Hello Tim,
thank you for your detailed response! You'll find my remarks and further
questions between what you wrote, below:
Tim Ikeda wrote:
>
> Hello Peter,
> You wrote:
> >Is there any _direct_ evidence for common ancestry between humans
> >and apes?
(snip)
> >Of course, there is a lot of evidence for this, particularly in the
> >field of DNA sequences.
>
> As well as the fossil record which provides information about when and
> where the lines could have diverged. That information can be used to
> calibrate and test the neutral mutation assumptions discussed
> below.
>
> > For various reasons, I am convinced humans
> >and apes are biologically related by common ancestry, but I am not
> >aware of any _direct_ evidence for this.
> >
> >Although the similarity between corresponding DNA sequences of, say,
> >human and chimpanzee may be statistically highly significant, common
> >natural selection may possibly account for this (parallel or convergent
> >evolution). Therefore, the significance of the evidence for common
> >ancestry is directly related to the _lack_ of functionality of the
> >sequences under consideration.
>
> I'll focus on one case.
> The often degenerate, third base of codons in sequences encoding proteins
> *may* have a selective effect in some cases. However, I think it would be
> exceptionally unlikely that *all* (or even most) such positions were
> subject to the level of selective pressure necessary to maintain such
> a degree of similarity or drive such a level of convergence. I believe
> that neutral theory provides a null hypothesis for sites thought to
> have been subject to selection. Additionally, we know from experiments
> in the lab and from sequences obtained from species with similar
> habitats and morphologies that sequence _convergence_ down to the third
> base in a codon is the exception, rather than the rule.
I agree with all this. But do you know of an example of a human-chimp
comparison where this question has been tested? (I would appreciate the
journal reference).
> On the other
> hand, sequences linked by presumed common descent tend to exhibit greater
> similarity at the third base.
Do you mean greater similarity than random? - or greater than expected
for neutral drift? The latter case would be very interesting! (If so, do
you have a conceivable explanation - and can you give me the reference
for this finding?)
> >Now, a pseudogene or other unused sequence which has evolved for the
> >last 6 million or more years in the ancestors of humans and chimps in an
> >exactly neutral way is, presumably, under no selective pressure. But is
> >it possible to demonstrate that such a sequence has not been used at any
> >time in either line of descent for any function, coded or non-coded?
>
> That goal is impossible to achieve even in studies of organisms of today.
> As you know, we cannot subject an organism to all possible environments
> and conclusively demonstrate that a change in a single base has absolutely
> no effect on an organism's fitness. For example, in wild-type
> S. typhimurium there had once been no documented examples of a growth
> variation in glutamate dehydrogenase knockout mutants. I found one
> growth condition unlikely to be encountered in the wild (alanine +
> ammonium) where such a phenotype could be found. That was a single
> gene knocked out with a few mutations. The amount of sequence divergence
> within humans is on the order of about 0.2% (?If I recall correctly?).
> We cannot evaluate the individual impact of those millions of base pairs
> let alone the effects of their interactions.
You are right, my request for demonstration of (absolute) non-use was
too demanding. But do you know of any work where pseudogenes or other
_usually_ non-functional sequences were compared between human and
chimp? Notice that, at this time, I am specifically concentrating on the
comparison between these two species, and on cases where the question of
selective pressures was investigated.
(snip)
> >Presumably, any single unused sequence will be too short to give a
> >sufficient signal-to-noise ratio to provide a definitive answer.
> >Therefore, large sets of such sequences would have to be tested
> >together.
> >
> >Have any such "phylogeny-indicator" sequence sets been documented?
>
> By the criteria you have chosen, no "phylogeny-indicator" sequence
> sets could be built. However, if we consider the rate at which
> mutations can be fixed by selection, the estimated mutation rates,
> and the time since the proposed divergence of human and ape lines,
> I think a case can be made to show that humans and apes exhibit
> far greater sequence divergence than could be attributed to selection
> alone.
Are you talking about selection for functions common to chimps and
humans, or about chimp- and human-specific ones? In the former case, one
would expect smaller than neutral divergence rates, in the latter case,
perhaps greater than neutral ones. In any case, selection effects would
be difficult to disentagle from neutral drift. Do you know of any
human-chimp comparisons of neutrally evolving sequence sets?
> >(By the way, the same argument applied here to similar sequences under
> >common selection is equally applicable to similar cladistic trees of
> >molecules which are interdependent in each organism. In this case,
> >independence would have to be demonstrated.)
>
> When I think about it, the same argument could be used to suggest that
> there is no direct evidence that the people who claim to be my mother
> and father really are my parents (aliens could have implanted an
> embryo in my mother instead) or that humans share a common origin.
> Perhaps the native people of Australia were "planted" there
> separately. Just because Australians can mate with other humans
> does not mean that they could not be products of convergence or separate
> creations. For the former case, convergence, there is a finite if
> astronomically unlikely possibility of occurring. I do not consider the
> "ultra-selectionist" arguments for convergent similarities to be terribly
> convincing in the case of human/ape sequence comparisons (for other
> individual cases perhaps, but not at the level of entire genomes or
> chromosomes). For the latter, alien seeding experiments and the like,
> there is simply no way of assessing relative probabilities. Given that
> there is no auxiliary evidence of an "intrusive intelligence" - eg.
> landing field burn marks, or artifacts like titanium tablets dating
> from that time, & etc. - at work on Earth during the period I will
> opt for an economy of explanations and ignore this possibility
> for now.
Now, excuse me, but this seems to me to be game-playing! You know that I
am neither trying to disprove evolution nor requesting absolute proofs
of given cases of common ancestry. No, I'm serious. If we want to
convince our Christian friends that humans were not only created in
God's image on the spiritual level, but also have a common ancestry with
apes on the biological level, we need very solid scientific evidence,
not just-so stories, jokes, and generalities.
> On the subjects of molecular evolution and sequence analyses, I've
> found these newsgroups to be exceptionally informative (perhaps not
> as good as chatting in the office of someone who does this work, but
> for the internet, these are pretty good sources):
>
> bionet.molbio.evolution
> bionet.molbio.info-theory
> (see also: sci.bio.evolution and sci.bio.systematics)
>
> http://groups.google.com/groups?hl=en&group=bionet.molbio.evolution
> From the bionet.molbio.evolution charter:
> "Bionet.molbio.evolution is a forum for scientific discussions and a
> source of information for the community of scientists interested in
> the study of the processes of how DNA, RNA, proteins and organisms
> have evolved at a molecular level. [...]"
>
> Those groups are visited be people who could better address your
> question. In fact, I suspect a search of past threads at www.deja.com
> might find the question already answered.
>
> Regards,
> Tim Ikeda (tikeda@sprintmail.com)
Thank you for these indications!
Regards,
Peter
-- Dr. Peter Ruest, CH-3148 Lanzenhaeusern, Switzerland <pruest@dplanet.ch> - Biochemistry - Creation and evolution "..the work which God created to evolve it" (Genesis 2:3)
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