Message 2001-02-0049: codes

Fri, 09 Feb 2001 16:12:00 -0600

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Date: Fri, 09 Feb 2001 16:12:00 -0600
From: "David M. Hillis" <>
Subject: codes

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<div>I had not intended to answer John Janovec's questions, since
these topics have been covered extensively before, but my perspective
is sufficiently different from one point in Phil's posting that I
felt compelled to respond:</div>
<div>At 2:24 PM -0500 2/9/01, Philip Cantino wrote:</div>
<blockquote type="cite" cite>The PhyloCode may or may not ever
<blockquote type="cite" cite>the rank-based system, but it certainly
won't replace it in the near<br>
future.&nbsp; Some magazine articles have emphasized the abandonment
&quot;Linnaean&quot; nomenclature (after all, journalists love
but it is clear to me that the two systems will operate in
for long while.&nbsp; Thus, the rank-based system will remain
for those who want to delimit and name phenetic groupings, and the<br>
PhyloCode will be available for those who wish to discover and
clades.&nbsp; People whose study groups are poorly known
may want to use both systems in the taxonomy of a single group.&nbsp;
so, symbols can be used used to indicate which names are governed
<blockquote type="cite" cite>which code.</blockquote>
<div>I don't see the two systems operating in parallel; I view the
PhyloCode as co-opting and improving the existing system. The way I
have used phylogenetic nomenclature, and will continue to use it, is
to define the existing names (as well as new taxa) in a phylogenetic
context. The existing codes don't actually define taxa in terms of
phylogeny; they restrict names based on type species and subjective
decisions of taxonomic limits. There are diagnoses of taxa rather
than phylogenetic definitions, and the diagnoses don't even have to
be correct. Ranks are required in the existing systems, but they are
optional (not necessarily eliminated) in phylogenetic nomenclature.
Thus, in my mind, we can do everything that we do with the existing
codes in the PhyloCode, but the added bonus is that we replace a
subjective, inherently non-evolutionary system with an objective
system that is designed to be positively informative about
evolutionary relationships. I would not throw out the old names, or
even how they are used (except where that usage conflicts with
evolutionary history, which many proponents of the existing codes
would do in any case); I would simply define the existing names in an
objective fashion, and remove the constraints of <i>mandatory</i>
ranks that are often misinformative. I agree with Phil that a big
advantage of the new system is that there are no <i>required</i>
ranks, so that if we have no information about the relationships at a
certain level, then we don't have to create artificial and
misinformative groups. Thus, the PhyloCode is even more compelling
for poorly studied groups than it is for well-studied ones.</div>
<div><x-tab>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </x-tab>It is
true that we could simply add phylogenetic definitions to existing
rules and accomplish some of these same goals. However, in addition,
the PhyloCode has these advantages:</div>
<div>1. ALL clades would be defined phylogenetically. Thus, we would
know what was meant by the use of a certain name, and be assured that
the group was actually a real historical group in the tree of Life.
Right now, we have no way of determining if a given name applies to a
real group, and 100 systematists could use that name in at least 100
different ways, since that is a subjective decision.</div>
<div>2. The PhyloCode makes ranking optional. I see this as a huge
advantage over the existing system. It eliminates a lot of endless
arguing about the rank of a given taxon, when this is obviously a
subjective decision. If ranks are useful, they can be applied in the
new system, but the taxa are applied to the same branch on the Tree
of Life no matter what arbitrary rank they are given.</div>
<div>3. The PhyloCode would incorporates a registration system for
all names. This will be critical to efforts to record and document
the world's biodiversity and recover the Tree of Life, and would be a
tremendous boon to basic systematic work.</div>
<div><x-tab>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </x-tab>In
summary, 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. Instead, I want to design the
PhyloCode so that the existing names and usages are defined
phylogenetically and incorporated into the new system. I want the
system to work so that names that are defined under the old codes can
be easily converted and incorporated into the new system in a manner
that will be transparent to &gt;99% of the users (most of whom will
not want to be bothered by the details, or inconvenienced by needless
name changes). I see the new system as a major upgrade of the old
system, not something that we would use in parallel. In other words,
I see the PhyloCode as version 2.0 of the combined old codes. I want
the work of people who still use version 1.0&nbsp; of one of the
taxon-specific codes to still be applicable, with a minor
translation, to version 2.0 (until such time as everyone uses version
2.0). However, it is clear to me that the old codes are simply not up
to the task of incorporating the needed improvements, especially if
we are going to have any hope of cataloging the world's biodiversity
and describing the Tree of Life.</div>
<div><x-tab>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </x-tab>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. In my vision for the PhyloCode, the only way to
distinguish if someone was using the old systems or the PhyloCode
would be whether or not there was value added: people who used the
PhyloCode would have explicit, phylogenetic definitions for their
taxa, all their taxa would be real historical groups, and the names
would be part of a registry so that information on the taxa
(including their definitions, authorship, publication history, etc.)
could be readily accessed. If ranks were deemed useful, they could be
used, but the use and limits of the names would not change because of
arbitrary ranking decisions. Thus, users of the old codes (versions
1.0) would be using basically the same names, but with less
information and stability of use.</div>
<div><x-tab>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </x-tab>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. That is why I have argued all along for a
system that can still be recognized and used with the old codes, but
adds value to the old system.</div>
<div><x-tab>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </x-tab>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.
I think it already does that for clades, and I will continue to argue
that it must do the same thing for species before it can be
<div>David Hillis</div>

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


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