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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
This is a multi-part message in MIME format. --Boundary_(ID_+57uGG/WrIiXNbbKSLHJuQ) Content-type: text/plain; charset="Windows-1252" Content-transfer-encoding: quoted-printable 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 --Boundary_(ID_+57uGG/WrIiXNbbKSLHJuQ) Content-type: text/html; charset="Windows-1252" Content-transfer-encoding: quoted-printable <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN"> <HTML><HEAD><TITLE>Re: on universaliy of Phylocode</TITLE> <META content=3D"text/html; charset=3Dwindows-1252" = http-equiv=3DContent-Type> <STYLE type=3Dtext/css>BLOCKQUOTE { PADDING-BOTTOM: 0px; PADDING-TOP: 0px } DL { PADDING-BOTTOM: 0px; PADDING-TOP: 0px } UL { PADDING-BOTTOM: 0px; PADDING-TOP: 0px } OL { PADDING-BOTTOM: 0px; PADDING-TOP: 0px } LI { PADDING-BOTTOM: 0px; PADDING-TOP: 0px } </STYLE> <META content=3D"MSHTML 5.00.2614.3500" name=3DGENERATOR></HEAD> <BODY bgColor=3D#ffffff> <DIV> </DIV> <BLOCKQUOTE=20 style=3D"BORDER-LEFT: #000000 2px solid; MARGIN-LEFT: 5px; MARGIN-RIGHT: = 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> </X-TAB>Our = e-mail=20 messages must have crossed each other. By the time you read = this, you=20 will have received some comments from me on your paper. As = 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> </X-TAB>Yes, = but=20 before, it has to become the "standard" method!</DIV> <DIV> </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 make = different=20 classificatory approaches just branches of the same biological=20 taxonomy.</FONT></BLOCKQUOTE> <BLOCKQUOTE cite type=3D"cite"> </BLOCKQUOTE> <BLOCKQUOTE cite type=3D"cite"><FONT size=3D-1>Of course, this = provides specific=20 problems considered recently by Marc Ereshefsky: for instance = the=20 Linnean species 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"> </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 than it is presumd by = any=20 law. Suppose you recognize and name a group as = monophyletic. And=20 someone else disapprove your conclusion or disagree with your = opinion =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 =20 considers such a situation? I gues it doesn't.</FONT></BLOCKQUOTE> <BLOCKQUOTE cite type=3D"cite"> </BLOCKQUOTE> <DIV><X-TAB> </X-TAB>On the=20 contrary, it does. Suppose that taxon A is defined as "the = smallest=20 clade that includes species B and C". Perhaps when the taxon is = defined,=20 species D is thought to be part of it, if the phylogeny is (B, (C, = D)). =20 Suppose that a later investigation yields the following phylogeny: (D, = (B,=20 C)). Species D is simply taken out of taxon A. There will = always=20 be a smallest clade that includes species B and C, but its contents = will=20 depend on the phylogeny. No problem!</DIV> <DIV> </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 FORMALLY IF ONLY 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> =20 </X-TAB>Sincerely,</DIV> <DIV><BR></DIV> <DIV><X-TAB> =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> --Boundary_(ID_+57uGG/WrIiXNbbKSLHJuQ)--