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Date: Thu, 10 Jun 2004 22:03:38 -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 1)
This recently announced volume contains a series of papers on the case of phylogenetic taxonomy and the PhyloCode, brought together from two symposia held early last year. Some works are vitriolic, others sound and wise, and most see the flaws inherent in the Linnaean system, and others reject the idea that any flaws exist. Some even other “fixes” to the Linnaean system, whereas most simply argue about hypotheses that phylogenetic taxonomists formed, or the PhyloCode itself, without offering a comparison, and by so doing, fail in their self-appointed task of bringing the PhyloCode down. he first paper, by Gerry Moore, is a drawn out, detailed comparison of how the two systems regard definitions and diagnoses, but there are enough fundamental errors that this paper stands out on its own, and thus, I have chosen to write up a detailed review of it and response to it on the list elsewhere. Janovec et al., in the second paper in the volume, attempt to determine the impact of the PhyloCode when or IF implemented on the Neotropical flora of the world, and refer to the manner by which this was done in the past (monographs and florists) --- Moore, G. 2003. Should taxon names be explicitly defined? _The Botanical Review_ 69(1): 2-21. Abstract: "Overviews are provided for traditional and phylogenetic nomenclature. In traditional nomenclature, a name is provided with a type and a rank. In the rankless phylogenetic nomenclature, a taxon name is provided with an explicit phylogenetic definition, which attaches the name to a clade. Linnaeus’s approach to nomenclature is also reviewed, and it is shown that, although the current system of nomenclature does use some Linnaean conventions (e.g., certain rank-denoting terms, binary nomenclature), it is actually quite different from Linnaean nomenclature. “The primary differences between traditional and phylogenetic nomenclature are reviewed. In phylogenetic nomenclature, names are provided with explicit phylogenetic definitions, whereas in traditional nomenclature names are not explicitly defined. In phylogenetic nomenclature, a name remains attached to a clade regardless of how future changes in phylogeny alter the clade’s content; in traditional nomenclature a name is not ‘married’ to any particular clade. In traditional nomenclature, names must be assigned ranks (an admittedly arbitrary process), whereas in phylogenetic nomenclature there are no formal ranks. Therefore, in phylogenetic nomenclature, the name itself conveys no hierarchical information, and the name conveys nothing regarding set exclusivity. “It is concluded that the current system is better able to handle new and unexpected change in ideas about taxonomic relationships. This greater flexibility, coupled with the greater information content that the names themselves (i.e., when used outside the context of a given taxonomy or phylogeny) provide, makes the current system better designed for use by all users of taxon names." There are too many things to say about this paper … I have a huge write up 7 MSWord pages long (10pt, with narrow-set margins) so that is a lot of text. Then I decided I might as well make this review about the volume with select quotes and arguments per paper, and how this effects the bulk of us. Moore’s thesis is the argument of definitions, but he begins by pointing out why it should be the “traditional” and not the “Linnaean” system, and how the evolution of the system differs from that of Linné’s day, and also, that the traditional system is “goverened” by his aphorisms. Needless to say, the best parts were at the end…. "For example, when crafting a definition for the name *Pinus* L., a phylogenetic nomenclator would certainly attempt to craft the definition so that the circumscription of the taxon would include all taxa currently recognized in the genus *Pinus* L. while excluding all taxa not currently placed in *Pinus* L. However, once the name is defined the taxonomist is forced to apply the definition regardless of how future revisions in phylogenetic hypotheses may lead to conflicts with historical usage." … "Let us say that Delta is defined as the least inclusive clade containing species E and species F. Let us also say that, under the original phylogenetic hypothesis, Delta was believed to be a taxon comprising three species (E, F, and G). However, let us now say that the original hypothesis regarding the phylogenetic relationship was drastically incorrect because species F is actually much less closely related to species E and G than originally believed and that .the least inclusive clade containing species E and F. is actually a clade that contains 500,000 species. Under phylogenetic nomenclature, the taxonomist would now be required to apply the name Delta to the clade that contains 500,000 species (the name Delta might become synonymized if there were an earlier name for this clade)." … We