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

Mon Jul 29 15:22:16 EDT 2013

Well, with the use of ontologies apomorphy-based definitions actually could be very practical.  This is something I am working on right now with Hilmar Lapp from Nescent.  We have a NSF grant due on 8/13 where we plan to ontologize phylogentic definitions, all of them, node-based, branch-based, apomorphy-based.  We have a prototype too and it works fairly well.  All so that we can navigate and query the tree of life using phyloreferences as coordinates, just like in any map.  Wish us luck.

Nico
P.S. I vote yes.

On Jul 29, 2013, at 3:08 PM, Kevin PADIAN wrote:

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<mailto: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<mailto:cantino at ohio.edu>>
Date: July 25, 2013 9:41:38 AM EDT
To: Committee on Phylogenetic Nomenclature <cpn at listserv.ohio.edu<mailto: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<mailto: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<mailto:cantino at ohio.edu>>, Committee on Phylogenetic Nomenclature <cpn at listserv.ohio.edu<mailto: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><mailto: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><mailto:cpn at listserv.ohio.edu>>
Cc: Kevin de Queiroz <dequeirozk at si.edu<mailto:dequeirozk at si.edu><mailto: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><mailto: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><mailto:cpn at listserv.ohio.edu>" <cpn at listserv.ohio.edu<mailto: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><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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