Striking a balance, weighting and Cladistics

[Richard Zander]

----- Original Message -----
From: "Thomas DiBenedetto" <TDibenedetto at DCCMC.ORG>
To: "'Richard Zander'" <rzander>; <TAXACOM at USOBI.ORG>
Sent: Monday, February 26, 2001 4:45 PM
Subject: RE: Striking a balance, weighting and Cladistics

> If there are a gazillion alternative trees for a set of taxa, then a bush
is
> merely a graphical representation of the statement: "the evidence does not
> support a preference for any of the gazillion trees over any other". You
> can't get a less exact solution than that. The question of whether the
> branches themselves are supported or not is simply outside of the scope of
> the analysis, we assume we are working with valid species.

A bush is _one_ graphical representation of the statement "the evidence does
not support a preference..." Another graphical representation is a well
resolved tree with little support. My whole point is that scientists should
"prefer" neither a bush and nor weakly supported trees. Prefer for what? To
use them in some way? What way?

>
> >With most cladograms, the null hypothesis of no phylogenetic
> >loading cannot be rejected by the data presented (when looking at an
> >entire tree of many taxa).
>
> Once again, there is no null hyothesis per se in play in the first place.
> This is not a statistical analysis. It is simply a procedure to detect the
> pattern in the data. The "significance" of the pattern is another matter
> entirely.

My point is that there is no acceptable pattern in the data when the
analytic result is a bush or a weakly supported tree. One can find
"patterns" in totally random data.



 Statistics is the spine of a certain type of science, dealing with the
> induction of general causal principles through the analysis of samples of
> the effects of those principles (as in your chicken example). This is not
> the only type of science that one can do.

Well, there's creation science...

The specific character
> transformations that are the currency of phylogenetic research are not the
> varied effects of a single causal principle or factor.

Shared evolutionary history?


> > An exact solution is publishable through the magic of the
> >philosophy of parsimony, even though there are doubtless . . . doubtless
> >many almost as well supported alternative trees.
>
> No magic needed. And I think you exaggerate the preponderance of well
> supported alternatives, at least in some cases.

Note the the sum of the probabilities of poorly supported alternatives may
be quite large. Only if you have a good theory that allows exclusion of
these alternatives can you ignore them. One theory is that if a branch is
bracketted above and below by well supported lineages, when one can ignore
these and focus on the branch and its alternatives.


> Intuitve evaluations fail to demand explicit, testable, and discuss-able
> character defintions. In addition, characters are weighted under a
> subjective, personal, and hence untestable standard.

"No weighting" is widely viewed as weighting of "1".

You know, I can pick out bits of your message (possibly out of context) and
respond vigorously, but I hope that my main point that exact solutions may
be no better than a bush is made.

R.


---------
From:
Richard H. Zander
Curator of Botany
Buffalo Museum of Science
1020 Humboldt Pkwy
Buffalo, NY 14211 USA
email: rzander at sciencebuff.org
voice: 716-896-5200 x 351