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

From: Terry M. Gray <grayt@lamar.colostate.edu>
Date: Sat Sep 17 2005 - 19:24:06 EDT

Cornelius,

There is nothing special about the vitamin C gene homology. I chose
it as a specific example of something my readers may not be familiar
with but which they could make sense of. I find the homology argument
in general to be totally compelling. Especially, molecular
homologies. The reasoning is nearly so obvious to me at least that
I'm not sure how to go about explaining it. (I do try in a little
more detail in my Perspectives article.) But, here's a shot.

We know that organisms reproduce and pass on their genetic
information to their descendants. So descendants have nearly
identical genetic information as their ancestors. Sometimes there are
mutations that alter this genetic information. These are observable
even among human populations and can be traced in family lines, etc.
(Often, if we have enough data, we can even identify the individual
in which the mutation occurred.) In the course of many generations,
you can tell which individuals belong in which line based on which
cluster of mutations they have accumulated. (very similar to the way
we trace Biblical manuscripts to come up with the originals).
Brothers and sisters are more similar to each other than cousins.
Cousins more than second cousins, etc. (This is not only true of
genetic information, but also phenotypic (external) characteristics
as we all know from identifiable family resemblances.) This is
exactly the pattern we observe in the biological world and thus infer
that ancestor-descendent relationships are the cause, i.e. evolution.
If all organisms are related by an evolutionary relationship then we
expect this kind of unity/diversity relationship.

Pseudo-genes are icing on the cake because they are evidence of the
ancestor-descendent relationship even though the biological function
is turned off by some control region (or otherwise mutation). It
doesn't appear that pseudo-genes are functional (although we don't
know everything), so why (this is not a theological why!) are they
there. Evolution provides an apt explanation. The gene was inherited
from an ancestor but at some point along the family line the mutation
knocked out the function. Apparently, knocking out the function is
not deleterious and the organism can survive without that function
(in the case of vitamin C and other essential vitamin syntheses, by
getting the essential metabolite from the diet).

If that's not an explanation or reasoning, I don't know what is. It's
not a mere assertion. And, there is no underlying theology here (at
least none that's any different than what undergirds my general
confidence in scientific methodologies). Also, I find it compelling.
Compelling on its own to accept evolution. But there are other
evidences--the fossil record and biogeography, in particular. These
force of all of these taken together makes evolution to be a solidly
established theory.

No doubt, there's lots of interesting puzzles and we have observed
mechanisms, especially lateral gene transfer mechanisms such as viral
and plasmid transfers that complicate things. In comparing organisms
it appears that other lateral transfer events have occurred over the
course of life's history as well such as acquiring genomes
(endosymbiosis), fluid genomes at life's earliest history, etc.) I
am also an advocate of "biological form" type arguments that
emphasize that not all biological phenomena are directly directed by
genes. Lots of interesting discussion nowadays from systems
biologists and complexity theorists. This may explain mysteries that
seem incongruent with common ancestry in the area of the different
larval forms. Despite all this puzzles, I have seen nothing that
suggests that the big picture originally suggest by Darwin and other
early evolutionists (despite their appeal to bad theology) should be
overturned.

TG

On Sep 17, 2005, at 3:15 PM, Cornelius Hunter wrote:

