM+NS is working.

What do you think about this experiment?
Posted by: Mark Iosim on Feb. 07 2008,04:58

Correction to my previous posting.

[quote]Mark Iosim I would like to use “Weasel program” to evaluate RM+NS mechanism in the development of drug resistance in bacteria.

....means....
     

---------------------QUOTE-------------------
Mark Iosim
I would like to use “Weasel program” to evaluate RM+NS mechanism in the development of drug resistance in bacteria.
---------------------QUOTE-------------------


Any body knows how to edit our own posts?
Posted by: oldmanintheskydidntdoit on Feb. 07 2008,05:28

Quote (Mark Iosim @ Feb. 07 2008,04:50)

As a software application for engineering problem GA is nothing else but optimization tool that among other banal things can “brainstorms” a predefined SET OF POTENTIAL SOLUTIONS.
---------------------QUOTE-------------------


Much like the POTENTIAL SOLUTIONS for any problem "exist" out there, somewhere. The point is that just because a solution exists it does not make it accessible.

You error is in thinking that the solutions are "predefined". If you mean "predefined" as in "the laws of physics determine which shapes will act as better antenna" then you are right. How else could it be? I don't see how that is a problem however? The point is that GA's allow us to reach solutions that otherwise remain inaccessible.
 

---------------------QUOTE-------------------
Almost forget! GA is also is used as propagandistic and deceiving tool to cause impression that Neo-Darwinism is standing on the solid scientific methodology.
---------------------QUOTE-------------------


You could prove that easily , if it were true. As you have not, but only claimed it is so, why should we listen to you?
 

---------------------QUOTE-------------------
The fact that you couldn’t find any better than GA argument in favor of random mutations as an engine of evolution, tells me about a lot about Neo-Darwinism theory.
---------------------QUOTE-------------------


You were given several examples. The fact you have not addressed them makes me thing you realize they cause your argument to fail and so you just ignore them. And in any case, you have not explained what is wrong with this example in any detail except for your opinions about why it is invalid.
 

---------------------QUOTE-------------------
To make “Weasel program” to evaluate RM+NS mechanism in the development of drug resistance I need to eliminates just the target that chooses “any line which, however slightly, most resembles the final target”. I expected to find a version of “Weasel program” that let me do this. But I didn’t find what I was looking for.
---------------------QUOTE-------------------



Then write one! The "Weasel" example is trivial to program. Like I said to Daniel, your options on these matters might start to matter if you provide proof. So learn to program and write some GA code. Then come back and show us.  

 

---------------------QUOTE-------------------
However this shouldn’t stop me testing RM+NS mechanism in the development of drug resistance using other tool. Peace of paper and calculator should work.
---------------------QUOTE-------------------



Try using the computer you are sat at?

 

---------------------QUOTE-------------------
What do you think about this experiment?
---------------------QUOTE-------------------



I tihnk you should be applauded for wanting to test your ideas, unlike Daniel.

Go ahead. I hear the Biologic people are looking for expirements to perform.

EDIT: I befroe e or something. Dunno. Too drunk to care.
Posted by: Daniel Smith on Feb. 07 2008,18:39

Quote (Albatrossity2 @ Feb. 06 2008,17:23)
                   
Quote (Daniel Smith @ Feb. 06 2008,17:42)
Which figure, and which table, and what exactly do they show that falsifies (but apparently doesn't destroy) Schindewolf's theory?  Try to be specific about how the data in "the figures and tables" falsifies Schindewolf.  If you say "it fills his gaps" - explain which gaps you are talking about and cite the quotation where Schindewolf made the claim that those specific gaps would never be filled.   Remember JAM, you're all about the evidence!
---------------------QUOTE-------------------


This is just too hilarious.

Recall that Daniel said, on the very first page of this thread                      

---------------------QUOTE-------------------
I decided what I needed was just to see the evidence for myself.
---------------------QUOTE-------------------


But now he can't see it, he needs a guide dog...
---------------------QUOTE-------------------


What's so "hilarious" about it.  I've been poring over the tables and figures in this paper and can find nothing that contradicts anything Schindewolf said.  Nothing.  Are you going to tell me there's evidence here that I can't see?  If so, what is it?
If you can see it so well (I doubt you can), then tell me specifically - what in the figures and tables falsifies Schindewolf?  (I can't get JAM to break his silence about this, so I'll try you).

Here's a list of the tables and figures in the < paper >:
 

---------------------QUOTE-------------------
Figure 1. Phylogenetic relationships between the hammatoceratins (black bars) and their descendants (grey bars). (a) Single lineage hypothesis (e.g. Donovan, Callomon & Howarth, 1981): hammatoceratins are classified in a single group, named the Hammatoceratinae, and give rise to all Bajocian families. (b) Two-lineage hypothesis (e.g. Rulleau, Elmi & Th´evenard, 2001): hammatoceratins are classified into two groups named the Hammatoceratidae and Erycitidae (both members of the Hammatocerataceae), and each of two families has descendants.
...
Table 1. List of characters used for cladistic analysis
...
Table 2. Data matrix used for cladistic analysis
...
Figure 2. The three most parsimonious cladograms with character state changes labelled. These trees share the same overall topology except for the connection of Abbasites, Riccardiceras, Docidoceras and Mollistephanus.
...
Table 3. Consistency, retention and rescale consistency indices (ci, ri, rc) for the characters used in this analysis; values are identical for the three most parsimonious cladograms
...
Figure 3. Strict consensus tree.
...
Figure 4. Phylostratigraphy of the Hammatocerataceae and initial members of Bajocian groups.

Cladistic analysis of the Middle Jurassic ammonite radiation
S. MOYNE & P. NEIGE

---------------------QUOTE-------------------



Follow the link, look at the data, and tell me what you see in this evidence that IYO falsifies Schindewolf.  I really doubt you will be able to do this because it would involve first learning what Schindewolf said about Jurassic ammonite evolution and his systems of classification -- something I just can't see you (or anyone else on this board) doing.

One thing I will tell you:  Schindewolf extensively utilized shell suture lines in his classifications of ammonites - something these authors -- because of the scope of their study -- were unable to do:  

---------------------QUOTE-------------------
Suture line characters are not used in this analysis because of their high variability between the different species of each genus. Moreover, using suture line characters for such different taxa would involve establishing clear homologies between the different sutural elements via an ontogenetic approach. The wide scope of the present study precludes this.
ibid. pg. 117
---------------------QUOTE-------------------


Schindewolf, on the other hand, extensively documented suture line evolution into the early ontogenetic stages.  You must realize that this was Schindewolf's area of expertise!

The interesting thing is that these authors and Schindewolf arrived at the same "two lineage" conclusion via two different classification methods.  Does that count for anything with you?  Or are you so dead set against Schindewolf that you are willing to dismiss him without even looking at the evidence?

Remember, this was a man about whom Stephen Jay Gould said:  

---------------------QUOTE-------------------
When I was a graduate student in 1965, I asked my advisor, Dr. Norman Newell: "who, in your opinion, is the world's greatest living paleontologist."  He replied, without hesitation, Otto H. Schindewolf.
Foreword, Basic Questions in Paleontology
---------------------QUOTE-------------------



So if you and JAM, (I'm lumping you two together because you're defending him), are going to just flippantly say that this paper somehow falsifies Schindewolf, you're not behaving at all like scientists.
Posted by: oldmanintheskydidntdoit on Feb. 08 2008,02:58

Quote (Daniel Smith @ Feb. 07 2008,18:39)
So if you and JAM, (I'm lumping you two together because you're defending him), are going to just flippantly say that this paper somehow falsifies Schindewolf, you're not behaving at all like scientists.
---------------------QUOTE-------------------


And you are?

In that case Daniel, do something sciency.
Posted by: mitschlag on Feb. 08 2008,04:35

Quote (Daniel Smith @ Feb. 07 2008,18:39)
Follow the link, look at the data, and tell me what you see in this evidence that IYO falsifies Schindewolf.  I really doubt you will be able to do this because it would involve first learning what Schindewolf said about Jurassic ammonite evolution and his systems of classification -- something I just can't see you (or anyone else on this board) doing.
---------------------QUOTE-------------------


Thanks for the link to the Moyne & Neige paper.

It would also be a kindness, and I hope not too much trouble, if you would either quote or give page citations to the relevant statements in Grundfragen that are in contention by JAM.

Kudos for stepping up to the plate in this fashion.
Posted by: oldmanintheskydidntdoit on Feb. 08 2008,06:20

Quote (mitschlag @ Feb. 08 2008,04:35)
Kudos for stepping up to the plate in this fashion.
---------------------QUOTE-------------------


Agreed.

It's all about the specifics.
Posted by: JAM on Feb. 08 2008,09:21

Quote (Daniel Smith @ Feb. 07 2008,18:39)

What's so "hilarious" about it.  I've been poring over the tables and figures in this paper and can find nothing that contradicts anything Schindewolf said.
---------------------QUOTE-------------------


Let's not forget that you frantically moved the goalposts, when this paper is about contradicting his assumption, on which his "theory" depends:
"The gaps that exist in the continuity of forms, which we always encounter at those very points, are not to be blamed on the fossil record; they are not illusions, but the expression of a natural, primary absence of transitional forms."
 

---------------------QUOTE-------------------
Nothing.
---------------------QUOTE-------------------


So, Dan, in the context of Schindewolf's claim above, tell me where in the nested hierarchy Schindewolf classified Riccardiceras.
 

---------------------QUOTE-------------------
Are you going to tell me there's evidence here that I can't see?
---------------------QUOTE-------------------


I'm telling you that you are afraid of evidence.

I'm telling you that you fabricate evidence when your political positions are threatened by real evidence, as you did when you claimed that the isthmus of Panama isolated Atlantic and Pacific humpback whale populations, a claim that an 8-year-old can see is false by glancing at a globe.

You also fabricated evidence when you made the inadvertent prediction (based on your hypothesis of how our bodies were designed by God) that "hind limb genes" even existed, a dishonest claim that you lack the integrity to either support or retract.


---------------------QUOTE-------------------
One thing I will tell you:  Schindewolf extensively utilized shell suture lines in his classifications of ammonites - something these authors -- because of the scope of their study -- were unable to do:        

---------------------QUOTE-------------------
Suture line characters are not used in this analysis because of their high variability between the different species of each genus. Moreover, using suture line characters for such different taxa would involve establishing clear homologies between the different sutural elements via an ontogenetic approach. The wide scope of the present study precludes this.
ibid. pg. 117
---------------------QUOTE-------------------


---------------------QUOTE-------------------


Dan, you twist the most obvious things to fit your sick political views so that they are unrecognizable.

Schindewolf's reliance on suture lines is the reason I keep asking you (and you keep ducking, because you know you are being dishonest) these questions:
1) How many nucleotide changes are required to change the number of mammalian vertebrae in an individual?
2) How many nucleotide changes are required to change the identity of a mammalian vertebra?

Surely we can agree that the genetic complexity involved in constructing the different vertebral morphologies is far, far greater than the genetic complexity of a suture line in an ammonite's shell.

 

---------------------QUOTE-------------------
Schindewolf, on the other hand, extensively documented suture line evolution into the early ontogenetic stages.  You must realize that this was Schindewolf's area of expertise!
---------------------QUOTE-------------------


I realize that. I also realize that EVEN LIMITING CONSIDERATION TO SUTURE LINES, Schindewolf's gaps have been filled:
 

---------------------QUOTE-------------------
Biological Reviews
May 1973 - Vol. 48 Issue 2 Page 159-194
EVOLUTION OR REVOLUTION OF AMMONOIDS AT MESOZOIC SYSTEM BOUNDARIES
JOST WIEDMANN
---------------------QUOTE-------------------


This is a review, so the evidence contradicting Schindewolf's claim is in the primary literature cited by Wiedmann, not in his words.
 

---------------------QUOTE-------------------
The interesting thing is that these authors and Schindewolf arrived at the same "two lineage" conclusion via two different classification methods.  Does that count for anything with you?
---------------------QUOTE-------------------


Nothing, because the reason I cited the evidence in this paper is to contradict Schindewolf's assumption: "The gaps that exist in the continuity of forms, which we always encounter at those very points, are not to be blamed on the fossil record; they are not illusions, but the expression of a natural, primary absence of transitional forms."

Why do you keep trying to move the goalposts to misrepresent my position as anything else, Dan?
 

---------------------QUOTE-------------------
Or are you so dead set against Schindewolf that you are willing to dismiss him without even looking at the evidence?
---------------------QUOTE-------------------


The issue here is that YOU have embraced Schindewolf's most arrogant, tenuous assumption without looking at ANY evidence. If you were all about the evidence, you would have undertaken a thorough review of the primary ammonite paleontology literature for the last half-century to determine if Schindewolf's assumption about gaps has held up. You didn't, which makes your statement above profoundly hypocritical. What does your Bible say about hypocrisy?
 

---------------------QUOTE-------------------
Remember, this was a man about whom Stephen Jay Gould said:        

---------------------QUOTE-------------------
When I was a graduate student in 1965, I asked my advisor, Dr. Norman Newell: "who, in your opinion, is the world's greatest living paleontologist."  He replied, without hesitation, Otto H. Schindewolf.
Foreword, Basic Questions in Paleontology
---------------------QUOTE-------------------


---------------------QUOTE-------------------


My God, Dan, your ego has damaged your reading comprehension. Gould isn't touting Schindewolf in that quote!
Posted by: Wesley R. Elsberry on Feb. 08 2008,11:16

Gould, later in the same foreword, specifically criticizes Schindewolf for paying attention only to confirming evidence, and ignoring disconfirming evidence.

It seems that Schindewolf has found an apt pupil.
Posted by: mitschlag on Feb. 08 2008,11:38

Quote (Wesley R. Elsberry @ Feb. 08 2008,11:16)
Gould, later in the same foreword, specifically criticizes Schindewolf for paying attention only to confirming evidence, and ignoring disconfirming evidence.

It seems that Schindewolf has found an apt pupil.
---------------------QUOTE-------------------


See, Dan, some of us have read Schindewolf's book.
Posted by: Albatrossity2 on Feb. 08 2008,11:45

Quote (Daniel Smith @ Feb. 07 2008,18:39)
So if you and JAM, (I'm lumping you two together because you're defending him), are going to just flippantly say that this paper somehow falsifies Schindewolf, you're not behaving at all like scientists.
---------------------QUOTE-------------------


I'm not defending JAM so much as I am enjoying his systematic take-down of your ever-fluid goalposts; he doesn't need my assistance.

As for pointing you to the exact line in the table or figure that indicates that Schindewolf is wrong, you have again putting words in my mouth. Read back through this thread and see if you can find where I said that this paper falsifies Schindewolf. You won't find it; I never said it. I don't claim to have read this paper; as noted before I am not a paleontologist. So I think that I am behaving like a scientist.

I'm not pretending that I know about all fields of science; I've stuck with what I know something about.

I'm not pretending to understand something that I don't understand.

I'm not constructing strawmen, moving the goalposts, or putting words in other's mouths.

I've admitted when I'm wrong, and clarified when it was pointed out to me that I was unclear.

Maybe if you behaved more like that, I wouldn't find your statements (I'm all about the evidence, but when I am looking at primary evidence, I don't know how to figure it out) so hilarious.
Posted by: Daniel Smith on Feb. 08 2008,13:44

Quote (mitschlag @ Feb. 08 2008,09:38)
 
Quote (Wesley R. Elsberry @ Feb. 08 2008,11:16)
Gould, later in the same foreword, specifically criticizes Schindewolf for paying attention only to confirming evidence, and ignoring disconfirming evidence.

It seems that Schindewolf has found an apt pupil.
---------------------QUOTE-------------------


See, Dan, some of us have read Schindewolf's book.
---------------------QUOTE-------------------


Correct me if I'm wrong, but I think Wesley has only read the foreword, and you have just skimmed through it (the book that is).  

Is that correct? (Wesley?)
Posted by: JAM on Feb. 08 2008,13:56

Quote (Daniel Smith @ Feb. 08 2008,13:44)
Quote (mitschlag @ Feb. 08 2008,09:38)
 
Quote (Wesley R. Elsberry @ Feb. 08 2008,11:16)
Gould, later in the same foreword, specifically criticizes Schindewolf for paying attention only to confirming evidence, and ignoring disconfirming evidence.

It seems that Schindewolf has found an apt pupil.
---------------------QUOTE-------------------


See, Dan, some of us have read Schindewolf's book.
---------------------QUOTE-------------------


Correct me if I'm wrong, but I think Wesley has only read the foreword, and you have just skimmed through it (the book that is).  
---------------------QUOTE-------------------


Why would that matter?

If he's read the foreword and can easily show that you are misrepresenting Gould in such a basic matter from a tiny sample, why would your claim to have read the book, especially given your rank mendacity wrt your evidentophobia, have any weight with us?

Where are those hind limb genes, btw?
Posted by: blipey on Feb. 08 2008,15:35

Quote (Daniel Smith @ Feb. 08 2008,13:44)
Quote (mitschlag @ Feb. 08 2008,09:38)
 
Quote (Wesley R. Elsberry @ Feb. 08 2008,11:16)
Gould, later in the same foreword, specifically criticizes Schindewolf for paying attention only to confirming evidence, and ignoring disconfirming evidence.

It seems that Schindewolf has found an apt pupil.
---------------------QUOTE-------------------


See, Dan, some of us have read Schindewolf's book.
---------------------QUOTE-------------------


Correct me if I'm wrong, but I think Wesley has only read the foreword, and you have just skimmed through it (the book that is).  

Is that correct? (Wesley?)
---------------------QUOTE-------------------


I've not read the book, but I have read other books--and some of them have even had forwards (though most of those didn't have pictures)  :angry:

If you are completely misrepresenting Gould once in what--a foreward is probably about  pages long?--3 pages, just think of the amount of lies you could tell over the whole book!

I'm guessing the number could run into the hundreds!
Posted by: mitschlag on Feb. 08 2008,15:54

Quote (Daniel Smith @ Feb. 08 2008,13:44)
 
Quote (mitschlag @ Feb. 08 2008,09:38)
     
Quote (Wesley R. Elsberry @ Feb. 08 2008,11:16)
Gould, later in the same foreword, specifically criticizes Schindewolf for paying attention only to confirming evidence, and ignoring disconfirming evidence.

It seems that Schindewolf has found an apt pupil.
---------------------QUOTE-------------------


See, Dan, some of us have read Schindewolf's book.
---------------------QUOTE-------------------


Correct me if I'm wrong, but I think Wesley has only read the foreword, and you have just skimmed through it (the book that is).  

Is that correct? (Wesley?)
---------------------QUOTE-------------------


My comment was intended in jest.  I guess I overestimate my comedic skills.  And my audience.
Posted by: Daniel Smith on Feb. 08 2008,18:44

Quote (Wesley R. Elsberry @ Feb. 08 2008,09:16)
Gould, later in the same foreword, specifically criticizes Schindewolf for paying attention only to confirming evidence, and ignoring disconfirming evidence.
---------------------QUOTE-------------------


I'm supposing you mean this:        

---------------------QUOTE-------------------
Schindewolf follows a conventional scientific conceit in claiming that he worked objectively, moving upward and outward from an empirical base in the groups he knew best--ammonites and corals.  In fact, this book represents the imposition of a worldview upon selected components of the empirical record.  Opposing views are scarcely discussed or even cited.
Stephen Jay Gould, foreword, Basic questions in Paleontology pg. xi
---------------------QUOTE-------------------



The interesting thing about that quote is that Schindewolf does speak often about opposing views in the book.  Gould specifically mentions George Gaylord Simpson later in the foreword as a "champion" of the Modern Synthesis, claiming that he has "laid to rest" Schindewolf's "ghosts", yet Schindewolf often speaks of Simpson's positions -- mentioning his name 9 times in his book.  So, I'm not sure exactly what Gould was getting at.  

I wonder though, since he was so often accused of advocating a saltational hypothesis himself, (punctuated equilibrium), if Gould wasn't attempting to distance himself from all such theories.  I know I was certainly struck by the parallels with Schindewolf when I read the Gould & Eldredge < paper > "Punctuated equilibrium comes of age" ---quick, almost invisible (as far as the fossil record is concerned) "speciation events" followed by long periods of evolutionary "stasis" ---it's not too distant a cousin to typogenesis and typostasis if you ask me.
Posted by: Daniel Smith on Feb. 08 2008,19:09

Quote (mitschlag @ Feb. 08 2008,02:35)
       
Quote (Daniel Smith @ Feb. 07 2008,18:39)
Follow the link, look at the data, and tell me what you see in this evidence that IYO falsifies Schindewolf.  I really doubt you will be able to do this because it would involve first learning what Schindewolf said about Jurassic ammonite evolution and his systems of classification -- something I just can't see you (or anyone else on this board) doing.
---------------------QUOTE-------------------


Thanks for the link to the Moyne & Neige paper.

It would also be a kindness, and I hope not too much trouble, if you would either quote or give page citations to the relevant statements in Grundfragen that are in contention by JAM.

Kudos for stepping up to the plate in this fashion.
---------------------QUOTE-------------------


Well, as to exactly what is in contention by JAM--you'll have to ask him.  He keeps talking about "gaps", but he doesn't seem to be able to recognize the context of Schindewolf's statements.  He then goes on to claim that there's "evidence" that Schindewolf said would never be found.  I don't know what that evidence is since he just says "it's in the figures and tables".  I've looked through the figures and tables and they list morphological characteristics of ammonite lineages that Schindewolf was probably well aware of - since most were discovered before Basic Questions was written.  JAM has specifically mentioned pages 105-106, and I quoted some from pages 102-103 in one of my responses.  I can't read his mind though.  

As for me though, I would recommend reading pages 125-145 to start -- this is where Schindewolf first goes into some detail on the topic of Ammonoid evolution as an "Introductory Example" for his theory.  The time period under discussion (for this one paper at least) is the Middle Jurassic.

Hope that helps!
Posted by: JAM on Feb. 08 2008,19:18

Quote (Daniel Smith @ Feb. 08 2008,19:09)

Well, as to exactly what is in contention by JAM--you'll have to ask him.

---------------------QUOTE-------------------

BS. I've quoted Schindewolf at least three times, and you've still tried to pretend that I'm challenging something else.


---------------------QUOTE-------------------
 I don't know what that evidence is since he just says "it's in the figures and tables".
---------------------QUOTE-------------------


IOW, you were lying when you claimed on the first page, "I decided what I needed was just to see the evidence for myself."

You've never really looked at evidence.



---------------------QUOTE-------------------
I've looked through the figures and tables and they list morphological characteristics of ammonite lineages that Schindewolf was probably well aware of - since most were discovered before Basic Questions was written.
---------------------QUOTE-------------------


What about the ones that were discovered after, doofus?


---------------------QUOTE-------------------
JAM has specifically mentioned pages 105-106, and I quoted some from pages 102-103 in one of my responses.  I can't read his mind though.
---------------------QUOTE-------------------


That's odd, as you've claimed to be able to several times before. What a hypocrite.  


---------------------QUOTE-------------------
As for me though, I would recommend reading pages 125-145 to start -- this is where Schindewolf first goes into some detail on the topic of Ammonoid evolution as an "Introductory Example" for his theory.
---------------------QUOTE-------------------


Why would someone interested in the evidence recommend the text over the limited amount of evidence in the book?

For that matter, why would someone interested in the evidence recommend a 50-year-old book instead of the primary literature?

You lie like a rug, Dan.
Posted by: Daniel Smith on Feb. 08 2008,19:22

Quote (Wesley R. Elsberry @ Feb. 08 2008,09:16)
Gould, later in the same foreword, specifically criticizes Schindewolf for paying attention only to confirming evidence, and ignoring disconfirming evidence.
---------------------QUOTE-------------------


I also noticed Wesley, while browsing the table of contents, that Schindewolf has a section entitled "The Pros and Cons of Typostrophism" in which he chronicles "Six Objections and Their Refutations".  This section begins at page 224 and goes to page 255.  That's over 30 pages devoted to the discussion of "opposing views".

So much for their "scarce discussion" I guess.
Posted by: Daniel Smith on Feb. 08 2008,19:36

Quote (JAM @ Feb. 08 2008,07:21)

I'm telling you that you are afraid of evidence.

I'm telling you that you fabricate evidence when your political positions are threatened by real evidence, as you did when you claimed that the isthmus of Panama isolated Atlantic and Pacific humpback whale populations, a claim that an 8-year-old can see is false by glancing at a globe.

You also fabricated evidence when you made the inadvertent prediction (based on your hypothesis of how our bodies were designed by God) that "hind limb genes" even existed, a dishonest claim that you lack the integrity to either support or retract.
---------------------QUOTE-------------------



Yes, I was wrong (although I was being a bit facetious) when I spoke of the "hind-leg gene".  I do know that there is no such thing - I just don't bother responding to most of your posts or accusations.  I'm only responding to this now because you continually bring it up as if it somehow defines me.

Also, I already explained the whale thing so let it go.

And now I'm going to rephrase my position on the Moyne & Neige paper specifically for your anal-retentive benefit:
I looked at their evidence and found that it supports Schindewolf's classifications of middle Jurassic ammonites.

Now, it is up to you to show that it does not.
Posted by: Albatrossity2 on Feb. 08 2008,19:51

Quote (Daniel Smith @ Feb. 08 2008,19:36)
Yes, I was wrong (although I was being a bit facetious) when I spoke of the "hind-leg gene".  I do know that there is no such thing - I just don't bother responding to most of your posts or accusations.  I'm only responding to this now because you continually bring it up as if it somehow defines me.
---------------------QUOTE-------------------


Well, it does define you, unfortunately.

I suspect that you had no idea of the ludicrousness of your position about "hind leg genes" when you first posted it. If you did, you would have said something at the time. But you didn't do that; you let it fester, hoping it would eventually subside. Now when you say you "know" that there is no such thing, it rings hollow. Why didn't you say that when it mattered, and admit that you were clueless about modern evo-devo evidence?

Sorry, Daniel, but it doesn't matter now. You had a chance to prove that you were indeed sincere in this discussion, by admitting that you were mistaken. By acting as if you knew it all along, you have defined yourself fairly concretely as just another creationist poser.
Posted by: blipey on Feb. 09 2008,04:05

Quote (Albatrossity2 @ Feb. 08 2008,19:51)
Quote (Daniel Smith @ Feb. 08 2008,19:36)
Yes, I was wrong (although I was being a bit facetious) when I spoke of the "hind-leg gene".  I do know that there is no such thing - I just don't bother responding to most of your posts or accusations.  I'm only responding to this now because you continually bring it up as if it somehow defines me.
---------------------QUOTE-------------------


Well, it does define you, unfortunately.

I suspect that you had no idea of the ludicrousness of your position about "hind leg genes" when you first posted it. If you did, you would have said something at the time. But you didn't do that; you let it fester, hoping it would eventually subside. Now when you say you "know" that there is no such thing, it rings hollow. Why didn't you say that when it mattered, and admit that you were clueless about modern evo-devo evidence?

Sorry, Daniel, but it doesn't matter now. You had a chance to prove that you were indeed sincere in this discussion, by admitting that you were mistaken. By acting as if you knew it all along, you have defined yourself fairly concretely as just another creationist poser.
---------------------QUOTE-------------------


God hates you.  And your tiny bunny rabbits, too.
Posted by: mitschlag on Feb. 09 2008,04:55

Quote (Daniel Smith @ Feb. 08 2008,19:09)
JAM has specifically mentioned pages 105-106, and I quoted some from pages 102-103 in one of my responses.  I can't read his mind though.  

As for me though, I would recommend reading pages 125-145 to start -- this is where Schindewolf first goes into some detail on the topic of Ammonoid evolution as an "Introductory Example" for his theory.  The time period under discussion (for this one paper at least) is the Middle Jurassic.

Hope that helps!
---------------------QUOTE-------------------


Thanks, I'll work on it!

In the meantime, I've read the Moyne & Neige paper, and I see that their cladistic analyses (which certainly took a large number of morphologic characters into account) led to the conclusion that  there were two middle Jurassic ammonite lineages.  It seems reasonable that later work would have refined the product of Schindewolf's labors.  So, like Daniel, I don't see anything in the paper that bears on the issue of orthogenesis vs natural selection.

And, like Daniel, I need HELP! in understanding JAM's points.
Posted by: mitschlag on Feb. 09 2008,05:07

Quote (Albatrossity2 @ Feb. 08 2008,19:51)
Sorry, Daniel, but it doesn't matter now. You had a chance to prove that you were indeed sincere in this discussion, by admitting that you were mistaken. By acting as if you knew it all along, you have defined yourself fairly concretely as just another creationist poser.
---------------------QUOTE-------------------


All of that notwithstanding, isn't it more interesting to focus on his arguments?

It's not easy for many of us to admit error.
Posted by: Albatrossity2 on Feb. 09 2008,07:36

Quote (mitschlag @ Feb. 09 2008,05:07)
 
Quote (Albatrossity2 @ Feb. 08 2008,19:51)
Sorry, Daniel, but it doesn't matter now. You had a chance to prove that you were indeed sincere in this discussion, by admitting that you were mistaken. By acting as if you knew it all along, you have defined yourself fairly concretely as just another creationist poser.
---------------------QUOTE-------------------


All of that notwithstanding, isn't it more interesting to focus on his arguments?
---------------------QUOTE-------------------


Sure it is. However, it would be a lot easier to focus on the arguments if they didn't change shape, or disappear altogether, when contradicting evidence is brought into his view.

His teleological definition of natural selection is a perfect example of this problem...
Posted by: Daniel Smith on Feb. 09 2008,11:02

Quote (Albatrossity2 @ Feb. 08 2008,17:51)
     
Quote (Daniel Smith @ Feb. 08 2008,19:36)
Yes, I was wrong (although I was being a bit facetious) when I spoke of the "hind-leg gene".  I do know that there is no such thing - I just don't bother responding to most of your posts or accusations.  I'm only responding to this now because you continually bring it up as if it somehow defines me.
---------------------QUOTE-------------------


Well, it does define you, unfortunately.

I suspect that you had no idea of the ludicrousness of your position about "hind leg genes" when you first posted it. If you did, you would have said something at the time. But you didn't do that; you let it fester, hoping it would eventually subside. Now when you say you "know" that there is no such thing, it rings hollow. Why didn't you say that when it mattered, and admit that you were clueless about modern evo-devo evidence?

Sorry, Daniel, but it doesn't matter now. You had a chance to prove that you were indeed sincere in this discussion, by admitting that you were mistaken. By acting as if you knew it all along, you have defined yourself fairly concretely as just another creationist poser.
---------------------QUOTE-------------------


Let me just say this about that:  Almost every post here has accused me of ignorance, lying, hypocrisy, or some other wrongdoing.  If I took the time to respond to every point raised in objection to my posts, I'd have very little time left in the day for other things.  So, I try to limit my responses (mostly anyway) to the most important matters regarding the current discussion.  JAM is bringing up things that were said weeks ago on a whole different topic.  What relevance does that have now?  Besides, I responded to JAMs objections to my mistake about humpback whales and he still brings it up!  So, I figure responding to his accusations is pretty much a lost cause.  I only do it occasionally when he repeats his accusations so often it starts to sway the debate.  I had hoped that reasonable people could see through his tactics and would give me the benefit of the doubt.  Maybe I was wrong about that.
Posted by: Albatrossity2 on Feb. 09 2008,13:35

Quote (Daniel Smith @ Feb. 09 2008,11:02)
If I took the time to respond to every point raised in objection to my posts, I'd have very little time left in the day for other things.
---------------------QUOTE-------------------


Maybe that should tell you something...
Posted by: JAM on Feb. 09 2008,13:51

Quote (Daniel Smith @ Feb. 08 2008,19:36)
     
Quote (JAM @ Feb. 08 2008,07:21)

I'm telling you that you are afraid of evidence.

I'm telling you that you fabricate evidence when your political positions are threatened by real evidence, as you did when you claimed that the isthmus of Panama isolated Atlantic and Pacific humpback whale populations, a claim that an 8-year-old can see is false by glancing at a globe.

You also fabricated evidence when you made the inadvertent prediction (based on your hypothesis of how our bodies were designed by God) that "hind limb genes" even existed, a dishonest claim that you lack the integrity to either support or retract.
---------------------QUOTE-------------------


Yes, I was wrong (although I was being a bit facetious) when I spoke of the "hind-leg gene".
---------------------QUOTE-------------------


BS. You even expanded upon it.
   

---------------------QUOTE-------------------
I do know that there is no such thing -
---------------------QUOTE-------------------


ORLY? Then why did you write the following?
   
Quote (Daniel Smith @ Nov. 18 2007,19:19)
       
Quote (JAM @ Nov. 18 2007,15:30)
  A) Do you predict that whales will be missing a hind-leg gene?
---------------------QUOTE-------------------

Not necessarily - though I predict it will be suppressed as to it's full development.  IOW, the non-coding "support cast" for that gene will be markedly different from animals that have fully developed hind legs.                    

---------------------QUOTE-------------------
Do you predict that monkeys have a tail gene that humans lack?
---------------------QUOTE-------------------

No.  I predict that their "tail gene(s)" (at least the protein coding parts) may be similar to ours, but all their various regulatory and support elements will be markedly different from ours.  Theirs will have much more activity and development in these non-coding areas - possibly evidenced by a markedly higher level of histone activity.  Ours will be suppressed.  
---------------------QUOTE-------------------


 

---------------------QUOTE-------------------
I just don't bother responding to most of your posts or accusations.
---------------------QUOTE-------------------


Non sequitur, as you did respond to this in a completely nonfacetious way.
 

---------------------QUOTE-------------------
I'm only responding to this now because you continually bring it up as if it somehow defines me.
---------------------QUOTE-------------------


It does. You responded to it before, and then you ran away, because you lack the integrity to admit that you were wrong.
 

---------------------QUOTE-------------------
Also, I already explained the whale thing so let it go.
---------------------QUOTE-------------------


No, you did not explain it. I still have no idea how you could have inferred something so spectacularly wrong from what you read.
 

---------------------QUOTE-------------------
And now I'm going to rephrase my position on the Moyne & Neige paper specifically for your anal-retentive benefit:
[b]I looked at their evidence</b> and found that it supports Schindewolf's classifications of middle Jurassic ammonites.
---------------------QUOTE-------------------


You're a fundamentally dishonest joke. I never challenged Schindewolf's classifications of anything. I challenged his assumption, that I have now quoted for you at least four times:
 

---------------------QUOTE-------------------
[b]"The gaps that exist in the continuity of forms, which we always encounter at those very points, are not to be blamed on the fossil record; they are not illusions, but the expression of a natural, primary absence of transitional forms."
---------------------QUOTE-------------------


What don't you understand about this?
 

---------------------QUOTE-------------------
Now, it is up to you to show that it does not.
---------------------QUOTE-------------------


No, arrogant, dishonest fake Christians like you do not get to revise my challenge. It stands perfectly well, and your repeated, deliberate misrepresentation of it shows that you know I'm right.
Posted by: mitschlag on Feb. 09 2008,16:17

JAM, you are most definitely a BOLD fellow.
Posted by: mitschlag on Feb. 09 2008,16:51

Quote (JAM @ Feb. 09 2008,13:51)
       

---------------------QUOTE-------------------
And now I'm going to rephrase my position on the paper specifically for your anal-retentive benefit:
I looked at their evidence and found that it supports Schindewolf's classifications of middle Jurassic ammonites.
---------------------QUOTE-------------------


You're a fundamentally dishonest joke. I never challenged Schindewolf's classifications of anything. I challenged his assumption, that I have now quoted for you at least four times:
           

---------------------QUOTE-------------------
"The gaps that exist in the continuity of forms, which we always encounter at those very points, are not to be blamed on the fossil record; they are not illusions, but the expression of a natural, primary absence of transitional forms."
---------------------QUOTE-------------------


What don't you understand about this?

---------------------QUOTE-------------------


So, what in the name of Darwin (may his name be eternally praised) does the Moyne & Neige paper have to do with    

---------------------QUOTE-------------------
"The gaps that exist in the continuity of forms, which we always encounter at those very points, are not to be blamed on the fossil record; they are not illusions, but the expression of a natural, primary absence of transitional forms."
---------------------QUOTE-------------------

?

Let the Delphic Oracle speak...
Posted by: JAM on Feb. 09 2008,17:15

Quote (mitschlag @ Feb. 09 2008,16:51)
So, what in the name of Darwin (may his name be eternally praised) does the Moyne & Neige paper have to do with      

---------------------QUOTE-------------------
"The gaps that exist in the continuity of forms, which we always encounter at those very points, are not to be blamed on the fossil record; they are not illusions, but the expression of a natural, primary absence of transitional forms."
---------------------QUOTE-------------------

?
---------------------QUOTE-------------------


The gaps are, to a large extent, blamed on the incompleteness of the fossil record in Schindewolf's day. Thus, they are largely illusory.

This negative assumption is integral to Schindewolf's thesis, and it's hooey.

Note also that to credibly assert a negative, one needs a LOT of evidence, and Daniel has zero interest in determining whether any gaps in the ammonite fossil record have been bridged in the last 50 years by new finds.
Posted by: mitschlag on Feb. 09 2008,18:30

Quote (JAM @ Feb. 09 2008,17:15)
     
Quote (mitschlag @ Feb. 09 2008,16:51)
So, what in the name of Darwin (may his name be eternally praised) does the Moyne & Neige paper have to do with              

---------------------QUOTE-------------------
"The gaps that exist in the continuity of forms, which we always encounter at those very points, are not to be blamed on the fossil record; they are not illusions, but the expression of a natural, primary absence of transitional forms."
---------------------QUOTE-------------------

?
---------------------QUOTE-------------------


The gaps are, to a large extent, blamed on the incompleteness of the fossil record in Schindewolf's day. Thus, they are largely illusory.

This negative assumption is integral to Schindewolf's thesis, and it's hooey.

Note also that to credibly assert a negative, one needs a LOT of evidence, and Daniel has zero interest in determining whether any gaps in the ammonite fossil record have been bridged in the last 50 years by new finds.
---------------------QUOTE-------------------


Yeah, of course you're right in principle.  And of course Schindewolf was insane to predict that transitional forms would never be found, because their existence would be "not even possible or conceivable" (page 106).

But, but , but isn't the devil in the details?  That Moyne and Neige and others have added new data is great.  But is it too much to ask you to point out how their data fill the gaps that Schindewolf made such a stink about?
Posted by: Daniel Smith on Feb. 09 2008,19:26

Quote (JAM @ Feb. 09 2008,11:51)
               
Quote (Daniel Smith @ Feb. 08 2008,19:36)
And now I'm going to rephrase my position on the Moyne & Neige paper specifically for your anal-retentive benefit:
I looked at their evidence and found that it supports Schindewolf's classifications of middle Jurassic ammonites.
---------------------QUOTE-------------------


You're a fundamentally dishonest joke. I never challenged Schindewolf's classifications of anything. I challenged his assumption, that I have now quoted for you at least four times:
                   

---------------------QUOTE-------------------
"The gaps that exist in the continuity of forms, which we always encounter at those very points, are not to be blamed on the fossil record; they are not illusions, but the expression of a natural, primary absence of transitional forms."
---------------------QUOTE-------------------


What don't you understand about this?
                   

---------------------QUOTE-------------------
Now, it is up to you to show that it does not.
---------------------QUOTE-------------------


---------------------QUOTE-------------------


Alright JAM, once and for all...

You are missing the point Schindewolf is making.

               

---------------------QUOTE-------------------
"The gaps that exist in the continuity of forms, which we always encounter at those very points, are not to be blamed on the fossil record; they are not illusions, but the expression of a natural, primary absence of transitional forms."
---------------------QUOTE-------------------



What are "those very points" of which Schindewolf speaks?

Here's the context of the quote you misrepresent:
             

---------------------QUOTE-------------------
When, therefore, the preserved material is sufficient to substantiate continuous evolutionary lineages within the individual structural designs, it should follow, if the assumption of a gradual bridging of the type boundaries by means of small developmental steps is correct, that the same situation applies between them.  Moreover, in view of the significant differences we see among the organizations of the individual types, a connecting series of the sort just referred to would not even have to have been very long or composed of many members.  However, there are no special conditions whatsoever in the fossil record that would indicate that gaps had repeatedly affected only the sequences that connect structural designs.  The gaps that exist in the continuity of forms, which we always encounter at those very points, are not to be blamed on the fossil record; they are not illusions, but the expression of a natural, primary absence of transitional forms.
Basic Questions in Paleontology, pg. 105, italics his, bold mine
---------------------QUOTE-------------------



It is quite easy to see, from the context you avoid, that Schindewolf is talking specifically about gaps between "types" - which he also refers to as "structural designs".  These types are said to have "significant differences" between them.  

Your contention that Schindewolf is just talking about "gaps in the fossil record" is a bogus strawman.  That is why you have convinced yourself that modern evidence, (which does fill up gaps within the individual structural designs, and even reveals new types), somehow falsifies Schindewolf's contention that the gaps between structural designs will not be filled.

Tell me specifically what Schindewolf meant by "types"?  Then explain to me which "gaps between types" were filled by the evidence in the Moyne & Neige paper?  You obviously know these things else surely you would not have made such a claim.

Have you ever bothered JAM, to look at the evidence Schindewolf has amassed in support of his claim?  His book is full of figures and tables.  There are even pictures!  You should really look into it a bit more before making assumptions such as these.
Posted by: blipey on Feb. 09 2008,19:41

Hey Daniel,

As has been explained to you those gaps of his don't exist--no matter where they are.  To argue that they really do exist, please tell me where my argument above goes wrong. Tell me why those gaps aren't the ones Schindewolf was proposing.  I'll reproduce it here for your convenience:



---------------------QUOTE-------------------
ToE (Common Descent)
----------------------------
            A
            /\
          B   C
         / \    \
       D    E   F
      / \    /   /\ \
    G   H  I   J K L


Schindewolf's Idea?
----------------------------
          A
         /
       B       C
                  \
   D              F
  /               / \
G   H     I    J    K          L

---------------------QUOTE-------------------


Posted by: JAM on Feb. 09 2008,22:13

Quote (Daniel Smith @ Feb. 09 2008,19:26)
Alright JAM, once and for all...

You are missing the point Schindewolf is making.
---------------------QUOTE-------------------


No, I understand the point he was trying to make, and moreover, I understand why it is untenable today. Schindewolf has an excuse, but you don't.
 

---------------------QUOTE-------------------
"The gaps that exist in the continuity of forms, which we always encounter at those very points, are not to be blamed on the fossil record; they are not illusions, but the expression of a natural, primary absence of transitional forms."
---------------------QUOTE-------------------


 

---------------------QUOTE-------------------
What are "those very points" of which Schindewolf speaks?
---------------------QUOTE-------------------


The discontinuities between what he refers to as "types," of course, which can mean anything from phyla to genera.
 

---------------------QUOTE-------------------
Here's the context of the quote you misrepresent:
---------------------QUOTE-------------------


I'm not misrepresenting anything.
 

---------------------QUOTE-------------------
When, therefore, the preserved material is sufficient to substantiate continuous evolutionary lineages within the individual structural designs,...
---------------------QUOTE-------------------


Yes, Dan, and that's why, in the context of "structural designs," which is bullshit if taken literally, I have been asking you questions that you have avoided, because in your shallow little soul, you know full well that you are wrong:
--------------
 
Quote (JAM @ Jan. 01 2008,20:33)
     
Quote (Daniel Smith @ Jan. 01 2008,18:53)
 
He tested his predictions as any paleontologist would - by excavating and sifting through fossils.
---------------------QUOTE-------------------


Dan, you lie like a rug. The way that paleontologists test predictions of their hypotheses is by predicting the locations, time of deposition, and morphologies of fossils BEFORE THEY FIND THEM, not after. Tiktaalik is a fine example of this sort of prediction.

SCHINDEWOLF PRODUCED NO DATA FROM TESTING THE PREDICTIONS OF HIS HYPOTHESIS. Do the caps help?
 

---------------------QUOTE-------------------
He produced much data himself during this period and continued his pursuit of fossils until his death in 1971.
---------------------QUOTE-------------------


You are a deeply dishonest man, Dan. I didn't claim that Schindewolf produced no data, I pointed out that SCHINDEWOLF PRODUCED NO DATA FROM TESTING THE PREDICTIONS OF THE HYPOTHESIS WITH WHICH YOU ARE ENAMORED.

Can't you read?
         

---------------------QUOTE-------------------
As of this date, I am not aware of anything found in the fossil record that falsifies his theory.  Are you?
---------------------QUOTE-------------------


You are blatantly dishonest, Dan, as Schindewolf's hypothesis makes clear predictions about the molecular evidence, and what we know about molecular and developmental biology falsifies his hypothesis.

For example,

1) What magnitude of genetic change is required to change the number of vertebrae in a vertebrate?
2) What magnitude of genetic change is required to change the IDENTITY of a vertebra in a vertebrate?
---------------------QUOTE-------------------

[/quote]
------------
Note that I was not avoiding context, I am PROVIDING context, while you are avoiding context.
 

---------------------QUOTE-------------------
 

---------------------QUOTE-------------------
it should follow, if the assumption of a gradual bridging of the type boundaries by means of small developmental steps is correct, that the same situation applies between them.
---------------------QUOTE-------------------


---------------------QUOTE-------------------


Dan, THIS ASSUMPTION IS FALSE. That's why I keep asking you those questions about vertebrae and "hind limb genes."
 

---------------------QUOTE-------------------
 

---------------------QUOTE-------------------
Moreover, in view of the significant differences we see among the organizations of the individual types,...
---------------------QUOTE-------------------


---------------------QUOTE-------------------


If you think the assumption is true, then define Schindewolf's "significant differences" in terms of numbers of nucleotide changes.

Can you face reality long enough to see that this has been the purpose of my questions that you are avoiding?

Can you park your inflated ego long enough to see that my harping on your false claims about "hind limb genes" and "tail genes" PROVIDES CONTEXT FOR YOU TO UNDERSTAND THE FALSEHOOD OF SCHINDEWOLF'S ASSUMPTIONS (despite the tales about his ego, at least he, unlike you, has the integrity to properly label some of his assumptions)?
 

---------------------QUOTE-------------------
It is quite easy to see, from the context you avoid, that Schindewolf is talking specifically about gaps between "types" - which he also refers to as "structural designs".  These types are said to have "significant differences" between them.
---------------------QUOTE-------------------


Yes, but referring to them as "structural designs" shows the circularity of his (and your) argument. I have been putting this in an evidentiary context for you, and you run away, because you know full well that you are lying.
 

---------------------QUOTE-------------------
Your contention that Schindewolf is just talking about "gaps in the fossil record" is a bogus strawman.
---------------------QUOTE-------------------


Yet I've been providing context, and you've been avoiding it.
 

---------------------QUOTE-------------------
Tell me specifically what Schindewolf meant by "types"?
---------------------QUOTE-------------------


Schindewolf uses the term "types" in many different contexts throughout the book; it simply means "taxa," and he uses it to refer to everything from phyla to genera. That is why it is profoundly stupid to take a translation literally.

Hmmm...can you think of another famous book for which that problem also exists? One that is full of obvious parables that some arrogant, ignorant idiots think we should take literally?
 

---------------------QUOTE-------------------
Have you ever bothered JAM, to look at the evidence Schindewolf has amassed in support of his claim?
---------------------QUOTE-------------------


Yes, and I'm not impressed. That's why I keep asking you these questions about vertebrae and "hind limb genes." If you were impressed, you'd take me up on them; in reality, you have no real faith in your position.
 

---------------------QUOTE-------------------
His book is full of figures and tables.  There are even pictures!
---------------------QUOTE-------------------


That's nice. But what about the evidence he omitted, and the mountains of evidence we've acquired since? You're dishonestly ignoring all that, because you have no faith that you can predict any of it.
 

---------------------QUOTE-------------------
You should really look into it a bit more before making assumptions such as these.
---------------------QUOTE-------------------


I did. That's why I have been asking you the contextual questions that show Schindewolf's most fundamental assumptions to be wrong.
Posted by: mitschlag on Feb. 10 2008,04:52

Quote (JAM @ Feb. 09 2008,22:13)

   

---------------------QUOTE-------------------
As of this date, I am not aware of anything found in the fossil record that falsifies his theory.  Are you?
---------------------QUOTE-------------------


You are blatantly dishonest, Dan, as Schindewolf's hypothesis makes clear predictions about the molecular evidence, and what we know about molecular and developmental biology falsifies his hypothesis.

For example,

1) What magnitude of genetic change is required to change the number of vertebrae in a vertebrate?
2) What magnitude of genetic change is required to change the IDENTITY of a vertebra in a vertebrate?
------------
Note that I was not avoiding context, I am PROVIDING context, while you are avoiding context.
         

