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Date: Mon, 18 Oct 2004 13:23:18 +0200
From: [unknown]
To: phylocode@ouvaxa.cats.ohiou.edu
Subject: Re: Mention of the Phylocode
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>Apart from being, I fear, hopelessly confusing, it could get us into=
some
>funny situations. For example... it could be illegal. If we tried to=
fix th=3D
e
>meaning of "t=3DE9trapode", we would be usurping the job of the Acad=
=3DE9mie
>Fran=3DE7aise; I wouldn't be surprised if that were illegal in Franc=
e.
>"Vernacular" doesn't only mean "English".
> This example may or may not be a wild exaggeration, but sup=
pose we
>give *Tetrapoda* to the crown-group and establish "tetrapod" for a m=
ember o=3D
f
>the apomorphy-based clade. How will we then call a member of *Tetrap=
oda*? A
>"tetrapodan", perhaps? Apart from (again) being very confusing, and
>_perpetuating_ the mistakes neontologists often make in ascribing fe=
atures
>of the crown-group to a larger clade, this couldn't be translated to=
German=3D
=3D2E
>I'm not sure, but probably even translating it to French would lead =
to
>problems.
=09Here, I completely agree with David. If=3D20
"tetrapod" means something else than "a member of=3D20
Tetrapoda", nomenclature will be in a state of=3D20
chaos and it will be difficult to determine what=3D20
authors mean. The two expressions must remain=3D20
synonymous.
> > "[...] These codes derive from
>> centuries of debate. For all their weaknesses, they are impressiv=
e
>> achievements that can be adapted to reflect new needs. [...]"
>
>Not if it is a new need to get rid of paraphyletic taxa.
>
>> Does the convention of attaching well-known
>> names to crown clades in all cases really bestow such advantages =
that th=3D
e
>> rest of the biological community will readily see the advantages =
and ado=3D
pt
>> this new system? (Heck, *I* am not convinced of this, and I am pr=
edispos=3D
ed
>> favourably to the PhyloCode.) Or will they react as these authors=
sugges=3D
t,
>> leaving PhyloCode supporters relatively isolated? We ignore our c=
olleagu=3D
es
>> at our own peril; I really do not think we have the critical numb=
ers tha=3D
t
>> our graduate students will multiply and spread the PhyloCode thro=
ughout
>> biology in future generations, as has been suggested by some.
>
>Well said.
=09Here, I agree that we have a dilemma, but=3D20
I would present it differently from Jason. Most=3D20
authors may THINK that Tetrapoda means "limbed=3D20
vertebrates", but in the neontological=3D20
literature, they use this word as if it meant=3D20
"the crown of limbed vertebrates". Yet, Jason=3D20
may be right that restricting many taxon names to=3D20
crowns will prove impopular in some fields.=3D20
However, do we want to tolerate a more imprecise=3D20
and sometimes misleading use of names because it=3D20
may prove more popular in some fields? I am not=3D20
being caricatural here; this question is a valid=3D20
one, and if necessary, it might perhaps be worth=3D20
asking the whole society (ISPN) or even many of=3D20
our colleagues outside the society what they=3D20
think. However, currently, there is nothing in=3D20
the PhyloCode that requires using popular names=3D20
for crowns (or to give a crown-clade definition=3D20
to popular names). See the following for an=3D20
example:
Note 10A.1. Recommendation 10A is not intended=3D20
either to encourage or to discourage the=3D20
application of preexisting names to crown,=3D20
apomorphy-based, or total clades, or to=3D20
node-based, apomorphy-based, or stem-based clades=3D20
generally. Because the associations of=3D20
preexisting names with precisely identified=3D20
clades commonly are ambiguous, reasonable=3D20
arguments can often be made for applying a=3D20
particular name to any one of several nested=3D20
clades.
=09Thus, under the current version of the=3D20
PhyloCode, how to define a popular name is a=3D20
matter of personal choice. Unless we plan to=3D20
change this, there may not be much point in doing=3D20
an extensive survey of how people feel about this=3D20
(unless most members of the ISPN want to take=3D20
this into consideration in their work). Under=3D20
the rank-based codes, I don't think that too many=3D20
taxonomists made opinion surveys before erecting=3D20
a new name or choosing a type.
=09However, I fully agree with Jason that we=3D20
have to be careful when deciding on whether or=3D20
not and how we implement the Pan-naming scheme.=3D20
This has been discussed a bit in the council of=3D20
the ISPN, and will be discussed more in the=3D20
PhyloCode Advisory Committee, but I agree with=3D20
Jason that the possible reactions of our=3D20
colleagues should be kept in mind when discussing=3D20
this.
Phil wrote:
> > For example, the notion that four-limbed
>> vertebrates that lie outside the crown are not
>> "tetrapods" understandably upsets people.
