paraplaying (and bullies)

[pierre deleporte]

At 18:04 07/04/2004 -0400, Frederick Schueler wrote:
>pierre deleporte wrote:
> >> Paraphyletic taxa are "natural", e.g. under the following criterion:
> >>members share one or several synapomorphy(ies) (= original homologous
> >>characters inherited by descent and effectively present...
>
> >* correct me if I'm wrong, but isn't paraphyly (above the species level)
> >an artifact of using categories? A consequence of the Aristotelian myth
> >that different taxa of the same category are somehow equivalent? 'Class
> >Mammalia' is paraphyletic only in relation to 'Class Reptilia' -
>'>Mammalia' is simply a monophyletic lineage within 'Amniota.'

A paraphyletic group is "incomplete" under the criterion "monophyletic = 
complete". This definition makes no reference to categorical ranks. Mono- 
or paraphyly is a phylogenetic property of the group in itself, class 
mammalia is monophyletic whatever the external referent, and classic 
incomplete reptilia (e.g. without birds) remain paraphyletic too. Only a 
change in the general phylogenetic topology may make a group change 
category (become para- or mono-, or explode...).

 >>The myth of the obvious, unique, optimal and all-purpose-fitting
 >>classification seems no longer tenable to me. It is a pre-scientific
 >>illusory quest (searching after "The" design of nature).

> >* ah, but if you want an "obvious, unique, optimal and all-purpose"
> >something, maybe you need Hegelian dialectical methodology.

I once was impressed by some form of "Hegelianism". Seems to me it was long 
ago. I'm now baffled by Hegelian confusion, specially "dialectics" (a 
methodology, you say? Where can I read the manual please?). "Hegel" now 
makes me turn on all my rational warnings.

> >If we start
> >with the grand fact of the natural subordination of organic beings in
> >groups under groups,

Should we? I don't start with "The" grand fact, because there are several 
"facts" of that kind. It depends on your systematization criteria: 
phylogenetic, or other.
Phylogeny is (roughly) a hierarchy, hence rather easily transposable into a 
formal  classification. But it's not the only hierarchy you can forge 
(because YOU class, you forge "natural" classes, not Nature). You can class 
on one or several scales according to biological properties other than 
common descent. Likely you will frequently group by analogy (marine / 
terrestrial, vocalizing / dumb, homeotherm / poikilotherm... and what you 
like), rather than by phylogenetic relatedness, and this you will know by 
confronting your classification with a phyloyeny. But of course there is 
strictly no law against this: just use the classification you need. 
Provided that you're conscious of your criteria, and warn your readers (my 
fishmonger puts shrimps close to mussels and calls them "sea fruits". I 
won't blame him. He can understand phylogeny anyway: other needs, other 
classification criteria. It's pure logic).

> >and accept that this subordination is due to descent with modification,

Some hierarchical patterns are phylogenetic, others are not. It depends on 
how you subordinate characters. Because you [sub]ordinate things your own 
way, Nature ordinates nothing by itself.

If you believe that a sound contemporaneous approach to systematics is:
- first check for some subordination pattern
- then try to explain it phylogenetically,
we can't disagree more.

One should not confuse:
- what possibly occurred in the little history of science (possibly, Darwin 
trying to interpret the standard typological systematics of his time a new, 
phylogenetic way), with:
- a sound contemporaneous scientific approach: we're no more struggling our 
way toward an evolutionary explanation of life, we have this scientific 
theory as a starting point, and it makes all the difference. Science itself 
evolves, from early groping to maturity (hegelians should at least 
understand evolution, some way...).

Thus I don't try to interpret a given subordination pattern an evolutionary 
way. All to the contrary, from the beginning I plan to explain my data set 
with a phylogeny. This is what mature (at least, maturing) science is about.
My data set is a data matrix [taxa x characters], and a data matrix is NOT 
hierarchically organized in itself, there is no unique evident 
subordination in it (rather a potentially illimited number of subordination 
patterns you can frame). I explain this data matrix phylogenetically, 
according to models of character evolution, and I get a topology. Then I 
can use it to class species phylogenetically (monophyletically for 
instance: I name clades; or paraphyletically: I name phylogenetically 
coherent grades, whatever grades can mean...).

> >there are two features to be accounted for -
> >when did the groups diverge, and how different are the diverged groups:
> >cladistics and phenetics.

Two classic logics in systematics...

>If descent is the thesis, and difference is the antithesis,

I understand nothing to the preceding sentence. It must be purely 
Hegelian   ;-)

Thesis and antithesis are notions concerning human logics, not descriptors 
of the external world. I never saw an encounter between a thesis and an 
antithesis in the real world out there. By the way, how do you identify 
them? (I'm ready for a third type encounter experience).
If you mean logics, not ontology, I still don't get the point: how comes 
that the notion of "descent" would be the "anti" (? a "dialectic anti"?) 
of  the notion of "difference"? You can descent and be the same, or descent 
and be different. More than this, divergence is the mark of common descent 
(synapomorphy). You simply can't compare or oppose these notions (unless 
the manual of logical dialectics explains this a convincing way... what 
manual?...).
But Hegel was an idealist, anti-materialist and anti-scientific, and his 
logic extremely confuse, so this must absolutely be Hegelian (= definitely 
not scientific).

>  then maybe
>the dialectical resolution

I even know of nobody explicitly attempting to use Hegelian dialectics in 
contemporaneous science. Your'e apparently one, but it looks like it 
doesn't work.
How do you conceive "dialectical resolution of biological evolutionary 
theses"? (not on "maybe" grounds, but with some intelligible method of course).

>  is a classification in which each taxon is
>tagged, not with a category, but with a date, and a differentiation
>measure.

Datation was effectively one of Hennig's propositions for overcoming the 
"ranking" problem. This has all to do with contemporaneous evolutionary 
biology, and hence nothing with Hegel.
Now, classing phylogenetically and tagging for distance to other groups is 
a "Kinmanian" proposition (with permission, Ken), i.e. a multi-code 
classification. Seems that modern "digital data banks" computing systems 
can easily deal with multiple searching entries and selection criteria (and 
computer assisted identification too: the good old dichotomic 
identification key seems obsolete; never really worked anyway). By the way, 
arn't we here on TAXACOM???

>  Estimating the date is a straight-forward hypothesis, and it's
>often done. I don't know what the differentiation measure might be -
>something related to the old phenetic goal of 'overall similarity,' and
>maybe derived from a discriminant function between sister groups.
>
>I think it's too bad phenetics didn't attach itself to cladistics at an
>early era, but by the time it became apparent that cladistics was going
>to succeed, perhaps the two schools had called each other so many hard
>names that a reconciliation wasn't feasible.

More on phenetics / cladistics in next post.

>imho,
>fred.

in mine,
Pierre


Pierre Deleporte
CNRS UMR 6552 - Station Biologique de Paimpont
F-35380 Paimpont   FRANCE
Téléphone : 02 99 61 81 66
Télécopie : 02 99 61 81 88