Tom DiBenedetto tdib at UMICH.EDU
Thu Feb 27 08:53:56 CST 1997

On Thu, 27 Feb 1997 06:37:40 -0800, James Francis Lyons-Weiler wrote:

>Consider the fact that when one decides to not weight morphological (or
>molecular) characters, one has decided that a transformation among states
>in character i has the same information (and therefore relative
>probability) as a transformation among states in character j.

One does not *necessarily* do that.  Only if you are approaching the
question from the perspective of presuming to be able to make
judgements as to the "information content" of a particular character
based on what has happened elsewhere within a similar class of

 >That is, a decision to use equaly weight is arbitrary, and requires
as much
>justification as any weight weighting scheme.

Unfortunatly, the decision to use any weight, equal or not, is
arbitrary in the probabilistic approach, because it must be based on
some sampling of presumed knowledge, often inferred from different
(hence irrelevant) systems or based on estimates drawn from
generalized understandings of process.
  This is a problem with the probabilistic approach. In a parsimony
approach, one does not assign probabilities to presumed
transformations; one attempts to group taxa in such a way that one
extracts the best-supported hierarchy of congruent transformations
amongst presumed homologies. This is supported by the basic
evolutionary insight that true homologies will be congruent. From
such a perspective, each transformation is a putative homology, a
hypothesized evolutionary event. As such, all have equal evidentiary

>(Felsenstein (1983); NATO symposium) made the excellent and astute point
>that parsimony requires implicit statements about the probability of
>character evolution; these probability statements are merely made explicit
>under generalized parsimony.

I find Felsenstein's point to be a rhetorical gambit to shore up
support for a probabilistic approach to phylogeny reconstruction. In
fact, a parsimony-based approach makes no such implicit statements,
for it does not operate in a probabilistic framework. And he
certainly knows that. Probabilism seems to run into at least two
fundamental limitations. First of all, one can only calculate the
probabilities of historical events from the perspective of a
sophisticated understanding of the course of history, This makes the
use of probabilism in the effort to lay out that understanding of
history rather problematical ("circular" works well here too).
Secondly, even if one were to arrive at an "accurate" estimate of the
probability of an historical event, that would only be useful on a
general level. The need, in phylogeny reconstruction, is to pass some
sort of judgement on unique, singular events, and these either
occurred or did not. Their "probability" is 1 or 0. Their calculated
probability in the context of presumed knowledge of general processes
is really irrelevant to the question of whether one particular
instance occurred or did not.

>        Quote taken out of context:
>                Date: Tue, 25 Feb 97 12:44:03
>                From: Tom DiBenedetto <tdib at umich.edu>
>                To: James Francis Lyons-Weiler <weiler at equinox.unr.edu>

>                >"I think you are right..."

did I say that????
gee, ya try to be nice, and it always comes back to haunt ya! :)

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