Classification, Evolution, and the Nature of Biology

Abstract

Historically, naturalists who proposed theories of evolution, including Darwin and Wallace, did so in order to explain the apparent relationship of natural classification. This book begins by exploring the intimate historical relationship between patterns of classification and patterns of phylogeny. However, it is a circular argument to use the data for classification. Alec Panchen presents other evidence for evolution in the form of a historically based but rigorously logical argument. This is followed by a history of methods of classification and phylogeny reconstruction including current mathematical and molecular techniques. The author makes the important claim that if the hierarchical pattern of classification is a real phenomenon, then biology is unique as a science in making taxonomic statements. This conclusion is reached by way of historical reviews of theories of evolutionary mechanism and the philosophy of science as applied to biology. The book is addressed to biologists, particularly taxonomists, concerned with the history and philosophy of their subject, and to philosophers of science concerned with biology. It is also an important source book on methods of classification and the logic of evolutionary theory for students, professional biologists, and paleontologists.

The practice of classification and the theory of evolution, and what the demise of Charles Darwin's tree of life hypothesis means for both of them

“…As Eric Bapteste and I have argued elsewhere , very much following Panchen (1992), what Darwin presents in The Origin is a hypothesis, not an observation or claimed-to-be true fact. The observation or fact to be explained (the explanandum) is hierarchical or tree-like classifications, their apparent robustness and their potential naturalness.…”

“…The practice of constructing multirank inclusive hierarchies (each group a member of one and only one grouping of the next higher rank, the whole representable as a tree) has an honoured place in Western natural history and philosophy, however. According to Panchen (1992), there are deep and complex historical connections between neo-Platonist practices of logical division (often illustrated by the Tree of Porphyry, whose successive bifurcations take us from Substance down to Socrates) and systematists' beliefs about the ontological status of supra-specific taxa. These varied: even Linnaeus (1707-1778) had doubts about the naturalness of taxa higher than genera.…”

Genome-Wide EST Data Mining Approaches to Resolving Incongruence of Molecular Phylogenies

“…Ginkgo biloba was specified as the outgroup. These species were selected because their phylogeny is firmly established by fossil records and morphological characteristics [22][23][24][25]. 144 shared genes of six species except for G. biloba and 36 shared genes of all six species were retrieved.…”

Constructing Phenetic and Phylogenetic Relationship Using Clad'97

“…This toolbox will close automatically when the construction process has been completed. Taking into account one OTU or group at a time, then the result is a dichotomous phenogram [3]. In principle, cluster analysis is a generic term for a mathematical method that shows which objects of concern in a set, along with many others [4].…”