---------------------QUOTE-------------------
         

---------------------QUOTE-------------------
it should follow, if the assumption of a gradual bridging of the type boundaries by means of small developmental steps is correct, that the same situation applies between them.
---------------------QUOTE-------------------


---------------------QUOTE-------------------


Dan, THIS ASSUMPTION IS FALSE. That's why I keep asking you those questions about vertebrae and "hind limb genes."

---------------------QUOTE-------------------


I don't think the student is going to get it on his own.

Here's a clue, Dan: "Endless forms most beautiful..."
Posted by: Daniel Smith on Feb. 10 2008,19:27

Quote (blipey @ Feb. 09 2008,17:41)
Hey Daniel,

As has been explained to you those gaps of his don't exist--no matter where they are.  To argue that they really do exist, please tell me where my argument above goes wrong. Tell me why those gaps aren't the ones Schindewolf was proposing.  I'll reproduce it here for your convenience:

       

---------------------QUOTE-------------------
ToE (Common Descent)
----------------------------
            A
            /\
          B   C
         / \    \
       D    E   F
      / \    /   /\ \
    G   H  I   J K L


Schindewolf's Idea?
----------------------------
          A
         /
       B       C
                  \
   D              F
  /               / \
G   H     I    J    K          L

---------------------QUOTE-------------------


---------------------QUOTE-------------------



Schindewolf's gaps are represented by the lines between the letters on your diagram.   It doesn't matter how many letters you add, it's the discontinuities between them that matter.  (Schindewolf advocated common descent BTW)

To clarify also:  His position is not based on the many and obvious gaps in the fossil record amongst most known forms - such as mammals.  His position is based on those forms that are well represented in the fossil record.

Here's an example:

            A
           /  \
          B   C
          B   /\
          B  D E
     
     

In this example, the lineage B extends through the period where the lineage C splits and forms D and E.  The problem, according to Schindewolf, is that although we have ample fossilized evidence of the B, C, D, and E lineages throughout this period, there is no evidence of the transition from 'C to D' or from 'C to E' at all.  C disappears and D and E appear suddenly while B is all the while well represented.

According to Schindewolf, this pattern is repeated throughout the fossil record.
Posted by: JAM on Feb. 10 2008,20:25

Quote (Daniel Smith @ Feb. 10 2008,19:27)
The problem, according to Schindewolf, is that although we have ample fossilized evidence of the B, C, D, and E lineages throughout this period, there is no evidence of the transition from 'C to D' or from 'C to E' at all.
---------------------QUOTE-------------------



Schindewolf's thesis is based on artifact if the gaps are filled. Organisms move, ocean currents shift, continents move.

The mechanistic problem (which in your soul you know is real, because you are too cowardly to answer my questions) is that neither you nor Schindewolf have quantified the evolutionary distance from 'C to D' or from 'C to E' in terms of mutations.

Schindewolf's thesis is mechanistically vapid if the number of mutations required is one, as no intermediate form would have existed.

I'll ask you again, just so you can feel the shame of running away from legitimate questions:
1) What magnitude of genetic change is required to change the number of vertebrae in a vertebrate?
2) What magnitude of genetic change is required to change the IDENTITY of a vertebra in a vertebrate?

Now, if you are a Christian who honestly believes that Schindewolf was correct, why won't you answer them and test his hypothesis against the evidence?

Schindewolf has an excuse now--he's dead. What's yours?
Posted by: mitschlag on Feb. 11 2008,09:45

Quote (Daniel Smith @ Feb. 10 2008,19:27)
Here's an example:

            A
           /  \
          B   C
          B   /\
          B  D E
     
     

In this example, the lineage B extends through the period where the lineage C splits and forms D and E.  The problem, according to Schindewolf, is that although we have ample fossilized evidence of the B, C, D, and E lineages throughout this period, there is no evidence of the transition from 'C to D' or from 'C to E' at all.  C disappears and D and E appear suddenly while B is all the while well represented.

According to Schindewolf, this pattern is repeated throughout the fossil record.
---------------------QUOTE-------------------


Help!  In the context of Grundfragen, pp 125-145 (Ammonoids) can you cite examples of C, D and E and what a "transition" would have looked like if it were to be found?   What was Schindewolf looking for that he couldn't find?

Those escargots look so much alike to the untrained eye, don't you know?
Posted by: Daniel Smith on Feb. 11 2008,18:44

Quote (mitschlag @ Feb. 11 2008,07:45)
                   
Quote (Daniel Smith @ Feb. 10 2008,19:27)
Here's an example:

            A
           /  \
          B   C
          B   /\
          B  D E
     
     

In this example, the lineage B extends through the period where the lineage C splits and forms D and E.  The problem, according to Schindewolf, is that although we have ample fossilized evidence of the B, C, D, and E lineages throughout this period, there is no evidence of the transition from 'C to D' or from 'C to E' at all.  C disappears and D and E appear suddenly while B is all the while well represented.

According to Schindewolf, this pattern is repeated throughout the fossil record.
---------------------QUOTE-------------------


Help!  In the context of Grundfragen, pp 125-145 (Ammonoids) can you cite examples of C, D and E and what a "transition" would have looked like if it were to be found?   What was Schindewolf looking for that he couldn't find?

Those escargots look so much alike to the untrained eye, don't you know?
---------------------QUOTE-------------------


OK,  keep in mind that these are my own interpretations of Schindewolf.  

Schindewolf held that:  
1) IF Darwin's gradualism was true, and
2) IF all creatures had somehow miraculously been fossilized (he knew they weren't so please don't go down that route),
3) THEN a perfect fossil record would look something like this:

                        AA
                      AA Aa
                     Ab    ac
                    AB      aC
                   bB         cC
                 BB bb        CC
               Bd                Ce
             Bf  dd           Cg  Ce
           bf       dD       cg     CE
         bF          DD    cG        eE
   
Notice that each graduation is a slight change from the one above and that a continuous chain is formed.  (Note: I have not depicted stasis at all in this example for the sake of space.)

Then, allowing for gaps in the fossilization of specimens, it would look something like this:


                      AA Aa
     
                    AB     aC
 
                 BB bb        CC
                Bd               Ce

            bf     dD       cg     CE
         bF         DD   cG          eE

Notice how, even with the missing links, it is fairly easy to hypothesize what they would have been based on the remaining links of the once continuous chain.

However, (again according to my interpretation of Schindewolf), the actual fossil record looks more like this:  
                         AA
                 BB    Aa     CC
         DD    BB    aA     CC
         Dd    Bb     aa     CC
         dD    bb              CC
         dd     bb             CC
                                 CC
                                 CC
                           EE   CC
                           Ee   CC  FF
               GG        eE         Ff
               GG        ee         fF
               GG                     ff

Two capital letters = basic body plan
One capital, one small = variation within the body plan
two small letters = overspecialized / degeneration

Notice how the CC lineage doesn't change much from the simple original body plan?  Schindewolf noticed that it was the more stable lineages that tended to continue longer and become the root stock for the next phase of typogenesis.  All the overspecialized lineages died out.  (For an example of this from Schindewolf's book, I would recommend pages 140-143 where he goes into some detail on the evolution of suture lines in the Triassic and Jurassic ammonoids.)  

As to your question of what a transitional ammonite might look like: To me (and you too apparently), they all look alike, but Schindewolf saw so many differences that he said he often could not envision what a transitional would look like between specific lineages.

This is why virtually every chart depicting the fossil record you'll ever see will have thick vertical lines (representing actual fossils found) and dotted horizontal and diagonal lines (representing projected descent) between them.
This is why also, such classifications are so hotly debated.

Also, I did find < BQiP online > - though there are many pages missing for copyright reasons.  Still, it's a good place for those without the book to look at it.  It's also a place to link to some of the charts and figures Schindewolf used, such as < this one >.
Posted by: Daniel Smith on Feb. 11 2008,19:12

[quote=JAM,Feb. 09 2008,20:13]    
Quote (Daniel Smith @ Feb. 09 2008,19:26)
   

---------------------QUOTE-------------------
What are "those very points" of which Schindewolf speaks?
---------------------QUOTE-------------------

The discontinuities between what he refers to as "types," of course, which can mean anything from phyla to genera.    

---------------------QUOTE-------------------
Tell me specifically what Schindewolf meant by "types"?
---------------------QUOTE-------------------


Schindewolf uses the term "types" in many different contexts throughout the book; it simply means "taxa," and he uses it to refer to everything from phyla to genera.
---------------------QUOTE-------------------


I'd recommend, for anyone interested in what Schindewolf meant by the term "type", the excellent analysis of the early and mid twentieth century German concept of typology as it relates to biological evolution, written by Georgy S. Levit and Kay Meister, entitled "The history of essentialism vs. Ernst Mayr’s ‘‘Essentialism Story’’: A case study of German idealistic morphology"
< link >
Here's the Abstract:    

---------------------QUOTE-------------------
Idealistic morphology as perhaps the most important historical manifestation of typology is
very suitable for a historical analysis of Ernst Mayr’s ‘‘Essentialism Story’’, which postulates an
antagonism between ‘‘typological thinking’’ and ‘‘population thinking’’. We show that German-language
idealistic-morphological theories consisted of two clearly distinguishable parts. The
cornerstone of these theories was the concept of the type as an abstract pattern representing a
certain class of phenomena and embodying the norm of this class. The primary objective of pure
typology was to create a non-phylogenetic classification system for living organisms based on
structurally explicable characters.
Thus, typology, as a non-phylogenetic foundation of idealistic
morphology, was conceptually neutral with respect to hypotheses of evolutionary mechanisms.
Typology was often accompanied by concepts such as Lamarckism, orthogenesis, creationism,
essentialism, etc. These peripheral (with respect to pure typology) concepts were autonomous
constructions and did not represent a direct logical consequence of typology. In our view
‘‘population thinking’’, as part of the Darwinian theory of evolutionary mechanism, could not be
directly opposed to ‘‘typological thinking’’. Rather, it was peripheral concepts such as essentialism
or creationism that led to conflicts between the Modern Synthesis and idealistic morphology.

(Emphasis mine)
---------------------QUOTE-------------------


Posted by: Richard Simons on Feb. 11 2008,19:15

Quote (Daniel Smith @ Feb. 11 2008,18:44)
As to your question of what a transitional ammonite might look like: To me (and you too apparently), they all look alike, but Schindewolf saw so many differences that he said he often could not envision what a transitional would look like between specific lineages.
---------------------QUOTE-------------------


If you can't see any differences then why do you accept Schindewolf's claim that they are so different that he could not envision what a transitional would look like? You should be paying attention to his evidence, not his views.
Posted by: Daniel Smith on Feb. 11 2008,20:18

Quote (JAM @ Feb. 09 2008,20:13)
But what about the evidence he omitted, and the mountains of evidence we've acquired since?
---------------------QUOTE-------------------


JAM, can you--for once--cite a legitimate example of evidence that Schindewolf ignored or of modern evidence that falsifies his theory?
Posted by: mitschlag on Feb. 12 2008,07:00

Quote (Daniel Smith @ Feb. 11 2008,18:44)
As to your question of what a transitional ammonite might look like: To me (and you too apparently), they all look alike, but Schindewolf saw so many differences that he said he often could not envision what a transitional would look like between specific lineages.
---------------------QUOTE-------------------


Thanks for your reply, Daniel, but it was not responsive to my request for examples of the ammonites that Schindewolf was discussing in his chapter.

Regarding the quote above, where did Schindewolf say that?  How could that be true in every case where a transitional might be posited?  How could he find (or fail to find) a transitional if he didn't know what it might look like?

I hope you will understand my confusion.
Posted by: oldmanintheskydidntdoit on Feb. 12 2008,07:39

Quote (Daniel Smith @ Feb. 11 2008,18:44)
As to your question of what a transitional ammonite might look like: To me (and you too apparently), they all look alike, but Schindewolf saw so many differences that he said he often could not envision what a transitional would look like between specific lineages.
---------------------QUOTE-------------------


It appears that you are mistaken.
 

---------------------QUOTE-------------------
The detailed succession of ammonites will be shown in the Lower Oxfordian and lowermost part of the Middle Oxfordian up to the Plicatilis/Transversarium boundary; the overlying Middle and Upper Oxfordian (up to Bifurcatus Zone) will be presented i.a. in the Zawodzie Quarry at Cz?stochowa. The youngest Oxfordian deposits including the famous Amoeboceras layers - the beds rich in Boreal and Subboreal ammonites within the Submediterranean ammonite succession of the Bimammatum Zone, will be shown in the Cz?stochowa Upland and the Wielu? Upland.
---------------------QUOTE-------------------


You missed that < field trip > however.
 

---------------------QUOTE-------------------
The Aalenian–Bajocian transition is a critical period in ammonite evolution; hence the Early Jurassic fauna are replaced by new ammonite families which become dominant throughout the Middle and Late Jurassic.
---------------------QUOTE-------------------


< http://tiny.cc/3Bdvw >
 

---------------------QUOTE-------------------
Based on a continuous succession of ammonite and calcareous nannofossil assemblages, the main purpose of this paper is the correlation between ammonite and calcareous nannofossil zone boundaries in two expanded sections from the Basque-Cantabrian area.
---------------------QUOTE-------------------


< http://users.unimi.it/rips/110/110N1.htm >
 

---------------------QUOTE-------------------
Yet among the tens of thousands of specimens dug up by collectors, no one has ever found a specimen that is part way between Hoplites dentatus and Euhoplites lautus or between lautus and Mortoniceras inflatum—or between any of the fourteen different ammonites.4
---------------------QUOTE-------------------


OK, I threw that last one in there from ICR as I suspect that's where you are coming from Daniel.
< http://www.icr.org/article/27/10/ >
Daniel, don't you think it's troublesome that you are taking the side of ICR in this "debate".

Any anyway Daniel, every time a "missing link" is filled people like you simply claim "ah-ha, but now there are TWO extra missing links".
Posted by: Daniel Smith on Feb. 12 2008,08:19

Quote (oldmanintheskydidntdoit @ Feb. 12 2008,05:39)
Quote (Daniel Smith @ Feb. 11 2008,18:44)
As to your question of what a transitional ammonite might look like: To me (and you too apparently), they all look alike, but Schindewolf saw so many differences that he said he often could not envision what a transitional would look like between specific lineages.
---------------------QUOTE-------------------


It appears that you are mistaken.
   

---------------------QUOTE-------------------
The detailed succession of ammonites will be shown in the Lower Oxfordian and lowermost part of the Middle Oxfordian up to the Plicatilis/Transversarium boundary; the overlying Middle and Upper Oxfordian (up to Bifurcatus Zone) will be presented i.a. in the Zawodzie Quarry at Cz?stochowa. The youngest Oxfordian deposits including the famous Amoeboceras layers - the beds rich in Boreal and Subboreal ammonites within the Submediterranean ammonite succession of the Bimammatum Zone, will be shown in the Cz?stochowa Upland and the Wielu? Upland.
---------------------QUOTE-------------------


You missed that < field trip > however.
   

---------------------QUOTE-------------------
The Aalenian–Bajocian transition is a critical period in ammonite evolution; hence the Early Jurassic fauna are replaced by new ammonite families which become dominant throughout the Middle and Late Jurassic.
---------------------QUOTE-------------------


< http://tiny.cc/3Bdvw >
   

---------------------QUOTE-------------------
Based on a continuous succession of ammonite and calcareous nannofossil assemblages, the main purpose of this paper is the correlation between ammonite and calcareous nannofossil zone boundaries in two expanded sections from the Basque-Cantabrian area.
---------------------QUOTE-------------------


< http://users.unimi.it/rips/110/110N1.htm >
   

---------------------QUOTE-------------------
Yet among the tens of thousands of specimens dug up by collectors, no one has ever found a specimen that is part way between Hoplites dentatus and Euhoplites lautus or between lautus and Mortoniceras inflatum—or between any of the fourteen different ammonites.4
---------------------QUOTE-------------------


OK, I threw that last one in there from ICR as I suspect that's where you are coming from Daniel.
< http://www.icr.org/article/27/10/ >
Daniel, don't you think it's troublesome that you are taking the side of ICR in this "debate".

Any anyway Daniel, every time a "missing link" is filled people like you simply claim "ah-ha, but now there are TWO extra missing links".
---------------------QUOTE-------------------


I looked at your links but they don't seem to correspond to your quotes.  Either way, nothing you've quoted or linked to - in and of itself - falsifies Schindewolf.  You have to show that they've discovered transitionals between types.  Schindewolf himself talked about many "continuous successions of ammonites" within specific types.
Posted by: Daniel Smith on Feb. 12 2008,08:21

Quote (mitschlag @ Feb. 12 2008,05:00)
 
Quote (Daniel Smith @ Feb. 11 2008,18:44)
As to your question of what a transitional ammonite might look like: To me (and you too apparently), they all look alike, but Schindewolf saw so many differences that he said he often could not envision what a transitional would look like between specific lineages.
---------------------QUOTE-------------------


Thanks for your reply, Daniel, but it was not responsive to my request for examples of the ammonites that Schindewolf was discussing in his chapter.

Regarding the quote above, where did Schindewolf say that?  How could that be true in every case where a transitional might be posited?  How could he find (or fail to find) a transitional if he didn't know what it might look like?

I hope you will understand my confusion.
---------------------QUOTE-------------------


Note my use of the word "often".  As to your other questions, I'll have to do some digging.
Posted by: oldmanintheskydidntdoit on Feb. 12 2008,08:23

Quote (Daniel Smith @ Feb. 12 2008,08:19)
I looked at your links but they don't seem to correspond to your quotes.  Either way, nothing you've quoted or linked to - in and of itself - falsifies Schindewolf.  You have to show that they've discovered transitionals between types.  Schindewolf himself talked about many "continuous successions of ammonites" within specific types.
---------------------QUOTE-------------------


The quoted text is from the links given, no question there.

Do you want screenshots with the text highlighted?
Posted by: Daniel Smith on Feb. 12 2008,10:44

Quote (oldmanintheskydidntdoit @ Feb. 12 2008,06:23)
 
Quote (Daniel Smith @ Feb. 12 2008,08:19)
I looked at your links but they don't seem to correspond to your quotes.  Either way, nothing you've quoted or linked to - in and of itself - falsifies Schindewolf.  You have to show that they've discovered transitionals between types.  Schindewolf himself talked about many "continuous successions of ammonites" within specific types.
---------------------QUOTE-------------------


The quoted text is from the links given, no question there.

Do you want screenshots with the text highlighted?
---------------------QUOTE-------------------


What I would like is for you to explain how these discoveries (in your opinion) falsify Schindewolf.
Posted by: oldmanintheskydidntdoit on Feb. 12 2008,10:52

Quote (Daniel Smith @ Feb. 12 2008,10:44)
What I would like is for you to explain how these discoveries (in your opinion) falsify Schindewolf.
---------------------QUOTE-------------------


The point is really, how do you know they don't?

And anyway what do you mean "falsify Schindewolf"?

Anything in specific? Or are you reducing the mans life work to "there are no transitions between forms"?

 

---------------------QUOTE-------------------
The detailed succession of ammonites will be shown in the Lower Oxfordian and lowermost part of the Middle Oxfordian up to the Plicatilis/Transversarium boundary;
---------------------QUOTE-------------------


 

---------------------QUOTE-------------------
suc·ces·sion      /s?k?s???n/ Pronunciation Key - Show Spelled Pronunciation[suhk-sesh-uhn] Pronunciation Key - Show IPA Pronunciation
–noun
1. the coming of one person or thing after another in order, sequence, or in the course of events: many troubles in succession.
2. a number of persons or things following one another in order or sequence.
3. the right, act, or process, by which one person succeeds to the office, rank, estate, or the like, of another.
4. the order or line of those entitled to succeed one another.
5. the descent or transmission of a throne, dignity, estate, or the like.
6. Also called ecological succession. Ecology. the progressive replacement of one community by another until a climax community is established.
---------------------QUOTE-------------------


Posted by: JAM on Feb. 12 2008,14:15

Quote (Daniel Smith @ Feb. 11 2008,18:44)
   
Quote (mitschlag @ Feb. 11 2008,07:45)
                         
Quote (Daniel Smith @ Feb. 10 2008,19:27)
According to Schindewolf, this pattern is repeated throughout the fossil record.
---------------------QUOTE-------------------



---------------------QUOTE-------------------


OK,  keep in mind that these are my own interpretations of Schindewolf.
---------------------QUOTE-------------------


So, when you say, "According to Schindewolf," that really means according to your interpretations of Schindewolf's opinions, and has nothing to do with the actual evidence. Do you not see more than a bit of dishonesty in your initial representation?   


---------------------QUOTE-------------------
Schindewolf held that:  
1) IF Darwin's gradualism was true...
---------------------QUOTE-------------------


Define "Darwin's gradualism" in detail. I smell more mendacity.


---------------------QUOTE-------------------
...Notice how the CC lineage doesn't change much from the simple original body plan?
---------------------QUOTE-------------------


No, I only notice a bunch of letters and no evidence. Do you not see how obviously you were lying when you claimed:
 
Quote (Daniel Smith @ Sep. 22 2007,04:48)
My main problem is that I want to see unbiased and unadulterated evidence; not evidence that is made-to-fit the observers viewpoint. ...I decided what I needed was just to see the evidence for myself.
---------------------QUOTE-------------------


You are afraid to look at the evidence for yourself. That's why you rely entirely on rhetoric.


---------------------QUOTE-------------------
As to your question of what a transitional ammonite might look like: To me (and you too apparently), they all look alike,...
---------------------QUOTE-------------------


So YOU aren't even convinced by any evidence. I second Richard Simons's question: if you aren't convinced by evidence, why would you accept Schindewolf's opinion as Gospel?


---------------------QUOTE-------------------
This is why virtually every chart depicting the fossil record you'll ever see will have thick vertical lines (representing actual fossils found) and dotted horizontal and diagonal lines (representing projected descent) between them.
---------------------QUOTE-------------------


And that's why new transitional finds resolve those dotted lines.


---------------------QUOTE-------------------
This is why also, such classifications are so hotly debated.
---------------------QUOTE-------------------


But they get resolved by new data, something no one in the ID movement has the integrity to produce.
Posted by: mitschlag on Feb. 12 2008,15:58

Would Schindewolf have recognized a transitional fossil if he saw one?

Apparently not:        

---------------------QUOTE-------------------
Even the initial joyous satisfaction that once greeted, for example, the discov­ery of the famous ancestral bird Archaeopteryx did not prove to be justified. Despite all its similarities to reptiles, Archaeopteryx is a true bird; the boundary between the reptile type and the bird type has not yet been bridged by a continu­ous, uninterrupted linking series.
---------------------QUOTE-------------------

Basic Concepts, p 103.

(Note the sarcasm: "initial joyous satisfaction."  Veddy scientific.)

Some reptilian features of Archaeopteryx (From < a post on IIDB >):

1. cervical vertebrae with simple concave articulation points (birds have long, saddle-shaped ones)
2. unfused trunk vertebrae
3. gastralia (abdominal ribs)
4. no uncinate processes on the rib cage and no articulation with the sternum
5. a sacrum with just 6 vertebrae (birds have between 11 and 23)
6. mobile elbow, wrist and finger bones (they're fused in birds)
7. downward-orientated shoulder socket
8. a long bony tail
9. teeth
10. theropod-like skull fenestrae
11. a short, heavy, forwardly-inclined quadrate
12. a thin straight jugal bone (as in reptiles)
13. a preorbital bar
14. an occipital condyle and foramen magnum above the back end of the quadrate, like that of therapods (birds have theirs below the quadrate) -- IOW the neck attaches to the head at the rear of the skull, not underneath.
15. no bill
16. unfused metatarsals
17. claws on three of the fingers

Blinded by ideology, was Otto Heinrich.
Posted by: Albatrossity2 on Feb. 12 2008,17:27

Quote (mitschlag @ Feb. 12 2008,15:58)
Would Schindewolf have recognized a transitional fossil if he saw one?
---------------------QUOTE-------------------


And, as pointed out before, are they necessary in all cases?

We don't know enough about the genetics of ammonites to say for sure, but given what we have learned in the past couple of decades about gene regulation in the development of form in insects (flies, butterflies, etc.) and mammals, it is certainly possible to hypothesize a situation where a single mutation in a homeotic gene led to a beneficial or even neutral morphological change in one generation. Naturally it would take lots of generations for this new morphology to become common enough to be fossilized, but there would not necessarily be ANY transitional forms.

Daniel, this is the reason that others have called you to task for your ignorant assumptions about hind-leg genes, or suggested that you read Endless Forms Most Beautiful, or even The Making of the Fittest. Schindewolf's assumptions about even the necessity of transitional forms might be in error, based on what has been discovered since he shuffled off this mortal coil.
Posted by: JAM on Feb. 12 2008,17:47

Quote (Daniel Smith @ Feb. 11 2008,20:18)
Quote (JAM @ Feb. 09 2008,20:13)
But what about the evidence he omitted, and the mountains of evidence we've acquired since?
---------------------QUOTE-------------------


JAM, can you--for once--cite a legitimate example of evidence that Schindewolf ignored or of modern evidence that falsifies his theory?
---------------------QUOTE-------------------


Sure. Assuming that your characterization of his assumption of gradualism is valid, he's ignoring the evidence from my brutha Greg, for starters.

As for modern evidence, why do you think I keep asking you about vertebrae?
Posted by: mitschlag on Feb. 13 2008,06:31

Quote (mitschlag @ Feb. 12 2008,15:58)
Would Schindewolf have recognized a transitional fossil if he saw one?

Apparently not:            

---------------------QUOTE-------------------
Even the initial joyous satisfaction that once greeted, for example, the discov­ery of the famous ancestral bird Archaeopteryx did not prove to be justified. Despite all its similarities to reptiles, Archaeopteryx is a true bird; the boundary between the reptile type and the bird type has not yet been bridged by a continu­ous, uninterrupted linking series.
---------------------QUOTE-------------------


---------------------QUOTE-------------------


In a book on paleontology comprising over 400 pages, it is revealing that the sole reference to Archaeopteryx is that short paragraph.

Two sentences that dismiss, without any analysis, one of the most important fossil finds in history.
Posted by: JAM on Feb. 13 2008,09:33

Quote (mitschlag @ Feb. 13 2008,06:31)
Quote (mitschlag @ Feb. 12 2008,15:58)
Would Schindewolf have recognized a transitional fossil if he saw one?

Apparently not:              

---------------------QUOTE-------------------
Even the initial joyous satisfaction that once greeted, for example, the discov­ery of the famous ancestral bird Archaeopteryx did not prove to be justified. Despite all its similarities to reptiles, Archaeopteryx is a true bird; the boundary between the reptile type and the bird type has not yet been bridged by a continu­ous, uninterrupted linking series.
---------------------QUOTE-------------------


---------------------QUOTE-------------------


In a book on paleontology comprising over 400 pages, it is revealing that the sole reference to Archaeopteryx is that short paragraph.

Two sentences that dismiss, without any analysis, one of the most important fossil finds in history.
---------------------QUOTE-------------------


And, to anticipate a dishonest attempt to regard Schindewolf's opinion as superior to actual evidence, numerous additional transitionals found since Schindewolf wrote his book do not support his airy dismissal.

There's also that pesky DNA evidence, which unequivocally demonstrates that birds and reptiles are monophyletic--in fact, birds are far more closely related to one group of reptiles than that group is to the remaining reptiles. What's funny is that another of Daniel's opinionated heroes, Denton, claims that this evidence somehow refutes evolution.
Posted by: Daniel Smith on Feb. 13 2008,19:37

Quote (mitschlag @ Feb. 12 2008,05:00)
           
Quote (Daniel Smith @ Feb. 11 2008,18:44)
As to your question of what a transitional ammonite might look like: To me (and you too apparently), they all look alike, but Schindewolf saw so many differences that he said he often could not envision what a transitional would look like between specific lineages.
---------------------QUOTE-------------------


Thanks for your reply, Daniel, but it was not responsive to my request for examples of the ammonites that Schindewolf was discussing in his chapter.

Regarding the quote above, where did Schindewolf say that?  How could that be true in every case where a transitional might be posited?  How could he find (or fail to find) a transitional if he didn't know what it might look like?

I hope you will understand my confusion.
---------------------QUOTE-------------------


Sorry for the delay mitschlag, but my time is limited.

I apologize also for not being able (yet) to find you a good example from Schindewolf's chapter on ammonites, (he doesn't give, very often, the specific names of the ammonites he speaks of, so it's hard to find the type of specific example you want), but I did find a pretty detailed example in one of Schindewolf's stony corals examples:  

It is found on pages 205 - 208 in the section entitled "The Origin Of Major Types".  Look at the figure on page 207, and read the corresponding description of it on the pages already outlined.  

What you are looking at here is Schindewolf's breakdown of the splitting off of the heterocorals from the pterocorals.  Like the suture line in ammonites, he uses the septal structure in the corals to retrace their evolution.

In this figure, 'e' is the mature Pterocorallia [Rugosa] with 'a-e' its ontogenetical developmental cycle.  'h' is the mature Heterophyllia with 'f-h' its ontogenetical developmental cycle.  'f' is also the most primitive heterocoral - Hexapyllia

Notice the transition from 'b to c' and 'b to f', about which Schindewolf says:            

---------------------QUOTE-------------------
Hexaphyllia (fig. 3.74f), the most primitive representative of the Heterocorallia, at first shows only a splitting of one lateral pair of protosepta (II) and holds to this very simple developmental stage throughout its life span.  The genus Heterophyllia, which follows it (fig. 3.74h), takes another large evolutionary step in the direction already established...
...As we determined earlier, these fundamental, qualitative character differences between the two structural designs make it appear to be completely impossible for the septal apparatus of the heterocorals to have arisen by gradual transformation from the differentiated septal apparatus of the pterocorals.  From the very beginning, their structural paths went in different directions.  Therefore, the breaking away of the heterocorals can only have come about during a developmental stage very early in ontogeny of the pterocorals, and we were able to pinpoint this stage precisely.  It occured in the early juvenile stage after the emplacement of protosepta pair II and before the appearance of protosepta pair III (fig. 3.74b).  At that point, immediately after the larva attached itself to the substrate and began to secrete its skeleton, the decisive switch to the new evolutionary direction occured, causing both the suppression of the heterocoral protoseptal pair III and the bifurcation of protoseptal pair II.
Gradual, smooth transitions between these two different developmental types are unknown and scarcely even imaginable.  It could be conceivable, of course, that the reduction of protoseptal pair III took place gradually; but with respect to either simple or bifurcate protoseptal pair II, there is a fundamental, dichotomous difference, which cannot be bridged by a gradual transformation.  The two characters are clearly correlated--perhaps owing to compensation of skeletal material; they are part of a coherent type-complex, which first appeared in or was produced by an early juvenile developmental stage of the ancestral type, suddenly, without any transition, in a single transformational step.
BQiP, pg. 206, emphasis his
---------------------QUOTE-------------------



While this is not exactly what you asked for, it does represent a pretty detailed account of one of the basic tenets of Schindewolf's theory - that the evolution of new types happens during an early ontogenetic stage and proceeds via a quite different developmental path to maturity.  

Remember that only 'e', 'h', and 'f' are mature corals, so when he says "Gradual, smooth transitions between these two different developmental types are unknown and scarcely even imaginable", he's talking about a gradual transition from 'e' (the mature Pterocorallia [Rugosa]) to 'f' (the mature Hexaphyllia).

He can't imagine that, but he can imagine a transition from 'b' (an early stage of ontogenetical development of  Pterocorallia [Rugosa]) to 'f' (the mature Hexaphyllia).

So this is what a saltational evolutionary event would look like to Schindewolf.

I'll continue to look for other specific examples for you, but I really think Schindewolf's book should be taken as a whole.  You should be able to read it for yourself and get a much better idea of his positions (given your background) than I can give you (given mine).
Posted by: JAM on Feb. 14 2008,01:09

Quote (Daniel Smith @ Feb. 09 2008,11:02)
So, I try to limit my responses (mostly anyway) to the most important matters regarding the current discussion.  JAM is bringing up things that were said weeks ago on a whole different topic.  What relevance does that have now?
---------------------QUOTE-------------------


It is the very same topic, but you're either too dim, too deluded, and/or too dishonest to see it. It's all about your patently false assumption, unsupported by any evidence, about the way that development works (or more to the point, how life was "designed").
Posted by: JAM on Feb. 14 2008,01:22

Quote (Daniel Smith @ Feb. 13 2008,19:37)
...What you are looking at here is Schindewolf's breakdown of the splitting off of the heterocorals from the pterocorals.  Like the suture line in ammonites, he uses the septal structure in the corals to retrace their evolution.
---------------------QUOTE-------------------


But where's the EVIDENCE that the septal structure or suture lines are genetically determined?

Why do you think I keep asking you how many base changes are required to change the identity of a vertebra, a much more complex structure than either of these?


---------------------QUOTE-------------------
Notice the transition from 'b to c' and 'b to f',
---------------------QUOTE-------------------


So how many mutations are required for this transition? How many mutations are required for the transition between a cervical vertebra and a thoracic one with ribs?


---------------------QUOTE-------------------
about which Schindewolf says: ...
---------------------QUOTE-------------------


Who cares what he said? What about the evidence?


---------------------QUOTE-------------------
...As we determined earlier, these fundamental, qualitative character differences between the two structural designs make it appear to be completely impossible for the septal apparatus of the heterocorals to have arisen by gradual transformation from the differentiated septal apparatus of the pterocorals.
---------------------QUOTE-------------------


It doesn't appear that way at all. It didn't then, and it definitely doesn't today, given what educated people know about developmental genetics.


---------------------QUOTE-------------------
From the very beginning, their structural paths went in different directions.
---------------------QUOTE-------------------


Where's the evidence that demonstrates that these fundamental, qualitative character differences weren't entirely due to environment, Dan?


---------------------QUOTE-------------------
Therefore, the breaking away of the heterocorals can only have come about during a developmental stage very early in ontogeny of the pterocorals, and we were able to pinpoint this stage precisely.  It occured in the early juvenile stage after the emplacement of protosepta pair II and before the appearance of protosepta pair III (fig. 3.74b).
---------------------QUOTE-------------------


So, now you allegedly realize that your "hind limb genes" and "tail genes" were total BS, but you're going to contradict yourself and assume that coral have "protoseptal genes" anyway?


---------------------QUOTE-------------------
At that point, immediately after the larva attached itself to the substrate and began to secrete its skeleton, the decisive switch to the new evolutionary direction occured, causing both the suppression of the heterocoral protoseptal pair III and the bifurcation of protoseptal pair II.
Gradual, smooth transitions between these two different developmental types are unknown and scarcely even imaginable.
---------------------QUOTE-------------------


What was known about inheritance at the time Schindewolf wrote this steaming pile of BS, Dan?


---------------------QUOTE-------------------
It could be conceivable, of course, that the reduction of protoseptal pair III took place gradually; but with respect to either simple or bifurcate protoseptal pair II, there is a fundamental, dichotomous difference, which cannot be bridged by a gradual transformation.
---------------------QUOTE-------------------


Where's the evidence that shows that it cannot be bridged by a single base change?


---------------------QUOTE-------------------
While this is not exactly what you asked for, it does represent a pretty detailed account of one of the basic tenets of Schindewolf's theory - that the evolution of new types happens during an early ontogenetic stage and proceeds via a quite different developmental path to maturity.
---------------------QUOTE-------------------


But it's BS hand-waving without testing any of its predictions in the real world.  


---------------------QUOTE-------------------
Remember that only 'e', 'h', and 'f' are mature corals, so when he says "Gradual, smooth transitions between these two different developmental types are unknown and scarcely even imaginable", he's talking about a gradual transition from 'e' (the mature Pterocorallia [Rugosa]) to 'f' (the mature Hexaphyllia).
---------------------QUOTE-------------------


Why would single mutations yield "gradual, smooth transitions" anyway?


---------------------QUOTE-------------------
I'll continue to look for other specific examples for you, but I really think Schindewolf's book should be taken as a whole.
---------------------QUOTE-------------------


I think the evidence is more important. You clearly were lying when you claimed an interest in evidence upon your arrival here.
Posted by: Daniel Smith on Feb. 14 2008,11:07

Quote (JAM @ Feb. 13 2008,23:22)
     
Quote (Daniel Smith @ Feb. 13 2008,19:37)
...What you are looking at here is Schindewolf's breakdown of the splitting off of the heterocorals from the pterocorals.  Like the suture line in ammonites, he uses the septal structure in the corals to retrace their evolution.
---------------------QUOTE-------------------


But where's the EVIDENCE that the septal structure or suture lines are genetically determined?
---------------------QUOTE-------------------


Where's the evidence that they're not?  They're definitely inherited from generation to generation.
     

---------------------QUOTE-------------------
Why do you think I keep asking you how many base changes are required to change the identity of a vertebra, a much more complex structure than either of these?
---------------------QUOTE-------------------


To change the subject after your embarassing attempt to falsify Schindewolf by "evidence" you refused to back up.
       

---------------------QUOTE-------------------
     

---------------------QUOTE-------------------
Notice the transition from 'b to c' and 'b to f',
---------------------QUOTE-------------------


So how many mutations are required for this transition? How many mutations are required for the transition between a cervical vertebra and a thoracic one with ribs?
---------------------QUOTE-------------------


You tell me -- you're the expert.

 

---------------------QUOTE-------------------
given what educated people know about developmental genetics.
...
What was known about inheritance at the time Schindewolf wrote this ...
...
Where's the evidence that shows that it cannot be bridged by a single base change?
...
Why would single mutations yield "gradual, smooth transitions" anyway?
---------------------QUOTE-------------------


So you've found Schindewolf's mechanism.

Bully for you!
Posted by: mitschlag on Feb. 14 2008,16:15

Quote (Daniel Smith @ Feb. 13 2008,19:37)
Sorry for the delay mitschlag, but my time is limited.

I apologize also for not being able (yet) to find you a good example from Schindewolf's chapter on ammonites, (he doesn't give, very often, the specific names of the ammonites he speaks of, so it's hard to find the type of specific example you want), but I did find a pretty detailed example in one of Schindewolf's stony corals examples:  

It is found on pages 205 - 208 in the section entitled "The Origin Of Major Types".  Look at the figure on page 207, and read the corresponding description of it on the pages already outlined.  

What you are looking at here is Schindewolf's breakdown of the splitting off of the heterocorals from the pterocorals.  Like the suture line in ammonites, he uses the septal structure in the corals to retrace their evolution.
---------------------QUOTE-------------------


I appreciate your diligence.  Regarding Ammonoid evolution, Schindwolf says on p 204,          

---------------------QUOTE-------------------
The examples cited of the transformation of type from the Triassic ceratites to the Jurassic ammonites or from the pterocorals to the cyclocorals show particularly well that each appearance of a new type signifies a radical break in the course of evolution.
---------------------QUOTE-------------------


I went back to pp 125-145, looking for his argument, but couldn't find a clear statement.  Such efforts are not helped by the author's reluctance to give page numbers for his backward- and forward-looking references and by a poor job of indexing by his translator-editors ("ceratite" isn't indexed, for example).

Anyway, regarding the corals, I grasp his point, and I agree that a gradualistic intervening sequence of adult forms between the heterocorals and the pterocorals is hard to envision.  His suggestion of an ontogenetic switch looks reasonable to me.

And that could have happened without divine intervention!
Posted by: JAM on Feb. 14 2008,16:19

Quote (Daniel Smith @ Feb. 14 2008,11:07)
   
Quote (JAM @ Feb. 13 2008,23:22)
           
Quote (Daniel Smith @ Feb. 13 2008,19:37)
...What you are looking at here is Schindewolf's breakdown of the splitting off of the heterocorals from the pterocorals.  Like the suture line in ammonites, he uses the septal structure in the corals to retrace their evolution.
---------------------QUOTE-------------------


But where's the EVIDENCE that the septal structure or suture lines are genetically determined?
---------------------QUOTE-------------------


Where's the evidence that they're not?
---------------------QUOTE-------------------


In the former case, in the primary literature on intraspecific (even intracolonial) variation in live corals, of course. Do you finally see what I mean about Schindewolf's hypothesis making testable empirical predictions?

How much variation is caused by environmental factors, BTW?
   

---------------------QUOTE-------------------
They're definitely inherited from generation to generation.
---------------------QUOTE-------------------


You are a compulsive liar, Dan. Only a profoundly dishonest person would label an aggressively ignorant guess with "definitely."

Besides, even if the differences are inherited, how much INTRAspecific genetic variation is known to exist in living corals?

If I'm wrong, I eagerly await your pointing me to the evidence that convinced you that these were "definitely" inherited.
   

---------------------QUOTE-------------------
   

---------------------QUOTE-------------------
Why do you think I keep asking you how many base changes are required to change the identity of a vertebra, a much more complex structure than either of these?
---------------------QUOTE-------------------


To change the subject after your embarassing attempt to falsify Schindewolf by "evidence" you refused to back up.
---------------------QUOTE-------------------


I did back it up, and I've been asking you the question long before that.

Do you see how your desperate claim that these matters I keep bringing up (your fantasy "hind limb genes," "tail genes," and the amount of genetic change required to produce complex phenotypic changes) aren't related to Schindewolf's BS hypothesis is completely false?

   

---------------------QUOTE-------------------
   

---------------------QUOTE-------------------
   

---------------------QUOTE-------------------
Notice the transition from 'b to c' and 'b to f',
---------------------QUOTE-------------------


So how many mutations are required for this transition? How many mutations are required for the transition between a cervical vertebra and a thoracic one with ribs?
---------------------QUOTE-------------------


You tell me -- you're the expert.
---------------------QUOTE-------------------


Zero.

Now tell me exactly how you know that the septal differences Schindewolf wrote about were "definitely inherited." It can't possibly be an innocent mistake when you emphasize it with "definitely;" it's a desperate attempt to lie to yourself while you are lying to others.

   

---------------------QUOTE-------------------
   

---------------------QUOTE-------------------

Why would single mutations yield "gradual, smooth transitions" anyway?
---------------------QUOTE-------------------


So you've found Schindewolf's mechanism.

Bully for you!
---------------------QUOTE-------------------


I didn't find the mechanism, it was known long before he wrote his book. That's why his hypothesis was DOA.

If this puzzles you, look at a junior-high-level biology textbook for a refresher, since your vapor-locked brain doesn't function well enough to get my joke about "brutha Greg."
Posted by: Daniel Smith on Feb. 14 2008,20:01

Quote (mitschlag @ Feb. 14 2008,14:15)
         
Quote (Daniel Smith @ Feb. 13 2008,19:37)
Sorry for the delay mitschlag, but my time is limited.

I apologize also for not being able (yet) to find you a good example from Schindewolf's chapter on ammonites, (he doesn't give, very often, the specific names of the ammonites he speaks of, so it's hard to find the type of specific example you want), but I did find a pretty detailed example in one of Schindewolf's stony corals examples:  

It is found on pages 205 - 208 in the section entitled "The Origin Of Major Types".  Look at the figure on page 207, and read the corresponding description of it on the pages already outlined.  

What you are looking at here is Schindewolf's breakdown of the splitting off of the heterocorals from the pterocorals.  Like the suture line in ammonites, he uses the septal structure in the corals to retrace their evolution.
---------------------QUOTE-------------------


I appreciate your diligence.  Regarding Ammonoid evolution, Schindwolf says on p 204,                      

---------------------QUOTE-------------------
The examples cited of the transformation of type from the Triassic ceratites to the Jurassic ammonites or from the pterocorals to the cyclocorals show particularly well that each appearance of a new type signifies a radical break in the course of evolution.
---------------------QUOTE-------------------


I went back to pp 125-145, looking for his argument, but couldn't find a clear statement.  Such efforts are not helped by the author's reluctance to give page numbers for his backward- and forward-looking references and by a poor job of indexing by his translator-editors ("ceratite" isn't indexed, for example).
---------------------QUOTE-------------------


Thanks mitschlag, for keeping this thread interesting, civil, and on-topic.  I really appreciate that!
I think what you're looking for is on page 140, in his section entitled "Mesozoic Ammonoids":          

---------------------QUOTE-------------------
This progressive evolution [Note: among Triassic ceratites - D.S.] from smooth shells to those with multibifurcate ribs takes place within a whole cluster of parallel lineages, not always absolutely simultaneously and in many conservative or prematurely extinct lines also not attaining the highest stage of sculpturing, but we can still speak, in general, of a directional, steady progression of sculpture.  All these lines then died off conspicuously, after having reached their highest degree of sculptural specialization, at the boundary between the Triassic and the Jurassic--all except one, which remained smooth and undifferentiated and survived this critical juncture to become the starting point of a new cycle of ammonoid evolution, of a renewed and profuse proliferation.
Exactly the same course of sculptural evolution that we see in the Triassic is repeated in the Jurassic-Cretaceous era in the Ammonitacea: at the beginning, there are once more smooth, unsculptured forms; these go on to develop simple ribs, then bifurcate ribs, then multibifurcate ribs (figs. 3.32 and 3.152).
BQiP, pg. 140, (my emphasis)
---------------------QUOTE-------------------



Does that help?
         

---------------------QUOTE-------------------
Anyway, regarding the corals, I grasp his point, and I agree that a gradualistic intervening sequence of adult forms between the heterocorals and the pterocorals is hard to envision.  His suggestion of an ontogenetic switch looks reasonable to me.

And that could have happened without divine intervention!
---------------------QUOTE-------------------

 
Perhaps, but I'd like to believe that--taken altogether--the sheer volume of such evolutionary steps lends itself more to a 'preprogrammed plan' explanation than to 'trial and error' and chance.  

That said, Schindewolf would agree with you, not me, about the need for 'divine intervention'.
Posted by: oldmanintheskydidntdoit on Feb. 15 2008,03:02

Quote (Daniel Smith @ Feb. 14 2008,20:01)
Perhaps, but I'd like to believe that--taken altogether--the sheer volume of such evolutionary steps lends itself more to a 'preprogrammed plan' explanation than to 'trial and error' and chance.  

That said, Schindewolf would agree with you, not me, about the need for 'divine intervention'.
---------------------QUOTE-------------------


Over what timescales are we talking about here Daniel?

And as 99%+ of everything that's ever lived is extinct it's not much of a plan is it really?
Posted by: mitschlag on Feb. 15 2008,09:54

Quote (Daniel Smith @ Feb. 14 2008,20:01)
I think what you're looking for is on page 140, in his section entitled "Mesozoic Ammonoids":                    

---------------------QUOTE-------------------
This progressive evolution [Note: among Triassic ceratites - D.S.] from smooth shells to those with multibifurcate ribs takes place within a whole cluster of parallel lineages, not always absolutely simultaneously and in many conservative or prematurely extinct lines also not attaining the highest stage of sculpturing, but we can still speak, in general, of a directional, steady progression of sculpture.  All these lines then died off conspicuously, after having reached their highest degree of sculptural specialization, at the boundary between the Triassic and the Jurassic--all except one, which remained smooth and undifferentiated and survived this critical juncture to become the starting point of a new cycle of ammonoid evolution, of a renewed and profuse proliferation.
Exactly the same course of sculptural evolution that we see in the Triassic is repeated in the Jurassic-Cretaceous era in the Ammonitacea: at the beginning, there are once more smooth, unsculptured forms; these go on to develop simple ribs, then bifurcate ribs, then multibifurcate ribs (figs. 3.32 and 3.152).
BQiP, pg. 140, (my emphasis)
---------------------QUOTE-------------------



Does that help?
---------------------QUOTE-------------------


Not really, though I appreciate the effort.  I hadn't picked up the reference to Fig 3.152 before, but neither the text nor that figure nor the other Ammonoid figures convey to me a level of discontinuity comparable to that shown in the corresponding text and figures on corals.  

---------------------QUOTE-------------------
...we can still speak, in general, of a directional, steady progression of sculpture.
---------------------QUOTE-------------------


Inasmuch as Schindewolf explicitly excluded teleological notions, he should have been more circumspect in making easily misconstrued pronouncements like this.  But he had another category of mysticism on his mind, unfortunately.
Posted by: mitschlag on Feb. 15 2008,10:05

Quote (Daniel Smith @ Feb. 14 2008,20:01)
       
Quote (mitschlag @ Feb. 14 2008,14:15)

And that could have happened without divine intervention!
---------------------QUOTE-------------------

 
Perhaps, but I'd like to believe that--taken altogether--the sheer volume of such evolutionary steps lends itself more to a 'preprogrammed plan' explanation than to 'trial and error' and chance.
---------------------QUOTE-------------------


Believe whatever you'd like, dear boy.   :)

The scientific question remains: How was it accomplished?



