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<div class="moz-cite-prefix">I vote for, even though I still think
that there are imprecisions in the formulation of apomorphy-based
definitions...<br>
<br>
Michel<br>
<br>
On 26/07/13 20:43, Cantino, Philip wrote:<br>
</div>
<blockquote cite="mid:F55A6EB3-AAC3-4E84-B06B-B3977DA2D0CE@ohio.edu"
type="cite">
<meta http-equiv="Content-Type" content="text/html;
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<div style="">
<div>Dear CPN members,</div>
<div><br>
</div>
<div>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.</div>
<div><br>
</div>
<div>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.</div>
<div><br>
</div>
<div>Your vote should be sent to the CPN listserv.</div>
<div><br>
</div>
<div>Thank you.</div>
<div><br>
</div>
<div>Phil</div>
<div><br>
</div>
</div>
<div style="">
<div><br>
<div><br>
<div>Begin forwarded message:</div>
<br class="x_Apple-interchange-newline">
<blockquote type="cite">
<div style="margin-top:0px; margin-right:0px;
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<span style="font-family:'Helvetica'; font-size:medium"><b>From:
</b></span><span style="font-family:'Helvetica';
font-size:medium">"Cantino, Philip" <<a
moz-do-not-send="true"
href="mailto:cantino@ohio.edu">cantino@ohio.edu</a>><br>
</span></div>
<div style="margin-top:0px; margin-right:0px;
margin-bottom:0px; margin-left:0px">
<span style="font-family:'Helvetica'; font-size:medium"><b>Date:
</b></span><span style="font-family:'Helvetica';
font-size:medium">July 25, 2013 9:41:38 AM EDT<br>
</span></div>
<div style="margin-top:0px; margin-right:0px;
margin-bottom:0px; margin-left:0px">
<span style="font-family:'Helvetica'; font-size:medium"><b>To:
</b></span><span style="font-family:'Helvetica';
font-size:medium">Committee on Phylogenetic
Nomenclature <<a moz-do-not-send="true"
href="mailto:cpn@listserv.ohio.edu">cpn@listserv.ohio.edu</a>><br>
</span></div>
<div style="margin-top:0px; margin-right:0px;
margin-bottom:0px; margin-left:0px">
<span style="font-family:'Helvetica'; font-size:medium"><b>Subject:
</b></span><span style="font-family:'Helvetica';
font-size:medium"><b>Fwd: [CPN] Fwd: Proposal to
reorganize Note 9.3.1--COMMENTS DUE BY WEDNESDAY</b><br>
</span></div>
<br>
<div style=""> 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.
<div><br>
</div>
<div>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.<br>
<div><br>
<div>Phil</div>
<div><br>
<div><br>
<div>Begin forwarded message:</div>
<br class="x_Apple-interchange-newline">
<blockquote type="cite">
<div style="margin-top:0px; margin-right:0px;
margin-bottom:0px; margin-left:0px">
<span style="font-family:'Helvetica';
font-size:medium"><b>From: </b></span><span
style="font-family:'Helvetica';
font-size:medium">"de Queiroz, Kevin" <<a
moz-do-not-send="true"
href="mailto:deQueirozK@si.edu">deQueirozK@si.edu</a>><br>
</span></div>
<div style="margin-top:0px; margin-right:0px;
margin-bottom:0px; margin-left:0px">
<span style="font-family:'Helvetica';
font-size:medium"><b>Subject: </b></span><span
style="font-family:'Helvetica';
font-size:medium"><b>Re: [CPN] Fwd:
Proposal to reorganize Note
9.3.1--COMMENTS DUE BY WEDNESDAY</b><br>
</span></div>
<div style="margin-top:0px; margin-right:0px;
margin-bottom:0px; margin-left:0px">
<span style="font-family:'Helvetica';
font-size:medium"><b>Date: </b></span><span
style="font-family:'Helvetica';
font-size:medium">July 24, 2013 3:14:35 PM
EDT<br>
</span></div>
<div style="margin-top:0px; margin-right:0px;
margin-bottom:0px; margin-left:0px">
<span style="font-family:'Helvetica';
font-size:medium"><b>To: </b></span><span
style="font-family:'Helvetica';
font-size:medium">"Cantino, Philip" <<a
moz-do-not-send="true"
href="mailto:cantino@ohio.edu">cantino@ohio.edu</a>>,
Committee on Phylogenetic Nomenclature
<<a moz-do-not-send="true"
href="mailto:cpn@listserv.ohio.edu">cpn@listserv.ohio.edu</a>><br>
</span></div>
<br>
<div>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.<br>
<br>
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).<br>
<br>
Kevin<br>
<br>
From: <Cantino>, Phil Cantino <<a
moz-do-not-send="true"
href="mailto:cantino@ohio.edu">cantino@ohio.edu</a><<a
moz-do-not-send="true"
href="mailto:cantino@ohio.edu">mailto:cantino@ohio.edu</a>>><br>
Date: Wednesday, July 24, 2013 9:44 AM<br>
To: Committee on Phylogenetic Nomenclature
<<a moz-do-not-send="true"
href="mailto:cpn@listserv.ohio.edu">cpn@listserv.ohio.edu</a><<a
moz-do-not-send="true"
href="mailto:cpn@listserv.ohio.edu">mailto:cpn@listserv.ohio.edu</a>>><br>
Cc: Kevin de Queiroz <<a
