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Date: Tue, 14 Sep 2004 11:50:38 -0500
From: [unknown]
To: phylocode@ouvaxa.cats.ohiou.edu
Subject: Re: Thoughts on the Paris meeting
--Boundary_(ID_2nZz+/qzL4KaFtURNGONcA)
Content-type: text/plain; charset=3Diso-8859-1; format=3Dflowed
Content-transfer-encoding: quoted-printable
Hi All (I accidentally sent this to the=3D20
PhyloAdvisors list - sorry to those who got it=3D20
before)
I think Scott's message and the rather negative=3D20
spin of the New Scientist article should be a=3D20
wake-up call. I agree with Scott that the=3D20
PhyloCode has become too concerned with the=3D20
narrow concerns of vertebrate paleontologists and=3D20
too little concerned with the much bigger issues=3D20
of facilitating the naming and analysis of extant=3D20
diversity. The way to achieve this it to strive=3D20
for a less legalistic and more computer-friendly=3D20
structure.
Our model should not just be the ICZN and ICBN=3D20
but GenBank, TreeBase etc. As I have said=3D20
before, the ideal would be a system that=3D20
circumvented traditional publication of names and=3D20
allowed direct submission of converted and new=3D20
clade and species names to a registry database.=3D20
The design of such a database and the rules=3D20
governing required fields and their content=3D20
would, in effect, be the "code." To be sure one=3D20
would need editorial process to avoid chaos due=3D20
to ill-informed or malicious individuals, but=3D20
whether the editorial input is at the=3D20
data-base/registry end or in the handling of=3D20
formal manuscripts it would seem that the load=3D20
put on the community would be the same (I for one=3D20
would find it easier to act as a reviewer of a=3D20
data-base entry in a predefined format than a=3D20
full manuscript).
As I attempted to argue to several people at the=3D20
meeting, making the PhyloCode a computer-based=3D20
endeavor would tend to argue for a simple system=3D20
employing only topology-based definitons (stem-=3D20
and node-based) - but there is room for=3D20
discussion.
While I was happy with the agreement that species=3D20
should be treated as epithet-derived uninomials,=3D20
I agree with Scott that the authorship mechanisms=3D20
may not be the best. Reference to a database=3D20
accession number would seem cleaner.
I would be very interested to know how many of=3D20
you (if any) share my concerns and, equally, how=3D20
many of you feel we have gone too far down the=3D20
legalistic Code route to change course now.
David
>As an interested observer, but currently not a=3D20
>full fledged Phylocode advocate, I was probably=3D20
>an anomaly at the Paris meeting. Also, I appear=3D20
>to have been the only mycologist there save for=3D20
>a half day attendance by a French colleague,=3D20
>whom unfortunately I never realized was there=3D20
>that day.
>
>Having said this, I have a few observations to=3D20
>share. But before that I would like to thank=3D20
>Michel Laurin for helping to arranging things=3D20
>and helping to host the meeting. It was a=3D20
>privilege to attend the meeting at the=3D20
>prestigious Mus=3DE9um National d'Histoire Naturelle=3D20
>and the examples of fine French cuisine arranged=3D20
>for the breaks and the social dinner were=3D20
>outstanding.
>
>As an outsider I was somewhat surprised by the=3D20
>number of palaeontologist at the meeting, which=3D20
>in retrospect perhaps should have been=3D20
>anticipated. I had expected the majority of=3D20
>Phylocode advocates to be those involved with=3D20
>DNA or protein sequence data. It now dawns on me=3D20
>why apomorphies are being used as specifiers,=3D20
>and it bewilders me as to how anatomical=3D20
>characters are objectively scored (as it is=3D20
>always slightly subjective when scoring=3D20
>morphological features). It was also an=3D20
>eye-opener to note the lack of representatives=3D20
>in microbiology and entomology, and the=3D20
>relatively few botanists. During one coffee=3D20
>break a contributor optimistically stated that=3D20
>within 10 years everybody in biology would be=3D20
>adopting the Phylocode, but I think that is=3D20
>naive, and unrealistic given the lack of=3D20
>interest in the code by major groups of=3D20
>biologists. The other disappointment was the=3D20
>fact that the registration database was not up=3D20
>and running smoothly for the meeting. There were=3D20
>still too many glitches.