Front-loaded?

Edited to add:  That is not a rat in the lower left-hand corner.
Posted by: Daniel Smith on Feb. 16 2008,21:45

Quote (mitschlag @ Feb. 15 2008,07:54)
             
Quote (Daniel Smith @ Feb. 14 2008,20:01)
I think what you're looking for is on page 140, in his section entitled "Mesozoic Ammonoids":                                    

---------------------QUOTE-------------------
This progressive evolution [Note: among Triassic ceratites - D.S.] from smooth shells to those with multibifurcate ribs takes place within a whole cluster of parallel lineages, not always absolutely simultaneously and in many conservative or prematurely extinct lines also not attaining the highest stage of sculpturing, but we can still speak, in general, of a directional, steady progression of sculpture.  All these lines then died off conspicuously, after having reached their highest degree of sculptural specialization, at the boundary between the Triassic and the Jurassic--all except one, which remained smooth and undifferentiated and survived this critical juncture to become the starting point of a new cycle of ammonoid evolution, of a renewed and profuse proliferation.
Exactly the same course of sculptural evolution that we see in the Triassic is repeated in the Jurassic-Cretaceous era in the Ammonitacea: at the beginning, there are once more smooth, unsculptured forms; these go on to develop simple ribs, then bifurcate ribs, then multibifurcate ribs (figs. 3.32 and 3.152).
BQiP, pg. 140, (my emphasis)
---------------------QUOTE-------------------



Does that help?
---------------------QUOTE-------------------


Not really, though I appreciate the effort.  I hadn't picked up the reference to Fig 3.152 before, but neither the text nor that figure nor the other Ammonoid figures convey to me a level of discontinuity comparable to that shown in the corresponding text and figures on corals.
---------------------QUOTE-------------------


mitschlag,

I'm sure this is not exactly what you're looking for either, but figure 3.37 (on page 134), gives an example of how Schindewolf used suture lines to draw similar conclusions about ammonoids to those he drew from the corals.  

Each suture line depicted there represents 1) an ontogenetic developmental stage of two specific ammonoids, ('a' = the Permian adrianitid, and 'b' = the Permian stacheoceratid),  AND,  2) a mature phylogenetic stage for various other forms of ammonoids, (with 'a6' and 'b3' being the mature suture lines for the adrianitid and the stacheoceratid respectively).  He goes into some detail about this on the surrounding pages, (I also found the same figure repeated later in the book [pg. 209, fig. 3.75] with more explanation there.)

The arrow from 'a3' to 'b1' illustrates the ontogentic stage at which the stacheoceratid splits off from the adrianitid (they share the same first 3 stages -- 'a1-3').  It's not as obvious to the untrained eye as it is from his coral diagrams, but if you study it closely, you can see that the same principle applies.
           

---------------------QUOTE-------------------
           

---------------------QUOTE-------------------
...we can still speak, in general, of a directional, steady progression of sculpture.
---------------------QUOTE-------------------


Inasmuch as Schindewolf explicitly excluded teleological notions, he should have been more circumspect in making easily misconstrued pronouncements like this.  But he had another category of mysticism on his mind, unfortunately.
---------------------QUOTE-------------------


I don't know what "mysticism" you're talking about.  Schindewolf felt that the "direction" was entirely constrained by the original saltational event.
Posted by: oldmanintheskydidntdoit on Feb. 17 2008,04:40

Quote (Daniel Smith @ Feb. 16 2008,21:45)
Quote (mitschlag @ Feb. 15 2008,07:54)
             
Quote (Daniel Smith @ Feb. 14 2008,20:01)
I think what you're looking for is on page 140, in his section entitled "Mesozoic Ammonoids":                                    

---------------------QUOTE-------------------
This progressive evolution [Note: among Triassic ceratites - D.S.] from smooth shells to those with multibifurcate ribs takes place within a whole cluster of parallel lineages, not always absolutely simultaneously and in many conservative or prematurely extinct lines also not attaining the highest stage of sculpturing, but we can still speak, in general, of a directional, steady progression of sculpture.  All these lines then died off conspicuously, after having reached their highest degree of sculptural specialization, at the boundary between the Triassic and the Jurassic--all except one, which remained smooth and undifferentiated and survived this critical juncture to become the starting point of a new cycle of ammonoid evolution, of a renewed and profuse proliferation.
Exactly the same course of sculptural evolution that we see in the Triassic is repeated in the Jurassic-Cretaceous era in the Ammonitacea: at the beginning, there are once more smooth, unsculptured forms; these go on to develop simple ribs, then bifurcate ribs, then multibifurcate ribs (figs. 3.32 and 3.152).
BQiP, pg. 140, (my emphasis)
---------------------QUOTE-------------------



Does that help?
---------------------QUOTE-------------------


Not really, though I appreciate the effort.  I hadn't picked up the reference to Fig 3.152 before, but neither the text nor that figure nor the other Ammonoid figures convey to me a level of discontinuity comparable to that shown in the corresponding text and figures on corals.
---------------------QUOTE-------------------


mitschlag,

I'm sure this is not exactly what you're looking for either, but figure 3.37 (on page 134), gives an example of how Schindewolf used suture lines to draw similar conclusions about ammonoids to those he drew from the corals.  

Each suture line depicted there represents 1) an ontogenetic developmental stage of two specific ammonoids, ('a' = the Permian adrianitid, and 'b' = the Permian stacheoceratid),  AND,  2) a mature phylogenetic stage for various other forms of ammonoids, (with 'a6' and 'b3' being the mature suture lines for the adrianitid and the stacheoceratid respectively).  He goes into some detail about this on the surrounding pages, (I also found the same figure repeated later in the book [pg. 209, fig. 3.75] with more explanation there.)

The arrow from 'a3' to 'b1' illustrates the ontogentic stage at which the stacheoceratid splits off from the adrianitid (they share the same first 3 stages -- 'a1-3').  It's not as obvious to the untrained eye as it is from his coral diagrams, but if you study it closely, you can see that the same principle applies.
           

---------------------QUOTE-------------------
             

---------------------QUOTE-------------------
...we can still speak, in general, of a directional, steady progression of sculpture.
---------------------QUOTE-------------------


Inasmuch as Schindewolf explicitly excluded teleological notions, he should have been more circumspect in making easily misconstrued pronouncements like this.  But he had another category of mysticism on his mind, unfortunately.
---------------------QUOTE-------------------


I don't know what "mysticism" you're talking about.  Schindewolf felt that the "direction" was entirely constrained by the original saltational event.
---------------------QUOTE-------------------


And, Daniel, at exactly what point did supernatural intervention take place?
Posted by: mitschlag on Feb. 17 2008,07:08

Quote (Daniel Smith @ Feb. 16 2008,21:45)
mitschlag,

I'm sure this is not exactly what you're looking for either, but figure 3.37 (on page 134), gives an example of how Schindewolf used suture lines to draw similar conclusions about ammonoids to those he drew from the corals.  

Each suture line depicted there represents 1) an ontogenetic developmental stage of two specific ammonoids, ('a' = the Permian adrianitid, and 'b' = the Permian stacheoceratid),  AND,  2) a mature phylogenetic stage for various other forms of ammonoids, (with 'a6' and 'b3' being the mature suture lines for the adrianitid and the stacheoceratid respectively).  He goes into some detail about this on the surrounding pages, (I also found the same figure repeated later in the book [pg. 209, fig. 3.75] with more explanation there.)

The arrow from 'a3' to 'b1' illustrates the ontogentic stage at which the stacheoceratid splits off from the adrianitid (they share the same first 3 stages -- 'a1-3' ).  It's not as obvious to the untrained eye as it is from his coral diagrams, but if you study it closely, you can see that the same principle applies.
---------------------QUOTE-------------------


Excellent.  Now I get it!  :)

I think the issue of suture lines was tainted for me by the statement in Moyne and Neige:    

---------------------QUOTE-------------------
Suture line characters are not used in this analysis because of their high variability between the different species of each genus.
---------------------QUOTE-------------------


So, I now see the parallel in Schindewolf's claims for corals and ammonoids: an ontogenetic switch.

Is that the gist of his saltationist hypothesis?  It looks testable.  Are there any molecular-genetic-devolopmental data pertaining thereto in the literature?
Posted by: mitschlag on Feb. 17 2008,08:05

Quote (Daniel Smith @ Feb. 16 2008,21:45)
 

---------------------QUOTE-------------------
   

---------------------QUOTE-------------------
...we can still speak, in general, of a directional, steady progression of sculpture.
---------------------QUOTE-------------------


Inasmuch as Schindewolf explicitly excluded teleological notions, he should have been more circumspect in making easily misconstrued pronouncements like this.  But he had another category of mysticism on his mind, unfortunately.
---------------------QUOTE-------------------


I don't know what "mysticism" you're talking about.  Schindewolf felt that the "direction" was entirely constrained by the original saltational event.
---------------------QUOTE-------------------


"Mysticism" was off the mark.  How about "metaphysics"?

I was trying to emphasize that it's too easy to read teleology into statements like this - and into his entire argument.  As you yourself have done.
Posted by: mitschlag on Feb. 17 2008,08:14

Regarding the picture of the  < Chihuahua and the Great Dane >...

Did the creator anticipate our need for Great Danes and Chihuahuas?
Posted by: JAM on Feb. 17 2008,13:58

Quote (mitschlag @ Feb. 17 2008,07:08)
I think the issue of suture lines was tainted for me by the statement in Moyne and Neige:          

---------------------QUOTE-------------------
Suture line characters are not used in this analysis because of their high variability between the different species of each genus.
---------------------QUOTE-------------------


---------------------QUOTE-------------------


[Daniel Smith]But that sentence doesn't mention Schindewolf! Therefore it (and the classification generated by using characters other than suture lines) can't possibly falsify his assumptions![/Daniel Smith]
 

---------------------QUOTE-------------------
So, I now see the parallel in Schindewolf's claims for corals and ammonoids: an ontogenetic switch.
---------------------QUOTE-------------------


Except that Schindewolf merely assumes that the switches represent huge genetic differences, Daniel blinds himself to Schindewolf's arrogance, and treats Schindewolf's opinions as evidence.
 

---------------------QUOTE-------------------
Is that the gist of his saltationist hypothesis?  It looks testable.  Are there any molecular-genetic-devolopmental data pertaining thereto in the literature?
---------------------QUOTE-------------------


Only morphological data are needed, which is why I kept pointing out to Dan that Schindewolf couldn't be bothered to test his hypothesis. It makes crystal-clear predictions about the limits of variation we should find in both living and fossilized corals.

< >Click to enlarge, from:

Journal of Paleontology; January 1987; v. 61; no. 1; p. 21-31
Intraspecific morphological variations in a Pleistocene solitary coral, Caryophyllia (Premocyathus) compressa Yabe and Eguchi
Kei Mori
Posted by: Daniel Smith on Feb. 17 2008,14:32

Quote (mitschlag @ Feb. 17 2008,05:08)
   
Quote (Daniel Smith @ Feb. 16 2008,21:45)
mitschlag,

I'm sure this is not exactly what you're looking for either, but figure 3.37 (on page 134), gives an example of how Schindewolf used suture lines to draw similar conclusions about ammonoids to those he drew from the corals.  

Each suture line depicted there represents 1) an ontogenetic developmental stage of two specific ammonoids, ('a' = the Permian adrianitid, and 'b' = the Permian stacheoceratid),  AND,  2) a mature phylogenetic stage for various other forms of ammonoids, (with 'a6' and 'b3' being the mature suture lines for the adrianitid and the stacheoceratid respectively).  He goes into some detail about this on the surrounding pages, (I also found the same figure repeated later in the book [pg. 209, fig. 3.75] with more explanation there.)

The arrow from 'a3' to 'b1' illustrates the ontogentic stage at which the stacheoceratid splits off from the adrianitid (they share the same first 3 stages -- 'a1-3' ).  It's not as obvious to the untrained eye as it is from his coral diagrams, but if you study it closely, you can see that the same principle applies.
---------------------QUOTE-------------------


Excellent.  Now I get it!  :)

I think the issue of suture lines was tainted for me by the statement in Moyne and Neige:          

---------------------QUOTE-------------------
Suture line characters are not used in this analysis because of their high variability between the different species of each genus.
---------------------QUOTE-------------------


So, I now see the parallel in Schindewolf's claims for corals and ammonoids: an ontogenetic switch.

Is that the gist of his saltationist hypothesis?  It looks testable.  Are there any molecular-genetic-devolopmental data pertaining thereto in the literature?
---------------------QUOTE-------------------


Yes this is the gist of his saltational hypothesis (and one of the cornerstones of his theory).  I don't know if anyone has tested it or not.  A quick search on Google Scholar turns up many articles that are unavailable, except for the abstracts, without a subscription.

I did find one interesting article (for which the < entire article > is available) dealing with the subject of chromosomal rearrangements.
Here's the abstract:

---------------------QUOTE-------------------
There has been limited corroboration to date for McClintock’s vision
of gene regulation by transposable elements (TEs), although her proposition on the
origin of species by TE-induced complex chromosome reorganizations in combination
with gene mutations, i.e., the involvement of both factors in relatively sudden formations
of species in many plant and animal genera, has been more promising. Moreover,
resolution is in sight for several seemingly contradictory phenomena such as the endless
reshuffling of chromosome structures and gene sequences versus synteny and the
constancy of living fossils (or stasis in general). Recent wide-ranging investigations
have confirmed and enlarged the number of earlier cases of TE target site selection (hot
spots for TE integration), implying preestablished rather than accidental chromosome
rearrangements for nonhomologous recombination of host DNA. The possibility of
a partly predetermined generation of biodiversity and new species is discussed. The
views of several leading transposon experts on the rather abrupt origin of new species
have not been synthesized into the macroevolutionary theory of the punctuated equilibrium
school of paleontology inferred from thoroughly consistent features of the fossil
record.
---------------------QUOTE-------------------


As you know, Schindewolf favored Goldschmidt's theory of macromutations via chromosomal rearrangements.  Davison has expanded on this as well.  I personally don't know enough about it to know if this is the direction you would go in looking for whether or not Schindewolf's saltational mechanism has been tested.  What do you think mitschlag?
Posted by: Daniel Smith on Feb. 17 2008,14:34

Quote (mitschlag @ Feb. 17 2008,06:05)
Quote (Daniel Smith @ Feb. 16 2008,21:45)
   

---------------------QUOTE-------------------
     

---------------------QUOTE-------------------
...we can still speak, in general, of a directional, steady progression of sculpture.
---------------------QUOTE-------------------


Inasmuch as Schindewolf explicitly excluded teleological notions, he should have been more circumspect in making easily misconstrued pronouncements like this.  But he had another category of mysticism on his mind, unfortunately.
---------------------QUOTE-------------------


I don't know what "mysticism" you're talking about.  Schindewolf felt that the "direction" was entirely constrained by the original saltational event.
---------------------QUOTE-------------------


"Mysticism" was off the mark.  How about "metaphysics"?

I was trying to emphasize that it's too easy to read teleology into statements like this - and into his entire argument.  As you yourself have done.
---------------------QUOTE-------------------


I can't help it if the shoe fits!  :D
Posted by: Daniel Smith on Feb. 17 2008,14:37

Quote (mitschlag @ Feb. 17 2008,06:14)
Regarding the picture of the  < Chihuahua and the Great Dane >...

Did the creator anticipate our need for Great Danes and Chihuahuas?
---------------------QUOTE-------------------


Apparently.

I thought you wanted to stick to science though!
Posted by: oldmanintheskydidntdoit on Feb. 17 2008,14:51

Quote (Daniel Smith @ Feb. 17 2008,14:37)
Quote (mitschlag @ Feb. 17 2008,06:14)
Regarding the picture of the  < Chihuahua and the Great Dane >...

Did the creator anticipate our need for Great Danes and Chihuahuas?
---------------------QUOTE-------------------


Apparently.

I thought you wanted to stick to science though!
---------------------QUOTE-------------------


Is there anything that could prove you are wrong?

Would you even be able to accept it if it were found?
Posted by: JAM on Feb. 17 2008,15:42

Quote (Daniel Smith @ Feb. 17 2008,14:32)
Yes this is the gist of his saltational hypothesis (and one of the cornerstones of his theory).  I don't know if anyone has tested it or not.
---------------------QUOTE-------------------


I just cited one in the post preceding yours. It failed miserably. Do you find that to be interesting?


---------------------QUOTE-------------------
A quick search on Google Scholar turns up many articles that are unavailable, except for the abstracts, without a subscription.
---------------------QUOTE-------------------


Dan, to serve as a test of his hypothesis, it doesn't need to be labeled as such. The question is, why didn't Schindewolf test the hypothesis that the morphological gaps he observed even represented inherited characters?


---------------------QUOTE-------------------
I did find one interesting article...
---------------------QUOTE-------------------


Why do you find opinion to more interesting than evidence, Dan?
Posted by: mitschlag on Feb. 17 2008,16:13

Quote (Daniel Smith @ Feb. 17 2008,14:37)
 
Quote (mitschlag @ Feb. 17 2008,06:14)
Regarding the picture of the  < Chihuahua and the Great Dane >...

Did the creator anticipate our need for Great Danes and Chihuahuas?
---------------------QUOTE-------------------


Apparently.

I thought you wanted to stick to science though!
---------------------QUOTE-------------------


Yes, I do.

What do you want to stick to?
Posted by: mitschlag on Feb. 18 2008,06:55

Quote (Daniel Smith @ Feb. 17 2008,14:32)
     
Quote (mitschlag @ Feb. 17 2008,05:08)
So, I now see the parallel in Schindewolf's claims for corals and ammonoids: an ontogenetic switch.

Is that the gist of his saltationist hypothesis?  It looks testable.  Are there any molecular-genetic-devolopmental data pertaining thereto in the literature?
---------------------QUOTE-------------------


Yes this is the gist of his saltational hypothesis (and one of the cornerstones of his theory).  I don't know if anyone has tested it or not.  A quick search on Google Scholar turns up many articles that are unavailable, except for the abstracts, without a subscription.
<snip>
As you know, Schindewolf favored Goldschmidt's theory of macromutations via chromosomal rearrangements.  Davison has expanded on this as well.  I personally don't know enough about it to know if this is the direction you would go in looking for whether or not Schindewolf's saltational mechanism has been tested.  What do you think mitschlag?
---------------------QUOTE-------------------


I think a look at < neoteny > is a start:
     

---------------------QUOTE-------------------
Neoteny plays a role in evolution, as a means by which, over generations, a species can undergo a significant physical change. In such cases, a species’ neotenous form becomes its “normal” mature form, no longer dependent upon environmental triggers to inhibit maturity. The mechanism for this could be a mutation in or interactions between genes involved in maturation, changing their function to impede this process...

---------------------QUOTE-------------------


Posted by: Daniel Smith on Feb. 18 2008,19:37

Quote (mitschlag @ Feb. 18 2008,04:55)
I think a look at < neoteny > is a start:
             

---------------------QUOTE-------------------
Neoteny plays a role in evolution, as a means by which, over generations, a species can undergo a significant physical change. In such cases, a species’ neotenous form becomes its “normal” mature form, no longer dependent upon environmental triggers to inhibit maturity. The mechanism for this could be a mutation in or interactions between genes involved in maturation, changing their function to impede this process...

---------------------QUOTE-------------------


---------------------QUOTE-------------------


     

---------------------QUOTE-------------------
"Neoteny is the retention, by adults in a species, of traits previously seen only in juveniles" (from your Wikipedia link).
---------------------QUOTE-------------------


Interesting.

I think that maybe Neoteny could apply to the coral example, but I don't see how it would apply to the ammonoid example - since both lineages continued in their respective development after the "switch" took effect.

It's food for thought.

What do you think of this?    

---------------------QUOTE-------------------
TE-induced and other gross chromosome rearrangements can lead to postzygotic isolating mechanisms that result in almost total cross-fertilization barriers between different lines of the same species in experimental organisms in a relatively short time period, as, for instance, in Pisum sativum (71).
CHROMOSOME REARRANGEMENTS AND TRANSPOSABLE ELEMENTS, Wolf-Ekkehard Lonnig and Heinz Saedler (my emphasis)
---------------------QUOTE-------------------



The footnote for 71 points to the following (unfortunately) German paper:
Lamprecht H. 1974. Monographie der Gattung Pisum. Graz: Steierm¨ark. Landesdruck. 655 pp.
Posted by: oldmanintheskydidntdoit on Feb. 19 2008,03:00

Quote (Daniel Smith @ Feb. 18 2008,19:37)
I think that maybe Neoteny could apply to the coral example
---------------------QUOTE-------------------


Calling all passengers. Your gap just got that bit smaller. Please note, all gods must now be re-sized to fit into the new, smaller gap. Mind the gap.
Posted by: mitschlag on Feb. 19 2008,06:42

Quote (Daniel Smith @ Feb. 18 2008,19:37)
I think that maybe Neoteny could apply to the coral example, but I don't see how it would apply to the ammonoid example - since both lineages continued in their respective development after the "switch" took effect.
---------------------QUOTE-------------------


Remember, you're dealing with enormous populations here, subject to differing environmental conditions (selective pressures) that vary over space and time.

There's no a priori reason to assume a global switchover independent of selective forces (despite Schindewolf's partiality to such notions).
Posted by: mitschlag on Feb. 19 2008,06:52

Quote (Daniel Smith @ Feb. 18 2008,19:37)
What do you think of this?        

---------------------QUOTE-------------------
TE-induced and other gross chromosome rearrangements can lead to postzygotic isolating mechanisms that result in almost total cross-fertilization barriers between different lines of the same species in experimental organisms in a relatively short time period, as, for instance, in Pisum sativum (71).
CHROMOSOME REARRANGEMENTS AND TRANSPOSABLE ELEMENTS, Wolf-Ekkehard Lonnig and Heinz Saedler (my emphasis)
---------------------QUOTE-------------------



The footnote for 71 points to the following (unfortunately) German paper:
Lamprecht H. 1974. Monographie der Gattung Pisum. Graz: Steierm¨ark. Landesdruck. 655 pp.
---------------------QUOTE-------------------


Haven't read the paper yet, but the reference is probably moot.  Such a mechanism for speciation looks perfectly reasonable to my relatively inexpert understanding of such matters.
Posted by: Daniel Smith on Feb. 19 2008,18:11

Quote (mitschlag @ Feb. 19 2008,04:52)
       
Quote (Daniel Smith @ Feb. 18 2008,19:37)
What do you think of this?                  

---------------------QUOTE-------------------
TE-induced and other gross chromosome rearrangements can lead to postzygotic isolating mechanisms that result in almost total cross-fertilization barriers between different lines of the same species in experimental organisms in a relatively short time period, as, for instance, in Pisum sativum (71).
CHROMOSOME REARRANGEMENTS AND TRANSPOSABLE ELEMENTS, Wolf-Ekkehard Lonnig and Heinz Saedler (my emphasis)
---------------------QUOTE-------------------



The footnote for 71 points to the following (unfortunately) German paper:
Lamprecht H. 1974. Monographie der Gattung Pisum. Graz: Steierm¨ark. Landesdruck. 655 pp.
---------------------QUOTE-------------------


Haven't read the paper yet, but the reference is probably moot.  Such a mechanism for speciation looks perfectly reasonable to my relatively inexpert understanding of such matters.
---------------------QUOTE-------------------


I think you should read the paper then, especially since they seem to be proposing this as a mechanism to explain the origin of higher categories ala Schindewolf:        

---------------------QUOTE-------------------
The question then centers on the extent to which TE-mediated chromosomal rearrangements can really explain the abrupt appearance not only of species but also of higher systematic categories in the face of the typical stasis of new life forms that so consistently characterizes the fossil record, i.e., the theory of punctuated equilibrium. Particularly apposite here are the following words of “so tough and influential a man” (52) as the German paleontologist Otto H. Schindewolf (116):
“According to Darwin’s theory, evolution takes place exclusively by way of slow, continuous formation and modification of species: the progressive addition of ever newer differences at the species level results in increasing divergence and leads to the formation of genera, families, and higher taxonomic and phylogenetic units. Our experience, gained from the observation of fossil material, directly contradicts this interpretation. We found that the organizing structure of a family or an order did not arise as the result of continuous modification in a long chain of species, but rather by means of a sudden, discontinuous direct refashioning of the type complex from family to family, from order to order, from class to class. The characters that account for the distinctions among species are completely different from those that distinguish one type from another.” (Italics by Schindewolf).
The existence in many animal groups such as foraminifers, brachiopods, corals, and others of an overwhelmingly rich fossil material consisting of literally millions (and generally in micropaleontology, billions) of individual exemplars led many paleontologists to emphasize that the objection most often raised against this view, i.e., the imperfection of the fossil record, is no longer valid [(15, 16, 37, 63, 116, 133, 139); see also discussion in (80, 85)]. Although Schindewolf’s causal explanations of evolution from inner compulsion are not accepted by most contemporary paleontologists, there is general agreement on his factual representation of the punctuated mode of appearance of new organisms in the fossil record. Given that Schindewolf’s description is phenotypically essentially correct, albeit with some exceptions (15, 56, 133), to what extent could TE-mediated small and gross chromosome rearrangements cope with the problem raised by the origin of families, orders, and classes?

CHROMOSOME REARRANGEMENTS AND TRANSPOSABLE ELEMENTS, pp 401–402, Wolf-Ekkehard Lonnig and Heinz Saedler, Annu. Rev. Genet. 2002. 36:389–410 (my emphasis)
---------------------QUOTE-------------------


Posted by: Daniel Smith on Feb. 19 2008,18:17

Quote (oldmanintheskydidntdoit @ Feb. 19 2008,01:00)
 
Quote (Daniel Smith @ Feb. 18 2008,19:37)
I think that maybe Neoteny could apply to the coral example
---------------------QUOTE-------------------


Calling all passengers. Your gap just got that bit smaller. Please note, all gods must now be re-sized to fit into the new, smaller gap. Mind the gap.
---------------------QUOTE-------------------


If you'd spent more time paying attention and less time jumping to conclusions, you'd know that I don't advocate a "god of the gaps".  I've been clear on a number of occasions that I believe God planned it all - even the stuff that's already been explained.
Posted by: oldmanintheskydidntdoit on Feb. 20 2008,03:00

Quote (Daniel Smith @ Feb. 19 2008,18:17)
 
Quote (oldmanintheskydidntdoit @ Feb. 19 2008,01:00)
     
Quote (Daniel Smith @ Feb. 18 2008,19:37)
I think that maybe Neoteny could apply to the coral example
---------------------QUOTE-------------------


Calling all passengers. Your gap just got that bit smaller. Please note, all gods must now be re-sized to fit into the new, smaller gap. Mind the gap.
---------------------QUOTE-------------------


If you'd spent more time paying attention and less time jumping to conclusions, you'd know that I don't advocate a "god of the gaps".  I've been clear on a number of occasions that I believe God planned it all - even the stuff that's already been explained.
---------------------QUOTE-------------------


You might believe it, but can you prove it?

You appear to have no evidence whatsoever to support your position.

For example, you quote
 

---------------------QUOTE-------------------
We found that the organizing structure of a family or an order did not arise as the result of continuous modification in a long chain of species, but rather by means of a sudden, discontinuous direct refashioning of the type complex from family to family, from order to order, from class to class. The characters that account for the distinctions among species are completely different from those that distinguish one type from another.
---------------------QUOTE-------------------



So, Daniel, did this "refashioning" take place because

a) god directly did it
b) god planned it that way

Daniel, is there really a difference between a and b?

And the thing about "god planned it" is that nothing can prove or disprove it.

Unicorns don't exist. god planned it that way

HIV kills innocent children. god planned it that way

We found that the organizing structure of a family or an order did not arise as the result of continuous modification in a long chain of species, but rather by means of a sudden, discontinuous direct refashioning of the type complex from family to family, from order to order, from class to class. god planned it that way.

So, Daniel, what makes you think that almost everything that's ever lived going extinct is planned? What's the point of that then? Oh, you can tell god planned it that way but you don't know why? Seems to me you can't have it both ways. You can't see a "plan" and not know why. Otherwise it's not really a plan is it?

For example, if you were attempting to escape from prison. Would a "plan" be to walk in a random direction and hope you escaped? Would somebody watching this behaviour think "oh, his plan to escape is good".

If it's "planned" Daniel can you use the same powers of observation that led you to believe that in the first place to make a prediction that might provide some support for your position? Use your understanding of the "plan" to predict something that has not yet happened? Or use the "plan" to predict something that has already happened, and where we can dig to see the fossils?

No?

Then what use is this insight into gods plan?

Something that explains everything is no use for anything. It's just in your brain. Stop trying to find evidence in the fossil record to support it. It's not there.

and if you are right then god planned me jumping to conclusions. Seems to me that your god wants you to lose these debates? I wonder why....Whatever the "why" it's planned you lose. And badly.
Posted by: mitschlag on Feb. 20 2008,07:40

Quote (Daniel Smith @ Feb. 19 2008,18:11)
I think you should read the paper then, especially since they seem to be proposing this as a mechanism to explain the origin of higher categories ala Schindewolf:
---------------------QUOTE-------------------


So?  The Loennig paper is a speculative review.  If it stimulates research, it will have made a contribution to our understanding.
Posted by: JAM on Feb. 20 2008,09:47

Quote (mitschlag @ Feb. 20 2008,07:40)
Quote (Daniel Smith @ Feb. 19 2008,18:11)
I think you should read the paper then, especially since they seem to be proposing this as a mechanism to explain the origin of higher categories ala Schindewolf:
---------------------QUOTE-------------------


So?  The Loennig paper is a speculative review.  If it stimulates research, it will have made a contribution to our understanding.
---------------------QUOTE-------------------


And such reviews are rarely peer-reviewed.
Posted by: Daniel Smith on Feb. 20 2008,11:02

Quote (oldmanintheskydidntdoit @ Feb. 20 2008,01:00)
Quote (Daniel Smith @ Feb. 19 2008,18:17)
   
Quote (oldmanintheskydidntdoit @ Feb. 19 2008,01:00)
       
Quote (Daniel Smith @ Feb. 18 2008,19:37)
I think that maybe Neoteny could apply to the coral example
---------------------QUOTE-------------------


Calling all passengers. Your gap just got that bit smaller. Please note, all gods must now be re-sized to fit into the new, smaller gap. Mind the gap.
---------------------QUOTE-------------------


If you'd spent more time paying attention and less time jumping to conclusions, you'd know that I don't advocate a "god of the gaps".  I've been clear on a number of occasions that I believe God planned it all - even the stuff that's already been explained.
---------------------QUOTE-------------------


You might believe it, but can you prove it?

You appear to have no evidence whatsoever to support your position.

For example, you quote
   

---------------------QUOTE-------------------
We found that the organizing structure of a family or an order did not arise as the result of continuous modification in a long chain of species, but rather by means of a sudden, discontinuous direct refashioning of the type complex from family to family, from order to order, from class to class. The characters that account for the distinctions among species are completely different from those that distinguish one type from another.
---------------------QUOTE-------------------



So, Daniel, did this "refashioning" take place because

a) god directly did it
b) god planned it that way

Daniel, is there really a difference between a and b?

And the thing about "god planned it" is that nothing can prove or disprove it.

Unicorns don't exist. god planned it that way

HIV kills innocent children. god planned it that way

We found that the organizing structure of a family or an order did not arise as the result of continuous modification in a long chain of species, but rather by means of a sudden, discontinuous direct refashioning of the type complex from family to family, from order to order, from class to class. god planned it that way.

So, Daniel, what makes you think that almost everything that's ever lived going extinct is planned? What's the point of that then? Oh, you can tell god planned it that way but you don't know why? Seems to me you can't have it both ways. You can't see a "plan" and not know why. Otherwise it's not really a plan is it?

For example, if you were attempting to escape from prison. Would a "plan" be to walk in a random direction and hope you escaped? Would somebody watching this behaviour think "oh, his plan to escape is good".

If it's "planned" Daniel can you use the same powers of observation that led you to believe that in the first place to make a prediction that might provide some support for your position? Use your understanding of the "plan" to predict something that has not yet happened? Or use the "plan" to predict something that has already happened, and where we can dig to see the fossils?

No?

Then what use is this insight into gods plan?

Something that explains everything is no use for anything. It's just in your brain. Stop trying to find evidence in the fossil record to support it. It's not there.

and if you are right then god planned me jumping to conclusions. Seems to me that your god wants you to lose these debates? I wonder why....Whatever the "why" it's planned you lose. And badly.
---------------------QUOTE-------------------


My belief in God is not based on science.  How sad would that be anyway?  You'd have to change your beliefs every time a new discovery was made!  No, my belief in God is purely subjective.  I do find however that the findings of science reinforce my beliefs.
Posted by: oldmanintheskydidntdoit on Feb. 20 2008,11:38

Quote (Daniel Smith @ Feb. 20 2008,11:02)
No, my belief in God is purely subjective.  I do find however that the findings of science reinforce my beliefs.
---------------------QUOTE-------------------


Give us an example then.

EDIT: Yay. I made it into a signature. Do you ever get drunk Daniel, or is that forbidden by your god?
Posted by: oldmanintheskydidntdoit on Feb. 20 2008,12:48

Quote (Daniel Smith @ Feb. 20 2008,11:02)
I do find however that the findings of science reinforce my beliefs.
---------------------QUOTE-------------------


That's a lucky coincidence eh?
Posted by: oldmanintheskydidntdoit on Feb. 20 2008,13:00

Interesting how you ignore the majority of my post Daniel to make a different point. Why did you quote it if you were only going to ignore it?

Was I indicating your belief in god arises from discontinuities in the fossil record?

I don't believe I was.

Here, let me refresh your memory of what you approvingly quoted earlier

 

---------------------QUOTE-------------------
the organizing structure of a family or an order did not arise as the result of continuous modification in a long chain of species, but rather by means of a sudden, discontinuous direct refashioning of the type complex from family to family, from order to order, from class to class.
---------------------QUOTE-------------------



and again
 

---------------------QUOTE-------------------

the organizing structure of a family or an order did not arise as the result of continuous modification in a long chain of species, but rather by means of a sudden, discontinuous direct refashioning of the type complex from family to family, from order to order, from class to class.

---------------------QUOTE-------------------



Now, why did you pick that particular quote? Just a coincidence that it mentions direct refashioning?

Was this "direct refashioning" because

a) natural but as yet unexplained events caused it
b) god did it directly there and then.
c) god planned it that way from the beginning.

or other?

Daniel, the point is here either you are trying to make a very  specific point about some mechanism of change that you are poorly qualified to argue, or you are saying there is direct evidence of gods intervention (or "plan") in the fossil record.

Which is it Daniel?
Posted by: Daniel Smith on Feb. 20 2008,17:46

Quote (mitschlag @ Feb. 20 2008,05:40)
     
Quote (Daniel Smith @ Feb. 19 2008,18:11)
I think you should read the paper then, especially since they seem to be proposing this as a mechanism to explain the origin of higher categories ala Schindewolf:
---------------------QUOTE-------------------


So?  The Loennig paper is a speculative review.  If it stimulates research, it will have made a contribution to our understanding.
---------------------QUOTE-------------------


Well, I didn't want you to read it so much for the opinions expressed but for the research they point to.  Particularly promising (IMO) is the research of A. Lima-de-Faria, B. McClintock, and J.A Shapiro.
If you don't want to read it, then don't.
I was just trying to answer your question:    
Quote (mitschlag @ Feb. 17 2008,05:08)

So, I now see the parallel in Schindewolf's claims for corals and ammonoids: an ontogenetic switch.

Is that the gist of his saltationist hypothesis?  It looks testable.  Are there any molecular-genetic-devolopmental data pertaining thereto in the literature?
---------------------QUOTE-------------------


Posted by: BWE on Feb. 20 2008,18:10

Quote (oldmanintheskydidntdoit @ Feb. 20 2008,11:38)
Quote (Daniel Smith @ Feb. 20 2008,11:02)
No, my belief in God is purely subjective.  I do find however that the findings of science reinforce my beliefs.
---------------------QUOTE-------------------


Give us an example then.

EDIT: Yay. I made it into a signature. Do you ever get drunk Daniel, or is that forbidden by your god?
---------------------QUOTE-------------------


I want to know if he's of the true faith, you know, sheep, etc...?
Posted by: Daniel Smith on Feb. 20 2008,18:11

Quote (oldmanintheskydidntdoit @ Feb. 20 2008,11:00)
Interesting how you ignore the majority of my post Daniel to make a different point. Why did you quote it if you were only going to ignore it?
---------------------QUOTE-------------------


OK, I admit it, I didn't read most of your post.
Frankly, you lost me at:        
Quote (oldmanintheskydidntdoit @ Feb. 20 2008,01:00)
You might believe it, but can you prove it?
---------------------QUOTE-------------------


I'm not interested in "proving" anything about God.  What kind of question is that anyway?  Can you "prove" 100% of what you believe?  Can you prove God doesn't exist?
Gimme a break!
Now, having gone back and actually read your post, I find it completely irrelevant to the subject at hand.
My belief in God (to repeat) is not based on the findings of man.  I already know God exists - for reasons science can't explain.  My belief is not based on objective reality - it is based on subjective, spiritual experiences.
So, when I look at science, I see the findings through believing eyes.  DNA is the coded language of life - written by God.  Proteins are his building blocks.  Evolution is his adaptive mechanism.  Etc.  No matter what man finds out, I'll still believe in God and I'll still believe that this world exists because of his plan.  Do you understand that?
I don't pretend to know the "Why?" for any of this either (which is what you're really asking).  I'll find that out soon enough.
Posted by: Daniel Smith on Feb. 20 2008,18:13

Quote (oldmanintheskydidntdoit @ Feb. 20 2008,09:38)
Yay. I made it into a signature. Do you ever get drunk Daniel, or is that forbidden by your god?
---------------------QUOTE-------------------


I just thought it was funny that's all.  No moral judgments here.
Posted by: Daniel Smith on Feb. 20 2008,18:42

Quote (oldmanintheskydidntdoit @ Feb. 20 2008,09:38)
   
Quote (Daniel Smith @ Feb. 20 2008,11:02)
No, my belief in God is purely subjective.  I do find however that the findings of science reinforce my beliefs.
---------------------QUOTE-------------------


Give us an example then.
---------------------QUOTE-------------------


How's this?    

---------------------QUOTE-------------------
Cells are capable of sophisticated information processing. Cellular signal transduction networks serve to compute data from multiple inputs and make decisions about cellular behavior. Genomes are organized like integrated computer programs as systems of routines and subroutines, not as a collection of independent genetic 'units'. DNA sequences which do not code for protein structure determine the system architecture of the genome. Repetitive DNA elements serve as tags to mark and integrate different protein coding sequences into coordinately functioning groups, to build up systems for genome replication and distribution to daughter cells, and to organize chromatin. Genomes can be reorganized through the action of cellular systems for cutting, splicing and rearranging DNA molecules.

Abstract: Transposable elements as the key to a 21st century view of evolution, Shapiro JA., Genetica. 1999;107(1-3):171-9.

---------------------QUOTE-------------------


That reinforces my belief that God programmed life.  What does it reinforce for you?
Posted by: Assassinator on Feb. 20 2008,19:03

Daniel, why do you value analogies like that to make certain things more clear so much? Those things aren't the real world, programming and IT isn't the same as the inner-workings of a cell, not even clóse.
Posted by: IanBrown_101 on Feb. 20 2008,23:18

Quote (Daniel Smith @ Feb. 21 2008,00:11)
I'm not interested in "proving" anything about God.  What kind of question is that anyway?  Can you "prove" 100% of what you believe?  Can you prove God doesn't exist?
Gimme a break!
---------------------QUOTE-------------------


Logical fallacy. You cannot prove (to the limits of the actual ability of people to prove anything) a negative.

Good grief man, that's basic stuff.
Posted by: oldmanintheskydidntdoit on Feb. 21 2008,02:58

Quote (oldmanintheskydidntdoit @ Feb. 20 2008,13:00)
Now, why did you pick that particular quote? Just a coincidence that it mentions direct refashioning?

Was this "direct refashioning" because

a) natural but as yet unexplained events caused it
b) god did it directly there and then.
c) god planned it that way from the beginning.

or other?

Daniel, the point is here either you are trying to make a very  specific point about some mechanism of change that you are poorly qualified to argue, or you are saying there is direct evidence of gods intervention (or "plan") in the fossil record.

Which is it Daniel?
---------------------QUOTE-------------------


I ask again. You are pointing to the fossil record here. The "subject at hand" if you will.

I'll keep asking.
Posted by: oldmanintheskydidntdoit on Feb. 21 2008,03:05

Quote (Daniel Smith @ Feb. 20 2008,18:42)
That reinforces my belief that God programmed life.  What does it reinforce for you?
---------------------QUOTE-------------------


It reinforces my belief that if your god exists he is a petulant moronic child who gives not a whit for the sufferings of it's creation and as such deserves only contempt.

Daniels god programmed HIV.
Daniels god programmed cancer.
Daniels god programmed the nerve that loops around a giraffe's neck and back when it could just have been a fraction of the length.
Daniels god programmed parasites that blind people, and worse.
Daniels god programmed malaria.

The fact you worship such a deity says lots about you.

And Daniel, I can't prove invisible unicorns don't exist either. I don't see that as a valid reason to worship them just in case.
Posted by: oldmanintheskydidntdoit on Feb. 21 2008,03:17

Quote (Daniel Smith @ Feb. 20 2008,18:11)
I'm not interested in "proving" anything about God.
---------------------QUOTE-------------------




---------------------QUOTE-------------------

I'm not interested in "proving" anything about God.  What kind of question is that anyway?
---------------------QUOTE-------------------


I think you are having a crisis of faith and are using this forum to convince yourself that evidence exists for your god.


---------------------QUOTE-------------------
Can you "prove" 100% of what you believe?  Can you prove God doesn't exist?
Gimme a break!
---------------------QUOTE-------------------


Silly question, shows how little you've thought about it, to my mind. I can't prove X does not exist so X exists? I don't think so.


---------------------QUOTE-------------------
Now, having gone back and actually read your post, I find it completely irrelevant to the subject at hand.
---------------------QUOTE-------------------


Which is what exactly? Some technical detail about how a particular detail of evolution recorded in the fossil record was achieved? Or how god intervened and made it so?


---------------------QUOTE-------------------
My belief in God (to repeat) is not based on the findings of man.
---------------------QUOTE-------------------


That's lucky then as the findings of man = no evidence so far!


---------------------QUOTE-------------------
I already know God exists - for reasons science can't explain.  My belief is not based on objective reality - it is based on subjective, spiritual experiences.
---------------------QUOTE-------------------


Yep, proof positive for all. Only thing is, not everybody believes so have you been chosen specially for this privilege?


---------------------QUOTE-------------------
So, when I look at science, I see the findings through believing eyes.
---------------------QUOTE-------------------


As has already been proven you see what you want to see, that's if you can even understand what it is you are seeing.


---------------------QUOTE-------------------
DNA is the coded language of life - written by God.
---------------------QUOTE-------------------


And quite a bad job it did eh? HIV etc?


---------------------QUOTE-------------------
Proteins are his building blocks.
---------------------QUOTE-------------------


And the parasites that burrow under your skin? Are they his "wikkle little worker parasites seeking out the guilty"?


---------------------QUOTE-------------------
Evolution is his adaptive mechanism.
---------------------QUOTE-------------------


And this was all revealed to you in a spiritual event yeah?


---------------------QUOTE-------------------
Etc.
---------------------QUOTE-------------------


See, ID'ers say that no evidence can falsify "darwinism" because it would adjust to fit it, but you are the case in point Daniel. No matter what is found, it'll reinforce your belief.


---------------------QUOTE-------------------
No matter what man finds out, I'll still believe in God and I'll still believe that this world exists because of his plan.
---------------------QUOTE-------------------


You keep going on about this plan. As I asked you already, what aspect of it makes you think it was a plan? Was it the parasites, badly designed spines or what?


---------------------QUOTE-------------------
 Do you understand that?
---------------------QUOTE-------------------


I understand that no amount of evidence that evolution without supernatural intervention will convince you that your god is not playing with the world behind the scenes.


---------------------QUOTE-------------------
I don't pretend to know the "Why?" for any of this either (which is what you're really asking).
---------------------QUOTE-------------------


And no doubt you have no interest in knowing as you are wrapped in the comfort blanket of "god knows best" and "it's all gods plan" and so you personally don't have to worry or try. It must be nice to know that your entire life is planned out Daniel? Takes some of the worry away right?


---------------------QUOTE-------------------
I'll find that out soon enough.
---------------------QUOTE-------------------


Why not go now? If it's so great in heaven what are all the god-botherers waiting for? If this earth is so corrupt then why hang around? I guess you subscribe to "the fall" and all that lark. Just seems odd to me why people who are 100% certain that a better life awaits don't just go to it.
Posted by: Louis on Feb. 21 2008,03:41

[JAD]

I love it so!

[/JAD]

After all the dancing around biology (which we all know isn't Danny's point anyway) we get back to "atheists believe there is no god, prove god doesn't exist" and badly done attempts at Pascal's Wager. Wonderful!

Tip for Danny: Atheism is strictly defined (in philosophical terms at least) as a lack of belief in a theistic deity, cast from your mind any and all confusions regarding morphed/popular versions of that word's meaning. Lack of belief does not equate to belief of lack. Period. If you want to refer to beief in a lack of a deity (as opposed to lack of belief in a deity) use a different word, it's less confusing for everyone concerned. I suggest one of the following: strong atheism, antitheism, anterotheism. Others may have their preferred term, personally I favour anterotheism simply because the Greek etymology is more apropos.

Second, proving a negative is, inductively at least, impossible. It is also a lovely little game called "shifting the burden of proof". The burden of proof rests on the positive claimant. I, and atheist, do not claim god does not exist, I wouldn't be so stupid, I also do not claim that unicorns don't exist, I wouldn't be that stupid either. What I do claim, and do so on the basis of a staggering amount of data, is that there is no clear cut, reliable, reproducible evidence, as free from bias and fallacious drivel as can be acheived, that either gods or unicorns exist. Therefore, and this is the personal bit, I act as if they did not. When there is evidence for their existence, then I shall act as though they do exist, which in this hypothetical case 'twould appear they do.

Thirdly and finally, if evolutionary biology needs to be modified or altered in some fashion which, as it is a scientific entity and thus only ever provisionally true, it undoubtedly will do, that alteration will be made on the available evidence. Reliable, reproducible evidence. There is no dogma to hold to, Darwin got lots of things wrong and lots of things right by the looks of it, science has moved forward in the last 150 years. Arguing against your own ignorant caricatures of the subject will only serve to make you look like a fool. Even if evolutionary biology is altered (on the basis of the evidence) beyond anything we recognise today it does not follow that your charmingly mysterious little deity is the default explanation. Deal with it.

Louis
Posted by: IanBrown_101 on Feb. 21 2008,06:24

Quote (Louis @ Feb. 21 2008,09:41)
your charmingly mysterious little deity
---------------------QUOTE-------------------


Now now Louis, lying is a sin. There is nothing charming about the Abrahamic god.
Posted by: mitschlag on Feb. 21 2008,07:06

Quote (Daniel Smith @ Feb. 20 2008,17:46)
   
Quote (mitschlag @ Feb. 20 2008,05:40)
           
Quote (Daniel Smith @ Feb. 19 2008,18:11)
I think you should read the paper then, especially since they seem to be proposing this as a mechanism to explain the origin of higher categories ala Schindewolf:
---------------------QUOTE-------------------


So?  The Loennig paper is a speculative review.  If it stimulates research, it will have made a contribution to our understanding.
---------------------QUOTE-------------------


Well, I didn't want you to read it so much for the opinions expressed but for the research they point to.  Particularly promising (IMO) is the research of A. Lima-de-Faria, B. McClintock, and J.A Shapiro.
If you don't want to read it, then don't.
I was just trying to answer your question:          
Quote (mitschlag @ Feb. 17 2008,05:08)

So, I now see the parallel in Schindewolf's claims for corals and ammonoids: an ontogenetic switch.

Is that the gist of his saltationist hypothesis?  It looks testable.  Are there any molecular-genetic-devolopmental data pertaining thereto in the literature?
---------------------QUOTE-------------------


---------------------QUOTE-------------------


Sorry for the misunderstanding.  :(

Kudos for finding the paper, which is relevant, as far as it goes, to my question.  And I have read it.

The point remains, however, that the paper's thesis is hypothetical.  Are there any subsequent confirming data?  For example, now that we have the complete genome sequences of chimps and humans, can we account for a saltational leap between them based on transposable element-mediated chromosomal rearrangements?

