[CPN] Fwd: Proposal to reorganize Note 9.3.1--COMMENTS DUE BY WEDNESDAY

[de Queiroz, Kevin]

Hmmm, Jim says that the reasons for the changes are exceedingly abstruse, but then he admits that the new terms are theoretically better, which was the reason for changing them.  :)  In addition, these abstruse issues are considered very important by some critics of the PhyloCode.

More importantly, I suppose we could deal with the continuity issue by mentioning the older terms either in a Note or in footnotes.

Kevin

From: "James A. Doyle" <jadoyle at ucdavis.edu<mailto:jadoyle at ucdavis.edu>>
Date: Tuesday, July 23, 2013 9:10 PM
To: "cpn at listserv.ohio.edu<mailto:cpn at listserv.ohio.edu>" <cpn at listserv.ohio.edu<mailto:cpn at listserv.ohio.edu>>
Subject: Re: [CPN] Fwd: Proposal to reorganize Note 9.3.1--COMMENTS DUE BY WEDNESDAY

Hello Phil et al.,

At the last minute I've finally gone through all the e-mails on these issues since April.  The one thing that has bothered me all along is Brian's point about continuity of old and new terms.  At first the change in terminology struck me as one of those annoyances that turn people off to nomenclature of all kinds - first we ask people to adopt one new set of terms, like node- and branch-based, and then just when they think they finally understand them we tell them to forget all about it and adopt a new set, for reasons that seem exceedingly abstruse (sorry, Kevin).  But now I'm coming around to the notion that the new terms are theoretically better and self-explanatory enough, actually more so than the old ones, and as a neo/paleo person I'm relieved that the terms crown clade and total clade maintain their conspicuous roles.  The idea that you'll change the terminology throughout the companion volume is also a big relief.

Nevertheless, I really would feel better if the old terms were explicitly acknowledged in the text where the new terms are introduced, not relegated to the glossary, since so many people have seen the old terms in the literature on phylogenetic nomenclature and have made efforts to understand them.  At the very least this could be done parenthetically in terms such as "see Glossary for the relations of these terms to the widely used terms node-based and branch-based."

Jim

Brian,

This is a good point.  My understanding is that we editors will be responsible for changing all the terminology throughout the companion volume before it is published, so it will not be a headache for the authors and there will be no discrepancy between the companion volume and the code.  (Kevin, please confirm whether this is your understanding as well.)

As for your suggestion that the old terms be mentioned in the new text for the sake of continuity, since the old (current) terms are widely known and used, I think the best place to do that might be the glossary.

Phil


On Jul 23, 2013, at 6:08 PM, Brian Andres wrote:

> Greetings all,
>
>   I like how this section has been fleshed out commensurate to its importance. If the proposed changes are voted down, I would suggest keeping most of the new text with the old terminology. However, I do have one reservation for the proposed changes in terminology. If we excise all the node- and branch-based terms, are we going to ask all the authors for Companion Volume to rewrite their entries with these terms removed? Both the Examples_for_Authors and Instructions_for_Authors use these terms, and #5 under Format for Entries in the Instructions requires their use. I for one use these the old terms seven times in my entries. There is a tradition of using this terminology in the literature and previous versions of the Code, and I wonder if they should be at least mentioned in the discussion of minimum- and maximum-clade definitions for continuity and for this discrepancy between the Code and Companion Volume.
>
> Best,
> £á
>
> On Jul 23, 2013, at 1:47 PM, "Cantino, Philip" <cantino at ohio.edu<mailto:cantino at ohio.edu>> wrote:
>
>> David,
>>
>> Thank you for spotting the omitted quotation mark.  You raise a good point about multiple apomorphies.  If I recall correctly, a definition of this type was also used in one of the entries for the companion volume (I was not the lead editor on that one, so I may be mis-remembering).  The use of multiple apomorphies is not very different from the use of a single complex apomorphy, which is addressed in Art. 9.10 and Rec. 9E.   It may well be worth expanding that article and recommendation to cover complex apomorphies as well, or perhaps covering them separately but with wording parallel to that of Art. 9.10 and Rec. 9E.  I also wonder whether that article and recommendation should be moved up into the section of Article 9 that we are now considering.  However, I'd prefer to delay considering these questions  until we find out whether the proposal already on the table is approved by the CPN.  I'll make a note to myself so I don't forget to come back to this later.
>>
>> Phil
>>
>>
>> On Jul 22, 2013, at 3:21 PM, David Marjanovic wrote:
>>
>>> Good point in Note 9.5.2 about the use of external specifiers for minimum-clade definitions.
>>>
>>> In the explanation of apomorphy-modified crown clade definitions, the quotation mark after "the crown clade characterized by apomorphy M (relative to other crown clades) as inherited by A" is missing.
>>>
>>> Should we explicitly acknowledge the possibility of multiple apomorphies in an apomorphy-based definition? I've seen at least one in the literature, along the lines of "the first ancestor that had all of the following list of apomorphies inherited by A, plus all its descendants".
>>>
>>> That's all. :-)
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James A. Doyle
Department of Evolution and Ecology
University of California
Davis, CA 95616, USA
Telephone:  1-530-752-7591; fax:  1-530-752-1449