Re: Classification: A Definition

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

Combined answer:

----- Original Message ----- 
From: "Jerry D. Harris" <jharris@dixie.edu>
Sent: Wednesday, May 09, 2007 11:26 PM

> > As David pointed out, phylogenetic nomenclature is not classification;
> it's an alternative to classification.
>
> I must admit, this comment has been nagging at me [...]
> Considering the following more or less typical definitions
> of "classification":
>
> MERRIAM-WEBSTER
> -------------------------
> 1: the act or process of classifying. 2 a: systematic arrangement in 
> groups or categories according to established criteria; specifically : 
> taxonomy b: class, category
>
> OXFORD ENGLISH DICTIONARY
> ---------------------------------------
> 1. The action of classifying or arranging in classes, according to common 
> characteristics or affinities; assignment to the proper class.
> 2. The result of classifying; a systematic distribution, allocation, or 
> arrangement, in a class or classes; esp. of things which form the 
> subject-matter of a science or of a methodic inquiry.

I agree with these definitions, and I maintain that phylogenetic 
nomenclature does not fit them. Assignment to the proper clade is not done 
by phylogenetic nomenclature, it's done by the science of phylogenetics. PN 
just takes those clades and names them; it's not concerned with what they do 
or should contain.

> The nomenclature is a means of providing names to entities (classes) that 
> exist/are ascertained to exist based on evolutionary descent; this differs 
> from the Linnean system of providing names to entities based on a few 
> gross physical similarities, sans regard to evolutionary relationships. 
> Either way, it's using a set of criteria to designate (i.e., name) groups.

Yes...

> [...] -- but still seems to me to be classification.  _Tyrannosaurus_
> is still classified as a member of the Coelurosauria, Tetanurae, 
> Theropoda,
> Dinosauria, Archosauria, Tetrapoda, Vertebrata, etc.

No, it's not. It is _found_ to be a member of all these groups.

Phylogenetics does that for us. We just take that tree with *Tyrannosaurus* 
in it and tie labels to the places the phylogenetic definitions of the 
labels tell us. We don't _put_ organisms into groups, we name groups, and we 
_find_ organisms to be in- or outside.

> I can see that phylogenetic NOMENCLATURE is _in itself_ not
> classification (not without the systematics part), but it also isn't an
> _alternative_ to classification.  Or am I missing the point here?

It's not really an alternative. Phylogenetics and PN together make 
classification completely superfluous; it just drops out of the equation; 
neither it nor any alternative is needed. "How should I translate a tree 
into a classification" turns out to be a wrong question, like Lowell & 
Dingus's famous "why did Napoleon cross the Mississippi".

----- Original Message ----- 
From: "Tim Williams" <twilliams_alpha@hotmail.com>
Sent: Thursday, May 10, 2007 2:28 AM

> Not only did the "Protista" concept vastly understate the huge 
> phylogenetic diversity of single-celled eukaryotes, but we even had a 
> situation where certain protists were classified as BOTH animals and
> plants (e.g., _Euglena_).

But not by the same people at the same time. In some classifications, they 
are animals; in others, they are plants; both at the same time is not 
allowed.

----- Original Message -----
From: "Colin McHenry" <cmchenry@westserv.net.au>
Sent: Thursday, May 10, 2007 3:15 AM

> Hear, hear.  The question is, if you're not putting together the phylocode 
> as an alternative classification system, then why are you doing it?

We have given up trying to solve the unsolvable problem. Instead we have 
eliminated it.

> I remember my high school biology
> teacher talking about Euglena: "it's a plant!
> No, it's an animal.  No, wait..."

I remember _my_ biology teachers saying that ("zoologists say it's an 
animal, botanists say it's a flagellated alga [like *Chlamydomonas* or so, 
presumably]" as late as the year _two thousand_ (the year I finished 
school).

Incidentally, I don't think the cytoskeleton comes from spirochaetes. All 
bacteria and archaea have a homolog of the tubulins (FtsZ) which performs a 
pretty similar function in the same way. That's taught these days in the 
cell biology lecture third-semester students of molecular biology are 
expected to take. (It was, of course, discovered long after Margulis came up 
with her idea... does she even still hold it?)

"Educate" is from "to lead out of".