Anything else pertaining thereto in other fully or partially sequenced genomes?
Posted by: Daniel Smith on Feb. 21 2008,18:26

Quote (IanBrown_101 @ Feb. 20 2008,21:18)
     
Quote (Daniel Smith @ Feb. 21 2008,00:11)
I'm not interested in "proving" anything about God.  What kind of question is that anyway?  Can you "prove" 100% of what you believe?  Can you prove God doesn't exist?
Gimme a break!
---------------------QUOTE-------------------


Logical fallacy. You cannot prove (to the limits of the actual ability of people to prove anything) a negative.

Good grief man, that's basic stuff.
---------------------QUOTE-------------------


I'm pretty sure you all collectively missed my point--which was that "beliefs" have nothing to do with "proof".  I was not arguing against atheism because it lacks proof, nor was I challenging you to prove a negative, I was simply saying that nobody holds their own beliefs to the standard of "proof".  

IOW, do you only believe what has been "proven"?  No, you don't.  Nobody does.  So I was actually making the opposite point: I don't ask you to prove what you believe, so don't ask me to prove my beliefs.

All this came about because oldmaninthesky asked me:    
Quote (oldmanintheskydidntdoit @ Feb. 20 2008,01:00)

You might believe it, but can you prove it?
---------------------QUOTE-------------------


Posted by: Daniel Smith on Feb. 21 2008,18:33

Quote (oldmanintheskydidntdoit @ Feb. 20 2008,13:00)
Was this "direct refashioning" because

a) natural but as yet unexplained events caused it
b) god did it directly there and then.
c) god planned it that way from the beginning.

or other?

---------------------QUOTE-------------------


I don't know - maybe all of the above.
     
Quote (oldmanintheskydidntdoit @ Feb. 20 2008,13:00)
Daniel, the point is here either you are trying to make a very  specific point about some mechanism of change that you are poorly qualified to argue, or you are saying there is direct evidence of gods intervention (or "plan") in the fossil record.

Which is it Daniel?
---------------------QUOTE-------------------


Maybe none of the above.
   
Quote (oldmanintheskydidntdoit @ Feb. 21 2008,00:58)
I ask again. You are pointing to the fossil record here. The "subject at hand" if you will.

I'll keep asking.
---------------------QUOTE-------------------


I know you will.
Posted by: Daniel Smith on Feb. 21 2008,19:26

Quote (mitschlag @ Feb. 21 2008,05:06)

Sorry for the misunderstanding.  :(

Kudos for finding the paper, which is relevant, as far as it goes, to my question.  And I have read it.

The point remains, however, that the paper's thesis is hypothetical.  Are there any subsequent confirming data?  For example, now that we have the complete genome sequences of chimps and humans, can we account for a saltational leap between them based on transposable element-mediated chromosomal rearrangements?

Anything else pertaining thereto in other fully or partially sequenced genomes?
---------------------QUOTE-------------------


I'm finding that the in-depth study of chromosomal evolution appears to be relatively new and most papers seem to reflect this.
I found < this paper >.  I haven't read it yet, but the abstract mentions evidence of "regions of extraordinarily rapid, localized genome evolution":      

---------------------QUOTE-------------------
Large-scale genome sequencing is providing a comprehensive view of the complex evolutionary forces that have shaped the structure of eukaryotic chromosomes. Comparative sequence analyses reveal patterns of apparently random rearrangement interspersed with regions of extraordinarily rapid, localized genome evolution. Numerous subtle rearrangements near centromeres, telomeres, duplications, and interspersed repeats suggest hotspots for eukaryotic chromosome evolution. This localized chromosomal instability may play a role in rapidly evolving lineage-specific gene families and in fostering large-scale changes in gene order. Computational algorithms that take into account these dynamic forces along with traditional models of chromosomal rearrangement show promise for reconstructing the natural history of eukaryotic chromosomes.

Structural Dynamics of Eukaryotic Chromosome Evolution, Evan E. Eichler and David Sankoff

---------------------QUOTE-------------------


If you're interested in more papers, just go to Google Scholar, search for "chromosome evolution", (or something more specific), and scroll through the results until you find a pdf file - the rest are usually just abstracts.  Although sometimes, if you click on the "All_ versions" link, there'll be a pdf there as well.

Good hunting!
Posted by: oldmanintheskydidntdoit on Feb. 22 2008,03:04

Quote (Daniel Smith @ Feb. 21 2008,19:26)
I'm finding that the in-depth study of chromosomal evolution appears to be relatively new and most papers seem to reflect this.
---------------------QUOTE-------------------


So you are here simply to discuss cutting edge science? And not to try and point out where your gods fingerprints can be seen?

Fine, whatever. Go for it.
Posted by: mitschlag on Feb. 22 2008,06:06

Quote (Daniel Smith @ Feb. 21 2008,19:26)
I'm finding that the in-depth study of chromosomal evolution appears to be relatively new and most papers seem to reflect this.
I found < this paper >.  I haven't read it yet, but the abstract mentions evidence of "regions of extraordinarily rapid, localized genome evolution":              

---------------------QUOTE-------------------
Large-scale genome sequencing is providing a comprehensive view of the complex evolutionary forces that have shaped the structure of eukaryotic chromosomes. Comparative sequence analyses reveal patterns of apparently random rearrangement interspersed with regions of extraordinarily rapid, localized genome evolution. Numerous subtle rearrangements near centromeres, telomeres, duplications, and interspersed repeats suggest hotspots for eukaryotic chromosome evolution. This localized chromosomal instability may play a role in rapidly evolving lineage-specific gene families and in fostering large-scale changes in gene order. Computational algorithms that take into account these dynamic forces along with traditional models of chromosomal rearrangement show promise for reconstructing the natural history of eukaryotic chromosomes.

Structural Dynamics of Eukaryotic Chromosome Evolution, Evan E. Eichler and David Sankoff

---------------------QUOTE-------------------


If you're interested in more papers, just go to Google Scholar, search for "chromosome evolution", (or something more specific), and scroll through the results until you find a pdf file - the rest are usually just abstracts.  Although sometimes, if you click on the "All_ versions" link, there'll be a pdf there as well.

Good hunting!
---------------------QUOTE-------------------


Dear boy, we really must focus.

Your job, as I understand it, is to justify and rehabilitate Schindewolf and your other authorities in defiance of the modern evolutionary synthesis.

My job, as I understand it, is to point out to you the futility of your job.

So when I ask you to come up with evidence to support your thesis, it does not advance the discussion for you to ask me to hunt for that evidence.    :)
Posted by: Daniel Smith on Feb. 22 2008,10:19

Quote (Assassinator @ Feb. 20 2008,17:03)
Daniel, why do you value analogies like that to make certain things more clear so much? Those things aren't the real world, programming and IT isn't the same as the inner-workings of a cell, not even clóse.
---------------------QUOTE-------------------


The question is not "why do I value these analogies?", but rather "why do these analogies work?".

Also, how is it that these analogies (in your words) "make certain things more clear" if they're (also in your words) "not even clóse"?
Posted by: Assassinator on Feb. 22 2008,10:37

Quote (Daniel Smith @ Feb. 22 2008,10:19)
Quote (Assassinator @ Feb. 20 2008,17:03)
Daniel, why do you value analogies like that to make certain things more clear so much? Those things aren't the real world, programming and IT isn't the same as the inner-workings of a cell, not even clóse.
---------------------QUOTE-------------------


The question is not "why do I value these analogies?", but rather "why do these analogies work?".

Also, how is it that these analogies (in your words) "make certain things more clear" if they're (also in your words) "not even clóse"?
---------------------QUOTE-------------------


They make things easier to understand for people outside the ivory tower of biology.
Sure, there are analogies, but they're A supperficial (yea, wrong spelling) and B even analogy's don't mean they're the same, because they simply aren't. Can't you see those things for yourself?
Posted by: mitschlag on Feb. 22 2008,11:09

Ah, analogies!   Sources of so many good ideas, but also of so many fundamental fallacies.  As stated in my ancient college textbook of logic:
   

---------------------QUOTE-------------------
An analogy doesn't prove anything; it merely calls to mind a possibility that might not have been thought of without the analogy. It's the experiment that counts in the end. Bohr's classic model of the atom is only a picture. It has clarified some points about the atom, it has hinted at some good hypotheses; but if you take it as proving anything about the atom, you are misusing the analogy. You can be fooled just as much by it as were those early inventors who tried to construct airplanes that flapped their wings, on the analogy with birds. Analogies illustrate, and they lead to hypotheses, but thinking in terms of analogy becomes fallacious when the analogy is used as a reason for a principle. This fallacy is called the argument from analogy.
---------------------QUOTE-------------------


Nota bene, Daniel:  "It's the experiment that counts in the end."
Posted by: JAM on Feb. 22 2008,11:12

Quote (Daniel Smith @ Feb. 22 2008,10:19)
Quote (Assassinator @ Feb. 20 2008,17:03)
Daniel, why do you value analogies like that to make certain things more clear so much? Those things aren't the real world, programming and IT isn't the same as the inner-workings of a cell, not even clóse.
---------------------QUOTE-------------------


The question is not "why do I value these analogies?", but rather "why do these analogies work?".
---------------------QUOTE-------------------


But their utility is strictly limited. If you had been paying attention to your own shifting positions, they've failed you every time you've made a prediction here, both explicit and implicit.


---------------------QUOTE-------------------
Also, how is it that these analogies (in your words) "make certain things more clear" if they're (also in your words) "not even clóse"?
---------------------QUOTE-------------------


They are explanatory devices. When they are used to make predictions, they always fall short.
Posted by: mitschlag on Feb. 22 2008,11:18

Hard to believe that we've been at this so long.  Remember this post?
 
Quote (Daniel Smith @ Sep. 22 2007,04:48)
There are many things I have yet to make up my mind about.  For instance; I have not made my mind up in regard to the age of the earth/cosmos as I have not seen all the evidence and probably do not have the expertise to rightly interpret it.

My main problem is that I want to see unbiased and unadulterated evidence; not evidence that is made-to-fit the observers viewpoint.  I'm finding that hard to do - since both sides of this issue tend to color the evidence with their own interpretive brush.

The first book I read on the subject (other than my high school science books) was "Scientific Creationism" by Dr. Henry Morris, and, although he makes some good points, I found some of his views to be a bit of a stretch and recognized his attempts to fit science to the bible.

I then spent quite some time on talk.origins and did much research on the internet looking at the case for the currently held theory of evolution.  I found that much of the evidence for the theory was being interpreted under the assumption of the theory.

I decided what I needed was just to see the evidence for myself.

This is the reason I have sought out authors such as Berg, Schindewolf, Denton, Davison and others.  First, they are true scientists - there are no religious views expressed in their books.  Second, they hold to no preconceived paradigm and they have (or had) nothing to gain by publishing their views.  Most were either ridiculed or shunned, or just put on a shelf and forgotten, but their works stand the test of time (at least so far).  These are the type of people I want to get my information from.
---------------------QUOTE-------------------


Have you made up your mind about the age of the earth yet?
Posted by: Henry J on Feb. 22 2008,11:47



---------------------QUOTE-------------------
Have you made up your mind about the age of the earth yet?
---------------------QUOTE-------------------



Just wait for its next birthday, then count the candles on the cake. :p

In other news, JAM's avatar almost had me reaching for a fly swatter...

Henry
Posted by: Daniel Smith on Feb. 22 2008,18:32

Quote (Assassinator @ Feb. 22 2008,08:37)
         
Quote (Daniel Smith @ Feb. 22 2008,10:19)
           
Quote (Assassinator @ Feb. 20 2008,17:03)
Daniel, why do you value analogies like that to make certain things more clear so much? Those things aren't the real world, programming and IT isn't the same as the inner-workings of a cell, not even clóse.
---------------------QUOTE-------------------


The question is not "why do I value these analogies?", but rather "why do these analogies work?".

Also, how is it that these analogies (in your words) "make certain things more clear" if they're (also in your words) "not even clóse"?
---------------------QUOTE-------------------


They make things easier to understand for people outside the ivory tower of biology.
Sure, there are analogies, but they're A supperficial (yea, wrong spelling) and B even analogy's don't mean they're the same, because they simply aren't. Can't you see those things for yourself?
---------------------QUOTE-------------------


OK, so let me get this straight: A paper published by James A. Shapiro (a scientist at the Department of Biochemistry and Molecular Biology, University of Chicago), in the Journal Genetica (which is listed as having the following subjects: Biomedical and Life Sciences, Life Sciences, Life Sciences, general, Animal Genetics and Genomics, Plant Genetics & Genomics, Human Genetics and Microbial Genetics and Genomics), contains analogies that are meant to "make things easier to understand for people outside the ivory tower of biology"?

So, you're saying his intended audience is people outside the ivory tower of biology?  Just how many of those people do you suppose read Genetica?

Also, if you really think these analogies are "supperficial", perhaps you should take that up with Mr. Shapiro himself, (jsha@uchicago.edu), because his < paper > is full of them.

Then maybe you could post your correspondences here so we can see how you straighten him out on his "supperficialities".

(PS. Nobody's saying that "analogous" = "the same".  That is a strawman)
Posted by: Daniel Smith on Feb. 22 2008,18:36

Quote (mitschlag @ Feb. 22 2008,09:18)
Hard to believe that we've been at this so long.  Remember this post?
     
Quote (Daniel Smith @ Sep. 22 2007,04:48)
There are many things I have yet to make up my mind about.  For instance; I have not made my mind up in regard to the age of the earth/cosmos as I have not seen all the evidence and probably do not have the expertise to rightly interpret it.

My main problem is that I want to see unbiased and unadulterated evidence; not evidence that is made-to-fit the observers viewpoint.  I'm finding that hard to do - since both sides of this issue tend to color the evidence with their own interpretive brush.

The first book I read on the subject (other than my high school science books) was "Scientific Creationism" by Dr. Henry Morris, and, although he makes some good points, I found some of his views to be a bit of a stretch and recognized his attempts to fit science to the bible.

I then spent quite some time on talk.origins and did much research on the internet looking at the case for the currently held theory of evolution.  I found that much of the evidence for the theory was being interpreted under the assumption of the theory.

I decided what I needed was just to see the evidence for myself.

This is the reason I have sought out authors such as Berg, Schindewolf, Denton, Davison and others.  First, they are true scientists - there are no religious views expressed in their books.  Second, they hold to no preconceived paradigm and they have (or had) nothing to gain by publishing their views.  Most were either ridiculed or shunned, or just put on a shelf and forgotten, but their works stand the test of time (at least so far).  These are the type of people I want to get my information from.
---------------------QUOTE-------------------


Have you made up your mind about the age of the earth yet?
---------------------QUOTE-------------------


Nope.  Not yet.  That's a rabbit trail I'm not prepared to go down at this time.
Posted by: Daniel Smith on Feb. 22 2008,19:19

Quote (mitschlag @ Feb. 22 2008,04:06)
   
Dear boy, we really must focus.

Your job, as I understand it, is to justify and rehabilitate Schindewolf and your other authorities in defiance of the modern evolutionary synthesis.

My job, as I understand it, is to point out to you the futility of your job.

So when I ask you to come up with evidence to support your thesis, it does not advance the discussion for you to ask me to hunt for that evidence.    :)
---------------------QUOTE-------------------


OK, fair enough.
Shapiro, in the same paper I quoted above, says:      

---------------------QUOTE-------------------
A recent example of world-wide evolutionary change has been the emergence over the past five decades of transmissible antibiotic resistance in bacteria. The role of transposable elements and other natural genetic engineering systems, such as conjugative plasmids and the gene casette/integron system for building up antibiotic resistance operons (Recchia & Hall, 1995), is extremely well documented at the molecular level in this major evolutionary event.
---------------------QUOTE-------------------


So I searched Google Scholar for "transposable elements" and "antibiotic resistance in bacteria", to see whether I could find any evidence of this, and I found this < paper >:
Transposable multiple antibiotic resistance in Streptococcus pneumoniae
Unfortunately, only the abstract is available, but I think you can see that it offers some support for the idea that evolution may proceed by saltational chromosomal rearrangements.  
         

---------------------QUOTE-------------------
A mobile genetic element, designated Tn1545, was detected in the chromosome of Streptococcus pneumoniae BM4200, a clinical isolate multiply resistant to antibiotics. The 25.3 kb element conferred resistance to kanamycin and structurally related aminoglycosides by synthesis of a 3prime-aminoglycoside phosphotranferase type III (aphA-3), to macrolide-lincosamide-streptogramin B-type antibiotics (ermAM), and to tetracycline (tetM). Tn1545 was self-transferable to a recombination deficient S. faecalis strain where it was able to transpose to various sites, induce insertional mutations and was apparently cleanly excised. The element also conjugated to and transposed to the chromosome of S. faecalis, S. lactis, S. diacetylactis, S. cremoris, S. sanguis, Staphylococcus aureus, and Listeria monocytogenes. The properties of the conjugative transposon Tn1545 could account for the sudden emergence, rapid dissemination, and stabilisation of multiple resistance to antibiotics in S. pneumoniae in the absence of plasmids.
---------------------QUOTE-------------------


Posted by: JAM on Feb. 22 2008,21:01

Quote (Henry J @ Feb. 22 2008,11:47)
In other news, JAM's avatar almost had me reaching for a fly swatter...
---------------------QUOTE-------------------


You liked it?
Posted by: Wesley R. Elsberry on Feb. 22 2008,21:33

Daniel Smith:

 

---------------------QUOTE-------------------

Unfortunately, only the abstract is available, but I think you can see that it offers some support for the idea that evolution may proceed by saltational chromosomal rearrangements.  

---------------------QUOTE-------------------



Since biologists already know about several different ways in which chromosomal rearrangements can yield pretty much instant speciation, there's nothing there that seems of relevance. You see, there's something missing from your statement that would make it relevant, but then the abstract would have nothing to do with supporting the claim anymore:

 

---------------------QUOTE-------------------

I think you can see that it offers support for the idea that evolution may ONLY proceed by saltation.

---------------------QUOTE-------------------



The trouble comes not in saying that saltation happens, but in saying that non-saltational change doesn't happen.
Posted by: oldmanintheskydidntdoit on Feb. 23 2008,06:09

Quote (Daniel Smith @ Feb. 22 2008,18:36)
Nope.  Not yet.  That's a rabbit trail I'm not prepared to go down at this time.
---------------------QUOTE-------------------


So you've not yet made your mind up regarding the age of the earth?

Let me remind you of a few < predictions > you made
 

---------------------QUOTE-------------------
Organisms will show evidence of preparation for anticipated environments; rudiments of organs not yet needed will be found.
When confronted with environmental changes, organisms will adapt using pre-existing features (already coded for in the genome) or will become extinct - no new features will develop slowly over time.
Patterns and laws will be found that govern how evolution works.
---------------------QUOTE-------------------


Very profound.
 

---------------------QUOTE-------------------
From the fossil record:
Lineages will be found to have begun before environments in which they later flourished began.
Mass extinctions will have been preceded by the introduction of new types that would dominate the next phase in earth’s cycle.
Organisms will be found to have begun the adaptive process before adaptation was necessary.
Patterns will be found in the origin, differentiation and eventual extinction of lineages that are not dependent upon environmental factors but exist across all manner of differing environments, geographical locations, types of organisms and ages.
---------------------QUOTE-------------------


Quite a sweeping set of predictions there Daniel!

 

---------------------QUOTE-------------------
Genetically:
Mathematical patterns not explainable by the current theory will be found when comparing sequences of different organisms.
The genetic code will be found to be more sophisticated and more robust than previously thought.
Embedded and overlapping coding will be found to be more prevalent than previously thought.
Careful examination of genomes will find preparatory and adaptive codes “waiting in the wings” ready to be utilized in case of environmental changes- many just a frame shift away.
Frame shifting will be found to be a more common mechanism for sudden evolutionary change than previously thought.
Every part of the entire genome of any organism will be found to either be used at some time in the organisms life, or be of future use.  There are no unusable “Leftovers”.
No adequate explanation other than design will ever be found for the origin of life’s most basic components - i.e. protein synthesis, cell division, sexual reproduction, etc.

Universally:
Because the earth, and the solar system were specifically designed for life, no life or signs of previous life will be found on any other planets within our field of exploration.

---------------------QUOTE-------------------


Even more sweeping!
For this one
 

---------------------QUOTE-------------------
Mathematical patterns not explainable by the current theory will be found when comparing sequences of different organisms.
---------------------QUOTE-------------------


It seems to me that you've since had the opportunity to compare sequences of different organisms.
What mathematical patterns did you find that are not explained by the current theory Daniel?
In that same message you said, in answer to me asking is there anything that design predicts that evolution does not:
 

---------------------QUOTE-------------------
I could say the same thing about the currently held theory.  Is there anything that will ever be found that you won't somehow make to fit and eventually make to be a prediction of the currently held theory?
---------------------QUOTE-------------------


And of course there any many things that if found would destroy "currently held theory" but it seems that over the course of this thread no amount of contrary evidence cannot be incorporated into your worldview.
I mean, it's like you < say >
 

---------------------QUOTE-------------------
I'm interested in the truth - that's all.  My goal is to find out what really happened.
---------------------QUOTE-------------------


And so let us continue. Some time later you < note >
 

---------------------QUOTE-------------------
I don't know why I started arguing against superimposable nested hierarchies - since that is entirely consistent with designed descent.  I guess it's just the old creationist in me that got me caught up in that.  I do admit that I don't have a real good grasp of the subject, and need to learn more.  Really my main objection to the current theory of evolution is in regards to mechanism.
---------------------QUOTE-------------------


That old time creationist in you? Seems to me that you've already made up your mind with regard to the age of the earth. And that's the funny thing - you are attempting to use the fossil record and what it shows as evidence for your position yet at the same time you think that it's all fake anyway and under 10,000 years old! It must be a strange place, the inside of your head. Lot's of Chinese walls.
From the same post:
 

---------------------QUOTE-------------------
First let me say that we have witnessed a saltational evolutionary event consistent with designed descent in our lifetime - the nylon bug.
---------------------QUOTE-------------------


So the designer knew that nylon would exist, when Daniel? Back at the start of time?At the beginning of the universe? Or more recently then that?
 

---------------------QUOTE-------------------
That the code for this enzyme was pre-existing also makes it consistent with designed descent.
---------------------QUOTE-------------------


So, under your "theory" it should be possible to go back to a previous "version" of the bug in question, before it started to be able to eat nylon and find the code in question but deactivated? Is that right?
In another < post > you say

 

---------------------QUOTE-------------------
If (as I'm alleging) genomes are replete with embedded codes just waiting for a signal, such as a frame shift, to set them in action, then a saltational change can happen with just one substitution.  These substitutions would be non-random of course.
---------------------QUOTE-------------------



Ah, so your position appears to be that your god makes these substitutions in real time. This appears to be at odds with what you recently said and with what I just quoted you as saying.
I asked you


---------------------QUOTE-------------------
Was this "direct refashioning" because

a) natural but as yet unexplained events caused it
b) god did it directly there and then.
c) god planned it that way from the beginning.

or other?
---------------------QUOTE-------------------


And you < said >



---------------------QUOTE-------------------
I don't know - maybe all of the above.
---------------------QUOTE-------------------


Which appears to contradict what you said...

The funny thing is that I keep asking you "< why >". And you keep saying you don't know. Yet previously you said



---------------------QUOTE-------------------
If we cannot directly ask a designer why they made certain choices, the best we can hope for is to examine their designs and try to make an educated guess based on what we observe.
---------------------QUOTE-------------------



So, Daniel, why did the designer (or "a" designer) make the choice regarding the overlong nerve in the giraffe neck? You did already in fact attempt an < answer >


---------------------QUOTE-------------------
The reason the nerve passes between the internal and external carotid arteries is because the giraffe evolved from a short-necked ancestor.  The giraffe most likely represents the over-specialized typolysis phase of Schindewolf's theory.

My guess is that the giraffe will exhibit low genetic variability when compared with other mammals also.

You have to remember that creation took place a long time ago, and lots of evolution and variation has happened since then.  The fact that so much of what remains is still functional is a testament to the brilliance of the Creator.
---------------------QUOTE-------------------


So my question to you is "a long time ago" about 6000 to 10000 years? Or is it longer?

You seem to be forgetting previous positions you've held Daniel. Some days the giraffe nerve is explained by "lots of evolution and variation" due to it being such a long time ago and some days it cannot be explained that way as the earth *might* not really be old at all.

Yet still, you can't seem to make up your mind as you've also < said >


---------------------QUOTE-------------------
I'll just say this and be done with it:
I'm perfectly content with a 4.5 billion year old earth, and I wouldn't cry if it turned out to be only 10,000 years old either.  IOW, it's not really an issue for me.

It's not how old things are; it's their chronological order that matters.
---------------------QUOTE-------------------



Perhaps the reason it's "not really an issue" for you is the general incoherence of your position. That's the trouble when you just make it all up for yourself, picking and choosing the bits you like and discarding the rest.

At that time I asked you this:


---------------------QUOTE-------------------
Daniel, in your opinion are  Schindewolf, Berg, and their theories of constrained evolution and evolution by law compatible with a 6000 year old earth and a global flood?

If not, what will you rule out?

Either way, progress will have been made.
---------------------QUOTE-------------------



Do you now care to rule one or the other out? Or is that rabbit hole still far to scary to enter?

In short Daniel, accept the fact you'll have nothing positive to contribute to this discussion or mankinds body of knowledge in general until you make up your mind about a few basic premises! And consider this - if your god can interfere at will and make changes such as the nylon bug frameshift then what happens to cause and effect? What happens to prediction? How can the whims of a designer be predicted? And yet predictions about how the physical world behave can be made with stunning accuracy, no god(s) required.
Posted by: mitschlag on Feb. 23 2008,07:13

Quote (Daniel Smith @ Feb. 22 2008,18:36)
     
Quote (mitschlag @ Feb. 22 2008,09:18)
Hard to believe that we've been at this so long.  Remember this post?
             
Quote (Daniel Smith @ Sep. 22 2007,04:48)
There are many things I have yet to make up my mind about.  For instance; I have not made my mind up in regard to the age of the earth/cosmos as I have not seen all the evidence and probably do not have the expertise to rightly interpret it.

My main problem is that I want to see unbiased and unadulterated evidence; not evidence that is made-to-fit the observers viewpoint.  I'm finding that hard to do - since both sides of this issue tend to color the evidence with their own interpretive brush.

<snip>

I decided what I needed was just to see the evidence for myself.

This is the reason I have sought out authors such as Berg, Schindewolf, Denton, Davison and others.  First, they are true scientists - there are no religious views expressed in their books.

<snip>

These are the type of people I want to get my information from.
---------------------QUOTE-------------------


Have you made up your mind about the age of the earth yet?
---------------------QUOTE-------------------


Nope.  Not yet.  That's a rabbit trail I'm not prepared to go down at this time.
---------------------QUOTE-------------------


You can't be serious, Daniel.

Here's what Schindewolf said:
 

---------------------QUOTE-------------------
THE BASIS FOR MEASURING TIME AND DETERMINING AGE

We have already said that a fundamental of geology, on which it stands or falls, is the possibility of determining the age of rocks and strata. Geology as a historical science with the goal of writing a history of the earth must have at its disposal a temporal system to date its events and arrange them within a time scale. Otherwise, geology would be a chaotic scrap heap of isolated facts and in no position to come up with systematic insights into the structure of the earth's crust and the mineral resources it holds. The same is true for paleontology, which must know the relative ages of the various faunas and floras if it wants to demonstrate their historical development.
---------------------QUOTE-------------------

Basic Questions, p 8.

Do you see the inconsistency in your thinking?

(Edited to add emphasis - and a tip of the hat to oldman, who just hit the same nail smartly on the head.)
Posted by: Daniel Smith on Feb. 23 2008,16:19

Quote (Wesley R. Elsberry @ Feb. 22 2008,19:33)
Daniel Smith:

   

---------------------QUOTE-------------------

Unfortunately, only the abstract is available, but I think you can see that it offers some support for the idea that evolution may proceed by saltational chromosomal rearrangements.  

---------------------QUOTE-------------------



Since biologists already know about several different ways in which chromosomal rearrangements can yield pretty much instant speciation, there's nothing there that seems of relevance. You see, there's something missing from your statement that would make it relevant, but then the abstract would have nothing to do with supporting the claim anymore:

   

---------------------QUOTE-------------------

I think you can see that it offers support for the idea that evolution may ONLY proceed by saltation.

---------------------QUOTE-------------------



The trouble comes not in saying that saltation happens, but in saying that non-saltational change doesn't happen.
---------------------QUOTE-------------------


But neither I nor Schindewolf ever said that.
Posted by: Daniel Smith on Feb. 23 2008,16:39

Quote (mitschlag @ Feb. 23 2008,05:13)
   
Quote (Daniel Smith @ Feb. 22 2008,18:36)
           
Quote (mitschlag @ Feb. 22 2008,09:18)
Hard to believe that we've been at this so long.  Remember this post?
                   
Quote (Daniel Smith @ Sep. 22 2007,04:48)
There are many things I have yet to make up my mind about.  For instance; I have not made my mind up in regard to the age of the earth/cosmos as I have not seen all the evidence and probably do not have the expertise to rightly interpret it.

My main problem is that I want to see unbiased and unadulterated evidence; not evidence that is made-to-fit the observers viewpoint.  I'm finding that hard to do - since both sides of this issue tend to color the evidence with their own interpretive brush.

<snip>

I decided what I needed was just to see the evidence for myself.

This is the reason I have sought out authors such as Berg, Schindewolf, Denton, Davison and others.  First, they are true scientists - there are no religious views expressed in their books.

<snip>

These are the type of people I want to get my information from.
---------------------QUOTE-------------------


Have you made up your mind about the age of the earth yet?
---------------------QUOTE-------------------


Nope.  Not yet.  That's a rabbit trail I'm not prepared to go down at this time.
---------------------QUOTE-------------------


You can't be serious, Daniel.

Here's what Schindewolf said:
       

---------------------QUOTE-------------------
THE BASIS FOR MEASURING TIME AND DETERMINING AGE

We have already said that a fundamental of geology, on which it stands or falls, is the possibility of determining the age of rocks and strata. Geology as a historical science with the goal of writing a history of the earth must have at its disposal a temporal system to date its events and arrange them within a time scale. Otherwise, geology would be a chaotic scrap heap of isolated facts and in no position to come up with systematic insights into the structure of the earth's crust and the mineral resources it holds. The same is true for paleontology, which must know the relative ages of the various faunas and floras if it wants to demonstrate their historical development.
---------------------QUOTE-------------------

Basic Questions, p 8.

Do you see the inconsistency in your thinking?

(Edited to add emphasis - and a tip of the hat to oldman, who just hit the same nail smartly on the head.)
---------------------QUOTE-------------------


I'd suggest you read pages 11-13 where Schindewolf makes it pretty clear that it's only the relative ages of fossils he's concerned with -- not the absolute ages.    

---------------------QUOTE-------------------
The only thing that concerns us in geology is the determination of the sequence of events...

...absolute age based on certain number of years is of no importance at all.  In this area, too, the only concern is to establish the relative age.

page 12 - his italics
---------------------QUOTE-------------------


Posted by: Daniel Smith on Feb. 23 2008,16:51

Quote (oldmanintheskydidntdoit @ Feb. 23 2008,04:09)
 
Quote (Daniel Smith @ Feb. 22 2008,18:36)
Nope.  Not yet.  That's a rabbit trail I'm not prepared to go down at this time.
---------------------QUOTE-------------------


So you've not yet made your mind up regarding the age of the earth?

Let me remind you of a few < predictions > you made
     

---------------------QUOTE-------------------
Organisms will show evidence of preparation for anticipated environments; rudiments of organs not yet needed will be found.
When confronted with environmental changes, organisms will adapt using pre-existing features (already coded for in the genome) or will become extinct - no new features will develop slowly over time.
Patterns and laws will be found that govern how evolution works.
---------------------QUOTE-------------------


Very profound.
     

---------------------QUOTE-------------------
From the fossil record:
Lineages will be found to have begun before environments in which they later flourished began.
Mass extinctions will have been preceded by the introduction of new types that would dominate the next phase in earth’s cycle.
Organisms will be found to have begun the adaptive process before adaptation was necessary.
Patterns will be found in the origin, differentiation and eventual extinction of lineages that are not dependent upon environmental factors but exist across all manner of differing environments, geographical locations, types of organisms and ages.
---------------------QUOTE-------------------


Quite a sweeping set of predictions there Daniel!

     

---------------------QUOTE-------------------
Genetically:
Mathematical patterns not explainable by the current theory will be found when comparing sequences of different organisms.
The genetic code will be found to be more sophisticated and more robust than previously thought.
Embedded and overlapping coding will be found to be more prevalent than previously thought.
Careful examination of genomes will find preparatory and adaptive codes “waiting in the wings” ready to be utilized in case of environmental changes- many just a frame shift away.
Frame shifting will be found to be a more common mechanism for sudden evolutionary change than previously thought.
Every part of the entire genome of any organism will be found to either be used at some time in the organisms life, or be of future use.  There are no unusable “Leftovers”.
No adequate explanation other than design will ever be found for the origin of life’s most basic components - i.e. protein synthesis, cell division, sexual reproduction, etc.

Universally:
Because the earth, and the solar system were specifically designed for life, no life or signs of previous life will be found on any other planets within our field of exploration.

---------------------QUOTE-------------------


Even more sweeping!
For this one
     

---------------------QUOTE-------------------
Mathematical patterns not explainable by the current theory will be found when comparing sequences of different organisms.
---------------------QUOTE-------------------


It seems to me that you've since had the opportunity to compare sequences of different organisms.
What mathematical patterns did you find that are not explained by the current theory Daniel?
In that same message you said, in answer to me asking is there anything that design predicts that evolution does not:
     

---------------------QUOTE-------------------
I could say the same thing about the currently held theory.  Is there anything that will ever be found that you won't somehow make to fit and eventually make to be a prediction of the currently held theory?
---------------------QUOTE-------------------


And of course there any many things that if found would destroy "currently held theory" but it seems that over the course of this thread no amount of contrary evidence cannot be incorporated into your worldview.
I mean, it's like you < say >
     

---------------------QUOTE-------------------
I'm interested in the truth - that's all.  My goal is to find out what really happened.
---------------------QUOTE-------------------


And so let us continue. Some time later you < note >
     

---------------------QUOTE-------------------
I don't know why I started arguing against superimposable nested hierarchies - since that is entirely consistent with designed descent.  I guess it's just the old creationist in me that got me caught up in that.  I do admit that I don't have a real good grasp of the subject, and need to learn more.  Really my main objection to the current theory of evolution is in regards to mechanism.
---------------------QUOTE-------------------


That old time creationist in you? Seems to me that you've already made up your mind with regard to the age of the earth. And that's the funny thing - you are attempting to use the fossil record and what it shows as evidence for your position yet at the same time you think that it's all fake anyway and under 10,000 years old! It must be a strange place, the inside of your head. Lot's of Chinese walls.
From the same post:
     

---------------------QUOTE-------------------
First let me say that we have witnessed a saltational evolutionary event consistent with designed descent in our lifetime - the nylon bug.
---------------------QUOTE-------------------


So the designer knew that nylon would exist, when Daniel? Back at the start of time?At the beginning of the universe? Or more recently then that?
     

---------------------QUOTE-------------------
That the code for this enzyme was pre-existing also makes it consistent with designed descent.
---------------------QUOTE-------------------


So, under your "theory" it should be possible to go back to a previous "version" of the bug in question, before it started to be able to eat nylon and find the code in question but deactivated? Is that right?
In another < post > you say

     

---------------------QUOTE-------------------
If (as I'm alleging) genomes are replete with embedded codes just waiting for a signal, such as a frame shift, to set them in action, then a saltational change can happen with just one substitution.  These substitutions would be non-random of course.
---------------------QUOTE-------------------



Ah, so your position appears to be that your god makes these substitutions in real time. This appears to be at odds with what you recently said and with what I just quoted you as saying.
I asked you
   

---------------------QUOTE-------------------
Was this "direct refashioning" because

a) natural but as yet unexplained events caused it
b) god did it directly there and then.
c) god planned it that way from the beginning.

or other?
---------------------QUOTE-------------------


And you < said >

   

---------------------QUOTE-------------------
I don't know - maybe all of the above.
---------------------QUOTE-------------------


Which appears to contradict what you said...

The funny thing is that I keep asking you "< why >". And you keep saying you don't know. Yet previously you said

   

---------------------QUOTE-------------------
If we cannot directly ask a designer why they made certain choices, the best we can hope for is to examine their designs and try to make an educated guess based on what we observe.
---------------------QUOTE-------------------



So, Daniel, why did the designer (or "a" designer) make the choice regarding the overlong nerve in the giraffe neck? You did already in fact attempt an < answer >
   

---------------------QUOTE-------------------
The reason the nerve passes between the internal and external carotid arteries is because the giraffe evolved from a short-necked ancestor.  The giraffe most likely represents the over-specialized typolysis phase of Schindewolf's theory.

My guess is that the giraffe will exhibit low genetic variability when compared with other mammals also.

You have to remember that creation took place a long time ago, and lots of evolution and variation has happened since then.  The fact that so much of what remains is still functional is a testament to the brilliance of the Creator.
---------------------QUOTE-------------------


So my question to you is "a long time ago" about 6000 to 10000 years? Or is it longer?

You seem to be forgetting previous positions you've held Daniel. Some days the giraffe nerve is explained by "lots of evolution and variation" due to it being such a long time ago and some days it cannot be explained that way as the earth *might* not really be old at all.

Yet still, you can't seem to make up your mind as you've also < said >
   

---------------------QUOTE-------------------
I'll just say this and be done with it:
I'm perfectly content with a 4.5 billion year old earth, and I wouldn't cry if it turned out to be only 10,000 years old either.  IOW, it's not really an issue for me.

It's not how old things are; it's their chronological order that matters.
---------------------QUOTE-------------------



Perhaps the reason it's "not really an issue" for you is the general incoherence of your position. That's the trouble when you just make it all up for yourself, picking and choosing the bits you like and discarding the rest.

At that time I asked you this:
   

---------------------QUOTE-------------------
Daniel, in your opinion are  Schindewolf, Berg, and their theories of constrained evolution and evolution by law compatible with a 6000 year old earth and a global flood?

If not, what will you rule out?

Either way, progress will have been made.
---------------------QUOTE-------------------



Do you now care to rule one or the other out? Or is that rabbit hole still far to scary to enter?

In short Daniel, accept the fact you'll have nothing positive to contribute to this discussion or mankinds body of knowledge in general until you make up your mind about a few basic premises! And consider this - if your god can interfere at will and make changes such as the nylon bug frameshift then what happens to cause and effect? What happens to prediction? How can the whims of a designer be predicted? And yet predictions about how the physical world behave can be made with stunning accuracy, no god(s) required.
---------------------QUOTE-------------------


I've read your post and I can't see all these inconsistencies you talk about.  The nylon bug frameshift is evidence of two working codes existing side by side.  One is activated when the other is deactivated.  I've been posting links to papers that have bits and pieces of confirmations for many of the other predictions.
I don't really care about the age of the earth.  I don't know why you think that's such a big deal anyway.  The sequence of events are already well established.  I'm arguing for a theory of evolution!  (or did that fact escape you?)
What's your beef?
Posted by: mitschlag on Feb. 23 2008,17:01

Quote (Daniel Smith @ Feb. 23 2008,16:39)
I'd suggest you read pages 11-13 where Schindewolf makes it pretty clear that it's only the relative ages of fossils he's concerned with -- not the absolute ages.            

---------------------QUOTE-------------------
The only thing that concerns us in geology is the determination of the sequence of events...

...absolute age based on certain number of years is of no importance at all.  In this area, too, the only concern is to establish the relative age.

page 12 - his italics
---------------------QUOTE-------------------


---------------------QUOTE-------------------


Please, Daniel, don't play these silly quotemining games.  If you look at the context, he's deflecting criticism about imprecisions in geological dating to emphasize the points about temporal succession that he wants to make.  Look at what else he has to say on page 12 about dating methods and at Fig 2.2, which gives "Absolute time span in millions of years" for the divisions of geologic history.

In any case, you should be concerned about the age of the earth and the universe if you want to have an understanding of evolution.  Or of much else in science.
Posted by: mitschlag on Feb. 23 2008,17:07

Quote (Daniel Smith @ Feb. 23 2008,16:51)
I don't really care about the age of the earth.  I don't know why you think that's such a big deal anyway.  The sequence of events are already well established.  I'm arguing for a theory of evolution!  (or did that fact escape you?)
What's your beef?
---------------------QUOTE-------------------


Because IT ALL HAS TO FIT TOGETHER TO MAKE SENSE!
Posted by: oldmanintheskydidntdoit on Feb. 23 2008,17:32

Quote (Daniel Smith @ Feb. 23 2008,16:51)
I've been posting links to papers that have bits and pieces of confirmations for many of the other predictions.
---------------------QUOTE-------------------


Call my bluff then.

Simply add a link to the list of predictions I quoted

That you also just quoted.

Lets take stock and see how you've done.

And if the papers themselves disagree with the conclusions you draw from them does that still count?
Posted by: JAM on Feb. 23 2008,17:33

Quote (Daniel Smith @ Feb. 23 2008,16:51)
I've read your post and I can't see all these inconsistencies you talk about.
---------------------QUOTE-------------------


I don't believe you. You have demonstrated a massive capacity for self-delusion. If you disagree, why don't you take the time to actually address all of the points made? If you're right, your response would be quite impressive.


---------------------QUOTE-------------------
The nylon bug frameshift is evidence of two working codes existing side by side.  One is activated when the other is deactivated.
---------------------QUOTE-------------------


Huh?


---------------------QUOTE-------------------
I've been posting links to papers that have bits and pieces of confirmations for many of the other predictions.
---------------------QUOTE-------------------


ORLY? Then why have most of them not been from the primary literature? Why wouldn't you just provide the links under each of the predictions, since they've been brought together in one place?
Posted by: rhmc on Feb. 23 2008,19:14

it's only a flesh wound...
Posted by: Wesley R. Elsberry on Feb. 23 2008,20:44

Hmmm? I thought the claim was that only saltation operated "between types". Did that change somewhere or get retracted when I wasn't paying attention?
Posted by: hereoisreal on Feb. 23 2008,21:03

2Pe 3:8 But, beloved, be not ignorant of this one thing, that one day
[is] with the Lord as a thousand years, and a thousand years as one day.

My thoughts:

One day = 1,000 years
1,000 years = 365,000,000 years (one day)
7,ooo years = 2,555,000,000 years (one week)

Zero
Posted by: keiths on Feb. 23 2008,22:54

Quote (hereoisreal @ Feb. 23 2008,21:03)
2Pe 3:8 But, beloved, be not ignorant of this one thing, that one day
[is] with the Lord as a thousand years, and a thousand years as one day.

My thoughts:

One day = 1,000 years
1,000 years = 365,000,000 years (one day)
7,ooo years = 2,555,000,000 years (one week)

---------------------QUOTE-------------------


Zero,

You and Dembski are peas in a pod.

From a chapel talk Dembski gave at Southwestern Bible and Taxidermy College:


---------------------QUOTE-------------------
For instance, the Scriptures teach that with God, a day is as a thousand years.  But if a day is as a thousand years, then each day in that thousand years is itself a thousand years.  Thus, if you run the numbers, a day with God is also as 365,000,000 years.  Follow the math to its logical conclusion, and with God, an instant is an eternity.
---------------------QUOTE-------------------


Posted by: mitschlag on Feb. 24 2008,04:42

When  that bug in JAM's avatar sprouts wings I'll believe in evolution.
Posted by: hereoisreal on Feb. 24 2008,04:50

Quote (keiths @ Feb. 23 2008,22:54)
Quote (hereoisreal @ Feb. 23 2008,21:03)
2Pe 3:8 But, beloved, be not ignorant of this one thing, that one day
[is] with the Lord as a thousand years, and a thousand years as one day.

My thoughts:

One day = 1,000 years
1,000 years = 365,000,000 years (one day)
7,ooo years = 2,555,000,000 years (one week)

---------------------QUOTE-------------------


Zero,

You and Dembski are peas in a pod.

From a chapel talk Dembski gave at Southwestern Bible and Taxidermy College:
 

---------------------QUOTE-------------------
For instance, the Scriptures teach that with God, a day is as a thousand years.  But if a day is as a thousand years, then each day in that thousand years is itself a thousand years.  Thus, if you run the numbers, a day with God is also as 365,000,000 years.  Follow the math to its logical conclusion, and with God, an instant is an eternity.
---------------------QUOTE-------------------


---------------------QUOTE-------------------


keiths, I had not seen Dembski's remarks. Thanks.

To me, time, like size and direction, has a middle, a reference point, zero.

So it goes:

BC/zero/AD

or

eternity past/timing mark/eternity future
Posted by: Bob O'H on Feb. 24 2008,04:58



---------------------QUOTE-------------------
To me, time, like size and direction, has a middle, a reference point, zero.

So it goes:

BC/zero/AD
---------------------QUOTE-------------------


And unfortunate example.  The first century AD only has 99 years: those poor Romans had to go from 1BC to 1AD.  There were riots that year, because the citizens were unhappy because they thought the Emperor was stealing a whole year from their lives.
Posted by: hereoisreal on Feb. 24 2008,08:30

Quote (Bob O'H @ Feb. 24 2008,04:58)


---------------------QUOTE-------------------
To me, time, like size and direction, has a middle, a reference point, zero.

So it goes:

BC/zero/AD
---------------------QUOTE-------------------


And unfortunate example.  The first century AD only has 99 years: those poor Romans had to go from 1BC to 1AD.  There were riots that year, because the citizens were unhappy because they thought the Emperor was stealing a whole year from their lives.
---------------------QUOTE-------------------


Bob, I'm open to suggestions.  How would
you measure time?  Where would you start?
Posted by: Arden Chatfield on Feb. 24 2008,10:36

Quote (Bob O'H @ Feb. 24 2008,04:58)


---------------------QUOTE-------------------
To me, time, like size and direction, has a middle, a reference point, zero.

So it goes:

BC/zero/AD
---------------------QUOTE-------------------


An unfortunate example.  The first century AD only has 99 years: those poor Romans had to go from 1BC to 1AD.  There were riots that year, because the citizens were unhappy because they thought the Emperor was stealing a whole year from their lives.
---------------------QUOTE-------------------


But the upside is, they could keep writing the same year on their checks for two years in a row.

But getting used to counting forwards after that was kind of tough.
Posted by: Daniel Smith on Feb. 24 2008,13:55

Quote (mitschlag @ Feb. 23 2008,15:01)
 
Quote (Daniel Smith @ Feb. 23 2008,16:39)
I'd suggest you read pages 11-13 where Schindewolf makes it pretty clear that it's only the relative ages of fossils he's concerned with -- not the absolute ages.                

---------------------QUOTE-------------------
The only thing that concerns us in geology is the determination of the sequence of events...

...absolute age based on certain number of years is of no importance at all.  In this area, too, the only concern is to establish the relative age.

page 12 - his italics
---------------------QUOTE-------------------


---------------------QUOTE-------------------


Please, Daniel, don't play these silly quotemining games.  If you look at the context, he's deflecting criticism about imprecisions in geological dating to emphasize the points about temporal succession that he wants to make.  Look at what else he has to say on page 12 about dating methods and at Fig 2.2, which gives "Absolute time span in millions of years" for the divisions of geologic history.

In any case, you should be concerned about the age of the earth and the universe if you want to have an understanding of evolution.  Or of much else in science.
---------------------QUOTE-------------------


Actually, it's only the gradual evolution of Darwinism that requires hundreds of millions of years to bring about 'life as we know it'.  A saltational evolution theory does not require that timespan.  So, I have not been really concerned about "proving" the age of the earth to myself.  It's not an issue for me.  A saltational theory can "take or leave" the hundreds of millions of years required by gradualism.  Schindewolf held to the currently accepted age of the earth, but it's in no way "quote-mining" to show that he wasn't too concerned about absolute age.  Relative age was the only real concern he had.  If you can show me a passage where he placed absolute age over relative age in importance, do so.
Posted by: JAM on Feb. 24 2008,14:10

Quote (Daniel Smith @ Feb. 24 2008,13:55)
   
Quote (mitschlag @ Feb. 23 2008,15:01)

Please, Daniel, don't play these silly quotemining games.  If you look at the context, he's deflecting criticism about imprecisions in geological dating to emphasize the points about temporal succession that he wants to make.  Look at what else he has to say on page 12 about dating methods and at Fig 2.2, which gives "Absolute time span in millions of years" for the divisions of geologic history.

