[Fwd: Re: Probabilities on Phylogenetic Trees]

James Francis Lyons-Weiler weiler at ERS.UNR.EDU
Wed Sep 17 19:45:11 CDT 1997

On Wed, 17 Sep 1997, Doug Yanega wrote:

> Loathe as I am to interrupt the heavyweight bout here, there's one thing
> James L-W wrote I can't let slip by:
> >> we are testing a set of hypotheses under a criterion which demands of
> >> them that they be congruent.  The most parsimonious solution is the
> >> set of homology hypotheses which survive this test, and since the
> >> homology hypotheses are also grouping hypotheses, the groups which
> >> emerge are accepted as those which are most consistent with what we
> >> have discovered about characters,
> >
> >        THIS is a great example of where the process of
> >        formulating a hypothesis and actually testing it
> >        is entirely conflated.  OF COURSE your data will
> >        be congruent, because you formulate a set of
> >        hypotheses under a criterion that demands that
> >        they be congruent... and then the set of hypotheses
> >        that survives the test of congruence is preferred.
> >        Yikes.
> The hypotheses are of *homology*, not of congruence. There is no
> "criterion" that is applied except whether or not the states of a given
> character are *potential* homologies and thus worth including in the
> analysis, and definitely no "demand" that one's hypotheses be congruent
> when one formulates them - that's the whole idea of the test! One is
> testing all of the hypotheses against each other, simultaneously, and the
> most parsimonious tree is the pattern that yields the fewest total
> rejections of all those (hopefully) independent hypotheses of homology
> (i.e., the solution with the greatest degree of congruence among hypotheses
> - and given how rarely cladists find complete congruence, I can't
> understand your "OF COURSE" claim above). I see no conflation there, what I
> see is Occam's Razor. Yikes.
> That's all I wanted to say, now back to our regularly scheduled program... ;-)

        My point remains because the only type of hypotheses of
        homology that are considered to begin with are those
        that have already passed a series of tests to distinguish
        homologies from non-homologies.  Explicitly, the degree of
        corrorboration afforded to the sets of congruent hypotheses
        is lower than it could be because previously screened
        hypotheses of homology have a a HIGH, not a LOW,
        probability, as so the presence of congruence has a HIGH, not
        a LOW logical probability, so boldness is low.


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