[Taxacom] Pasimony and base alignment

[Richard Zander]

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?

******************************
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
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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

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"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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