Re: DNA sequence space

From: Terry M. Gray <grayt@lamar.colostate.edu>
Date: Fri Sep 30 2005 - 01:13:16 EDT

On Sep 29, 2005, at 9:55 PM, Cornelius Hunter wrote:
>
> Terry:
>
>
>> Terry, you wrote:
>>
>>
>> --------------
>> If so, then what does such divine action look like empirically? In
>> the fossil record, in the genetic record, etc?
>> --------------
>>
>>
>> How about a code?
>>
>>
>> A bit cryptic there. Are you talking about the genetic code?
>>
>
> Yes, sorry.
>
>
>
>> So, are you saying that the genetic code is not evolvable?
>>
>
> That is what the empirical evidence is pointing to. Experiments to
> change it
> show it resists change. See, for example:
>
> Doring V, Marliere P., "Reassigning cysteine in the genetic code of
> Escherichia coli," Genetics. 1998 Oct;150(2):543-51.
>

This is not what I mean here. Everyone agrees that the genetic code
is resistant to change. Evolutionists (advocates of common ancestry)
see its resistance to change as a key argument for evolution--i.e.
amid other changes there's a commonality that's readily explained by
common ancestry.

What I mean is "Could the code have come into being by other than
"special" divine action?

>
>
>
>
> And that its existence
>
>> undermines all the other arguments for common ancestry
>>
>
> Not sure what you mean. What other arguments make evolution
> compelling?

I'm afraid we'll be going round and round on this one. The cytochrome
c sequence comparison alone is a compelling argument to me. Coupled
with general taxonomic arguments (nested hierarchies) and the
progression of the fossil record, it's virtually a slam dunk
confirmation. I know you disagree, but what more can I say. I find
the textbook arguments convincing--you don't.

>
>
>
> (that's what I mean
>
>> by evolution, in case it's not clear)? And is this "simply" a
>> negative argument? I can't explain the origin of the code so
>> therefore it's "special" divine action.
>>
>
> What's wrong with negative evidence?

Most of the time negative evidence simply means "I haven't been able
to come up with a good idea (yet)". In general, plausible
speculations without details and with some uinresolved issues are
much more satisfying (to me) than "I can't see how it can happen that
way."

>
>
> Or do you have a positive argument based on the existence of
>
>> the code?
>>
>
> One if by land, and two if by sea (hope that isn't too cryptic ...
> 8^).
> Point is we have examples that intelligent agents create codes.

That doesn't mean that all codes come about by intelligent agents,
right?

>
>
>
> We know somehow that codes come about only by intelligent agents.
>
>> Etc.
>>
>>
>> For what it's worth, since the genetic code is more or less
>> identical across all organism (see my discussion of exceptions in
>> the chapter in Perspectives on an Evolving Creation), this doesn't
>> seem to get you very far.
>>
>
> I don't see why.

Because evolution is vastly more than the origin of the genetic code.
I disagree with your statement below that if one accepts a
supernatural origin of the genetic code (not that I do), that one is
not an evolutionist.

>
>
> Suppose I'm
>
>> willing to say that God "specially created" the genetic code at
>> the outset of life. Don't forget, I fully believe that divine
>> action is always at work. (Although I have to say that I'm not
>> sure I can tell the difference between "ordinary" divine action
>> and "extraordinary" divine action, miracle, or whatever you want
>> to call it, when it comes to things like the origin of the genetic
>> code.)
>>
>
> Let me add another possibility:
>
> 1. Suppose I'm willing to say that God "specially created" the
> genetic code
> at the outset of life.
>
> 2. Suppose I'm willing to say that regardless of *how* God created the
> genetic code at the outset of life (eg, secondary or primary
> causes), the
> result (ie, the DNA code) can in principle be used to infer such. For
> instance, God could have used secondary causes, but the causes
> and / or
> initial conditions could perhaps be shown to be so finely tuned or
> otherwise
> suspicious that a design inference can be fairly made.

This is the heart of my question. I don't see how you make this
inference. Besides, I already know that God created the genetic code
at the outset of life (since God created everything). Your bottom
line argument, as I see it here, is that, I can't explain how the
code originated given what I know now, so I conclude that God did it
using extraordinary means. Can you tell me at what point do we "give
up" on "naturalistic" explanations? How do we decide not only that we
don't know, but that we will never know?

>
> Notice that #2 is not the front-loading hypothesis discussed by
> some TEs,
> because in this case the front-loading is inferred from the
> evidence. Also,
> the inference is not a fact. Just a reasonable, and perhaps best,
> inference.
>
> If a person is willing to say #1 or #2 then he is not a traditional
> evolutionist.

So what? That doesn't negate all the other reasons for finding common
ancestry compelling.

>
>
>
>>
>> What other sorts of special, "non-natural" divine action can you
>> point to?
>>
>
> Well I'm more interested in studying nature free of
> presuppositional shackles about natural history, and allowing for
> design ideas to be included in the study. For instance, one can do
> classification without requiring the relationships to fit an
> evolutionary tree.
>

Nothing really wrong with this, but I would argue that we're not
dealing with presuppositions here. We're dealing with a theoretical
framework that has significant empirical roots. It's not just that
evolution makes sense when you presuppose evolution. Evolution is a
reasonable conclusion based on the data at hand. It continues to be a
productive comprehensive framework in which to do lots of biology. As
I've said before, evolution gives a powerful explanation to
classification. Nothing else comes close. It's Ptolemy vs. Copernicus/
Kepler. One merely computes planetary motions, the other actually
explains them. Classification on its own is merely a brute force
"that's the way things are" or "that's the way God made them" (if
that's the way it is then I guess we'll deal with it), but, if
classification is in fact rooted in natural history, then it is a
unifying explanation that is "deeper" than the brute force
explanation. Many of us in the sciences, Christian and non-Christian
alike, find that desire to explain and find unifying explanation to
be powerful motivators. I will be the first to admit that such things
are "meta-science", but nonetheless they are driving factors.
Classification with evolution still prods us to ask why and we
hypothesize about the roles of "biological form" and the like (back
to the homology/analogy debate). The point is that we "want" to
explain the way things are because we believe that there are knowable
and discoverable explanations. Lots of philosophy of science in this
paragraph but that's part of my (and everyone's argument).

TG

>
>>
>>
>> TG
>>
>
>
>
> --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 Fri Sep 30 01:16:44 2005

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