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Date: Thu, 10 Jun 2004 22:04:50 -0700 (PDT)
From: "Jaime A. Headden" <qilongia@yahoo.com>
To: List PhyloCode <phylocode@ouvaxa.cats.ohiou.edu>
Subject: Anti-Phylogenetic Comments in The Botanical Review (part 2)
Carpenter, J.M. 2003. Critique of pure folly. _The Botanical Review_ 69(1): 79-92. Abstract: “A critique of the draft PhyloCode is presented. Its stated goals cannot be met by the proposals in the current draft, which also fails to uphold its stated principles. Its internal contradictions include a cumbersome reinvention of the very aspect of the current Linnaean system that advocates of the PhyloCode most often decry.” This paper offers a rundown of his problems with the Phylocode rule by rule. Well, selective rules. But first, issues of stability and (again) rank: “A name is used in two different senses if it does not refer to the same set of taxa in two applications; that is instability, in taxonomy and in language. By contrast, if a name is used in one case, say, for a family, and another for a subfamily, but in each case circumscribes exactly the same included taxa, that is trivial for communicating the meaning -- the content -- of the name. Any experienced taxonomist understands this, but advocates of the PhyloCode completely fail to grasp this point.” “[A]dvocates of the PhyloCode have ignored the actual measure of taxonomic stability in terms of content,” by which is meant, that undergoing a conversion from traditional to phylogenetic system and name alterations (rather than coining), it was “demonstrated” (also by Kojima) that more changes occur in converting a relationship (A ((B, C)(D (E, F)))) into phylogenetic terms than into traditional terms, whereas it is ignored the opposite would occur for a “comb-like arrangement” where (A (B (C (D (E, F))))) [this example requiring 5 names for each “family,” and the necessary 1-3 superfamilies to group them all as required under the ICBN and ICZN, not to mention suborders, orders, etc. So, while Carpenter criticized phylogenetic nomenclators for one thing, he ignores the system that de Quieroz used to prove his point, and vice versa. Mutual values of change between systems; neither has a foothold on the other. Yet THIS is what it thought by the authors in this volume as “stability.” “Any hierarchy is inherently ranked, whether a cladogram or formal Linnaean classification. The named categories in a Linnaean classification convey information on exclusivity: Taxa at the same rank are not included within one another; taxa at higher ranks are not contained within taxa of lower ranks. This information is immediately communicated in a given case simply by stating the ranks or, even more efficiently, by the use of standardized suffixes for family-group categories in the classification and binominal nomenclature for species. The suffixes are relatively few in number, and readily learned, as is the convention of binomina, even by nonspecialists or the general public. In contrast, in so-called phylogenetic rankless classifications no indication of relationships of taxa is communicated by the names at all. Reference to a cladogram is required to communicate any information on group membership, thus a so-called phylogenetic classification would be understood and used only by specialists.” I can easily call comment on how I would need to be stupid and silly for the ranked system to make sense to me. I am, afterall, a specialist in another group altogether different than botany. But then, who will be reading my papers? Geochemists interested on the arguments of cranial kinesis in a group of theropods whose number totals less than 100 specimens world-wide? Indeed, a cladogram is usually neccesary for most specialists IN the group to understand character transformation and evolutionary relationships. The conveyance of Suborder Theropoda to me is virtually meaningless, because it connotes NO special data on the NUMBER of species. Indeed, the Class Aves is included within this Suborder, but not ONE systematist has offered a change in ranks that has ever made it to print. At this point, the rank system, and the accompanying easily-learned chart and mnemonic (which I ignore because I know the order anyway), are virtually useless to me when I am studying the relationships of organisms, not how to address them to the “stupid, silly” public. -- Now, that’s a good boy, eat your bread; you couldn’t comprehend the nature of the bread anyway, but you can eat it, can’t you? -- It seems a proxy to stay with something familiar. Principles: “ ‘1. Reference. The primary purpose of taxon names is to provide a means of referring to taxa, as opposed to indicating their characters, relationships, or membership.’ As if taxa can be referred to without some indication of attributes or membership, let alone the fact that for clades to be specified there has to be some indication of relationships.” A definition. A name is a reference to a clade; the clade is determined by it’s definition; it’s membership by its application to the cladogram; the characters by the common features of the membership, or of the basal members of the group named. “ ‘2. Clarity. Taxon names should be unambiguous in their designation of particular taxa. Nomenclatural clarity is achieved through explicit definitions.’ It is scarcely unambiguous if a name does not change but its meaning (content, or ‘designation of particular taxa’) does.” They would only be ambiguous if one felt the name was equal to its content at time of naming; if this is not so, there is no ambiguity. The definition makes the clade VERY clear from that point on, even though membership is only hinted at by one or two species as specifiers. “ ‘3. Uniqueness. To promote clarity, each taxon should have only one accepted name, and each accepted name should refer to only one taxon.’ Names can scarcely be unique if they can apply to taxa differing greatly in content.” This being a big difference between the two systems. The content defines the use of the name … yet in the traditional system, you can move a name around, change it -- what-have-you -- as you see fit, depending on what you think it should apply at. There are no criteria for the determination of which name goes to which clade, as there shouldn’t be, because a name only labels a point in the tree one wishes to bring attention to. The name, itself, is unique, and never changes, even if content does. This means, “THE NAME ITSELF NEVER CHANGES, ONLY ITS REFERENT CLADE.” “ ‘4. Stability. The names of taxa should not change over time. As a corollary, it must be possible to name newly discovered taxa without changing the names of previously discovered taxa.’ It is scarcely stable if names do not ‘change’ while at the same time changing greatly in content.” This is similar to point 3. Content is married to the affixes and rank, so the name is unstable in traditional taxonomy. YET, content is never specified. No one has, to my knowledge, been able to get many different workers to agree that the family rank refers to a certain number of genera, especially since it is mandatory for there to be a family including a genus, no matter what. “‘5. Phylogenetic context. The PhyloCode is concerned with the naming of taxa and the application of taxon names within a phylogenetic context.’ But the first principle stated that taxa are to be referred to without indication of relationships.” Yeah … the problems of grasping the separation of these qualities to people who feel they are bound at the hip. “ ‘6. The PhyloCode permits freedom of taxonomic opinion with regard to hypotheses about relationships; it only concerns how names are to be applied within the context of a given phylogenetic hypothesis.’ True, but it is precisely how those names are applied that is the source of the instability of the PhyloCode names relative to the Linnaean system (see above, and Nixon & Carpenter, 2000).” And some would argue it’s the lack of rules on application of names and ranks that makes the traditional system more unstable. This, my friends and colleagues, is the reason why there are so many systematic arguments: too many assumptions. We move on to the rules break-down: Article 6 did not receive much comment apart for a vitriolic comment on some of the recommendations of treating names in either phylogenetic or traditional systems, as in adding P or L for these systems to the names, respectively, or applying “Clade” or name of the rank to your nomen to show how you are using the name under the system. Carpenter was not fond of either idea, but preferred the latter to the former as it seems to appeal to his sense of former versus informal recognition of names and ranks. Carpenter says that the application and the nature of Article 9 contradicts the first principle (above), but as hopefully clarified by my comments, this is not the case. His biggest problem seems to be with the _recommendation_ that a clade name be accompanied by reference to include a “description or diagnosis, a list of synapomorphies, and/or a list of included taxa[,]” and “should be done with a thorough knowledge of the group concerned, including its taxonomic and nomenclatural history and previously used diagnostic features” (Recommendations 9c and 9e). I, personally, agree that these should be mandatory, but they are already accepted this way for most works that accept new names. Article 11 is considered the most “revealing” so far. This is governing specifiers, and if you thought that the authors in this volume had a problem with type vs specifier before, hold on. Carpenter feels that, while the PhyloCode can work with other codes, it is apparently _dependant_ on them for some reasons, including references to species, and I felt I should make a point that NO code has come even close to making secure statements on the security and identification of a species. It is not just left to defining the rank and type and describing it as a species to be one, since the quality of evolution in phylogenetics (including current use of the ICZN and ICBN) versus phyletics and typology treat species succinctly differently. Carpenter cites Articles 11.5, 11.8, and 11.9, and I don’t understand then why he feels (as noted earlier) that the code will cause chaos? Or as other’s feel, ignore the entirety of the historical record. “Ordinal names are not regulated in the International Code of Zoological Nomenclature, but in ranked Linnaean classification Pinnipedia is an order. As such, it is not contained within the order Carnivora, and vice versa. If in fact the support for a sister-group relationship between part of Pinnipedia and part of Carnivora is deemed sufficiently strong [oops -- sorry, that doesn’t matter], so that reclassification is required to reflect changed ideas on phylogeny [oops, sorry again -- I forgot that Linnaean classification can’t reflect phylogeny], then the sense in which each ordinal name is used would have to change.” Here we see another reflection of the problem of abandoning ranks. All recent phylogenies show that the entirety of Pinnipedia is within Carnivora, requiring that the use of orders as ranks being abandoned, changed to fit the actual phylogeny, rather than forcing the phylogeny to fit the ranks, and that the understanding that this segregation or equivalency of groups by “equal” rank is precisely what is meant when “Linnaean classification can’t reflect phylogeny.” Carpenter tries to show through examples in attempting to define nested nodes or node-stem triplets and how a different phylogeny will “mess up” the definitions, and how it “really illustrates nothing more than the inability of so-called phylogenetic nomenclature to retain the intended meaning of a name as ideas on phylogeny change[,]” among other things, and that ranking of these taxa performs this mutually exclusive effect … except that names at ranks are supposed to be flexible, mutable, can move about, even if their rank is fixed (which, as one can easily show, it is not -- without encountering that “they are both orders, one can’t contain the other!” argument). So, it would be easy to indicate that, for example, Dinosauria be defined classically so that it excludes bird, which can be done with ranks by using Mayr’s preferred example of “keeping Aves as a class:” “How exactly the name Dinosauria would be specified so that it does not contain birds is not detailed[.]” Rather, such a definition is easy, by providing a stem-modified node, one can detail a clade’s composition, and include an exclusive specifier of Aves, Avialae, etc. That is, of course, if you enjoy the paraphyly of clades. Carpenter is laughing at this point because he doesn’t see the irony of his bringing this up right after his Pinnipedia refutal. Carpenter seems to be laughing outright when it comes to bringing up article 15, concerning conservation and rejection, when “names do not change” under the PhyloCode. This is the final comments short of his repeating conclusion and references to the foundation of the SPN upon the founders of the PhyloCode itself being “funny.” Oh well, it amuses some people…. -- Keller, R.A.; Boyd, R.N.; and Wheeler, Q.D. 2003. The illogical basis of phylogenetic nomenclature. _The Botanical Review_ 69(1): 93-110. Abstract: “The current advocacy for the so-called PhyloCode has a history rooted in twentieth-century arguments among biologists and philosophers regarding a putative distinction between classes and individuals. From this seemingly simple and innocuous discussion have come supposed distinctions between definitions and diagnosis, classification and systematization, and now Linnaean and ‘phylogenetic’ nomenclature. Nevertheless, the metaphysical dichotomy of class versus individual, insofar as its standard applications to the issue of biological taxonomy are concerned, is an outdated remnant of early logical positivist thinking. Current views on natural kinds and their definitions under a scientific realist perspective provide grounds for rejecting the class versus individual dichotomy altogether insofar as biological entities are concerned. We review the role of natural kinds in scientific practice and the nature of definitions and scientific classifications. Although inherent instabilities of the PhyloCode are clearly sufficient to argue against the general application of this nominally phylogenetic system, our goal here is to address serious and fundamental flaws in its very foundation by exposing the unsubstantiated philosophical assumptions preceding and subtending it.” Keller et al. is, by itself, a singular drive to point out a particular heavy-handed approach to calling “phylogenetic” taxonomy a hypocrisy. No counting to the fact that their sources are at odds with one another: they imply that work in the early 90’s by de Quieroz and Gauthier contradicts work in the mid-90’s by Ghiselin, among other things, and that while traditional taxonomy would point at individuals (and their special meanings), the PhyloCode rejects individuals because it defines taxa by relation to an ancestor, rather than defined by the characters, and thus endorses “classes.” The bandied about “Aristotelian” system becomes the scapegoat for why the PhyloCode is “bad.” Let’s ignore that arguments for “individual” vs “class” are not apparent in the works cited, because this is