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Archiver > GENEALOGY-DNA > 2006-11 > 1162591657


From: "John McEwan" <>
Subject: Re: [DNA] Molecular clocks: when times are a-changin'
Date: Sat, 4 Nov 2006 11:07:37 +1300
In-Reply-To: <REME20061103161425@alum.mit.edu>


John C said
.....
In fact, we *know*
the underlying mechanisms for the discrepancy between rate
calculations based on direct observation and those based on
millennium-scale population studies -- random extinction and
population expansion.
.....
This certainly has a major impact

also
.....
There is no way to invoke natural selection on
junk DNA in the first place and certainly no way to invoke selection
based on correlations between the vastly different time-scale
behaviors of STR's and coding mutations on the tiny handful of genes
on the Y chromosome.
.....

Sigh... we have been through this all before a number of times, junk DNA
(aka the assumption that non protein coding regions have no function and
therefore changes in it are selectively neutral) is a concept that is
now dated in light of emerging knowledge of mammalian genomes. In fact,
lets be honest, as a concept it is incorrect. I have also detailed a
number of times how genetic variation in an individuals capacity to
repair mutations produces correlated changes in both STR and SNP
mutation rates across the genome. Therefore "observed" father son rates
will be by definition be an overestimate of the observed change over a
longer time frame because the effect of purifying selection has not been
explicitly accounted for. Currently the magnitude of this effect is
difficult to estimate, but it should not be ignored.

John McEwan


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