>
>The debate on incorporating species into the=3D20
>code took a worrying direction by the shift=3D20
>towards using current species epithets (stripped=3D20
>of generic names) but leaving attached authors'=3D20
>names, year and page (or reference) if=3D20
>necessary. One of the burden's of the current=3D20
>codes (ICBN, ICZN, ICNB) is the author=3D20
>citations, particularly for the botanical code=3D20
>that involves authors of new combinations being=3D20
>added on. Adding authors' names on taxon names=3D20
>always introduces the ego factor (no matter how=3D20
>noble one might believe themselves to be). The=3D20
>historic codes in part did this to help track=3D20
>names through literature. Such is unnecessary=3D20
>when every single name in this code is in a=3D20
>database. Authorship is irrelevant and can be=3D20
>eliminated because each has a unique=3D20
>registration number. There is the grand=3D20
>opportunity to rise above everyone's collective=3D20
>egos (but of course nobody wanted to do this).=3D20
>Suggesting now that authors names (year of=3D20
>publication or validation) become part of=3D20
>species names actually goes several steps=3D20
>further in an illogical direction.
>
>With regard to fungi, I noted in the current draft the following:
>
>Recommendation 10 E. Names referring to mitotic=3D20
>asexual morphs (anamorphs) of ascomycete and=3D20
>basidiomycete fungi are treated by the ICBN and=3D20
>Draft BioCode as applicable only to the organ or=3D20
>morph represented by their type, not to the=3D20
>fungus in all its morphs (holomorph), which is=3D20
>considered to be represented by the teleomorph,=3D20
>i.e. the morph characterized by the production=3D20
>of asci/ascospores, basidia/basidiospores,=3D20
>teliospores, or other basidium-bearing organs.=3D20
>Because of the frequent polyphyly of the sets of=3D20
>species to which anamorph names traditionally=3D20
>apply, the names of clades of ascomycete and=3D20
>basidiomycete fungi should not be based on the=3D20
>names of anamorphs unless there is reason to=3D20
>believe that the group generally associated with=3D20
>the anamorph name is monophyletic.
>
>For those of you unfamiliar with nomenclature of=3D20
>fungi as governed by the botanical code, fungi=3D20
>are the only group of extant organisms where=3D20
>species with multiple reproductive morphs have=3D20
>been allowed multiple accepted valid scientific=3D20
>names, one for the entire organism, based upon a=3D20
>sexual morphotype, and others based upon asexual=3D20
>morphological features. Article 59 of the=3D20
>current ICBN covers this issue and undoubtedly=3D20
>led to the incorporation of recommendation 10E=3D20
>in the Phylocode.
>
>It is intriguing to see such a melding of=3D20
>definitions from an existing code with the=3D20
>Phylocode while missing the point that the=3D20
>current article dealt with pleomorphic fungi.=3D20
>There are some that only reproduce asexually and=3D20
>their anamorph (asexual morph-based) name is in=3D20
>fact the holomorph name, applicable to the=3D20
>entire organism. In some cases it would make=3D20
>more sense to adopt the anamorph name for a=3D20
>clade that encompasses both sexual and asexual=3D20
>species regardless of whether existing names are=3D20
>typified by teleomorphs (sexual reproductive=3D20
>organs) or anamorphs (asexual reproductive=3D20
>organs).
>
>Scott A. Redhead, Ph.D.
