[Taxacom] orangutan outrage

Richard Pyle deepreef at bishopmuseum.org
Thu Jun 25 13:30:20 CDT 2009


John:

Is it your contention that there is phylogenetically informative information
contained within morphology that is not *somewhere* in the genome?

Or, is it merely your contention that we are not yet able to extract the
phylogenetically informative information from the genome yet, and therefore
morphology serves as a more reliable indicator in many/most circumstances?

I could be persuaded about the latter, but the former is a very tough sell.
If there is phylogenetically informative aspects of morphology that are not
*somewhere* in the genome (independent of our current ability to decipher
it), then I'm struggling to understand how that information can exist (i.e.,
if it's phylogenetically informative, then it really must be heritable).

Don't get me wrong -- I'm certainly in the camp who believe that molecular
data are often over-rated, and lead to a false sense of confidence in
results.  However, I see this not as a failure of the *concept* (i.e., that
the genome is rich with information useful for reconstructing phylogeneies),
but rather as a failure in our ability to put molecular data in its proper
context, given our current state of understanding for how to interpret it
properly.  I am confident that we will eventually (perhaps within my
lifetime) have the necessary understanding to fully extract the
phylogenetically valuable information from the Genome, at which point
morphology will be useful primarily for bridging extant organisms to fossil
organisms.

I'm also keeping an open mind to the possibilities that:
1) There may be phylogenetically useful information observable in morphology
that does not exist somewhere in the genome (though I'm struggling with
imagining a mechanism);

2) It may not be possible (ever) to extract all of the phylogenetically
useful information from the genome (hard to fathom, given that the
phylogenetically informitive morphology is almost by definition derived from
the genome, and if the biomolecules know how to extract that information,
then we should eventually be able to do so as well);

3) Human civilization may collapse before we achieve the necessary level of
understanding of the phylogenetic aspects of genomic information.

Aloha,
Rich

> -----Original Message-----
> From: taxacom-bounces at mailman.nhm.ku.edu 
> [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of John Grehan
> Sent: Thursday, June 25, 2009 2:32 AM
> To: taxacom at mailman.nhm.ku.edu
> Subject: Re: [Taxacom] orangutan outrage
> 
> Comparisons of whole genomes of great apes will do no better 
> than partial genomes as it would lack outgroup comparison to 
> provide a braod comparative context for the distribution of 
> bases. Whole genome comparaison are also no solution anyway 
> because of the underlying problem of not being able to 
> individually recognize apomorphic states for base relationships.
> 
> Its popular to believe in molecular simiarlity as the proof 
> of phylogeny, but its never been more than a belief system 
> based on assumptions that have never been serously challenged 
> from morphology.
> There are many instances of molecular-morphological 
> incongruence, but for most groups no one really cares. In the 
> case of human origins the problem cannot be ignored, efforts 
> to do so notwithstanding.
> 
> If the molecualr theorists and Ken are correct, then 
> morphological systematics is no longer a science as it cannot 
> stand as independent evidence. The fossil record is also 
> rendered scientifically meaningless as there would be no 
> emprical way of making an informed judgement of relationship 
> in the absence of molecular support. There will no longer be 
> scientific justification for employing morphological 
> systematists (one museum director of a natural history museum 
> who himself studied fossil 'hominids' said as much). 
> Morphological systematics would be little more than 
> mysticism. These are the bottom line implicaitons that no one 
> seems to want to recognize. Even morphological systematists 
> (including almost all paleoanthropologists) are willing to 
> gut themselves of any scientific substance.
> 
> John Grehan
> 
> 
> > -----Original Message-----
> > From: taxacom-bounces at mailman.nhm.ku.edu [mailto:taxacom- 
> > bounces at mailman.nhm.ku.edu] On Behalf Of Kenneth Kinman
> > Sent: Wednesday, June 24, 2009 11:11 PM
> > To: taxacom at mailman.nhm.ku.edu
> > Subject: [Taxacom] orangutan outrage
> > 
> > Dear All,
> >       It seems to me that all of this will soon be settled by a
> thorough
> > comparison of the WHOLE genomes of the great apes.  The most
> convincing
> > synapomorphies will probably be more complex molecular signals (not 
> > substitutions, additions, or deletions of just single bases).
> >       The big question in my mind is still whether chimps clade 
> > exclusively with gorillas or with humans.  If, on the other hand, 
> > orangutans and humans do exclusively clade together, I will be very 
> > surprised.  I still believe that the morphological similarities
> between
> > orangutans and humans will turn out to be plesiomorphies (especially
> if
> > chimps and gorillas form an exclusive clade).  I wouldn't call
> Grehan's
> > hypothesis either "wacky" or "loopy", but I still think it 
> is highly 
> > unlikely.
> >           --------Cheers,
> >                           Ken Kinman
> > 
> > 
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