Re: Is evolution really the central theory for all of biology?

From: Terry M. Gray <grayt@lamar.colostate.edu>
Date: Tue Sep 20 2005 - 02:38:50 EDT

Cornelius,

No one is ignoring evidence. I really wish you'd get off that song.
You just don't like the explanation. As I've said repeatedly biology
is complicated and there are mechanisms to accomplish all the
exceptional stuff you talk about.

I'll join David in underscore biological (form and function),
chemical, and physical constraint. Perhaps there are only a few
solutions to some problems. BTW, in the biochemistry world trypsin-
like serine proteases and subtilisn-like serine proteases constitute
an example of convergence, at least of catalytic mechanism. The
active site arrangement is one of just a few ways to skin the
protease cat chemically. That is likely to be a powerful drive to
convergence. What other mechanisms for convergence are there?
Mutational hotspots? Lateral gene transfer? Retroviruses and mobile
genetic elements? All of those things are EASILY part of an
evolutionary model. Messy, perhaps. Like biology. This ain't physics,
you know. But all consistent with known biological mechanisms.

If we "assume" that evolution is true, it's because there is
significant warrant for doing so. One or even several exception or
problem or anomaly doesn't break a well established there. My sense
is that many puzzles are being solved. I'm still not clear on what
you are saying about vitamin C pseudo-genes. Are you suggesting that
it's just as plausible to suggest that the mutation that existing in
many (if not all) primates arose independently in each case due to
some mutational hotspot? OK, maybe so. But does that negate all the
other homology (molecular and morphological)? I don't think so.

I'd be interested in your list of massive and detailed convergences
in biology. Not sure we'll come up with answers for them all, but it
might be interested to see in detail what you're talking about and
how it stacks up against what many of consider to be the massive
evidence for evolution.

TG

On Sep 19, 2005, at 6:48 PM, Cornelius Hunter wrote:

> Terry, Douglas and David:
>
>
> Terry and Douglas :
>
> Evolution can explain:
>
> 1. Dramatic differences in otherwise highly similar species.
> 2. Dramatic similarities in otherwise distant species.
>
> In this "homology vs analogy" space, it is not clear what real
> limits there are to evolutionary prediction. In any case, the
> limits certainly cannot be drawn very tightly. This means that
> evolution can explain a wide range of outcomes. This means that any
> one particular outcome does not confer much increased confidence in
> the validity of the hypothesis. Terry, you write:
>
> "It's not special pleading if there are real examples of
> convergence, i.e. it's part of what we expect in the complex
> biological world and there are ways to distinguish between them."
>
> Real examples of convergence are precisely why evidential claims,
> such as the vitamin C pseudogene, constitute special pleading. The
> only examples of "real" convergence we know are these mutational
> hotspots where identical mutations are observed to occur
> independently. Hence claiming that the vitamin C pseudogene
> mutations are evidence for common descent *is* special pleading.
>
> The massive and detailed convergence in biology was a surprise for,
> not a prediction of, evolution. Nor do there exist unambiguous ways
> to distinguish homologies from analogies. Ultimately it is both
> subjective and circular. Subjective because the evolutionist must
> draw from a variety of criteria to decide how make his judgement.
> Circular because he must assume evolution occurred. Without first
> assuming evolution, then the evolutionist would have to reckon with
> all the negative evidence which is being ignored.
>
>
>
> David:
>
>
>
>>> This is special pleading when the similar designs are claimed as
>>>
>>>
>> evidence for evolution (as in #1), but not when similar designs are
>> used as mere explanations (eg, "ah, these designs are similar because
>> they arose from a common ancestor").<
>>
>> Not real sure what you mean.
>>
>>
>
> Kuhn described those working within a scientific paradigm as doing
> "normal" science. In normal science, the paradigm is assumed to be
> true, for purposes of convenience, progress, and so forth. Normal
> science is not concerned with proving the paradigm to be true,
> accumulating evidence and presenting it to outsiders, etc. They've
> assumed it to be true and are working away.
>
> In fact, it is tricky for normal science activities to cast their
> findings as evidence because they have presupposed the paradigm to
> be true. The evolution paradigm is so thoroughly baked in that it
> is difficult for evolutionists to step outside the paradigm and
> make the case to an outsider. It is difficult for them to seriously
> engage in the hypothesis: "could evolution be false, and how do I
> counter this idea to someone who is not committed to the paradigm?"
>
> Instead of seriously engaging, what evolutionsts often respond with
> speculative explanations, such as, "these designs are similar
> because they arose from a common ancestor". Yes, we all know this
> is the explanation -- evolution can explain such similarities. And
> when they appear in distant species we are told this is due to
> convergence. And when dramatic differences are found in otherwise
> similar species, we're told of some freak contingent explanation.
> But why is any of this *evidence* as opposed to mere hand-waving
> explanation which amounts to little more than a tautology.
>
> To make the case for evolution we need two things. First, we need
> good strong evidences and arguments that do not fall apart under
> inspection. And second, we need good defenses against the problems
> that exist. Right now we have neither one of these.
>
> --Cornelius
>
>
> =================
> Cornelius,
>
> It's not special pleading if there are real examples of
> convergence, i.e. it's part of what we expect in the complex
> biological world and there are ways to distinguish between them.
> The main way to distinguish them is whether or not there are other
> arguments/evidences for common ancestry. If not, convergence; if
> so, most likely, common ancestry. I, for one, wouldn't rule out
> convergence among related lineages, but then it becomes very
> difficult to tell without nearly complete molecular pedigree data.
>
> TG
>
>
>
>
>
>> Yes, evolution has it both ways because the pattern of data (to
>> borrow a
>> phrase from ID) has specified complexity that exactly corresponds to
>> understood evolutionary mechanisms (i.e., that mutation is
>> probablistic in
>> being able to produce point mutations AND the environment exerts
>> the same
>> general physical "challenges" to form and function).
>>
>> This variety of possibilities is exactly what evolution would
>> predict, but
>> it such a mixture of true homologies and convergences is unlike any
>> "intelligent design" that our human minds would likely envision.
>>
>> Douglas
>>
>>
>
> ====================
>
> David:
>
> Again, we're talking about evidence, not explanation. I did not
> present convergence as a challenge to evolutionary explanations. I
> presented it as a challenge to evolutionary evidence. Here is the
> general form of the evolutionary claim:
>
> 1. Evolution claims similar designs as evidence for evolution.
> 2. Similar designs that cannot be ascribed to common descent are
> chalked up as examples of convergence.
>
> So evolution is having it both ways. This is special pleading when
> the similar designs are claimed as evidence for evolution (as in
> #1), but not when similar designs are used as mere explanations
> (eg, "ah, these designs are similar because they arose from a
> common ancestor").
>
>
> --Cornelius
>
>

________________
Terry M. Gray, Ph.D.
Computer Support Scientist
Chemistry Department
Colorado State University
Fort Collins, CO 80523
(o) 970-491-7003 (f) 970-491-1801
Received on Tue Sep 20 02:41:53 2005

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