[CPN] Fwd: Fwd: Proposal to reorganize Note 9.3.1--CALL FOR A VOTE
Kevin PADIAN kpadian at berkeley.eduMon Jul 29 15:08:10 EDT 2013
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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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