> Terry and George:
>
> Terry:
>
> You say:
>
> "For what it's worth, and this may be a discussion stopper, I
> simply disagree with your argument that pseudo-genes and other
> molecular homologies and other homologies for that matter aren't
> compelling."
>
> But why? This is crucial. It would be very important if pseudo-
> genes provided compelling scientific evidence for evolution. But
> you do not explain why, you simply make the assertion Please don't
> take that as criticism, I realize you were simply pounding out an
> email. But evolutionists never explain why this evidence is
> compelling, in a scientific sense, whereas it is easy to find the
> theological argument made.
>
> I explained how this evidence is typically used with theological
> premises, and why without such premises the argument is a case of
> special pleading. You say this might be a discussion stopper. Well
> I'm afraid it will be if you don't give your reasoning. I cannot
> respond to bare assertions. For all the research I've done, I have
> been unable to discover why the vitamin C pseudogene is compelling
> scientific evidence. Indeed, it seems clear that it does not
> qualify as such. I've given the reason why this argument fails
> scientifically. Can you explain why I am wrong?
>
> You suggest this might be a case of different thresholds of what
> qualifies as compelling. I don't understand this. How could this be
> a case of different thresholds when no explanation for why this is
> compelling has been given, here or in the literature (that I can
> find). The only way I can try to cast this as scientific evidence
> for evolution is the following:
>
> 1. Evolution predicts more similarities between more closely
> related species.
> 2. The vitamin C pseudo gene contains some similarities between
> closely related species.
> 3. Therefore, this is a successful prediction.
>
> But even this fails. First, this is hardly compelling evidence for
> evolution. It places the evidence at the same level as any other
> similarity. It is the same as every homologous feature between the
> primates. There are millions of these (gall bladder, lower lip,
> hemoglobin, etc, etc). Why then is the vitamin C pseudogene used,
> if it has nothing to do with the theological "God wouldn't do it
> that way" argument?
>
> Furthermore, as I've pointed out, it is special pleading anyway.
> How can this be counted as scientific evidence, as minor as it is,
> when we find the same evidence in cases where common descent and
> evolution could *not* be the cause. In those cases, the
> evolutionist must ascribe the similarity to independent mutation
> events. But if that explanation works for amazingly repeated
> mutations, why can't it be used for the vitamin C repeats?
>
> So I don't see how this can be a case of different thresholds of
> what qualifies as compelling. I have yet to see the scientific case
> made at all.
>
> --Cornelius
>
>
>
> George:
>
> I don't understand why you think I am imposing evolutionary views
> on your position. I'm simply taking your statements at face value,
> which are:
>
> ------------------------
> It's true that God does not do all the things that take place
> directly - i.e., without creatures - but this doesn't mean that God
> is absent or distant from what takes places. "God concurs, he does
> nor precur" is a classic formula. Thus I don't see this at all as
> a "break in the link between God and creation" anymore than I would
> say that the link between a carpenter & a nail being put through a
> board is broken because the carpenter uses a hammer instead of
> pushing the nail though with his hand.
>
> and,
>
>
>> Ah, but then doesn't God's activity have to be deterministic?
>> No. If there is a basic indeterminancy at the quantum level which
>> is involved in changes in DNA & if there is some flexibility even
>> in larger scale processes because of sensitivity to initial
>> conditions, & if God limits divine activity to what can be
>> accomplished through natural processes, then God may leave some
>> element of chance in what happens in the world. If you want a very
>> crude analogy, the carpenter closes his eyes before putting the
>> nail in place.
>>
>
> and,
>
>
>> In any case I don't think it's necessary to equate the divine
>> governance with micro-management of all events. I think that God
>> intended for intelligent life to evolve so that the Incarnation
>> could take place but that needn't mean, e.g., that bipedalism -
>> which seems to have been a significant step in the development of
>> _our_ intelligence - was a requirement that God built in in the
>> beginning.
>>
> ------------------------
>
> What you are saying easily fits into my phrase "break in the link
> between God and creation." It sounds like you are pouring more
> meaning into my phrase than is there. Part of the problem may be
> that I am addressing evolutionary thinking, and you, I think, are
> not primarily focusing on evolution but rather developing a
