I analyze a number of widespread misconceptions concerning species. The species category, defined by a concept, denotes the rank of a species taxon in the Linnaean hierarchy. Biological species are reproducing isolated from each other, which protects the integrity of their genotypes. Degree of morphological difference is not an appropriate species definition. Unequal rates of evolution of different characters and lack of information on the mating potential of isolated populations are the major difficulties in the demarcation of species taxa.

Recent discussion of mechanism has suggested new approaches to several issues in the philosophy of science, including theory structure, causal explanation, and reductionism. Here, I apply what I take to be the fruits of the 'new mechanical philosophy' to an analysis of a contemporary debate in evolutionary biology about the role of natural selection in speciation. Traditional accounts of that debate focus on the geographic context of genetic divergence--namely, whether divergence in the absence of geographic isolation is possible (or significant). (...) Those accounts are at best incomplete, I argue, because they ignore the mechanisms producing divergence and miss what is at stake in the biological debate. I argue that the biological debate instead concerns the scope of particular speciation mechanisms which assign different roles to natural selection at various stages of divergence. The upshot is a new interpretation of the crux of that debate--namely, whether divergence with gene flow is possible (or significant) and whether the isolating mechanisms producing it are adaptive. (shrink)

The longstanding species problem in biology has a history that suggests a solution, and that history is not the received history found in many texts written by biologists or philosophers. The notion of species as the division into subordinate groups of any generic predicate was the staple of logic from Aristotle through the middle ages until quite recently. However, the biological species concept during the same period was at first subtly and then overtly different. Unlike the logic sense, which relied (...) on definitions of the essence of both genus and species, biological species from the time of Epicurus were consistently considered to involve a reproductive element: in short, living species relied not on essential definitions, but on the generative cause, which might not be definable. I term this the generative conception of species: species were the generation by reproduction of form. This undercuts the claim that species before Darwin were essentialist, and divorces the notion of a type from that of essence. In fact, as late as the end of the nineteenth century, logicians explicitly treated biological “species” as a homonym only of logical essentialist species, and permitted considerable deviation from the type or form. At every point, species in logic were thought to be a subset, in effect, of some more general notion. I sketch a history of both philosophical and biological traditions of the species concept, before turning to the current conceptions. These are reconsidered in the light of this history, and in particular Mayr’s changing views are shown to be somewhat Whiggish, historiographically. Of the many touted biological species concepts, only one of which (Mayr’s) is called _the_ Biological Species Concept, none appears to capture all the relevant facts, intuitions, and operational requirements of biology. Cladistic conceptions, however, have much in common with the older philosophical literature, in that the natural group of cladism is the clade, or monophyletic group. After considering the Individuality Thesis, and the metaphysics of species, we see that species are the most particular terminal taxa in a clade, and that they are “defined” in terms of the particular synapomorphies, or evolved characters, that are causally responsible for keeping the lineages that organisms form distinct from one another. In this way, we can remain within the generative conception of species that has been in play for over two millennia, and yet avoid the pitfalls of prior attempts to find a universal conception of species. (shrink)

Recent discussion of mechanism has suggested new approaches to several issues in the philosophy of science, including theory structure, causal explanation, and reductionism. Here, I apply what I take to be the fruits of the Ônew mechanical philosophyÕ to an analysis of a contemporary debate in evolutionary biology about the role of natural selection in speciation. Traditional accounts of that debate focus on the geographic context of genetic divergence— namely, whether divergence in the absence of geographic isolation is possible (or (...) significant). Those accounts are at best incomplete, I argue, because they ignore the mechanisms producing divergence and miss what is at stake in the biological debate. I argue that the biological debate instead concerns the scope of particular speciation mechanisms which assign different roles to natural selection at various stages of divergence. The upshot is a new interpretation of the crux of that debate—namely, whether divergence with gene flow is possible (or significant) and whether the isolating mechanisms producing it are adaptive. Ó 2005 Elsevier Ltd. All rights reserved. (shrink)

The paper characterizes Darwin's theory, providing a synthesis of recent historical investigations in this area. Darwin's reading of Malthus led him to appreciate the importance of population pressures, and subsequently of natural selection, with the help of the wedge metaphor. But, in itself, natural selection did not furnish an adequate account of the origin of species, for which a principle of divergence was needed. Initially, Darwin attributed this to geographical isolation, but later, following his work on barnacles which underscored the (...) significance of variation, and arising from his work on botanical arithmetic, he supposed that diversity allowed more places to be occupied in a given region. So isolation was not regarded as essential. Large regions with intense competition, and with ample variation spread by blending, would facilitate speciation. The notion of place was different from niche, and it is questioned whether Darwin's views on ecology were as modern as is commonly supposed. Two notions of struggle are found in Darwin's theory; and three notions of variation. Criticisms of his theory led him to emphasize the importance of variation over a range of forms. Hence the theory was populational rather than typological. The theory required a Lamarckian notion of inheritable changes initiated by the environment as a source of variation. Also, Darwin deployed a use/habit theory; and the notion of sexual selection. Selection normally acted at the level of the individual, though kin selection was possible. Group selection was hinted at for man. Darwin's thinking (and also the exposition of his theory) was generally guided by the domestic-organism analogy, which satisfied his methodological requirement of a vera causa principle. (shrink)

