Re: DNA sequence space

Terry, Ted (toward bottom):

Terry:

>>> 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?

This is a remarkable claim. The DNA code is resistant to change and this, we
are to believe, is a key argument *for* evolution. In fact, if the code is
resistant to change, then science is telling us it did not evolve, not that
it did evolve.

>> 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.

Well for starters you could try explaining *why* you find these arguments
convincing in the face of major problems. You did not reply to my
explanation why this is not compelling evidence a few days back when we
discussed this. Now you assert this claim again, and again with no
justification. Here, again, is why this claim is bad science:

###############################################

Here are 3 criteria for judging the quality of evidence:

----
A. The evidence should not include significant problems for the theory 
(obviously).
B. The evidence should be the fulfillment of a somewhat narrow prediction of 
the theory. That is, if the evidence as well as several other outcomes are 
all accommodated by the theory, then the evidence is not compelling.
C. The evidence severely damages all alternative theories (need to be 
careful not to misrepresent or ignore the alternative theories, of course).
----
The nested hierarchy data suggest or reveal:
1. The designs of the species seem to be clustered, and the clusters seem to 
cluster in larger groups, and so on, in what is called a nested hierarchical 
pattern.
2. There are a great many exceptions that violate the pattern, at all 
levels, such that, for example, a paper out of Doolittle's lab has called 
for a "relaxation of tree thinking."
3. There is massive convergence, meaning similar designs show up in distant 
clusters.
#3 fails on A. #2 fails on A and 1-3 all fail on B. Also, none succeed on C. 
So as with the fossil evidence, pseudogenes, small-scale adaptation, etc., 
this is not compelling evidence for evolution.
###############################################
> 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.
Evolution says naturalistic processes are sufficient to explain the origin 
of species.
>> 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."
See next ...
>>
>>> 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?
Right, see next ...
>> 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?
We don't. There is no point at which we "give up" on "naturalistic" 
explanations. See next ...
>>> 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.
Evolution does not give a powerful explanation for classification. Massive 
convergence, identical sequences, obvious differences in cousin species ...; 
these are all surprises to evolution.    Again, see next ...
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).
>
OK, here is the "see next." It is remarkable of these discussions parallel 
the 17th - 18th c. debate between the English empricists in the Royal 
Society and the dogmatic thinkers from the Aristotelian and Cartesian 
traditions.
Terry you asked for a positive argument in addition to the negative 
argument, vis a vis the DNA code. There is an obvious positive argument, 
which I provided. Are you now requiring that my positive argument to be 
conclusive -- to prove that *only* intelligent agents can make a code?
Evolutionists claim their idea is a fact, and when presented with counter 
evidence they convert it into a falsification test. We might have mountains 
of evidence against evolution, but unless one can absolutely prove evolution 
is impossible, we conclude nothing from it.
Here are the characteristics of the two modes of thinking :
RS/ID:
1. Against a priori's (metaphysical and metholodical)
2. Against making truth claims. "This is what we know right now ..."
3. Epistemology largely based in probabilities.
4. Humanity has an impaired intellect. Skeptical of extrapolating on a 
little bit of knowledge to grand truth claims; however, not a group of 
skeptics. Knowledge possible, but not easy.
5. Lack a tidy, well-defined philosophy of science, by choice.
Aristotelians/Cartesians/evolutionists/skeptics
1. Embrace a priori's (metaphysical and metholodical)
2. Routinely make truth claims. "A slam dunk confirmation ... evolution is a 
fact"
3. Epistemology largely based in a priori's.
4. Humanity easily knows truth. "Pseudogenes prove design is false..."
5. Have powerful, well-defined philosophies of science.
Terry and Ted:
Perhaps Ted will chime in here. The parallel is striking, and for those 
interested in delving into this I would recommend Chapter 2 ("Science and 
Religion in England in the Seventeenth Century") in R.M. Burns's *The Great 
Debate on Miracles: From Joseph Glanvill to David Hume,* 1981.
Terry, later you wrote:
"If "special creation" was indeed God's method of creation, He went to great 
efforts to make it look like evolution (common ancestry) occurred. "
So how do non homologous development pathways, UCEs, massive convergence, 
apparent bounds on and preprogramming of adaptation, myriad high 
complexities, etc., make life appear to have been created via evolution?
--Cornelius