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Date: Mon, 18 Oct 2004 18:42:05 -0700
From: [unknown]
To: "'phylocode@ouvaxa.cats.ohiou.edu'" <phylocode@ouvaxa.cats.ohiou.=
Subject: RE: Re: use of vernacular names
I've been thinking about the discussion quite a bit over the weekend,= and a few points have clarified for me. This is probably too long of a post= , but writing this out helps me crystallize my thinking, and your feedback = is always valued. Firstly, when I speak of "general biologists" I really= refer to systematists, because most biologists will follow the opinion prev= alent in the field--a point well made by Kevin de Queiroz in Paris, as I re= call. Philip D. Cantino wrote: > Having read David's and Michel's comments, I will concede that my > suggestion about how "tetrapod" might be used was probably > incorrect--but only because it is not a true vernacular name, as > pointed out by David: >=20 > >I don't know how else we could get people to apply "tetrapod" to a= nything > >other than Tetrapoda. "Tetrapod" is in reality not vernacular at a= ll. This is a key observation I think. The swirling issue over whether Te= trapoda and tetrapod should refer to the same group of animals drove me back = to my opinion survey, where there were on the whole mixed feelings about wh= ether vernacular and technical terms should correspond. Those who felt most strongly that they should were also those who felt most strongly for = or against the PhyloCode. Interestingly, these are for the most part all workers who specialize on basal tetrapods (organisms that fall outsid= e of crown tetrapods for the most part). This is a battleground issue, cle= arly. Also interestingly, the opponents have adopted the one revolutionary = change that underpins the PhyloCode: attaching names to clades. They have co= nverted traditional names to clade names, and have coined new clade names, so= I wonder how strongly their opposition is tied to the issue of Tetrapod= a, or how much it is over the general issue of taxonomic freedom, or over s= ome other provision of the PhyloCode?=20 The issues of Tetrapoda and Anthracosauria are what initially drew me= into the PhyloCode discussion. As you are aware, Michel extended the first= work of Jacques and Kevin admirably, and followed the rules of priority se= t forth at the time he respected their original definitions which tied both n= ames to the crown. I can't say how much I appreciate his doing this, given th= e practice common at the time of each author coining their own definiti= ons, even after discussing established definitions. (Sean Modesto and I ou= tline a couple of examples of this practice in the early to mid 90s in our up= coming opinion piece in Syst Biol.) We have to have rules to develop our nomenclature. But the result of doing so came with a price, given his= new tree topology--the taxonomic content of these taxa changed dramatical= ly, so that much of the diversity of limbed vertebrates was left outside Tet= rapoda, and Anthracosaurus was no longer an anthracosaur. But, recognizing th= ese clades were still important to paleontologists, Michel gave them new = names by converting other names, Stegocephali and Embolomeri, which require= d changing the meanings of these names too. This all logically flows fr= om first principles in my opinion. When Michel did this most of our coll= eagues were quite upset in the radical change in meaning of these names, and= their response was to ignore his work.=20 Instead of ignoring this work because I didn't like the nomenclatural implications, I decided to look at the reason why the name should be attached to the crown in the first place, and see if their might be r= ecourse following the ideas of Phylogenetic Nomenclature, which I thought mad= e a lot of sense (the PhyloCode not existing at this point). To my surprise I discovered it was just a convention, a preference whose initial justifications had been found wanting. I also discovered that even Ke= vin and Jacques at the very beginning of Phylogenetic Nomenclature admitted t= hat the best definition for Tetrapoda was an apomorphy-based definition, but = decided against it because of problems they perceived with these definitions. Obviously, they have since changed their minds on apomorphy-based definitions. So, the justifications for always attaching well-known n= ames to the crown have been found wanting, and the opposition for using apomorphy-based definitions have been dropped by many of the most influential members of the Advisory Committee. Thus, I raised the que= stion of the definition of Tetrapoda. In any event, this is observation num= ber two for me: I never appreciated how Michel has operated as if a system ha= s been in place this whole time, because it is via a system that stability w= ill be sustained. I agree completely that a system is necessary for this app= roach to be stable. I have, in contrast to Michel, asked whether the origin= al definition is the most appropriate before we are "stuck" with it. The consensus was that the original definition for Anthracosauria was not correct and it was amended. I have suggested Tetrapoda is similarly n= eeding correction, but so far it appears that the consensus at least among t= he Advisory Committee is comfortable with things are they are, and I am = left scratching my head as to why because I think I've presented a logical argument. The one and only reason I have been offered for why a crown-based def= inition is best is Michel's line of argument, encapsulated in the following r= ecent quote:=20 "Most authors may THINK that Tetrapoda means "limbed vertebrates", bu= t in the neontological literature, they use this word as if it meant "the = crown of limbed vertebrates". Yet, Jason may be right that restricting man= y 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 becau= se it may prove more popular in some fields?" Michel nails the two additional issues I have identified over the