Message 2005-12-0053: Re: Repost: An alternative to the Companion Volume?

Tue, 22 Nov 2005 13:07:02 -0500

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Date: Tue, 22 Nov 2005 13:07:02 -0500
From: [unknown]
To: David Marjanovic <>
Subject: Re: Repost: An alternative to the Companion Volume?

Hi David,

Kevin and I have been discussing your proposal and will continue to=
think about how to expedite the implementation of the PhyloCode.  We=
have a prospective publisher (and a contract) for both the companion=
volume and the code itself: University of California Press.  The=20
manuscripts are due early in 2007.  Although we are behind schedule=
on the project, we have every intention of completing it.  However,=
we have been discussing whether the volume should try to represent=
all clades of life (some far more thoroughly than others), as=20
currently planned, or whether we should request permission from UC=
Press to reduce the coverage in the first volume to certain groups=
(primarily plants and vertebrates) for which many specialists who are=
sympathetic to phylogenetic nomenclature are currently available.=
The first scenario would lead to there being a single starting date=
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=
time before starting volumes for some major clades (particularly=20
arthropods) were completed.

Although, as Mike Taylor pointed out, your proposals could be carried=
out in conjunction with the companion volume, I have concerns about=
some of the specifics.  For one thing, I don't think it is realistic=
for the CPN to be responsible for assessing the acceptance of all=
published phylogenetically defined names after five or ten years.=
This would be an immense job. Publication of names in the Society's=
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=
names and definitions would have to consider all uses of the names in=
the full range of biological journals in which they may have been=

Furthermore, the decision whether a particular name was being=20
accepted, used, or ignored would be difficult to assess.  There would=
be some clear cases, but a decision as to how many uses of a name=
would constitute enough support to register it durably would be=20
arbitrary.  You suggest that names that are being ignored could be=
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=
of the clade not being a popular one for study or discussion.  For=
names of little studied groups, it might not be possible to get an=
accurate assessment of acceptance after even 10 years.=20

David, although I do not support this particular proposal, I will=
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=
set of proposed changes that the CPN is now considering includes=20
several that are based on your suggestions.


>I am reposting this (with a few small modifications) because I think=
>year's congress season is over, so more people might read it now tha=
n the
>first time...
>----- Original Message -----
>From: "David Marjanovic" <>
>Sent: Friday, October 21, 2005 7:14 PM
>I apologize for the somewhat unusual length; I think this matter is =
>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=
>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=
>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=
>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=
>foreseeable ways.
>The balance between these dangers is probably _very_ difficult to fi=
>and if we run out of luck, that balance might itself lie in an undes=
>place (like containing many largely wise but rather unpopular names =
>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=
>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=
>we post a notice that people are encouraged to publish papers (prefe=
>collaboratively) on the nomenclature of their favorite clades. Such =
>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=
>Society's journal. This way we would make sure that we wouldn't miss=
>of them, and that all would abide to the PhyloCode. The disadvantage=
>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=
>thereof) looks what has become of the names in that paper: Are they =
>used? Are they being ignored? Are they still being discussed?
>_____If they are in general use, the CPN changes their registration =
>provisional to durable (except maybe if the authors do not want this=
>see the fourth point.
>_____If they are being ignored, the CPN deletes them from the regist=
>_____If the discussion is still going on, it won't be interrupted --=
>CPN extends the time of provisional registration by another term.
>_____Depending on the CPN's workload, the duration of a term should =
>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=
>should change to reflect the date of durable registration, or whethe=
r they
>should stay, too, which might make the Code retroactive. This issue =
>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=
>immediately register them durably, but should maybe not need to do s=
>(This should probably be restricted to new, as opposed to converted,=
>In other words, each part of the tree gets its own Companion Volume =
>its own date for the implementation of the PhyloCode.
>_____There is, by the way, a precedent for this: under the ICZN, pri=
>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=
>impact factor of PaleoBios by an order of magnitude ;-) )!
>It may not be easy to just cancel the Companion Volume; I hear there=
>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=
>define Hexapoda, Insecta, Pterygota etc. ourselves and let the
>entomologists discuss that. Ideally this would force them to familia=
>themselves with PN and to start discussing definitions with each oth=
>- It might speed up publication because it would spare the editors t=
>decision of whose preferred names get into the Companion Volume -- s=
>include all of them! On the other hand, it might (!) be a good thing=
>our first publication were internally consistent. :-)
>- Walter G. Joyce, John F. Parham & Jacques Gauthier: Developing a p=
>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
>- Michael P. Taylor & Darren Naish: The phylogenetic taxonomy [sic] =
>Diplodocoidea (Dinosauria: Sauropoda), PaleoBios 25(2), 1 -- 7 (2005=
>downloadable from

Philip D. Cantino
Professor and Associate 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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