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  Topic: Evolution of the horse; a problem for Darwinism?, For Daniel Smith to present his argument< Next Oldest | Next Newest >  
jeannot



Posts: 1201
Joined: Jan. 2006

(Permalink) Posted: 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.

  
Henry J



Posts: 5786
Joined: Mar. 2005

(Permalink) Posted: 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.

Not over short time frames, anyway. When the universe is gets old enough for all the stars to have burned out, maybe.

Henry

  
Reciprocating Bill



Posts: 4265
Joined: Oct. 2006

(Permalink) Posted: 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.

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).

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).

--------------
Myth: Something that never was true, and always will be.

"The truth will set you free. But not until it is finished with you."
- David Foster Wallace

"Here’s a clue. Snarky banalities are not a substitute for saying something intelligent. Write that down."
- Barry Arrington

  
Richard Simons



Posts: 425
Joined: Oct. 2006

(Permalink) Posted: 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?

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.

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?

--------------
All sweeping statements are wrong.

  
Richard Simons



Posts: 425
Joined: Oct. 2006

(Permalink) Posted: Oct. 03 2007,21:02   

In the previous post I said
Quote
(and other comments like tells me that you are just starting

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.

--------------
All sweeping statements are wrong.

  
Alan Fox



Posts: 1556
Joined: Aug. 2005

(Permalink) Posted: 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

  
Daniel Smith



Posts: 970
Joined: Sep. 2007

(Permalink) Posted: 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.

--------------
"If we all worked on the assumption that what is accepted as true is really true, there would be little hope of advance."  Orville Wright

"The presence or absence of a creative super-intelligence is unequivocally a scientific question."  Richard Dawkins

  
Alan Fox



Posts: 1556
Joined: Aug. 2005

(Permalink) Posted: 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?


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.


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. :)

  
Reciprocating Bill



Posts: 4265
Joined: Oct. 2006

(Permalink) Posted: 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.

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?

--------------
Myth: Something that never was true, and always will be.

"The truth will set you free. But not until it is finished with you."
- David Foster Wallace

"Here’s a clue. Snarky banalities are not a substitute for saying something intelligent. Write that down."
- Barry Arrington

  
JAM



Posts: 517
Joined: July 2007

(Permalink) Posted: 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.

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.

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.

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.

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
How do you explain artificial evolution of random sequences, then?  
Quote
- especially as genomes are found to contain more embedded, overlapping codes.

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).

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.

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.

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.

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.

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?

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?

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)?

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?

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?

  
Daniel Smith



Posts: 970
Joined: Sep. 2007

(Permalink) Posted: 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.

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?

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 ...)

--------------
"If we all worked on the assumption that what is accepted as true is really true, there would be little hope of advance."  Orville Wright

"The presence or absence of a creative super-intelligence is unequivocally a scientific question."  Richard Dawkins

  
Reciprocating Bill



Posts: 4265
Joined: Oct. 2006

(Permalink) Posted: 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.

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?

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 ...)

OK - but the question was: Does this fairly summarize your view?

--------------
Myth: Something that never was true, and always will be.

"The truth will set you free. But not until it is finished with you."
- David Foster Wallace

"Here’s a clue. Snarky banalities are not a substitute for saying something intelligent. Write that down."
- Barry Arrington

  
Daniel Smith



Posts: 970
Joined: Sep. 2007

(Permalink) Posted: Oct. 06 2007,03:15   

Quote (Reciprocating Bill @ Oct. 05 2007,21:25)
OK - but the question was: Does this fairly summarize your view?

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.

--------------
"If we all worked on the assumption that what is accepted as true is really true, there would be little hope of advance."  Orville Wright

"The presence or absence of a creative super-intelligence is unequivocally a scientific question."  Richard Dawkins

  
oldmanintheskydidntdoit



Posts: 4999
Joined: July 2006

(Permalink) Posted: 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?

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.

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.


Try to avoid sounding like them huh?

Link

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I also mentioned that He'd have to give me a thorough explanation as to *why* I must "eat human babies".
FTK

if there are even critical flaws in Gauger’s work, the evo mat narrative cannot stand
Gordon Mullings

  
Daniel Smith



Posts: 970
Joined: Sep. 2007

(Permalink) Posted: 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?


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.

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).
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.


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)

"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. :)

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!

--------------
"If we all worked on the assumption that what is accepted as true is really true, there would be little hope of advance."  Orville Wright

"The presence or absence of a creative super-intelligence is unequivocally a scientific question."  Richard Dawkins

  
Daniel Smith



Posts: 970
Joined: Sep. 2007

(Permalink) Posted: 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?
Yes.    
Quote

If so, how do you propose going to look for it?
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?