>> However, if we continue to allow the vernacular
>> name "tetrapod" to be used freely as individual
>> people see fit, it can be applied to the crown o
>> the total group or anything in between, as
>> desired by the user. If Tetrapoda is applied to
>> the crown, members of Pan-Tetrapoda could (and no
>> doubt would) be referred to as tetrapods.
=09This would be confusing to all, because=3D20
some "tetrapods" would be part of Tetrapoda and=3D20
others would not, and because some members of=3D20
Pan-Tetrapoda would have limbs, and others would=3D20
not (many known members of Pan-Tetrapoda are=3D20
finned sarcopterygians, such as Euthenopteron,=3D20
Osteolepis, Panderichthys, etc.). Thus, in this=3D20
case, I agree with David's response (below).
> > Permitting this reduces the intensity of feeling
>> about which clade (crown, total, or
>> apomorphy-based) a particular scientific name is
>> applied to.
David replied:
>I think this is not true. It just wouldn't happen. Most workers woul=
d apply
>"tetrapod" only to *Tetrapoda* and to nothing else.
> Anyone who didn't, however, would hopelessly confuse their =
student=3D
s,
>who would conclude in the opposite direction that *Tetrapoda* corres=
ponds t=3D
o
>whatever the professor calls a tetrapod. Researchers outside the fie=
ld of
>Devonian and Carboniferous tetrapod paleontology would find "tetrapo=
ds" in
>the literature and then write in their own works that *Tetrapoda* po=
ssesses
>such and such characteristics when it doesn't. Or they'd calibrate t=
heir
>molecular trees with the appearance of "tetrapods", get bogus result=
s, and
>publish them as sensations -- and then people would have to find out=
what
>precisely the original author meant with "tetrapods". (There are sev=
eral
>just such cases in the literature.)
> It would be almost as if phylogenetic definitions would sti=
ll not
>exist. It would be almost as if the PhyloCode had still not been int=
roduced=3D
=3D2E
>This is precisely the state of affairs we want to end, I think.
=09Exactly. I think that one of the=3D20
greatest benefits of the PhyloCode is to end=3D20
"fuzzy tree thinking", and using a vernacular=3D20
word in another meaning as its formal counterpart=3D20
would perpetuate this problem. I know of several=3D20
erroneous statements in the literature made=3D20
because of such nomenclatural problems. Here, we=3D20
have a real dilemma: do we tolerate a fuzzy or=3D20
variable meaning because it will not hurt=3D20
anybody's feelings (but then, why not simply=3D20
continue with the ICZN and ICBN?), or do we pick=3D20
ONE of these meanings? Even if we opt for the=3D20
latter, we can try to pick the most popular=3D20
option, and the recommendations currently in the=3D20
PhyloCode certainly advocate this or something=3D20
very close to this.
=09Finally, as far as I know, in the French=3D20
literature, a "t=3DE9trapode" is always thought of as=3D20
a member of the taxon Tetrapoda, just like a=3D20
"oiseau" (bird) is always thought of as a member=3D20
of the taxon Avis. The variety of meanings that=3D20
can be found for these terms just reflect "fuzzy=3D20
tree thinking"; paleontologists put all limbed=3D20
vertebrates in Tetrapoda or consider them=3D20
tetrapods, just like they consider all flying,=3D20
feathered dinosaurs to be part of Avis (birds),=3D20
but neontologists, when talking about tetrapods=3D20
and birds make statements that are known to be=3D20
true only of the crown, and when they date their=3D20
origin, that is really the origin of the crown.=3D20
I believe that some neontologists who made such=3D20
statements simply did not think that these two=3D20
entities were different, or if they were aware of=3D20
the difference (and this was probably common),=3D20
they did not bother to indicate that their=3D20
description applied to a subset of birds and=3D20
tetrapods. Since they have no access to fossils,=3D20
for many of them, the difference may appear=3D20
unimportant. However, conceptually and=3D20
biologically, the differences may be very=3D20
important.
