[Taxacom] quote of the week

John Grehan jgrehan at sciencebuff.org
Tue Mar 25 13:04:37 CDT 2008

From: Pierre Deleporte [mailto:pierre.deleporte at univ-rennes1.fr] 

>>here John  Grehan is (as recently predicted) reaching the point where
he is implicitly exposing his >>'clique analysis' method (as explained
to him years ago); an extreme form of clique analysis in fact, for >>not
only he tries to select a clique (possibly the largest?) of completely
mutually compatible characters, >>but he discards all but homoplasy-free
characters (however inconsistently in his own morphological data 
>>analysis 'by hand', as also explained years ago)

I'm a bit confused by the above as I thought homoplasy could be
identified only after the analysis.

>>John seems (?) to have evolved in his consideration of outgroup
criterion for rooting (he once rejected 
>>the possibility of performing any molecular phylogeny at all, 

If I did then I should not have. I only question whether molecular
phylogenies are really cladistic when they purport to be, and whether
molecular phylogenies can necessarily falsify a contradictory
morphological phylogeny.

>>and also using parsimony optimization programs, because molecular
characters could not, supposedly, be 
>>polarized a priori one by one, as morphological characters were
supposed to do, and programs did not 
>>explicitly asked for a priori polorization)

At least we agree on this. Yes I am either old fashioned or misguided in
looking to include characters that can be polarized individually before
the analysis as potential synapomorphies.

>>it would also seem that John is possibly (?) implicitly renouncing to
his characterization of molecular >>data as being "phenetic in

Sorry, not yet.

>>(if not, all his current discussion about ougroups in molecular
analysis would be nonsensical: one could >>logically not improve
parsimony analysis of intrinsically "phenetic data", if such a notion
could mean 
>>anything at all)

The other alternative is that the cladistic claims of molecular
systematics are nonsensical.

>>but up to this date, John refused to analyse molecular data such a

In the background - Cheers, cheers! (sorry that was just my imagination)

>>and refused to use existing computer programs for performing his own
morphological analysis as well (e.g. >>using some 'clique' option in
Felsenstein 's Phylogeny Inference Package - accessible for free on the

Sorry, you must have misunderstood me somewhere along the way. I thought
I had mentioned on this list that I am currently working on a
morphological analysis. Maybe I did not specifically mention computer
programs, but I am using PAUP - principally because that is what all the
other primate morphologists have used. But in addition I did to a Bremer
support analysis, which the others did not do.

>>hence, for those interested, we still don't know what would be the
result of such a molecular analysis, be >>it only for 'a few species',
rooted or not, and much less for 'complete outgroup comparison' 
>>including all primates


>>please note, for curiosity and clarity, that John is not proposing
>>(below) to perform a complete parsimony analysis of all primates, but
to check in all primates except 5 
>>species for absence of 'derived' (i.e. 
>>original) states present in (human, orang), which is consistent with
the diagnostic of an implicit 'clique >>+ homoplasy-free' analysis
mentioned above 

Not quite correct. We are looking at all character states that may be
found within humans and the great apes that support any relationships
between any of them. In other words, character states unique to humans
and orangutans, humans and chimps, humans and both African apes, chimps
and gorillas. We have not focused so much on other combinations although
some may be valid. Further research required on such claims in the
literature (and morphological claims are traditionally very poorly

>>I'm not trying to promote John Grehan's quite peculiar method, these
precisions have no other intention 
>>than possibly helping to avoid going round through all this discussion

Thanks for trying to be helpful, although going around again may be
inevitable as long as the orangutan question is ignored in the
scientific literature.

John Grehan

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