More on the 'cladistics' of sequences

[John Grehan]

-----Original Message-----
From: Taxacom Discussion List [mailto:TAXACOM at LISTSERV.NHM.KU.EDU] On
Behalf Of pierre deleporte
Sent: Monday, June 07, 2004 7:59 AM


And you now know that this is exactly what programs do when they perform

cladistic analysis of molecular data like for any other data. I know
that 
you know that. Via the outgroup criterion, each and every molecular 
character state (i.e. a given base at a given site in aligned sequences)

has an a priori polarization in putative plesio-apomorphy (for each and 
every character = site).

If the program carries out this function then there would seem to be no
a priori polarization. If there is an a priori polarization of sequences
I would be interested to read an example.

And you also know that there is nothing like "rooting after the
analysis", 
or "rooting during the analysis", because you know that one can perform
the 
analysis the following way and get exactly the same result:

Rooting either way as you describe does not change the contrast between
identifying potential synapomorphies before the analysis, or identifying
synapomorphies using the analysis.

And you also know that the program begins with discarding cladistically 
non-informative characters. This is the first thing it does. Thus, only 
cladistically putatively informative characters remain in the analysis, 
i.e. characters with putative plesiomorphic state and apomorphic ones. 

But the program can only get rid of what are identified as
non-informative and that depends on what one puts in the first place. An
algorithm might treat characters as informative, but if they are
mis-identified in the first place then would still appear to be garbage
in garbage out.

Hence, all outgroup-polarized molecular characters are "cladistic" in
your 
(very peculiar) acception of the term, i.e. they are individually, 
putatively polarized a priori, via the outgroup criterion, 

Please give me a citation of a paper showing where someone has gone
through molecular sequences, and argued for the plesiomorphic and
apmorphic states for each individual gene before any analysis is done. I
am looking for an analysis where a gene is shown to have a constant
pattern of bases throughout various species of the outgroup, and then is
apomorphic for other base sequences in the ingroup.

and the analysis 
is performed the classic cladistic way for molecules just like for 
morphology. Same criteria, same procedures.

That remains to be seen.

and I still cannot understand why you persist in taxing 
molecular cladistic phylogeny of being non-cladistic.

I sympathize with your plight.

>One can document each character for the outgroup and ingroup. By this
>documentation it is possible for each character to be independently
>verified or refuted by another individual

This you can do, exactly this, with molecular data as treated by modern 
programs.

Sorry, in morphology 'programs' cannot do this. A person has to evaluate
each character and make an assessment of its status, and then defend the
assigned status by comparative documentation (even though in actual fact
this is not very well done if at all in hominid systematics - just look
at the dreadful stuff published in Nature and Science. Even Homo appears
to lack a synapomorphy.

Just try it, as I suggested you repeatedly. But apparently you 
don't try... Why don't you try and verify by yourself that this is all
the 
same approach? Same logic giving same result?

Because you are asking the wrong thing.

I admit that the fact that everybody tells you the same thing will not 
change your mind the slightest way, for it's quite imaginable that the 
whole community of specialists of morphological and molecular cladistic 
analysis on earth is wrong and you are right. 

Well, imaginable or not one can suppose that the majority is always
right. Then one may also suppose the opposite. Who cares?

Science is not a democraty. 

True. Since I have not commented on the politics why bring it up?

But why don't you try and verify? Because it's also imaginable that you
are 
wrong, and this you can check by yourself:
- take some molecular data
- root them a priori character by character via the outgroup criterion

I want to see how others have done this.

>No, but if one cannot polarize the characters and determine which are
>potential synapomorphies before the analysis then the implication is
that
>such individuals do not know their group very well.

But this is exactly what the program does, 

Again, programs are just recipes and recipes lack intelligence (and I
will avoid making any jokes on that one).

Look forward to the citation example.

John Grehan