[CPN] Article 1 and "taxon"

[David Marjanovic]

As I said, I've been wondering about Article 1 and its similarity to the 
Glossary entry for "taxon". So I looked up what the rank-based codes 
have instead, and searched the PhyloCode for "tax".

== The rank-based codes ==

Art. 1 of the ICZN 
http://www.nhm.ac.uk/hosted-sites/iczn/code/includes/page.jsp?article=1 
is titled "Definition and scope" -- not of the ICZN, but of "zoological 
nomenclature": Art. 1.1 reads "Zoological nomenclature is the system of 
scientific names applied to taxonomic units (taxa; singular: taxon) of 
extant or extinct animals." Art. 1.1.1 explains what is meant by 
"animals". Art. 1.2 makes explicit what is included (e. g. fossils that 
don't contain any substance that belonged to the  living animal), 1.3 
makes explicit what is excluded, 1.4 asserts independence from the other 
rank-based codes. Art. 2 deals with taxa classified as animals at one 
time but not another, Art. 3 defines the starting point.

Art. 1.1 of the ICBN (2006) 
http://ibot.sav.sk/icbn/frameset/0005Ch1Art001.htm reads: "Taxonomic 
groups of any rank will, in this _Code_, be referred to as taxa 
(singular: taxon)." Art. 1.2 and 1.3 introduce morphotaxa; Art. 2 and 3 
introduce ranks.

The ICNB, as of 1992, never explains "taxon". There isn't even a 
glossary! The term "taxa" appears for the first time in General 
Consideration 4 http://www.ncbi.nlm.nih.gov/books/n/icnb/A154/ -- it is 
evidently assumed that the code will be read by taxonomists, who already 
know what a taxon is.

== Search results from the PhyloCode==

Apart from Principle 5, for which see below, "taxon"/"taxa"/"subtaxa" 
occurs in four different ways:

-- Where it could simply be omitted: 6.4, Art. 7.2, Example 1 of 11A 
(first occurrence), Glossary entry: phylogenetic definition. The first 
two cases have "name of a taxon"; in many other places, the PhyloCode 
just uses "name" instead.
-- Where it could be replaced by "clade": Principles 1 through 4, Art. 
6.5, 6.6, 9.10 (arguably), 10.1 (later "paraphyletic group" three 
times), 11.8 with both Notes, Example 1 of 11.9, 13.1, 13.3, 13.5, 14.1, 
Example 1 of Note 15.11.1, all Examples of 15.13, 21A, Glossary entries: 
accepted name, apomorphy-modified node-based definition, branch-modified 
node-based definition (first two occurrences). Many of these were 
probably written when we still expected to add rules for species names 
before implementation.
-- Where it refers to taxa (potentially) recognized under rank-based 
codes: 9.8 (incl. Note 9.8.2 with Example), Example 2 of Note 9.8A.1, 
10.1B (arguably), 10D, 10E (arguably), 10G (probably), Example 2 of 
11.9, 11A (main text), Example 1 of 11A (second and third occurrence), 
11C, 17.1, Notes 21.4A2 and -3, 21.4B with Examples 2 and 5, Example 3 
of Note 21A.3, Glossary entries: categorical rank, definition, 
description, diagnosis, epithet, extant (arguably), homonym (arguably -- 
see 13.1), hybrid formula (arguably), phylogenetic system, rank, 
rank-based system, synonym (arguably -- see 14.1), taxon (first 
sentence), type. This usage is, importantly, _not_ covered by Art. 1 or 
by Phil's proposal for the Glossary entry of "taxon".
-- Where it clearly refers specifically to clades and species: Glossary 
entries: apomorphy-based definition, branch-modified node-based 
definition (third occurrence), taxon (second sentence). In the Glossary 
entry for "branch-modified node-based definition", "taxa" could be 
replaced by "organisms".

What, actually, is the status of the Glossary? Are its entries meant to 
have the force of Articles and apply exclusively to the PhyloCode, or 
are they meant to merely explain the terms used in nomenclature, as far 
as they happen to occur in the PhyloCode? Different entries seem to 
assume one or the other, sometimes apparently even both.

== Suggestions ==

Abandon the implication that the PhyloCode is about the names of taxa. 
It is, for now at least, specifically about the names of clades. Therefore:

-- Omit "taxon"/"taxa" where the term is unnecessary; replace it by 
"clade" or "organisms" where that is meant; keep it elsewhere. I'm not 
sure what to do with the Glossary entry for "apomorphy-based definition".
-- Restrict the glossary entry for "taxon" to the following: "A grouping 
of organisms (e.g., a clade) that has been, or could be, given a name 
under a code of nomenclature. Taxa can be nested." This assumes that the 
Glossary is meant to explain the terms, not define them specifically for 
the PhyloCode.
-- Delete Article 1. We might replace it with an article about scope and 
the starting point, but all that is already explained in the Preamble 
and the Principles.

== What else I found during the search of the PhyloCode ==

-- The Example to Note 9.8.2 cites "Olmstead and Judd (20xx)". That 
should be rectified.
-- Example 1 to Note 15.11.1 says that Angiospermae has synapomorphies. 
But Hennig was pickier than that. Being one clade, it has autapomorphies 
(auto- = self); only two or more taxa can share synapomorphies (syn- = 
together).
-- Preamble item 1 should contain a reference to Art. 2, where "clade" 
is defined and explained.
-- Perhaps "permits" should be replaced by "does not restrict" in 
Principle 6; that sounds less authoritarian. Also in Principle 6, 
"taxonomic opinion" should be shortened to "opinion" -- it is already 
explained immediately afterwards as "with regard to hypotheses about 
relationships"; to this explanation, we should probably add "or ranks" 
and reference Art. 3.
-- Perhaps we should rewrite Principle 5. How about: "Phylogenetic 
context. This code assumes evolution (descent with heritable 
modification); it is concerned with the naming of clades and the 
application of clade names in the context of phylogenetic hypotheses." 
But, actually, this is all already implied in Preamble item 1, so maybe 
we should simply delete Principle 5.