In any case, you should be concerned about the age of the earth and the universe if you want to have an understanding of evolution.  Or of much else in science.
---------------------QUOTE-------------------


Actually, it's only the gradual evolution of Darwinism that requires hundreds of millions of years to bring about 'life as we know it'.
---------------------QUOTE-------------------


Dan, this is preposterous. We aren't "Darwinists." Darwin merely observed existing variation and posited that at least some of it is heritable.

We clearly know that every mutational event is quantal (saltational), not gradual.
   

---------------------QUOTE-------------------
A saltational evolution theory does not require that timespan.
---------------------QUOTE-------------------


Schindewolf only proposed that SOME evolution is saltational.

Wesley patiently explained that single translocations have been shown to cause speciation.



---------------------QUOTE-------------------
So, I have not been really concerned about "proving" the age of the earth to myself.  It's not an issue for me.
---------------------QUOTE-------------------


The evidence isn't relevant for you, belying your claims when you first showed up here. You'd rather use straw men, ancient discredited opinions, and speculation that you are afraid to test against the evidence.


---------------------QUOTE-------------------
...it's in no way "quote-mining" to show that he wasn't too concerned about absolute age.
---------------------QUOTE-------------------


Actually, the most egregious quote-mining you've done is to use Schindewolf's painting of Darwin's position and falsely attribute it to us, as though no one has done any work to understand evolutionary mechanisms.

Mutations are digital, quantal, saltational, varying in their effects by multiple orders of magnitude. That comes from the evidence that you lied about your interest in, and it supercedes anything Darwin wrote 150 years ago and anything that  Schindewolf tried to attribute to him 50 years ago.
Posted by: Daniel Smith on Feb. 24 2008,14:18

Quote (oldmanintheskydidntdoit @ Feb. 23 2008,15:32)
 
Quote (Daniel Smith @ Feb. 23 2008,16:51)
I've been posting links to papers that have bits and pieces of confirmations for many of the other predictions.
---------------------QUOTE-------------------


Call my bluff then.

Simply add a link to the list of predictions I quoted

That you also just quoted.

Lets take stock and see how you've done.

And if the papers themselves disagree with the conclusions you draw from them does that still count?
---------------------QUOTE-------------------


Have you read any of the papers I've linked to?

If you had, you'd already know the truth of my statement and would not require me to spend half a day rehashing what's already been covered.

Personally, I don't think you've shown any interest in anything I've posted here - other than trying to discredit it.

Here's a 'for instance':

Here's the < "nylon bug" paper >.
The abstract makes this statement:
 

---------------------QUOTE-------------------
Analysis of the published base sequence residing in the pOAD2 plasmid of Flavobacterium Sp. K172 indicated that the 392-amino acid-residue-long bacterial enzyme 6-aminohexanoic acid linear oligomer hydrolase involved in degradation of nylon oligomers is specified by an alternative open reading frame of the preexisted coding sequence that originally specified a 472-residue-long arginine-rich protein.
---------------------QUOTE-------------------



Yet you ask:
 
Quote (oldmanintheskydidntdoit @ Feb. 23 2008,04:09)

So, under your "theory" it should be possible to go back to a previous "version" of the bug in question, before it started to be able to eat nylon and find the code in question but deactivated? Is that right?

---------------------QUOTE-------------------



So you obviously did not look at the paper or you'd have known that the "code in question but deactivated" was "the preexisted coding sequence that originally specified a 472-residue-long arginine-rich protein".

If you're too lazy to even bother to click on the links I post, or read the papers (or even the abstracts) these links point to, don't act as if you've somehow discredited my statements.

It's a very shallow "science" you practice oldman.
Posted by: Daniel Smith on Feb. 24 2008,14:25

Quote (Wesley R. Elsberry @ Feb. 23 2008,18:44)
Hmmm? I thought the claim was that only saltation operated "between types". Did that change somewhere or get retracted when I wasn't paying attention?
---------------------QUOTE-------------------


"Between types" - Yes.  Exclusively - No.
Schindewolf expressly said that gradual evolution occurred on a regular basis - during the typostasis and typolosis phases of his theory.
IOW, the saltational events were rare, but gradual evolution was common.  So we'd expect to find mostly evidence of gradual evolution in the fossil record except at the beginnings of types.
Posted by: JAM on Feb. 24 2008,14:37

Quote (Daniel Smith @ Feb. 24 2008,14:18)
   
Quote (oldmanintheskydidntdoit @ Feb. 23 2008,15:32)
       
Quote (Daniel Smith @ Feb. 23 2008,16:51)
I've been posting links to papers that have bits and pieces of confirmations for many of the other predictions.
---------------------QUOTE-------------------


Call my bluff then.

Simply add a link to the list of predictions I quoted

That you also just quoted.

Lets take stock and see how you've done.

And if the papers themselves disagree with the conclusions you draw from them does that still count?
---------------------QUOTE-------------------


Have you read any of the papers I've linked to?

If you had, you'd already know the truth of my statement and would not require me to spend half a day rehashing what's already been covered.

Personally, I don't think you've shown any interest in anything I've posted here - other than trying to discredit it.

Here's a 'for instance':

Here's the < "nylon bug" paper >.
The abstract makes this statement:
---------------------QUOTE-------------------


Abstracts aren't evidence.



---------------------QUOTE-------------------
Yet you ask:
       
Quote (oldmanintheskydidntdoit @ Feb. 23 2008,04:09)

So, under your "theory" it should be possible to go back to a previous "version" of the bug in question, before it started to be able to eat nylon and find the code in question but deactivated? Is that right?

---------------------QUOTE-------------------



So you obviously did not look at the paper or you'd have known that the "code in question but deactivated" was "the preexisted coding sequence that originally specified a 472-residue-long arginine-rich protein".
---------------------QUOTE-------------------


There's absolutely zero evidence that the "code" was "deactivated." Deactivation is an action. Who performed it and when?

 

---------------------QUOTE-------------------
If you're too lazy to even bother to click on the links I post, or read the papers (or even the abstracts) these links point to, don't act as if you've somehow discredited my statements.
---------------------QUOTE-------------------


You're projecting your laziness onto others.
 

---------------------QUOTE-------------------
It's a very shallow "science" you practice oldman.
---------------------QUOTE-------------------


More projection. Where is there any evidence even suggesting deactivation, Dan? There are very, very obvious predictions (not to someone as lazy as you, of course) that must be true if this had been the case.
Posted by: Daniel Smith on Feb. 24 2008,14:42

Quote (JAM @ Feb. 24 2008,12:10)
Mutations are digital, quantal, saltational, varying in their effects by multiple orders of magnitude.
---------------------QUOTE-------------------


So Schindewolf was right - there is a genetic mechanism for saltational evolution.  This mechanism is (I'm guessing) chromosomal and multiplies the effects of single nucleotide substitutions "by multiple orders of magnitude".  Goldschmidt called these "macromutations" and is also then shown to have been correct by modern evidence.  

So what are we arguing about here JAM?

Is it simply my attempt to bring God into the picture?  If so, that's unfair to Schindewolf and Goldschmidt - as neither of them did that - so why attempt to discredit them because of me?
Posted by: Daniel Smith on Feb. 24 2008,14:57

Quote (JAM @ Feb. 24 2008,12:37)

Abstracts aren't evidence.
---------------------QUOTE-------------------


Geez JAM, do I need to quote the whole paper?  Take a look at it.  It's even got figures!
Posted by: Daniel Smith on Feb. 24 2008,15:51

Here's another theory that parallels Schindewolf's by applying a macromutational mechanism to mammalian evolution:

Karyotypic fissioning and Canid phylogeny < (link) >    

---------------------QUOTE-------------------
Abstract

A theory is advanced which holds that mammalian evolution has been largely dependent on extensive chromosomal changes. These take the form of occasional simultaneous massive increase in diploid number through centric mis-division, here called karyotypic fissioning. This event occurs in a single individual and subsequently spreads through a population depending on chance, meiotic compatibility, dynamics of the population and natural selection. The possibility that fusions also occur sporadically is not precluded, although such events are not seen as abundant. This theory accounts for the wide variation in diploid number among the Mammalia and relates the presumed episodes of karyotypic fissioning with known periods of explosive speciation and adaptive radiation. Finally, the traditional evolutionary concept of mutant allele substitution through gene frequency shift under the influence of natural selection is placed in a new perspective. While it is still seen as a primary mechanism of evolution, it is seen as more significant as a “fine-tuning” mechanism, perhaps often responding to exigencies precipitated by chromosomal changes.

The theory is tested by integrating its assumptions with the phylogeny of the recent Canidae as previously reconstructed from the fossil record and classical studies of anatomy. The correlation between increase in diploid number and adaptive radiation within this group is obvious. Within the family it is possible to specify approximate times and places of karyotypic fissioning which have been found to be consistent with known paleontogical and zoogeographic facts. It has also been possible to suggest relationships among living species which had not been previously recognized, but which are testable by independent techniques.
---------------------QUOTE-------------------



Which led to this:
Kinetochore reproduction in animal evolution: Cell biological explanation of karyotypic fission theory < (link) >    

---------------------QUOTE-------------------
Abstract

Karyotypic fission theory of Todd offers an explanation for the diverse range of diploid numbers of many mammalian taxa. Theoretically, a full complement of acrocentric chromosomes can be introduced into a population by chromosomal fission. Subsequent inheritance of ancestral chromosomes and paired fission derivatives potentially generates a diploid range from the ancestral condition to double its number of chromosomes. Although it is undisputed that both chromosomal fission and fusion (“Robertsonian rearrangements”) have significantly contributed to karyological diversity, it is generally assumed that independent events, the fission of single chromosomes or the fusion of two chromosomes, are the sources of such change. The karyotypic fission idea by contrast posits that all mediocentric chromosomes simultaneously fission. Here I propose a specific cell biological mechanism for Todd's karyotypic fission concept, “kinetochore reproduction theory,” where a complete set of dicentric chromatids is synthesized during gametogenesis, and kinetochore protein dephosphorylation regulates dicentric chromatid segregation. Three postulates of kinetochore reproduction theory are: (i) breakage of dicentric chromosomes between centromere pairs forms acrocentric derivatives, (ii) de novo capping of newly synthesized acrocentric ends with telomeric DNA stabilizes these derivatives, and (iii) mitotic checkpoints regulate chromosomal disjunction to generate fissioned karyotypes. Subsequent chromosomal rearrangement, especially pericentric inversion, increases the probability of genetic isolation amongst incipient sympatric species polytypic for fission-generated acrocentric autosomes. This mechanism obviates the requirement for numerous independent Robertsonian rearrangements and neatly accounts for mammalian karyotype evolution as exemplified in analyses of Carnivora, Artiodactyla, and Primates.
---------------------QUOTE-------------------



So you have a chromosomal evolution theory for mammalian evolution and a hypothesized cellular mechanism - both of which are testable.

In my uneducated opinion, current evolutionary thought is more in line with Schindewolf and Goldschmidt than with Darwin.
Posted by: mitschlag on Feb. 24 2008,16:32

Quote (Daniel Smith @ Feb. 24 2008,13:55)

Actually, it's only the gradual evolution of Darwinism that requires hundreds of millions of years to bring about 'life as we know it'.  A saltational evolution theory does not require that timespan.
---------------------QUOTE-------------------


Well, then, what timespan does it require?  I believe that you've been asked this before.  Is it 6,000 years?
Posted by: mitschlag on Feb. 24 2008,16:35

Quote (Daniel Smith @ Feb. 24 2008,13:55)
 
Quote (mitschlag @ Feb. 23 2008,15:01)
In any case, you should be concerned about the age of the earth and the universe if you want to have an understanding of evolution.  Or of much else in science.
---------------------QUOTE-------------------


---------------------QUOTE-------------------


Did you get my point?
Posted by: oldmanintheskydidntdoit on Feb. 24 2008,16:48

Quote (Daniel Smith @ Feb. 24 2008,15:51)
In my uneducated opinion, current evolutionary thought is more in line with Schindewolf and Goldschmidt than with Darwin.
---------------------QUOTE-------------------


I believe there is a sentence missing. The one that describes how this supports your point.

And even my uneducated opinion knows that "current evolutionary thought" is very far away from what Darwin would have thought. The clue is in the date. 12 February 1809 – 19 April 1882.

Things have changed since 1882.
Posted by: Lou FCD on Feb. 24 2008,19:45

Quote (oldmanintheskydidntdoit @ Feb. 24 2008,17:48)
 
Quote (Daniel Smith @ Feb. 24 2008,15:51)
In my uneducated opinion, current evolutionary thought is more in line with Schindewolf and Goldschmidt than with Darwin.
---------------------QUOTE-------------------


I believe there is a sentence missing. The one that describes how this supports your point.
---------------------QUOTE-------------------


That tickled me.  Thanks.
Posted by: JAM on Feb. 24 2008,20:09

Quote (Daniel Smith @ Feb. 24 2008,14:57)
Quote (JAM @ Feb. 24 2008,12:37)

Abstracts aren't evidence.
---------------------QUOTE-------------------


Geez JAM, do I need to quote the whole paper?  Take a look at it.  It's even got figures!
---------------------QUOTE-------------------


No, you need to examine the evidence, which is not synonymous with anyone's opinion about the meaning of the evidence. At least you could admit that you were deliberately lying when you claimed:

Quote (Daniel Smith @ Sep. 22 2007,04:48)
I decided what I needed was just to see the evidence for myself.
---------------------QUOTE-------------------


Posted by: JAM on Feb. 24 2008,20:41

Quote (Daniel Smith @ Feb. 24 2008,14:42)
 
Quote (JAM @ Feb. 24 2008,12:10)
Mutations are digital, quantal, saltational, varying in their effects by multiple orders of magnitude.
---------------------QUOTE-------------------


So Schindewolf was right - there is a genetic mechanism for saltational evolution.  This mechanism is (I'm guessing) chromosomal
---------------------QUOTE-------------------


This is ludicrous. WTF does "chromosomal" mean in this context? Are you trying to make some chromosomal/episomal distinction, or are you just trying to pretend that you know what you are talking about?
 

---------------------QUOTE-------------------
...and multiplies the effects of single nucleotide substitutions "by multiple orders of magnitude".
---------------------QUOTE-------------------


You have no reading comprehension, Dan. Mutations, including all types, vary in their phenotypic effects by many orders of magnitude. IOW, there is virtually no correlation between the extent of the mutation as you look at the DNA and its phenotypic effect.

Put in more concrete terms, so that it might sink into a brain that is addled by wishful thinking and dishonesty, large interstitial deletions can have no detectable phenotype, even when homozygous, while single-base substitutions can be lethal, even when heterozygous.

Do you have any idea how dishonest it was for you to replace the beginning of my sentence with something completely different, and pretend that you were accurately representing my position?

 

---------------------QUOTE-------------------
Goldschmidt called these "macromutations" and is also then shown to have been correct by modern evidence.
---------------------QUOTE-------------------


You don't know what you are talking about. Anyone who can conflate:

1) Mutations are digital, quantal, saltational, varying in their effects by multiple orders of magnitude.

with

2) This mechanism is (I'm guessing) chromosomal and multiplies the effects of single nucleotide substitutions "by multiple orders of magnitude".

isn't operating with a full deck.
 

---------------------QUOTE-------------------
So what are we arguing about here JAM?
---------------------QUOTE-------------------


Your fundamental dishonesty and avoidance of evidence, primarily. Secondarily, your unwillingness to admit that your failed predictions made you less confident in the hypotheses you arrived with. Your pretense that opinion = evidence is an implicit admission that you lack faith.    

---------------------QUOTE-------------------
Is it simply my attempt to bring God into the picture?
---------------------QUOTE-------------------


No, it's your position that your desire to bring God into the picture somehow justifies multiple, deliberate lies (as well as pretending to know things that you don't) in direct violation of the Ninth Commandment. Christianity is supposed to be about demanding truthfulness from one's self, not trumping it with the need to defend a literal reading of a parable, considered to be a parable by the majority of your fellow Christians as well as the majority of Christian theologians.
Posted by: JAM on Feb. 24 2008,20:47

Quote (oldmanintheskydidntdoit @ Feb. 24 2008,16:48)
Quote (Daniel Smith @ Feb. 24 2008,15:51)
In my uneducated opinion, current evolutionary thought is more in line with Schindewolf and Goldschmidt than with Darwin.
---------------------QUOTE-------------------


I believe there is a sentence missing. The one that describes how this supports your point.

And even my uneducated opinion knows that "current evolutionary thought" is very far away from what Darwin would have thought. The clue is in the date. 12 February 1809 – 19 April 1882.

Things have changed since 1882.
---------------------QUOTE-------------------


Come on! Dan has no problem ignoring any data from the last 120 years if it helps him preserve his political position.

Will Dan respond to the criticism that he is being dishonest by holding up Schindewolf's representation of Darwin as the embodiment of our understanding of evolutionary mechanisms in 2008?

I say no, at least not honestly. He simply has to believe that we all worship Darwin (and that Schindewolf wasn't fudging yet again) or his house of cards falls down yet again.
Posted by: JAM on Feb. 24 2008,20:56

Quote (Daniel Smith @ Feb. 24 2008,15:51)
Here's another theory that parallels Schindewolf's by applying a macromutational mechanism to mammalian evolution:
---------------------QUOTE-------------------


I don't see the parallels. To illustrate, here's a question for you to dodge:

Would the chromosomal rearrangements cited by Wesley (translocations, inversions, breaks, fusions, etc.) be more likely to cause "pretty much instant speciation" via huge changes in phenotype, or via an entirely genetic mechanism that's covered in undergraduate genetics courses, as well as in some advanced high-school genetics courses?
Posted by: Wesley R. Elsberry on Feb. 25 2008,00:11

Quote (Daniel Smith @ Feb. 24 2008,14:25)
Quote (Wesley R. Elsberry @ Feb. 23 2008,18:44)
Hmmm? I thought the claim was that only saltation operated "between types". Did that change somewhere or get retracted when I wasn't paying attention?
---------------------QUOTE-------------------


"Between types" - Yes.  Exclusively - No.
Schindewolf expressly said that gradual evolution occurred on a regular basis - during the typostasis and typolosis phases of his theory.
IOW, the saltational events were rare, but gradual evolution was common.  So we'd expect to find mostly evidence of gradual evolution in the fossil record except at the beginnings of types.
---------------------QUOTE-------------------


Where one would *never* see it?
Posted by: Daniel Smith on Feb. 25 2008,19:10

Quote (Wesley R. Elsberry @ Feb. 24 2008,22:11)
   
Quote (Daniel Smith @ Feb. 24 2008,14:25)
     
Quote (Wesley R. Elsberry @ Feb. 23 2008,18:44)
Hmmm? I thought the claim was that only saltation operated "between types". Did that change somewhere or get retracted when I wasn't paying attention?
---------------------QUOTE-------------------


"Between types" - Yes.  Exclusively - No.
Schindewolf expressly said that gradual evolution occurred on a regular basis - during the typostasis and typolosis phases of his theory.
IOW, the saltational events were rare, but gradual evolution was common.  So we'd expect to find mostly evidence of gradual evolution in the fossil record except at the beginnings of types.
---------------------QUOTE-------------------


Where one would *never* see it?
---------------------QUOTE-------------------


In a sense yes.  If we saw something (in the fossil record that is), it would mean there was a gradual enough transition that it probably wasn't saltational.  So we should expect to *never* see it.  I would think we should see evidence of it in the chromosomes of related genomes however.
Posted by: Daniel Smith on Feb. 25 2008,19:18

Quote (mitschlag @ Feb. 24 2008,14:32)
 
Quote (Daniel Smith @ Feb. 24 2008,13:55)

Actually, it's only the gradual evolution of Darwinism that requires hundreds of millions of years to bring about 'life as we know it'.  A saltational evolution theory does not require that timespan.
---------------------QUOTE-------------------


Well, then, what timespan does it require?  I believe that you've been asked this before.  Is it 6,000 years?
---------------------QUOTE-------------------


I don't know what it would require.  As far as I can tell, the only required time period would be for the saltational events to spread to whatever extent they did population-wise.  The saltational event itself would require (at the most) one life-cycle for the organism in question.
Posted by: Daniel Smith on Feb. 25 2008,19:24

Quote (mitschlag @ Feb. 24 2008,14:35)
   
Quote (Daniel Smith @ Feb. 24 2008,13:55)
     
Quote (mitschlag @ Feb. 23 2008,15:01)
In any case, you should be concerned about the age of the earth and the universe if you want to have an understanding of evolution.  Or of much else in science.
---------------------QUOTE-------------------


---------------------QUOTE-------------------


Did you get my point?
---------------------QUOTE-------------------


I got it.  I've got no problem with the currently accepted age of the earth either.  All I said was that this saltational theory does not require that timespan.
Did you get my point?
Posted by: oldmanintheskydidntdoit on Feb. 26 2008,03:00

Quote (Daniel Smith @ Feb. 25 2008,19:24)
All I said was that this saltational theory does not require that timespan.
---------------------QUOTE-------------------


 
Quote (Daniel Smith @ Feb. 24 2008,13:55)
I don't know what it would require.
---------------------QUOTE-------------------



So you don't know what timespan it would require and at the same time you know it does not require *that* timespan?

How come you know what it does not need yet don't know what it does need?

Seems somewhat odd to me. Almost like you are making it up as you go along.
Posted by: oldmanintheskydidntdoit on Feb. 26 2008,03:13

Quote (Daniel Smith @ Feb. 25 2008,19:24)
I've got no problem with the currently accepted age of the earth either.  All I said was that this saltational theory does not require that timespan.
---------------------QUOTE-------------------



What's the minimum period required for your saltational theory Daniel? 6000 to 10,000 years perhaps?

It seems you won't rule out a 6000 year old earth? Sure, your saltational theory does not require a millions of years old earth but the fossils we're talking about do! You can't use fossil evidence and then claim it *could* be less then 6000 years old (which you are doing by implication).

Just say it Daniel.

Tell me Daniel, do you still think the jury is out on if the sun orbits the earth? Is there a case for both points of view? Or can we only progress if we unambiguously rule out one option and move on? By taking this stand you can rule out all sorts of things that cannot be accommodated under a 6000 year old earth.
Posted by: mitschlag on Feb. 26 2008,05:13

[parody]

Listen up, Brethren:

In contradiction to the Genesis story, GOD did not create all living things IN THE BEGINNING.  Each TYPE was CREATED in a saltational event.  (Especially the pinnacle of CREATION, MAN.)   A more leisurely approach befitting a BEING with eternity on HIS hands.

It doesn't matter WHEN in history each TYPE was created, as long as we keep the RELATIVE ORDER of CREATION straight.   Because we must keep it SCIENTIFIC.

Indeed, it's prudent to disbelieve evidence of an OLD EARTH, because that supports the DARWINIST interpretation. For DARWINISM (a work of the DEVIL) leads to UNBELIEF in saltation, and thus to unbelief in CREATION.   And GOD gets irritated when we don't believe in his ALMIGHTY POWER!

[/parody]
Posted by: Daniel Smith on Feb. 26 2008,19:10

Quote (oldmanintheskydidntdoit @ Feb. 26 2008,01:00)
 
Quote (Daniel Smith @ Feb. 25 2008,19:24)
All I said was that this saltational theory does not require that timespan.
---------------------QUOTE-------------------


   
Quote (Daniel Smith @ Feb. 24 2008,13:55)
I don't know what it would require.
---------------------QUOTE-------------------



So you don't know what timespan it would require and at the same time you know it does not require *that* timespan?

How come you know what it does not need yet don't know what it does need?

Seems somewhat odd to me. Almost like you are making it up as you go along.
---------------------QUOTE-------------------


Have you read any of those papers yet oldman?
Or are you just going to continually move the goalposts?
Posted by: oldmanintheskydidntdoit on Feb. 27 2008,03:00

Quote (Daniel Smith @ Feb. 26 2008,19:10)
Quote (oldmanintheskydidntdoit @ Feb. 26 2008,01:00)
   
Quote (Daniel Smith @ Feb. 25 2008,19:24)
All I said was that this saltational theory does not require that timespan.
---------------------QUOTE-------------------


     
Quote (Daniel Smith @ Feb. 24 2008,13:55)
I don't know what it would require.
---------------------QUOTE-------------------



So you don't know what timespan it would require and at the same time you know it does not require *that* timespan?

How come you know what it does not need yet don't know what it does need?

Seems somewhat odd to me. Almost like you are making it up as you go along.
---------------------QUOTE-------------------


Have you read any of those papers yet oldman?
Or are you just going to continually move the goalposts?
---------------------QUOTE-------------------


Why, are you looking to discuss them with somebody other then JAM?

While I can perhaps understand why, I've no sympathy. Try engaging JAM on the evidence maybe?

Daniel, how come you don't know what timespan your favoured theory require yet know what timespan they don't require?

Daniel, you say time does not matter, only the order in which things happened. If we rewind right back, in your theory, do we get to the garden of Eden by any chance? A literal genesis?

Or is that too silly even for you?
Posted by: Daniel Smith on Feb. 27 2008,17:58

Quote (oldmanintheskydidntdoit @ Feb. 27 2008,01:00)
   
Quote (Daniel Smith @ Feb. 26 2008,19:10)
   
Have you read any of those papers yet oldman?
Or are you just going to continually move the goalposts?
---------------------QUOTE-------------------


Why, are you looking to discuss them with somebody other then JAM?
---------------------QUOTE-------------------


You claim I have "no evidence" to back my statements, yet when I produce papers that have the evidence you say you need to see, you refuse to look.
Again I'll ask, how many of those papers have you read?
Posted by: Daniel Smith on Feb. 27 2008,18:05

Quote (oldmanintheskydidntdoit @ Feb. 26 2008,01:13)
Sure, your saltational theory does not require a millions of years old earth but the fossils we're talking about do!
---------------------QUOTE-------------------


How do you know that oldman?  How long does fossilization take?  What's the timespan needed to produce "the fossils we're talking about"?  How did you arrive at that figure?  Have you even thought about it?  Or are you just parotting what you've heard someone else say?
Posted by: JAM on Feb. 27 2008,18:43

Quote (Daniel Smith @ Feb. 27 2008,17:58)
Again I'll ask, how many of those papers have you read?
---------------------QUOTE-------------------


I looked at the two you most recently cited, but I have no idea why you cited them. They are about karyotypic changes within mammalian families (I'm only sure that Canidae is a family; I'm just guessing that the others are too).

Are you claiming that you see anything resembling Schindewolf's morphological gaps within any of those taxa?

If not, what's your point?
Posted by: IanBrown_101 on Feb. 27 2008,21:20

Quote (Daniel Smith @ Feb. 28 2008,00:05)
Quote (oldmanintheskydidntdoit @ Feb. 26 2008,01:13)
Sure, your saltational theory does not require a millions of years old earth but the fossils we're talking about do!
---------------------QUOTE-------------------


How do you know that oldman?  How long does fossilization take?  What's the timespan needed to produce "the fossils we're talking about"?  How did you arrive at that figure?  Have you even thought about it?  Or are you just parotting what you've heard someone else say?
---------------------QUOTE-------------------


Hi Mr Smith, come in, I'd like to introduce you to Mr Radiometric Dating.
Posted by: Daniel Smith on Feb. 28 2008,11:10

Quote (IanBrown_101 @ Feb. 27 2008,19:20)
 
Quote (Daniel Smith @ Feb. 28 2008,00:05)
 
Quote (oldmanintheskydidntdoit @ Feb. 26 2008,01:13)
Sure, your saltational theory does not require a millions of years old earth but the fossils we're talking about do!
---------------------QUOTE-------------------


How do you know that oldman?  How long does fossilization take?  What's the timespan needed to produce "the fossils we're talking about"?  How did you arrive at that figure?  Have you even thought about it?  Or are you just parotting what you've heard someone else say?
---------------------QUOTE-------------------


Hi Mr Smith, come in, I'd like to introduce you to Mr Radiometric Dating.
---------------------QUOTE-------------------


How much do you actually know about radiometric dating?
Posted by: IanBrown_101 on Feb. 28 2008,11:41

Quote (Daniel Smith @ Feb. 28 2008,17:10)
Quote (IanBrown_101 @ Feb. 27 2008,19:20)
 
Quote (Daniel Smith @ Feb. 28 2008,00:05)
   
Quote (oldmanintheskydidntdoit @ Feb. 26 2008,01:13)
Sure, your saltational theory does not require a millions of years old earth but the fossils we're talking about do!
---------------------QUOTE-------------------


How do you know that oldman?  How long does fossilization take?  What's the timespan needed to produce "the fossils we're talking about"?  How did you arrive at that figure?  Have you even thought about it?  Or are you just parotting what you've heard someone else say?
---------------------QUOTE-------------------


Hi Mr Smith, come in, I'd like to introduce you to Mr Radiometric Dating.
---------------------QUOTE-------------------


How much do you actually know about radiometric dating?
---------------------QUOTE-------------------


Well considering I finished my science education at my A-levels, and the only one I continued that far was biology, only what I've read and so on, so not a huge amount.

Why, do you know more about it than, say, the people who use it?
Posted by: mitschlag on Feb. 28 2008,12:32

Quote (IanBrown_101 @ Feb. 28 2008,11:41)
 
Quote (Daniel Smith @ Feb. 28 2008,17:10)
 
Quote (IanBrown_101 @ Feb. 27 2008,19:20)
     
Quote (Daniel Smith @ Feb. 28 2008,00:05)
     
Quote (oldmanintheskydidntdoit @ Feb. 26 2008,01:13)
Sure, your saltational theory does not require a millions of years old earth but the fossils we're talking about do!
---------------------QUOTE-------------------


How do you know that oldman?  How long does fossilization take?  What's the timespan needed to produce "the fossils we're talking about"?  How did you arrive at that figure?  Have you even thought about it?  Or are you just parotting what you've heard someone else say?
---------------------QUOTE-------------------


Hi Mr Smith, come in, I'd like to introduce you to Mr Radiometric Dating.
---------------------QUOTE-------------------


How much do you actually know about radiometric dating?
---------------------QUOTE-------------------


Well considering I finished my science education at my A-levels, and the only one I continued that far was biology, only what I've read and so on, so not a huge amount.

Why, do you know more about it than, say, the people who use it?
---------------------QUOTE-------------------


Brace yourself.  Strong tard on the horizon.

That's my fear, at any < rate >
Posted by: swbarnes2 on Feb. 28 2008,14:35

Quote (Daniel Smith @ Feb. 28 2008,00:05)
 
How much do you actually know about radiometric dating?
---------------------QUOTE-------------------

 

It's just astonishing.

We had already seen tons of evidence that, when given a choice between his Creationist beliefs, and his integrity, Daniel chooses his Creationist beliefs.

And now, given the choice between his Creationism, and pretty much all of science, he again throws science away, and clings to his Creationism.

There is no falsehhod transparent enough, no stupidity blatent enough to prevent Daniel from trampling every moral principle he possesses to embrace it, if it supports his Creationism.

It's not just that creationism requires you to throw away facts and reason.  But that defending it requires that it requries you to throw away your honesty and integrity.  It kills not only your mind, but your soul.
Posted by: mitschlag on Feb. 28 2008,16:12

Quote (swbarnes2 @ Feb. 28 2008,14:35)
 
Quote (Daniel Smith @ Feb. 28 2008,00:05)
 
How much do you actually know about radiometric dating?
---------------------QUOTE-------------------

 

It's just astonishing.

We had already seen tons of evidence that, when given a choice between his Creationist beliefs, and his integrity, Daniel chooses his Creationist beliefs.

And now, given the choice between his Creationism, and pretty much all of science, he again throws science away, and clings to his Creationism.

There is no falsehhod transparent enough, no stupidity blatent enough to prevent Daniel from trampling every moral principle he possesses to embrace it, if it supports his Creationism.

It's not just that creationism requires you to throw away facts and reason.  But that defending it requires that it requries you to throw away your honesty and integrity.  It kills not only your mind, but your soul.
---------------------QUOTE-------------------


That's OK.  Creationist souls are expendable.   :D
Posted by: oldmanintheskydidntdoit on Feb. 28 2008,16:49

Quote (Daniel Smith @ Feb. 27 2008,18:05)
 
Quote (oldmanintheskydidntdoit @ Feb. 26 2008,01:13)
Sure, your saltational theory does not require a millions of years old earth but the fossils we're talking about do!
---------------------QUOTE-------------------


How do you know that oldman?  How long does fossilization take?  What's the timespan needed to produce "the fossils we're talking about"?  How did you arrive at that figure?  Have you even thought about it?  Or are you just parotting what you've heard someone else say?
---------------------QUOTE-------------------


 

---------------------QUOTE-------------------
How long does fossilization take?
---------------------QUOTE-------------------


I think it depends. This is an interesting article:
< nonmineralized_tissues_in_fossils >
 

---------------------QUOTE-------------------
The standard textbook account of “fossilization” might be termed the “Tin Man” story: soft tissues decay, the resulting cavities are filled with minerals precipitated from groundwater, and the original biominerals transform into or are replaced by other substances. This process results in a replica of the original object in which the original substance has been heavily altered and largely or entirely replaced by other materials
---------------------QUOTE-------------------


And later
 

---------------------QUOTE-------------------
Indeed, it is only in the past 15 years that paleontological geochemists begun to address, in a serious and organized way, basic questions about why some things endure long enough to become fossils. To date, these efforts have revealed important details about the chemical behavior of some fossils in some settings, but we are a long way from the kind of systematic knowledge implied by the cited passages.
---------------------QUOTE-------------------


Now, I'm not a paleontological geochemist. Neither, I suspect are you. So perhaps a firsthand account will be useful?
< John W. Bebout, Ph.D., Sr. Technical Specialist, Oil and Gas, Fluid Minerals Group, Bureau of Land Management >
 

---------------------QUOTE-------------------
How long it takes for petrification to occur depends on a lot of factors like pH and temperature, but all things being equal, groundwater saturated with calcium carbonate(calcite)acts the fastest because calcite is more
soluble than silica or other petrifying minerals.  In the parking garage where I work, which is only 3 years old, 4 inch stalactites have already formed from rainwater leaching calcium carbonate out of the concrete floors.

So if we accept the fact that petrification occurs as a continuum (in other words, a gradual process from partial to complete replacement/recrystallization/permineralization), and we assume the replacement material is calcite under ideal chemical conditions, petrification can certainly occur just a few hundred years or even less.
---------------------QUOTE-------------------



So, how long does fossilization take? It takes as long as it takes. Those bones, in the right conditions can sit around for a long time. Long enough to fossilise at any rate.
;) I'd say more towards hundreds of years then thousands.
 

---------------------QUOTE-------------------
What's the timespan needed to produce "the fossils we're talking about"?
---------------------QUOTE-------------------


A mindbendengly far away long long time. Amazingly un-understandable. The timespan appears to be about 2/3 of the Mesozoic era. Is this a quiz?
 

---------------------QUOTE-------------------
How did you arrive at that figure?
---------------------QUOTE-------------------


I did not conduct any of the research myself. I read the information at sources that I trust to tell me at the very least the truth as they see it. Part of them earning that trust in the first place is telling a story that has no, or few inconsistencies. A story that has consilience in fact, rather then "no inconsistencies". Overall. And the "story" that has consilience? Well, there's no Noah and his ark in it, that's for sure. What's your take on the Ark Daniel? Did all the ammonites climb aboard the ark or will even you dismiss that has a childs tale?
 

---------------------QUOTE-------------------
Have you even thought about it?
---------------------QUOTE-------------------


I got three words for you buster.

< AFDave >
< Cailbration Curves >


Go look it up.
 

---------------------QUOTE-------------------
Or are you just parotting what you've heard someone else say?
---------------------QUOTE-------------------


No, I find the subject fascinating and am grateful for the occasional bout of free education that goes on when folks like AFDave need correcting, in detail. Over and over.

What about you Daniel? You ever thought about it? Consider this then - if our understanding of the workings of matter is so far off that dating can be "wrong" then it's unlikely the computer you are sitting in front of with all it's quantum weirdness (tunneling is exploited don't ya know) would work as expected. And so, er, it's not wrong? Or you know something we don't know?

Do share.
Posted by: JAM on Feb. 28 2008,17:47

Quote (swbarnes2 @ Feb. 28 2008,14:35)
Quote (Daniel Smith @ Feb. 28 2008,00:05)
 
How much do you actually know about radiometric dating?
---------------------QUOTE-------------------

 

It's just astonishing.

We had already seen tons of evidence that, when given a choice between his Creationist beliefs, and his integrity, Daniel chooses his Creationist beliefs.

And now, given the choice between his Creationism, and pretty much all of science, he again throws science away, and clings to his Creationism.

There is no falsehhod transparent enough, no stupidity blatent enough to prevent Daniel from trampling every moral principle he possesses to embrace it, if it supports his Creationism.

It's not just that creationism requires you to throw away facts and reason.  But that defending it requires that it requries you to throw away your honesty and integrity.  It kills not only your mind, but your soul.
---------------------QUOTE-------------------


For me, the striking thing is the incredible weakness of faith that Dan's behavior reveals.
Posted by: EoRaptor013 on Feb. 28 2008,22:20

Jam,
If I break my screen smacking that damned bug every time I see it out of the corner of my eye, I'm gonna send you the bill via my friends Rocco and Bufo, to pay for it! :angry:



With love,
FormicaBane
Posted by: oldmanintheskydidntdoit on Feb. 29 2008,09:29

Quote (Daniel Smith @ Feb. 28 2008,11:10)
Quote (IanBrown_101 @ Feb. 27 2008,19:20)
   
Quote (Daniel Smith @ Feb. 28 2008,00:05)
   
Quote (oldmanintheskydidntdoit @ Feb. 26 2008,01:13)
Sure, your saltational theory does not require a millions of years old earth but the fossils we're talking about do!
---------------------QUOTE-------------------


How do you know that oldman?  How long does fossilization take?  What's the timespan needed to produce "the fossils we're talking about"?  How did you arrive at that figure?  Have you even thought about it?  Or are you just parotting what you've heard someone else say?
---------------------QUOTE-------------------


Hi Mr Smith, come in, I'd like to introduce you to Mr Radiometric Dating.
---------------------QUOTE-------------------


How much do you actually know about radiometric dating?
---------------------QUOTE-------------------


It seems Daniel is bluffing:


---------------------QUOTE-------------------
Sorry Dr. Davison.
Speaking of your PEH, I've been reading "Questions of Paleontology" by Otto Schindewolf, and it occured to me:
If evolution was saltational, doesn't that eliminate the need for long time frames?
I'm new to the concept of dating and determining ages, and I haven't got far enough in the book to see if Schindewolf covers this, but I'm getting the impression that the entire dating framework is based on the long periods of time thought necessary for gradual evolution to take place. Since all evidence points to sudden, directed evolution, aren't the methods of dating and their calibrations subject to reassessment?
---------------------QUOTE-------------------


My bolding.
< Link >
Posted by: Henry J on Feb. 29 2008,10:17

Even if saltation did remove the requirement for long time frames, that wouldn't change the fact that the time frames that actually occurred have been measured.

(It would also of course depend on the degree of saltation, and the amount of recovery time needed between saltation events. Also it might take more than salt; sometimes pepper and other spices may be needed.)

Henry
Posted by: Daniel Smith on Feb. 29 2008,10:54

Quote (swbarnes2 @ Feb. 28 2008,12:35)
Quote (Daniel Smith @ Feb. 28 2008,00:05)
 
How much do you actually know about radiometric dating?
---------------------QUOTE-------------------

 

It's just astonishing.

We had already seen tons of evidence that, when given a choice between his Creationist beliefs, and his integrity, Daniel chooses his Creationist beliefs.

And now, given the choice between his Creationism, and pretty much all of science, he again throws science away, and clings to his Creationism.

There is no falsehhod transparent enough, no stupidity blatent enough to prevent Daniel from trampling every moral principle he possesses to embrace it, if it supports his Creationism.

It's not just that creationism requires you to throw away facts and reason.  But that defending it requires that it requries you to throw away your honesty and integrity.  It kills not only your mind, but your soul.
---------------------QUOTE-------------------


You got all that from my question?

Wow!
Posted by: Daniel Smith on Feb. 29 2008,10:59

Quote (oldmanintheskydidntdoit @ Feb. 29 2008,07:29)
 
Quote (Daniel Smith @ Feb. 28 2008,11:10)
   
Quote (IanBrown_101 @ Feb. 27 2008,19:20)
     
Quote (Daniel Smith @ Feb. 28 2008,00:05)
       
Quote (oldmanintheskydidntdoit @ Feb. 26 2008,01:13)
Sure, your saltational theory does not require a millions of years old earth but the fossils we're talking about do!
---------------------QUOTE-------------------


How do you know that oldman?  How long does fossilization take?  What's the timespan needed to produce "the fossils we're talking about"?  How did you arrive at that figure?  Have you even thought about it?  Or are you just parotting what you've heard someone else say?
---------------------QUOTE-------------------


Hi Mr Smith, come in, I'd like to introduce you to Mr Radiometric Dating.
---------------------QUOTE-------------------


How much do you actually know about radiometric dating?
---------------------QUOTE-------------------


It seems Daniel is bluffing:
   

---------------------QUOTE-------------------
Sorry Dr. Davison.
Speaking of your PEH, I've been reading "Questions of Paleontology" by Otto Schindewolf, and it occured to me:
If evolution was saltational, doesn't that eliminate the need for long time frames?
I'm new to the concept of dating and determining ages, and I haven't got far enough in the book to see if Schindewolf covers this, but I'm getting the impression that the entire dating framework is based on the long periods of time thought necessary for gradual evolution to take place. Since all evidence points to sudden, directed evolution, aren't the methods of dating and their calibrations subject to reassessment?
---------------------QUOTE-------------------


My bolding.
< Link >
---------------------QUOTE-------------------


I'm not "bluffing".  I'm still asking the same question.  Do you know the answer?
Posted by: oldmanintheskydidntdoit on Feb. 29 2008,11:02

Quote (Daniel Smith @ Feb. 29 2008,10:59)
I'm not "bluffing".  I'm still asking the same question.  Do you know the answer?
---------------------QUOTE-------------------


Er, What's the question again? If it's "how much do you know about radiometric dating" the answer is "Exactly as much as I know".

And I already answered several of your other questions on the previous page.
Posted by: Dr.GH on Feb. 29 2008,12:09

Quote (Daniel Smith @ Feb. 28 2008,09:10)
Quote (IanBrown_101 @ Feb. 27 2008,19:20)
 
Quote (Daniel Smith @ Feb. 28 2008,00:05)
   
Quote (oldmanintheskydidntdoit @ Feb. 26 2008,01:13)
Sure, your saltational theory does not require a millions of years old earth but the fossils we're talking about do!
---------------------QUOTE-------------------


How do you know that oldman?  How long does fossilization take?  What's the timespan needed to produce "the fossils we're talking about"?  How did you arrive at that figure?  Have you even thought about it?  Or are you just parotting what you've heard someone else say?
---------------------QUOTE-------------------


Hi Mr Smith, come in, I'd like to introduce you to Mr Radiometric Dating.
---------------------QUOTE-------------------


How much do you actually know about radiometric dating?
---------------------QUOTE-------------------


I am an expert.  What do you know about radiometric, or anyother dating mrthod?
Posted by: Tracy P. Hamilton on Feb. 29 2008,13:06



---------------------QUOTE-------------------
Speaking of your PEH, I've been reading "Questions of Paleontology" by Otto Schindewolf, and it occured to me:
If evolution was saltational, doesn't that eliminate the need for long time frames?
I'm new to the concept of dating and determining ages, and I haven't got far enough in the book to see if Schindewolf covers this, but I'm getting the impression that the entire dating framework is based on the long periods of time thought necessary for gradual evolution to take place. Since all evidence points to sudden, directed evolution, aren't the methods of dating and their calibrations subject to reassessment?
---------------------QUOTE-------------------



There never was a need for long time frames.  Don't project your shortcomings (needing to have X be true for emotional reasons) onto scientists.  Scientists need to understand the universe as it is.

The dating framework is not based on "periods of time thought necessary".  The dating framework is based on physical processes that enable ages to be derived reliably.

You are also making a logic error:  if speciation is faster than previously thought, that does not mean the ages need to be reassessed.  Suppose I find out that a house can be built in 7 days by watching extreme makeover, rather than the 6 months I thought should take.  Is that a reason to reassess the age of my house?  Have you forgotten the statements about stasis?  That takes time, too, you know.
Posted by: JAM on Feb. 29 2008,13:26

Quote (EoRaptor013 @ Feb. 28 2008,22:20)
Jam,
If I break my screen smacking that damned bug every time I see it out of the corner of my eye, I'm gonna send you the bill via my friends Rocco and Bufo, to pay for it! :angry:



With love,
FormicaBane
---------------------QUOTE-------------------


Is this better?
Posted by: Lou FCD on Feb. 29 2008,15:28

Quote (JAM @ Feb. 29 2008,14:26)
Is this better?
---------------------QUOTE-------------------


I was actually growing kinda fond of the bug.
Posted by: mitschlag on Feb. 29 2008,15:46

Quote (JAM @ Feb. 29 2008,13:26)
Is this better?
---------------------QUOTE-------------------


I may vomit.
Posted by: JonF on Feb. 29 2008,17:53

Quote (Daniel Smith @ Feb. 29 2008,11:59)
Quote (oldmanintheskydidntdoit @ Feb. 29 2008,07:29)
   
Quote (Daniel Smith @ Feb. 28 2008,11:10)
     
Quote (IanBrown_101 @ Feb. 27 2008,19:20)
       
Quote (Daniel Smith @ Feb. 28 2008,00:05)
         
Quote (oldmanintheskydidntdoit @ Feb. 26 2008,01:13)
Sure, your saltational theory does not require a millions of years old earth but the fossils we're talking about do!
---------------------QUOTE-------------------


How do you know that oldman?  How long does fossilization take?  What's the timespan needed to produce "the fossils we're talking about"?  How did you arrive at that figure?  Have you even thought about it?  Or are you just parotting what you've heard someone else say?
---------------------QUOTE-------------------


Hi Mr Smith, come in, I'd like to introduce you to Mr Radiometric Dating.
---------------------QUOTE-------------------


How much do you actually know about radiometric dating?
---------------------QUOTE-------------------


It seems Daniel is bluffing:
     

---------------------QUOTE-------------------
Sorry Dr. Davison.
Speaking of your PEH, I've been reading "Questions of Paleontology" by Otto Schindewolf, and it occured to me:
If evolution was saltational, doesn't that eliminate the need for long time frames?
I'm new to the concept of dating and determining ages, and I haven't got far enough in the book to see if Schindewolf covers this, but I'm getting the impression that the entire dating framework is based on the long periods of time thought necessary for gradual evolution to take place. Since all evidence points to sudden, directed evolution, aren't the methods of dating and their calibrations subject to reassessment?
---------------------QUOTE-------------------


My bolding.
< Link >
---------------------QUOTE-------------------


I'm not "bluffing".  I'm still asking the same question.  Do you know the answer?
---------------------QUOTE-------------------


I also am an expert. Are you preparing to regurgitate the same tired "based on three assumptions" crap that creationists typically copy from some ill-informed web site in a vain attempt to exhibit some knowledge? Or do you really have something to say or ask?

If you wish to criticize the methodology of radiometric dating, be sure to discuss Ar-Ar, isochron, and U-Pb methods. After all, they  make up the vast majority of geological radiometric dating results; comparatively few studies use the K-Ar method (although it does have its place)

You can leave Pb-Pb isochrons, U-Th disequilibrium dating, and a few other topics for later; they require more knowledge. But if the discussion develops they may come up.

Oh, and don't bother with accelerated radioactive decay unless you have a way to get rid of the heaat and radiation.
Posted by: Daniel Smith on Feb. 29 2008,20:11

Quote (JAM @ Feb. 27 2008,16:43)
         
Quote (Daniel Smith @ Feb. 27 2008,17:58)
Again I'll ask, how many of those papers have you read?
---------------------QUOTE-------------------


I looked at the two you most recently cited, but I have no idea why you cited them. They are about karyotypic changes within mammalian families (I'm only sure that Canidae is a family; I'm just guessing that the others are too).

Are you claiming that you see anything resembling Schindewolf's morphological gaps within any of those taxa?

If not, what's your point?
---------------------QUOTE-------------------


Both of these papers advance a saltational mechanism for evolution, similar to what Schindewolf proposed.  That such mechanisms require far fewer transitional steps than the gradualism Darwin proposed is IMO vindication for Schindewolf.  If these karyotypic changes resulted in morphological changes, these transitional steps would be next to invisible in the fossil record - thus explaining Schindewolf's gaps between types.

