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Date: Tue, 22 Nov 2005 13:07:02 -0500
To: David Marjanovic <email@example.com>
Subject: Re: Repost: An alternative to the Companion Volume?
Hi David, Kevin and I have been discussing your proposal and will continue to= =20 think about how to expedite the implementation of the PhyloCode. We= =20 have a prospective publisher (and a contract) for both the companion= =20 volume and the code itself: University of California Press. The=20 manuscripts are due early in 2007. Although we are behind schedule= =20 on the project, we have every intention of completing it. However,= =20 we have been discussing whether the volume should try to represent= =20 all clades of life (some far more thoroughly than others), as=20 currently planned, or whether we should request permission from UC= =20 Press to reduce the coverage in the first volume to certain groups= =20 (primarily plants and vertebrates) for which many specialists who are= =20 sympathetic to phylogenetic nomenclature are currently available.= =20 The first scenario would lead to there being a single starting date= =20 for all organisms. The second scenario would entail different=20 starting dates for different major clades, an option that the=20 Advisory Group had previously considered, and it might be quite some= =20 time before starting volumes for some major clades (particularly=20 arthropods) were completed. Although, as Mike Taylor pointed out, your proposals could be carried= =20 out in conjunction with the companion volume, I have concerns about= =20 some of the specifics. For one thing, I don't think it is realistic= =20 for the CPN to be responsible for assessing the acceptance of all= =20 published phylogenetically defined names after five or ten years.= =20 This would be an immense job. Publication of names in the Society's= =20 journal would help reduce the scope of task, but we are far from=20 having our own journal, and the assessment of frequency of use of= =20 names and definitions would have to consider all uses of the names in= =20 the full range of biological journals in which they may have been= =20 used. Furthermore, the decision whether a particular name was being=20 accepted, used, or ignored would be difficult to assess. There would= =20 be some clear cases, but a decision as to how many uses of a name= =20 would constitute enough support to register it durably would be=20 arbitrary. You suggest that names that are being ignored could be= =20 deleted from the registration database, but this would require=20 distinguishing lack of use that resulted from rejection by the=20 systematics community from lack of use that was simply a consequence= =20 of the clade not being a popular one for study or discussion. For= =20 names of little studied groups, it might not be possible to get an= =20 accurate assessment of acceptance after even 10 years.=20 David, although I do not support this particular proposal, I will= =20 take this opportunity to tell you how much both Kevin and I=20 appreciate your many efforts to improve the code, which are made=20 possible by your careful reading and thorough understanding of it. A= =20 set of proposed changes that the CPN is now considering includes=20 several that are based on your suggestions. Phil >I am reposting this (with a few small modifications) because I think= this >year's congress season is over, so more people might read it now tha= n the >first time... > >----- Original Message ----- >From: "David Marjanovic" <firstname.lastname@example.org> >Sent: Friday, October 21, 2005 7:14 PM > >I apologize for the somewhat unusual length; I think this matter is = very >important. Please bear with me. > >The idea of having a Companion Volume is to avoid having a gold rush= , a >competitive race where people run to get their favorite names and >definitions registered first. I wholeheartedly agree with this inten= tion. >But the Companion Volume may not be an effective way to implement it= . It >has two potential big problems: > >- If too few people contribute as authors and editors, the risk rise= s that >unwise* or unpopular names or definitions could be set in stone. Thi= s >would just about automatically lead the LARGE number of systematists >who have never heard of phylogenetic nomenclature to despise it, and >perhaps it would even drive away some current adherents. If the numb= er >of people in EITHER group becomes too large, the PhyloCode will go >the way of the BioCode. >- If too many people are involved, it will never reach publication. > >* =3D will produce confusion when the topology changes in unforeseen= but >foreseeable ways. > >The balance between these dangers is probably _very_ difficult to fi= nd, >and if we run out of luck, that balance might itself lie in an undes= irable >place (like containing many largely wise but rather unpopular names = and >definitions _and_ being published 10 years from now). > >Therefore I would like to suggest an, in my humble opinion, safer >alternative: Instead of having one volume published at once, we coul= d >spread the work over time -- by implementing the PhyloCode piecemeal= . >Here's how I imagine that: > >1. On the website, and maybe in the first issue of the Society's jou= rnal, >we post a notice that people are encouraged to publish papers (prefe= rably >collaboratively) on the nomenclature of their favorite clades. Such = papers >already exist; two examples (from tetrapods, where -- unfortunately = -- >almost all of the current discussion on PN happens) are cited below. >_____Maybe the publication of such papers should be restricted to th= e >Society's journal. This way we would make sure that we wouldn't miss= any >of them, and that all would abide to the PhyloCode. The disadvantage= would >be that it would (probably) slow down the whole process. > >2. The names in such a publication become _provisionally registered_= . > >3. A certain amount of time later (what about some five to ten years= ?) the >Committee on Phylogenetic Nomenclature (or whatever part or appointe= es >thereof) looks what has become of the names in that paper: Are they = being >used? Are they being ignored? Are they still being discussed? >_____If they are in general use, the CPN changes their registration = =66rom >provisional to durable (except maybe if the authors do not want this= anymore); >see the fourth point. >_____If they are being ignored, the CPN deletes them from the regist= ration >database. >_____If the discussion is still going on, it won't be interrupted --= the >CPN extends the time of provisional registration by another term. >_____Depending on the CPN's workload, the duration of a term should = be >considered a minimum (if the CPN has too much to do, it can simply >consider the issue later; all terms are automatically extended to th= e point at >which the CPN makes a decision). > >4. Upon durable registration, the authors of the names stay the same= , and >priority sets in. I'm not sure if the year and the registration numb= er >should change to reflect the date of durable registration, or whethe= r they >should stay, too, which might make the Code retroactive. This issue = needs >discussion. > >5. After the nomenclature of a part of the tree has been set in ston= e in >this way, anyone can name newly discovered clades in that part and c= an >immediately register them durably, but should maybe not need to do s= o. >(This should probably be restricted to new, as opposed to converted,= names.) > >In other words, each part of the tree gets its own Companion Volume = and >its own date for the implementation of the PhyloCode. >_____There is, by the way, a precedent for this: under the ICZN, pri= ority >starts in 1758, except for the spiders which start in 1751. (This >particular publication is simply declared by the ICZN to have been >published in 1758. We don't need to do such nonsense, we have the >registration numbers.) > >I hope to have started a vigorous discussion (and to have elevated t= he >impact factor of PaleoBios by an order of magnitude ;-) )! > >Addendum: >It may not be easy to just cancel the Companion Volume; I hear there= is >already a hopeful publisher, and so on. But dropping it may not be >necessary. As Mike Taylor has pointed out onlist: > >"I'd just like to point out that David's proposal does not=20 >[necessarily] entail >discarding the Companion Volume -- merely that the definitions >proposed in that volume, like all others, would originally be >_provisionally_ registered, to be affirmed or rejected after a >reasonable length of time. That way, we'd avoid painting ourselves >into a corner." > >I can see two potential advantages in this particular approach: > >- It would greatly lower the threshold on who is enough of an "exper= t" to >contribute. So if, for example, we don't find an entomologist, we si= mply >define Hexapoda, Insecta, Pterygota etc. ourselves and let the >entomologists discuss that. Ideally this would force them to familia= rize >themselves with PN and to start discussing definitions with each oth= er. >- It might speed up publication because it would spare the editors t= he >decision of whose preferred names get into the Companion Volume -- s= imply >include all of them! On the other hand, it might (!) be a good thing= if >our first publication were internally consistent. :-) > >References: >- Walter G. Joyce, John F. Parham & Jacques Gauthier: Developing a p= rotocol >for the conversion of rank-based taxon names to phylogenetically def= ined clade >names, as exemplified by turtles, Journal of Paleontology 78(5), 989= -- 1013 >(2004) >- Michael P. Taylor & Darren Naish: The phylogenetic taxonomy [sic] = of >Diplodocoidea (Dinosauria: Sauropoda), PaleoBios 25(2), 1 -- 7 (2005= ) >downloadable from http://www.miketaylor.org.uk/dino/pubs/ --=20 Philip D. Cantino Professor and Associate Chair Department of Environmental and Plant Biology Ohio University Athens, OH 45701-2979 U.S.A. Phone: (740) 593-1128; 593-1126 Fax: (740) 593-1130 e-mail: email@example.com