That would be logical.    
Quote

If not, what exactly do you mean by "front loaded" if not "contains instructions for dealing with future events"?
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.


Try to avoid sounding like them huh?

Link

Never read that, but I can't say that I disagree with it.

--------------
"If we all worked on the assumption that what is accepted as true is really true, there would be little hope of advance."  Orville Wright

"The presence or absence of a creative super-intelligence is unequivocally a scientific question."  Richard Dawkins

  
Reciprocating Bill



Posts: 4265
Joined: Oct. 2006

(Permalink) Posted: 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?

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.

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.

--------------
Myth: Something that never was true, and always will be.

"The truth will set you free. But not until it is finished with you."
- David Foster Wallace

"Here’s a clue. Snarky banalities are not a substitute for saying something intelligent. Write that down."
- Barry Arrington

  
improvius



Posts: 807
Joined: Jan. 2006

(Permalink) Posted: Oct. 06 2007,10:58   

oops, wrong thread

--------------
Quote (afdave @ Oct. 02 2006,18:37)
Many Jews were in comfortable oblivion about Hitler ... until it was too late.
Many scientists will persist in comfortable oblivion about their Creator ... until it is too late.

  
Daniel Smith



Posts: 970
Joined: Sep. 2007

(Permalink) Posted: 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?

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.

--------------
"If we all worked on the assumption that what is accepted as true is really true, there would be little hope of advance."  Orville Wright

"The presence or absence of a creative super-intelligence is unequivocally a scientific question."  Richard Dawkins

  
JAM



Posts: 517
Joined: July 2007

(Permalink) Posted: 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?

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.

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.

  
Daniel Smith



Posts: 970
Joined: Sep. 2007

(Permalink) Posted: 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.

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.

--------------
"If we all worked on the assumption that what is accepted as true is really true, there would be little hope of advance."  Orville Wright

"The presence or absence of a creative super-intelligence is unequivocally a scientific question."  Richard Dawkins

  
Daniel Smith



Posts: 970
Joined: Sep. 2007

(Permalink) Posted: 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?

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.

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.

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.

--------------
"If we all worked on the assumption that what is accepted as true is really true, there would be little hope of advance."  Orville Wright

"The presence or absence of a creative super-intelligence is unequivocally a scientific question."  Richard Dawkins

  
Reciprocating Bill



Posts: 4265
Joined: Oct. 2006

(Permalink) Posted: 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".

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.

--------------
Myth: Something that never was true, and always will be.

"The truth will set you free. But not until it is finished with you."
- David Foster Wallace

"Here’s a clue. Snarky banalities are not a substitute for saying something intelligent. Write that down."
- Barry Arrington

  
JAM



Posts: 517
Joined: July 2007

(Permalink) Posted: 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.

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.

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?

  
stevestory



Posts: 13407
Joined: Oct. 2005

(Permalink) Posted: 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.

   
Daniel Smith



Posts: 970
Joined: Sep. 2007

(Permalink) Posted: 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.

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.

--------------
"If we all worked on the assumption that what is accepted as true is really true, there would be little hope of advance."  Orville Wright

"The presence or absence of a creative super-intelligence is unequivocally a scientific question."  Richard Dawkins

  
oldmanintheskydidntdoit



Posts: 4999
Joined: July 2006

(Permalink) Posted: 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.

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.

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

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?

--------------
I also mentioned that He'd have to give me a thorough explanation as to *why* I must "eat human babies".
FTK

if there are even critical flaws in Gauger’s work, the evo mat narrative cannot stand
Gordon Mullings

  
Daniel Smith



Posts: 970
Joined: Sep. 2007

(Permalink) Posted: 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.

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.

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?

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?

--------------
"If we all worked on the assumption that what is accepted as true is really true, there would be little hope of advance."  Orville Wright

"The presence or absence of a creative super-intelligence is unequivocally a scientific question."  Richard Dawkins

  
Daniel Smith



Posts: 970
Joined: Sep. 2007

(Permalink) Posted: 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.

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.

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

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?

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.

--------------
"If we all worked on the assumption that what is accepted as true is really true, there would be little hope of advance."  Orville Wright

"The presence or absence of a creative super-intelligence is unequivocally a scientific question."  Richard Dawkins

  
mitschlag



Posts: 236
Joined: Sep. 2006

(Permalink) Posted: 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?

You are the scientist, DS.  You are responsible for devising the test.

--------------
"You can establish any “rule” you like if you start with the rule and then interpret the evidence accordingly." - George Gaylord Simpson (1902-1984)

  
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