[Taxacom] orangutan outrage

Steve Manning sdmanning at asub.edu
Thu Jun 25 16:03:44 CDT 2009


At 01:30 PM 6/25/2009, Richard Pyle wrote:

>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).

Well, if paleoclimates are known and if present climates are known to 
correspond with morphological differences (phenotypic plasticity), I 
guess when examining a fossil, one could extrapolate and say the 
morphology is more phylogenetically informative than the genome.  (I 
am not aware of any such correlations in humans, orangutans, chimps 
or other relatives.)


>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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