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+--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? >
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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?
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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.      

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

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Can you supply that quote from Darwin?
 

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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.

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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.
   

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

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

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Denton's last book supports directed evolution.

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

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

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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.

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

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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?

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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.        

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

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

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OK,
       

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

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Does that qualify?
       

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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.

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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

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No, those were already sequenced.

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OK my bad.
       

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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?

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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.

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OK
       

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

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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.                

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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.

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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?

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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.      
       

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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.

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

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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.

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Can you supply that quote from Darwin?
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< Here >.
Posted by: Wesley R. Elsberry on Sep. 26 2007,06:42



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

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<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:  

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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.

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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)


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



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

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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]
     

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 Most components can also be organized into nested hierarchies.
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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.
       

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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.
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Then show us the data.
       

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

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

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Where did Denton assume a ladder?  I don't remember that part.
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< http://www.talkorigins.org/faqs/denton.html >
Read the last half of part III.
     

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Like I said, I'm willing to look at any and all evidence.  I'm less interested in opinions though.
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Then why have you offered nothing but opinions?
     

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

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

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OK,    

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you have the appealing quality of massive arrogance, made even more appealing by massive ignorance... so please save your lying for ignorant lay people.
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Does that qualify?
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No, because there's not a single name in there.
[quote]    

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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.

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OK
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Then why do you go back on that below?
   

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

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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.
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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.
   

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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.

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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?

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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.
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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.
   

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I need to see the evidence for myself - I won't just take your word for it.
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I'm showing you evidence and you are denying that it is evidence.     
   

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The tree is theoretical in that it is just a graphic representation of a proposed relationship.
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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?
   

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How do you know these genes are not convergent?
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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)


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

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We don't have to wait to know that Denton's assertion is < incorrect >.
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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)
     

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

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<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>
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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)
 

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

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We don't have to wait to know that Denton's assertion is < incorrect >.
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That's a much more lucid explanation than the TO page to which I pointed Daniel, thanks.
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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)
 

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

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We don't have to wait to know that Denton's assertion is < incorrect >.
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That's a much more lucid explanation than the TO page to which I pointed Daniel, thanks.
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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.
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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?
     

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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.

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That's not true.  
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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



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The another drama about fossils proving evolution of man:

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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)
 

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

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I am convinced of one thing: whatever happened was by design.
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???
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:
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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.
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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:                          

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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.

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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?
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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 bindin