recently underwent the "pan-stem" clade argument on the DML of the utility of recognizing clades by sight of their names. Which is precisely the measure by which Moore argues retention of ranks: “[T]he plant taxonomist can determine that the names Pinophyta, *Ephedra* L., *Rhynchospora* subg. *Haplostylis* Pax, Sapindaceae, Liliopsida, Acorales, *Pyxidanthera barbulata* Michx., and *Viola pedata* var. *lineariloba* D.C. represent taxa at the ranks of division, genus, subgenus, family, class, order, species, and variety, respectively." … "No such conclusions can be made under the phylogenetic system of nomenclature, because the name conveys nothing regarding rank assignment and therefore indicates nothing about set exclusivity." Erroneous, as much as I have no problem telling that Oviraptoridae is included in Caenagnathoidea, within Oviraptorosauria, and that this is in turn inside Maniraptora, but Oviraptorosauria is NOT within Paraves. Perhaps not to a plant taxonomist, but _I_ don't need ranks to tell me the order. Definitions (because his thesis is about definitions) force the name into a particular part of any tree as best it can. If it cannot fit to the tree, it should not be used. In this manner, names gain hierarchy by proxy, by the arrangement of their taxa: they do not need another set of names (aka, ranks) telling them what order they should be in. I can later say that because I don't like how Acorales is being used, it's a Class now, rather than an Order, and it's "equivalent" to Liliopsida. Moore then goes on to describe how a name by itself means nothing if it's not applied as a rank to other elements of ranked nature, using the example of a grocers argument of table salt, being a spice, which is a type of food item; Moore argues that by themselves, these are meaningless terms, which is erroneous. "Food items" include things used to provide sustenance, "spices" are things that flavor other food items, and "salt" is one such spice with a bland, granular texture and taste. If using the same language, this relationship is almost certainly impossible to confuse without using ranks. Another fundamental argument of PhyloCode is lost upon the thesis: "Because phylogenetic nomenclature would abandon ranks, the system would also force the abandonment of functional binary nomenclature." … "Under the phylogenetic nomenclature approach, I envision the classification process being placed on automatic pilot. Taxonomists would provide the explicit phylogenetic definitions and phylogenies, and the nomenclatural system would take care of the rest. This appears to be fine to some, such as Donoghue, who recently complained (quoted in Milius, 1999: 269) that ‘Renaming goes on on a daily basis. We’re busy. We have better things to do. It doesn’t make sense for scientists to be doing things like this.’ However, as opposed to having an explicit system (where the definitions do all the work), having an inexplicit system of nomenclature with the taxonomist playing a key role in the classification process (i.e., our current system) recognizes the ‘balancing act’ (see Bowker & Star, 1999) that must go on in classification. As Bowker & Star (1999: 324.325) put it: ‘Classification schemes always represent multiple constituencies. They can do so most effectively through the incorporation of ambiguity -- leaving certain terms open for multiple definitions across different social worlds: they are in this sense boundary objects. Designers must recognize these zones of ambiguity, protecting them where necessary to leave free play for the schemes to do their organizational work.’ I regard the current system as providing a higher level of ‘free play.’ This is best summarized by Wheeler (2001: 15), who stated that traditional nomenclature ‘is stable enough to say what we know, flexible enough to accommodate what we learn; independent of specific theories, yet reflective of known empirical data; compatible with phylogenetic theory, but not a slave to it; particular enough for precise communication, general enough to reflect refuted hypotheses.’ Therefore, I answer ‘No’ to the question I raised in the title of this article.” -- Janovec, J.P.; Clark, L.G.; and Mori, S.A. 2003. Is the Neotropical flora ready for the PhyloCode? _The Botanical Review_ 69(1): 22-43. Abstract: Nomenclatural systems are structured around classification, and together they enable increasingly informed communication about biological diversity. Challengers of Linnaean classification and nomenclature have proposed the PhyloCode, a new set of rules that would govern the way systematists classify and name the diversity of life. Monographs and floras are two fundamental vehicles for communicating information about plant diversity. These works provide a comprehensive foundation of botanical research upon which other scientific studies are based. Information conveyed by monographs and floras is utilized directly or indirectly both within and outside the scientific arena by a wide range of consumers, such as