Message 2004-02-0011: Re: on universaliy of Phylocode

Fri, 06 Feb 2004 15:28:06 +0300

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Date: Fri, 06 Feb 2004 15:28:06 +0300
From: "Igor Ya. Pavlinov" <igor_pavlinov@zmmu.msu.ru>
To: Michel Laurin <laurin@ccr.jussieu.fr>
Cc: PhyloCode <phylocode@ouvaxa.cats.ohiou.edu>
Subject: Re: on universaliy of Phylocode

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Re: on universaliy of Phylocode
  ----- Original Message -----=20
  From: Michel Laurin=20
  To: Igor Ya. Pavlinov=20
  Sent: Friday, February 06, 2004 2:39 PM
  Subject: Re: on universaliy of Phylocode


  Dear Igor,


          Our e-mail messages must have crossed each other.  By the time =
you read this, you will have received some comments from me on your =
paper.  As  for your comments on the PhyloCode, I respond to your most =
specific comment below.


    Dear Michel,
    if you ever read my paper I've sent you you woudl see that my =
somewhat sceptical position in respect to the phylocode is caused by my =
"historical" view of that fates of various classificatory approaches. =
You just recall that "the new systematics" and phenetics were dominating =
prior to cladistics in XX century while the pre-phylogenetic taxonomy of =
XIX century was based on naturphilosophie. And where they all are now? =
So, I suspect there will come time when cladistics along with the =
phylocode will become "old-fashioned".


          Yes, but before, it has to become the "standard" method!

  BLESSED THOSE WHO BELIEVE

    It is neither bad nor good, it is just a general law of development =
of any scientific discipline. And unity of language is one of the most =
strong "glue" factors that make different classificatory approaches just =
branches of the same biological taxonomy.

    Of course, this provides specific problems considered recently by =
Marc Ereshefsky: for instance the Linnean species are not the Darwinian =
ones although they are both called "species". But then we have to =
acknowledge that "eco-species" are not the same as "phylo-species". =
Following the logic of the phylocode promoters, we have to adopt =
different nomenclature to different kinds of species, and each author, =
before naming his/her species properly would be oblidged to decide first =
with which kind of species he/she deals with.

    And this returns us to the phylocode again. It is applied to =
monophyletic taxa which is excellent in theory. But practice is much =
more diverse than it is presumd by any law. Suppose you recognize and =
name a group as monophyletic. And someone else disapprove your =
conclusion or disagree with your opinion  - say, just because that =
someone disagree with your method or a programm employed (Farris vs =
Felsenstein vs Estabrook vs Swofford). What it may mean from the =
phylocode standpoint? How one has to treat names of taxa which supposed =
monophyletic status is falsified by other studies or is not acknowledged =
by other members of taxonomic community? Does phylocode  considers such =
a situation? I gues it doesn't.

          On the contrary, it does.  Suppose that taxon A is defined as =
"the smallest clade that includes species B and C".  Perhaps when the =
taxon is defined, species D is thought to be part of it, if the =
phylogeny is (B, (C, D)).  Suppose that a later investigation yields the =
following phylogeny: (D, (B, C)).  Species D is simply taken out of =
taxon A.  There will always be a smallest clade that includes species B =
and C, but its contents will depend on the phylogeny.  No problem!

  YOUR ARGUMENTATION IS CORRECT AS MUCH AS IT APPEALS TO THE ANCESTOR OF =
A, B AND ALL ITS DESCENDANTS. BUT IT DOESN'T SEEM TO BE CORRECT FORMALLY =
IF ONLY MONOPHYLY OF CLAD (B+C) DEFINES A: THE LATTER IS FALSIFIED BY =
(B(C+D)) IN WHICH (B+C) IS PARAPHYLETIC. THANKS FOR THIS DISCUSSION, NOW =
I SEE WHY ANCESTOR IS INCLUDED IN DEFINITION.

          Sincerely,


          Michel
--=20

  Michel Laurin
  FRE 2696, CNRS
  Universit=E9 Paris 7 - Denis Diderot
  2, place Jussieu
  case 7077
  75005 Paris
  FRANCE

  tel. (33 1) 44 27 36 92
  fax. (33 1) 44 27 56 53
  http://tolweb.org/tree/laurin/Laurin_Home_page.html

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0px; PADDING-LEFT: 5px; PADDING-RIGHT: 0px">
  <DIV style=3D"FONT: 10pt arial">----- Original Message ----- </DIV>
  <DIV=20
  style=3D"BACKGROUND: #e4e4e4; FONT: 10pt arial; font-color: =
black"><B>From:</B>=20
  <A href=3D"mailto:laurin@ccr.jussieu.fr" =
title=3Dlaurin@ccr.jussieu.fr>Michel=20
  Laurin</A> </DIV>
  <DIV style=3D"FONT: 10pt arial"><B>To:</B> <A=20
  href=3D"mailto:igor_pavlinov@zmmu.msu.ru" =
title=3Digor_pavlinov@zmmu.msu.ru>Igor=20
  Ya. Pavlinov</A> </DIV>
  <DIV style=3D"FONT: 10pt arial"><B>Sent:</B> Friday, February 06, 2004 =
2:39=20
  PM</DIV>
  <DIV style=3D"FONT: 10pt arial"><B>Subject:</B> Re: on universaliy of=20
  Phylocode</DIV>
  <DIV><BR></DIV>
  <DIV>Dear Igor,</DIV>
  <DIV><BR></DIV>
  <DIV><X-TAB>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </X-TAB>Our =
e-mail=20
  messages must have crossed each other.&nbsp; By the time you read =
this, you=20
  will have received some comments from me on your paper.&nbsp; As&nbsp; =
for=20
  your comments on the PhyloCode, I respond to your most specific =
comment=20
  below.</DIV>
  <DIV><BR></DIV>
  <BLOCKQUOTE cite type=3D"cite"><FONT size=3D-1>Dear =
Michel,</FONT></BLOCKQUOTE>
  <BLOCKQUOTE cite type=3D"cite"><FONT size=3D-1>if you ever read my =
paper I've=20
    sent you you woudl see that my somewhat sceptical position in =
respect to the=20
    phylocode is caused by my "historical" view of that fates of various =

