Traditionally, species have been treated as classes. In fact they may be considered individuals. The logical term “individual” has been confused with a biological synonym for “organism.” If species are individuals, then: 1) their names are proper, 2) there cannot be instances of them, 3) they do not have defining properties, 4) their constituent organisms are parts, not members. “ Species " may be defined as the most extensive units in the natural economy such that reproductive competition occurs among their (...) parts. Species are to evolutionary theory as firms are to economic theory: this analogy resolves many issues, such as the problems of “reality” and the ontological status of nomenclatorial types. (shrink)

Different chemical species are often cited as paradigm examples of structurally delimited natural kinds. While classificatory monism may thus seem plausible for simple molecules, it looks less attractive for complex biological macromolecules. I focus on the case of proteins that are most plausibly individuated by their functions. Is there a single, objective count of proteins? I argue that the vagaries of function individuation infect protein classification. We should be pluralists about macromolecular classification.

Biologists and philosophers of biology typically regard essentialism about speciesas incompatible with modern Darwinian theory. Analytic metaphysicians such asKripke, Putnam and Wiggins, on the other hand, believe that their essentialist thesesare applicable to biological kinds. I explore this tension. I show that standard anti-essentialist considerations only show that species do not have intrinsic essential properties. I argue that while Putnam and Kripke do make assumptions that contradict received biological opinion, their model of natural kinds, suitably modified, is partially applicable to (...) biological species. However, Wiggins'' thesis that organisms belong essentially to their species is untenable, given modern species concepts. I suggest that Putnam''s, Kripke''s and Wiggins'' errors stem from adopting an account of the point of scientific classification which implies that relationally-defined kinds are likely to be of little value, an account which is inapplicable to biology. (shrink)

Ernst Mayr has argued that Darwinian theory discredited essentialist modes of thought and replaced them with what he has called "population thinking". In this paper, I characterize essentialism as embodying a certain conception of how variation in nature is to be explained, and show how this conception was undermined by evolutionary theory. The Darwinian doctrine of evolutionary gradualism makes it impossible to say exactly where one species ends and another begins; such line-drawing problems are often taken to be the decisive (...) reason for thinking that essentialism is untenable. However, according to the view of essentialism I suggest, this familiar objection is not fatal to essentialism. It is rather the essentialist's use of what I call the natural state model for explaining variation which clashes with evolutionary theory. This model implemented the essentialist's requirement that properties of populations be defined in terms of properties of member organisms. Requiring such constituent definitions is reductionistic in spirit; additionally, evolutionary theory shows that such definitions are not available, and, moreover, that they are not needed to legitimize population-level concepts. Population thinking involves the thesis that population concepts may be legitimized by showing their connections with each other, even when they are not reducible to concepts applying at lower levels of organization. In the paper, I develop these points by describing Aristotle's ideas on the origins of biological variation; they are a classic formulation of the natural state model. I also describe how the development of statistical ideas in the 19th century involved an abandoning of the natural state model. (shrink)

Essentialism is widely regarded as a mistaken view of biological kinds, such as species. After recounting why (sections 2-3), we provide a brief survey of the chief responses to the “death of essentialism” in the philosophy of biology (section 4). We then develop one of these responses, the claim that biological kinds are homeostatic property clusters (sections 5-6) illustrating this view with several novel examples (section 7). Although this view was first expressed 20 years ago, and has received recent discussion (...) and critique, it remains underdeveloped and is often misrepresented by its critics (section 8). (shrink)

