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Date: Fri, 09 Feb 2001 16:12:00 -0600
From: "David M. Hillis" <dhillis@mail.utexas.edu>
To: PhyloCode@ouvaxa.cats.ohiou.edu
Subject: codes
<!doctype html public "-//W3C//DTD W3 HTML//EN"> <html><head><style type="text/css"><!-- blockquote, dl, ul, ol, li { margin-top: 0 ; margin-bottom: 0 } --></style><title>codes</title></head><body> <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><br></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 replace</blockquote> <blockquote type="cite" cite>the rank-based system, but it certainly won't replace it in the near<br> future. Some magazine articles have emphasized the abandonment of<br> "Linnaean" nomenclature (after all, journalists love controversy),<br> but it is clear to me that the two systems will operate in parallel<br> for long while. Thus, the rank-based system will remain available<br> for those who want to delimit and name phenetic groupings, and the<br> PhyloCode will be available for those who wish to discover and name<br> clades. People whose study groups are poorly known phylogenetically<br> may want to use both systems in the taxonomy of a single group. If<br> so, symbols can be used used to indicate which names are governed by</blockquote> <blockquote type="cite" cite>which code.</blockquote> <div><br></div> <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> </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> </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 >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 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> </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> </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> </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 implemented.</div> <div>David Hillis</div> <div><br> 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> E-mail: dhillis@mail.utexas.edu</div> </body> </html>