Re: [asa] Two questions...Ayala's article

> I must also classify myself as "not an expert" in this field. However, I
> find it quite interesting to look at how often the words "presume" and
> "presumption" are used in the Ayala article. If you look at this article
> specifically and the field as a whole, there is significant controversy over
> the various models and how to interpret the results…more so than I am
> comfortable with. This is reflected in the comment in reply to the Ayala
> article, as well as several other articles (see below).

I have heard (within a conventional biological context) the claim that
there seemed to be multiple population genetics model to match any
situation.

> Ayala's point is that, for a given chunk of DNA, including mtDNA chunks, you
> may be able to trace that chunk back to a common ancestor. However, the next
> chunk of DNA will be from a *different* ancestor, not the same one, implying
> not one, but a population of "Eves". I am NOT familiar enough to state for
> certainty, but I thought that the mtDNA was looked at more as a whole than
> other DNA? It's size is about 15-17 kbp, and codes for 37 genes.

mtDNA is thought in most animals to undergo recombination only rarely,
so it is typically thought to be a single "chunk" (I've had reviewers
make that complaint for a paper using only mitochondrial genes, but
unfortunately we don't yet know any reliable rapidly evolving nuclear
sequences to look at in mollusks.) However, in ordinary chromosomal
DNA, mixing up of chunks happens all the time. If there is a
population bottleneck, then in fact several chunks probably come from
one individual, but still there's a mix. Of course, this doesn't rule
out a single pair in the much more distant past.

> When we get to the point of whether there was a n=2 vs an n=X, Ayala puts X
> at ~100,000. He describes how it would be impossible for all the alleles of
> the MHC to survive a population smaller than (I think) about 10,000 sexually
> active humans, which equates to a total population that is of course larger.
> The issue here of course is the MHC region. If one is going to look at
> comparative regions and molecular clocks, it seems to me that the MHC has
> got to be the *worst* possible choice to use. Within the field of
> immunology, this region of the genetic code is sometimes called the G.O.D.
> (interesting, yes?) region, for Generator (or Generation) Of Diversity.
> Mutation rates here can be quite rapid. See the Hogstrand or Carrington
> articles below.

Yes, the assumption that the MHC alleles survive rather than
convergently re-evolve is highly dubious. After all, when you're
trying to generate a random DNA sequence, you only have A, G, T, and C
to choose from. On average, there will be about 25% similarity
between genuinely random DNA sequences. The MHC alleles must be
functional, so there are some constraints makign them less than fully
random. It has such high mutation rates that it should be possible to
look at some well-documented modern genealogies and check out the
patterns. I don't know how well one can calculate a probable
bottleneck diversity given the extreme overprinting of positive
selection for high variation.

Also, any one individual has multiple MHC alleles.

A somewhat analogous situation arose in bacterial studies. Bacteria
were placed with a sugar that they couldn't metabolize. Some evolved
the ability to use it. These bacteria were re-mutated to remove the
ability and put back in similar conditions. They evolved the ability
to use the sugar much faster than before. Lamarckian evolution?? No,
it turned out that the bacteria had evolved a high mutation rate,
thereby increasing their chances of having beneficial (or harmful or
neutral) mutations.

> The only way to have an n=2 bottleneck is if this couple were quite special in some way or ways, and that isn't "natural".<

Or to put them fairly far back in time. Actually, this aspect in part
reflects population genetics, too. If you have a finite population
with multiple alleles of a particular gene and no further mutation,
after enough generations there will only be a single allele in the
population because individuals do not all have equal reproductive
success and because each allele in a parent has a probability, but not
a certainty, of getting into the next generation. In smaller
populations, it's quicker. Two chunks may have different ancestors,
but those two individuals have a common ancestor if you go back far
enough, etc.

Certainly trying to go back far enough to have a single pair
physically ancestral to all modern humans runs into difficulties with
the fact that Gen. 4 seems to depict late Neolithic technology-about
10,000 years ago or so. Not absolutely insurmountable, but difficult.

An analogy to the more spiritual interpretation of Adam and Eve's
parental status is the way that Jesus is the new Adam. He isn't
biologically ancestral to anyone, but spiritually what He did
transfers out to a large number of people.

-- 
Dr. David Campbell
425 Scientific Collections
University of Alabama
"I think of my happy condition, surrounded by acres of clams"
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