Scientific realism has three dimensions: a metaphysical commitment to the existence of a mind-independent world; a semantic commitment to a literal interpretation of scientific claims; and an epistemological commitment to scientific knowledge of both observable and unobservable entities. The semantic dimension is uncontroversial, and the epistemological dimension, though contested, is well articulated in a number of ways. The metaphysical dimension, however, is not even well articulated. In this paper, I elaborate a plausible understanding of mind independence for the realist – (...) plausible in conceding the force of sceptical arguments to the effect that there is no one correct way to carve nature at its joints, but realist in proposing an objective basis for carving nonetheless. Walking this line between implausible realism and full-blown constructivism leads down the path of three forms of relativism or pluralism: one concerning the ways in which scientists “package” properties into entities; another concerning the precise metaphysical natures of these entities; and another concerning the context relativity of their behaviour. (shrink)

In this article I assess the problems and prospects of a microstructural approach to chemical substances. Saul Kripke and Hilary Putnam famously claimed that to be gold is to have atomic number 79 and to be water is to be H2O. I relate the first claim to the concept of element in the history of chemistry, arguing that the reference of element names is determined by atomic number. Compounds are more difficult: water is so complex and heterogeneous at the molecular (...) level that `water is H2O' seems false under some interpretations. I sketch a response to this problem. (shrink)

The paper defends the doctrine that Linnaean taxa, including species, have essences that are, at least partly, underlying intrinsic, mostly genetic, properties. The consensus among philosophers of biology is that such essentialism is deeply wrong, indeed incompatible with Darwinism. I argue that biological generalizations about the morphology, physiology, and behavior of species require structural explanations that must advert to these essential properties. The paper concludes by summarizing my responses to the objection that, according to current “species concepts,” species are relational, (...) and to the objection that essentialism cannot accommodate features of Darwinism associated with variation and change. (shrink)

This paper considers two recent arguments that structure should not be regarded as the fundamental individuating property of proteins. By clarifying both what it might mean for certain properties to play a fundamental role in a classification scheme and the extent to which structure plays such a role in protein classification, I argue that both arguments are unsound. Because of its robustness, its importance in laboratory practice, and its explanatory centrality, primary structure should be regarded as the fundamental distinguishing characteristic (...) of protein taxonomy. (shrink)

Microstructuralism in the philosophy of chemistry is the thesis that chemical kinds can be individuated in terms of their microstructural properties (Hendry in Philos Sci 73:864–875, 2006 ). Elements provide paradigmatic examples, since the atomic number should suffice to individuate the kind. In theory, Microstructuralism should also characterise higher-level chemical kinds such as molecules, compounds, and macromolecules based on their constituent atomic properties. In this paper, several microstructural theses are distinguished. An analysis of macromolecules such as moonlighting proteins suggests that (...) all the forms of microstructuralism cannot accommodate them. (shrink)

In this paper I take issue with the doctrine that organisms belong of their very essence to the natural kinds (or biological taxa, if these are not kinds) to which they belong. This view holds that any human essentially belongs to the species Homo sapiens, any feline essentially belongs to the cat family, and so on. I survey the various competing views in biological systematics. These offer different explanations for what it is that makes a member of one species, family, (...) etc. a member of that taxon. Unfortunately, none of them offers an explanation that is compatible with the essentialism in question. (shrink)

It is commonly held that objects in the world form natural kinds. Rabbits form a natural kind and so do all pieces of gold. The traditional account of natural kinds asserts that the members of a kind share a common essence. The essence of gold, for example, is its unique atomic structure. That structure occurs in all and only pieces of gold, and it is a property that all pieces of gold must have.

Moonlighting – the performance of more than one function by a single protein – is becoming recognized as a common phenomenon with important implications for systems biology and human health. The different functions of a moonlighting protein may use different regions of the protein structure, or alternative structures that occur due to post-translational modifications and/or differences in binding partners. Often the different functions of moonlighting proteins are used at different times or in different places. The existence of moonlighting functions complicates (...) efforts to under- stand metabolic and regulatory networks, as well as physiological and pathological processes in organisms. Because moonlighting functions can play important roles in disease processes, an improved understanding of moonlighting proteins will provide new opportunities for pharmacological manipulations that specifically target a function involved in pathology while sparing physiologically important functions. (shrink)