parsimony/biology (was: Striking a balance...)

[Brad McFall]

On Thu, 22 Feb 2001 13:09:03 +0100, Pierre Deleporte <Pierre.Deleporte at UNIV-
RENNES1.FR> wrote:

>(I renamed this part of the thread so that Peter Hovenkamp can delete it
>more easily).
>
>At 12:42 21/02/01 Tom Di Benedetto wrote:
>
>>>Pierre Deleporte wrote:
>>>...under what biological criteria do we apply the "parsimony criterion"?
>>
>>This use of the parsimony criterion makes no reference to biology or
>>evolutionary theory per se; it is used as a logical tool in the process of
>>extracting patterns from evidence that is not entirely consistent.
>
>Well, I think this is exactly what you logically cannot pretend to do. And
>Kirk Fitzhugh stated it well in his last message.
>A colleague suggested me a reformulation for "biological criteria" (may be
>confused with "optimality criterion"). I meant : under which biological
>explanatory law do you apply parsimony?
>
>"Descent with modification" in itself is not sufficient to distinguish
>between different phylogenetic methods.
>
>I believed that my allusion to "Theorem 5" of Tuffley and Steel (1997) was
>sufficient to put light on this:
>"Theorem 5: Maximum parsimony and maximum likelihood with no common
>mechanism are equivalent in the sense that both choose the same tree or
>trees."
>
>ML corresponds to "some common mechanism", MP corresponds to "no common
>mechanism" (local optimization of homology).
>
>The original data matrix (primary homology) is the same for ML and MP (and
>for a phenetic/molecular clock approach too).
>
>The particular vision of the evolutionary process in standard MP ("no
>common mechanism") is definitely NOT included inside the mere definition of
>primary homology (data matrix).
>
>I agree that standard MP globally optimizes evolutionary scenarios for
>characters, but it does this SOME WAY ("no common mechanism" etc...). Other
>ways are imaginable.
>
>If you agree with these points (and you agreed with some of them in your
>previous messages), how can you pretend that the choice of parsimony as
>applied in MP has no biological implication?
>
>Alternative proposition (silly proposition given the current most popular
>vision of the evolutionary process): I could parsimoniously maximise
>homoplasy instead of parsimoniously optimize character state contiguity.
>The explanatory law would be : horizontal transfer of characters is the
>overwhelming evolutionary mechanism, and primary homology is systematically
>misleading.
>
>But some models in ML implement some notion of decreased confidence in the
>informativeness of primary homology in some circumstances... long branches
>etc... and they do this with a notion of "common mechanism" throughout the
>tree.
>
>Given the matrix of putatively homologous characters, applying parsimony
>the standard way for optimizing character state contiguity with "no common
>mechanism" IS a biological decision, not a mere general application of
>Occam's
>razor "like that".
>
>Occam's razor may be used to cut off a lot of different things, under
>different logics.
>
>Pierre
>
>
>Pierre Deleporte
>CNRS UMR 6552 - Station Biologique de Paimpont
>F-35380 Paimpont   FRANCE
>Téléphone : 02 99 61 81 66
>Télécopie : 02 99 61 81 88

To any, every OR all;

What if you could describe the space of phylogenetic methodology
(Simpson's "kinetic phylogeny") and approach cladistic topologies from a
spatial understanding defined (man-made) in terms of cellular automata +
graph theory?  Would't this be some notion of Lewontin's as to the use of a
kind of "a priori"??

I am suprised to find again in biology that the "hermenutics" depends on
the particular plurivocal aspect of a word.

Whatever "criteria" or max-min may mean, I have felt that logic has not
been properly taught falling pedagogically under 'mathematical maturity'
but I don't even have fresh this, memory.

Similarity is not resemblence and contiguity is not connection.
communication. BSM.