Weights, probability

Richard Zander bryo at AGIS.AG.NET
Tue Mar 4 01:00:28 CST 1997

Doug Yanega wrote:
> Richard Zander commented:
> >The heavy discussion on weighting characters has tended finally to light
> >upon phylogenetic differences in character importance. Now, I figure
> >that, since we don't know the mutation rates of state changes in the
> >different character we use, we pretty much depend on Keynes' "princicple
> >of indifference" which says if we don't know the different importances
> >of various variable, use equal importance since there is a good chance
> >it will average out. This is pooh-poohed by experts in probability with
> >good reason, so what have we other than a system of classification with
> >good Darwinian intentions ("like produces like") and a whole lot of
> >argument about the relationships of details for which we have no
> >information. Method alone guarantees precision not truth.

I think we have a classification bettered by grouping terminal taxa by
mathematical evaluations of advanced derived character states, given a
lot of assumptions. We have, however, more of a useful classification
than a useful analysis of phylogeny, though, given those obviously
indefensible assumptions (judging from the weighty arguments: "The boots
get heavy when blood muddies the field").

> What I don't quite understand is how this a priori pattern-testing is going
> to be fundamentally different from a circular application of parsimony
> itself; it's like building a tree, then concluding "Aha! Character 33
> appears to have a homoplasious state 1 in taxa 4 and 17, so character 33 is
> only 85% informative! Now let's plug that probability in with the others and
> run the data again." The only difference is that there is no actual tree
> constructed in that first pattern-testing step, just an algorithm (without a
> graphic representation) which gives you estimated probabilities of
> "informativeness" based on some overall comparison of each character to the
> others in the matrix. I find the concept of making a "relative determination
> of which comparisons are misleading" *before* an analysis to be hard to
> swallow, and my gut feeling is that it is equivalent to parsimony analysis
> in itself (i.e., looking for incongruence in a pattern).
> Just trying to make some sense of this,
Clear thinking, Doug. That's good point. I also second your hesitation
about using "a priori" to refer to pre-algorithm weighting. The phrase
refers to conclusions not based on reason, if you look it up, but has
been used by numerical taxonomists since the sixties to refer to
anybody's inferences other than the particular algorithm in style at the
moment. Who started that? I used to think it was a ploy, since a priori
has always had negative connotations to scientists, but now I think it's
just ignorant.


Richard H. Zander, Buffalo Museum of Science
1020 Humboldt Pkwy, Buffalo, NY 14211 USA bryo at ag.net

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