=09Sincerely,
=09Michel
--=20
Michel Laurin
=3D46RE 2696, CNRS
Universit=3DE9 Paris 7 - Denis Diderot
2, place Jussieu
case 7077
75005 Paris
=3D46RANCE
tel. (33 1) 44 27 36 92
http://tolweb.org/tree/laurin/Laurin_Home_page.html
Secretary of the International Society for Phylogenetic Nomenclature=
=3D
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<html><head><style type=3D3D"text/css"><!--
blockquote, dl, ul, ol, li { padding-top: 0 ; padding-bottom: 0 }
--></style><title>Re: Mention of the Phylocode</title></head><body>
<blockquote type=3D3D"cite" cite>Apart from being, I fear, hopelessly
confusing, it could get us into some<br>
funny situations. For example... it could be illegal. If we tried to
fix the<br>
meaning of "t=3DE9trapode", we would be usurping the job of
the Acad=3DE9mie<br>
=3D46ran=3DE7aise; I wouldn't be surprised if that were illegal in
=3D46rance.<br>
"Vernacular" doesn't only mean "English".<br>
This example may or may no=
t
be a wild exaggeration, but suppose we<br>
give *Tetrapoda* to the crown-group and establish "tetrapod"=
;
for a member of<br>
the apomorphy-based clade. How will we then call a member of
*Tetrapoda*? A<br>
"tetrapodan", perhaps? Apart from (again) being very
confusing, and<br>
_perpetuating_ the mistakes neontologists often make in ascribing
features<br>
of the crown-group to a larger clade, this couldn't be translated to
German.<br>
I'm not sure, but probably even translating it to French would lead
to<br>
problems.</blockquote>
<div><br></div>
<div><x-tab> </x-tab>Here, =
I
completely agree with David. If "tetrapod" means
something else than "a member of Tetrapoda", nomenclature
will be in a state of chaos and it will be difficult to determine wha=
t
authors mean. The two expressions must remain synonymous.</div>
<div><br></div>
<blockquote type=3D3D"cite" cite>> "[...] These codes derive
=66rom<br>
> centuries of debate. For all their weaknesses, they are
impressive<br>
> achievements that can be adapted to reflect new needs.
[...]"<br>
<br>
Not if it is a new need to get rid of paraphyletic taxa.<br>
<br>
> Does the convention of attaching well-known<br>
> names to crown clades in all cases really bestow such advantages
that the<br>
> rest of the biological community will readily see the advantages
and adopt<br>
> this new system? (Heck, *I* am not convinced of this, and I am
predisposed<br>
> favourably to the PhyloCode.) Or will they react as these author=
s
suggest,<br>
> leaving PhyloCode supporters relatively isolated? We ignore our
colleagues<br>
> at our own peril; I really do not think we have the critical
numbers that<br>
> our graduate students will multiply and spread the PhyloCode
throughout<br>
> biology in future generations, as has been suggested by some.<br=
>
<br>
Well said.</blockquote>
<div><br></div>
<div><x-tab> </x-tab>Here, =
I
agree that we have a dilemma, but I would present it differently from
Jason. Most authors may THINK that Tetrapoda means "limbed
vertebrates", but in the neontological literature, they use this
word as if it meant "the crown of limbed vertebrates". =
;
Yet, Jason may be right that restricting many taxon names to crowns
will prove impopular in some fields. However, do we want to
tolerate a more imprecise and sometimes misleading use of names
because it may prove more popular in some fields? I am not bein=
g
caricatural here; this question is a valid one, and if necessary, it
might perhaps be worth asking the whole society (ISPN) or even many o=
f
our colleagues outside the society what they think. However,
currently, there is nothing in the PhyloCode that requires using
popular names for crowns (or to give a crown-clade definition to
popular names). See the following for an example:</div>
<div><br></div>
<div><font face=3D3D"Times" size=3D3D"-1" color=3D3D"#000000">Note 10=
A.1.
Recommendation 10A is not intended either to encourage or to
discourage the application of preexisting names to crown,
apomorphy-based, or total clades, or to node-based, apomorphy-based,
or stem-based clades generally. Because the associations of
preexisting names with precisely identified clades commonly are
ambiguous, reasonable arguments can often be made for applying a
particular name to any one of several nested clades.</font></div>
<div><br></div>
<div><x-tab> </x-tab>Thus,
under the current version of the PhyloCode, how to define a popular
name is a matter of personal choice. Unless we plan to change
this, there may not be much point in doing an extensive survey of how
people feel about this (unless most members of the ISPN want to take
this into consideration in their work). Under the rank-based
codes, I don't think that too many taxonomists made opinion surveys
before erecting a new name or choosing a type.</div>
<div><br></div>
<div><x-tab>
</x-tab>However, I fully agree with Jason that we have to be careful
when deciding on whether or not and how we implement the Pan-naming
scheme. This has been discussed a bit in the council of the
ISPN, and will be discussed more in the PhyloCode Advisory Committee,
but I agree with Jason that the possible reactions of our colleagues
