<!doctype html public "-//W3C//DTD W3 HTML//EN">
<html><head><style type="text/css"><!--
blockquote, dl, ul, ol, li { padding-top: 0 ; padding-bottom: 0 }
--></style><title>Re: [CPN] Fwd: Proposal to reorganize Note
9.3.1--COMMENTS</title></head><body>
<div>Hello Phil et al.,</div>
<div><br></div>
<div>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.</div>
<div><br></div>
<div>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."</div>
<div><br></div>
<div>Jim</div>
<div><br></div>
<blockquote type="cite" cite>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>
> Greetings all,<br>
><br>
><x-tab> </x-tab>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>
><br>
> Best,<br>
> ��<br>
><br>
> On Jul 23, 2013, at 1:47 PM, "Cantino, Philip"
<cantino@ohio.edu> wrote:<br>
><br>
>> David,<br>
>><br>
>> 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.</blockquote>
<blockquote type="cite" cite>>><br>
>> Phil<br>
>><br>
>><br>
>> On Jul 22, 2013, at 3:21 PM, David Marjanovic wrote:<br>
>><br>
>>> Good point in Note 9.5.2 about the use of external
specifiers for minimum-clade definitions.<br>
>>><br>
>>> 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>
>>><br>
>>> 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 type="cite" cite>>>> That's all. :-)</blockquote>
<blockquote type="cite" cite>>>>
_______________________________________________<br>
>>> CPN mailing list<br>
>>> CPN@listserv.ohio.edu<br>
>>> http://listserv.ohio.edu/mailman/listinfo/cpn<br>
>><br>
>><br>
>> _______________________________________________<br>
>> CPN mailing list<br>
>> CPN@listserv.ohio.edu<br>
>> http://listserv.ohio.edu/mailman/listinfo/cpn<br>
><br>
><br>
> _______________________________________________<br>
> CPN mailing list<br>
> CPN@listserv.ohio.edu<br>
> http://listserv.ohio.edu/mailman/listinfo/cpn<br>
<br>
<br>
_______________________________________________<br>
CPN mailing list<br>
CPN@listserv.ohio.edu<br>
http://listserv.ohio.edu/mailman/listinfo/cpn</blockquote>
<div><br></div>
<div><br></div>
<x-sigsep><pre>--
</pre></x-sigsep>
<div>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</div>
</body>
</html>
<html><head><style type="text/css"><!--
blockquote, dl, ul, ol, li { padding-top: 0 ; padding-bottom: 0 }
--></style><title>Re: [CPN] Fwd: Proposal to reorganize Note
9.3.1--COMMENTS</title></head><body>
<div>Hello Phil et al.,</div>
<div><br></div>
<div>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.</div>
<div><br></div>
<div>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."</div>
<div><br></div>
<div>Jim</div>
<div><br></div>
<blockquote type="cite" cite>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>
> Greetings all,<br>
><br>
><x-tab> </x-tab>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>
><br>
> Best,<br>
> ��<br>
><br>
> On Jul 23, 2013, at 1:47 PM, "Cantino, Philip"
<cantino@ohio.edu> wrote:<br>
><br>
>> David,<br>
>><br>
>> 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.</blockquote>
<blockquote type="cite" cite>>><br>
>> Phil<br>
>><br>
>><br>
>> On Jul 22, 2013, at 3:21 PM, David Marjanovic wrote:<br>
>><br>
>>> Good point in Note 9.5.2 about the use of external
specifiers for minimum-clade definitions.<br>
>>><br>
>>> 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>
>>><br>
>>> 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 type="cite" cite>>>> That's all. :-)</blockquote>
<blockquote type="cite" cite>>>>
_______________________________________________<br>
>>> CPN mailing list<br>
>>> CPN@listserv.ohio.edu<br>
>>> http://listserv.ohio.edu/mailman/listinfo/cpn<br>
>><br>
>><br>
>> _______________________________________________<br>
>> CPN mailing list<br>
>> CPN@listserv.ohio.edu<br>
>> http://listserv.ohio.edu/mailman/listinfo/cpn<br>
><br>
><br>
> _______________________________________________<br>
> CPN mailing list<br>
> CPN@listserv.ohio.edu<br>
> http://listserv.ohio.edu/mailman/listinfo/cpn<br>
<br>
<br>
_______________________________________________<br>
CPN mailing list<br>
CPN@listserv.ohio.edu<br>
http://listserv.ohio.edu/mailman/listinfo/cpn</blockquote>
<div><br></div>
<div><br></div>
<x-sigsep><pre>--
</pre></x-sigsep>
<div>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</div>
</body>
</html>