More on the 'cladistics' of sequences

[Richard Jensen]

Dear John,

It is becoming abundantly clear that (a) you have no desire to read the
comprehensive literature that explains how (from beginning to end; including
being a competent systematist who understands that characters being used)
cladistic analyses are performed or (b) you simply reject that notion that
molecular data can provide good hypotheses of phylogenetic relationships
(fully testable, etc.; I know this is not the case, but your ignoring the
extensive and informative comments provided by members of this list
certainly gives that impression), or (c) you are simply being a gadfly.

The reference to uninformative characters is a classic example of your not
paying attention: any good cladistic algorithm can determine, as can any
competent systematist, whether or not a character is informative.
Uninformative characters are ignored because they don't provide any
information about sister-group relationships.  I don't have to be a hominid
systematist to take a look at a data matrix and tell you whether or not a
character is informative.  This is the "intelligent ignoramus" aspect of
analysis that was raised when numerical taxonomy was in its infancy.  Some
claimed that numerical taxonomy would reduce the science to a purely
algorithmic exercise that required no understanding of the organisms.  Well,
that's never been the case.  Morphological data are especially difficult to
evaluate and, in fact, are unlikely to provide "accurate" phylogenies (see
Lamboy, 1994. Systematic Botany 19: 489-505). Yes, Lamboy's analyses were
based on simulated data, but the data matrices generated were not unlike
real morphological data matrices.

Respectfully,

Dick


John Grehan wrote:

> -----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

--
Richard J. Jensen              | tel: 574-284-4674
Department of Biology      | fax: 574-284-4716
Saint Mary's College         | e-mail: rjensen at saintmarys.edu
Notre Dame, IN 46556    | http://www.saintmarys.edu/~rjensen