Circularity & testing.

James Lyons-Weiler weiler at ERS.UNR.EDU
Sat Oct 19 13:57:35 CDT 1996

On Sat, 19 Oct 1996, Tom DiBenedetto wrote:

> >The shift of the focus towards homology really misses the point of whether
> >reciprocal illumination is circular or not.
> Whether reciprocal illumination is circular or not, it is ubiquitous
> in science. No, I dont think it is circular.
It is not ubiquitous in science.  Just because a pattern is sensible does
not mean that the sensing of the patter constitutes a test of how sensible
that pattern is.  See how ridiculous it is?

 > >Hypotheses can't be used to test hypotheses.

> Hypotheses are combined parsimoniously under the expectation that
> they will be congruent if they are true (and yes the fact that they
> may be congruent doesnt PROVE they are true). They are tested against
> an expectation deduced from basic evolutionary principles.

I never expect any test to PROVE anything.  My point was that trees, as
hypotheses, can't test hyotheses of homology.  The trees are derived from
the hypotheses of homology, and then are supposed to provide a test of
homology?  Posh.

> > > Even when the assessment of homology is good, the
> >tree that has the most among character agreement can be erroneous (this we
> >know from simulation and known phylogenies).
> Everyone has always known that; what do you think this is an argument
> for or against?
I think it's an argument against using trees to test hypotheses of

> >Cladistic parsimony alone cannot test anything, except for the hypothesis
> >that tree T is indeed the shortest tree for a given data set.  Who would
> >want to use an erroneous tree to test otherwise excellent hypotheses of
> >homology?
> ??? If the hypotheses are so excellent, then the tree is gonna be
> equally excellent, for it is nothing but the combination of the
> hypotheses, with a bit of fracturing done on those characters which
> are incongruent with the preponderant pattern.

No, when homology is dead on, the trees can be dead wrong.  Where is the

James Lyons-Weiler

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