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molecular clock question

Tom Schneider toms at fcs260c2.ncifcrf.gov
Mon Sep 9 09:47:13 EST 1991

In article <9109052236.AA17124 at bambi.ccs.fau.edu> tomh at BAMBI.CCS.FAU.EDU (Tom Holroyd)
>Hi.  I'm doing a report on molecular clocks, and I thought I might find
>some folks to talk to on the mol-evol list.

>I've noticed that there is a lot of controversy over the "rate" of

I think you are right, these so called molecular clocks are only an
approximation.  Besides, what they measure is the changes which DON'T matter!
The changes in cytochrome C are equivalent to the rearrangements of water
molecules in a glass of water.  I wouldn't call that evolution, but in the
perverted way people think these days, it is.  (Those who want to defend this
idiocy, flame away!)  The really interesting evolution is harder to capture
(eg the creation of a whole new gene) so people tend to ignore it!

>Life exists on the side of a sandpile, if you know what that means.

Yes, interesting point.

>A side note: how likely are totally neutral mutations?

Taking the viewpoint of information theory, I have never understood this big
argument about neutral mutations.  I think this is because the arguments are
not too good (I mean, let's measure it in bits folks!!!).  It is quite clear
from information analysis of binding sites that some positions are more
important than others (See: JMB 188: 415, 1986, NAR 18:6097, 1990).  The answer
to your question is:  neutral mutations are 100% likely!  With respect to LexA
binding sites (for example) there are neutral mutations more than 20 bases away
from the center of the site.  By 'neutral' I mean that the information content
is measurably close to zero (within the noise of the measurement), and changes
there have no effect on that particular system.  I can't believe that every
base in the genome will be part of a functioning entity (binding site, gene,
etc).  So what's the big fight about??  We should dump this stupid term
'neutral' and get some numbers, measured in bits.  The complete answer to your
question would be a distribution of the information content of bases (running
from 0 to 2 bits of course!) versus their frequency in the genome.  We don't
know enough to do this for the whole genome yet, but we can do it for

Nice posting.

>Tom Holroyd
>Center for Complex Systems
>Florida Atlantic University
>tomh at bambi.ccs.fau.edu

  Tom Schneider
  National Cancer Institute
  Laboratory of Mathematical Biology
  Frederick, Maryland  21702-1201
  toms at ncifcrf.gov

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