[Taxacom] Pasimony and base alignment

[Steve Manning]

At 10:45 AM 9/8/2006 -0500, Richard Zander wrote:
>In my message about high Bayesian posterior probabilities, I asserted
>that gauging reliability by optimality alone has been shifted to
>alignment of DNA sequences. We are thus still left with optimality
>alone, certainly when gaps are inserted to make alignments the same
>length (such that moving a gap a bit to the right or left yields a
>different branch arrangement or different posterior probability). Gaps
>do not come ready-inserted, we insert them ourselves to make a "best"
>alignment.
>
>Kirk F. has shifted the problem to something else again, pooh-poohing
>parsimony and posteriors alike in a rather absolute philosophical
>fashion. Somewhere there is a judicious mesocosm between joyous
>overconfidence in phylogenetic analysis as a process generating
>knowledge (or at least hypotheses that someone else will confirm
>someday), and dour condemnation of the whole bit. Are there any comments
>along the lines of a middle view?

Sure - I think of it as a probability analysis.  Roughly, the most 
parsimonious cladogram is the one with the highest probability, unless 
other measurable factors alter the probabilities.

It would be interesting if attempts were routinely made to assess the 
probabilities of correctness of each cladogram published, weighting 
molecular and macromorphological data as well as possible with current 
knowledge.  Of course that would usually result in the most probable 
phylogeny still having a probability of less than 0.5 but would emphasize 
how statistically insignificant the differences between the most 
parsimonious and other possible phylogenies usually are.  Sort of analogous 
to predicting results of a basketball tournament or gambling casino. (Note: 
I am not a statistician.)

Steve

>******************************
>Richard H. Zander
>NOTE: NEW PHONE NUMBER 314-577-0276
>Missouri Botanical Garden
>PO Box 299
>St. Louis, MO 63166-0299 USA
>richard.zander at mobot.org
>Web sites: http://www.mobot.org/plantscience/resbot/
>and http://www.mobot.org/plantscience/bfna/bfnamenu.htm
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>******************************
>
>-----Original Message-----
>From: taxacom-bounces at mailman.nhm.ku.edu
>[mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of J. Kirk
>Fitzhugh
>Sent: Wednesday, August 30, 2006 1:42 PM
>To: taxacom at mailman.nhm.ku.edu
>Subject: Re: [Taxacom] Pasimony and base alignment
>
>At 10:06 AM 8/30/2006 -0500, Richard Zander wrote:
> >Given that trees are commonly presented nowadays with high Bayesian
> >posterior probabilities on branch arrangements, or the equivalent in
> >bootstrap values, and given that the additional uncertainty of
> >alignments requires joint probability (multiply the chance that the
> >branch arrangement is correct by the chance that the alignment is
> >correct when not being correct gives a different answer), then one
>might
> >advance the idea that maximum parsimony alone as a measure of
> >reliability (converges on the truth, scientists always accept the
> >simplest theory, least falsifiable, etc.) has been shifted from
> >tree-making to alignment.
>
>Parsimony, as applied in the inference of explanatory hypotheses like
>cladograms, has nothing to do with truth or reliability. The simplest
>hypothesis is one that applies one premise to other premises to the
>greatest extent possible in the act of deriving a conclusion. This
>allows
>for multiple, mutually exclusive hypotheses, all of which are equally
>acceptable for future consideration, given the premises, such that any
>notions of truth or reliability become irrelevant. The conjunction of
>'descent with modification' with shared similarities, leading to a
>'minimum-length tree,' cannot warrant any view regarding the truth or
>reliability of that tree. Bayesian thinking is also precluded since the
>relevant test evidence has not been applied, and rarely ever is, in the
>context of phylogenetic hypotheses.
>
>Kirk
>
>------------------------------------------
>"No good idea avoids the fate of being taken to a ludicrous extreme."
>
>I. Tattersal, The Fossil Trail
>
>------------------------------------------
>J. Kirk Fitzhugh, Ph.D.
>Curator of Polychaetes
>Research & Collections Branch
>Los Angeles County Museum of Natural History
>900 Exposition Blvd
>Los Angeles CA 90007
>Phone:   213-763-3233
>FAX:       213-746-2999
>e-mail:  kfitzhug at nhm.org
>http://www.nhm.org/research/annelida/index.html
>------------------------------------------
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Dr. Steve Manning
Arkansas State University--Beebe
Mathematics and Science
Professor of Biology
P.O. Box 1000
Beebe, AR  72012
Phone: 501-882-8203
Fax: 501-882-4437