# [Fwd: Re: Probabilities on Phylogenetic Trees]

Doug Yanega dyanega at MONO.ICB.UFMG.BR
Wed Sep 17 21:17:22 CDT 1997

```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
>
>        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... ;-)

Sincerely,

Doug Yanega    Depto. de Biologia Geral, Instituto de Ciencias Biologicas,
Univ. Fed. de Minas Gerais, Cx.P. 486, 30.161-970 Belo Horizonte, MG   BRAZIL
phone: 031-448-1223, fax: 031-44-5481  (from U.S., prefix 011-55)
http://www.icb.ufmg.br/~dyanega/
"There are some enterprises in which a careful disorderliness
is the true method" - Herman Melville, Moby Dick, Chap. 82

```