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

From: Terry M. Gray <grayt@lamar.colostate.edu>
Date: Sat Sep 17 2005 - 23:05:14 EDT

Cornelius,

Did you hear me? There's nothing special about the vitamin C pseudo-
gene. The argument from homology is compelling in its own right using
the reasoning I explained. The vitamin C story is just a permutation
of the general homology argument. Evolution is well-established
before anything about vitamin C synthesis genes was known. And, yes,
some vitamin C synthesis gene mutation happened independently in both
the primate line and in the guinea pigs (I don't know if it's the
same mutation in guinea pigs as it is in primates). No one who
recognizes that identical mutations can occur independently by some
mechanism would argue that the presence of the vitamin C pseudo-gene
in all primates is an example. Common ancestry based on a host of
other evidences is a much simpler explanation. I think it's special
pleading to suggest that it happened independently in every primate
species when all other evidence suggests that primates are all related.

And, as I said, I'm not afraid of "negative" data nor is an
evolutionist I've met. We are puzzled over it and work to sort out an
explanation--basic science in my opinion. I've just never seen enough
negative data to warrant throwing out all the positive data and
overturning the general theory. There are plausible explanations for
much of the "negative" data. Perhaps mutational hotspots are the
explanation for identical mutations in non-related lineages.

I'm sure you'll accuse me of switching the focus here but let me
introduce this less scientific aspect of the discussion. I'm not
afraid to continue the debate about whether arguments for evolution
are compelling, but I am also not afraid to address the Biblical/
theological/philosophical issues. Let me ask you. Is your opposition
to evolution simply due to your belief that the arguments for it are
not compelling or do you have Biblical/theological/philosophical
reasons that primarily inform your opposition? I can respect your
opposition either way, but I have to say, that if you think the
scientific arguments for evolution are weak then you stand in a
significant minority among life scientists. Minorities are sometimes
right in the long run. However, the objections you give are exactly
the objects that Michael Denton, Phil Johnson, Mike Behe, and young-
earth creationists have given for the past 50 years. They are old and
worn. And, few professionals are convinced. Most are easily refuted
by professional biologists. The laity who have been brainwashed into
thinking that it's either evolution OR creation find the arguments
persuasive because it supports their fundamental belief in God and
creationism (belief I share, by the way). School boards, popular
media, conservative Christian groups and churches (and, yes, I am
even in one of those conservative churches), even the President of
the United States (and, yes, I am a general supporter of George W.
Bush), are convinced. So there seems to be a huge resurgence of anti-
evolutionary thought. And, yes, there is enormous political clout
with all of that. Fortunately, truth doesn't depend on politics
(think of the abortion issue or 18th and 19th century slavery), but
politics can set the wide-spread acceptance of truth back.
Personally, i think that Johnson, Denton, Behe, you, and other anti-
evolutionist writers have set us back in the discussion in the
evangelical community 50 or 100 years.

I'm very confident that whole genome analysis of many different
species are going to radically confirm common ancestry and help us
sort out some of the anomalies. Time will tell, but, as I read the
literature, so far so good.

TG

On Sep 17, 2005, at 8:22 PM, Cornelius Hunter wrote:

> Terry:
>
>
>> If that's not an explanation or reasoning, I don't know what is.
>>
>
> The exchange we just had followed a pattern that is typical. It
> seems quite often that when an evolutionist claims the evidence
> overwhelmingly supports evolution; that evolution is a fact,
> etc.,etc., and I ask for the details, what the evolutionist
> responds with is merely the textbook evolutionary *explanation*,
> and omitting all the negative evidence. You claimed that the
> vitamin C pseudogene is compelling evidence, and then wound up with
> the conclusion that
>
>
>> Evolution provides an apt explanation.
>>
>
> Yes, no doubt evolution provides an explanation, but that doesn't
> make the pseudogene compelling evidence. I'll explain for a third
> time now why this evidence does not seem compelling, and in fact
> why such a claim seems to be a logical fallacy (ie, special
> pleading). The reason is this: the independent occurrence of
> identical mutations is well known in biology, both experimentally
> and inferred from genome data. That is, identical mutations are
> observed and inferred in different species where common ancestry
> cannot be the cause. The mutations occurred independently yet are
> identical. When we see these data, no one, not even evolutionists,
> attempts to ascribe them to common ancestry. So, the claim that the
> identical mutations in the vitamin C pseudogene constitute
> compelling evidence for evolution ignores the fact that a non
> evolutionary explanation not only exists, but is routinely used
> (when the common ancestry hypothesis is otherwise ruled out). Thus,
> this claim that the vitamin C pseudogene is compelling evidence for
> evolution seems to me to be a logical fallacy. If I'm wrong about
> this I'd like to know why.
>
> --Cornelius
>
>
>
>
>
>
>
>
>
>> 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
>>
>>
>
>

________________
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 23:07:34 2005

This archive was generated by hypermail 2.1.8 : Sat Sep 17 2005 - 23:07:34 EDT