From Kinetochore reproduction in animal evolution: Cell biological explanation of karyotypic fission theory:          

---------------------QUOTE-------------------
Karyotypic fission theory recently applied to lemurs (prosimian primates) explains their karyotypic diversity (2n = 20–70) with a minimum of four evolutionary steps, whereas prior explanations required at least 100 independent chromosomal mutations (4).
---------------------QUOTE-------------------

         

---------------------QUOTE-------------------
Recent advances in cell-cycle regulation, chromosome behavior, fossil record, and phylogenetic inferences dispute that the primary direction of karyotypic evolution by sequential fusion of chromosomes is toward an arbitrary reduction in diploid number. Rather the tendency of kinetochores to reproduce, of telomerases to cap newly synthesized chromosome ends, and of mitotic checkpoints to regulate disjunction and generate freshly fissioned karyotypes in ancestral animals supports Todd's concept of saltatory chromosomal evolution.
---------------------QUOTE-------------------


From Karyotypic fissioning and Canid phylogeny:
         

---------------------QUOTE-------------------
This theory accounts for the wide variation in diploid number among the Mammalia and relates the presumed episodes of karyotypic fissioning with known periods of explosive speciation and adaptive radiation. Finally, the traditional evolutionary concept of mutant allele substitution through gene frequency shift under the influence of natural selection is placed in a new perspective. While it is still seen as a primary mechanism of evolution, it is seen as more significant as a “fine-tuning” mechanism, perhaps often responding to exigencies precipitated by chromosomal changes.
---------------------QUOTE-------------------


This is almost exactly what Schindewolf's theory proposed - that types were produced saltationally, (called here "periods of explosive speciation and adaptive radiation"), and then gradually evolved into specialized forms within that type, (here inferred by relegating gradual evolution to "a “fine-tuning” mechanism... responding to exigencies precipitated by chromosomal changes").

I'm not sure how you can not see the parallels with Schindewolf JAM, but then you know a lot more about this stuff than I do.
Posted by: Daniel Smith on Feb. 29 2008,20:19

Quote (JonF @ Feb. 29 2008,15:53)
 
Quote (Daniel Smith @ Feb. 29 2008,11:59)
   
Quote (oldmanintheskydidntdoit @ Feb. 29 2008,07:29)
     
Quote (Daniel Smith @ Feb. 28 2008,11:10)
       
Quote (IanBrown_101 @ Feb. 27 2008,19:20)
           
Quote (Daniel Smith @ Feb. 28 2008,00:05)
           
Quote (oldmanintheskydidntdoit @ Feb. 26 2008,01:13)
Sure, your saltational theory does not require a millions of years old earth but the fossils we're talking about do!
---------------------QUOTE-------------------


How do you know that oldman?  How long does fossilization take?  What's the timespan needed to produce "the fossils we're talking about"?  How did you arrive at that figure?  Have you even thought about it?  Or are you just parotting what you've heard someone else say?
---------------------QUOTE-------------------


Hi Mr Smith, come in, I'd like to introduce you to Mr Radiometric Dating.
---------------------QUOTE-------------------


How much do you actually know about radiometric dating?
---------------------QUOTE-------------------


It seems Daniel is bluffing:
       

---------------------QUOTE-------------------
Sorry Dr. Davison.
Speaking of your PEH, I've been reading "Questions of Paleontology" by Otto Schindewolf, and it occured to me:
If evolution was saltational, doesn't that eliminate the need for long time frames?
I'm new to the concept of dating and determining ages, and I haven't got far enough in the book to see if Schindewolf covers this, but I'm getting the impression that the entire dating framework is based on the long periods of time thought necessary for gradual evolution to take place. Since all evidence points to sudden, directed evolution, aren't the methods of dating and their calibrations subject to reassessment?
---------------------QUOTE-------------------


My bolding.
< Link >
---------------------QUOTE-------------------


I'm not "bluffing".  I'm still asking the same question.  Do you know the answer?
---------------------QUOTE-------------------


I also am an expert. Are you preparing to regurgitate the same tired "based on three assumptions" crap that creationists typically copy from some ill-informed web site in a vain attempt to exhibit some knowledge? Or do you really have something to say or ask?

If you wish to criticize the methodology of radiometric dating, be sure to discuss Ar-Ar, isochron, and U-Pb methods. After all, they  make up the vast majority of geological radiometric dating results; comparatively few studies use the K-Ar method (although it does have its place)

You can leave Pb-Pb isochrons, U-Th disequilibrium dating, and a few other topics for later; they require more knowledge. But if the discussion develops they may come up.

Oh, and don't bother with accelerated radioactive decay unless you have a way to get rid of the heaat and radiation.
---------------------QUOTE-------------------


I know next to nothing about the subject, so I'm not trying to advance anything.  I'm just asking.  Somehow, I got the impression that radiometric dating methods were calibrated originally by the "known" length of time it took for evolution to take place.  I'm not sure where I heard that - it could've been from a creationist website or something - and I'm not saying it's true.  I'm just asking!
Posted by: oldmanintheskydidntdoit on Mar. 01 2008,04:10

Quote (Daniel Smith @ Feb. 29 2008,20:19)
Somehow, I got the impression that radiometric dating methods were calibrated originally by the "known" length of time it took for evolution to take place.  I'm not sure where I heard that - it could've been from a creationist website or something - and I'm not saying it's true.  I'm just asking!
---------------------QUOTE-------------------


Then you are wrong.

Daniel, why are you even reading creationist websites?

I thought you were after the truth?

EDIT: Daniel, you should also know that the first wave of geologists were creationists who went digging to prove the account of the bible (ok, this is a simplified version of the real events) and found instead that the evidence they were digging up could not support the biblical account. And changed their minds. I'm sure somebody can provide a good reference to these events, if not I'll dig one up for you.

They found out what really happened.

EDIT EDIT: This site might appeal, < http://www.answersincreation.org/geology.htm >
Rebuttals to many standard creationist talking points but from a biblical POV. I thought it might be better then the usual "reality based community" rebuttals you no doubt will refuse to read.
Posted by: oldmanintheskydidntdoit on Mar. 01 2008,04:44

< http://www.answersincreation.org/radiometricdating.htm >
< http://www.talkorigins.org/faqs/dating.html >

Also, as I mentioned before, the question you have to ask is why do all the calibration curves match up? Sure you can attempt to poke holes in a single method of dating, but you'll still have to explain the curves....
Posted by: mitschlag on Mar. 01 2008,05:52

Quote (Daniel Smith @ Feb. 29 2008,20:11)
Both of these papers advance a saltational mechanism for evolution, similar to what Schindewolf proposed.  That such mechanisms require far fewer transitional steps than the gradualism Darwin proposed is IMO vindication for Schindewolf.  If these karyotypic changes resulted in morphological changes, these transitional steps would be next to invisible in the fossil record - thus explaining Schindewolf's gaps between types.

From Kinetochore reproduction in animal evolution: Cell biological explanation of karyotypic fission theory:

<snip>

From Karyotypic fissioning and Canid phylogeny:
---------------------QUOTE-------------------


You  pays your  money and you takes your choice.*  Try this one on for size:

< A test of the karyotypic fissioning theory of primate evolution >
 

---------------------QUOTE-------------------
Stanyon R.

Karyotypic fissioning theory has been put forward by a number of researchers as a possible driving force of mammalian evolution. Most recently, Giusto and Margulis (BioSystems, 13 (1981) 267-302) hypothesized that karyotypic fissioning best explains the evolution of Old World monkeys, apes, and humans. According to their hypothesis, hominoid karyotypes were derived from the monkey chromosome complement by just such a fissioning event. That hypothesis is tested here by comparing the G-banded chromosomes of humans and great apes with eight species of Old World monkeys. Five submetacentric chromosomes between apes and monkeys have identical banding patterns and nine chromosomes share the same pericentric inversion. Such extensive karyological similarities are not in accordance with, or predicted by karyotypic fissioning. Apparently, karyotypic fissioning is an extremely uneconomical model of chromosomal evolution. The strong conservation of banding patterns sometimes involving the retention of identical chromosomes indicates that ancient linkages of genes have probably been maintained through many speciation events.
---------------------QUOTE-------------------

(Emphasis added)

*Cherry-picking the literature is a  favored Creationist tactic.
Posted by: mitschlag on Mar. 01 2008,07:24

Quote (Daniel Smith @ Feb. 29 2008,20:19)
Somehow, I got the impression that radiometric dating methods were calibrated originally by the "known" length of time it took for evolution to take place.
---------------------QUOTE-------------------


A classic Creationist canard.

If that were the case, it would be an example of CIRCULAR REASONING, wouldn't it?

Stupid scientists, assuming what they want to conclude!   :angry:
Posted by: JonF on Mar. 01 2008,12:04

Quote (Daniel Smith @ Feb. 29 2008,21:19)
I know next to nothing about the subject, so I'm not trying to advance anything.  I'm just asking.  Somehow, I got the impression that radiometric dating methods were calibrated originally by the "known" length of time it took for evolution to take place.  I'm not sure where I heard that - it could've been from a creationist website or something - and I'm not saying it's true.  I'm just asking!
---------------------QUOTE-------------------


OK, true "just asking" from a creationist is rare. My apologies.

The answer is no. Radiometric dates are calibrated by known physics, comparison between different radiometric methods ("radioactivity" subsumes several very different and independent processes), comparison with non-radiometric methods (e.g. ice cores, varves, tree rings), and comparison with known dates (e.g. the eruption of Vesuvius in AD 79).
Posted by: JonF on Mar. 01 2008,12:09

Quote (oldmanintheskydidntdoit @ Mar. 01 2008,05:10)
Daniel, you should also know that the first wave of geologists were creationists who went digging to prove the account of the bible (ok, this is a simplified version of the real events) and found instead that the evidence they were digging up could not support the biblical account. And changed their minds. I'm sure somebody can provide a good reference to these events, if not I'll dig one up for you.
---------------------QUOTE-------------------


< History of the Collapse of "Flood Geology" and a Young Earth >, adapted from a book by an evangelical Christian, adapted by an evangelical Christian.
Posted by: JonF on Mar. 01 2008,12:10

ABE: remove duplicate
Posted by: JAM on Mar. 01 2008,13:18

Quote (Daniel Smith @ Feb. 29 2008,20:11)
   
Quote (JAM @ Feb. 27 2008,16:43)
               
Quote (Daniel Smith @ Feb. 27 2008,17:58)
Again I'll ask, how many of those papers have you read?
---------------------QUOTE-------------------


I looked at the two you most recently cited, but I have no idea why you cited them. They are about karyotypic changes within mammalian families (I'm only sure that Canidae is a family; I'm just guessing that the others are too).

Are you claiming that you see anything resembling Schindewolf's morphological gaps within any of those taxa?

If not, what's your point?
---------------------QUOTE-------------------


Both of these papers advance a saltational mechanism for evolution, similar to what Schindewolf proposed.
---------------------QUOTE-------------------


No, they don't. You're evading.

Schindewolf defined "saltation" MORPHOLOGICALLY, the papers you cited only discuss KARYOTYPIC differences. Fossils don't have karyotypes.

I'll ask you again: do any of these KARYOTYPIC events result in MORPHOLOGICAL "saltation" events? If you don't know, was it ethical for you to have cited these papers?

"That such mechanisms require far fewer transitional steps than the gradualism Darwin proposed is IMO vindication for Schindewolf."

Dan, it's 2008.

Darwin didn't know about genetics. These are single mutational events. At the genetic level, it's impossible to be any more gradual than single mutations.

Schindewolf and you are using a straw man fallacy. If Darwin was wrong, how do you infer that we must also be wrong?

 

---------------------QUOTE-------------------
If these karyotypic changes resulted in morphological changes, these transitional steps would be next to invisible in the fossil record - thus explaining Schindewolf's gaps between types.
---------------------QUOTE-------------------



Hence my question--are there any morphological correlates to any of the karyotypic changes described in those papers? If not, or if you don't know, this has nothing to do with Schindewolf and your citation of them constitutes a deliberate violation of the Ninth Commandment.

 

---------------------QUOTE-------------------
From Kinetochore reproduction in animal evolution: Cell biological explanation of karyotypic fission theory:                

---------------------QUOTE-------------------
Karyotypic fission theory recently applied to lemurs (prosimian primates) explains their karyotypic diversity (2n = 20–70) with a minimum of four evolutionary steps, whereas prior explanations required at least 100 independent chromosomal mutations (4).
---------------------QUOTE-------------------


---------------------QUOTE-------------------


Therefore, macroevolution is within easy reach of mutations. This has nothing to do with Darwin, as Darwin came before Mendel, Morgan, et al.

               

---------------------QUOTE-------------------
 

---------------------QUOTE-------------------
Recent advances in cell-cycle regulation, chromosome behavior, fossil record, and phylogenetic inferences dispute that the primary direction of karyotypic evolution by sequential fusion of chromosomes is toward an arbitrary reduction in diploid number. Rather the tendency of kinetochores to reproduce, of telomerases to cap newly synthesized chromosome ends, and of mitotic checkpoints to regulate disjunction and generate freshly fissioned karyotypes in ancestral animals supports Todd's concept of saltatory chromosomal evolution.
---------------------QUOTE-------------------


---------------------QUOTE-------------------


Schindewolf's hypothesis was about MORPHOLOGICAL saltation. Can't you read and comprehend the adjective CHROMOSOMAL?

Did Schindewolf even mention chromosomes in his Bib--er, book?
 

---------------------QUOTE-------------------
From Karyotypic fissioning and Canid phylogeny:
               

---------------------QUOTE-------------------
This theory accounts for the wide variation in diploid number among the Mammalia and relates the presumed episodes of karyotypic fissioning with known periods of explosive speciation and adaptive radiation. Finally, the traditional evolutionary concept of mutant allele substitution through gene frequency shift under the influence of natural selection is placed in a new perspective. While it is still seen as a primary mechanism of evolution, it is seen as more significant as a “fine-tuning” mechanism, perhaps often responding to exigencies precipitated by chromosomal changes.
---------------------QUOTE-------------------


---------------------QUOTE-------------------


There's nothing in there that supports your position.
 

---------------------QUOTE-------------------
This is almost exactly what Schindewolf's theory proposed - that types
---------------------QUOTE-------------------

...which he defined MORPHOLOGICALLY.  

---------------------QUOTE-------------------
were produced saltationally, ...I'm not sure how you can not see the parallels with Schindewolf JAM, but then you know a lot more about this stuff than I do.
---------------------QUOTE-------------------


Yes, but that doesn't seem to matter to you. You only see what you desperately want to see (you can't see the important difference between karyotypic and morphologic events), but what I find immoral about your actions is that you lie like a rug when your wishful thinking is pointed out to you.

Let me summarize: Darwin didn't know genetics. Claiming that creationism is correct because Darwin didn't know that all mutations are particulate, digital events is ludicrous.
Posted by: Daniel Smith on Mar. 01 2008,21:17

Quote (mitschlag @ Mar. 01 2008,03:52)
 
Quote (Daniel Smith @ Feb. 29 2008,20:11)
Both of these papers advance a saltational mechanism for evolution, similar to what Schindewolf proposed.  That such mechanisms require far fewer transitional steps than the gradualism Darwin proposed is IMO vindication for Schindewolf.  If these karyotypic changes resulted in morphological changes, these transitional steps would be next to invisible in the fossil record - thus explaining Schindewolf's gaps between types.

From Kinetochore reproduction in animal evolution: Cell biological explanation of karyotypic fission theory:

<snip>

From Karyotypic fissioning and Canid phylogeny:
---------------------QUOTE-------------------


You  pays your  money and you takes your choice.*  Try this one on for size:

< A test of the karyotypic fissioning theory of primate evolution >
     

---------------------QUOTE-------------------
Stanyon R.

Karyotypic fissioning theory has been put forward by a number of researchers as a possible driving force of mammalian evolution. Most recently, Giusto and Margulis (BioSystems, 13 (1981) 267-302) hypothesized that karyotypic fissioning best explains the evolution of Old World monkeys, apes, and humans. According to their hypothesis, hominoid karyotypes were derived from the monkey chromosome complement by just such a fissioning event. That hypothesis is tested here by comparing the G-banded chromosomes of humans and great apes with eight species of Old World monkeys. Five submetacentric chromosomes between apes and monkeys have identical banding patterns and nine chromosomes share the same pericentric inversion. Such extensive karyological similarities are not in accordance with, or predicted by karyotypic fissioning. Apparently, karyotypic fissioning is an extremely uneconomical model of chromosomal evolution. The strong conservation of banding patterns sometimes involving the retention of identical chromosomes indicates that ancient linkages of genes have probably been maintained through many speciation events.
---------------------QUOTE-------------------

(Emphasis added)

*Cherry-picking the literature is a  favored Creationist tactic.
---------------------QUOTE-------------------


Here's the paper they refer to:
Karyotypic fission theory and the evolution of old world monkeys and apes.
< link >
Abstract:  

---------------------QUOTE-------------------
The karyotypes of living catarrhines are correlated with the current concepts of their fossil record and systematic classification. A phylogeny, beginning at the base of the Oligocene, for those animals and their chromosome numbers is presented. Todd's (1970) theory of karyotypic fissioning is applied to this case - three fissioning events are hypothesized. A late Eocene event (the primary catarrhine fissioning) is hypothesized to underlie the diversification of the infraorder Catarrhini into its extant families, the second fissioning underlies the radiation of the pongidae/Hominidae in the Miocene and the third accounts for the high chromosome numbers (54 - 72) and the Neogene(Miocene-Pliocene-Pleistocene) radiation of members of the genus Cercopithecus. Published catarrhine chromosome data, including that for "marked" chromosomes (those with a large achromatic region that is the site for ribosomal RNA genes) are tabulated and analysed. The ancestral X chromosome is always retained in the unfissioned metacentric state. The Pongidae/Hominidae have 15 pairs of mediocentric chromosomes that survived the second fissioning whereas the other chromosomes (besides the X) are thought to be fission-derived acrocentrics. Both the detailed karyology and the trend from low to high numbers is best interpreted to support Todd's concept of adaptive radiations correlated with karyotypic fissioning in ancestral populations.
---------------------QUOTE-------------------


So I guess the jury's still out on this one.
Posted by: Daniel Smith on Mar. 01 2008,21:46

Quote (JAM @ Mar. 01 2008,11:18)
Schindewolf's hypothesis was about MORPHOLOGICAL saltation. Can't you read and comprehend the adjective CHROMOSOMAL?

Did Schindewolf even mention chromosomes in his Bib--er, book?
---------------------QUOTE-------------------


Yes, in notes 21 and 22 on pages 349 and 352 where he speaks of Goldschmidt's Systemmutationen.  
On page 352 he says:        

---------------------QUOTE-------------------
This repatterning, or Systemmutation, is attributed to cytologically provable breaks in the chromosomes, which evoke inversions, duplications, and translocations.  A single modification of an embryonic character produced in this way would then regulate a whole series of related ontogenetic processes, leading to a completely new developmental type.
(his emphasis)
---------------------QUOTE-------------------



         

---------------------QUOTE-------------------
Claiming that creationism is correct because Darwin didn't know that all mutations are particulate, digital events is ludicrous.
---------------------QUOTE-------------------


Yes it would be - if that's what I was doing.  However, I am not claiming anything regarding creationism when I'm defending Schindewolf.  His theory has nothing whatsoever to do with creationism.

So, unless you have a completely different definition of "creationism" than I do, your statement is a complete strawman.
Posted by: Daniel Smith on Mar. 01 2008,21:50

Quote (JonF @ Mar. 01 2008,10:09)
 
Quote (oldmanintheskydidntdoit @ Mar. 01 2008,05:10)
Daniel, you should also know that the first wave of geologists were creationists who went digging to prove the account of the bible (ok, this is a simplified version of the real events) and found instead that the evidence they were digging up could not support the biblical account. And changed their minds. I'm sure somebody can provide a good reference to these events, if not I'll dig one up for you.
---------------------QUOTE-------------------


< History of the Collapse of "Flood Geology" and a Young Earth >, adapted from a book by an evangelical Christian, adapted by an evangelical Christian.
---------------------QUOTE-------------------


Thank you for that.  I'll give it a read - along with the other links posted by oldman.
Like I've said before, I haven't really studied this, so I really have no opinion on it yet.  I only raise questions to check whether those who would presume to teach me something here have actually studied this area themselves.
Posted by: blipey on Mar. 01 2008,22:51



---------------------QUOTE-------------------
Like I've said before, I haven't really studied this, so I really have no opinion on it yet.  I only raise questions to check whether those who would presume to teach me something here have actually studied this area themselves.
---------------------QUOTE-------------------



How exactly would you be in a position to judge those you question?  It is your opinion that you are able to judge the level of knowledge of others in a topic you know nothing about?  How would you know they aren't feeding you a line of shit?  Bizarre.
Posted by: IanBrown_101 on Mar. 01 2008,22:57

Quote (Daniel Smith @ Mar. 02 2008,03:46)


---------------------QUOTE-------------------
Claiming that creationism is correct because Darwin didn't know that all mutations are particulate, digital events is ludicrous.
---------------------QUOTE-------------------


Yes it would be - if that's what I was doing.  However, I am not claiming anything regarding creationism when I'm defending Schindewolf.  His theory has nothing whatsoever to do with creationism.

So, unless you have a completely different definition of "creationism" than I do, your statement is a complete strawman.
---------------------QUOTE-------------------


Lovely, I note that you aren't actually addressing the point JAM is making, to whit, you are arguing as if science had not advanced since Darwin.
Posted by: JAM on Mar. 02 2008,00:10

[quote=Daniel Smith,Mar. 01 2008,21:46]
Quote (JAM @ Mar. 01 2008,11:18)
Schindewolf's hypothesis was about MORPHOLOGICAL saltation. Can't you read and comprehend the adjective CHROMOSOMAL?

Did Schindewolf even mention chromosomes in his Bib--er, book?
---------------------QUOTE-------------------


Yes, in notes 21 and 22 on pages 349 and 352 where he speaks of Goldschmidt's Systemmutationen.  
On page 352 he says:          

---------------------QUOTE-------------------
This repatterning, or Systemmutation, is attributed to cytologically provable breaks in the chromosomes, which evoke inversions, duplications, and translocations.  A single modification of an embryonic character produced in this way would then regulate a whole series of related ontogenetic processes, leading to a completely new developmental type.
(his emphasis)
---------------------QUOTE-------------------


Schindewolf was wrong.

The point you keep missing is that these karyotypically visible events (fission, fusion, inversion, translocation, etc.) can produce speciation with absolutely zero change in phenotype.

On the other hand, a single nucleotide substitution can cause massive phenotypic changes.

Can you manage to wrap your brain around that fundamental point?
Posted by: JAM on Mar. 02 2008,00:19

Quote (IanBrown_101 @ Mar. 01 2008,22:57)
Quote (Daniel Smith @ Mar. 02 2008,03:46)


---------------------QUOTE-------------------
Claiming that creationism is correct because Darwin didn't know that all mutations are particulate, digital events is ludicrous.
---------------------QUOTE-------------------


Yes it would be - if that's what I was doing.  However, I am not claiming anything regarding creationism when I'm defending Schindewolf.  His theory has nothing whatsoever to do with creationism.

So, unless you have a completely different definition of "creationism" than I do, your statement is a complete strawman.
---------------------QUOTE-------------------


Lovely, I note that you aren't actually addressing the point JAM is making, to whit, you are arguing as if science had not advanced since Darwin.
---------------------QUOTE-------------------


So was Schindewolf, who should've known better.
Posted by: mitschlag on Mar. 02 2008,04:40

Quote (Daniel Smith @ Mar. 01 2008,21:17)
 
Quote (mitschlag @ Mar. 01 2008,03:52)
     
Quote (Daniel Smith @ Feb. 29 2008,20:11)
Both of these papers advance a saltational mechanism for evolution, similar to what Schindewolf proposed.  That such mechanisms require far fewer transitional steps than the gradualism Darwin proposed is IMO vindication for Schindewolf.  If these karyotypic changes resulted in morphological changes, these transitional steps would be next to invisible in the fossil record - thus explaining Schindewolf's gaps between types.

From Kinetochore reproduction in animal evolution: Cell biological explanation of karyotypic fission theory:

<snip>

From Karyotypic fissioning and Canid phylogeny:
---------------------QUOTE-------------------


You  pays your  money and you takes your choice.*  Try this one on for size:

< A test of the karyotypic fissioning theory of primate evolution >
         

---------------------QUOTE-------------------
Stanyon R.

Karyotypic fissioning theory has been put forward by a number of researchers as a possible driving force of mammalian evolution. Most recently, Giusto and Margulis (BioSystems, 13 (1981) 267-302) hypothesized that karyotypic fissioning best explains the evolution of Old World monkeys, apes, and humans. According to their hypothesis, hominoid karyotypes were derived from the monkey chromosome complement by just such a fissioning event. That hypothesis is tested here by comparing the G-banded chromosomes of humans and great apes with eight species of Old World monkeys. Five submetacentric chromosomes between apes and monkeys have identical banding patterns and nine chromosomes share the same pericentric inversion. Such extensive karyological similarities are not in accordance with, or predicted by karyotypic fissioning. Apparently, karyotypic fissioning is an extremely uneconomical model of chromosomal evolution. The strong conservation of banding patterns sometimes involving the retention of identical chromosomes indicates that ancient linkages of genes have probably been maintained through many speciation events.
---------------------QUOTE-------------------

(Emphasis added)

*Cherry-picking the literature is a  favored Creationist tactic.
---------------------QUOTE-------------------


Here's the paper they refer to:
Karyotypic fission theory and the evolution of old world monkeys and apes.
< link >
Abstract:      

---------------------QUOTE-------------------
The karyotypes of living catarrhines are correlated with the current concepts of their fossil record and systematic classification. A phylogeny, beginning at the base of the Oligocene, for those animals and their chromosome numbers is presented. Todd's (1970) theory of karyotypic fissioning is applied to this case - three fissioning events are hypothesized. A late Eocene event (the primary catarrhine fissioning) is hypothesized to underlie the diversification of the infraorder Catarrhini into its extant families, the second fissioning underlies the radiation of the pongidae/Hominidae in the Miocene and the third accounts for the high chromosome numbers (54 - 72) and the Neogene(Miocene-Pliocene-Pleistocene) radiation of members of the genus Cercopithecus. Published catarrhine chromosome data, including that for "marked" chromosomes (those with a large achromatic region that is the site for ribosomal RNA genes) are tabulated and analysed. The ancestral X chromosome is always retained in the unfissioned metacentric state. The Pongidae/Hominidae have 15 pairs of mediocentric chromosomes that survived the second fissioning whereas the other chromosomes (besides the X) are thought to be fission-derived acrocentrics. Both the detailed karyology and the trend from low to high numbers is best interpreted to support Todd's concept of adaptive radiations correlated with karyotypic fissioning in ancestral populations.
---------------------QUOTE-------------------


So I guess the jury's still out on this one.
---------------------QUOTE-------------------


The HYPOTHESIS presented in the Giusto and Margulis paper that you cited has a time stamp of 1981.  The TEST of their hypothesis by Stanyon that found their hypothesis wanting was published in 1983.

Unless subsequent work has further enriched the topic, the judgment of Stanyon holds.
Posted by: mitschlag on Mar. 02 2008,04:56

Quote (Daniel Smith @ Mar. 01 2008,21:50)
Quote (JonF @ Mar. 01 2008,10:09)
   
Quote (oldmanintheskydidntdoit @ Mar. 01 2008,05:10)
Daniel, you should also know that the first wave of geologists were creationists who went digging to prove the account of the bible (ok, this is a simplified version of the real events) and found instead that the evidence they were digging up could not support the biblical account. And changed their minds. I'm sure somebody can provide a good reference to these events, if not I'll dig one up for you.
---------------------QUOTE-------------------


< History of the Collapse of "Flood Geology" and a Young Earth >, adapted from a book by an evangelical Christian, adapted by an evangelical Christian.
---------------------QUOTE-------------------


Thank you for that.  I'll give it a read - along with the other links posted by oldman.
Like I've said before, I haven't really studied this, so I really have no opinion on it yet.  I only raise questions to check whether those who would presume to teach me something here have actually studied this area themselves.
---------------------QUOTE-------------------


You made a smart move coming here.  The light is so much better than in that cave.
Posted by: Albatrossity2 on Mar. 02 2008,08:32

Quote (JAM @ Mar. 02 2008,00:10)
The point you keep missing is that these karyotypically visible events (fission, fusion, inversion, translocation, etc.) can produce speciation with absolutely zero change in phenotype.

On the other hand, a single nucleotide substitution can cause massive phenotypic changes.

Can you manage to wrap your brain around that fundamental point?
---------------------QUOTE-------------------


And I predict that Daniel will keep on missing this point; I have become convinced that he doesn't understand it...
Posted by: JAM on Mar. 02 2008,09:23

Quote (Albatrossity2 @ Mar. 02 2008,08:32)
Quote (JAM @ Mar. 02 2008,00:10)
The point you keep missing is that these karyotypically visible events (fission, fusion, inversion, translocation, etc.) can produce speciation with absolutely zero change in phenotype.

On the other hand, a single nucleotide substitution can cause massive phenotypic changes.

Can you manage to wrap your brain around that fundamental point?
---------------------QUOTE-------------------


And I predict that Daniel will keep on missing this point; I have become convinced that he doesn't understand it...
---------------------QUOTE-------------------


He could if he put his mind to it. IMO, it's more accurate to say that he refuses to understand it.
Posted by: Daniel Smith on Mar. 02 2008,12:40

Quote (JAM @ Mar. 01 2008,22:10)
 
Quote (Daniel Smith @ Mar. 01 2008,21:46)
   
Quote (JAM @ Mar. 01 2008,11:18)
Schindewolf's hypothesis was about MORPHOLOGICAL saltation. Can't you read and comprehend the adjective CHROMOSOMAL?

Did Schindewolf even mention chromosomes in his Bib--er, book?
---------------------QUOTE-------------------


Yes, in notes 21 and 22 on pages 349 and 352 where he speaks of Goldschmidt's Systemmutationen.  
On page 352 he says:              

---------------------QUOTE-------------------
This repatterning, or Systemmutation, is attributed to cytologically provable breaks in the chromosomes, which evoke inversions, duplications, and translocations.  A single modification of an embryonic character produced in this way would then regulate a whole series of related ontogenetic processes, leading to a completely new developmental type.
(his emphasis)
---------------------QUOTE-------------------


---------------------QUOTE-------------------


Schindewolf was wrong.

The point you keep missing is that these karyotypically visible events (fission, fusion, inversion, translocation, etc.) can produce speciation with absolutely zero change in phenotype.

On the other hand, a single nucleotide substitution can cause massive phenotypic changes.

Can you manage to wrap your brain around that fundamental point?
---------------------QUOTE-------------------


I'm aware of the former, but can you give me examples of the latter?
Posted by: Daniel Smith on Mar. 02 2008,12:44

Quote (oldmanintheskydidntdoit @ Mar. 01 2008,02:10)
Daniel, why are you even reading creationist websites?

I thought you were after the truth?
---------------------QUOTE-------------------


I am, which is why I go straight to the source.  Are you suggesting I should find out what creationists are saying by not visiting their websites?  How open-minded is that?
Posted by: Daniel Smith on Mar. 02 2008,12:56

Quote (mitschlag @ Mar. 02 2008,02:40)
Quote (Daniel Smith @ Mar. 01 2008,21:17)
   
Quote (mitschlag @ Mar. 01 2008,03:52)
       
Quote (Daniel Smith @ Feb. 29 2008,20:11)
Both of these papers advance a saltational mechanism for evolution, similar to what Schindewolf proposed.  That such mechanisms require far fewer transitional steps than the gradualism Darwin proposed is IMO vindication for Schindewolf.  If these karyotypic changes resulted in morphological changes, these transitional steps would be next to invisible in the fossil record - thus explaining Schindewolf's gaps between types.

From Kinetochore reproduction in animal evolution: Cell biological explanation of karyotypic fission theory:

<snip>

From Karyotypic fissioning and Canid phylogeny:
---------------------QUOTE-------------------


You  pays your  money and you takes your choice.*  Try this one on for size:

< A test of the karyotypic fissioning theory of primate evolution >
           

---------------------QUOTE-------------------
Stanyon R.

Karyotypic fissioning theory has been put forward by a number of researchers as a possible driving force of mammalian evolution. Most recently, Giusto and Margulis (BioSystems, 13 (1981) 267-302) hypothesized that karyotypic fissioning best explains the evolution of Old World monkeys, apes, and humans. According to their hypothesis, hominoid karyotypes were derived from the monkey chromosome complement by just such a fissioning event. That hypothesis is tested here by comparing the G-banded chromosomes of humans and great apes with eight species of Old World monkeys. Five submetacentric chromosomes between apes and monkeys have identical banding patterns and nine chromosomes share the same pericentric inversion. Such extensive karyological similarities are not in accordance with, or predicted by karyotypic fissioning. Apparently, karyotypic fissioning is an extremely uneconomical model of chromosomal evolution. The strong conservation of banding patterns sometimes involving the retention of identical chromosomes indicates that ancient linkages of genes have probably been maintained through many speciation events.
---------------------QUOTE-------------------

(Emphasis added)

*Cherry-picking the literature is a  favored Creationist tactic.
---------------------QUOTE-------------------


Here's the paper they refer to:
Karyotypic fission theory and the evolution of old world monkeys and apes.
< link >
Abstract:        

---------------------QUOTE-------------------
The karyotypes of living catarrhines are correlated with the current concepts of their fossil record and systematic classification. A phylogeny, beginning at the base of the Oligocene, for those animals and their chromosome numbers is presented. Todd's (1970) theory of karyotypic fissioning is applied to this case - three fissioning events are hypothesized. A late Eocene event (the primary catarrhine fissioning) is hypothesized to underlie the diversification of the infraorder Catarrhini into its extant families, the second fissioning underlies the radiation of the pongidae/Hominidae in the Miocene and the third accounts for the high chromosome numbers (54 - 72) and the Neogene(Miocene-Pliocene-Pleistocene) radiation of members of the genus Cercopithecus. Published catarrhine chromosome data, including that for "marked" chromosomes (those with a large achromatic region that is the site for ribosomal RNA genes) are tabulated and analysed. The ancestral X chromosome is always retained in the unfissioned metacentric state. The Pongidae/Hominidae have 15 pairs of mediocentric chromosomes that survived the second fissioning whereas the other chromosomes (besides the X) are thought to be fission-derived acrocentrics. Both the detailed karyology and the trend from low to high numbers is best interpreted to support Todd's concept of adaptive radiations correlated with karyotypic fissioning in ancestral populations.
---------------------QUOTE-------------------


So I guess the jury's still out on this one.
---------------------QUOTE-------------------


The HYPOTHESIS presented in the Giusto and Margulis paper that you cited has a time stamp of 1981.  The TEST of their hypothesis by Stanyon that found their hypothesis wanting was published in 1983.

Unless subsequent work has further enriched the topic, the judgment of Stanyon holds.
---------------------QUOTE-------------------


I agree.
Posted by: JAM on Mar. 02 2008,18:47

Quote (Daniel Smith @ Mar. 02 2008,12:40)
 
Quote (JAM @ Mar. 01 2008,22:10)
   
Quote (Daniel Smith @ Mar. 01 2008,21:46)
     
Quote (JAM @ Mar. 01 2008,11:18)
Schindewolf's hypothesis was about MORPHOLOGICAL saltation. Can't you read and comprehend the adjective CHROMOSOMAL?

Did Schindewolf even mention chromosomes in his Bib--er, book?
---------------------QUOTE-------------------


Yes, in notes 21 and 22 on pages 349 and 352 where he speaks of Goldschmidt's Systemmutationen.  
On page 352 he says:                

---------------------QUOTE-------------------
This repatterning, or Systemmutation, is attributed to cytologically provable breaks in the chromosomes, which evoke inversions, duplications, and translocations.  A single modification of an embryonic character produced in this way would then regulate a whole series of related ontogenetic processes, leading to a completely new developmental type.
(his emphasis)
---------------------QUOTE-------------------


---------------------QUOTE-------------------


Schindewolf was wrong.

The point you keep missing is that these karyotypically visible events (fission, fusion, inversion, translocation, etc.) can produce speciation with absolutely zero change in phenotype.

On the other hand, a single nucleotide substitution can cause massive phenotypic changes.

Can you manage to wrap your brain around that fundamental point?
---------------------QUOTE-------------------


I'm aware of the former,...
---------------------QUOTE-------------------


Since you know he was wrong about that, why would you claim that he was vindicated?


---------------------QUOTE-------------------
...but can you give me examples of the latter?
---------------------QUOTE-------------------


Yes; oligodontia, orofacial cleft, optic atrophy, absence of radius, radioulnar synostosis, absence of thumbs, chondrodysplasia, GH insensitivity, split-hand/foot malformation with long bone deficiency, etc.
Posted by: jhbbunch on Mar. 02 2008,22:54

Evolution of the horse is a problem for Darwinism? How about it being a problem for YEC's? They have yet to show me one fossil bed containing the fossil remains of an ancestor to the horse that contains the remains, fossilized or otherwise of a modern horse. Darwinist prediction: no fossil remains of a modern elephant, rhino .lion, human, etc. will be found in a fossil bed containing an eohippus. The YEC predict they will all be found together. How is my prediction doing, and how is theirs doing?
Posted by: IanBrown_101 on Mar. 03 2008,02:55

Quote (Daniel Smith @ Mar. 02 2008,18:44)
Quote (oldmanintheskydidntdoit @ Mar. 01 2008,02:10)
Daniel, why are you even reading creationist websites?

I thought you were after the truth?
---------------------QUOTE-------------------


I am, which is why I go straight to the source.  Are you suggesting I should find out what creationists are saying by not visiting their websites?  How open-minded is that?
---------------------QUOTE-------------------


Why do you care what they say at all?

If you want to know about the science, go to the science, not to people who say science is a lie.
Posted by: mitschlag on Mar. 03 2008,07:06

Quote (JAM @ Mar. 02 2008,18:47)
         
Quote (Daniel Smith @ Mar. 02 2008,12:40)
           
Quote (JAM @ Mar. 01 2008,22:10)
               
Quote (Daniel Smith @ Mar. 01 2008,21:46)
                 
Quote (JAM @ Mar. 01 2008,11:18)
Schindewolf's hypothesis was about MORPHOLOGICAL saltation. Can't you read and comprehend the adjective CHROMOSOMAL?

Did Schindewolf even mention chromosomes in his Bib--er, book?
---------------------QUOTE-------------------


Yes, in notes 21 and 22 on pages 349 and 352 where he speaks of Goldschmidt's Systemmutationen.  
On page 352 he says:                            

---------------------QUOTE-------------------
This repatterning, or Systemmutation, is attributed to cytologically provable breaks in the chromosomes, which evoke inversions, duplications, and translocations.  A single modification of an embryonic character produced in this way would then regulate a whole series of related ontogenetic processes, leading to a completely new developmental type.
(his emphasis)
---------------------QUOTE-------------------


---------------------QUOTE-------------------


Schindewolf was wrong.

The point you keep missing is that these karyotypically visible events (fission, fusion, inversion, translocation, etc.) can produce speciation with absolutely zero change in phenotype.

On the other hand, a single nucleotide substitution can cause massive phenotypic changes.

Can you manage to wrap your brain around that fundamental point?
---------------------QUOTE-------------------


I'm aware of the former,...
---------------------QUOTE-------------------


Since you know he was wrong about that, why would you claim that he was vindicated?
         

---------------------QUOTE-------------------
...but can you give me examples of the latter?
---------------------QUOTE-------------------


Yes; oligodontia, orofacial cleft, optic atrophy, absence of radius, radioulnar synostosis, absence of thumbs, chondrodysplasia, GH insensitivity, split-hand/foot malformation with long bone deficiency, etc.
---------------------QUOTE-------------------


Remember < this >?



--------------------------------------------------------------------------------
< Science 6 April 2007: >
Vol. 316. no. 5821, pp. 112 - 115

 

---------------------QUOTE-------------------
A Single IGF1 Allele Is a Major Determinant of Small Size in Dogs

The domestic dog exhibits greater diversity in body size than any other terrestrial vertebrate. We used a strategy that exploits the breed structure of dogs to investigate the genetic basis of size. First, through a genome-wide scan, we identified a major quantitative trait locus (QTL) on chromosome 15 influencing size variation within a single breed. Second, we examined genetic variation in the 15-megabase interval surrounding the QTL in small and giant breeds and found marked evidence for a selective sweep spanning a single gene (IGF1), encoding insulin-like growth factor 1. A single IGF1 single-nucleotide polymorphism haplotype is common to all small breeds and nearly absent from giant breeds, suggesting that the same causal sequence variant is a major contributor to body size in all small dogs.
---------------------QUOTE-------------------


Posted by: mitschlag on Mar. 03 2008,07:39

As I exercise due diligence in reading Schindewolf, I've been working on the concept of Orthogenesis, which looms large in his thought.

I ran across < this account > (among many others) on the Web, and I wonder whether Daniel Smith thinks that it fairly represents the concept:
 

---------------------QUOTE-------------------
Orthogenesis is the notion that evolution proceeds in straight lines. This can refer to the idea that evolution proceeds straight from species A to species B without any side branches. More importantly, it refers to the idea that an evolutionary lineage changes steady, uniform way with no reversals. Sometimes, but not always, it was imagined that species were evolving steadily towards a goal. Usually this trend was supposed to be caused by some “mysterious inner force” (to use Simpson’s words) of the species that compelled it to evolve. Some supporters of orthogenesis would say that once a trend got started in a lineage that it would unchangingly continue until extinction occurred.

Lets use some concrete examples to illustrate what this meant. Supporters of orthogenesis had pointed to the sabertooths. They claimed that the sword-like canine teeth of these cats over evolutionary time continuously got bigger until they were overgrown to the degree which they caused the animals extinction...
---------------------QUOTE-------------------


Posted by: JAM on Mar. 03 2008,12:06

Quote (mitschlag @ Mar. 03 2008,07:06)
< Science 6 April 2007: >
Vol. 316. no. 5821, pp. 112 - 115

 

---------------------QUOTE-------------------
A Single IGF1 Allele Is a Major Determinant of Small Size in Dogs

The domestic dog exhibits greater diversity in body size than any other terrestrial vertebrate. We used a strategy that exploits the breed structure of dogs to investigate the genetic basis of size. First, through a genome-wide scan, we identified a major quantitative trait locus (QTL) on chromosome 15 influencing size variation within a single breed. Second, we examined genetic variation in the 15-megabase interval surrounding the QTL in small and giant breeds and found marked evidence for a selective sweep spanning a single gene (IGF1), encoding insulin-like growth factor 1. A single IGF1 single-nucleotide polymorphism haplotype is common to all small breeds and nearly absent from giant breeds, suggesting that the same causal sequence variant is a major contributor to body size in all small dogs.
---------------------QUOTE-------------------


---------------------QUOTE-------------------


Point of clarification--

The single nucleotide in this case was not shown to cause the phenotype; it was just a marker (SNP). The likely cause is variation in the promoter.

IOW, it still counts as evidence against Schindewolf's claim of correlation between the magnitude of events at the DNA and phenotypic levels, it just doesn't fit into the category of single-nucleotide substitutions.
Posted by: mitschlag on Mar. 03 2008,15:48

Quote (JAM @ Mar. 03 2008,12:06)
Point of clarification--

The single nucleotide in this case was not shown to cause the phenotype; it was just a marker (SNP). The likely cause is variation in the promoter.

IOW, it still counts as evidence against Schindewolf's claim of correlation between the magnitude of events at the DNA and phenotypic levels, it just doesn't fit into the category of single-nucleotide substitutions.
---------------------QUOTE-------------------


Thanks.

(Hey, Daniel, see how science works?)
Posted by: Daniel Smith on Mar. 04 2008,18:33

Quote (mitschlag @ Mar. 03 2008,05:39)
As I exercise due diligence in reading Schindewolf, I've been working on the concept of Orthogenesis, which looms large in his thought.

I ran across < this account > (among many others) on the Web, and I wonder whether Daniel Smith thinks that it fairly represents the concept:
     

---------------------QUOTE-------------------
Orthogenesis is the notion that evolution proceeds in straight lines. This can refer to the idea that evolution proceeds straight from species A to species B without any side branches. More importantly, it refers to the idea that an evolutionary lineage changes steady, uniform way with no reversals. Sometimes, but not always, it was imagined that species were evolving steadily towards a goal. Usually this trend was supposed to be caused by some “mysterious inner force” (to use Simpson’s words) of the species that compelled it to evolve. Some supporters of orthogenesis would say that once a trend got started in a lineage that it would unchangingly continue until extinction occurred.

Lets use some concrete examples to illustrate what this meant. Supporters of orthogenesis had pointed to the sabertooths. They claimed that the sword-like canine teeth of these cats over evolutionary time continuously got bigger until they were overgrown to the degree which they caused the animals extinction...
---------------------QUOTE-------------------


---------------------QUOTE-------------------


Schindewolf speaks at length about Orthogenesis.  If I understand it correctly, his views were that evolution followed repeatable patterns, was irreversible, eventually led to overspecialization and ultimately ended in extinction.

Of the description you quote I'd say this much applies to Schindewolf's view:  

---------------------QUOTE-------------------
Orthogenesis ... refers to the idea that an evolutionary lineage changes [in a] steady, uniform way with no reversals. Species [are not] evolving steadily towards a goal, [rather the path they were set on was "decided" by the saltational event that first formed that type].  [T]his trend was [not] caused by some “mysterious inner force” (to use Simpson’s words) of the species that compelled it to evolve. [Rather, Schindewolf] would say that once a trend got started in a lineage, it would unchangingly continue until extinction occurred.

Lets use some concrete examples to illustrate what this meant. Supporters of orthogenesis had pointed to the sabertooths. They claimed that the sword-like canine teeth of these cats over evolutionary time continuously got bigger until they were overgrown to the degree which they caused the animals extinction... [Schindewolf uses this example for his typolosis phase]
---------------------QUOTE-------------------


Posted by: Daniel Smith on Mar. 04 2008,18:35

Quote (mitschlag @ Mar. 03 2008,13:48)
 
Quote (JAM @ Mar. 03 2008,12:06)
Point of clarification--

The single nucleotide in this case was not shown to cause the phenotype; it was just a marker (SNP). The likely cause is variation in the promoter.

IOW, it still counts as evidence against Schindewolf's claim of correlation between the magnitude of events at the DNA and phenotypic levels, it just doesn't fit into the category of single-nucleotide substitutions.
---------------------QUOTE-------------------


Thanks.

(Hey, Daniel, see how science works?)
---------------------QUOTE-------------------


Condescension noted.
Posted by: Daniel Smith on Mar. 04 2008,18:47

Quote (JAM @ Mar. 02 2008,16:47)
   
Quote (Daniel Smith @ Mar. 02 2008,12:40)
       
Quote (JAM @ Mar. 01 2008,22:10)

The point you keep missing is that these karyotypically visible events (fission, fusion, inversion, translocation, etc.) can produce speciation with absolutely zero change in phenotype.

On the other hand, a single nucleotide substitution can cause massive phenotypic changes.

Can you manage to wrap your brain around that fundamental point?
---------------------QUOTE-------------------


I'm aware of the former,...
---------------------QUOTE-------------------


Since you know he was wrong about that, why would you claim that he was vindicated?
---------------------QUOTE-------------------


Come on JAM.  The authors themselves were claiming that these mechanisms could explain "periods of explosive speciation and adaptive radiation".  These periods are what Schindewolf refers to as the evolution of types.  No one is claiming that every instance produces morphological changes though.  Schindewolf merely claimed that it was possible.  He felt such discussions were best left to geneticists.
     

---------------------QUOTE-------------------
 

---------------------QUOTE-------------------
...but can you give me examples of the latter?
---------------------QUOTE-------------------


Yes; oligodontia, orofacial cleft, optic atrophy, absence of radius, radioulnar synostosis, absence of thumbs, chondrodysplasia, GH insensitivity, split-hand/foot malformation with long bone deficiency, etc.
---------------------QUOTE-------------------

 
I see.  You're talking about deformities.
Do you know of any speciation events based on these types of deformities?
Posted by: Daniel Smith on Mar. 04 2008,19:22

Here's a prediction I made < a while back >:        

---------------------QUOTE-------------------
3.  What are presently considered neutral sites will be found to be "instructional" - that is, they will carry the instructions that tell the various proteins, RNA and enzymes where to go, when to go and what to do when they get there.