educators, agronomists, ecologists, conservationists, amateur naturalists, and even lawmakers, to name a few. Both classification and nomenclature are essential to the process of synthesis that leads to monographic and floristic treatments and the communication that they facilitate. Conversion to a new system would have far-reaching consequences for the flow of information from systematics to other scientific disciplines, and to society. The purposes of this article are to address the proposed conversion from the perspective of monographic and floristic research focused on Neotropical plant diversity and to point out some difficulties in applying the PhyloCode to the Neotropical flora. Although we welcome improvements in the current nomenclatural system, we conclude that the PhyloCode is not prepared to replace the Linnaean system as a new way to communicate information about Neotropical plant diversity.” This is one of the more cogent papers of he volume for many reasons. For example, it’s not antagonistic. They even propose questions: “1. Is the power of inference an important part of the way we communicate about the Neotropical flora? From where does this power arise in our stream of communication, and how does this relate to nomenclatural code? 2. Are name changes really a problem? Will absence of ranks, a nomenclatural freeze, and severing the tie between nomenclature and classification (taxonomic concept) be better than name changes that now reflect taxonomic change and concept? 3. How will the problems of newly discovered species, discovery of new characters, and changes in outgroups be resolved? 4. Do we really have an adequate number of phylogenies for diverse regions such as the Neotropical flora? 5. Based on partial evidence, is it really possible to reconstruct a phylogeny that is robust enough to stand the test of time and support a frozen nomenclature? 6. How can we treat higher-level taxonomic patterns before we discover, describe, classify, and name at the lower taxonomic levels—the species?” Kojima J. 2003. Apomorphy-based definition also pinpoints a node, and PhyloCode names prevent effective communication. _The Botanical Review_ 69(1): 44-58. Abstract: “Acceptable methods of defining taxon (or clade) names in the draft PhyloCode, or so-called phylogenetic nomenclature, are ‘node based,’ ‘stem based,’ and ‘apomorphy based.’ All of them define a clade name by pinpointing a node; whereas node-based and stem-based definitions require two or more taxon .specifiers. to define names, an apomorphy-based definition requires two specifiers of different types; namely, a single-taxon specifier and a character specifier. The taxon specifier in an apomorphy-based definition is completely different from the ‘type’ in the Linnaean system. Taxon (or clade) names in the PhyloCode are characterized in two entirely different manners: One is a name that does not change, either in its orthography or in the contents of the taxon referred to by it (or its meaning) over time; the other is a name that is just like a pure mark and thus has no meaning. Communication through such PhyloCode names is very ineffective or impossible.” A few quotes: “The only difference between node-based and stem-based definitions is whether a name is restricted to ‘crown clades’ or includes also the ‘stem clade’ (Nixon & Carpenter, 2000).” “Even if referring to a taxonomic hypothesis, however, neither a taxon name nor a taxon is defined in terms of the type and the taxonomic category. Again the type is a single reference point and, therefore, can define only itself; the taxonomic hierarchical categories are for assigning taxa into a nested pattern (or a hierarchical arrangement) but do not define any taxa or taxon names.” This makes me curious about the purpose of the ranks…. The taxonomic hypothesis itself puts the taxa into a co-called hierarchical arrangement, to which the ranks are assigned at points that feel wise to the taxonomist. Kojima spent half the paper, actually, in describing a situation wherein one can track changes to the system between traditional and phylogenetic systems, with two data sets, and how the two systems treat them. I am, for sake of space, not including these, and urge the reader to get this paper for their own intellectual perusal. However, suffice it to say, his conclusion was: “I presented these hypothesized examples not to support so-called phylogenetic classification but to show that such a comparison of the stability of names is worth doing only within the Linnaean system when change is required but does not make sense contrasting the PhyloCode and Linnaean names because they are completely different in the effect of changes in included taxa on names.” Which is an important point to make. “A name (up to the family-group rank), under the codes in current use -- or in the Linnaean system -- is established when its rank is specified by the orthography, description of diagnostic characters is provided, and the type is designated (e.g., Article 13 of the International Code of Zoological Nomenclature [ICZN, 2000]).” How is rank specified? By the affix applied to the name? What defines the ranks, historical usage? “Stuessy (2001: 185) mentioned ‘Words in a dictionary are, indeed, defined. . . . [They] serve as labels for concepts, objects, ideas, etc. Names are, of course, words, but they are different kinds of words -- they are solely labels for purposes of communication.’ This statement is incorrect. It is concepts, objects, or ideas that are defined, and in a dictionary those definitions are given under words that are labels to those defined concepts, objects, or ideas. Labels (= words) are not defined, but their meanings are given. Names are the same kind of words as those in a dictionary; that is, they are labels for persons, institutions, goods, and so on. Without objects, concepts, or ideas that names label, those names do not function as communication media.” Though Kojima has the application correct, where names are the same as words, the quality or means by which the definitions are formed are different for taxonomic nomenclature than they are for lay nomenclature. A “chamber” is different than the application of the sense of “Aster” and it’s use in taxonomy. For instance, how will you define in a dictionary *Aster*? Or *Canis*? “*Canis* (n). An organism belonging to the family Canidae, which includes *C. familiaris*”? It’s certainly not synonymous with “dog” to many people, who’ve never heard of it. It was the same as “dog” in ancient Rome, but no longer, and its meaning has shifted in a taxonomic sense. traditional taxonomy will require the use of the type species, the type specimen, the rank, the describer, and his description, to “define” it. Well, Kojima says it’s not defined, but that is precisely how one will go about it under traditional taxonomy. “In the so-called phylogenetic nomenclature, ‘taxa [or clades] are circumscribed [by a particular phylogenetic hypothesis] before they are named, . . . are named through acts similar to christening, and . . . taxon names are labels’ (de Queiroz, 2000: 535). This statement implies that a taxon name is not defined but labels a taxon concept circumscribed by a phylogenetic definition.” Kojima describes a “problem” with phylogenetic definitions by proceeding on to a discussion of a dummy data set and dummy definitions that concludes: “’Gamma’ may include only ‘epsilon’ and ‘gamma’ but could include all organisms on Earth (or in space). The name ‘Gamma’ is not a label for any particular concept; thus it has no meaning.” Au contraire, but it has a lot of meaning … the name “Gamma,” as in the example under Moore’s paper with “Delta,” provides us with a very clear, and very secure definition: it shall only apply in this way, and no matter the change in content, to that group of taxa and whatever shall be included. “ ‘phylogenetic definitions’ mean not phylogenetic hypotheses but whether they are node-based, stem-based, or apomorphy-based definitions.” That, I think, is the point. The name in traditional taxonomy often refers to a hypothesis, which can be shifted around, flexed, bent, and broken at will. “ ‘Synonyms are names that are spelled differently but refer to the same taxon[; they] . . . must be established and may be homodefinitional (based on the same definition) or heterodefinitional (based on different definitions).’ If the names have to be defined, they must be homodefinitional to be synonymous.” Kojima does not understand that the content and thus application of a heterodefinitional clade can be the same (i.e., synonymous) with that of another clade. -- Schuh, R.T. 2003. The Linnaean system and its 250-year persistence. _The Botanical Review_ 69(1): 59-78. Abstract: “The Linnaean system of nomenclature has been used and adapted by biologists over a period of almost 250 years. Under the current system of codes, it is now applied to more than 2 million species of organisms. Inherent in the Linnaean system is the indication of hierarchical relationships. The Linnaean system has been justified primarily on the basis of stability. Stability can be assessed on at least two grounds: the absolute stability of names, irrespective of taxonomic concept; and the stability of names under changing concepts. Recent arguments have invoked conformity to phylogenetic methods as the primary basis for choice of nomenclatural systems, but even here stability of names as they relate to monophyletic groups is stated as the ultimate objective. The idea of absolute stability as the primary justification for nomenclatural methods was wrong from the start. The reasons are several. First, taxa are concepts, no matter the frequency of assertions to the contrary; as such, they are subject to change at all levels and always will be, with the consequence that to some degree the names we use to refer to them will also be subject to change. Second, even if the true nature of all taxa could be agreed upon, the goal would require that we discover them all and correctly recognize them for what they are. Much