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

From: Cornelius Hunter <ghunter2099@sbcglobal.net>
Date: Tue Sep 20 2005 - 10:23:57 EDT

Terry and Pim:

Pim mentions that "trees inferred from for instance morphological data are
largely substantiated by the underlying genetic data." Again, one hardly
needs evolution here. This is common sense. I wouldn't expect the
arabidopsis blueprint not to correspond to its morphology. Of course there
is going to be some sort of correlation between genetic data and morphology.
On the other hand, there are many examples where the correlation breaks
down, and evolution has difficulty explaining these because the observed
genetic differences / similarities would not have arisen according to
gradual change occurring over time with common descent. So various epicycles
need to be invoked.

Pim also mentions that "As I understand it there are very few if any
examples of convergence at the sequence level." I guess he is not familiar
with the so-called UCE's (ultra conserved sequences) where vast stretches of
genetic sequences between distant species are identical, yet not
functionally constrained. This is something that should falsify evolution
(indeed, that is precisely what an evolutionist told me a few years ago
before these findings came out), but when these findings came out, of
course, the possibility that they could harm the theory was not so much as
whispered. Terry, this is yet another example of folks ignoring evidence
that you seem to be sure is not happening. Terry you write:

> 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.

Again, this is fine for normal science where it is assumed that novel
proteins somehow can evolve. But without first presupposing evolution, this
story is anything but easy. This is another example of ignoring negative
evidence. Everything we know points away from the idea of novel proteins
evolving. If one does not at least recognize and acknowledge a difficulty
here, then we're ignoring negative evidence.

> If we "assume" that evolution is true, it's because there is significant
> warrant for doing so.

Yes, evolution is supposed to be a fact. What we need are compelling
evidences though. How about this: start by supplying *one* compelling
evidence.

> 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?

I'm suggesting this is a more plausible explanation.

> OK, maybe so. But does that negate all the other homology (molecular and
> morphological)? I don't think so.

Of course not. You said it was compelling evidence and I was addressing that
point.

> I'd be interested in your list of massive and detailed convergences in
> biology.

The UCEs I mentioned above are good place to start. A general source is
Simon Conway Morris's *Life's Solutions.*

--Cornelius

> 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 10:28:00 2005

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