The biological species (biospecies) concept applies only to sexually reproducing species, which means that until sexual reproduction evolved, there were no biospecies. On the universal tree of life, biospecies concepts therefore apply only to a relatively small number of clades, notably plants andanimals. I argue that it is useful to treat the various ways of being a species (species modes) as traits of clades. By extension from biospecies to the other concepts intended to capture the natural realities of what keeps (...) taxa distinct, we can treat other modes as traits also, and so come to understand that theplurality of species concepts reflects the biological realities of monophyletic groups.We should expect that specialists in different organisms will tend to favour those concepts that best represent the intrinsic mechanisms that keep taxa distinct in their clades. I will address the question whether modes ofreproduction such as asexual and sexual reproduction are natural classes, given that they are paraphyletic in most clades. (shrink)

Several stages can be identified in Darwin's effort to formulate natural selection. The first stage corresponded, roughly speaking, to the period up to 1844. It was characterized by Darwin's attempt to base his model of geographic speciation on an individualistic dynamics, with species understood as reproductively isolated populations. Toward the end of this period, Darwin's ignorance of the laws of variations and heredity led him to adopt varieties and species as the units of variations. This had the extremely important effect (...) of stimulating him to consider the process of speciation as involving populations. At the end of this period, Darwin also began to regard adaptation as being exclusively toward places in the economy of nature. Thus he faced the problem of integrating the process of natural selection with the process of speciation. Individual variants were the units that fueled the first process, whereas varieties produced new speices. There was no link between adaptation and speciation, except whatever could be supplied by a quasi-historical, developmental idea of optimizing the amount of life.In the second stage, I contend, Darwin's reading of Milne-Edwards crystallized his previous insights into a coherent whole. Milne-Edwards' comments on the advantage of functional specialization could readily be understood in terms of the advantage accruing to the individual, relative to other members of its species, from occupying a different niche. Milne-Edwards' discussion of the division of labor suggested that organisms which moved into unoccupied niches would enjoy reduced competition, and hence a differential advantage in survival and reproduction; thus they would induce the species to do likewise. Rather than base his explanation on an analogy with the artificial economy, Darwin chose the principle of the optimalization of the amount of life per unit area as the overall explanatory principle. The difficulties connected with integrating different levels of description were therefore circumvented, insofar as the problem of diversity and speciation was concerned. Although natural selection considered individuals as the units of selection, and the units of variations were varieties and species, the dynamics of the process understood in terms of natural selection, competition, division of labor and niches could give a plausible account of how individual advantage could be transferred to the species, and how diversity resulted from this mechanism. The problem of the different levels of descriptions was confined to how the properties of variations in individuals (in particular, the frequency of variations and their transmission) were responsible for the assumed variability characteristic of varieties and species. This problem Darwin never solved.A third stage occurred in 1858 with the amalgamation of the tree-of-life vizualization of the process of speciation. Speciation, geographic distribution, and systematics were all then embedded in a conceptual matrix with vast explanatory powers. (shrink)

Traditional logical empiricist and more recent historicist positions on the logic of discovery are briefly reviewed and both are found wanting. None have examined the historical detail now available from recent research on Darwin, from which there is evidence for gradual transition in descriptive and explanatory concepts. This episode also shows that revolutionary research can be directed by borrowed metascientific objectives and heuristics from other disciplines. Darwin's own revolutionary research took place within an ontological context borrowed from non evolutionary predecessors (...) with methodological objectives borrowed from and justified by their success in Newton's physics. The logic of discovery is not a special form of inference from observation to theory, but rather a theory of the rationality of research, including principles bearing upon the rational choice of problems, or epistemic objectives, and heuristic, or means to solving the problems. Such choices can be justified only locally in the context of a relatively stable background ontology and substantive epistemology, not globally for all science. (shrink)

Historians and philosophers of science agree that Darwin had an understanding of species which led to a workable theory of their origins. To Darwin species did not differ essentially from ‘varieties’ within species, but were distinguishable in that they had developed gaps in formerly continuous morphological variation. Similar ideas can be defended today after updating them with modern population genetics. Why then, in the 1930s and 1940s, did Dobzhansky, Mayr and others argue that Darwin failed to understand species and speciation? (...) Mayr and Dobzhansky argued that reproductively isolated species were more distinct and ‘real’ than Darwin had proposed. Believing species to be inherently cohesive, Mayr inferred that speciation normally required geographic isolation, an argument that he believed, incorrectly, Darwin had failed to appreciate. Also, before the sociobiology revolution of the 1960s and 1970s, biologists often argued that traits beneficial to whole populations would spread. Reproductive isolation was thus seen as an adaptive trait to prevent disintegration of species. Finally, molecular genetic markers did not exist, and so a presumed biological function of species, reproductive isolation, seemed to delimit cryptic species better than character-based criteria like Darwin’s. Today, abundant genetic markers are available and widely used to delimit species, for example using assignment tests: genetics has replaced a Darwinian reliance on morphology for detecting gaps between species. In the 150th anniversary of The Origin of Species , we appear to be returning to more Darwinian views on species, and to a fuller appreciation of what Darwin meant. (shrink)