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Maximum Likelihood Analysis Question

Ron Kagan rkagan at ewald.mbi.ucla.edu
Thu Aug 22 15:09:39 EST 1996

In article <4vbpoi$8s9 at nntp3.u.washington.edu> Wnn System Account,
wnn at evolution.genetics.washington.edu writes:
>>Since when is the molecular clock a reasonable null hypothesis?!!!
>>Molecular phylogenetics in the late 20th century... limited by the 
>>arbitrariness of Joe Felsenstein's imagination and Linus Pauling's 
>>[no offense Joe... ].
>(1) Sure I take offense!   But come to think of it you have put me in
>    awesomely good company there!   So, thanks.
>(2) The molecular clock is a good, useful, fruitful approximation.
>    It is more true the more closely related are the species.  If you're
>    comparing archaebacteria to eubacteria to eukaryotes, it is wierd to
>    assume it.  If you're doing phylogenies within a genus of
>    it is a natural thing to test.   Does anyone imagine that they would
>    have grossly-different rates of molecular evolution?  It would be
>    strange if they did.  Morphology is, of course, a different matter.
>(3) The molecular clock has been denounced so loudly as nonexistent by
>    phylogenetic systematists (and non-parsimony methods frequently, and
>    wildly inaccurately, asserted to inherently assume it) that it would
>    helpful to science to have it defended.  It is not true.  But it is
>    often pretty nearly true for closely related beasts.  It is therefore
>    often worth testing.
>Molecular phylogenetics in the early 21st century ... limited by
>myths of the total invalidity of the clock?
>Joe Felsenstein         joe at genetics.washington.edu     (IP No.
> Dept. of Genetics, Univ. of Washington, Box 357360, Seattle, WA
98195-7360 USA

It seems that I have stepped in the middle of quite a bit of controversy
over the molecular clock.  

In the Jan. 26, 1996 issue of _Science_ 271:470-477, R.F. Doolittle et
al. published a research article titled _Determining Divergence Times of
the Major Kingdoms of Living Organisms with a Protein Clock_.  In this
paper, Doolittle and coworkers used sequence data for 57 different groups
of proteins and reasonably well-fixed divergence times to calibrate a
molecular clock and establish a 2,000 Myr procaryote-eucaryote divergence

Would anybody here care to comment on the validity/invalidity of
Doolittle's results based on the molecular clock?

"If you love wealth better than liberty, the tranquility of servitude
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that ye were our countrymen." 

                        - Samuel Adams, 1776
Ron Kagan, Ph.D.
Dept. of Chemistry and Biochemistry, UCLA
rkagan at ewald.mbi.ucla.edu

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