Keller et al.’s apparent observation of the matter; however, let’s jump straight to the conclusions: “The PhyloCode is intended to rest on the philosophy of individualism -- a dubious philosophy about the nature of species and higher taxa. Individualism purposed to ‘solve’ the species problem by endorsing a problematic and outdated theory of meaning and definition. Arguments about species-as-individuals and their supposed compatibility with evolutionary theory are commonly deployed to persuade biologists to accept phylogenetic nomenclature (e.g., Brochu & Sumrall, 2001; Bryant & Cantino, 2002); however, their own methodological tools, ‘phylogenetic definitions,’ are logically incompatible with those views. The Linnaean system, rather than having been an obstacle to biological progress within an evolutionary worldview, is a paradigmatic example of a natural language: a language that has been able to incorporate the immense acquisition of knowledge about the diversity of the organic world during more than 200 years and that is consistent with the phylogenetic explanations behind our classifications. Perhaps it may require revision or abandonment (Ereshefsky, 1999, 2001), but this cannot be established by simple philosophical arguments. It is ironic to see that de Queiroz’s claim that ‘taxonomists have been largely unaware of the philosophical positions implied by their views’ (1994: 499) holds even more truly among the fervent followers of the PhyloCode than among taxonomists in general.” This is all at once erroneous. Keller et al. spend the entirety of the paper describing how “phylogenetic” nomenclators are contradicting themselves because someone, at one point, argued that definitions should follow character assignments, rather than relationship to ancestors. This is ignoring the nature of the term “diagnosis.” Their big support for the “Linnaean” or traditional system? As noted in another paper in the same volume: because it’s been around for over 200 years. No attempt was made to compare the two systems or how they treat individuals, lineages, and ancestors (they do so in VERY different ways), as well as the dichotomy of separation of taxa (traditional system) vs joining them (phylogenetic system). As for the philosophical arguments, the authors chose ONE version of recognition of recognizing relation of taxa as the “fundamental” means by which they reject the PhyloCode, rather than, as in their introduction, by synthesizing all of their philosophical arguments into one cohesive counter-argument. By this, Keller et al. fail in their task of rejecting the PhyloCode, as they clearly have yet to read the document and how it treats taxa. You CAN still use ranks, if you want to. -- Nixon, K.C.; Carpenter, J.M.; and Stevenson, D.W. 2003. The PhyloCode is fatally flawed, and the “Linnaean” system easily can be fixed. _the Botanical Review_ 69(1): 111-120. Abstract: “Promoters of the PhyloCode have mounted an intensive and deceptive publicity campaign. At the centerpiece of this campaign have been slogans such as that the Linnaean System will ‘goof you up,’ that the PhyloCode is the ‘greatest thing since sliced bread,’ and that systematists are ‘afraid’ to propose new names because of ‘downstream consequences.’ Aside from such subscientific spin and sloganeering, proponents of the PhyloCode have offered nothing real to back up claims of greater stability for their new system. They have also misled many into believing that the PhyloCode is the only truly phylogenetic system. The confusion that has been fostered involves several discrete arguments, concerning: a new ‘method’ of ‘designating’ names, rank-free taxonomy, uninomial nomenclature, and issues of priority. Claims that the PhyloCode produces a more stable nomenclature are false, as shown with the example of ‘paleoherbs.’ A rank-free system of naming requires an annotated reference tree for even the simplest exchanges of information. This would be confusing at best and would cripple our ability to teach, learn, and use taxonomic names in the field or in publications. We would be confronted by a mass of polynomial names, tied together only by a tree graphic, with no agreed name (except a uninomial, conveying no hierarchy) to use for any particular species. The separate issue of stability in reference to rules of priority and rank can be easily addressed within the current codes, by implementation of some simple changes, as we will propose in this article. Thus there is no need to ‘scrap’ the current Linnaean codes for a poorly reasoned, logically inconsistent, and fatally flawed new code that will only bring chaos.” I have actually not read this one yet... sorry. ===== Jaime A. Headden Little steps are often the hardest to take. We are too used to making leaps in the face of adversity, that a simple skip is so hard to do. We should all learn to walk soft, walk small, see the world around us rather than zoom by it. "Innocent, unbiased observation is a myth." --- P.B. Medawar (1969) __________________________________ Do you Yahoo!? Friends. Fun. Try the all-new Yahoo! Messenger. http://messenger.yahoo.com/