Now, the third prediction is more of a guess, but I think it makes sense.  We know about sequences that code for proteins, and we know about sequences that regulate them, but we don't know how a certain protein "knows" where to go, what to do and when to do it.  My guess is that these instructions are carried in what are presently considered neutral sites and - for that reason - these sites resist mutations just like all other evolutionarily constrained sites.
---------------------QUOTE-------------------



And here's a paper that makes me at least feel I'm on the right track:

< Why repetitive DNA is essential to genome function >

     

---------------------QUOTE-------------------
ABSTRACT
There are clear theoretical reasons and many well-documented examples which show that repetitive DNA is essential for genome function. Generic repeated signals in the DNA are necessary to format expression of unique coding sequence files and to organise additional functions essential for genome replication and accurate transmission
to progeny cells. Repetitive DNA sequence elements are also fundamental to the cooperative molecular interactions forming nucleoprotein complexes. Here, we review the surprising abundance of repetitive DNA in many genomes, describe its structural diversity, and discuss dozens of cases where the functional importance of repetitive elements has been studied in molecular detail. In particular, the fact that repeat elements serve either as initiators or boundaries for heterochromatin domains and provide a significant fraction of scaffolding/matrix attachment regions (S/MARs) suggests that the repetitive component of the genome plays a major architectonic role in higher order physical structuring. Employing an information science model, the ‘functionalist’ perspective on repetitive DNA leads to new ways of thinking about the systemic organisation of cellular genomes and provides several novel possibilities involving repeat elements in evolutionarily significant genome reorganisation. These ideas may facilitate the interpretation of comparisons between sequenced genomes, where the repetitive DNA component is often greater than the coding sequence component.
---------------------QUOTE-------------------


Posted by: JAM on Mar. 04 2008,23:19

Quote (Daniel Smith @ Mar. 04 2008,18:47)
 
Quote (JAM @ Mar. 02 2008,16:47)
       
Quote (Daniel Smith @ Mar. 02 2008,12:40)
         
Quote (JAM @ Mar. 01 2008,22:10)

The point you keep missing is that these karyotypically visible events (fission, fusion, inversion, translocation, etc.) can produce speciation with absolutely zero change in phenotype.

On the other hand, a single nucleotide substitution can cause massive phenotypic changes.

Can you manage to wrap your brain around that fundamental point?
---------------------QUOTE-------------------


I'm aware of the former,...
---------------------QUOTE-------------------


Since you know he was wrong about that, why would you claim that he was vindicated?
---------------------QUOTE-------------------


Come on JAM.  The authors themselves were claiming that these mechanisms could explain "periods of explosive speciation and adaptive radiation".  These periods are what Schindewolf refers to as the evolution of types.

---------------------QUOTE-------------------


You're dead wrong. The authors themselves are talking about evolution WITHIN what Schindewolf calls types. Canids are a single type, Daniel, no matter how much speciation and radiation goes on.


---------------------QUOTE-------------------
No one is claiming that every instance produces morphological changes though.  Schindewolf merely claimed that it was possible.
---------------------QUOTE-------------------


I don't think so. He was claiming that as the mechanism, when in fact there's not even a correlation.


---------------------QUOTE-------------------
He felt such discussions were best left to geneticists.
---------------------QUOTE-------------------


Then why did he discuss them, and why are you so blatantly fudging his definition of "type"?
       

---------------------QUOTE-------------------
     

---------------------QUOTE-------------------
...but can you give me examples of the latter?
---------------------QUOTE-------------------


Yes; oligodontia, orofacial cleft, optic atrophy, absence of radius, radioulnar synostosis, absence of thumbs, chondrodysplasia, GH insensitivity, split-hand/foot malformation with long bone deficiency, etc.
---------------------QUOTE-------------------

 
I see.  You're talking about deformities.[/quote]
I'm talking about single-nucleotide changes that result in huge changes in morphology. They happen to be deformities because most geneticists are in the game to help people, unlike you.


---------------------QUOTE-------------------
Do you know of any speciation events based on these types of deformities?
---------------------QUOTE-------------------


What? Are you drunk, Dan?

I'm arguing that there's NO CORRELATION BETWEEN SPECIATION EVENTS AND BIG MORPHOLOGICAL CHANGES.

Damn, Dan, you're either incredibly dishonest, a complete idiot, or both.

I choose both.

BTW, the movement of the nostrils from the front to the top of the head has been clearly attributed to changes in the regulation of a gene that is mutated in human craniofacial "deformities," so another one of your incredibly dishonest attempts to place Schindewolf's Ancient Holy Word above real data fails miserably.
Posted by: JAM on Mar. 04 2008,23:19

Quote (Daniel Smith @ Mar. 04 2008,18:35)
Quote (mitschlag @ Mar. 03 2008,13:48)
 
Quote (JAM @ Mar. 03 2008,12:06)
Point of clarification--

The single nucleotide in this case was not shown to cause the phenotype; it was just a marker (SNP). The likely cause is variation in the promoter.

IOW, it still counts as evidence against Schindewolf's claim of correlation between the magnitude of events at the DNA and phenotypic levels, it just doesn't fit into the category of single-nucleotide substitutions.
---------------------QUOTE-------------------


Thanks.

(Hey, Daniel, see how science works?)
---------------------QUOTE-------------------


Condescension noted.
---------------------QUOTE-------------------


And ever so richly deserved.
Posted by: JAM on Mar. 04 2008,23:25

Quote (Daniel Smith @ Mar. 04 2008,19:22)
And here's a paper that makes me at least feel I'm on the right track:

< Why repetitive DNA is essential to genome function >
---------------------QUOTE-------------------


Wouldn't the authors have produced some actual data by testing their hypothesis if they were on the right track?

Tell me about Sternberg's expertise in molecular genetics while you're at it, OK?

As well as his ethics; just for fun, let's limit it to his publication of a paper for which the author could not legally assign the copyright because the author had previously published most of it elsewhere.
Posted by: mitschlag on Mar. 05 2008,06:38

Quote (Daniel Smith @ Mar. 04 2008,18:33)
Schindewolf speaks at length about Orthogenesis.  If I understand it correctly, his views were that evolution followed repeatable patterns, was irreversible, eventually led to overspecialization and ultimately ended in extinction.

Of the description you quote I'd say this much applies to Schindewolf's view:        

---------------------QUOTE-------------------
Orthogenesis ... refers to the idea that an evolutionary lineage changes [in a] steady, uniform way with no reversals. Species [are not] evolving steadily towards a goal, [rather the path they were set on was "decided" by the saltational event that first formed that type].  [T]his trend was [not] caused by some “mysterious inner force” (to use Simpson’s words) of the species that compelled it to evolve. [Rather, Schindewolf] would say that once a trend got started in a lineage, it would unchangingly continue until extinction occurred.
---------------------QUOTE-------------------


---------------------QUOTE-------------------


Thanks for the clarification.

GG Simpson and others who worked in the field found that Schindewolf's orthogenesis theory did not fit the evidence of horse evolution:


Posted by: Daniel Smith on Mar. 05 2008,11:00

Quote (JAM @ Mar. 04 2008,21:25)
 
Quote (Daniel Smith @ Mar. 04 2008,19:22)
And here's a paper that makes me at least feel I'm on the right track:

< Why repetitive DNA is essential to genome function >
---------------------QUOTE-------------------


Wouldn't the authors have produced some actual data by testing their hypothesis if they were on the right track?

Tell me about Sternberg's expertise in molecular genetics while you're at it, OK?

As well as his ethics; just for fun, let's limit it to his publication of a paper for which the author could not legally assign the copyright because the author had previously published most of it elsewhere.
---------------------QUOTE-------------------


There are two authors JAM.  Here is their info:  

---------------------QUOTE-------------------
James A. Shapiro1,* and Richard von Sternberg2,3
1 Department of Biochemistry and Molecular Biology, University of Chicago, 920 E. 58th Street, Chicago, IL 60637, USA
(E-mail : jsha@uchicago.edu)
2 National Center for Biotechnology Information – GenBank Building 45, Room 6AN.18D-30, National Institutes of Health, Bethesda,
Maryland 20894 (E-mail: sternber@ncbi.nlm.nih.gov)
3 Department of Systematic Biology, NHB-163, National Museum of Natural History, Smithsonian Institution,Washington, D.C., 20013-7012
(E-mail : Sternberg.Richard@NMNH.SI.EDU)
---------------------QUOTE-------------------


Posted by: blipey on Mar. 05 2008,12:13

Wow.  Your response is "There are two authors"?

Really.  No address of the issue of evidence and testing of hypothesis?  Just noting the fact that there are two authors?

Did the second author bother to test anything?  Does there being a second author somehow advance your case? Or answer the question?
Posted by: oldmanintheskydidntdoit on Mar. 05 2008,12:52

Quote (blipey @ Mar. 05 2008,12:13)
Wow.  Your response is "There are two authors"?

Really.  No address of the issue of evidence and testing of hypothesis?  Just noting the fact that there are two authors?

Did the second author bother to test anything?  Does there being a second author somehow advance your case? Or answer the question?
---------------------QUOTE-------------------


I suspect Daniel is beginning to see the error of his ways.

Say it ain't so Daniel, say it ain't so.....
Posted by: swbarnes2 on Mar. 05 2008,14:12

I think that a fair bit of what any of us would have to say has already been covered in the panda's thumb review of this paper.

< Another example of “scholarship” >

I also add the contents of "the onion test"

< Junk DNA, Junk Science, and The Onion Test >

And Daniel, if you fail to say anything intelligent or fact-based in response...well, we'll know that you have neither anything intelligent nor factual to say.

No one will be surprised.
Posted by: Daniel Smith on Mar. 05 2008,18:41

Quote (blipey @ Mar. 05 2008,10:13)
Wow.  Your response is "There are two authors"?

Really.  No address of the issue of evidence and testing of hypothesis?  Just noting the fact that there are two authors?

Did the second author bother to test anything?  Does there being a second author somehow advance your case? Or answer the question?
---------------------QUOTE-------------------


I was at work.  I didn't have time for a thorough response.  

As for evidence, there's a table that spans six pages listing the evidence for functional repetitive DNA.

Did you look at it?
Posted by: Dr.GH on Mar. 05 2008,19:12

My new copy of Davis A. Young's book, "The Biblical Flood" came today.  So did John Allen Paulos's "Irreligion," and Neil Shubin's, "Your Inner Fish."  I needed a chaser for all the biblical literature and creationst tomes I have been reading.

Even creationsits can lead to some good reading.
Posted by: blipey on Mar. 05 2008,19:18

Quote (Daniel Smith @ Mar. 05 2008,18:41)
Quote (blipey @ Mar. 05 2008,10:13)
Wow.  Your response is "There are two authors"?

Really.  No address of the issue of evidence and testing of hypothesis?  Just noting the fact that there are two authors?

Did the second author bother to test anything?  Does there being a second author somehow advance your case? Or answer the question?
---------------------QUOTE-------------------


I was at work.  I didn't have time for a thorough response.  

As for evidence, there's a table that spans six pages listing the evidence for functional repetitive DNA.

Did you look at it?
---------------------QUOTE-------------------


Yes. The table you speak of is found in a section titled "DOCUMENTATION OF DIVERSE GENOMIC
FUNCTIONS ASSOCIATED WITH DIFFERENT
CLASSES OF REPETITIVE DNA ELEMENTS".

It is a list of repetitive DNA elements just as it says.  It is not really (I may be wrong--not reading biology papers for a living) evidence of their conclusion.

It seems to be a list of things that exist.  To cite that as evidence of their conclusion seems incorrect.  It would rather be like me concluding "Baseball is the Best Sport" and claiming as evidence the following table:

1.  There are 4 bases
2.  3 strikes and you're out
3.  There are 90 feet between bases

I may be wrong, of course.  I'll leave it to professionals to correct me (as I often need correcting).
Posted by: swbarnes2 on Mar. 05 2008,19:37

Quote (Daniel Smith @ Mar. 05 2008,18:41)

As for evidence, there's a table that spans six pages listing the evidence for functional repetitive DNA.
---------------------QUOTE-------------------



And how many of those functions for repetative DNA were found by Creationists?

If Creationists were so sure that their hypotheses would be borne out, why aren't they collecting all that evidence?

For goodness sake, no one sensible is claiming that no repetitive DNA has any function at all.

But with all the evidence you claim is in this paper, can you draw a conclusion as to what percentage of repetative stuff has a vital function?

Or is that, when asked a real, specific question, all your so-called evidence doens't actually support the grandiose claims you think it does?

We all remember the last time you made a quantitative claim.  You claimed that 50% of human genes would have no mouse ortholog.  

And we all also know that when you jettisoned your integrity in favor of supporting Creationism, you rendered yourself incapable of remembering things like that.  Thank goodness this board remains, with its nunmerous testements to your absurd dishonesty.
Posted by: Lou FCD on Mar. 05 2008,20:01

Quote (Dr.GH @ Mar. 05 2008,20:12)
My new copy of Davis A. Young's book, "The Biblical Flood" came today.  So did John Allen Paulos's "Irreligion," and Neil Shubin's, "Your Inner Fish."  I needed a chaser for all the biblical literature and creationst tomes I have been reading.

Even creationsits can lead to some good reading.
---------------------QUOTE-------------------


Please be very careful, Dr. GH.

I really don't want to see you < wind up like Steve Story >.

Sad, sad, sad.
Posted by: Daniel Smith on Mar. 06 2008,19:03

Quote (swbarnes2 @ Mar. 05 2008,12:12)
I think that a fair bit of what any of us would have to say has already been covered in the panda's thumb review of this paper.

< Another example of “scholarship” >

I also add the contents of "the onion test"

< Junk DNA, Junk Science, and The Onion Test >

And Daniel, if you fail to say anything intelligent or fact-based in response...well, we'll know that you have neither anything intelligent nor factual to say.

No one will be surprised.
---------------------QUOTE-------------------


I read the panda's thumb review.  One thing I noticed is that Ian Musgrave, the panda's thumb author, focused in on one fairly insignificant element in the paper - reproductive rates - and used perceived mistakes relating to said rates as an excuse to ignore the rest of the paper.  Hardly fair I'd say, since Shapiro and Sternberg don't make much of an issue about reproduction rates. Here's a portion of the review:        

---------------------QUOTE-------------------
One of the challenges to the idea that the majority of non-coding DNA is doing something useful is the existence of organisms like the puffer fish Fugu. Despite being a fairly complex vertebrate, with roughly similar number of genes to humans, it has between half to one-third the non-coding DNA that other vertebrates (and non-vertebrates) have. So what do Shapiro and von Sternberg say about Fugu? Their only mention is this:

   “Rapidly reproducing organisms, like Caenorhabditis, Drosophila, Fugu and Arabidopsis, tend to have stripped-down genomes with relatively less abundant repetitive DNA, while organisms with longer life cycles, such as humans and maize, have larger genomes with correspondingly more repetitive elements (Table 1).”

However, their own table shows that this is nonsense.

In order of reproductive rate
Organism,  % Genome repetitive DNA,  Reproduction rate
Caenorhabditis briggsae, 22%,  approx 25-50 times per year
Drosophila (fuit fly),  34-57%*,  6-12 times per year
Clionia(tunicate),  35%,  several times to once per year
Mouse,  40%,  3-4 times a year
Fugu,  15%,  Once per year
Dog,  31%,  Once per year+
---------------------QUOTE-------------------



First off, the quote leaves out an important part of the context.  Here's the whole thing:        

---------------------QUOTE-------------------
The second overlooked aspect is the significance of
genome size and of distance between distinct regions of the
genome
. Rapidly reproducing organisms, like Caenorhabditis,
Drosophila, Fugu and Arabidopsis tend to have stripped-down
genomes with relatively less abundant repetitive DNA, while
organisms with longer life cycles, such as humans and
maize, have larger genomes with correspondingly more
repetitive elements (Table 1; Cavalier-Smith, 1985).
---------------------QUOTE-------------------

They are talking about trends here - not hard fast rules.  Their main focus being not reproduction rates, but the "genome size and of distance between distinct regions of the genome".
If you look at < the table > as it appears in the paper, you'll see that it is just a listing showing significant statistics related to 1) Genome size, 2) % repetitive DNA, and 3) % coding sequences.  Musgrave's table adds reproduction rates and leaves out 'genome size' and '% coding sequences'.  These elements add an important ratio to the equation.  When left out, it gives the false impression that the authors are falsifying data.

So Musgrave finds an insignificant perceived flaw and magnifies it to such a level as to give the impression that none of Shapiro and Sternberg's work can be trusted.

Of course no one here will let that influence them.  I'm sure you would all rather make up your own minds about this.   So you'll go and read the paper yourselves, with an open mind, to see if Shapiro and Sternberg actually make a good case.

Right?
Posted by: Daniel Smith on Mar. 06 2008,19:11

Quote (blipey @ Mar. 05 2008,17:18)
 
Quote (Daniel Smith @ Mar. 05 2008,18:41)
   
Quote (blipey @ Mar. 05 2008,10:13)
Wow.  Your response is "There are two authors"?

Really.  No address of the issue of evidence and testing of hypothesis?  Just noting the fact that there are two authors?

Did the second author bother to test anything?  Does there being a second author somehow advance your case? Or answer the question?
---------------------QUOTE-------------------


I was at work.  I didn't have time for a thorough response.  

As for evidence, there's a table that spans six pages listing the evidence for functional repetitive DNA.

Did you look at it?
---------------------QUOTE-------------------


Yes. The table you speak of is found in a section titled "DOCUMENTATION OF DIVERSE GENOMIC
FUNCTIONS ASSOCIATED WITH DIFFERENT
CLASSES OF REPETITIVE DNA ELEMENTS".

It is a list of repetitive DNA elements just as it says.  It is not really (I may be wrong--not reading biology papers for a living) evidence of their conclusion.

It seems to be a list of things that exist.  To cite that as evidence of their conclusion seems incorrect.  It would rather be like me concluding "Baseball is the Best Sport" and claiming as evidence the following table:

1.  There are 4 bases
2.  3 strikes and you're out
3.  There are 90 feet between bases

I may be wrong, of course.  I'll leave it to professionals to correct me (as I often need correcting).
---------------------QUOTE-------------------


The first column in the table is labeled "Function", the last is labeled "Reference".  The rows of the table are sorted for... "Function".  There are columns labeled "Structural Class" and "Example" which would qualify as "things that exist".  But, as a whole, the table is designed so you can look at the claimed functions for these "things that exist" and check the cited references to see if the claims are valid.

Apparently you skimmed through it so fast, you missed those key elements.
Posted by: Daniel Smith on Mar. 06 2008,19:13

Quote (swbarnes2 @ Mar. 05 2008,17:37)
 
Quote (Daniel Smith @ Mar. 05 2008,18:41)

As for evidence, there's a table that spans six pages listing the evidence for functional repetitive DNA.
---------------------QUOTE-------------------



And how many of those functions for repetative DNA were found by Creationists?
---------------------QUOTE-------------------


So you're hip to them being "functions" now?
Posted by: Daniel Smith on Mar. 06 2008,19:21

Quote (mitschlag @ Mar. 05 2008,04:38)
 
Quote (Daniel Smith @ Mar. 04 2008,18:33)
Schindewolf speaks at length about Orthogenesis.  If I understand it correctly, his views were that evolution followed repeatable patterns, was irreversible, eventually led to overspecialization and ultimately ended in extinction.

Of the description you quote I'd say this much applies to Schindewolf's view:          

---------------------QUOTE-------------------
Orthogenesis ... refers to the idea that an evolutionary lineage changes [in a] steady, uniform way with no reversals. Species [are not] evolving steadily towards a goal, [rather the path they were set on was "decided" by the saltational event that first formed that type].  [T]his trend was [not] caused by some “mysterious inner force” (to use Simpson’s words) of the species that compelled it to evolve. [Rather, Schindewolf] would say that once a trend got started in a lineage, it would unchangingly continue until extinction occurred.
---------------------QUOTE-------------------


---------------------QUOTE-------------------


Thanks for the clarification.

GG Simpson and others who worked in the field found that Schindewolf's orthogenesis theory did not fit the evidence of horse evolution:


---------------------QUOTE-------------------


Schindewolf used the example of horse evolution as evidence for an orthogenetic trend towards phyletic size increase. (See figures 3.130-35 on page 292)

I think your chart fairly supports that conclusion as well.

The thing I'm finding most often is that those who criticized Schindewolf often don't seem to have taken the time to try to fully understand his positions and the reasoning behind them.
Posted by: swbarnes2 on Mar. 06 2008,20:14

[quote=Daniel Smith,Mar. 06 2008,19:03]


---------------------QUOTE-------------------
They are talking about trends here - not hard fast rules.”
---------------------QUOTE-------------------



Sigh.

Do the data they present support the claim to see?  Yes, or no?



---------------------QUOTE-------------------
If you look at the table as it appears in the paper, you'll see that it is just a listing showing significant statistics related to 1) Genome size, 2) % repetitive DNA, and 3) % coding sequences.”
---------------------QUOTE-------------------



Okay, so when you graph the data they present, does the graph support the “trend” they claim?  Or is their trend nonsense, and they threw data in the paper to make it look factual, when it’s not?  Does it support a “trend” between less repetitive DNA and reproductive cycle times?  



---------------------QUOTE-------------------
Musgrave's table adds reproduction rates and leaves out 'genome size' and '% coding sequences'.  These elements add an important ratio to the equation.”
---------------------QUOTE-------------------



He leaves out the coding percentage but since the claim isn’t about coding percentages, but repetitive percentages, leaving that out doesn’t alter a thing.

Musgrave’s table has the percentage of repetitive sequences.  For goodness sakes, we can all go to the link and see that ourselves.  

Oh wow…you honestly don’t think that a percentage is a ratio, do you?

This is priceless, and very Creationist of you to not understand middle school math. Okay, I won’t accuse you of dishonesty on this one.  I’ll do you the charity of assuming that you are too stupid to realize that what you said is nonsense.

Well, I think we can scratch "intelligent" off the list of adjectives describgin this post.



---------------------QUOTE-------------------
When left out, it gives the false impression that the authors are falsifying data.”
---------------------QUOTE-------------------



No, it doesn’t.  It gives the correct impression that the authors’ conclusion can’t be drawn from their data.

But one doesn’t expect a person who thinks that percentages aren’t ratios to understand that.



---------------------QUOTE-------------------
So you'll go and read the paper yourselves, with an open mind, to see if Shapiro and Sternberg actually make a good case.”
---------------------QUOTE-------------------



Sure, some repetitive DNA has function.  But that case was made years ago, by all the real scientists who did the research and wrote the papers that those two guys cited.

But that doesn’t prove that all, or even most of non-coding DNA does anything.

You want to impress us with your scientific integrity, it’s very simple.

What do you predict would happen if say, a chunk of DNA a million bases long which was known to have no coding DNA were totally deleted from, say, the mouse genome?

What do you predict the mouse would be like?

Put your money where your mouth is, or continue to prove that you have thrown your integrity in the toilet for Creationism.
Posted by: Tracy P. Hamilton on Mar. 06 2008,21:20

Quote (Daniel Smith @ Mar. 06 2008,19:21)
Quote (mitschlag @ Mar. 05 2008,04:38)
 
Quote (Daniel Smith @ Mar. 04 2008,18:33)
Schindewolf speaks at length about Orthogenesis.  If I understand it correctly, his views were that evolution followed repeatable patterns, was irreversible, eventually led to overspecialization and ultimately ended in extinction.

Of the description you quote I'd say this much applies to Schindewolf's view:            

---------------------QUOTE-------------------
Orthogenesis ... refers to the idea that an evolutionary lineage changes [in a] steady, uniform way with no reversals. Species [are not] evolving steadily towards a goal, [rather the path they were set on was "decided" by the saltational event that first formed that type].  [T]his trend was [not] caused by some “mysterious inner force” (to use Simpson’s words) of the species that compelled it to evolve. [Rather, Schindewolf] would say that once a trend got started in a lineage, it would unchangingly continue until extinction occurred.
---------------------QUOTE-------------------


---------------------QUOTE-------------------


Thanks for the clarification.

GG Simpson and others who worked in the field found that Schindewolf's orthogenesis theory did not fit the evidence of horse evolution:


---------------------QUOTE-------------------


Schindewolf used the example of horse evolution as evidence for an orthogenetic trend towards phyletic size increase. (See figures 3.130-35 on page 292)

I think your chart fairly supports that conclusion as well.

The thing I'm finding most often is that those who criticized Schindewolf often don't seem to have taken the time to try to fully understand his positions and the reasoning behind them.
---------------------QUOTE-------------------


< florida natural history museum says >

"Were all fossil horses larger than their ancestors?
Archaeohippus means ancient horse
Though many horses became larger than their ancestors, Archaeohippus actually became quite a bit smaller! Archaeohippus descended from the larger Miohippus. Nannippus is another example of a horse that was smaller than its ancestors."

Another theory slain by TWO ugly facts.
Posted by: JAM on Mar. 06 2008,21:27

Quote (Daniel Smith @ Mar. 06 2008,19:03)
So you'll go and read the paper yourselves, with an open mind, to see if Shapiro and Sternberg actually make a good case.

Right?
---------------------QUOTE-------------------


Dude, wouldn't we look at the EVIDENCE before deciding whether they make a good case?

You're all about evidence, right?
Quote (Daniel Smith @ Sep. 22 2007,04:48)

My main problem is that I want to see unbiased and unadulterated evidence; not evidence that is made-to-fit the observers viewpoint...I decided what I needed was just to see the evidence for myself.

---------------------QUOTE-------------------


Daniel, you're citing a review in a low-tier journal. It's clear that you're afraid of unbiased and unadulterated evidence, and that you are afraid to examine the evidence for yourself. You desperately need someone to tell you what to think.

Why did you tell such blatant lies when you arrived here?
Posted by: Tracy P. Hamilton on Mar. 06 2008,21:40

Quote (Daniel Smith @ Mar. 06 2008,19:03)
 
Quote (swbarnes2 @ Mar. 05 2008,12:12)
I think that a fair bit of what any of us would have to say has already been covered in the panda's thumb review of this paper.

< Another example of “scholarship” >

I also add the contents of "the onion test"

< Junk DNA, Junk Science, and The Onion Test >

And Daniel, if you fail to say anything intelligent or fact-based in response...well, we'll know that you have neither anything intelligent nor factual to say.

No one will be surprised.
---------------------QUOTE-------------------


I read the panda's thumb review.  One thing I noticed is that Ian Musgrave, the panda's thumb author, focused in on one fairly insignificant element in the paper - reproductive rates - and used perceived mistakes relating to said rates as an excuse to ignore the rest of the paper.
---------------------QUOTE-------------------



In other words, Ian Musgrave points out that their explanation for Fugu's lack of junk doesn't hold water, and you call it a fairly insignificant point about a paper that claims junk is essential????



---------------------QUOTE-------------------
Ian:"The Fugu data is not the only evidence that most non-coding DNA is functionless. To start with the single celled amoeba has a genome 200 times larger than the human genome, most of it repetitive DNA. It would be hard to argue that the amoeba needs far more repetitive DNA than humans to organise its genome."
---------------------QUOTE-------------------



Doesn't sound like ignoring the evidence for junk being junk, and just nitpicking about reproductive rates.



---------------------QUOTE-------------------
Ian:
"Furthermore, we have evidence from sequence conservation. If the repetitive DNA has a function, then its sequence should be conserved (for example if it serves as binding sites for regulatory proteins). However, the majority of the repetitive DNA is not conserved. Indeed, Kimura famously predicted that humans should have around about 1% protein coding genes based on mutation patterns (Kimura and Ohta, 1971). We actually have roughly 1-2% of our genome coding for protein (Nusbaum et al 2005). The sequence conservation data is compatible with over 90% of our genome doing not very much at all (either as regulatory sequences or protein coding sequences). Now, about 3-5% of repetitive DNA is conserved, which suggests that it might do something (Nobrega et al, 2004; Nusbaum et al 2005). So, what happens when this conserved repetitive DNA is removed?

The answer is “beggar all”."
---------------------QUOTE-------------------



What's that?  Somebody actually deleted this DNA that is claimed to have a function, and it makes no difference to the organism?  Another idea that doesn't survive scrutiny.

How do you choose which papers you accept at face value, and which you do not?  Is it based on the fact that you like the conclusions, or on the reasoning used to arrive at them?
Posted by: Daniel Smith on Mar. 07 2008,00:10

Quote (Daniel Smith @ Mar. 06 2008,17:03)
They are talking about trends here - not hard fast rules.
---------------------QUOTE-------------------


That sentence should read: "They are talking about tendencies here - not hard fast rules."
Posted by: oldmanintheskydidntdoit on Mar. 07 2008,03:10

Quote (Daniel Smith @ Mar. 07 2008,00:10)
 
Quote (Daniel Smith @ Mar. 06 2008,17:03)
They are talking about trends here - not hard fast rules.
---------------------QUOTE-------------------


That sentence should read: "They are talking about tendencies here - not hard fast rules."
---------------------QUOTE-------------------


What no edit button?  :D

Daniel, ever heard of < phlostigon >?

Have a read, then let us know if you think current thinking is in error.
 

---------------------QUOTE-------------------
"Phlogisticated" substances are those that contain phlogiston and are "dephlogisticated" when burned; "in general, substances that burned in air were said to be rich in phlogiston; the fact that combustion soon ceased in an enclosed space was taken as clear-cut evidence that air had the capacity to absorb only a definite amount of phlogiston. When air had become completely phlogisticated it would no longer serve to support combustion of any material, nor would a metal heated in it yield a calx; nor could phlogisticated air support life, for the role of air in respiration was to remove the phlogiston from the body."[4] Thus, phlogiston as first conceived was a sort of anti-oxygen.
---------------------QUOTE-------------------


Posted by: Daniel Smith on Mar. 07 2008,19:25

[quote=swbarnes2,Mar. 06 2008,18:14]        
Quote (Daniel Smith @ Mar. 06 2008,19:03)

         

---------------------QUOTE-------------------
They are talking about trends here - not hard fast rules.”
---------------------QUOTE-------------------



Sigh.

Do the data they present support the claim to see?  Yes, or no?
---------------------QUOTE-------------------


Sigh.

Yes it does.  (Hint: reproductive rates are not the focus of their claim and are not part of their data.)  If you search their paper for the partial term "reproduc" (which should catch all references to reproduction) there are only three matches (and the other two are about reproductive isolation).  So making a big deal about reproductive rates is a classic strawman argument.
         

---------------------QUOTE-------------------
       

---------------------QUOTE-------------------
If you look at the table as it appears in the paper, you'll see that it is just a listing showing significant statistics related to 1) Genome size, 2) % repetitive DNA, and 3) % coding sequences.”
---------------------QUOTE-------------------



Okay, so when you graph the data they present, does the graph support the “trend” they claim?  Or is their trend nonsense, and they threw data in the paper to make it look factual, when it’s not?  Does it support a “trend” between less repetitive DNA and reproductive cycle times?
---------------------QUOTE-------------------

 
First off, I should have said "tendency" not "trend" - since "tend to" was the phrase they used.  (I have not been given the privilege of editing my own posts, so I was unable to go back and change that.)
Secondly, is that their claim?  If so, why do they not expound upon it?  Like I said before, it's not presented as if it's a rule - it's a tendency.  There are exceptions to tendencies.  Here are the other places where they reference that table (Table 1) in the paper.  You tell me if reproductive rates are the focus:        

---------------------QUOTE-------------------
Fifty years of DNA-based molecular genetics and genome sequencing have revolutionised our ideas about the physical basis of cell and organismal heredity. We now understand many processes of genome expression and transmission in considerable molecular detail, and whole genome sequences allow us to think about the principles that underlie the organisation of cellular DNA molecules. There have been many surprises and new insights. In the human genome, for example, the protein-coding component represents about 1.2% of the total DNA, while 43% of the sequenced euchromatic portion of the genome consists of repeated and mobile DNA elements (International Human Genome Consortium, 2001; Table 1). In addition to dispersed elements, most of the unsequenced heterochromatic portion of the human genome (about 18% of the total) consists of repetitive DNA, both mobile elements and tandemly repeated ‘ satellite ’ DNA. Thus, over half the human genome is repetitive DNA. Table 1 shows that the human genome is far from exceptional in containing a major fraction of repeats. Even in bacteria, repetitive sequences may account for upwards of 5–10% of the total genome (Hofnung & Shapiro, 1999; Parkhill et al., 2000)....

...It is important to note here the little known fact that phenotypic effects of heterochromatin are not necessarily limited to adjacent genetic loci. The strength of heterochromatic silencing on the three large D. melanogaster chromosomes is sensitive to the total nuclear content of heterochromatin carried on the Y chromosome (see Table 1). ...

...Another frequently ignored feature of genome system architecture associated with repeat elements is overall genome size (Cavalier-Smith, 1985). In plants, genome size correlates with an increase in repetitive DNA abundance (Table 1). Plant molecular geneticists have suggested that the total length of each genome is an important functional characteristic, which influences replication time, a characteristic that correlates with the length of the life cycle (Bennett, 1998; Bennetzen, 2000; Petrov, 2001; Vinogradov, 2003). It makes sense that amplification of mobile genetic elements is an efficient method of altering total DNA content in the genome. Similarly, distance between regulatory and coding sequences may be an important control parameter (Zuckerandl, 2002).
---------------------QUOTE-------------------


Well?    

---------------------QUOTE-------------------
       

---------------------QUOTE-------------------
Musgrave's table adds reproduction rates and leaves out 'genome size' and '% coding sequences'.  These elements add an important ratio to the equation.”
---------------------QUOTE-------------------



He leaves out the coding percentage but since the claim isn’t about coding percentages, but repetitive percentages, leaving that out doesn’t alter a thing.

Musgrave’s table has the percentage of repetitive sequences.  For goodness sakes, we can all go to the link and see that ourselves.
---------------------QUOTE-------------------

 
There are two percentages listed in the table.  Those two percentages, (along with the genome size), paint a picture of "the significance of genome size and of distance between distinct regions of the genome" - which was the part of their claim Musgrave left out.
     

---------------------QUOTE-------------------
Oh wow…you honestly don’t think that a percentage is a ratio, do you?

This is priceless, and very Creationist of you to not understand middle school math. Okay, I won’t accuse you of dishonesty on this one.  I’ll do you the charity of assuming that you are too stupid to realize that what you said is nonsense.

Well, I think we can scratch "intelligent" off the list of adjectives describgin this post.
---------------------QUOTE-------------------


Sigh...
         

---------------------QUOTE-------------------
     

---------------------QUOTE-------------------
When left out, it gives the false impression that the authors are falsifying data.”
---------------------QUOTE-------------------



No, it doesn’t.  It gives the correct impression that the authors’ conclusion can’t be drawn from their data.
---------------------QUOTE-------------------


Which data is that?  Reproduction rates?  That's not their data!
     

---------------------QUOTE-------------------
But one doesn’t expect a person who thinks that percentages aren’t ratios to understand that.
---------------------QUOTE-------------------


Sigh...
         

---------------------QUOTE-------------------
     

---------------------QUOTE-------------------
So you'll go and read the paper yourselves, with an open mind, to see if Shapiro and Sternberg actually make a good case.”
---------------------QUOTE-------------------



Sure, some repetitive DNA has function.  But that case was made years ago, by all the real scientists who did the research and wrote the papers that those two guys cited.

But that doesn’t prove that all, or even most of non-coding DNA does anything.
---------------------QUOTE-------------------


So is that a "Yes" or a "No" about whether or not you'll actually read the paper?  

---------------------QUOTE-------------------
You want to impress us with your scientific integrity, it’s very simple.

What do you predict would happen if say, a chunk of DNA a million bases long which was known to have no coding DNA were totally deleted from, say, the mouse genome?

What do you predict the mouse would be like?

Put your money where your mouth is, or continue to prove that you have thrown your integrity in the toilet for Creationism.
---------------------QUOTE-------------------

 
I already know the answer to that (You see, I actually read the panda's thumb review).  But just because the deletion produced no observable effects doesn't mean the DNA was not functional.
I could probably delete a big chunk of the files on my hard drive with no ill effects.  I would not even notice they were gone until I needed them - which could be months or years later.  The again, I might never notice if they were files used for the one-time setup of my computer.  Yet they are all functional files.

Maybe the chunk deleted from the mouse genome was used during ontogeny and then not used again.  Deleting it would produce no ill effects then.
Posted by: JAM on Mar. 08 2008,02:22

Quote (Daniel Smith @ Mar. 07 2008,19:25)
I could probably delete a big chunk of the files on my hard drive with no ill effects.  I would not even notice they were gone until I needed them - which could be months or years later.

---------------------QUOTE-------------------


If you never needed them or used them for anything, they are not functional.


---------------------QUOTE-------------------
The again, I might never notice if they were files used for the one-time setup of my computer.  Yet they are all functional files.
---------------------QUOTE-------------------


Are you claiming that these repetitive sequences were deleted after the setup (development) of the mouse?

Do you realize how brain-dead these ID arguments from analogies are, particularly since you aren't even constructing a true analogy?


---------------------QUOTE-------------------
Maybe the chunk deleted from the mouse genome was used during ontogeny and then not used again.  Deleting it would produce no ill effects then.
---------------------QUOTE-------------------


Dan, that has to be one of the most ignorant things you have ever written here, which is saying a lot.

What do we real scientists do when we delete a chunk of the mouse genome?

Are you so dense that you think that a chunk of the genome could be deleted from an adult mouse? How would we get into every cell to do it?

Oh, and when you see that your entire premise was false, will that affect your claimed confidence in your conclusion?
Posted by: JAM on Mar. 08 2008,02:26

Quote (Daniel Smith @ Mar. 07 2008,19:25)
Quote (swbarnes2 @ Mar. 06 2008,18:14)
         
Quote (Daniel Smith @ Mar. 06 2008,19:03)

           

---------------------QUOTE-------------------
They are talking about trends here - not hard fast rules.”
---------------------QUOTE-------------------



Sigh.

Do the data they present support the claim to see?  Yes, or no?
---------------------QUOTE-------------------


Sigh.

Yes it does.  (Hint: reproductive rates are not the focus of their claim and are not part of their data.)
---------------------QUOTE-------------------



None of the data are theirs. They don't have sufficient faith in their position to produce any new data. Actions speak louder than words.

"If you search their paper for the partial term "reproduc" (which should catch all references to reproduction) there are only three matches (and the other two are about reproductive isolation)."
---------------------QUOTE-------------------


The question was about the data, not about the text.

Can't you distinguish the difference?
Posted by: Daniel Smith on Mar. 08 2008,11:11

Quote (JAM @ Mar. 08 2008,00:22)
 
Quote (Daniel Smith @ Mar. 07 2008,19:25)
I could probably delete a big chunk of the files on my hard drive with no ill effects.  I would not even notice they were gone until I needed them - which could be months or years later.

---------------------QUOTE-------------------


If you never needed them or used them for anything, they are not functional.
 

---------------------QUOTE-------------------
The again, I might never notice if they were files used for the one-time setup of my computer.  Yet they are all functional files.
---------------------QUOTE-------------------


Are you claiming that these repetitive sequences were deleted after the setup (development) of the mouse?

Do you realize how brain-dead these ID arguments from analogies are, particularly since you aren't even constructing a true analogy?
 

---------------------QUOTE-------------------
Maybe the chunk deleted from the mouse genome was used during ontogeny and then not used again.  Deleting it would produce no ill effects then.
---------------------QUOTE-------------------


Dan, that has to be one of the most ignorant things you have ever written here, which is saying a lot.

What do we real scientists do when we delete a chunk of the mouse genome?

Are you so dense that you think that a chunk of the genome could be deleted from an adult mouse? How would we get into every cell to do it?

Oh, and when you see that your entire premise was false, will that affect your claimed confidence in your conclusion?
---------------------QUOTE-------------------


I realized that after my post.  I was thinking "Oh no, JAMs going to have a field day with that one!"  Oh well.  That's how science works - right?

Oh, and the files on my hard drive are still functional whether I use them or not.  They may not be "functioning" at the moment, but they are still "functional".

Whether or not they are analogous in any way to functioning and functional parts of genomes, I don't know, but I'd suspect they are.
Posted by: Daniel Smith on Mar. 08 2008,11:14

Quote (JAM @ Mar. 08 2008,00:26)
 
Quote (Daniel Smith @ Mar. 07 2008,19:25)

"If you search their paper for the partial term "reproduc" (which should catch all references to reproduction) there are only three matches (and the other two are about reproductive isolation)."
---------------------QUOTE-------------------


The question was about the data, not about the text.

Can't you distinguish the difference?
---------------------QUOTE-------------------


Yes.  They present no data on reproduction rates for the organisms discussed.
Posted by: Daniel Smith on Mar. 08 2008,15:26

Quote (JAM @ Mar. 02 2008,16:47)
 
Quote (Daniel Smith @ Mar. 02 2008,12:40)
     
Quote (JAM @ Mar. 01 2008,22:10)
       
Quote (Daniel Smith @ Mar. 01 2008,21:46)
         
Quote (JAM @ Mar. 01 2008,11:18)
Schindewolf's hypothesis was about MORPHOLOGICAL saltation. Can't you read and comprehend the adjective CHROMOSOMAL?

Did Schindewolf even mention chromosomes in his Bib--er, book?
---------------------QUOTE-------------------


Yes, in notes 21 and 22 on pages 349 and 352 where he speaks of Goldschmidt's Systemmutationen.  
On page 352 he says:                    

---------------------QUOTE-------------------
This repatterning, or Systemmutation, is attributed to cytologically provable breaks in the chromosomes, which evoke inversions, duplications, and translocations.  A single modification of an embryonic character produced in this way would then regulate a whole series of related ontogenetic processes, leading to a completely new developmental type.
(his emphasis)
---------------------QUOTE-------------------


---------------------QUOTE-------------------


Schindewolf was wrong.

The point you keep missing is that these karyotypically visible events (fission, fusion, inversion, translocation, etc.) can produce speciation with absolutely zero change in phenotype.

On the other hand, a single nucleotide substitution can cause massive phenotypic changes.

Can you manage to wrap your brain around that fundamental point?
---------------------QUOTE-------------------


I'm aware of the former,...
---------------------QUOTE-------------------


Since you know he was wrong about that, why would you claim that he was vindicated?
   

---------------------QUOTE-------------------
...but can you give me examples of the latter?
---------------------QUOTE-------------------


Yes; oligodontia, orofacial cleft, optic atrophy, absence of radius, radioulnar synostosis, absence of thumbs, chondrodysplasia, GH insensitivity, split-hand/foot malformation with long bone deficiency, etc.
---------------------QUOTE-------------------


Let me just clarify something here.  Schindewolf did not spend a lot of time talking about genetic mechanisms because he was not a genetecist.  He knew however, that there had to be some form of mechanism because he saw evidence for it in the fossil record.  He produced extensive data (JAM) documenting the reality of an ontogenetic switch from an established developmental path to a new and different developmental pathway during the early ontogenetic stages of fossilized ammonites and corals.

So he knew evolution happened that way - he had observed it as directly as a paleontologist could - he just didn't know what exact mechanism was behind the observed switch.

He embraced Goldschmidt's systemmutationen because it closely resembled his own observations, but the switch does not have to be chromosomal rearrangements, it could be single nucleotide substitutions (I suppose) provided they affected an early enough stage in ontogeny.

The point being, Schindewolf's theory was based on his direct observations of 'ontogenetical evolution' in the fossil record (as "direct" as can be deduced from the fossil record that is).
Posted by: JAM on Mar. 08 2008,19:10

Quote (Daniel Smith @ Mar. 08 2008,11:14)
Quote (JAM @ Mar. 08 2008,00:26)
   
Quote (Daniel Smith @ Mar. 07 2008,19:25)

"If you search their paper for the partial term "reproduc" (which should catch all references to reproduction) there are only three matches (and the other two are about reproductive isolation)."
---------------------QUOTE-------------------


The question was about the data, not about the text.

Can't you distinguish the difference?
---------------------QUOTE-------------------


Yes.  They present no data on reproduction rates for the organisms discussed.
---------------------QUOTE-------------------


So why your brain-dead text search as a response?

Isn't the point that their claim:


---------------------QUOTE-------------------
Rapidly reproducing organisms, like Caenorhabditis,
Drosophila, Fugu and Arabidopsis tend to have stripped-down
genomes with relatively less abundant repetitive DNA, while
organisms with longer life cycles, such as humans and
maize, have larger genomes with correspondingly more
repetitive elements (Table 1 ; Cavalier-Smith, 1985).
---------------------QUOTE-------------------



Is not only false, but utterly unsupported by the data in Table 1?
Posted by: Wesley R. Elsberry on Mar. 08 2008,19:27

I think Daniel thinks it is a win if whoever he's backing at the moment can't be accused of obvious self-contradiction. Right or wrong seem to be merely arguable. If someone doesn't support a liked argument with data, that is not only not a fault, but prevents anyone from being able to say that they shot themselves in the foot.
Posted by: blipey on Mar. 08 2008,19:57



---------------------QUOTE-------------------
I realized that after my post.  I was thinking "Oh no, JAMs going to have a field day with that one!"  Oh well.  That's how science works - right?

Oh, and the files on my hard drive are still functional whether I use them or not.  They may not be "functioning" at the moment, but they are still "functional".

Whether or not they are analogous in any way to functioning and functional parts of genomes, I don't know, but I'd suspect they are.
---------------------QUOTE-------------------



So your response, though self-admittedly wrong, should have no bearing on whether or not the rest of your conclusions can be trusted?  Even when you are so cavalier about being wrong and don't seem to care to alter your argument, explain why you used such a bogus argument, or anything?

As to the functionality argument vis computer files:

Isn't the conclusion that the paper draws: the repeated sequences are necessary FOR the function OF the genome?  This is not the same thing as merely having a function.

Your analogy of computer files is terrible.  If a file is not necessary to the functionality OF the computer, it is not functional in the way that the authors see repeated DNA sequences.

edited to put right quote up front
Posted by: Daniel Smith on Mar. 09 2008,11:10

Quote (JAM @ Mar. 08 2008,17:10)
     
Quote (Daniel Smith @ Mar. 08 2008,11:14)
     
Quote (JAM @ Mar. 08 2008,00:26)
         
Quote (Daniel Smith @ Mar. 07 2008,19:25)

"If you search their paper for the partial term "reproduc" (which should catch all references to reproduction) there are only three matches (and the other two are about reproductive isolation)."
---------------------QUOTE-------------------


The question was about the data, not about the text.

Can't you distinguish the difference?
---------------------QUOTE-------------------


Yes.  They present no data on reproduction rates for the organisms discussed.
---------------------QUOTE-------------------


So why your brain-dead text search as a response?

Isn't the point that their claim:
     

---------------------QUOTE-------------------
Rapidly reproducing organisms, like Caenorhabditis,
Drosophila, Fugu and Arabidopsis tend to have stripped-down
genomes with relatively less abundant repetitive DNA, while
organisms with longer life cycles, such as humans and
maize, have larger genomes with correspondingly more
repetitive elements (Table 1 ; Cavalier-Smith, 1985).
---------------------QUOTE-------------------



Is not only false, but utterly unsupported by the data in Table 1?
---------------------QUOTE-------------------



Let's look at the claim:
     

---------------------QUOTE-------------------
The second overlooked aspect is the significance of
genome size and of distance between distinct regions of the
genome
. Rapidly reproducing organisms, like Caenorhabditis,
Drosophila, Fugu and Arabidopsis tend to have stripped-down
genomes
with relatively less abundant repetitive DNA while
organisms with longer life cycles, such as humans and
maize, have larger genomes with correspondingly more
repetitive elements (Table 1 ; Cavalier-Smith, 1985).
---------------------QUOTE-------------------


So what do they mean by "relatively less" and "correspondingly more"?  Is it in relation to their own genome size or is it relative to the amount of repetitive elements in the other category (rapidly reproducing vs. longer life cycles)?  Since they say "stripped-down genomes with relatively less abundant repetitive DNA" and "larger genomes with correspondingly more repetitive elements" and immediately before that say that they are talking about "the significance of genome size and of distance between distinct regions of the genome", I'd say it is the latter.

From that perspective, I think the data in Table 1 does support their claim - especially if you look at the specific species mentioned.
Posted by: oldmanintheskydidntdoit on Mar. 09 2008,11:29

Daniel, just wondering if you had any thoughts on how the humble onion fits into all of this?
 

---------------------QUOTE-------------------

< Junk DNA, Junk Science, and The Onion Test >
The onion test is a simple reality check for anyone who thinks they have come up with a universal function for non-coding DNA. Whatever your proposed function, ask yourself this question: Can I explain why an onion needs about five times more non-coding DNA for this function than a human?

