Message 2001-02-0056: Codes

Mon, 12 Feb 2001 11:16:24 -0500

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Date: Mon, 12 Feb 2001 11:16:24 -0500
From: Gerry Moore <>
Subject: Codes

Through some glitch my last message was incomplete. I try again below. 
Thanks to those who pointed this out to me.

I. Co-opting existing codes

In contrast to P. Cantino’s "two systems operating in parallel
approach", D. Hillis recently wrote that he viewed the PhyloCode as
an "upgrade" ("version 2") of the of the old system ("version 1")
and one that should "co-opt" the existing system. Such a view is
quite different than that put forward in the Preface of the PhyloCode. Also, 
Hillis noted that most of the resistance he had seen to the PhyloCode was 
from people who objected to the creation of a competing parallel system. 
This is different from the perspective I took away from the Nomenclatural 
Section at the 1999 International Botanical Congress (note: the symposia on 
phylogenetic nomenclature was not part of the Section). Phylogenetic 
nomenclature was discussed in an official capacity because a proposal was 
put before the Section to consider permitting the valid publication of 
"unranked" taxon names (it was defeated by a simple show of hands)and there 
was also much watercooler discussion of the topic during breaks. My take on 
those discussions was that most felt that it was fine for advocates of 
phylogenetic nomenclature to construct a different system so long as it did 
not co-opt or take over the existing system. Creating two systems parallel 
would allow people to use both systems and see for themselves which one 
worked better for their particular needs. Back in October 2000 a lengthy 
phylo nom thread developed on TAXACOM. Many of the comments were strongly 
critical of phylo nom. Phil C. performed the Herculean task of responding to 
almost all of the posts. He basically made the "parallel" argument, and it 
had a remarkably assuasive effect on that thread. Some who were strongly 
opposed even conceded that they might actually test drive phylogenetic 
nomenclature. I suspect that had he characterized the PhyloCode as the 
version 2 that would co-opt the version 1 (the exisitng codes) his comments 
would have generated much more heat than calm.

II. Under the PhyloCode we can do everything that we do with the
    existing codes

If this were the case then it would certainly make sense to regard
the PhyloCode as the "version 2" of the existing system. However, I
disagree with this assessment. Under phylogenetic nomenclature a name
is formally attached to a clade. Barring intervention by a
committee, it remains attached to that clade regardless of how the
content of the clade changes with changes in ideas about phylogeny.
Under traditional nomenclature names are not formally attached to
clades. I regard this difference between the two systems as so fundamental 
that it is inappropriate to characterize one as simply a
newer version of the other. Thus I do not agree with Hillis’s
assessment that "the PhyloCode can be designed so that it does
everything the old codes do…" . The two systems may use many of the
same names but the names are defined in very different ways. The
task before the systematic community now is to decide which one is
better. I believe that there is not enough evidence yet to make a
clear judgment here. It is simply not enough to develop a phylogenetic 
nomenclature for a group of organisms. We must allow these new nomenclatures 
to age to see how they handle changes in phylogenetic concepts. Having both 
systems in use parallel would allow us to study each system in the face of 
changing phylogenetic concepts. Hillis was critical of the existing system, 
noting that it required "diagnoses of taxa rather than phylogenetic 
definitions, and the diagnoses don't even have to be correct." However under 
the PhyloCode one can define taxon names under a phylogenetic hyopthesis 
that is also later proven incorrect. It is important to study what happens 
to the applications of these names in these cases (e.fg., how much content 
change occurs, how much need for formal conservation is there).

III. The Species problem

In his recent posts Hillis has stressed that the PhyloCode should
incorporate rules for species before any official status is accorded
to the code. Under such a set of rules what would the status of
names be that were created under the existing system? Would species
names also require formal conversion from the traditional system
into the phylogenetic system? Who would be responsible for handling
the issues relating to conservation and rejection of species names?
Would the standing committees that deal with these matters under the
existing system be "co-opted" by new committees under the PhyloCode?

Gerry Moore

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