of biology is far from that goal at the species level and even further for supraspecific taxa. Nomenclature serves as a tool for biology. Absolute stability of taxonomic concepts -- and nomenclature -- would hinder scientific progress rather than promote it. It can been demonstrated that the scientific goals of systematists are far from achieved. Thus, the goal of absolute nomenclatural stability is illusory and misguided. The primary strength of the Linnaean system is its ability to portray hierarchical relationships; stability is secondary. No single system of nomenclature can ever possess all desirable attributes: i.e., convey information on hierarchical relationships, provide absolute stability in the names portraying those relationships, and provide simplicity and continuity in communicating the identities of the taxa and their relationships. Aside from myriad practical problems involved in its implementation, it must be concluded that ‘phylogenetic nomenclature’ would not provide a more stable and effective system for communicating information on biological classifications than does the Linnaean system.” “Under the Linnaean system, as currently applied, information on hierarchical relationships is conveyed directly. At the least inclusive level, species are nested within genera. Because species names comprise a combination of generic and species epithets, the placement -- and therefore relationships -- of species are self-evident from the use of their names. At more inclusive levels the endings of the taxon names connote relative positions in the hierarchical system, up to a given point, depending on whether we are using the botanical or zoological code. Thus, within the limits of the number of levels recognized in the hierarchy, the system directly conveys information on group membership and on group relationships.” The previously indicated and repeated reason for ranks … notability at a glance from the name that it should be HIGHER than the others, or include other affixes. This is the ONLY reason granted to offer for retention of ranks. Genera and species don’t have affixes, but are italicized and capitalized or in lower cases, respectively, so you will _always_ know a rank when you see the name. The issue of group membership has been pointed out before. Insect genera and plant genera often include MANY more species than do, say, avian genera. The relative composition of ranks as a value of the rank depends on the group studied; as a counter to this, the hoatzin order Opisthocomiformes has a staggering ONE genus in it … and it’s not even a fossil. The magical rank refers to the number of taxa in there … so why aren’t there fewer orders, families, and genera in vertebrates? There used to be 20+ species in *Megalosaurus* and a few others representative taxa. Mike Keesey offered a synthesis to reflect this jokingly, but maybe we can do this to reflect rank? “Most taxon names in biology have little or no meaning in and of themselves. Although the hierarchical system of Linnaean nomenclature can be quickly learned -- and therefore the rank order and inclusion/exclusion relationships of names comprehended -- information on the meanings of the names is still dependent on knowledge of biology.” So, ranks still have no meaning … just an easy to recall inclusion/exclusion series for themselves? As argued elsewhere, taxon names all have meaning, whether considered or not, relative to their content. “Taxon concepts exist in the form of diagnoses.” [Read: not definitions.] It is the diagnosis that provides what a taxon is, and what it isn’t. Not rank, not definition, etc. This is true on the one hand, but untrue on the other. Apomorphy-based clades are defined on their relationship to the diagnosis, in a sense, much as node- and stem-based clades are divorced from the diagnosis, as in crown- and pan-stem-clades. “A completely dichotomous hierarchical system would require n -1 higher taxa, where n is the number of species. Nowhere near that many higher-taxon concepts exist.” Actually, only one taxon concept is required: they are all clades defined by their relationship to one another. Something that seems to shock most of the authors and especially THIS one is that the number of actual nodes and stems can get names. No one has to name them, and in fact phylogenetic taxonomy as in the PhyloCode desires NOT to name most of them, just those that are considered important for communication. “The Linnaean system provides a relatively simple and effective system of communicating hierarchical information. It is not the only possible system capable of communicating such information, but it now has a nearly 250-year history of doing so. It is that continuity which provides one of the strongest arguments for the persistence of the Linnaean approach and also for maintaining it. With at least 2 million names for biological taxa now in existence, any efforts to replace Linnaean nomenclature should be very well founded indeed. Otherwise, massive confusion will result, and much of the