---------------------QUOTE-------------------


How dos that fit into your understanding of the significance of genome size?
Posted by: JAM on Mar. 09 2008,13:37

Quote (Daniel Smith @ Mar. 09 2008,11:10)
Let's look at the claim:
         

---------------------QUOTE-------------------
The second overlooked aspect is the significance of
genome size and of distance between distinct regions of the
genome
. Rapidly reproducing organisms, like Caenorhabditis,
Drosophila, Fugu and Arabidopsis tend to have stripped-down
genomes
with relatively less abundant repetitive DNA while
organisms with longer life cycles, such as humans and
maize, have larger genomes with correspondingly more
repetitive elements (Table 1 ; Cavalier-Smith, 1985).
---------------------QUOTE-------------------


So what do they mean by "relatively less" and "correspondingly more"?
---------------------QUOTE-------------------


They mean that they can't support their claim.
 

---------------------QUOTE-------------------
Is it in relation to their own genome size or is it relative to the amount of repetitive elements in the other category (rapidly reproducing vs. longer life cycles)?
---------------------QUOTE-------------------


Dan, the paper is pure hackery.

1) Genome size is very highly correlated with the amount of repeated DNA; in fact, because the same fundamental set of genes is there (remember how spectacularly wrong your prediction was?) and most DNA without a known function is repetitive, genome size is basically a function of the amount of repeated DNA.

2) The opposite of "rapidly reproducing" is "slowly reproducing," not "longer life cycles."
 

---------------------QUOTE-------------------
Since they say "stripped-down genomes with relatively less abundant repetitive DNA" and "larger genomes with correspondingly more repetitive elements" and immediately before that say that they are talking about "the significance of genome size and of distance between distinct regions of the genome", I'd say it is the latter.
---------------------QUOTE-------------------


It doesn't matter; it's BS either way.
 

---------------------QUOTE-------------------
From that perspective, I think the data in Table 1 does support their claim - especially if you look at the specific species mentioned.
---------------------QUOTE-------------------


Why would you italicize your bad grammar? Data (plural) either do or don't support a claim.

1) The data in the table couldn't possibly support their claim even if their claim was correct, because they offered no data on either speed of reproduction or length of life cycle (which aren't the same thing).

2) Look at two of the specific species mentioned: dog and mouse. The claimed relationship doesn't hold at all for them. IOW, they are incompetent even at dishonest cherry-picking.

If you really wanted to see if this is true, you'd look at more closely-related organisms, such as within < the genus Allium. > The evidence (remember, that stuff you lied about being interested in?) shows that genome size is amazingly plastic.
Posted by: mitschlag on Mar. 09 2008,13:55

And now, a brief interlude, as we return to those thundering hoofs of yesteryear...
         
Quote (Tracy P. Hamilton @ Mar. 06 2008,21:20)
           
Quote (Daniel Smith @ Mar. 06 2008,19:21)
             
Quote (mitschlag @ Mar. 05 2008,04:38)
               
Quote (Daniel Smith @ Mar. 04 2008,18:33)
Schindewolf speaks at length about Orthogenesis.  If I understand it correctly, his views were that evolution followed repeatable patterns, was irreversible, eventually led to overspecialization and ultimately ended in extinction.

Of the description you quote I'd say this much applies to Schindewolf's view:                          

---------------------QUOTE-------------------
Orthogenesis ... refers to the idea that an evolutionary lineage changes [in a] steady, uniform way with no reversals. Species [are not] evolving steadily towards a goal, [rather the path they were set on was "decided" by the saltational event that first formed that type].  [T]his trend was [not] caused by some “mysterious inner force” (to use Simpson’s words) of the species that compelled it to evolve. [Rather, Schindewolf] would say that once a trend got started in a lineage, it would unchangingly continue until extinction occurred.
---------------------QUOTE-------------------


---------------------QUOTE-------------------


Thanks for the clarification.

GG Simpson and others who worked in the field found that Schindewolf's orthogenesis theory did not fit the evidence of horse evolution:


---------------------QUOTE-------------------


Schindewolf used the example of horse evolution as evidence for an orthogenetic trend towards phyletic size increase. (See figures 3.130-35 on page 292)

I think your chart fairly supports that conclusion as well.

The thing I'm finding most often is that those who criticized Schindewolf often don't seem to have taken the time to try to fully understand his positions and the reasoning behind them.
---------------------QUOTE-------------------


< florida natural history museum says >

"Were all fossil horses larger than their ancestors?
Archaeohippus means ancient horse
Though many horses became larger than their ancestors, Archaeohippus actually became quite a bit smaller! Archaeohippus descended from the larger Miohippus. Nannippus is another example of a horse that was smaller than its ancestors."

Another theory slain by TWO ugly facts.
---------------------QUOTE-------------------



Cogent points, Tracy P. Hamilton (typically ignored by Mr Smith).  We will see more on that below, but first let's hear what Otto Heinrich Schindewolf himself had to say:
           

---------------------QUOTE-------------------
Schindewolf, pp. 290-291

Phyletic Increase in Size

A special case of an orthogenetic trend is size increase during the course of evolution. This may even be the essential, central process of orthogenesis and one that contributes to and effects at least a portion of the other phenomena.
<snip>
The genus Eohippus, of the Lower Eocene of North America, which stands at the beginning of the horse lineage, had a shoulder height of twenty-five centi­meters and was the size of a cat. The subsequent forms were, in order, the size of a fox terrier and then of a sheep before gradually attaining the size and proportions of the modern horse. A yardstick for the increase in size is provided by the series of skulls of some horse forms, shown to scale in figure 3.109, and by the reconstructions in figures 3.130—35. A further example is the evolution of camels, which also begins with dwarf species about the size of a rabbit, miniatures of the Recent representatives (pl.27A).

In these examples, the size of the body increases with the approach to modern times, and the Recent forms, as the provisional terminal stages of the lineages in question, are the largest of their respective kinds...
---------------------QUOTE-------------------


Here is GG Simpson's rejoinder:
     

---------------------QUOTE-------------------
GG Simpson, The Meaning of Evolution, revised 1967, pp. 136-137:

The horses even provide us with exceptions to the rule that animals tend to increase in size in their evolution. Dur­ing the Eocene the record, contrary to a rather general im­pression, does not show any net or average increase in size. In fact the known late Eocene horses average rather smaller than eohippus in the early Eocene. Then still later, in the Miocene and Pliocene, there were at least three different branches of the horse family characterized by miniature or decreased size (Archaeohippus, Nannippus, Calippus), while at the same time other lines were, according to “rule,” in­creasing in size. At that time, too, others were fluctuating around a mean size without notable change and still others developed different species of decidedly different sizes — as, indeed, is the case in Equus today.

There is increasing evidence that mammals in general, especially some of the relatively large forms, have tended to decrease in average size since the Pleistocene ice age. In it­self this negates any invariability in the rule of increase of size, and it certainly strongly suggests adaptive response to climatic conditions as opposed to size control by some inner tendency or life urge within the organisms alone. We know that climates have tended to become warmer since the Pleistocene. We also know that closely related living mam­mals show the adaptive phenomenon of being, on an average, relatively smaller in warmer climates. It is certainly reason­able to suppose that this is the same sort of phenomenon in­volved in size decrease from Pleistocene to Recent.
---------------------QUOTE-------------------


To be concluded...
Posted by: mitschlag on Mar. 09 2008,13:56

Otto Heinrich, the cherry-picker:
 

---------------------QUOTE-------------------
Schindewolf, pp. 291-295 (continuing from the previous excerpt):

...And yet, this [he means inexorable increase in size] is by no means always the case; extremely often it is just the opposite, that extinct, ancient animal forms are characterized by unusual size, and the layman is indeed inclined to imagine these, without exception, as gigantic monsters.

In fact, we know that among extinct tigers, bears, elephants, rhinoceroses, and so on, there are some  extinct species that were considerably larger than those living today. A particularly conspicuous example is the mighty Baluchitherium, from the Oligocene of Asia, which is assigned to the rhinoceros group even though (like most ancient rhinoceroses) it has no horn on its nose (fig. 3.136). The shoulder height of this animal comes to about 5.3 meters, and the length of the torso is as much as 10 meters, making it one of the largest terrestrial mammals that ever lived. The enormous size of this animal is clearly seen in the comparison of a reconstruction of Baluchitherium with the Recent Indian rhi­noceros, both shown to scale in figure 3. 137.

These examples, however, by no means represent a contradiction to our rule of phyletic increase in size, for the extinct forms in question are not the imme­diate predecessors of the smaller Recent species. They are only members of a broader, related group within which they represent the terminal forms of extinct collateral lines (fig. 3.138). To this extent, they thoroughly confirm the general rule that gigantic forms mark the end of evolution.

Unquestionable examples of a once-attained body size being secondarily re­duced are almost unknown except in instances where such a reduction is suc­ceeded by a thorough remodeling to a completely new typal structure, which, itself, begins again with small forms. The exceptions occasionally cited are prob­ably only apparent, for in those cases it has not been shown that the forms with the supposed reduction in size really issued from larger ancestral forms of the same genetic lineage; only in such a situation would our rule be contradicted.

Accordingly, the evolution of size is, in general, irreversible. However, it is immediately clear that gigantic forms are indicators of dying lineages, for ulti­mately a point would be reached beyond which continued increase in size would be impossible for physiological reasons.
---------------------QUOTE-------------------


However, you are full of it, Schindewolf:
 

---------------------QUOTE-------------------
Simpson, op. cit., pp.137-138:

In this connection, it is known that many large animals of the past became extinct and are not the ancestors of their smaller living relatives. Mammoths were not ancestral to smaller elephants. (As a matter of fact, most mammoths were no larger than some living elephants, but a few were.) The elephantine ground sloths were not ancestral to the little living tree sloths. The dinosaurs were not the ancestors of the small lizards of later times. But this does not mean that forms that were the ancestors of living animals were not also somewhat larger than the latter at one time or another, and such does appear to be the case for some of them.

Some paleontologists have been so impressed by the fre­quent trend for animals to become larger as time goes on that they have tried to work it the other way around. If they find, say, a Pleistocene bison that is somewhat larger than a Recent bison (so-called Bison taylori, associate and prey of early man in America, is a good example), then they conclude that it is not ancestral to later bison because it is larger. You can establish any “rule” you like if you start with the rule and then interpret the evidence accordingly.
---------------------QUOTE-------------------


That last line is a keeper.
Posted by: JAM on Mar. 09 2008,16:20

Quote (Daniel Smith @ Mar. 08 2008,15:26)
Let me just clarify something here.
---------------------QUOTE-------------------


You misspelled "obfuscate."
   

---------------------QUOTE-------------------
Schindewolf did not spend a lot of time talking about genetic mechanisms because he was not a genetecist.
---------------------QUOTE-------------------


So what? Dan, we're talking about a false claim that he made about genetics. Not being a geneticist is no excuse for making a false claim. Schindewolf had zero excuse for not knowing the relevant genetics.
   

---------------------QUOTE-------------------
He knew however, that there had to be some form of mechanism because he saw evidence for it in the fossil record.
---------------------QUOTE-------------------


But he was WRONG about the mechanism, just as he was wrong about the horse data. It's that simple.
   

---------------------QUOTE-------------------
He produced extensive data (JAM) documenting the reality of an ontogenetic switch from an established developmental path to a new and different developmental pathway during the early ontogenetic stages of fossilized ammonites and corals.
---------------------QUOTE-------------------


He produced exactly ZERO data to support his claim about the genetic mechanisms underlying the "switches." If he really was interested in testing his hypothesis, he would have observed and documented the huge morphological gaps WITHIN coral species AND EVEN WITHIN INDIVIDUAL COLONIES. I pointed you to that evidence, and you, proving beyond any doubt that you were lying when you claimed to want to see the evidence for yourself, ignored it.

Schindewolf was wrong. Deal with it.
   

---------------------QUOTE-------------------
So he knew evolution happened that way - he had observed it as directly as a paleontologist could - he just didn't know what exact mechanism was behind the observed switch.
---------------------QUOTE-------------------


And he hypothesized a mechanism, but could not be bothered to test his hypothesis. He was wrong.
   

---------------------QUOTE-------------------
He embraced Goldschmidt's systemmutationen because it closely resembled his own observations,...
---------------------QUOTE-------------------


Now you're just lying. It didn't "resemble his observations." Even if it *was consistent with* them, it still wasn't consistent with the data that we have now, and that you so dishonestly ignore.

Why did you lie and claim to be interested in evidence, Dan?
   

---------------------QUOTE-------------------
... but the switch does not have to be chromosomal rearrangements,...
---------------------QUOTE-------------------


Uh, Dan, the huge differences we observe within living coral species and colonies suggest that most of that morphological variation isn't even genetic.
[/quote] it could be single nucleotide substitutions (I suppose) provided they affected an early enough stage in ontogeny.[/quote]
Even then, it doesn't contradict neo-Darwinian evolutionary theory at all. Single-nucleotide substitutions are the smallest particulate change possible.
 

---------------------QUOTE-------------------
The point being, Schindewolf's theory was based on his direct observations of 'ontogenetical evolution' in the fossil record (as "direct" as can be deduced from the fossil record that is).
---------------------QUOTE-------------------


The point being that his hypothesis made clear predictions about what he would not be observed within live coral species. He didn't test his hypothesis. Other people did, and it's not consistent with the data. That's why his hypothesis is on the trash heap of science. His data are still useful.
Posted by: mitschlag on Mar. 09 2008,17:27

Quote (JAM @ Mar. 09 2008,16:20)
That's why his hypothesis is on the trash heap of science. His data are still useful.
---------------------QUOTE-------------------


Gotta give credit where credit is due.

And it's due.
Posted by: Daniel Smith on Mar. 09 2008,19:17

Quote (JAM @ Mar. 09 2008,11:37)
 
Quote (Daniel Smith @ Mar. 09 2008,11:10)
Let's look at the claim:
             

---------------------QUOTE-------------------
The second overlooked aspect is the significance of genome size and of distance between distinct regions of the genome. Rapidly reproducing organisms, like Caenorhabditis, Drosophila, Fugu and Arabidopsis tend to have stripped-down genomes with relatively less abundant repetitive DNA while
organisms with longer life cycles, such as humans and
maize, have larger genomes with correspondingly more
repetitive elements (Table 1 ; Cavalier-Smith, 1985).
---------------------QUOTE-------------------


So what do they mean by "relatively less" and "correspondingly more"?
---------------------QUOTE-------------------


They mean that they can't support their claim.
     

---------------------QUOTE-------------------
Is it in relation to their own genome size or is it relative to the amount of repetitive elements in the other category (rapidly reproducing vs. longer life cycles)?
---------------------QUOTE-------------------


Dan, the paper is pure hackery.

1) Genome size is very highly correlated with the amount of repeated DNA; in fact, because the same fundamental set of genes is there (remember how spectacularly wrong your prediction was?) and most DNA without a known function is repetitive, genome size is basically a function of the amount of repeated DNA.

2) The opposite of "rapidly reproducing" is "slowly reproducing," not "longer life cycles."
     

---------------------QUOTE-------------------
Since they say "stripped-down genomes with relatively less abundant repetitive DNA" and "larger genomes with correspondingly more repetitive elements" and immediately before that say that they are talking about "the significance of genome size and of distance between distinct regions of the genome", I'd say it is the latter.
---------------------QUOTE-------------------


It doesn't matter; it's BS either way.
     

---------------------QUOTE-------------------
From that perspective, I think the data in Table 1 does support their claim - especially if you look at the specific species mentioned.
---------------------QUOTE-------------------


Why would you italicize your bad grammar? Data (plural) either do or don't support a claim.

1) The data in the table couldn't possibly support their claim even if their claim was correct, because they offered no data on either speed of reproduction or length of life cycle (which aren't the same thing).

2) Look at two of the specific species mentioned: dog and mouse. The claimed relationship doesn't hold at all for them. IOW, they are incompetent even at dishonest cherry-picking.

If you really wanted to see if this is true, you'd look at more closely-related organisms, such as within < the genus Allium. > The evidence (remember, that stuff you lied about being interested in?) shows that genome size is amazingly plastic.
---------------------QUOTE-------------------


I'm looking at the Allium paper right now and I can see what you're talking about w/regard to genome size.  Looking at the data, I notice that all the species from the Subgenus Amerallium have larger genomes.  The authors also note "a correlation between genome size and ploidy level", but it doesn't seem to me to be a strong correlation.

---------------------QUOTE-------------------
A comparative analysis conducted using Mesquite (Maddison and Maddison 2003) revealed the existence of a correlation between genome size and ploidy level (Fig. 2, P = 0.031): tetraploidy is correlated with a small genome size.
---------------------QUOTE-------------------


Nevertheless, I think I'm in way over my head on this one!  I will defer to you that the paper proves your point.  I'm not going to be able to defend the Shapiro/Sternberg paper very effectively - I'm just too new to this.  I've made the mistake in the past of making grandiose claims that I could not back up and I'm beginning to see the error of my ways.  So, the Shapiro/Sternberg paper must stand or fall on its own merits.
Posted by: Daniel Smith on Mar. 09 2008,19:55

Quote (JAM @ Mar. 09 2008,14:20)
   
Quote (Daniel Smith @ Mar. 08 2008,15:26)
Let me just clarify something here.
---------------------QUOTE-------------------


You misspelled "obfuscate."
         

---------------------QUOTE-------------------
Schindewolf did not spend a lot of time talking about genetic mechanisms because he was not a genetecist.
---------------------QUOTE-------------------


So what? Dan, we're talking about a false claim that he made about genetics. Not being a geneticist is no excuse for making a false claim. Schindewolf had zero excuse for not knowing the relevant genetics.
         

---------------------QUOTE-------------------
He knew however, that there had to be some form of mechanism because he saw evidence for it in the fossil record.
---------------------QUOTE-------------------


But he was WRONG about the mechanism, just as he was wrong about the horse data. It's that simple.
         

---------------------QUOTE-------------------
He produced extensive data (JAM) documenting the reality of an ontogenetic switch from an established developmental path to a new and different developmental pathway during the early ontogenetic stages of fossilized ammonites and corals.
---------------------QUOTE-------------------


He produced exactly ZERO data to support his claim about the genetic mechanisms underlying the "switches." If he really was interested in testing his hypothesis, he would have observed and documented the huge morphological gaps WITHIN coral species AND EVEN WITHIN INDIVIDUAL COLONIES. I pointed you to that evidence, and you, proving beyond any doubt that you were lying when you claimed to want to see the evidence for yourself, ignored it.

Schindewolf was wrong. Deal with it.
         

---------------------QUOTE-------------------
So he knew evolution happened that way - he had observed it as directly as a paleontologist could - he just didn't know what exact mechanism was behind the observed switch.
---------------------QUOTE-------------------


And he hypothesized a mechanism, but could not be bothered to test his hypothesis. He was wrong.
         

---------------------QUOTE-------------------
He embraced Goldschmidt's systemmutationen because it closely resembled his own observations,...
---------------------QUOTE-------------------


Now you're just lying. It didn't "resemble his observations." Even if it *was consistent with* them, it still wasn't consistent with the data that we have now, and that you so dishonestly ignore.

Why did you lie and claim to be interested in evidence, Dan?
         

---------------------QUOTE-------------------
... but the switch does not have to be chromosomal rearrangements,...
---------------------QUOTE-------------------


Uh, Dan, the huge differences we observe within living coral species and colonies suggest that most of that morphological variation isn't even genetic.
 

---------------------QUOTE-------------------
it could be single nucleotide substitutions (I suppose) provided they affected an early enough stage in ontogeny.
---------------------QUOTE-------------------


Even then, it doesn't contradict neo-Darwinian evolutionary theory at all. Single-nucleotide substitutions are the smallest particulate change possible.
       

---------------------QUOTE-------------------
The point being, Schindewolf's theory was based on his direct observations of 'ontogenetical evolution' in the fossil record (as "direct" as can be deduced from the fossil record that is).
---------------------QUOTE-------------------


The point being that his hypothesis made clear predictions about what he would not be observed within live coral species. He didn't test his hypothesis. Other people did, and it's not consistent with the data. That's why his hypothesis is on the trash heap of science. His data are still useful.
---------------------QUOTE-------------------


To be fair to Schindewolf, at the time of the books printing, he was "not yet familiar" with Goldschmidt's The Material Basis of Evolution though he says that Goldschmidt's "earlier communications on this subject" had "considerable influence" on his thinking.  He says quite specifically that    

---------------------QUOTE-------------------
the concepts described here grew out of my own analysis of the paleontological material.
---------------------QUOTE-------------------

 
The genetic mechanism of chromosome repatterning was not even mentioned in the first printing of his book.  He only mentioned it in subsequent footnotes.
In the original publication he makes the case for an ontogenetic change of developmental direction.  In fact, on page 353, Fig. 3.156, he charts his views of the ontogentic switch:    

---------------------QUOTE-------------------
Consequently, there is no fundamental difference between micromutations... and macromutations, which appear in early stages and are distinguished only by the profoundness of their effects.
---------------------QUOTE-------------------


So his embracing of Goldschmidt's mechanism was based on, as he put it, "the broad agreement in our views" with the caveat that "Goldschmidt goes further than I and is in a position to support his phylogenetic conclusions genetically."

So, I've made a mish-mash out of Schindewolf's case by conflating it with Goldschmidt's.  

As for the evidence presented regarding the horse and living corals, I'll have to give all of it some thought.  Was the coral evidence the picture you posted?
Posted by: JAM on Mar. 09 2008,23:26

Quote (Daniel Smith @ Mar. 09 2008,19:17)
I'm looking at the Allium paper right now and I can see what you're talking about w/regard to genome size.  Looking at the data, I notice that all the species from the Subgenus Amerallium have larger genomes.  The authors also note "a correlation between genome size and ploidy level", but it doesn't seem to me to be a strong correlation.    

---------------------QUOTE-------------------
A comparative analysis conducted using Mesquite (Maddison and Maddison 2003) revealed the existence of a correlation between genome size and ploidy level (Fig. 2, P = 0.031): tetraploidy is correlated with a small genome size.
---------------------QUOTE-------------------


Nevertheless, I think I'm in way over my head on this one!
---------------------QUOTE-------------------


I salute you for being honest. At the risk of pissing you off, I hope that I can get you to understand that you are in over your head because you are placing opinion above evidence. When you arrived here, there seemed to be hope because you claimed to be interested in evidence and you seemed to be interested until your predictions were all shown to be wrong. Then you reverted to standard IDer/creationist behavior.
 

---------------------QUOTE-------------------
I will defer to you that the paper proves your point.
---------------------QUOTE-------------------


You should never grant that ANYTHING is proven in science. We don't deal in proof--that's the best way to put evidence above opinion, even expert opinion.
 

---------------------QUOTE-------------------
I'm not going to be able to defend the Shapiro/Sternberg paper very effectively - I'm just too new to this.
---------------------QUOTE-------------------


You don't have to understand the minutiae of the field to see that it is hackery--all you need to do is to see whether Shapiro or Sternberg have produced any data in the process of testing the hypothesis you find so appealing. They haven't and they won't.
 

---------------------QUOTE-------------------
I've made the mistake in the past of making grandiose claims that I could not back up and I'm beginning to see the error of my ways.
---------------------QUOTE-------------------


Good! Can you see the error of Sternberg's? Of Behe's? Of Schindewolf's?
 

---------------------QUOTE-------------------
So, the Shapiro/Sternberg paper must stand or fall on its own merits.
---------------------QUOTE-------------------


It doesn't have any. Here's why you're getting in trouble:

Your method: start with a hypothesis you find appealing and look for quotes that agree or seem to agree with your POV.

The scientific method: start with the evidence, try to explain the evidence with a hypothesis, and then do everything you can to demolish YOUR OWN hypothesis (or anyone else's hypothesis with which you become enamored) before you come to any conclusion, which still is only provisional--nothing is ever proven.

Your method is instinctive and easy. The scientific method goes against our instincts, but is the most powerful way to gain practical understanding about nature.

Are you beginning to see that even famous, productive scientists can lose track of the scientific method when they yield to ego and instinct, but that lay people, armed only with an understanding of the scientific method, can easily determine when this happens?

If Schindewolf had been a truly great scientist, he would have studied living corals. Being unable to move into a new field is an incredibly lame excuse.
Posted by: Daniel Smith on Mar. 10 2008,10:58

Quote (JAM @ Mar. 09 2008,21:26)
 
Quote (Daniel Smith @ Mar. 09 2008,19:17)
I'm looking at the Allium paper right now and I can see what you're talking about w/regard to genome size.  Looking at the data, I notice that all the species from the Subgenus Amerallium have larger genomes.  The authors also note "a correlation between genome size and ploidy level", but it doesn't seem to me to be a strong correlation.      

---------------------QUOTE-------------------
A comparative analysis conducted using Mesquite (Maddison and Maddison 2003) revealed the existence of a correlation between genome size and ploidy level (Fig. 2, P = 0.031): tetraploidy is correlated with a small genome size.
---------------------QUOTE-------------------


Nevertheless, I think I'm in way over my head on this one!
---------------------QUOTE-------------------


I salute you for being honest. At the risk of pissing you off, I hope that I can get you to understand that you are in over your head because you are placing opinion above evidence. When you arrived here, there seemed to be hope because you claimed to be interested in evidence and you seemed to be interested until your predictions were all shown to be wrong. Then you reverted to standard IDer/creationist behavior.
   

---------------------QUOTE-------------------
I will defer to you that the paper proves your point.
---------------------QUOTE-------------------


You should never grant that ANYTHING is proven in science. We don't deal in proof--that's the best way to put evidence above opinion, even expert opinion.
   

---------------------QUOTE-------------------
I'm not going to be able to defend the Shapiro/Sternberg paper very effectively - I'm just too new to this.
---------------------QUOTE-------------------


You don't have to understand the minutiae of the field to see that it is hackery--all you need to do is to see whether Shapiro or Sternberg have produced any data in the process of testing the hypothesis you find so appealing. They haven't and they won't.
   

---------------------QUOTE-------------------
I've made the mistake in the past of making grandiose claims that I could not back up and I'm beginning to see the error of my ways.
---------------------QUOTE-------------------


Good! Can you see the error of Sternberg's? Of Behe's? Of Schindewolf's?
   

---------------------QUOTE-------------------
So, the Shapiro/Sternberg paper must stand or fall on its own merits.
---------------------QUOTE-------------------


It doesn't have any. Here's why you're getting in trouble:

Your method: start with a hypothesis you find appealing and look for quotes that agree or seem to agree with your POV.

The scientific method: start with the evidence, try to explain the evidence with a hypothesis, and then do everything you can to demolish YOUR OWN hypothesis (or anyone else's hypothesis with which you become enamored) before you come to any conclusion, which still is only provisional--nothing is ever proven.

Your method is instinctive and easy. The scientific method goes against our instincts, but is the most powerful way to gain practical understanding about nature.

Are you beginning to see that even famous, productive scientists can lose track of the scientific method when they yield to ego and instinct, but that lay people, armed only with an understanding of the scientific method, can easily determine when this happens?

If Schindewolf had been a truly great scientist, he would have studied living corals. Being unable to move into a new field is an incredibly lame excuse.
---------------------QUOTE-------------------


JAM,

Can you please point me again to the living coral evidence you spoke about?

Thanks.
Posted by: JAM on Mar. 10 2008,12:46

Quote (Daniel Smith @ Mar. 10 2008,10:58)
Can you please point me again to the living coral evidence you spoke about?

Thanks.
---------------------QUOTE-------------------


I had started with FOSSIL coral intraspecific morphological variation, because it should have been clear, even to you, that Schindewolf was avoiding testing his hypothesis. Since you completely ignored that evidence, there was no reason to cite evidence from living corals:

< http://www.antievolution.org/cgi-bin....ry97708 >

You confidently claimed, "They're definitely inherited from generation to generation," Dan. Please tell me:

1) What evidence you used to reach this explicitly DEFINITE conclusion, and
2) If it was inherited, what evidence do you have on the amount of polymorphism within coral species or colonies.

Thanks!
Posted by: Daniel Smith on Mar. 10 2008,19:17

Quote (JAM @ Mar. 10 2008,10:46)
     
Quote (Daniel Smith @ Mar. 10 2008,10:58)
Can you please point me again to the living coral evidence you spoke about?

Thanks.
---------------------QUOTE-------------------


I had started with FOSSIL coral intraspecific morphological variation, because it should have been clear, even to you, that Schindewolf was avoiding testing his hypothesis. Since you completely ignored that evidence, there was no reason to cite evidence from living corals:

< http://www.antievolution.org/cgi-bin....ry97708 >

---------------------QUOTE-------------------


That link just takes me back to page 1 of this thread.
   

---------------------QUOTE-------------------
You confidently claimed, "They're definitely inherited from generation to generation," Dan. Please tell me:

1) What evidence you used to reach this explicitly DEFINITE conclusion, and
2) If it was inherited, what evidence do you have on the amount of polymorphism within coral species or colonies.

Thanks!
---------------------QUOTE-------------------


For 1: I was going exclusively on the evidence presented for the "developing" suture lines in Schindewolf's book (see Fig. 3.46 on pg. 151 for an example).  I then made the assumption that, because these suture lines changed over time, they represented an inherited factor.  I did not seek out any other sources.  So, in retrospect, I should have never said "definitely".

For 2: I don't have any.  That's not to say that there isn't any in Schindewolf's book, but I'm not remembering any right now.

BTW, Schindewolf did study living corals, he mentions studying the living coral Scleractinia on page 151.  

One of my biggest problems JAM is that I can't seem to retain much of what I read (especially when it's over my head).  I'm learning this stuff in bits and pieces so I might not be able to give you specific answers to your questions - which is why I often speak in generalities.

I just ran across this in Schindewolf's book:

---------------------QUOTE-------------------
With corals, too, if preservational conditions have been favorable we are fortunate to have access to the entire developmental history of the skeletal elements of a singel individual, from its first appearance on.  We can take a series of cross sections from the calcareous corallite and, using them, follow in every detail the origin and transformation of the septa,
pg.149
---------------------QUOTE-------------------


I wasn't aware that it was possible to actually see the development of an individual in the fossil record!  Not that this proves anything, I just found it interesting.
Posted by: Daniel Smith on Mar. 10 2008,19:26

Quote (mitschlag @ Mar. 09 2008,11:56)
Otto Heinrich, the cherry-picker:
     

---------------------QUOTE-------------------
Schindewolf, pp. 291-295 (continuing from the previous excerpt):

...And yet, this [he means inexorable increase in size] is by no means always the case; extremely often it is just the opposite, that extinct, ancient animal forms are characterized by unusual size, and the layman is indeed inclined to imagine these, without exception, as gigantic monsters.

In fact, we know that among extinct tigers, bears, elephants, rhinoceroses, and so on, there are some  extinct species that were considerably larger than those living today. A particularly conspicuous example is the mighty Baluchitherium, from the Oligocene of Asia, which is assigned to the rhinoceros group even though (like most ancient rhinoceroses) it has no horn on its nose (fig. 3.136). The shoulder height of this animal comes to about 5.3 meters, and the length of the torso is as much as 10 meters, making it one of the largest terrestrial mammals that ever lived. The enormous size of this animal is clearly seen in the comparison of a reconstruction of Baluchitherium with the Recent Indian rhi­noceros, both shown to scale in figure 3. 137.

These examples, however, by no means represent a contradiction to our rule of phyletic increase in size, for the extinct forms in question are not the imme­diate predecessors of the smaller Recent species. They are only members of a broader, related group within which they represent the terminal forms of extinct collateral lines (fig. 3.138). To this extent, they thoroughly confirm the general rule that gigantic forms mark the end of evolution.

Unquestionable examples of a once-attained body size being secondarily re­duced are almost unknown except in instances where such a reduction is suc­ceeded by a thorough remodeling to a completely new typal structure, which, itself, begins again with small forms. The exceptions occasionally cited are prob­ably only apparent, for in those cases it has not been shown that the forms with the supposed reduction in size really issued from larger ancestral forms of the same genetic lineage; only in such a situation would our rule be contradicted.

Accordingly, the evolution of size is, in general, irreversible. However, it is immediately clear that gigantic forms are indicators of dying lineages, for ulti­mately a point would be reached beyond which continued increase in size would be impossible for physiological reasons.
---------------------QUOTE-------------------


However, you are full of it, Schindewolf:
   

---------------------QUOTE-------------------
Simpson, op. cit., pp.137-138:

In this connection, it is known that many large animals of the past became extinct and are not the ancestors of their smaller living relatives. Mammoths were not ancestral to smaller elephants. (As a matter of fact, most mammoths were no larger than some living elephants, but a few were.) The elephantine ground sloths were not ancestral to the little living tree sloths. The dinosaurs were not the ancestors of the small lizards of later times. But this does not mean that forms that were the ancestors of living animals were not also somewhat larger than the latter at one time or another, and such does appear to be the case for some of them.

Some paleontologists have been so impressed by the fre­quent trend for animals to become larger as time goes on that they have tried to work it the other way around. If they find, say, a Pleistocene bison that is somewhat larger than a Recent bison (so-called Bison taylori, associate and prey of early man in America, is a good example), then they conclude that it is not ancestral to later bison because it is larger. You can establish any “rule” you like if you start with the rule and then interpret the evidence accordingly.
---------------------QUOTE-------------------


That last line is a keeper.
---------------------QUOTE-------------------


mitschlag,

I don't think Schindewolf was of the opinion that all lineages always increased in size.  I remember him talking about exceptions such as pygmy and dwarf species.  He also talked at length, and provided septal and suture line data that showed that some lineages didn't change much at all for long periods of time.  He does claim that there's a definite tendency towards gigantism towards the end of many lineages, and your quote form Simpson agrees with that:  

---------------------QUOTE-------------------
Some paleontologists have been so impressed by the fre­quent trend for animals to become larger as time goes on that they have tried to work it the other way around.
---------------------QUOTE-------------------


Schindewolf might have overstated its extent, but I don't think that means his statements should be ignored altogether.  Perhaps they should just be taken with a grain of salt.
Posted by: IanBrown_101 on Mar. 10 2008,22:20

Quote (Daniel Smith @ Mar. 11 2008,01:26)
I remember him talking about exceptions such as pygmy and dwarf species.
---------------------QUOTE-------------------


Ah, superb. Obviously Schindewolf must be right because he addresses these MAJOR problems for evilution. PYGMIES AND DWARFS!!!!!!!!!!1111!1
Posted by: JAM on Mar. 10 2008,23:17

This doesn't say much for your searching abilities:

Quote (JAM @ Feb. 17 2008,13:58)
 
Quote (mitschlag @ Feb. 17 2008,07:08)
I think the issue of suture lines was tainted for me by the statement in Moyne and Neige:            

---------------------QUOTE-------------------
Suture line characters are not used in this analysis because of their high variability between the different species of each genus.
---------------------QUOTE-------------------


---------------------QUOTE-------------------


[Daniel Smith]But that sentence doesn't mention Schindewolf! Therefore it (and the classification generated by using characters other than suture lines) can't possibly falsify his assumptions![/Daniel Smith]
     

---------------------QUOTE-------------------
So, I now see the parallel in Schindewolf's claims for corals and ammonoids: an ontogenetic switch.
---------------------QUOTE-------------------


Except that Schindewolf merely assumes that the switches represent huge genetic differences, Daniel blinds himself to Schindewolf's arrogance, and treats Schindewolf's opinions as evidence.
     

---------------------QUOTE-------------------
Is that the gist of his saltationist hypothesis?  It looks testable.  Are there any molecular-genetic-devolopmental data pertaining thereto in the literature?
---------------------QUOTE-------------------


Only morphological data are needed, which is why I kept pointing out to Dan that Schindewolf couldn't be bothered to test his hypothesis. It makes crystal-clear predictions about the limits of variation we should find in both living and fossilized corals.

< >Click to enlarge, from:

Journal of Paleontology; January 1987; v. 61; no. 1; p. 21-31
Intraspecific morphological variations in a Pleistocene solitary coral, Caryophyllia (Premocyathus) compressa Yabe and Eguchi
Kei Mori
---------------------QUOTE-------------------


Posted by: oldmanintheskydidntdoit on Mar. 11 2008,06:15

Quote (Daniel Smith @ Mar. 10 2008,19:17)
I did not seek out any other sources.  So, in retrospect, I should have never said "definitely".
---------------------QUOTE-------------------


   

---------------------QUOTE-------------------
One of my biggest problems JAM is that I can't seem to retain much of what I read (especially when it's over my head).
---------------------QUOTE-------------------



So go back to the beginning and start over. Start your education from the ground up, don't try and leap in areas even you admit you do not properly understand. How can you possible expect to prove your (any) point if you don't even understand the arguments you are getting back when you make a point!?!

Daniel, there's only room in my sig for one quote at a time, please stop!

So, is horse evolution a problem for Darwinism or not? I don't care if it was Alan that picked that subject, I'm asking you now, with your new knowledge that's been hard earned, do you see it as a problem for Darwinism or not?

If yes, why?
If no, well, teh win.
Posted by: Henry J on Mar. 11 2008,15:40



---------------------QUOTE-------------------
So, is horse evolution a problem for Darwinism or not?
---------------------QUOTE-------------------



Neigh!

:)
Posted by: Daniel Smith on Mar. 11 2008,19:06

Quote (JAM @ Mar. 10 2008,21:17)
This doesn't say much for your searching abilities:

 
Quote (JAM @ Feb. 17 2008,13:58)
   
Quote (mitschlag @ Feb. 17 2008,07:08)
I think the issue of suture lines was tainted for me by the statement in Moyne and Neige:              

---------------------QUOTE-------------------
Suture line characters are not used in this analysis because of their high variability between the different species of each genus.
---------------------QUOTE-------------------


---------------------QUOTE-------------------


[Daniel Smith]But that sentence doesn't mention Schindewolf! Therefore it (and the classification generated by using characters other than suture lines) can't possibly falsify his assumptions![/Daniel Smith]
       

---------------------QUOTE-------------------
So, I now see the parallel in Schindewolf's claims for corals and ammonoids: an ontogenetic switch.
---------------------QUOTE-------------------


Except that Schindewolf merely assumes that the switches represent huge genetic differences, Daniel blinds himself to Schindewolf's arrogance, and treats Schindewolf's opinions as evidence.
       

---------------------QUOTE-------------------
Is that the gist of his saltationist hypothesis?  It looks testable.  Are there any molecular-genetic-devolopmental data pertaining thereto in the literature?
---------------------QUOTE-------------------


Only morphological data are needed, which is why I kept pointing out to Dan that Schindewolf couldn't be bothered to test his hypothesis. It makes crystal-clear predictions about the limits of variation we should find in both living and fossilized corals.

< >Click to enlarge, from:

Journal of Paleontology; January 1987; v. 61; no. 1; p. 21-31
Intraspecific morphological variations in a Pleistocene solitary coral, Caryophyllia (Premocyathus) compressa Yabe and Eguchi
Kei Mori
---------------------QUOTE-------------------


---------------------QUOTE-------------------


JAM,

Thanks for finding that for me.  I've been looking at the pictures and can see a lot of variety in septal arrangement - though many follow a similar format with three shorter septa between the longer ones.

I can not access the paper though.  Can you tell me if these corals were all contemporaries of one another?  I see that they are all from the Pleistocene epoch, but that epoch spans from 1,808,000 to 11,550 years BP.  Also I need to know if these are all adult forms?

Thanks.
Posted by: Daniel Smith on Mar. 11 2008,19:12

Quote (oldmanintheskydidntdoit @ Mar. 11 2008,04:15)
 
Quote (Daniel Smith @ Mar. 10 2008,19:17)
I did not seek out any other sources.  So, in retrospect, I should have never said "definitely".
---------------------QUOTE-------------------


     

---------------------QUOTE-------------------
One of my biggest problems JAM is that I can't seem to retain much of what I read (especially when it's over my head).
---------------------QUOTE-------------------



So go back to the beginning and start over. Start your education from the ground up, don't try and leap in areas even you admit you do not properly understand. How can you possible expect to prove your (any) point if you don't even understand the arguments you are getting back when you make a point!?!

Daniel, there's only room in my sig for one quote at a time, please stop!

So, is horse evolution a problem for Darwinism or not? I don't care if it was Alan that picked that subject, I'm asking you now, with your new knowledge that's been hard earned, do you see it as a problem for Darwinism or not?

If yes, why?
If no, well, teh win.
---------------------QUOTE-------------------


The only part of horse evolution that I ever claimed was a problem for Darwinism was the [disputed] claim that the reduction in toes began before it was beneficial.
Posted by: Henry J on Mar. 11 2008,23:10



---------------------QUOTE-------------------
The only part of horse evolution that I ever claimed was a problem for Darwinism was the [disputed] claim that the reduction in toes began before it was beneficial.
---------------------QUOTE-------------------



As long as it wasn't detrimental, why would it be a problem?

Henry
Posted by: oldmanintheskydidntdoit on Mar. 12 2008,03:45

Quote (Daniel Smith @ Mar. 11 2008,19:12)

The only part of horse evolution that I ever claimed was a problem for Darwinism was the [disputed] claim that the reduction in toes began before it was beneficial.
---------------------QUOTE-------------------


So, is that a "Yes" or a "No"?

You are very good at answering a different question to the one that was asked Daniel....
Posted by: Daniel Smith on Mar. 12 2008,11:09

Quote (oldmanintheskydidntdoit @ Mar. 12 2008,01:45)
 
Quote (Daniel Smith @ Mar. 11 2008,19:12)

The only part of horse evolution that I ever claimed was a problem for Darwinism was the [disputed] claim that the reduction in toes began before it was beneficial.
---------------------QUOTE-------------------


So, is that a "Yes" or a "No"?

You are very good at answering a different question to the one that was asked Daniel....
---------------------QUOTE-------------------


I don't know enough about the particulars of horse evolution to say whether it (the entire evolutionary history of the horse lineage) is a problem for Darwinism or not.  I was merely pointing out that I (as far as I can remember) only made one reference to horse evolution being a problem for a Darwinist interpretation and that was regarding the pre-adaptive selection for the reduction in toes.  It has never been the focus of my arguments here however.
Posted by: mitschlag on Mar. 12 2008,14:24

Quote (Daniel Smith @ Mar. 12 2008,11:09)
I don't know enough about the particulars of horse evolution to say whether it (the entire evolutionary history of the horse lineage) is a problem for Darwinism or not.  I was merely pointing out that I (as far as I can remember) only made one reference to horse evolution being a problem for a Darwinist interpretation and that was regarding the pre-adaptive selection for the reduction in toes.  It has never been the focus of my arguments here however.
---------------------QUOTE-------------------


That might be a problem if it were supported by evidence.  How can one be confident that a trait is non-adaptive if one does not have a clear picture of the environment at the time the trait emerged?

Note that the plains came before the one-toed horses, contrary to Schindewolf's belief.  (You can't have plains without grazing animals, and you don't need to be one-toed to be a grazing animal.)

Note that three-toed horses were running on plains (and eating grass) capably enough to survive for millions of years.

Note that one-toed horses became extinct in the Americas despite an abundance of plains for them to run on and grass to graze on.

Schindewolf appears to have selected evidence to fit his  orthogenetic preconceptions.
Posted by: Daniel Smith on Mar. 12 2008,18:54

I think I'm done here.

I'm just getting tired of arguing.

There's really no point to it anymore.  We're starting to cover topics we've already covered - sometimes several times.

I've learned lots since coming here.  Thanks to everyone who challenged me on things.  You forced me to take a long hard look at myself and my beliefs.  I'm sorry I came across as defensive and unwilling to learn because I really was listening.

I'd like to especially thank JAM for showing me the importance of evidence, data and TESTING!  I'm going to do everything in my power to destroy my own hypotheses and beliefs from now on.  Maybe I'll come back and let you all know how it turns out.

Later.
Posted by: Dr.GH on Mar. 12 2008,22:30

Good start.  Warm regards.  Bye Bye
Posted by: JAM on Mar. 12 2008,23:20

Quote (Daniel Smith @ Mar. 12 2008,18:54)
I think I'm done here.

I'm just getting tired of arguing.

There's really no point to it anymore.  We're starting to cover topics we've already covered - sometimes several times.

I've learned lots since coming here.  Thanks to everyone who challenged me on things.  You forced me to take a long hard look at myself and my beliefs.  I'm sorry I came across as defensive and unwilling to learn because I really was listening.

I'd like to especially thank JAM for showing me the importance of evidence, data and TESTING!  I'm going to do everything in my power to destroy my own hypotheses and beliefs from now on.  Maybe I'll come back and let you all know how it turns out.

Later.
---------------------QUOTE-------------------


Dan,

I'm glad I could help. Good luck. You might want to look into the concept of NOMA:

< http://en.wikipedia.org/wiki/Non-overlapping_magisteria >
Posted by: mitschlag on Mar. 13 2008,06:25

Tough love rocks!

Congratulations, Daniel Smith, as you continue your adventure.


(Anybody interested in a slightly used copy of Grundfragen?)
Posted by: swbarnes2 on Mar. 13 2008,13:30

Quote (Daniel Smith @ Mar. 12 2008,18:54)
I'm going to do everything in my power to destroy my own hypotheses and beliefs from now on.
---------------------QUOTE-------------------



Transparently dishonest to the last.
Posted by: Alan Fox on Mar. 13 2008,13:32

Quote (Daniel Smith @ Mar. 12 2008,13:54)
I think I'm done here.

I'm just getting tired of arguing.

There's really no point to it anymore.  We're starting to cover topics we've already covered - sometimes several times.

I've learned lots since coming here.  Thanks to everyone who challenged me on things.  You forced me to take a long hard look at myself and my beliefs.  I'm sorry I came across as defensive and unwilling to learn because I really was listening.

I'd like to especially thank JAM for showing me the importance of evidence, data and TESTING!  I'm going to do everything in my power to destroy my own hypotheses and beliefs from now on.  Maybe I'll come back and let you all know how it turns out.

Later.
---------------------QUOTE-------------------


Farewell, Dan.

Glad you feel there was some benefit to your experience here.
I second JAM's point about NOMA. You should give "The Ancestor's Tale" a try too.

Best wishes
Alan
Posted by: VMartin on Mar. 14 2008,12:36

Daniel,

it's a pity you have finished the discussion here. But you are right. There were some interesing links you sent. It's more usefull to read those materials. I was again inspired by the link you sent on German idealistic morphology and borrowed Pflanzenmorphology by professor Wilhelm Troll. It has more than 700 pages and it deals with interesting idea that all seed-plants are just variations of ideal "Urpflanze". Wilhelm Troll crucial works  - as those of A. Portmann - haven't been translated into English.
Posted by: Erasmus, FCD on Mar. 14 2008,21:48



---------------------QUOTE-------------------
it deals with interesting idea that all seed-plants are just variations of ideal "Urpflanze"
---------------------QUOTE-------------------



that is indeed an interesting idea.  it reminds me of another interesting idea that all left nipples are regrets in the mind of lesser gods.



---------------------QUOTE-------------------
Wilhelm Troll crucial works  - as those of A. Portmann - haven't been translated into English.
---------------------QUOTE-------------------



as shitty as it actually works in practice, the law of supply and demand provides an explanation for this phenomenon.



Get back to work Martin!  Them sows ain't gonna inseminate themselves, boy.
Posted by: Lou FCD on Mar. 17 2008,11:52





---------------------QUOTE-------------------
< but I know what I like, by mondoagogo >
---------------------QUOTE-------------------



I moved some off topic comments yesterday.


Posted by: oldmanintheskydidntdoit on Oct. 15 2008,17:17

Quote (Daniel Smith @ Oct. 01 2007,21:26)
 
Quote (Alan Fox @ Oct. 01 2007,07:31)
Re the search for evidence of life on Mars, there are three possible outcomes that I can foresee.

1:Evidence is found for a life-form totally different from anything seen on Earth, say, not even based on carbon, but, for instance, built on silicon.

2: Evidence is found for a life-form bearing distinct similarities to terrestrial lifeforms.

3; No evidence found.

If 1, abiogenesis is almost inevitable on any suitable planet, given enough time.

If 2, lifeforms such as bacterial spores may travel across space as passengers in meteorites. (Panspermia)

If 3, we still don't know.
---------------------QUOTE-------------------


One other option for #2:

If we find life on another planet that is distinctly similar to our own, it could mean that abiogenesis acts according to laws as well.

Denton's position, as expressed in "Nature's Destiny", was that any life, anywhere else in the universe, would have to be remarkably similar to our own.
---------------------QUOTE-------------------


But now you'll write him? Tell him abiogenesis is impossible?
Posted by: oldmanintheskydidntdoit on Jan. 16 2009,03:04

Oops, wrong thread :)
end


Powered by Ikonboard 3.0.2a
Ikonboard © 2001 Jarvis Entertainment Group, Inc.