Re: Mitochondrial Eve
Wed, 19 May 1999 21:54:59 EDT

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

Speaking of handling people in a rough and condescending manner....

> I've resisted the temptation to do battle with Kevin on this line of
> thought, but enough is enough. His bashing of others over trivial and
> sometimes erroneous points (his error) has gone too far.

It is you who are arguing trivialities. You do not demonstrate that I am in
error in my basic position, that it has been experimentally established that
the rate of mutation for any one gene is largely constant and that any
observed differences in the rates of mutation of different genes is to
expected, which is the crux of my dispute with Gordon. All you have
demonstrated is that I did not know what microsatellites were. And you
yourself demonstrate that they are no threat to the established fact of the
constancy of rates of mutation. Is your dislike for me so big that you would
make a mountain out of a molehill in an attempt to discredit me rather than
discuss the real issue?

And if you define "bashing" as pointing out other people's errors and
misconceptions, what are you doing to me if it is not the same? Especially
since you are deliberately trying to be offensive, whereas I was merely being
bluntly honest.

> First of all, different genes MAY have different mutation rates but this is
> not necessarily true.

I never said it was necessarily true; instead of jumping to erroneous
conclusions, why not ask what I meant? Or is your own arrogance so great
that you cannot make yourself do that?

> Kevin earlier criticized a list of papers Gordon listed suggesting that
> they may be relevant to the discussion. However, Kevin's reply to each
> title was that each paper considered "different genes" and hence were
> uninformative because, as Kevin claims, different genes have different
> mutation rates. This is NOT a given.

Of course it isn't a given. However, since the papers were obviously
investigating different genes it is therefore no surprise that they were
found to have different mutation rates. See _Fundamentals of Molecular
Evolution_ by Wen-Hsiung Li and Dan Graur (Sinauer Associates, 1991) for more
details. What you are ignoring is that Gordon Simons has implied that the
constancy of the rate of mutation means that all mutation rates for any gene
must be the same, so that if you can find even one gene that has a mutation
rate different from that of another gene you have disproved the claim that
the rate of mutation is constant. Why did you not critique that? All I ever
did was point out that different genes can (not must) have different mutation
rates, but that for each gene its own mutation rate would be constant.

> Then he criticized Gordon for just
> basing his interest on the titles of the papers rather than reading them.
> Isn't it interesting then that Kevin only critiqued the papers based on
> their titles and not content?

Since Gordon used the titles to imply that those references critiqued the
established fact of the constancy of rates of mutation, it was only
appropriate to demonstrate how the titles in fact show that the papers were
NOT critiques of the constancy of rates of mutation, but rather were
critiques of the constancy of rates of molecular evolution. If as you imply
these papers in fact do support Gordon, why are you not quoting from them to
prove me wrong? Is it because you are not familiar with their contents
either? Or is it because you are and you know that my analysis based on the
titles is correct?

> Kevin's claim that different alleles of microsatellite loci are different
> genes is just crap.

Since the definition of allele is "an alternative form of a gene at a locus"
(Li and Graur, _Fundamentals of Molecular Evolution_ 1991, pg. 233) I would
say that it was in fact a reasonable interpretation considering my ignorance
(see below). Or are you saying that Li and Graur are spouting crap as well?

> Microsatellites are highly repetitive sequences of
> dinucleotide or trinucleotide repeats and different alleles simply differ
> in the number of repeats of the repetitive sequence. Microsatellites are
> not genes.

Then the fact that their "alleles" have different rates of mutation is not a
refutation of the established fact that the mutation rates of true genes are
constant. Of course, the obvious question is, are the mutation rates of
these microsatellite "alleles" changing constantly or do they change only
when the "alleles" mutate? If the latter, then what I said about alleles
having different mutational rates because they are different from their
parent gene but that their mutational rates are still constant as long as
they do not undergo any further change is still correct.

> Nevertheless they are heritable and show allelic variation.
> Apparently Kevin has a serious problem with the definition of gene.

No problem at all, which is why the reference to alleles in the title threw
me. I freely admit that I was not familiar with the term microsatellite
(sometimes called minisatellite), but I have read up on them since. Had I
known what they really were when I wrote my reply I would have pointed out
that they still have nothing to do with with whether the mutation rates of
genes are constant, for the reasons explained above. Funny how my worst
error still refutes Gordon's claims.

Kevin L. O'Brien