Re: Mitochondrial Eve
Fri, 21 May 1999 15:26:21 EDT

Here are Steve Clark's additional comments, which I have have just discovered
thanks to Steve, and my responses.

In a message dated 5/19/99 5:25:43 PM Mountain Daylight Time, writes:

> >This is a hair-splitting rebutal. Of course if genes change then so can
> >their mutation rates, but if they change they are technically no longer
> >same genes they were before they changed. After all, different genes
> >different rates of mutation. What Gordon Simons is talking about are the
> >rates of mutation of STABLE genes; ie, genes that do not change. Any
> >that does not change has a constant rate of mutation; if it changes then
> >its
> >rate of mutation may also change, but genes that do not change do not
> >changing rates of mutation.
> This is rather circular.

Then explain how it is circular to say that the mutation rate of a gene does
not change unless the gene itself changes? Is it also circular to say that
the decay rate of an isotope does not change unless the isotope itself
changes? It is certainly true that if a gene changes it's mutation rate may
not change, but I'm not arguing that. What I am arguing is that if the
mutation rate does change it is because the gene itself changed in some
fashion (eg, mutation or transposition); if instead the gene does not change,
the mutation rate will not change on its own. I don't see anything circular
about that.

> >Excellent. Then you have learned something new. Alleles are genes that
> >produce the same (or essentially the same) protein product that differ
> >by slight mutations yet can be differentiated and separated by Mendelian
> >genetics. The fact that they are very similar is irrelevant; they act
> >separate genes and fundamentally they are different genes, hence each can
> >have its own rate of mutation.
> This is not necessarily true. Alleles of a gene do not act like separate
> genes and are not inherited like separate genes.

According to basic Mendelian genetics they are; how is basic Mendelian
genetics wrong?

> They are inherited like alleles of the same gene.

Which according to basic Mendelian genetics is the same thing as saying that
they are inherited as separate independent inherited factors that just happen
to determine different forms of the same trait (or code for different
versions of the same polypeptide). In this phrasing gene is best defined as
the DNA nucleotide sequence found at a particular locus. One chromosome may
have one sequence while the second has a different sequence, but since the
sequences are mostly the same and occur at the same locus they can in a sense
be called the same gene. However, they are also different alleles because
they have different sequences. And they are separate genes because they sit
on separate chromosomes. Since each chromosome is inherited as an
independent unit, each allele is also inherited as an independent factor. As
such, to say "they are inherited like alleles of the same gene" is from the
basic Mendelian point of view to say that they are inherited as independent
factors that determine different forms of the same trait.

> Different alleles of a gene may or may not have
> different rates of mutation. This is not a given.

Already dealt with in my original reply. In a nutshell, I never said it was
a given that different alleles would have different rates of mutation. In
fact, it is more likely that they would have similar rates of mutation but
different rates of substitution. However, it should be no surprise if they
do have different rates, since they are different genes.

> Finally, microsatellite
> alleles are not genes. They do not encode a protein product.

Also dealt with in my original response. I screwed up and I freely admit it.
However, this really has no bearing on my debate with either Gordon Simons
or Marcio Pie.

Kevin L. O'Brien