[Taxacom] DNA homologies

[pierre deleporte]

A 08:30 04/10/2006 -0400, you wrote :

>I would agree that in an absolute sense they are not unique because the
>same condition occurs in other taxa. However, I can individually make
>the case to predict they are uniquely derived because of their rarity or
>the outgroup distance in which they occur.

the problem is that you allow such an exception only for characters 
supporting your pet phylogeny, which constitutes an obvious bias

>If others can algorithmically refute my contention about their status then 
>fine.

I just refuted it "non-algorithmically" I think ?
now, computer-assisted "algorithmic" treatment of the data would greatly 
help you avoiding such bias as mentioned above : the computer has no 
preference for Homo-Pongo

>But most of the proposed derived characters can be shown not
>to show up in other taxa - something that one can individually do for
>each proposed character state in morphology.

and molecular data as well, no problem at all (except for you, if you 
persist in refusing to consider this reality) : it's compatibility 
analysis, implemented for instance in some programs of Joe Felsenstein's 
PHYLIP program package
and it's free ! ...   (I don't mean recommended...)
and PHYLIP has no bias in favor of or against Homo-Pongo, super !

>Please give me a citation of a molecular paper that does not use some
>kind of optimization process to balance gaps and substitutions to match
>bases for sequences of different lengths.

Vahteraz and Muona 2006, Cladistics 22 p. 222-229, right on the shelf in 
front of you -
quoting : "using the optimization alignment program POY, with parsimony as 
the optimality criterion", hence not overall sequence similarity at all, 
hence apparently not "phenetic data" in your jargon... but who knows.. 
please check by yourself (initial basic training)

now if "optimization" itself is evil, whatever the extremely vague notion 
of "kind of... process to balance..." can be, OK you winn, no problem, and 
you'll always winn against "optimizers" of all kinds...
including all morphologists trying to "optimize" their alignments of 
morphological data.

I you really mean this, I must consider that, logically (!), you are 
proceeding yourself counter-optimally, or at least deliberately 
non-optimally, when aligning teeth occurring in different numbers in 
different mammalian mandibles... you likely align (homologize) the more 
different teeth standing in the more different places in the sequence... of 
pick them at random... whatever your criteria, you should not optimize 
their implementation, it's evil

but if you are aligning (= putatively homologizing) the more similar teeth 
standing in the more similar relative positions in the sequence, then you 
are not worth better than all those molecular optimizers, and shame on you 
(this is an opinion, fitting your own standards I mean)...

but I fear that every (rational) body must implement some optimality 
criterion for any classification

now, as a great polemist (I really mean it), you are once more escaping the 
Q question :
do it yourself, align yourself "without an optimality criterion for 
balancing" anything at all, and compare your results with those of other 
people, then treat the data your way, and tell us whether or not this 
changes the molecular phylogeny of anthropoids

you can refuse to do that, hence forever protecting your "opinion" against 
critics... but to your own eyes only

>Well those molecular systematists who use alignment say otherwise.

beyond whatever can be said, just show me how you perform alignment and why 
- it's the best way to overcome questions of vocabulary

> > no, logics is first in rational debates
>According to whatever form of logic you chose to accept.

increasingly fascinating.. post-modernism is really opening illimited 
routes for wild speculation...

I wondered why some discussions seemed to lead nowhere : now I get it, 
there must be a special (and unpublished) Grehanesc form of logic that of 
course I cannot understand, because everybody can have his own personal 
form of logic after all
great news : science is impossible, let's engage in extensive propaganda

we can even do better : everyone his logic and his proper vocabulary, if I 
can schtroumpf this smurf

>But you DO express a lot of opinions !

please ignore all of them them and just consider my logical statements, 
this is the way of science

the inconsistence of your analysis is not an opinion : it's the result of 
the logical analysis of your procedure, showing an avowedly biased 
compatibility analysis for constructing the data matrix, but standard 
parsimony for analysing the resulting data set, with no justification for 
changing your logic according to the arbitrary phylogenetic depth of the 
analysis

there is hardly any opinion inthere

now, if you treat all relevant data like callosities and enamel, you are 
plainly performing standard cladistic analysis, and the whole polemic is 
(logically) over, both for data matrix construction and subsequent data 
analysis

still not an opinion

Pierre


Pierre Deleporte
CNRS UMR 6552 - Station Biologique de Paimpont
F-35380 Paimpont   FRANCE
Téléphone : 02 99 61 81 63
Télécopie : 02 99 61 81 88