Re: [asa] Exaptation

From: wjp <wjp@swcp.com>
Date: Tue Jun 23 2009 - 13:18:30 EDT

Cameron:

Randy pointed out in his email that certain random genetic mixing processes
could produce "significant" changes in the individual.

One expects this mixing process to occur amongst physically "close" coding.
I don't know this, but perhaps we can guess that at least within chromosomes
that physical closeness might reflect "functional" closeness. Over time, of
course, the random mixing could conceivably trace out the entire genetically
coded strand.

Our experience with human coding suggests that this would be a delicate and
unstable process. However, it is possible to imagine a code in which such
mixing could be endured and "meaning" remain. For example, text messaging
points to the redundancy of English spelling. Coding might also be
redundant. The problem, of course, is not merely to be able to express the
same message, but to express a new (survival) one.

It is this latter aspect that, for me, is conceptually problematic. You point
to the problem, I think, when you ask why "unused" parts should just lie around
waiting to be used.

It may well be that we simply do not have the appropriate language to speak of
these things. Functionality is conceptual. The random process of genetic variation
knows nothing of functionality. Two functions, no matter how close, are as distant
as the east is from the west from the perspective of random selection. Selection
is not only blind; it is Dumb.

What we must imagine is that the genetic soup gets stirred up; something different
arises, perhaps it survives, perhaps not. If it survives, it gets mixed up again,
and something new arises. There is no functionality. That is our perspective.
It is just something new.

The possibility of a "hopeful monster" comes about because we are messing with a
code. The mixing of the letters of a written message might produce almost anything.
Since meaning is not physical, possibility is difficult to map, and surely need
not be continuous, or even related.

It seems to me that "new functionality" in a blind, dumb process must emerge
almost miraculously. I cannot imagine a blind, dumb random process whereby
a jaw bone would become vital for the correct functioning of hearing, unless
perhaps the jaw bone were always involved with hearing, in which case it
is not a new functionality.

I know that the biological community believe that it has been firmly
established that the jaw bone "evolved" into the middle ear.
Indeed, they regard it as one of the great accomplishments of
evolutionary biology. They claim to have found an historical trace
from reptile to humans. It seems to me that if they are correct then
something is going on in evolutionary development that is more than
random and natural selection, at least that's how it seems to my
naive mind.

What might be going on is something like what Conway Morris suggests:
that many paths lead to similar forms. It may be that there is something
about biological possibility that is more constrained than its random
development suggests. This could be a sign of divine intervention, or
some physical principle as yet unknown. After all, who would have
thought that H2O could produce such beautiful structures in winter
skies.

I believe that it just these kinds of issues that are associated with
irreducible complexity. But I won't pursue that here.

