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Date: Thu, 15 Feb 2001 10:00:37 -0600 (CST)
From: znc14@TTACS.TTU.EDU
To: "Janovec, John" <jjanovec@nybg.org>
Cc: "'PhyloCode@ouvaxa.cats.ohiou.edu'" <PhyloCode@ouvaxa.cats.ohiou.edu>, znc14@TTU.EDU
Subject: Re: On the Other Phylogenetic Systematics, Nixon and Carpenter
On Wed, 14 Feb 2001, Janovec, John wrote: > Dear Phylocode listserv participants, > > I am very curious to know what the take is on the recent "OOPS" (On the > Other Phylogenetic Systematics) paper published in a recent issue of > Cladistics. I too have been wondering if anyone has been working on a politely worded reply (if you are, you are welcome ot my thoughts on the subject). Personally, I don't think I can do it, my bloodpressure is not so great, and I have trouble with the somewhat... strident tone of this paper. I guess it could be worse, it could have been titled "the PhyloCode is vapor." > Does it not bring up some very good points to consider regarding > the proposed Phylocode? It makes the argument recently summarized by Dr. Cantino, although in a somewhat reactionary way (a common theme of recent "critiques" of phylogenetic nomenclature). Some workers would prefer a system in which species are grouped _a priori_ of knowledge of their phylogeny. A name is tied explicitly to these groups, and their exclusiveness (relative to other known species) can be tested by analysis. However, instead of discarding the name if the group if it does not pass the test (which might make more sense), the group is reconstituted to exclude some members. Presumably, if too much change is called for, the group is then disbanded. There are not objective guides for how much change is too much, or which ones must be kept in the group. This approach, considered the "traditional" one, has some advantages, in that associations of particular species with particular taxa are conserved (of course, this is also possible in the phylogenetic scheme, through careful definition). However, in a nomenclautral system that exclusively recognizes monphyletic groups, it can be a little disturbing. Such traditional schemes do not recognize clades explicitly (since there is no effort to encompass unidentified descendants of the common ancestor of a group). Further, they do not recognize, nor do they associate with the group, the most recent common ancestor of the included forms. On a more practical side, the most recent common ancestor, and therefore the clade itself, changes regularly with new hypotheses of phylogeny, as does the content of the clade (in terms of unknown or poorly known members). Essentially, yuou are constantly changing the clade which is named, in the name of a stable assocaition of a name with a set of species. While Nixon and Carpenter do make a valid point, that composition probably changes more in phylogenetic nomenclature, they fail to appreciate the value of the fact that a phylogenetic definition always refers to one and only one clade and common ancestor... ALL that changes in composition... this is valuable, in that *all* that is testable is clade membership. We cannot objectively test the membership of an _a priori_ grouping based on a clade that WILL change with the results of our analysis (because the limits of the group may be changed to accomodate new hypotheses of phylogeny). This is comparable to trying to solve for two variables with one equation; the solution changes constantly and by the fiat of the systmatist. It is important to remember, in such discussion, that a clade is not a group, it is a monophyletic entity, and clades are indicated by an anlysis, not fully discovered. The Nixon and Carpenter approach to taxonomy is firmly grounded in the notion of naming groups based on essentialist characteristics, and associating a name with a "taxon concept." This perspective is antithetical to the methods espoused by many advocates of phylogenetic nomenclature, in which the natural ordering of life (through phylogenetic relationships) is discovered, and clades are named with the intention of discovering the known descendants of the specified common ancestor. Nixon and Carpenter (and other authors) are obsessed with the concept of stability of analytical taxonomic content, a concept as elusive as the name is cumbersome. They skirt the fact that a phylogenetic name ALWAYS refers to the same clade, and therefore the same included species. The crux of phylogenetic nomenclature is that the included species are HYPOTHESIZED (ala the scientific method, and all that...), and not forced into a group at the expense of a constant common ancestor. Remember, the common ancestor is the root of a clade... Although they effectivley demonstrate that the content of phylogenetic "taxa" is unstable, these authors do so through an extremely loaded example. In all cases, when a name is tied to a group of very specious groups with poorly resolved interrelationships, the content will change. However, of the X,000 species they show changing membership, all of these are retaining their membership at the next most exclusive level. Thus, the bazillion specie of Angiospermae do not necessarily change their assocation with this name, even though they may change their association with the name "paleoherbs," a name which the original authors chose NOT to name (for reasons Nixon and Carpenter make obvious). Of course, the other point these authors miss is that, under phylogenetic nomenclature, these taxa eitherc ARE or ARE NOT members of this clade, their actual relationships do not