Re: Taxon Search

[David Marjanovic <david.marjanovic@gmx.at>]

From: "Jaime A. Headden" <qilongia@yahoo.com>
Date: Sun, 04 Dec 2005 21:15:41 -0800 (PST)

> Meanwhile, enjoy an excellent paper:
>
>  Sereno, P. C. 2005. The logical basis of phylogenetic taxonomy.
>   _Systematic Biology_ 54:595-619.

It is quite interesting and makes several very good points, but I wouldn't 
quite call it "excellent". This starts with the (somewhat overblown) title 
-- there is no "phylogenetic taxonomy", only phylogenetic nomenclature. 
(The term "taxonomy" was invented as "the theory of classifications". 
People who apply phylogenetic nomenclature _do not classify_ -- they don't 
hack the Tree of Life apart and try to shoehorn the pieces into a set of 
boxes of predetermined sizes; instead they tie labels to defined places on 
the intact tree.)

On Paul Sereno's own request (I still don't know why he values my opinion 
that much...), I have written down all my comments to this paper. This is 
done in the format I reply to e-mails -- a quote followed by my comments. 
As a result, it is a Word document with 11 pages. If this doesn't scare 
you, feel free to request a copy!

>  "Abstract.?Phylogenetic taxonomy, like modern Linnean taxonomy, was
> modeled on a phylogenetic tree rather than a cladogram

Doesn't make any difference, except it allows somewhat more illustrative 
terminology.

> and, like its predecessor,
> perpetuates the use of morphology as a means of recognizing clades.

(This is about apomorphy-based definitions -- so it's about defining taxa, 
not just recognizing them.)

> (2) a complete notational scheme for phylogenetic definitions is
> presented that distinguishes symbolic notation from shorthand and
> longhand versions;

Better than the scheme currently used in the examples of the PhyloCode, 
but I hear a paper is in press which will offer much better 
alternatives...

TaxonSearch is clearly a good thing (apart from the criteria for 
determining "active" and "inactive" status, I'd say). I can't wait for it 
to grow!

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