bill

On Tue, 23 Jun 2009 12:04:55 -0400, "Cameron Wybrow" <wybrowc@sympatico.ca> wrote:
> Bill and Randy:
>
> I think these considerations regarding incrementalism are important. Of
> course you both already know that even within the broadly Darwinian camp,
> Gould had pointed out that the fossil record did not comport with
> Darwinian
> gradualism. Michael Denton, in his first book, *Evolution: A Theory in
> Crisis*, confirmed Gould's observations with reference to biochemistry,
> pointing out that not only morphologically, but even with regard to
> certain
> important proteins, the animal kingdom was characterized by gappiness and
> clusters rather than gradualism and continuity, as classical neo-Darwinism
> would predict.
>
> I think that in Denton's second book, *Nature's Destiny* (which is not a
> repudiation of the first book, as some suppose, but rather an attempt to
> go
> beyond it), he suggests exactly what Bill is suggesting below, i.e., that
> major changes in the phenotype could be built up by gradual changes in the
> genotype. This would preserve Darwinian gradualism at the genetic level,
> while explaining the discrepant phenomena observed by Gould, Denton and
> others at the morphological and other levels. So Darwin would be both
> right
> and wrong; right, in insisting upon gradualism, but wrong, in expecting
> that
> all the gradual change would show up morphologically and be selected for.
> Thus, Bill's remark about not necessarily being able to find transitional
> species on the morphological level is quite a propos.
>
> I see some problems with Denton's solution. He supposes (contra Darwin)
> that most of the genetic changes aren't immediately expressed
> morphologically or in any other way, but are "saved up", and then, when a
> certain cluster of changes "makes sense", the whole cluster is expressed.
> So genetic changes might accumulate over a million years, and then a new
> creature might appear which would be quite different from its parents. It
> would perhaps (though Denton doesn't say this; I'm just trying to make
> sense
> of what he does say) look like a "hopeful monster" to the outsider, maybe,
> I
> don't know, a bat born to a rodent mother (I'm making this example up;
> Denton doesn't give any). But to the genetic observer over the
> million-year-period, only gradualism would ever be seen: "random" looking
> mutations. I have two tentative objections to this view: (a) how much
> different could the offspring be from the parent, and survive?
> Particularly
> in the case of mammals, who require maternal care after birth? Could a
> bat-like creature, for example, still nurse from its rodent mother? Would
> the milk, the nipples, etc. be compatible? More important, might the
> mother
> not instinctively reject the freak child and refuse to nurse it? And even
> in the case of reptiles, the mother crocodile carries around her tiny
> young
> for a period in her mouth, to keep them safe; would she do so for some
> (again, just a tentative example) some freak offspring that was hairy like
> a
> mammal? (b) How does the genome know not to express the minor gradual
> changes until they are all assembled? Why wouldn't it express each
> genetic
> change right away? What internal mechanism "holds back" certain changes
> from being expressed? Is there a timing mechanism of some kind? How
> would
> it work? For Denton's theory to be correct, the operation of DNA must
> have
> layers of sophistication that we have not yet fathomed. Of course that is
> exactly his thesis, that the DNA is just part of the cosmic computer
> program, so to speak, which was written before Creation and is meant to
> "output" man. The question is, how do we go about confirming this
> teleological aspect of the operation of DNA? Isn't such a view, while not
> contradicted by the facts, at this point extremely speculative, and very
> problematic?
>
> Hopefully Denton will address this question in his third book, which is
> due
> out later this year.
>
> Cameron.
>
>
>
>
>
>
>
> ----- Original Message -----
> From: "Bill Powers" <wjp@swcp.com>
> To: "Randy Isaac" <randyisaac@comcast.net>
> Cc: <asa@calvin.edu>
> Sent: Tuesday, June 23, 2009 7:55 AM
> Subject: Re: [asa] Exaptation
>
>
>> Randy:
>>
>> I will try looking at some of the articles you reference.
>>
>> I take you to be saying that incrementalism on the genetic scale may
>> produce "discontinuity" on the morphological scale.
>>
>> I suspected the same some 20 years ago when I first started studying
>> evolutionary theory, which is why I thought at the time that we really
>> don't know what a transitional species would look like.
>>
>> My experience with nonlinear and chaotic systems suggested to me that
> the
>> same might be possible for biological systems.
>>
>> If this is the case, one ought to be at least suspect of any proposed
>> transitional history since almost all are based upon morphological
>> similarity, although I imagine the theory has begun to rely upon