    classificatory approaches. You just recall that "the new =
systematics" and=20
    phenetics were dominating prior to cladistics in XX century while =
the=20
    pre-phylogenetic taxonomy of XIX century was based on =
naturphilosophie. And=20
    where they all are now? So, I suspect there will come time when =
cladistics=20
    along with the phylocode will become =
"old-fashioned".</FONT></BLOCKQUOTE>
  <DIV><BR></DIV>
  <DIV><X-TAB>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </X-TAB>Yes, =
but=20
  before, it has to become the "standard" method!</DIV>
  <DIV>&nbsp;</DIV>
  <DIV><FONT color=3D#ff0000 face=3D"Arial Cyr" size=3D2>BLESSED THOSE =
WHO=20
  BELIEVE<BR></FONT></DIV>
  <BLOCKQUOTE cite type=3D"cite"><FONT size=3D-1>It is neither bad nor =
good, it is=20
    just a general law of development of any scientific discipline. And =
unity of=20
    language is one of the most strong "glue" factors that&nbsp;make =
different=20
    classificatory approaches just branches of the same biological=20
    taxonomy.</FONT></BLOCKQUOTE>
  <BLOCKQUOTE cite type=3D"cite">&nbsp;</BLOCKQUOTE>
  <BLOCKQUOTE cite type=3D"cite"><FONT size=3D-1>Of course, this =
provides specific=20
    problems considered&nbsp;recently by Marc Ereshefsky: for instance =
the=20
    Linnean species&nbsp;are not the Darwinian ones although they are =
both=20
    called "species". But then we have to acknowledge that "eco-species" =
are not=20
    the same as "phylo-species". Following the logic of the phylocode =
promoters,=20
    we have to adopt different nomenclature to different kinds of =
species, and=20
    each author, before naming his/her species properly would be =
oblidged to=20
    decide first with which kind of species he/she deals =
with.</FONT></BLOCKQUOTE>
  <BLOCKQUOTE cite type=3D"cite">&nbsp;</BLOCKQUOTE>
  <BLOCKQUOTE cite type=3D"cite"><FONT size=3D-1>And this returns us to =
the=20
    phylocode again. It is applied to monophyletic taxa which is =
excellent in=20
    theory. But practice is much more diverse&nbsp;than it is presumd by =
any=20
    law. Suppose you recognize and name a group as =
monophyletic.&nbsp;And=20
    someone else disapprove your conclusion or disagree with your =
opinion&nbsp;=20
    - say, just because that someone disagree with your method or a =
programm=20
    employed (Farris vs Felsenstein vs Estabrook vs Swofford). What it =
may mean=20
    from the phylocode standpoint? How one has to treat names of taxa =
which=20
    supposed monophyletic status is falsified by other studies or is not =

    acknowledged by other members of taxonomic community? Does =
phylocode&nbsp;=20
    considers such a situation? I gues it doesn't.</FONT></BLOCKQUOTE>
  <BLOCKQUOTE cite type=3D"cite">&nbsp;</BLOCKQUOTE>
  <DIV><X-TAB>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </X-TAB>On the=20
  contrary, it does.&nbsp; Suppose that taxon A is defined as "the =
smallest=20
  clade that includes species B and C".&nbsp; Perhaps when the taxon is =
defined,=20
  species D is thought to be part of it, if the phylogeny is (B, (C, =
D)).&nbsp;=20
  Suppose that a later investigation yields the following phylogeny: (D, =
(B,=20
  C)).&nbsp; Species D is simply taken out of taxon A.&nbsp; There will =
always=20
  be a smallest clade that includes species B and C, but its contents =
will=20
  depend on the phylogeny.&nbsp; No problem!</DIV>
  <DIV>&nbsp;</DIV>
  <DIV><FONT color=3D#ff0000 face=3D"Arial Cyr" size=3D2>YOUR =
ARGUMENTATION IS CORRECT=20
  AS MUCH AS IT APPEALS TO THE ANCESTOR OF A, B AND ALL ITS DESCENDANTS. =
BUT IT=20
  DOESN'T SEEM TO BE CORRECT&nbsp;FORMALLY IF ONLY&nbsp;MONOPHYLY OF =
CLAD (B+C)=20
  DEFINES A: THE LATTER IS FALSIFIED BY (B(C+D)) IN WHICH (B+C) IS =
PARAPHYLETIC.=20
  THANKS FOR THIS DISCUSSION, NOW I SEE WHY ANCESTOR IS INCLUDED IN=20
  DEFINITION.<BR></FONT></DIV>
  <DIV><X-TAB>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=20
</X-TAB>Sincerely,</DIV>
  <DIV><BR></DIV>
  <DIV><X-TAB>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=20
  </X-TAB>Michel</DIV><X-SIGSEP><PRE>--=20
</PRE></X-SIGSEP>
  <DIV>Michel Laurin<BR>FRE 2696, CNRS<BR>Universit=E9 Paris 7 - Denis=20
  Diderot<BR>2, place Jussieu<BR>case 7077<BR>75005 =
Paris<BR>FRANCE<BR><BR>tel.=20
  (33 1) 44 27 36 92<BR>fax. (33 1) 44 27 56=20
  =
53<BR>http://tolweb.org/tree/laurin/Laurin_Home_page.html</DIV></BLOCKQUO=
TE></BODY></HTML>

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