[Taxacom] orangutan outrage

John Grehan jgrehan at sciencebuff.org
Thu Jun 25 13:35:12 CDT 2009


> -----Original Message-----
> From: Richard Pyle [mailto:deepreef at bishopmuseum.org]
> John:
> 
> Is it your contention that there is phylogenetically informative
> information
> contained within morphology that is not *somewhere* in the genome?

No - as I pointed out in response to Ken, the genome in its
morphological manifestation already demonstrates the human-orangutan
clade

> 
> 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?

Yes

> 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. 

Agreed

 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.

Or morphology will be the necessary corroboration. It may be that
obtaining the pertinent information from the DNA strand will only be
possible if the developmental link to its morphological aspect is known.

> 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);

There have been some recent theories about cytoplasmic molecules that
interact with DNA. But I have not kept up with that field.

> 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);

That's the unknown for the present.

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

Quite likely I think.

John Grehan
> 
> 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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