should be kept in mind when discussing this. </div>
<div><br></div>
<div>Phil wrote:</div>
<div><br></div>
<blockquote type=3D3D"cite" cite>> For example, the notion that
four-limbed<br>
> vertebrates that lie outside the crown are not<br>
> "tetrapods" understandably upsets people.<br>
> However, if we continue to allow the vernacular<br>
> name "tetrapod" to be used freely as individual<br>
> people see fit, it can be applied to the crown o<br>
> the total group or anything in between, as<br>
> desired by the user. If Tetrapoda is applied to<br>
> the crown, members of Pan-Tetrapoda could (and no<br>
> doubt would) be referred to as tetrapods.</blockquote>
<div><br></div>
<div><x-tab> </x-tab>This
would be confusing to all, because some "tetrapods" would b=
e
part of Tetrapoda and others would not, and because some members of
Pan-Tetrapoda would have limbs, and others would not (many known
members of Pan-Tetrapoda are finned sarcopterygians, such as
Euthenopteron, Osteolepis, Panderichthys, etc.). Thus, in this
case, I agree with David's response (below).</div>
<div><br></div>
<blockquote type=3D3D"cite" cite>> Permitting this reduces the
intensity of feeling<br>
> about which clade (crown, total, or<br>
> apomorphy-based) a particular scientific name is<br>
> applied to.</blockquote>
<div><br></div>
<div>David replied:<br>
</div>
<blockquote type=3D3D"cite" cite>I think this is not true. It just
wouldn't happen. Most workers would apply<br>
"tetrapod" only to *Tetrapoda* and to nothing else.<br>
Anyone who didn't, however=
,
would hopelessly confuse their students,<br>
who would conclude in the opposite direction that *Tetrapoda*
corresponds to<br>
whatever the professor calls a tetrapod. Researchers outside the fiel=
d
of<br>
Devonian and Carboniferous tetrapod paleontology would find
"tetrapods" in<br>
the literature and then write in their own works that *Tetrapoda*
possesses<br>
such and such characteristics when it doesn't. Or they'd calibrate
their<br>
molecular trees with the appearance of "tetrapods", get
bogus results, and<br>
publish them as sensations -- and then people would have to find out
what<br>
precisely the original author meant with "tetrapods". (Ther=
e
are several<br>
just such cases in the literature.)<br>
It would be almost as if
phylogenetic definitions would still not<br>
exist. It would be almost as if the PhyloCode had still not been
introduced.<br>
This is precisely the state of affairs we want to end, I
think.</blockquote>
<div><br></div>
<div><x-tab>
</x-tab>Exactly. I think that one of the greatest benefits of
the PhyloCode is to end "fuzzy tree thinking", and using a
vernacular word in another meaning as its formal counterpart would
perpetuate this problem. I know of several erroneous statements
in the literature made because of such nomenclatural problems.
Here, we have a real dilemma: do we tolerate a fuzzy or variable
meaning because it will not hurt anybody's feelings (but then, why no=
t
simply continue with the ICZN and ICBN?), or do we pick ONE of these
meanings? Even if we opt for the latter, we can try to pick the
most popular option, and the recommendations currently in the
PhyloCode certainly advocate this or something very close to
this.</div>
<div><br></div>
<div><x-tab>
</x-tab>Finally, as far as I know, in the French literature, a
"t=3DE9trapode" is always thought of as a member of the tax=
on
Tetrapoda, just like a "oiseau" (bird) is always thought of
as a member of the taxon Avis. The variety of meanings that can
be found for these terms just reflect "fuzzy tree thinking"=
;
paleontologists put all limbed vertebrates in Tetrapoda or consider
them tetrapods, just like they consider all flying, feathered
dinosaurs to be part of Avis (birds), but neontologists, when talking
about tetrapods and birds make statements that are known to be true
only of the crown, and when they date their origin, that is really th=
e
origin of the crown. I believe that some neontologists who made
such statements simply did not think that these two entities were
different, or if they were aware of the difference (and this was
probably common), they did not bother to indicate that their
description applied to a subset of birds and tetrapods. Since
they have no access to fossils, for many of them, the difference may
appear unimportant. However, conceptually and biologically, the
differences may be very important.</div>
<div><br></div>
<div><x-tab>
</x-tab>Sincerely,</div>
<div><br></div>
<div><x-tab>
</x-tab>Michel</div>
<x-sigsep><pre>--=20
</pre></x-sigsep>
<div><font color=3D3D"#000000">Michel Laurin<br>
=3D46RE 2696, CNRS<br>
Universit=3DE9 Paris 7 - Denis Diderot<br>
2, place Jussieu<br>
case 7077<br>
75005 Paris<br>
=3D46RANCE<br>
<br>
tel. (33 1) 44 27 36 92</font></div>
<div><font
color=3D3D"#000000">http://tolweb.org/tree/laurin/Laurin_Home_page.ht=
ml</font
></div>
<div><br></div>
<div><font color=3D3D"#000000">Secretary of the<i> International Soci=
ety
for Phylogenetic Nomenclature</i></font></div>
</body>
</html>=3D
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