Circularity & testing.

James Lyons-Weiler weiler at ERS.UNR.EDU
Sat Oct 19 16:02:11 CDT 1996

On Sat, 19 Oct 1996, Tom DiBenedetto wrote:

> One more time....the tree itself is not turned back to test the
> hypotheses, the test is a test of congruence; the tree is the result.
> What is so difficult about this?

What is so difficult about it is that there the test you describe does not
manifest itself in any measureable manner. Tree length does not provide
any measure of congruence; homoplasy indices are unreliable.  Again, where
is the test?

>  Do you know what a hypothesis of homology is?

Wiley (p. 139)

"  the "problem of homology" can be broken by simply realizing that
homologies can be treated as hypotheses that are tested by other
hypotheses of homology and their associated phylogenetic hypotheses".

Like I said, hypotheses can't be tested by other hypotheses; where are the
critical values?  Where are the probability distributions?  Where are
error terms?  The argument revolves around what one considers to be a
critical test; I simply reject that whatever you mean by congruence
provides anything resembling a critical test.  The rest of the biological
sciences see the danger of circular reasoning, and Hull (in 1967!) warned
us about the limitations of the same within the context of phylogenetic

 > 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
> >> for or against?
> >I think it's an argument against using trees to test hypotheses of
> >homology.
> I think you wrong.

Good for you.

> > No, when homology is dead on, the trees can be dead wrong. Where is
> > the test?
> HUH? That is absurd.

How?  Why?

James Lyons-Weiler

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