>Curator - National Mycological Herbarium=3D20
>/ Curator de l'herbier mycologique national
>Research Scientist / Chercheur scientifique
>Biodiversity (Mycology and Botany) /=3D20
>Biodiversit=3DE9 (Mycologie et Botanique)=3D20
>Agriculture and Agri-Food Canada/Agriculture et=3D20
>Agroalimentaire Canada 960 Carling Avenue/960=3D20
>Carling Avenue Saunder's Bldg./ Edifice de=3D20
>Saunder Ottawa, Ontario/Ottawa (Ontario) K1A 0C6
>Telephone/T=3DE9l=3DE9phone: 613-759-1384
>Facsimile/T=3DE9l=3DE9copieur: 613-759-1599
>redheads@agr.gc.ca
>
--
David Baum=20
Department of Botany =09=09Off.:(608)265-5385
University of Wisconsin=09 =09Lab.:(608)265-7929
430 Lincoln Drive =09Fax :(608)262-7509
Madison, WI 53706 =09dbaum@wisc.edu
http://www.botany.wisc.edu/baum
--=20
David Baum=20
Department of Botany =09=09Off.:(608)265-5385
University of Wisconsin=09 =09Lab.:(608)265-7929
430 Lincoln Drive =09Fax :(608)262-7509
Madison, WI 53706 =09dbaum@wisc.edu
http://www.botany.wisc.edu/baum=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: Thoughts on the Paris
meeting</title></head><body>
<div>Hi All (I accidentally sent this to the PhyloAdvisors list -
sorry to those who got it before)</div>
<div><br></div>
<div>I think Scott's message and the rather negative spin of the New
Scientist article should be a wake-up call. I agree with Scott
that the PhyloCode has become too concerned with the narrow concerns
of vertebrate paleontologists and too little concerned with the much
bigger issues of facilitating the naming and analysis of extant
diversity. The way to achieve this it to strive for a less
legalistic and more computer-friendly structure.</div>
<div><br></div>
<div>Our model should not just be the ICZN and ICBN but GenBank,
TreeBase etc. As I have said before, the ideal would be a syste=
m
that circumvented traditional publication of names and allowed direct
submission of converted and new clade and species names to a registry
database. The design of such a database and the rules governing
required fields and their content would, in effect, be the
"code." To be sure one would need editorial
process to avoid chaos due to ill-informed or malicious individuals,
but whether the editorial input is at the data-base/registry end or i=
n
the handling of formal manuscripts it would seem that the load put on
the community would be the same (I for one would find it easier to ac=
t
as a reviewer of a data-base entry in a predefined format than a full
manuscript).</div>
<div><br></div>
<div>As I attempted to argue to several people at the meeting, making
the PhyloCode a computer-based endeavor would tend to argue for a
simple system employing only topology-based definitons (stem- and
node-based) - but there is room for discussion.</div>
<div><br></div>
<div>While I was happy with the agreement that species should be
treated as epithet-derived uninomials, I agree with Scott that the
authorship mechanisms may not be the best. Reference to a
database accession number would seem cleaner.</div>
<div><br></div>
<div>I would be very interested to know how many of you (if any) shar=
e
my concerns and, equally, how many of you feel we have gone too far
down the legalistic Code route to change course now.</div>
<div><br></div>
<div>David</div>
<div><br></div>
<div><br></div>
<blockquote type=3D3D"cite" cite>As an interested observer, but curre=
ntly
not a full fledged Phylocode advocate, I was probably an anomaly at
the Paris meeting. Also, I appear to have been the only mycologist
there save for a half day attendance by a French colleague, whom
unfortunately I never realized was there that day.</blockquote>
<blockquote type=3D3D"cite" cite><font
face=3D3D"Times New Roman"> </font></blockquote>
<blockquote type=3D3D"cite" cite><font face=3D3D"Times New Roman">Hav=
ing said
this, I have a few observations to share. But before that I would lik=
e
to thank Michel Laurin for helping to arranging things and helping to
host the meeting. It was a privilege to attend the meeting at the
prestigious<i> Mus=3DE9um National d'Histoire Naturelle</i></font> an=
d
the examples of fine French cuisine arranged for the breaks and the
social dinner were outstanding.</blockquote>
<blockquote type=3D3D"cite" cite><font
face=3D3D"Times New Roman"> </font></blockquote>
<blockquote type=3D3D"cite" cite><font face=3D3D"Times New Roman">As =
an
outsider I was somewhat surprised by the number of palaeontologist at
the meeting, which in retrospect perhaps should have been anticipated=
.