> theology that happens to accommodate evolution nicely.
>
> It is interesting that biologists tend to use random mutations and
> physicists tend to use quantum indeterminacy, chaos theory, or some
> such. In any case, the effect is the same. You write:
>
>
>> I realize that this idea may be intolerable to those with some
>> views of divine sovereignty. It's legitimate to criticize what I
>> say from such a standpoint but don't try to force my views into
>> some Procrustean bed of "evolutionary thinking."
>>
>
> I certainly do not want to be forcing your views anywhere you don't
> want to go. I do not think, however, that the issue is over divine
> sovereignty. One need not hold to a high view of divine sovereignty
> to take exception to evolution's theological premises or the
> theology of the cross.
>
> --Cornelius
>
>
>
>
>
>>> George:
>>>
>>> Your carpenter analogy does not does not accurately describe the
>>> evolution (or your) position. Yes, the carpenter may use his hand
>>> or a hammer, but in both cases he drives the nail in where he
>>> want the nail to be. The design reflects his will. Evolutionary
>>> thinking is that what we observe in nature does not generally
>>> reflect divine will. So there must be a break in the link. This
>>> is where the distancing of God from nature comes in. It is fine
>>> for you to say you do not distance God from nature, but this is
>>> true only in certain regards. You do distance God from nature
>>> with regard to creative acts.
>>>
>>> You might try using the analogy of a sculptor rather than a
>>> carpenter. One can imagine describing God using evolution as the
>>> sculptor uses his chisel. In this case evolution, like the
>>> chisel, is merely a deterministic tool and there is no break in
>>> the link between creator and creation. The process is error-free,
>>> and both God and the sculptor achieve exactly their desired
>>> designs. The tool or mechanism adds nothing to the process. This
>>> is not evolutionary thinking.
>>>
>>
>> Cornelius -
>>
>> Again you are trying to tell me what I think by, inter alia,
>> assuming that because I accept evolution my ideas must be
>> conformed to what you think is "evolutionary thinking." &
>> although one could certainly use a sculptor instead of a carpenter
>> as an analogy for divine cooperation, the way you set out the
>> sculptor analogy suggests that you've missed my point. It is not
>> that the sculptor uses "evolution" as a tool but that he/she uses
>> all the detailed physical processes involved in genetic change,
>> animal behavior &c as tools at every step of the process. To say
>> that "evolution" is the tool suggests that God is only involved at
>> some very high level & is thus remote from the details, whereas my
>> point is that God is involved in the details.
>>
>> Ah, but then doesn't God's activity have to be deterministic?
>> No. If there is a basic indeterminancy at the quantum level which
>> is involved in changes in DNA & if there is some flexibility even
>> in larger scale processes because of sensitivity to initial
>> conditions, & if God limits divine activity to what can be
>> accomplished through natural processes, then God may leave some
>> element of chance in what happens in the world. If you want a very
>> crude analogy, the carpenter closes his eyes before putting the
>> nail in place.
>>
>> I realize that this idea may be intolerable to those with some
>> views of divine sovereignty. It's legitimate to criticize what I
>> say from such a standpoint but don't try to force my views into
>> some Procrustean bed of "evolutionary thinking."
>>
>> OTOH the fact that there is scientific indeterminancy means that
>> God has some freedom to act in the world without going beyond the
>> limits of the laws of physics.
>> This means that God may be able to give some direction to
>> evolution even though the process appears to scientific
>> observation to be "undirected." I have some hesitation about the
>> idea (suggested by Pollard & Russell) that God exerts such
>> direction by collapsing quantum wave packets in appropriate ways
>> but remain open to some version of that idea. (I comment on this
>> briefly on pp.82 & 119-120 of _The Cosmos in the Light of the
>> Cross_ .)
>>
>> In any case I don't think it's necessary to equate the divine
>> governance with micro-management of all events. I think that God
>> intended for intelligent life to evolve so that the Incarnation
>> could take place but that needn't mean, e.g., that bipedalism -
>> which seems to have been a significant step in the development of
>> _our_ intelligence - was a requirement that God built in in the
>> beginning. God's purpose for creation can really be seen only
>> escatologically - Eph.1:10.
>>
>>
>> Shalom
>> George
>> http://web.raex.com/~gmurphy/
>>
>>
>
>

________________
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 Sat Sep 17 19:28:42 2005

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