change, only our hypothesis does. So, in a sense, the traditional methodology advocated by Nixon and Carpenter is rooted only to groups of species associated _a priori_ of analysis, with the acknowledgement that these groups may change, or even be abandoned alltogether. I fail to see any real stability in such a system. We certainly cannot expect nature to respect the groupings we force upon it (a point readily acknowledged by most traditionalists). However, some systematists do not see the need for a foundation for systematics, for any logical referrent. In the old days, this attitude was combated by the twin demons phenetics and phylogenetic systematics. Now, with the victory of phylogenetic systematics in providing a reproducable basis for phylogenetic analysis, many adovocate complacency and non-reproducability in our nomenclature. You may decide for yourself if you would like to see some science in your scientific nomenclature. In another recent paper, Benton has argued points similar to Nixon and Carpenter, but from the more pragmatic perspective of constructing a classification. While he appears to have missed the explicit point of phylogenetic nomenclature, that it is NOT a classification, and is meant to replace the use of classification in biological nomenclature, his points are somewhat more tangible. PN does not necessarily work well as a classification, in that it abandons the (artificial) structure, and therefore the "morphological key" of the Linnean System. However, the traditional method also fails to be a good classification, in that it is inextricably interwoven with interpretation. The "good Linnean taxonomist" of Benton does not arrange his groups to best classify his subjects for information storage and retrieval purposes, if he did so, he would be a pheneticist. Instead, he complicates his classificationo with consideration of phylogeny. Of course, as Benton points out, this is not done each time new information presents itself, the "good Linnean taxonomist" waits for an unspecified time, until the new phylogeny is better established. Thus, even in his attempts to formulate a deliberately incomplete phylogenetic reference within the classification, the traditionalist fails. Although Benton claims to favor monphyletic taxa, he allows for content to remain constant for long periods at the expense of phylogenetic information. What Benton advocates is the least effective of all possible systems, a poor classification, a poor phlogenetic reference, and either way a poor systematic nomenclature. Practitioners of phylogenetic nomenclature have been characterized as purists (among other things). However, I fail to see what other alternative there is. Traditional nomenclature fails to formulate explicit, scientific, or even useful classifications. By compromising two of the possible goals of a nomencaltural scheme, those of effectively capturing phylogenetic and morphological information, traditional nomenclature fails to be at all useful or scientific. It is only useful as an information-storage system for either type of data if the preferences of the authors, with regard to which sort of information takes priority at each "level," a criterion which does not seem to be constant even within a single work by a single author. Of course, any heirarchy based solely on morphological information is inherently subjective anyway, a point which eventually lead to the demise of phenetics. Anyway, a traditional taxonomy does serve a third goal well; it is a good key for recovering inforation from the literature. However, even in this it regularly fails, as new concepts and new nomenclatural schemes rewrite taxonomy, and require every graduate student to develop his own mental map of arcahic and arcane taxonomy (Predentata = Orntihischia, Lambeosauridae = Lambeosaurinae, Trachodon = Thespesius = Claosaurus = Anatosaurus = Edmontosaurus = Anatotitan, etc.). Indeed, although some practitioners convert traiditional taxa with poorly thought-out phylognetic defintions (often based on one particular tree, and that tree alone), I advocate (and will do so in print) a more careful approach to ensuring access to the literature (although I like crown clades, myself). Another point concerning Nixon and Carpenter's paper (albeit a minor one) which I have touched on earlier, is that ANY system claiming to name only monophyletic taxa is, by definition, a "node-pointing system." In the case of traditional taxonomists, this point is lost, because these workers tend not to consider the undiscovered members of a clade (such as the common ancestor). However, a clade is an ancestor and all of its descendants, and therefore a node (do not be confused by recent papers, such as Padian, Hutchinson and Holtz's excellent terhopod nomenclature article... node-, stem-, and apomoprhy-based definitions all identify the same class of entity, a clade, they are just different ways of specifiying *which* clade is being named). Thus, a way of attaching a name to a monophyetic group is a way of attatching a name to a clade, is a way of pointing out a clade, is a way of pointing out a node, is a "node-pointing system." Nixon and Carpenter seem to be objecting to the fact that Phylognetic Nomenclature does so explicitly... given this paragraph, I feel they might benefit from some explicitness in their own system. I hope this helps. Jonathan R. Wagner P.S. I apoligize if this post seems a bit disorganized, I am using an outdated e-mail interface (since I am on "company" time... the joys of graduate funding).