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Cracking the Code

To the Editors:

Two items in the July-August issue addressed the PhyloCode, a system for governing the names of biological taxa (taxonomic groups) based on evolutionary principles. As a co-author of that document, I would like to clarify points raised in both articles.

In her From the President message, Lynn Margulis states that the PhyloCode uses a conceptually flawed topology of evolutionary trees. The PhyloCode, however, is not based on evolutionary trees but on definitions that specify the references of taxon names in terms of common ancestry relationships. Such definitions can be applied in the context either of trees or of more extensively connected graphs, which are necessary to represent evolutionary fusions. In the latter case, they result in names being applied to partially overlapping groups. Consequently, names governed by the PhyloCode would do a better job of representing the symbiogenetic origins, as Dr. Margulis advocates for certain taxa,  than do the traditional taxonomic and nomenclatural systems. As a unified code, the PhyloCode would also solve the problem pointed out by Dr. Margulis concerning organisms that are neither plants nor animals but have been given different names under the traditional botanical and zoological codes. 

In "Attacks on Taxonomy" (Science Observer), Roger Harris aptly describes the controversy surrounding the PhyloCode. He states, however, that the system of nomenclature represented by the PhyloCode is meant to replace the system developed by Carl von Linné (Linnaeus). The system of nomenclature that the PhyloCode is meant to replace was developed roughly 100 years after the time of Linnaeus and ties names strongly to taxonomic ranks. The PhyloCode represents a return to an approach more similar to that adopted by Linnaeus and other early naturalists in that names are more strongly tied to taxa (now conceptualized in evolutionary terms) than to ranks. Nevertheless, abandoning the Linnean hierarchical ranks is not a core proposition of the PhyloCode, which does not prohibit the use of ranks but only replaces their function in specifying the references of names with methods based on evolutionary principles.

Kevin de Queiroz
National Museum of Natural History
Smithsonian Institution
Washington, D.C.

Dr. Margulis responds:

I laud Dr. de Queiroz's expertise and the PhyloCode's desire to stabilize the names of taxa when their associated ranks change. Were we to know common ancestry relationships among a majority of species, definitions that specify the references of taxon names might be properly descriptive.

However, we know very few of the estimated 30 million species of extant organisms. Therefore, the ability to employ partially overlapping taxonomic groups does not solve any problems of names and ranks. Rather, it will likely generate more esoteric confusion and grant license to those who yearn to replace groupings of messy live beings with neatly quantifiable computer categories. For this reason, I reiterate the need to open the acute problem of the naming and evolutionary classification of all life to the broader research community that Sigma Xi represents.

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