[CPN] Proposal to reorganize Note 9.3.1--revised in light of Michel's comments
Cantino, Philip
cantino at ohio.edu
Mon Jul 8 13:13:05 EDT 2013
Dear CPN members,
I sent you a proposed revision of Note 9.3.1 on July 3, asking that comments be sent by July 24. Michel read it very promptly and sent comments on July 5. Kevin and I have discussed Michel's suggested changes and incorporated three of them in the attached revision. I made the changes using Track Changes so you should easily find them.
Michel, you raised a fourth issue but we do not agree with you on that one, which concerns the recommended wordings for apomorphy-based definitions. You wrote: "None of these formulations seem sufficiently clear. They seem to allow use of homoplasy to define mutiple clades, although the singular would imply that only one of the clades possessing the apomorphy is designated (though not necessarily the one in which it is synapomorphic with A. Note that “as inherited by A” is ambiguous; a homoplasy may be indistinguishable from a synapomrophy, at the primary (historical) homology level. Take a very simple example, a substitution of a nucleotide (say, from A to T); it can happen in three clades, and it is indistinguishable. It is “as inherited in A” in all three. I think that the definitions should use “synapomorphic with A”, instead of “as inherited by A”. I raised this problem in the preliminary version; I am surprised that my comments were not incorporated into this version."
Regarding the final sentence of your comment, the wording you objected to in the preliminary version was "as exhibited by A". David M suggested changing this to "as inherited by A", we agreed, and that wording is used in the present version. I understand your objection to the "exhibited by" wording, but I don't see how "inherited by A" would lead to the homoplasy problem you described. Using your example, if state T is inherited by specifier A from an ancestor, the state T inherited by A only originated once, even if an indistinguishable state T originated in parallel elsewhere. In discussing this with Kevin, he added the following comment: "The fact that certain nucleotides are indistinguishable to us does not prevent us from inferring that they are homoplastic from the tree structure. And if they are homoplastic, then only the one that was inherited by A would count as satisfying the definition."
I am still asking that comments be sent by July 24, but please use the attached version (4b) instead of the one I sent on July 3.
Regards,
Phil
On Jul 5, 2013, at 7:40 AM, Michel LAURIN wrote:
Dear Phil et al.,
Indeed, I am currently in Lisbon, hence the delay. I have inserted a
few comments and suggestions (using tracked changes) in the attached
version (I hope that I used the latest version because Phil's message
seemed to include two slightly different versions).
Cheers,
Michel
Quoting "Cantino, Philip" <cantino at ohio.edu<mailto:cantino at ohio.edu>>:
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
UMR 7207
Mus?um National d?Histoire Naturelle
Batiment de G?ologie
Case postale 48
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F-75231 Paris cedex 05
FRANCE
http://www2.mnhn.fr/hdt203/info/laurin.php
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