wee= kend. Michel has quite rightly noted that there is imprecision with the way nomenclature is sometimes being used, but we disagree with 1) the sev= erity of the problem, and thus 2) the best solution. Until I really tried t= o understand what Michel was saying in our debate paper I never appreci= ated that there might be a problem with researchers who speak of "tetrapod= s" expressing gene Y while "fish" express gene Z, say, because I never r= ead this as anything other than "Extant tetrapods they sampled" and "what= ever 'fish' they sampled" and I would then mentally map the characters ont= o the tree in my head, and proceed from there. Taking the informal, nonrigo= rous wording of some neontologists strictly literally was never a possibil= ity to me--because it makes no sense to allege that fossil taxa express a ge= ne because we can't know such things directly. Larry Whitmer has written= an entire monograph on a cladistically-based method for inferring "soft = tissue" data using fossils, and I am very sensitive to the extent we can infe= r the presence of structures not directly preserved. Its my training. Do pe= ople really read papers in such a literal manner, or is this a rhetorical = device? I honestly cannot conceive of how one can read a paper in the literal= sense because it is so far from how my thinking works, and this has admitte= dly blinded me to the possibility. If the latter, I can see why Michel would be troubled by this potenti= al imprecision in discussion. I also understand why he would seek to cha= nge the meaning of the name Tetrapoda since neontologists likely to use the t= erm loosely are many and paleo types, who tend to think about these thing= s more (since alpha taxonomy is a huge part of what we do) and are fewer in = number, are more likely to adopt new names. It makes complete sense, and foll= ows =66rom first principles. I note however that paleontologists are amon= g the harshest critics of the PhyloCode. Part of me feels similarly to Davi= d, that changing the meaning of this name is abrogating our responsibility to educate nonsystematists of the importance of careful rigor in use of technical names, and is allowing the ignorance of some workers to dri= ve our decisions in name conversion, rather than honestly evaluating how peo= ple working with these technical names use them currently. And I think th= at is a distinction that should be considered. I do think that some, perhaps even most, well-known taxa should be ti= ed to the crown, and I have said so all along. I also now see that, when sp= eaking of historical continuity, I myself refer to the post-Darwinian era, w= hen fossils started to be found and incorporated into the Linnean classification. I concede that concepts of taxa are plastic, and have differed from worker to worker to the point that working out predomin= ant usage can be sometimes difficult. I wonder if there is a difference i= n the way systematists who work primarily on extant species and paleontolog= ists conceive taxa and clades. I can imagine it is easier to think of taxa= as relatively fixed if my primary concern were those species alive today--because what we see is what we get. However, speaking for myse= lf, I think of taxa as unknowable in any precise way (a probability cloud w= ould be an apt analogy), because there is always another fossil to be found t= hat might possibly completely alter my understanding of relationships. I = prefer stem-based taxa as a result, which can always be subdivided later, wh= en more plesiomorphic forms, perhaps less morphologically distinct from a "well-known" but descendant group, are found. I have a new appreciati= on for node-based taxa after the Paris meeting (but still think there is too= much "top-down" thinking). Yes, to those who would characterize me as being concerned about my "= special taxa", you bet I am fond of this name, and all of the names of the gr= oups I work with. All specialists are, more or less; its our life's work. An= d yes, I care less about the names used for other clades I do not work with.= Its easy for me to make pronouncements about my preference for, say, Mamm= alia to be a crown-based clade. I have nothing invested in it emotionally. So= , shouldn't the specialists make these decisions, since they are stuck = with the result? Might the feeling that one is being told which name shoul= d be used for the group one works on by a small, self-appointed group not engender resentment among some systematists who might otherwise be on= side? However, I refuse to consider myself as working against "the greater = good of biology". I believe that maintaining continuity with the literature a= nd clear, precise communication to be all about what is best for biology= .=20 I remain open minded. Thus, as I asked in my first email and ask agai= n now, why are we persisting on keeping Tetrapoda attached to the crown, and= use Holotetrapoda for the apomorphy-based definition, when using Tetrapod= a and Neotetrapoda (or whatever) is logically just as consistent, but additionally, will maintain consistency with the literature, and more= over might help to bring more workers onside? Does an apomorphy-based defi= nition this really create more confusion and "fuzzy tree thinking" among wor= kers? Will "fixing" the issue of imprecise name use by some nonsystematists= bring greater advantages to us than using this name in the sense that most = people believe it means already (as even Michel admits) or will it cause gre= ater confusion? How on earth can we possibly evaluate the pros and cons of= either option in a rigorous manner? Will this decision come down the subject= ive preference of the Advisory Committee or Editorial Board for the proce= edings volume? Thank you for your patience with this message. You may feel safe from= future messages of this length, because I have a ton and a half of deadlines looming and cannot take this chunk of time again until January. Best, Jason