I had expected the majority of Phylocode advocates to be those
involved with DNA or protein sequence data. It now dawns on me why
apomorphies are being used as specifiers, and it bewilders me as to
how anatomical characters are objectively scored (as it is always
slightly subjective when scoring morphological features). It was also
an eye-opener to note the lack of representatives in microbiology and
entomology, and the relatively few botanists. During one coffee break
a contributor optimistically stated that within 10 years everybody in
biology would be adopting the Phylocode, but I think that is naive,
and unrealistic given the lack of interest in the code by major group=
s
of biologists. The other disappointment was the fact that the
registration database was not up and running smoothly for the meeting=
.
There were still too many glitches.</font></blockquote>
<blockquote type=3D3D"cite" cite><font
face=3D3D"Times New Roman"> </font></blockquote>
<blockquote type=3D3D"cite" cite><font face=3D3D"Times New Roman">The=
debate
on incorporating species into the code took a worrying direction by
the shift towards using current species epithets (stripped of generic
names) but leaving attached authors' names, year and page (or
reference) if necessary. One of the burden's of the current codes
(ICBN, ICZN, ICNB) is the author citations, particularly for the
botanical code that involves authors of new combinations being added
on. Adding authors' names on taxon names always introduces the ego
factor (no matter how noble one might believe themselves to be). The
historic codes in part did this to help track names through
literature. Such is unnecessary when every single name in this code i=
s
in a database. Authorship is irrelevant and can be eliminated because
each has a unique registration number. There is the grand opportunity
to rise above everyone's collective egos (but of course nobody wanted
to do this). Suggesting now that authors names (year of
publication or validation) become part of species names actually goes
several steps further in an illogical direction.</font></blockquote>
<blockquote type=3D3D"cite" cite><font
face=3D3D"Times New Roman"> </font></blockquote>
<blockquote type=3D3D"cite" cite><font face=3D3D"Times New Roman">Wit=
h regard
to fungi, I noted in the current draft the
following:</font></blockquote>
<blockquote type=3D3D"cite" cite><font
face=3D3D"Times New Roman"> </font></blockquote>
<blockquote type=3D3D"cite" cite><font face=3D3D"Times New Roman"
size=3D3D"-2">Recommendation 10 E. Names referring to mitotic asexual
morphs (anamorphs) of ascomycete and basidiomycete fungi are treated
by the ICBN and Draft BioCode as applicable only to the organ or morp=
h
represented by their type, not to the fungus in all its morphs
(holomorph), which is considered to be represented by the teleomorph,
i.e. the morph characterized by the production of asci/ascospores,
basidia/basidiospores, teliospores, or other basidium-bearing organs.
Because of the frequent polyphyly of the sets of species to which
anamorph names traditionally apply, the names of clades of ascomycete
and basidiomycete fungi should not be based on the names of anamorphs
unless there is reason to believe that the group generally associated
with the anamorph name is monophyletic.</font></blockquote>
<blockquote type=3D3D"cite" cite><font
face=3D3D"Times New Roman"> </font></blockquote>
<blockquote type=3D3D"cite" cite><font face=3D3D"Times New Roman">For=
those of
you unfamiliar with nomenclature of fungi as governed by the botanica=
l
code, fungi are the only group of extant organisms where species with
multiple reproductive morphs have been allowed multiple accepted vali=
d
scientific names, one for the entire organism, based upon a sexual
morphotype, and others based upon asexual morphological features.