moz-do-not-send="true"
href="mailto:dequeirozk@si.edu">dequeirozk@si.edu</a><<a
moz-do-not-send="true"
href="mailto:dequeirozk@si.edu">mailto:dequeirozk@si.edu</a>>><br>
Subject: Fwd: [CPN] Fwd: Proposal to
reorganize Note 9.3.1--COMMENTS DUE BY
WEDNESDAY<br>
<br>
Dear CPN members,<br>
<br>
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.)<br>
<br>
Others of you who have not commented and
wish to, please go ahead and do so today.<br>
<br>
Thank you.<br>
<br>
Regards,<br>
Phil<br>
<br>
<br>
<br>
Begin forwarded message:<br>
<br>
From: James Doyle <<a
moz-do-not-send="true"
href="mailto:jadoyle@ucdavis.edu">jadoyle@ucdavis.edu</a><<a
moz-do-not-send="true"
href="mailto:jadoyle@ucdavis.edu">mailto:jadoyle@ucdavis.edu</a>>><br>
Date: July 23, 2013 9:10:24 PM EDT<br>
To: "<a moz-do-not-send="true"
href="mailto:cpn@listserv.ohio.edu">cpn@listserv.ohio.edu</a><<a
moz-do-not-send="true"
href="mailto:cpn@listserv.ohio.edu">mailto:cpn@listserv.ohio.edu</a>>"
<<a moz-do-not-send="true"
href="mailto:cpn@listserv.ohio.edu">cpn@listserv.ohio.edu</a><<a
moz-do-not-send="true"
href="mailto:cpn@listserv.ohio.edu">mailto:cpn@listserv.ohio.edu</a>>><br>
Subject: Re: [CPN] Fwd: Proposal to
reorganize Note 9.3.1--COMMENTS DUE BY
WEDNESDAY<br>
<br>
Hello Phil et al.,<br>
<br>
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.<br>
<br>
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."<br>
<br>
Jim<br>
<br>
Brian,<br>
<br>
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.)<br>
<br>
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.<br>
<br>
Phil<br>
<br>
<br>
On Jul 23, 2013, at 6:08 PM, Brian Andres
wrote:<br>
<br>
<blockquote type="cite">Greetings all,<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite"> 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.<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">Best,<br>
</blockquote>
<blockquote type="cite">£á<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">On Jul 23, 2013, at
1:47 PM, "Cantino, Philip" <<a
moz-do-not-send="true"
href="mailto:cantino@ohio.edu">cantino@ohio.edu</a><<a
moz-do-not-send="true"
href="mailto:cantino@ohio.edu">mailto:cantino@ohio.edu</a>>>
wrote:<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">David,<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">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.<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">Phil<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">On Jul 22, 2013,
at 3:21 PM, David Marjanovic wrote:<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">Good point in
Note 9.5.2 about the use of external
specifiers for minimum-clade
definitions.<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">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.<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">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".<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">That's all. :-)<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">_______________________________________________<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">CPN mailing list<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><a
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<blockquote type="cite">
<blockquote type="cite">
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<blockquote type="cite"><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">_______________________________________________<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">CPN mailing list<br>
</blockquote>
</blockquote>
<blockquote type="cite">
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<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">_______________________________________________<br>
</blockquote>
<blockquote type="cite">CPN mailing list<br>
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_______________________________________________<br>
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<br>
<br>
--<br>
<br>
<br>
James A. Doyle<br>
Department of Evolution and Ecology<br>
University of California<br>
Davis, CA 95616, USA<br>
Telephone: 1-530-752-7591; fax:
1-530-752-1449<br>
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<pre class="moz-signature" cols="72">--
Michel Laurin
UMR 7207
Muséum National d’Histoire Naturelle
Batiment de Géologie
Case postale 48
43 rue Buffon
F-75231 Paris cedex 05
FRANCE
<a class="moz-txt-link-freetext" href="http://www2.mnhn.fr/hdt203/info/laurin.php">http://www2.mnhn.fr/hdt203/info/laurin.php</a></pre>
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