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

>
>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.

No, you also have small insertions, deletions, inversions, Alu
insertions, etc. It is easy to see these things in the alignments
between primates, because the genomes are so similar that alignment
is usually easy.

>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.

No more that 4 at any locus, although a locus might get duplicated in
various ways, which could effectively give you more 4 versions of the
same proteins after a while.

>
>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.

Just to clarify, they only evolved the new ability at a rate that
could be detected in a laboratory sized population because they had a
dormant gene that could be activated by a mutation or two.

Many experiments show that when you take a microbial clonal
population, divide it up and put them under all under the same new
culture conditions, they will optimize for the new conditions in a
variety of ways. There may be common mutations that occur in multiple
cultures because they can occur at high rates and are strongly
selected for under the new conditions, but there are almost always a
variety of mutations that contribute to the optimization and only
occur in one or a few of the cultures. It is naive to think that
there is only one general set of alleles possible at each locus in
the HMC, and that they would be regenerated faithfully over and over
again.

I have suggested ways to test what actually happened in the e-mail I
sent the other day.

>
>> 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.

Doesn't this ignore the possibility of selection at the population
level for maintaining many alleles at a given locus? Having many
alleles at a given locus of the MHC, which encodes proteins having to
do with immunity, means that when new pathogens or new variants of
existing pathogens arise, it is more likely that some portion of the
population will be able to respond effectively to the pathogen. If
new pathogens arise regularly, which they do, there is continuing
pressure to maintain many alleles at these loci. The idea that
multiple alleles must eventually be reduced to one or a few assumes
that there is no selective pressure for maintaining a large number of
alleles. It makes sense to me that, over the long haul, there is all
kinds of selective pressure for the maintenance of many alleles at
many loci of the MHC.

>
>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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Received on Wed Feb 25 15:41:21 2009