Turning around

[John Grehan]

Tindall has already indicated the complexity of questions about DNA and
morphology. As for molecular traits accumulating with each speciation
event the "logic is great" which is another way of saying that it is an
assumption. Assuming the assumption is correct, it is another step to
saying that the accumulation of changes will actually correlate in some
necessary way with the phylogenetic sequence. 

As for statistical support, any measure of overall similarity might be
statistically sound without it necessarily being any more accurate about
the phylogenetic sequence if there is no a priori exclusion of
plesiomorphic states. With bases potentially flipping between one or
other base alternatives, and that base alternative (or even loss or
gain) providing no indication of what came before, it all seems to come
down to statistical imagination of what is inherently untestable
(Probably sticking my neck out on that one). Of course one can invoke
any number of statistical and theoretical models to accommodate this
problem - which is what molecular theorist do.

And then here is the problem of apples and oranges (not orangs). What if
a statistically well supported morphology contradicts a statistically
well supported sequence pattern? I suppose some would say that the DNA
is always better because one can always have more characters (what seems
to me to be another kind of phenetic argument [phenetic as in overall
similarity]). Then there are others who say combine the data as if
apples were oranges.

As for the assertion that "morphology does seem to show a set of ancient
orangutan genes reactivated in homo in selective response to particular
environmental conditions" that is factually incorrect. It's just an ad
hoc hypothesis to protect DNA models from falsification [actually its
interesting that this popped up because one prominent hominoid
systematist has more or less admitted to me that the morphological
support for humans and African apes [let along chimpanzees which is
pretty well non existent] is far less than support for the human and
orangutan and so has come up with the very same assertion. Anything to
protect the deification of DNA bases.

"As an explanation, it works, but proof is so far lacking". Any
explanation works in some way or other according to the purposes of the
author.

Successful historical predictions about past tectonic events based on
the phylogenetic classification of plants and animals shows that these
classifications do reflect something of a "true" phylogeny at least to
the point of being able to successfully predict something of the real
world. So perhaps one is not wasting time over the question of the
"true" phylogeny. 

The great thing about the orangutan is that the issue of human origin is
so prominent and so it raises the profile of an issue over morphology
and genetics that is otherwise generally buried or conveniently ignored
(or there is propaganda about a dialogue between genetics and morphology
as in Science). The real question (in my mind) is whether the 'science'
of systematics can acknowledge this scientific problem and rather than
suppressing it (as through editorial politics), encourage the
dissemination of both the evidence and the different theoretical
perspectives. Primatologists, for example, apply the principle of
mediocrity by taking the position that the suppression of Schwartz's
theory is justified simply because it has been suppressed by everyone
(i.e. if it were any good it would not have been suppressed). 

Perhaps primatology has yet to experience the Renaissance.

John Grehan



> -----Original Message-----
> From: Taxacom Discussion List [mailto:TAXACOM at LISTSERV.NHM.KU.EDU] On
> Behalf Of Richard.Zander at MOBOT.ORG
> Sent: Tuesday, February 21, 2006 4:13 PM
> To: TAXACOM at LISTSERV.NHM.KU.EDU
> Subject: Re: [TAXACOM] Turning around
> 
> The whole point of molecular systematics is that it is hoped that
> differences in DNA usually or mostly do NOT reflect evolution
directly,
> because if they did, we would have the same problem with convergence
as is
> the case with morphology and molecular analysis would then not be a
> second,
> independent test. Molecular traits are, it is hoped, not connected to
> anything in morphology. They just accumulate with each event of
> speciation,
> and the ones shared the most are the most ancestral. The logic is
great,
> the
> execution so far problematic, possibly because of the inclusion of
many
> apparently noncoding or codon-synonymous sequences that are actually
> subject
> to selection pressures.
> 
> Regarding orang-homo morphological similarity in the face of
contradictory
> molecular data that statistically well-supports pan-homo as terminal
in
> the
> clade, my suggestion of a theoretically understandable violation of
> Dollo's
> law by long silenced and recently reactivated gene clusters does not
> falsify
> anything. Molecular analysis does seem to show orangutan left in the
> evolutionary dust, yet morphology does seem to show a set of ancient
> orangutan genes reactivated in homo in selective response to
particular
> environmental conditions. As an explanation, it works, but proof is so
far
> lacking.
> 
> It is a waste of time to worry which is the "true" evolution:  the
> phylogenetic tree that infers nested sets of genetic isolation events,
> presumably with associated fixation of incrementally established new
> traits,
> OR the (theoretical) jump of a highly preadaptive gene complex from
> orangutan to homo. If you decide that the latter is a better theory or
the
> only theory, you need to be able to defend it well in the marketplace
of
> ideas. In my case, I think both processes occur, and much that is
> problematic about our understanding of phylogeny may not be soluble
with
> current methods.
> 
> ______________________
> Richard H. Zander
> Bryology Group, Missouri Botanical Garden
> PO Box 299, St. Louis, MO 63166-0299 USA
> richard.zander at mobot.org <mailto:richard.zander at mobot.org>
> Voice: 314-577-5180;  Fax: 314-577-0828
> Websites
> Bryophyte Volumes of Flora of North America:
> http://www.mobot.org/plantscience/bfna/bfnamenu.htm
> <http://www.mobot.org/plantscience/bfna/bfnamenu.htm>
> Res Botanica:
> http://www.mobot.org/plantscience/resbot/index.htm
> <http://www.mobot.org/plantscience/resbot/index.htm>
> Shipping address for UPS, etc.:
> Missouri Botanical Garden
> 4344 Shaw Blvd.
> St. Louis, MO 63110 USA
> 
> 
> 
>   _____
> 
> From: John Grehan [mailto:jgrehan at sciencebuff.org]
> Sent: Tuesday, February 21, 2006 2:35 PM
> To: Richard Zander; TAXACOM at LISTSERV.NHM.KU.EDU
> Subject: RE: [TAXACOM] Turning around
> 
> 
> 
> I don't always keep track of all postings on TAXACOM. As for
alternative
> explanation (or at least possible explanation) - I've made them on
TAXACOM
> already. My principal thinking is that linear patterns of DNA sequence
> similarities comprise both primitive and derived states that cannot be
> identified without knowing what they are connected to in morphology.
So
> simply reading of linear sequence patterns is just measuring overall
> similarity - whether or not it is rooted.
> 
> 
> 
> Regarding the orangutan-homo similarities being explained in terms of
> violation of Dollo's law - am I correct this is being invoked to
'explain'
> why the morphology is wrong and sequences right - or is the point
> something
> else? Got a bit lost on that.
> 
> 
> 
> John Grehan