Turning around

[Richard.Zander at MOBOT.ORG]

Well, John . . .

Statistics is based on a phenomenon in physics called the binomial
distribution. It is not imaginary or supportive of empty explanations. In
speculative phylogenetics, scientific data (facts, or well-documented
observations) plus a scientific model yields (with a particular method) a
scientific hypothesis. Of course, the Bayesian one-time retrodiction of a
historical event is fraught with problems, but it is still scientific. Based
on sequence facts and a model generated from facts, it does give you a
theory that is a scientific approach to scientific truth, in the sense that
if there is no argument against, and plenty of statistical support (in terms
of not-to-be-expected-from-random-generation of data) for, then one can base
one's conduct (further research) and bet one's science on the hypothesis.
The scientific results are not empty explanations by armchair scholars, but
are actual guides to conduct (or you can reject them if you think technique,
model or data are not up to snuff, but then you should have an idea of
exactly why not). Another guide to conduct is in the artistic or spiritual
realm, involving the apprehension of Truths that powerfully affect the
psyche. If you have a third Guide, let us know.

What happens when strongly supported morphological results contradict
strongly supported molecular results? One can come up with a hypothesis to
test, like I did for the situation with orang-homo-pan. Contradictions are
not always a sign of faulty data or model or method, they may be a clue to
new processes to be discovered or further investigated.

Some philosopher wrote that often if you can state the problem clearly
enough, the answer is obvious). If the problem is that there is too much
focus on molecular analyses while ignoring morphological analyses, you are
preaching to the choir. If you have a new way of combining the two without
just throwing out the molecular end, let us know.

______________________
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
Res Botanica:
http://www.mobot.org/plantscience/resbot/index.htm
Shipping address for UPS, etc.:
Missouri Botanical Garden
4344 Shaw Blvd.
St. Louis, MO 63110 USA

-----Original Message-----
From: John Grehan [mailto:jgrehan at sciencebuff.org]
Sent: Wednesday, February 22, 2006 7:58 AM
To: Richard Zander; TAXACOM at LISTSERV.NHM.KU.EDU
Subject: RE: Re: [TAXACOM] Turning around

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