Such expressions as that famous one of Linnæus, and which we often meet with in a more or less concealed form, that the characters do not make the genus, but that the genus gives the characters, seem to imply that something more is included in our classification, than mere resemblance. I believe that something more is included; and that propinquity of descent,—the only known cause of the similarity of organic beings,—is the bond, hidden as it is by various degrees of modification, which is partially revealed to us by our classifications (Darwin, 1859, p. 413f).
Monday, 29 October 2007
The Great Phenetic Revival 2 Revisted: A Reply to Felsenstein
Recently on our blog we received a reply to our posting on The Great Phenetic Revival 2: Phenetics from Joseph Felsenstein (University of Washington). We thought it would be a pity to relegate our reply to the comments section and instead include it as separate post.
Felsenstein claims not to have been "trying to give the history of "phylogenetic methods" in his chapter 10. Nevertheless, this seems not to have prevented him from making sweeping (and damning) statements concerning classification - some published before the publication of his book: "The focus of systematics has shifted massively away from classification: it is the phylogenies that are central, and it is nearly irrelevant how they are then used in taxonomy" (Felsenstein 2001: 467), "Systematists get so worked up declaiming the centrality of classification in systematics that I have argued the opposite' (Felsenstein in Franz 2005, p. 495); others see things in much the same light: "Many phylogeneticists now see nomenclature and classification as largely irrelevant to phylogenetics..." (Hillis 2007: 331).
Still, Felsenstein sees himself as commenting only upon "algorithmic methods", when, of course, any method proposed can be made 'algorithmic' and many attempted to do so in constructing early versions of data matrices, way before Sneath or Sokal (see figure above as well as Tillyard 1919, Abel 1910 and Willman 2003).
Cladistics and phenetics might (erroneously) be seen as methods. Felsenstein wished to drop the terminology: "Making this distinction [between phenetics and cladistics] implies that something fundamental is missing from the 'phenetic' methods, that they are ignoring information that the 'cladistic' methods do not. In fact, both methods can be considered to be statistical methods, making their estimates in slightly different ways ... In this book we will give the terms 'cladistic' and 'phenetic' a rest and consider all approaches as methods of statistical inference of the phylogeny" (Felsenstein 2004: 145-146). Our comment on Felsenstein's wish to drop the terms 'cladistic' and 'phenetic', was "to grant equal time to all quantitative (numerical) methodologies", which now leaves us puzzled as to what, exactly, in this passage was "an outrageous misrepresentation of the content of my Chapter 10".
Further, "... numerical phylogenetics is not 'based on simple similarity'. It just isn't. There is no way you can compute either a parsimony tree, or a likelihood tree, from a table of similarities between species". What, then, is it based upon? The matrices that grace our systematic accounts certainly look to us as if they are sets of similarities.
To many (us included), cladistics was about the reform of palaeontology rather than the elaboration, support and promotion of one kind of method or another. That reform began in the 1960s almost entirely independent of the numerical development of data manipulation, of which the latter manifests itself as the ever present pernicious influence of phenetics (regardless of that manifestation as 'parsimony', 'compatibility', 'likelihood', etc.). Felsenstein doesn't mention palaeontology in his history chapter but does later in "Phylogenies and Paleontology" (Felsenstein 2004: 547 et seq.). Here his imprecision seems a little troubling: "...If the fossil record of a group has been searched thoroughly enough, then we should not only be allowed to interpret fossils as ancestors, we should be encouraged to do so" (Felsenstein 2004, p. 547) - searched thoroughly enough; we should not only be allowed to...we should be encouraged to do so. How thorough is enough? And since when has the scientific endeavour required 'permission' to be 'allowed' and 'encouraged' to 'believe' something? It was with such 'beliefs' that the first cladistic revolution was necessary. It is from the ever present phenetics that the second cladistic revolution will (eventually) be born.
Abel, O. 1910. Kritische Untersuchungen über die palaogenen Rhinocerotiden Europas. Abhandlungen Kaiserlich-Koenigliche Geologische Reichsanstalt 20: 1-22.
Felsenstein, J., 2001. The troubled growth of statistical phylogenetics. Systematic Biology 50: 465-467.
Felsenstein, J., 2004. A digression on history and philosophy. In: Felsenstein, J. (Ed.), Inferring Phylogenies. Sinauer Associates, Sunderland, MA, pp. 123-146.
Franz, N. 2005. On the lack of good scientific reasons for the growing phylogeny/classification gap. Cladistics 21: 495-500.
Hillis, D. M. 2007. Constraints in naming parts of the Tree of Life. Molecular Phylogenetics and Evolution 42: 331-338.
Tillyard R. J., 1919. The panorpoid complex. Part 3: the wing venation. Proceedings of the Linnean Society of New South Wales 44: 533-717.
Willman, R. 2003. From Haeckel to Hennig: the early development of phylogenetics in German-speaking Europe. Cladistics 19: 449-479.