[Fwd: Re: Probabilities on Phylogenetic Trees]

Tom DiBenedetto tdib at UMICH.EDU
Thu Sep 18 20:19:49 CDT 1997

 James Francis Lyons-Weiler wrote:
>        I am NOT talking about the probability that the
>        shortest tree is true.  I am talking about whether
>        or not the parsimony criterion affords any amount
>        of corroboration...

So lets keep this simple so we dont talk past eachother. I enter into
my algorithm a matrix of homology hypotheses. Different stuff comes
out. Some emerge the same way I put them in,,,others are fractured,
maybe completely. Something has happened to my hypotheses,,,yes? I am
using the words "corroborated" and "falsified" because it seems
obvious to me that they are accurate. Maybe you want to use different
words. Like what? And why?  You tried "confirmed" instead of
corroborated, but I agree with myself that that is not right. If you
hold up a hypothesis to a standard and say "either this hypothesis is
congruent with the standard or I will abandon it", you are testing,
not seeking confirmation.

>         The fact
>        that the boldest hypothesis is, in fact, the longest
>        tree is irrelevant to the suitability of parsimony
>        to the task of being a critical test.

huh? you mean the shortest tree, right? The longest tree is an
unresolved bush, which says nothing.

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