> presumed
>> ancestry.
>>
>> bill
>>
>> On Tue, 23 Jun 2009, Randy Isaac wrote:
>>
>>> Interesting point, Bill. I think we need to be careful about an
> argument
>>> based on the a requirement of incrementalism. We still have so much to
>>> learn about the quantization of descent with modification. In contrast
> to
>>> Darwin's view of gradualism, the discovery of DNA led to a quantization
>>> of changes at the molecular level but we still have so little awareness
>>> of what that might mean macroscopically in the functional realm.
>>>
>>> There have been several good articles in Science News recently that
> talk
>>> about this. In January, an article showed some support for Conway
>>> Morris's approach.
>>>
> http://www.sciencenews.org/view/feature/id/40006/title/Molecular_Evolution
>>> Molecular Evolution
>>> Investigating the genetic books of life reveals new details of 'descent
>>> with modification' and the forces driving it
>>> By Tina Hesman Saey
>>> January 31st, 2009; Vol.175 #3 (p. 26).
>>>
>>> Even more relevant was a story in March on structure variants.
>>>
> http://www.sciencenews.org/view/generic/id/40922/title/Jumping_genes_provide_unexpected_diversity
>>> Jumping genes provide unexpected diversity
>>> Mobile DNA elements help shape human genomes
>>> By Tina Hesman Saey
>>> March 14th, 2009; Vol.175 #6 (p. 16)
>>>
>>> The above articles are too long to copy and post but most of you
> probably
>>> have access to either paper or electronic copies.
>>>
>>> The net is that incremental changes at the molecular level may be more
>>> significant than we expected and the resulting functional impact may be
>>> even greater.
>>>
>>> Randy
>>>
>>> ----- Original Message ----- From: "Bill Powers" <wjp@swcp.com>
>>> To: <asa@calvin.edu>
>>> Cc: <wjp@swcp.com>
>>> Sent: Tuesday, June 23, 2009 12:14 AM
>>> Subject: [asa] Exaptation
>>>
>>>
>>>> I'm continuing to think about Irreducible Complexity. A closely
> related
>>>> concept is that of exaptation, wherein some biological structure or
>>>> process
>>>> used for one function is later used for a different function.
>>>>
>>>> Exaptation is apparently a well accepted doctrine and there a few
>>>> carefully
>>>> documented arguments to support the notion, including the development
>>>> from the
>>>> jaw bone for use in the middle ear, the bone spur of the panda
>>>> developing into
>>>> a thumb, and the development of feathers from thermal insulation into
>>>> feathers
>>>> for flight. The last two have problems in my mind conceptually, the
>>>> first is
>>>> perhaps the best.
>>>>
>>>> Nonetheless, exaptation appears to present theoretical problems, and
>>>> here is why.
>>>>
>>>> It appears to me that Darwinian (random) evolution, not only presumes,
>>>> but
>>>> must be committed to a principle of incrementalism, whereby evolution
>>>> sensibly
>>>> proceeds according to small incremental changes.
>>>>
>>>> This principle appears necessary because of the random nature of the
>>>> process.
>>>> Significant, but random, changes are highly likely to be deadly,
>>>> producing a
>>>> non-survivable species. This is because it is likely that survival
>>>> large
>>>> changes are likely to be complex and highly integrated, but to expect
> a
>>>> random
>>>> process to be able to accomplish such a feat seems to ask far too
> much.
>>>> On
>>>> the other hand, small changes are more likely to leave the species
> still
>>>> survivable. Such changes, while small, can be mildly advantageous,
>>>> neutral,
>>>> or even mildly disadvantageous.
>>>>
>>>> The principle of incrementalism presumes that in some sense that
> changes
>>>> are
>>>> near each other. But this nearness is not conceptual nearness,
>>>> something
>>>> utterly foreign to a blind process, but probablistic.
>>>>
>>>> Prima facie, exaptation violates this principle of incrementalism.
> This
>>>> is so
>>>> because the previous function is not probabilistically near the new
>>>> function.
>>>> It is conceptually near perhaps, but how can it be probabilistically
>>>> near?
>>>>
>>>> Functionality is conceptual. I don't know how else to say it. In a
>>>> sense the
>>>> very notion of functionality is suspicious in a non-teleological
>>>> process. But
>>>> what then do we mean when we say in exaptation that an old function is
>>>> used
>>>> for a new one?
>>>>
>>>> To take, but one example, if one reviews, even in cartoon form the
>>>> evolutionary development of the jaw bone into the middle ear, it
> appears
>>>> to me
>>>> to be miraculous if viewed as a random process. It only seems
>>>> reasonable
>>>> "conceptually," but not, to me, as a blind process.
>>>>
>>>> Can anyone help?
>>>>
>>>> thanks,
>>>>
>>>> bill
>>>>
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>>>>
>>>
>>>
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>>
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Received on Tue Jun 23 13:19:20 2009

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