Message 2001-02-0051: Fwd: codes

Sat, 10 Feb 2001 19:58:42 -0500

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Date: Sat, 10 Feb 2001 19:58:42 -0500
From: Philip Cantino <>
Subject: Fwd: codes

Responding to David Hillis's most recent message:

Let me start by emphasizing the points of agreement between me and
David.  As he pointed out, we agree on many of the advantages
of the PhyloCode.  In addition, we agree that the code should
ultimately govern the naming of species as well as clades; we
disagree only on the timing of this.  He feels that it would be best
not to implement the rules for clades until rules for species have
been added, whereas I feel it would be better to implement the rules
for clades before adding rules for species.  Perhaps we should
discuss the reasoning behind each of these views, but that is not my
purpose here.  Rather, I want to respond to David's juxtaposition of
our views about the relationship between the PhyloCode and the
existing system.

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.

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.

David wrote:

>I see the new system as a major upgrade of the old system, not
>something that we would use in parallel.

When I say that the systems will operate in parallel, I don't mean
that an individual systematist will necessarily use both (although
one may want to use both when working with groups that are very
poorly known phylogenetically, as I suggested in an earlier message).
Rather, both systems will be available for those who wish to use
them, and it will, by and large, be different people who will use the
PhyloCode than the current system.  I hope that all phylogenetic
systematists will eventually use the PhyloCode--and perhaps only the
PhyloCode.  However, I  suspect that many systematists who are
primarily interested in species-level descriptive taxonomy and have a
phenetic perspective on supraspecific groupings will prefer to stick
with the rank-based system.

>	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.

>	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.

>	I think this represents a fundamental difference in
>perspective and goals between Phil and myself, and at some point we
>are going to have to go one way or the other. Some people may not
>want to go along with the effort if we go one way, and some will not
>want to go along if we go the other. I think most of the resistance
>I've seen to the PhyloCode is from people who object to the creation
>of a competing, parallel system, and I agree with their perspective.
>However, there is no reason that the PhyloCode has to do that: the
>PhyloCode can be designed so that it does everything the old codes
>do, but adds value at the same time, and brings nomenclature up to
>the third millennium.

 From the perspective of those who prefer traditional taxonomy, the
PhyloCode doesn't do "everything the old codes do."  Because the
PhyloCode is designed to link names explicitly to particular clades,
it doesn't have the flexibility that the existing codes do to modify
the boundaries of taxa in order to maintain the taxonomic content
associated with a name.  For those who place priority on naming
clades, this reduced flexibility is an acceptable price to pay for
the increased stability of clade names provided by the PhyloCode, but
for those who have no objection to paraphyletic groups and who are
mainly interested in grouping species into easily recognizable (even
if artificial) groups, and even for some cladists who put a lot of
emphasis on clade content (see Benton, 2000 and Nixon & Carpenter,
2000), the existing codes are preferable.  We are not going to bring
these people around to preferring the PhyloCode--hence the
inevitability of two parallel systems.


Philip D. Cantino
Professor and Chair
Department of Environmental and Plant Biology
Ohio University
Athens, OH 45701-2979

Phone: (740) 593-1128; 593-1126
Fax: (740) 593-1130


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