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

[de Queiroz, Kevin]

Although I appreciate the fact that contributors would like for the Companion Volume to be moving along faster than it is, griping about it really doesn't help.  The editors could also complain about some of the authors, including those who complain the most.  If both sides would just stick to doing their part, the project would move forward more quickly.

Changing the names of the definitions in the contributions will not be overly time-consuming.  That's the least of our problems with keeping the volume moving forward.

Finally, I'm not sure why some people are worried that other people (who are not involved in phylogenetic nomenclature or the PhyloCode) think that the project might be dead.  They're just wrong.  It doesn't really matter what they think.

Kevin

From: Michel Laurin <michel.laurin at upmc.fr<mailto:michel.laurin at upmc.fr>>
Date: Wednesday, July 24, 2013 2:31 AM
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

Dear colleagues,

    I also strongly prefer that the old terms be mentioned in the text, not only in the glossary, for reasons that Jim just explained very well.

    I am also relieved that the editors will handle this change in terminology in the Companion Volume contributions, for which the editorial process has been nightmarish, in my opinion. Never in my career have I seen a book be in preparation for so long, nor the papers come back to me so often or after so long (like a couple of years between submission or revision and feedback on that version). I still have a few to revise but I have not found time to do so simply because I have more urgent things to do, like finalizing papers or revising papers that I know will get decisions within a couple of months, as opposed to this book which may be published in the next decade... But I will try to get to those revisisons this Fall, after my long Latino-American trip (which means in November). In these revisions, I will not worry about the change in terminology because I have enough to do with these short, extremely densely-commented contributions. And when I discussed the CV with another contributor, whose name I will not disclose because I did not ask for his permission to cite him, he told me that he was annoyed because his contributions kept coming back with more comments, and that if they came back once more, he would just give up... So, this is a touchy issue and I sure hope that Phil's understanding about how the CV editors will handle this is shared by Jacques and Kevin.

    Incidentally, the long delay in implementing our code because of the CV is still leading colleagues to wonder if the project is dead; at ICVM-10 in Barcelona, a couple of weeks ago, I have a discussion about this with J. Hanken, and I cleared up this issue. But I have no idea how many others think like him... So I just hope that the extra work for the CV editors will not mean adding another couple of years in publication of this much-overdue book.

    Michel

On 24/07/13 03:10, James Doyle wrote:
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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