existing literature might be rendered essentially useless.” It is the “longevity” of the system that means it should be retained? Not all names were coined following or even strictly adhering to the principles of the codes now favored to be retained, but most were, in fact, not. As for the existing literature, this is unfounded. The abandonment of ranks and the literature’s historical import is still very much an issue here, and in phylogenetic nomenclature. Just look at papers remarking on phylogenies and nomenclature using the phylogenetic system, and the use of the literature remains strong indeed going back centuries. Schuh goes on to resolve how he thinks of phylogenetic nomenclature, including defining “Defininition” as where taxa, rather than names, are defined, and only as a node-, stem-, or apomorphy-based definition -- not entirely true, as definitions of crown-clades, pan-stems, and stem-defined nodes exist and will likely be used. He argues that the traditional system is controlled by types, whereas not understanding that the “types” in phylogenetic nomenclature are effectively specifiers. “Mayr was attacking working taxonomists as essentialists, he was also complaining about what he viewed as the defects of Hennig.s then recently introduced methods and the fact that they would undoubtedly reduce the Aves to a status lower than .class. (in a phylogenetic classification), the rank to which birds were truly deserving in his view.” The application of rank is always thus. “De Queiroz […] has argued that there are two primary kinds of taxonomic and nomenclatural systems: Linnaean and phylogenetic […] taxonomic systems can be both Linnaean and phylogenetic, whereas nomenclatural systems ‘must be one or the other.’ The statement suggests that the Linnaean system of nomenclature cannot be used in a phylogenetic context, an idea that will strike most practicing taxonomists as absurd.” Referring to the nomenclatural system of applying names to ranks, and ranks to names, and that names were defined by some form of “magical” number of taxonomic importance, such as Mayr’s comments. The SYSTEM can be used interchangeably. This has been shown in the past to some degrees, but the methods of naming and recognition of entities are VERY different between the two. “From this limited sample, we must conclude that taxonomy is by its very nature not a stable enterprise, and consequently neither can be the nomenclature that is tied to it.” “[T]axonomists have long used the terms ‘definition,’ ‘description,’ and ‘diagnosis’ as being virtually synonymous […]As such, ‘definition,’ ‘diagnosis,’ and ‘description’ all have the intended meaning of listings or summaries of the attributes of taxa, the first two terms usually referring to a more restricted list of attributes than the last.” And this is the fundamental means by which the nomenclatural methods disagree. “The definition of Asteraceae […] would certainly be treated by the bulk of practicing taxonomists as ‘the set of attributes shared by *Aster* and other plant taxa grouped together and placed at that categorical level.’ […] The continued insistence by de Queiroz, and others infatuated with the idea of phylogenetic nomenclature, that placement of a taxon at some level in the Linnaean hierarchy confers some ‘essential’ quality to that taxon is simply misguided. Asteraceae can maintain its status as monophyletic, while retaining its position in the hierarchy of relationships at a level other than family.” Which begs the question: “why give it a rank?” The hierarchy of a system can be known and communicated without ranks. “How nomenclature can remain entirely stable in the face of revised concepts has not been satisfactorily explained by de Queiroz, and it is certainly not explained by Ereshefsky.” Revision of an hypothesis does not reflect instability; it is the ability for the nomenclature to be stabilized relative to their constituents (and in this case, a very few specifiers that the clade named will ALWAYS contain) that provides the stability. I have noted throughout this volume the same difficulty in achieving this point, which means only that this point, the issue of heterodefinitional synonymy, and that it’s OKAY for one’s historical usage to change with the content shifts but the name would seem not to. In fact, the phylogeny shifts, the name stays stable, as much as happens in ANY system. There are NO checks and balances in traditional taxonomy to insure the name retains its given implied and original meaning, or accepted current meaning, without attempting to validate the necessity for providing ranks to stabilize the names into a series. I hope THAT explains stability in revised hypothesis of relationship. Schuh also appears to be under the mistaken impression that any affix is mandatory in phylogenetic nomenclature or under the PhyloCode, though it has been suggested that –ina be applied to some clades, this was a _suggestion_. [I will continue this...] ===== 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/