Felsenstein versus Ockham?

R. Zander bryo at PARADOX.NET
Mon Jan 25 11:55:41 CST 1999


Tom:
Scientists in general are interested in prediction of testable hypotheses. Cladists are interested in retroduction of a
single, complex phenomenon. Simplicity is justified in prediction when selecting hypotheses to test, since you have a testable
hypothesis and you can always get more data. Simplicity applies to evolution to the extent that observation has told up
(inference) that like produces like, that much convergence is not associated with most observed evolutionary processes. Thus,
optimality criteria can be used in eliminated unreasonable hypotheses, or in the case of cladistics, hypotheses of homology
associated with long trees. Homology as observed and theorized in evolutionary processes is mostly maximized. Mostly, but not
all. There is no evidence a priori that a data set

species A 1 2 3 4 5 6 7 8 9
species B 1 2 3 4 5 0 0 0 0
species C 0 0 0 0 0 6 7 8 9

with species A and B sharing characters 1-5 must be more closely related than species A and C sharing characters 6-9.

Your use of the term "prefer" demonstrates a fatal weakness (associated with optimality criteria) in cladistics as generally
practiced. Philosophers "prefer," "select" or "choose" theories, scientists act upon them by basing other analyses on them:
biogeographic, other phylogenetic analyses, etc. A probabilistic (or actionable or dependable) hypothesis should have more
going for it than "preference."

Construct a win-loss table for a 2X2 matrix of prefering (and acting upon) or rejecting (and not acting at all) a particular
hypothesis. Rejecting anything dubious gives an evanescent satisfaction, "prefering" anything dubious is rewarded with glory
and money. Surely there is some loss to science in a Type II error in phylogenetics!

In the case of parsimony, I recommend a high Bremer support value for a clade before a cladistic hypothesis can be seen as a
genuine probabilistic reconstruction that is better than any other method of grouping taxa by characters influenced by
evolutionary processes. We all like phylogenetic reconstruction methods that model evolution (parsimony, likelihood, Bayesian)
and prefer them to pure distance methods, but for what? I prefer to claim only a best, predictive classification with no or
little help from probabilistic phylogenetic reconstruction of the details.

Tom DiBenedetto wrote:

> >In my opinion, simplicity is justified to the extent that
> >nature is parsimonious; it is, but not optimally so.
>
> That may be your view, but it is not the justification used by cladists, nor, I think, by scientists in general who use a
> parsimony critereon. Parsimony is a logical discipline; it states that for any given set of adequate explanations for real
> world phenomena, one prefers the less complex. As Newton ( I think it was) put it; "do not postulate complexity
> unneccesarily".

And I said, in a recent publication, "...a corollary to Occam's Razor is that explanations must remain multiple when no one of
them is probabilistically adequate." Those who object to "probabilistic" can substitute "adequate as a basis for action." I'm
glad you cited Newton. Occam apparently was not refering to hypotheses in science but to real things in religion and
philosophy; he cautioned that just because a word exists does not mean that a real thing must be associated with it. He cited
many words as logically and epistemologically synonymous and his school required a minimal acceptance of real things in and
out of the world.


> This says nothing about how complex or parsimonious the real world is. One must explain whatever
> complexity one discovers,

No, I don't think so. One does not have to explain whatever complexity one discoveres, most especially when the data is
contradictory and more than one reasonable hypothesis is possible. In the context of action, you are arguing that, of a lineup
of criminals, one must find some one of them guilty, namely the one with the most evidence against him/her, even if there is
reasonable doubt.


> and there is nothing about the parsimony principle which constrains such discoveries.
>
> > Both the parsimonists and t
> >he statistical phylogeneticists err when they use optimality criteria to estimate a
> >point when an interval is better justified by contradictions in the data.
>
> I dont understand what you mean by this. The only optimality critereon in cladistic parsimony is that one report only
> those evolutionary transformations that are indicated by the data

But you select those that you report. Autapomorphies are not reported. Contrary evolutionary transformations in a tree one
step longer are not reported.


> and by the assumptions of a hierarchical branching
> pattern.
>


Richard


--


Richard H. Zander, Curator of Botany
Patricia M. Eckel, Research Fellow in Botany
Buffalo Museum of Science
1020 Humboldt Pkwy, Buffalo, NY 14211 USA
bryo at paradox.net   voice: 716-896-5200 ext. 351




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