[CPN] Fwd: Proposal to reorganize Note 9.3.1--USE THIS VERSION INSTEAD

Thu Jul 4 10:19:09 EDT 2013

Dear CPN members,

The version of the Note 9.3.1 reorganization that I sent you yesterday included some notes to ourselves and to David that I forgot to delete.  More importantly, I forgot to add some related changes in Articles 2 and 11 from a separate document.  Please discard the version I sent you yesterday and use the one attached to this message instead.

Thank you.

Phil

Begin forwarded message:

From: "Cantino, Philip" <cantino at ohio.edu<mailto:cantino at ohio.edu>>
Date: July 3, 2013 1:49:52 PM EDT
To: Committee on Phylogenetic Nomenclature <cpn at listserv.ohio.edu<mailto:cpn at listserv.ohio.edu>>
Subject: Fwd: [CPN] Proposal to reorganize Note 9.3.1

Dear CPN members,

You were probably beginning to wonder if I had dropped off the face of the earth, since I told you in mid-May that I would be able to send a revised proposal by early June.  Here it is at last, though you may not immediately recognize it as fundamentally the same proposal you looked over in April.

Partly in response to David Marjanovic's May 1 comments about the last version of our proposal, and partly out of Kevin's and my own feelings that it is inappropriate for something that is as central to the PhyloCode as phylogenetic definitions to be covered in a complex Note, Kevin took the initiative to draft an expansion of Note 9.3.1 into a series of articles.  After he and I did some fine-tuning, we sent it to David M. for comments.  David suggested several changes, most of which we adopted, and in some cases expanded on.  Because all three of us (Kevin, David and I) were slow to respond at various stages in this process due to other responsibilities, it has taken longer than I expected.  Although the resulting set of rules and notes is considerably longer than Note 9.3.1, this is not inappropriate given the importance of this section, which is likely to be the most frequently consulted portion of the code.

These rules include some references to other articles, some of which are numbered differently than in the current version of the code because of changes that have already been approved by the CPN or will be necessary if this expansion of Note 9.3.1 is adopted.  Specifically, Arts. 9.4 - 9.9 are the new articles included here.  Art 9.10 cited here is Art. 9.4 in the current online version of the code.  Art. 11.12, cited here is Art. 11.9 in the current code.

With many CPN members likely to be traveling during the summer, we should give ourselves enough time so that everyone can read the proposed changes carefully.  I suggest July 24 (three weeks) as a target date to send comments, but please let me know if your plans for this period make it difficult for you to do so in that time frame.  I am not asking for any voting at this time.  Please send your comments to the listserv, not to me personally.

Regards,
Phil

Begin forwarded message:

From: "Cantino, Philip" <cantino at ohio.edu<mailto:cantino at ohio.edu>>
Date: May 13, 2013 2:49:40 PM EDT
To: Committee on Phylogenetic Nomenclature <cpn at listserv.ohio.edu<mailto:cpn at listserv.ohio.edu>>
Subject: Fwd: [CPN] Proposal to reorganize really just Note 9.3.1 this time

Dear CPN members,

Although I had hoped to be able to generate a new revision of the proposals related to Note 9.3.1 last week, it is not ready.  Kevin and I worked on it via email last week and came up with wording we are both comfortable with on some issues, but we haven't had time yet to consider all of the aspects of David M's proposed reorganization of that Note (and related matters in that message).  Unfortunately, I am leaving town on Wednesday for nine days and will not be dealing with CPN business during that period, so it is going to have to wait a few weeks.  I will do my best to get to it soon after I return, but realistically, I think it is likely to be late May or early June before we can send you a revised proposal.

Regards,
Phil

Begin forwarded message:

From: "Cantino, Philip" <cantino at ohio.edu<mailto:cantino at ohio.edu>>
Date: May 3, 2013 2:08:01 PM EDT
To: Committee on Phylogenetic Nomenclature <cpn at listserv.ohio.edu<mailto:cpn at listserv.ohio.edu>>
Subject: Fwd: [CPN] Proposal to reorganize really just Note 9.3.1 this time

Dear CPN members,

Quite a few changes were suggested on Wednesday, and it may take a while for Kevin and me to work through them by email and generate a new revision of the original set of proposals.  I hope to be able to send it to you by the middle of next week but it could be later.

Regards,
Phil

Begin forwarded message:

From: Michel Laurin <michel.laurin at upmc.fr<mailto:michel.laurin at upmc.fr>>
Date: May 1, 2013 8:20:20 PM EDT
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] Proposal to reorganize really just Note 9.3.1 this time

Hi all,

    It is late, but I will be busy with something else tomorrow (technically, later today because it is 2:20AM), so I just want to add that after reading Kevin's and David's comments, with which I agree (at least at first glance), if the changes outlined by both are done, I think that I will feel comfortable voting for the amendment.

    Good night,

    Michel

On 02/05/13 02:10, David Marjanovic wrote:
The entire text of the version I propose follows. Because it is so different from the current wording, I have not marked additions and deletions, except where I propose to delete entire paragraphs.

=================================

Note 9.3.1. The definition of "clade" is "an ancestor (an organism, population, or species) and all of its descendants" (Art. 2.1). Building on this definition, clade names can be defined by pointing at such an ancestor, creating a phylogenetic definition. This can be done in different ways, such as the following:

 *   The ancestor can be mentioned directly in an ancestor-based definition: "A and all its descendants", where A is a specific organism, population, or species.
 *   Usually, however, the intended ancestor is not directly known. Thus, the ancestor can be indicated by its relation to two or more specifiers (Art. 11) that are mentioned directly:
    *   A minimum-clade definition [note the hyphen which makes clear that the clade, not the definition, is a minimum] may take the form [...]
    *   A maximum-clade definition may take the form [...]
    *   An apomorphy-based definition may take the form [...]
 *   The ancestor can be indicated by its relation to two or more specifiers that are not mentioned directly, but described as members of another clade that fulfill certain criteria. Such definitions may first describe an unnamed clade and then use its extant members (or those fulfilling another criterion) as specifiers for a minimum-clade definition:
    *   A maximum-modified crown clade definition [note the addition of "-modified" to avoid confusion because crown clades are minimum clades] may take the form [...]
    *   An apomorphy-modified crown clade definition may take the form [...]
 *   A crown clade in its entirety, mentioned by name, can be the internal specifier in the definition of the name of a total clade under the conditions specified in Art. 10.5. [This fact contradicts a claim in Note 11.1.2.]

[deletion of the two paragraphs that follow this list in the proposal we're currently discussing]

The above list is not exhaustive. Most importantly, definitions may contain qualifying clauses that restrict their applications to specific phylogenetic hypotheses (Art. 11.9).

The system of abbreviations used here [...]

For abbreviations involving qualifying clauses, see Note 11.9.1.

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--
Michel Laurin
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Mus�um National d�Histoire Naturelle
Batiment de G�ologie
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http://www2.mnhn.fr/hdt203/info/laurin.php

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