Re: What goes around comes around

From: Preston Garrison <>
Date: Wed Oct 12 2005 - 02:13:03 EDT

Cornelius and all,

I have been away from the computer for several days, so hi again.

"Common mechanism" is not a hypothesis that is specific enough to be
evaluated. I pointed out the paper to show that there is more than a
handful of evidence that has to be accounted for. (There are
somewhere over a million sites in the chimp/human comparison. The
chimp genome hasn't been fully evaluated so the total is uncertain.)
Common descent provides a very simple explanation for the
overwhelming majority of millions of individual events. For the
"common mechanism" hypothesis (independent occurrence in separate
organisms) to be taken seriously outside of anti-evolution circles,
you would have to make a detailed proposal for how each subsubtype of
L1 and Alu (and other classes of transposable elements) could have a
complex but well defined spectrum of target sites which is different
from all the others. You also have to show that most of these
elements achieved something near saturation of all the sites in the
genomes that each was compatible with. This is because the possible
sites would be randomly sampled separately in each species, and the
observed fraction of total events that is common to the two species
is high. This could be made somewhat more plausible if there was
positive selection for all the insertions. There are a few insertions
of HERVs that seem to have a function, and there is some evidence
that L1 elements participate in X chromosome inactivation for dosage
compensation in females. Seems pretty hard to think of a function
that would select individually for all those L1s and Alus, though.
L1s don't code for anything but the enzymes necessary for
transposition and Alus don't code for anything at all. And of course
to be taken seriously, all this would have to show that your
hypothesis made some predictions that were confirmed.

There are conceivable ways to test the hypothesis. You might get some
evidence by studying the genome sequences carefully. (The details are
left to the student.) :) You can make the master elements transpose
in cultured cells by forcing expression of the element. There has
been some work to do this and look at the target sites to see if
there is any sequence specificity, but I haven't looked at that work
in any detail. You could pursue this. Maybe the people funding the
Discovery Institute would fund you. :) Maybe you could get a
post-doc in a transposon lab that studies this and not tell them what
your motivation is. :) Are you confident enough of your hypothesis
to spend your time and other peoples' money?

Received on Wed Oct 12 02:14:46 2005

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