[CPN] Fwd: Proposal to reorganize Note 9.3.1--COMMENTS DUE BY WEDNESDAY
James Doyle
jadoyle at ucdavis.edu
Tue Jul 23 21:10:24 EDT 2013
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> 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
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