[CPN] Fwd: Fwd: Proposal to reorganize Note 9.3.1--CALL FOR A VOTE

Mon Jul 29 15:08:10 EDT 2013

I hate apomorphy-based definitions, personally, because I don't think they
can be practically distinguished from diagnoses in most cases, even if
theoretically they are different.  But the perfect is sometimes the enemy
of the good.  -- kp

Kevin Padian
Professor and Curator
Department of Integrative Biology and Museum of Paleontology
University of California, Berkeley CA 94720

On Mon, Jul 29, 2013 at 11:32 AM, Michel Laurin <michel.laurin at upmc.fr>wrote:

>  I vote for, even though I still think that there are imprecisions in the
> formulation of apomorphy-based definitions...
>
>     Michel
>
> On 26/07/13 20:43, Cantino, Philip wrote:
>
>  Dear CPN members,
>
>  A new version of the proposal we have been discussing is attached
> (version 4d).  This version includes parenthetical references to the old
> terminology, as requested by several of you, and addresses Kevin de Q's
> concern with a new footnote.  The missing quotation mark pointed out by
> David has also been corrected.
>
>  At this point, I'd like to call for a vote on this set of proposed
> changes.   I assume that everyone has read it by now, but I also realize
> that there are various conferences going on right now, not to mention
> fieldwork and vacations, so I think we should give ourselves at least ten
> days.   I'm going to set Monday, August 5 as the target date to conclude
> the voting, but if anyone feels this is insufficient time, please let me
> know.
>
>  Your vote should be sent to the CPN listserv.
>
>  Thank you.
>
>  Phil
>
>
>
> Begin forwarded message:
>
>  *From: *"Cantino, Philip" <cantino at ohio.edu>
>  *Date: *July 25, 2013 9:41:38 AM EDT
>  *To: *Committee on Phylogenetic Nomenclature <cpn at listserv.ohio.edu>
>  *Subject: **Fwd: [CPN] Fwd: Proposal to reorganize Note 9.3.1--COMMENTS
> DUE BY WEDNESDAY*
>
>  I don't mind deleting the references to "stem-based", but I agree with
> Brian, Jim and Michel that the terms node-based and branch-based should be
> referenced in some way in these articles.  I'll have to delay the vote on
> this set of proposals until Kevin and I discuss this issue and hopefully
> come up with wording that everyone can live with.
>
>  Yesterday was the deadline for comments, so I am going to assume that
> everyone has read the proposal and, in the absence of other comments, the
> only issue that needs further attention before we vote is the referencing
> of the terms currently used for these definition types.
>
> Phil
>
>
> Begin forwarded message:
>
>  *From: *"de Queiroz, Kevin" <deQueirozK at si.edu>
>  *Subject: **Re: [CPN] Fwd: Proposal to reorganize Note 9.3.1--COMMENTS
> DUE BY WEDNESDAY*
>  *Date: *July 24, 2013 3:14:35 PM EDT
>  *To: *"Cantino, Philip" <cantino at ohio.edu>, Committee on Phylogenetic
> Nomenclature <cpn at listserv.ohio.edu>
>
> Well, as Phil noted, "nothing in a code of rules is ever as simple as it
> first appears."  I have reservations about these insertions, because they
> make it seem as though the pairs of terms are equivalent (i.e., that the
> newer terms are simply more accurate descriptively, but that both sets of
> terms are names for the same concepts).  In fact, the concepts themselves
> are not strictly equivalent.  This situation is illustrated by the
> following examples:  1) A directly-specified-ancestor definition is a
> special case of a minimum-clade definition, but it is not necessarily a
> special case of a node-based definition (it could also be branch-based).
>  2) A maximum-crown-clade definition is a special case of a maximum clade
> definition, but its supposed equivalent, the branch-modified node-based
> definition, is a special case of a node-based (rather than branch-based)
> definition.  Because the concepts are not strictly equivalent, I think it
> might cause unanticipated future confusion to treat them as if they are.
>
> In addition, even if we decide to include the insertions, I favor deleting
> reference to "stem-based definition" and "stem-modified node-based
> definition".  Those terms go back an additional generation and probably
> don't need to be covered here (they are covered in the Preface).  Moreover,
> they are misleading in that the term "stem" properly refers to a subset of
> branches (those that are parts stem lineages).
>
> Kevin
>
> From: <Cantino>, Phil Cantino <cantino at ohio.edu<mailto:cantino at ohio.edu<cantino at ohio.edu>
> >>
> Date: Wednesday, July 24, 2013 9:44 AM
> To: Committee on Phylogenetic Nomenclature <cpn at listserv.ohio.edu<
> mailto:cpn at listserv.ohio.edu <cpn at listserv.ohio.edu>>>
> Cc: Kevin de Queiroz <dequeirozk at si.edu<mailto:dequeirozk at si.edu<dequeirozk at si.edu>
> >>
> Subject: Fwd: [CPN] Fwd: Proposal to reorganize Note 9.3.1--COMMENTS DUE
> BY WEDNESDAY
>
> Dear CPN members,
>
> In light of the comments from Brian, Jim and Michel, I have modified the
> text to insert parenthetical references to the old terms for these
> definitions (see attached draft).  Kevin and I normally run drafts by each
> other before presenting them to the CPN, but this modification seems
> uncomplicated (though this is probably a rash comment on my part, as
> nothing in a code of rules is ever as simple as it first appears).  To save
> time, I am sending it to you at the same time as Kevin receives it.
>  (Kevin, if you could comment on this quickly, it would be helpful.)
>
> Others of you who have not commented and wish to, please go ahead and do
> so today.
>
> Thank you.
>
> Regards,
> Phil
>
>
>
> Begin forwarded message:
>
> From: James Doyle <jadoyle at ucdavis.edu<mailto:jadoyle at ucdavis.edu<jadoyle at ucdavis.edu>
> >>
> Date: July 23, 2013 9:10:24 PM EDT
> To: "cpn at listserv.ohio.edu<mailto:cpn at listserv.ohio.edu<cpn at listserv.ohio.edu>>"
> <cpn at listserv.ohio.edu<mailto:cpn at listserv.ohio.edu<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 <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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> Michel Laurin
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