Message 2001-02-0057: Re: Fwd: codes

Mon, 12 Feb 2001 11:33:31 -0600

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Date: Mon, 12 Feb 2001 11:33:31 -0600
From: "David M. Hillis" <>
Subject: Re: Fwd: codes

>David says: "Phil and I agree on many of the advantages of the
>PhyloCode, but we differ in that I do not want to create a competing,
>parallel system of nomenclature as Phil does."   This
>characterization of my view is not entirely accurate.  It is not
>that I "want" there to be parallel systems, but rather that I think
>that parallel systems are inevitable (at least for a while).
>Although David may envision the PhyloCode as merely an "upgrade" of
>the current system, there are many other people who see the
>differences between the two systems as quite fundamental. People who
>feel that the differences are fundamental and prefer the current
>system are not going to be willing to abandon it.  We can introduce
>the PhyloCode and promote its advantages, but we certainly can't
>force anyone to use it.

This is exactly the reason that the PhyloCode has to be forward- and 
reverse-compatible with the existing codes. Although we can't force 
people to use the PhyloCode rules, we can devise the PhyloCode in 
such a way that as people name new species or clades under the old 
codes, then all one has to do is register the name and provide a 
phylogenetic definition to make the new taxon fit under the 
PhyloCode. Since people will want to do this themselves with their 
own names (rather than have their names converted by someone else), 
they will do it as a matter of course, as long as the PhyloCode 
requirements don't conflict with the traditional Code requirements. 
Thus, although there may be parallel codes for a while, one set (the 
old ones) will basically be a subset of the other (PhyloCode), unless 
will do something stupid like make the forms of the names different. 
That is why I think it is important for the PhyloCode to use the same 
form of names as the old codes, so that descriptions under PhyloCode 
will also satisfy the requirements of the old codes. If we don't do 
this, then we really will force people to use one code or the other, 
rather than providing an upgrade of the old codes. Creating taxon 
descriptions that fit a new set of rules, but not the old set, would, 
in my opinion, create taxonomic chaos and two  parallel competing 
systems of nomenclature.

>David's perspective also seems to assume that everyone shares his
>(and my) preference for monophyletic taxonomy--i.e., the view that
>only species and clades should be given formal taxonomic recognition.
>However, there are many systematists who still have a phenetic
>perspective and are entirely comfortable with delimiting and naming
>paraphyletic groups (this may be more true in my field--botany--than
>in David's--vertebrate zoology).  Surely these people are not going
>to abandon the familiar system they grew up with in favor of the
>PhyloCode.  For this reason if no other, the two systems will operate
>in parallel for a time.  I would like to think that the entire
>taxonomic community will eventually adopt monophyletic taxonomy.  If
>this proves correct, and if phylogenetic nomenclature does not
>contain unforeseen flaws, the rank-based system may eventually be
>abandoned in favor of the PhyloCode.  But to think this will occur
>soon is, in my opinion, very naive.  I also think it would be unwise
>to abandon the traditional system until the PhyloCode has been tested
>for a number of years.  Can we be ABSOLUTELY SURE that it will work
>as well as we think it will?  What if we are wrong?   I prefer not to
>demolish the old highway bridge before the durability of the new
>improved one has been tested for a few years.

In this sense, we have two systems in operation now under the old 
codes. Many (the vast majority in my experience, although I realize 
that I have a biased sample) systematists reject paraphyletic groups 
now, and only use names that have been given to paraphyletic groups 
if the group concept is changed to include all the descendants of the 
common ancestor. That is the same under the old and new codes. I 
can't remember the last time I heard of someone purposefully 
supporting the naming or recognition of a paraphyletic group. 
However, if they did, other people would choose not to recognize it, 
even under the old codes. Nonetheless, if there are still people 
describing paraphyletic groups, then I'd want their descriptions to 
be easily convertible under the PhyloCode: as part of this 
conversion, the definition would make it clear that all the 
descendants of the common ancestor were a part of the group, and any 
synonyms with other names would become clear.

>>	This difference in goals explains why Phil and I have very
>>different perspectives about systems for naming species, for
>>instance. I want to use a system that uses names in exactly the same
>>form as the old codes, with the addition of a registration system
>>and phylogenetic context. That way, the old names can still be used,
>>but with value added. Phil wants new species names that can easily
>>be distinguished from the old ones, so that the two systems could be
>>used in parallel and combination.
>This is a little misleading.  The "new species names" I am in favor
>of differ only in form from the old ones--e.g., Quercus-alba versus
>Quercus alba.  Strictly speaking, David's preferred system (Method M
>in the 1999 Cantino et al. paper) changes species names more than my
>preferred system does; e.g., "Quercus alba" would become "alba" under
>Method M; however, Quercus could (and generally would) be placed
>before the species name to provide phylogenetic context and make the
>new name look like a Linnaean binomial.  So although the name "alba"
>(Method M) is more different from "Quercus alba" (the current name)
>than is "Quercus-alba" (Method B--my preferred approach), it is
>possible for the species name plus a "taxonomic address" (Quercus in
>this case) to look identical to a Linnaean binomial in Method M,
>whereas the name looks slightly different by inclusion of a hyphen in
>Method B.

Under Method M (and only under Method M among the Cantino et al. 
methods), the same species description can meet the requirements of 
both the old and new codes. Under Phil's preferred system, a 
description under the new rules would not fit the old rules, so one 
would either have to only describe  species under one set of rules, 
or publish two descriptions for the same species (one under each set 
of rules). That little hyphen causes all kinds of problems, and also 
fixes the name alba with a clade name that may be found to be 
misleading in the future (or, alternatively, the actual names keep 
changing). Only under Method M would the species still be referred to 
as Quercus alba (even though technically, the species name would be 
alba), and a single species description could serve any of the Codes 
(both old and new).

>>	I think the PhyloCode needs to be reverse-compatible. If I
>>switch to version 2.0 of a program, I still want to be able to read
>>and use files created in version 1.0, and I know that some friends
>>will probably not upgrade for a while and still send me files
>>created in version 1.0. I also want them to be able to read files
>>that I've created in 2.0, even if they can't take advantage of all
>>the new features. However, since version 2.0 has added features,
>>pretty soon everyone wants to upgrade, and once I get version 2.0 I
>>don't want to create files partly with 1.0 and partly with 2.0.
>>I see the PhyloCode in that context as well.
>I'm not convinced that "pretty soon everyone [will want] to upgrade."
>Systematists who don't buy into the phylogenetic paradigm that David
>and I (and presumably most people on this listserv) accept are
>unlikely to want to "upgrade" to the PhyloCode--hence the
>inevitability of two parallel systems for a while.

Certainly, if we don't make the new system an upgrade of the old 
system, but instead change the basic form of the new system so that 
it doesn't fit the rules of the old, then many people will be 
resistant to change. If the advantages of the system can be achieved 
without threatening the rules of the old system, then I expect that 
most people will want to "upgrade." There wouldn't be any penalty of 
doing so, and plenty of advantages. On the other hand, if the rules 
for describing a new species (for instance) under PhyloCode are such 
that the species description would not be applicable under the old 
codes, then the penalty is great and few people (including myself) 
would participate.


David M. Hillis
Director, School of Biological Sciences
Director's office: 512-232-3690 (FAX: 512-232-3699)
Alfred W. Roark Centennial Professor
Section of Integrative Biology
University of Texas
Austin, TX 78712
Research Office: 512-471-5792
Lab: 512-471-5661
FAX: 512-471-3878


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