Article 59 of the current ICBN covers this issue and undoubtedly led
to the incorporation of recommendation 10E in the
Phylocode.</font></blockquote>
<blockquote type=3D3D"cite" cite><font
face=3D3D"Times New Roman"> </font></blockquote>
<blockquote type=3D3D"cite" cite><font face=3D3D"Times New Roman">It =
is
intriguing to see such a melding of definitions from an existing code
with the Phylocode while missing the point that the current article
dealt with pleomorphic fungi. There are some that only reproduce
asexually and their anamorph (asexual morph-based) name is in fact th=
e
holomorph name, applicable to the entire organism. In some case=
s
it would make more sense to adopt the anamorph name for a clade that
encompasses both sexual and asexual species regardless of whether
existing names are typified by teleomorphs (sexual reproductive
organs) or anamorphs (asexual reproductive
organs).</font></blockquote>
<blockquote type=3D3D"cite" cite><font face=3D3D"Arial"
size=3D3D"-1"> </font></blockquote>
<blockquote type=3D3D"cite" cite><font face=3D3D"Courier New" size=
=3D3D"-1">Scott
A. Redhead, Ph.D.</font><br>
<font face=3D3D"Courier New" size=3D3D"-1">Curator - National Mycolog=
ical
Herbarium /</font> <font face=3D3D"Courier New" size=3D3D"-1">Cu=
rator de
l'herbier mycologique national</font><br>
<font face=3D3D"Courier New" size=3D3D"-1">Research Scientist / Cherc=
heur
scientifique</font><br>
<font face=3D3D"Courier New" size=3D3D"-1">Biodiversity (Mycology and=
Botany)
/ Biodiversit=3DE9 (Mycologie et Botanique) Agriculture and Agri-Food
Canada/Agriculture et Agroalimentaire Canada 960 Carling Avenue/960
Carling Avenue Saunder's Bldg./ Edifice de Saunder Ottawa,
Ontario/Ottawa (Ontario) K1A 0C6</font></blockquote>
<blockquote type=3D3D"cite" cite><font face=3D3D"Courier New"
size=3D3D"-1">Telephone/T=3DE9l=3DE9phone: 613-759-1384</font><br>
<font face=3D3D"Courier New" size=3D3D"-1">Facsimile/T=3DE9l=3DE9copi=
eur:
613-759-1599</font><br>
<font face=3D3D"Courier New"
size=3D3D"-1">redheads@agr.gc.ca</font></blockquote>
<blockquote type=3D3D"cite" cite><font
face=3D3D"Times New Roman"> </font></blockquote>
<div><br></div>
<div><br></div>
<div><tt>--</tt></div>
<div>David Baum <br>
<br>
Department of Botany <x-tab> =
</x-tab><x-tab>
</x-tab>Off.:(608)265-5385<br>
University of Wisconsin<x-tab>
</x-tab
> &n=
bsp;<x-=3D
tab
> </x-tab>Lab.:(608)265-7929<br>
430 Lincoln
Drive <spa=
n
></span
> <x=
-tab
> </x-tab>Fax
:(608)262-7509<br>
Madison, WI
53706 <spa=
n
></span> <=
x-tab
> </x-tab>dbaum@wisc.edu</div>
<div>http://www.botany.wisc.edu/baum</div>
<x-sigsep><pre>--=20
</pre></x-sigsep>
<div>David Baum <br>
<br>
Department of Botany <x-tab> =
</x-tab><x-tab>
</x-tab>Off.:(608)265-5385<br>
University of Wisconsin<x-tab>
</x-tab
> &n=
bsp;<x-=3D
tab
> </x-tab>Lab.:(608)265-7929<br>
430 Lincoln
Drive <spa=
n
></span
> <x=
-tab
> </x-tab>Fax
:(608)262-7509<br>
Madison, WI
53706 <spa=
n
></span> <=
x-tab
> </x-tab>dbaum@wisc.edu<br>
http://www.botany.wisc.edu/baum</div>
</body>
</html>=3D
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