Positivism vs Realism

[John Trueman]

James Francis Lyons-Weiler wrote:
>>        Parsimony is a criterion, but the belief that
>>        the criterion will lead to meaningful estimates of the past
>>        requires a bolus of faith I'd rather not choke on.

and Thomas Pape wrote
>I cannot quite understand this scepticism towards parsimony. Why should you
>EVER choose an estimate of the 'truth' that requires a LESS SIMPLE
>explanation? How can an estimate which requires MORE AD-HOC explanations
>ever be superior?

... and I agree with Thomas's point, but ...

What puzzles me most in this and in all such discussions on tree-estimation
(or reconstruction) versus The Truth is that of all tree estimation
procedures the only one which regularly causes this level of angst is
PARSIMONY.  What about likelihood trees or distance trees, doesn't the
exact same argument apply?  We have a criterion for preferring one tree
over another (max likelihood) or at least a criterion for deciding which
tree is the estimated tree (the one produced by the algorithm: NJ or
whatever).  There still must be what James has called "a bolus of faith" to
raise that tree to the status of a meaningful phylogenetic estimate.

In this regard there is nothing special about parsimony. WHATEVER
estimation method we use, we still should distinguish "the tree that comes
from the method" from "a good/valid/meaningful estimate of the phylogeny".
Knowledge of the conditions under which each given method will and will not
recover a known hierarchic signal are useful here.  Parsimony is good
sometimes, various likelihood models are good sometimes,  NJ and even UPGMA
will work provided the data (hence, the underlying evolutionary process)
are appropriate, but EVERY method has its "Felsenstein zone" or equivalent:
a set of circumstances in which to add more data will lead with increasing
certainty to the wrong tree.

Tests on the data can be of some help in picking up problem cases in which
the key assumptions of one (or more) methods are violated.  And if the
chosen method is appropriate to the data, then tests (eg, bootstraps and
TPTPs) against the possibility that recovered groups are attributable to
chance alone can help in distinguishing the bits of the tree which are
meaningful from the bits which are not.

But until the data are tested, and until the tests on nodes of the tree
have been done, a tree estimate is just a tree estimate, it cannot be a
hypothesis about phylogeny.

John

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John Trueman
Bioinformatics Unit
Research School of Biological Sciences
Australian National University        -------------------------------
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