At least 22 concepts of species are in use today and many of these are notably incompatible in their accounts of biological diversity. Much of the traditional turmoil embodied in the species problem ultimately derives from the packaging of inappropriate criteria for species into a single concept. This results from a traditional conflation of function of concepts with their applications, definitions with concepts, taxonomic categories with groups, and the ontological status of real species with teleological approaches to recover them. Analogous (...) to classifications of supraspecific taxa, our forging inappropriate and ambiguous information relating to theoretical and operational discussions of species ultimately results in a trade-off between convenience, accuracy, precision, and the successful recovery of natural biological diversity. Hence, none of these expectations or intentions of species or classifications is attainable through composite, and possibly discordant, concepts of biological diversity or its descent. Reviewing and evaluating the concepts of species for their theoretical and operational qualities illustrates that a monistic, primary concept of species, applicable to the various entities believed to be species, is essential. This evaluation reveals only one theoretical concept as appropriate for species, the Evolutionary Species Concept. This conceptualization functions as a primary concept and is essential in structuring our ideas and perceptions of real species in the natural world. The remaining concepts are secondary, forming a hierarchy of definitional guidelines subordinate to the primary concept, and are essential to the study of species in practice. Secondary concepts should be used as operational tools, where appropriate, across the variance in natural diversity to discover entities in accord with the primary concept. Without this theoretical and empirical structuring of concepts of species our mission to achieve reconciliation and understanding of pattern and process of the natural world will fail. (shrink)

Stem cell scientists and ethicists have focused intently on questions relevant to the developmental stage and developmental capacities of stem cells. Comparably less attention has been paid to an equally important set of questions about the nature of stem cells, their common characteristics, their non‐negligible differences and their possible developmental species specificity. Answers to these questions are essential to the project of justly inferring anything about human stem cell biology from studies in non‐human model systems—and so to the possibility of (...) eventually developing human therapies based on stem cell biology. After introducing and discussing these questions, I conclude with a brief discussion of the creation of novel model systems in stem cell biology: human‐to‐animal embryonic chimeras. Such novel model systems may help to overcome obstacles to extrapolation, but they are also scientifically and ethically contentious. BioEssays 26:1005‐1012, 2004. © 2004 Wiley Periodicals, Inc. (shrink)

SummaryThis paper addresses the question of what scientific realism implies and what it does not when it is articulated so as to provide the best defense against plausible philosophical alternatives. A summary is presented of “abductive” arguments for scientific realism, and of the epistemological and semantic conceptions upon which they depend. Taking these arguments to be the best current defense of realism, it is inquired what, in the sense just mentioned, realism implies and what it does not. It is concluded (...) that realism implies the strong rejection of epistemological foundationalism, a non‐Humean conception of causation and of explanation, and a causal rather than conceptual account of the unity of natural definitions. It is denied that realism implies bivalence or the existence of one true theory, one preferred vocabulary or one distinctly privileged science. It is further denied that realism implies that there are no unrecognized conventional aspects to scientific theorizing and it is denied that realism implies that scientists routinely do good experimental metaphysics. (shrink)

The essentialism story is a version of the history of biological classification that was fabricated between 1953 and 1968 by Ernst Mayr, who combined contributions from Arthur Cain and David Hull with his own grudge against Plato. It portrays pre-Darwinian taxonomists as caught in the grip of an ancient philosophy called essentialism, from which they were not released until Charles Darwin's 1859 Origin of Species. Mayr's motive was to promote the Modern Synthesis in opposition to the typology of idealist morphologists; (...) demonizing Plato served this end. Arthur Cain's picture of Linnaeus as a follower of 'Aristotelian' (scholastic) logic was woven into the story, along with David Hull's application of Karl Popper's term, 'essentialism', which Mayr accepted in 1968 as a synonym for what he had called 'typological thinking'. Although Mayr also pointed out the importance of empiricism in the history of taxonomy, the essentialism story still dominates the secondary literature. The history of the first telling of the essentialism story exposes its scant basis in fact. (shrink)

Individuals are a prominent part of the biological world. Although biologists and philosophers of biology draw freely on the concept of an individual in articulating both widely accepted and more controversial claims, there has been little explicit work devoted to the biological notion of an individual itself. How should we think about biological individuals? What are the roles that biological individuals play in processes such as natural selection (are genes and groups also units of selection?), speciation (are species individuals?), and (...) organismic development (do genomes code for organisms)? Much of our discussion here will focus on organisms as a central kind of biological individual, and that discussion will raise broader questions about the nature of the biological world, for example, about its complexity, its organization, and its relation to human thought. (shrink)

Richard Owen has been condemned by Darwinians as an anti-evolutionist and an essentialist. In recent years he has been the object of a revisionist analysis intended to uncover evolutionary elements in his scientific enterprise. In this paper I will examine Owen's evolutionary hypothesis and its connections with von Baer's idea of divergent development. To give appropriate importance to Owen's evolutionism is the first condition to develop an up-to-date understanding of his scientific enterprise, that is to disentagle Owen's contribution to the (...) modernization of typology and morphology. I will argue that Owen's Platonic essentialism is rhetorical and incongruous. On the contrary, an interpretation of the archetype based on Aristotle's biological works makes possible a new conception of type, based on a homeostatic mechanism of stability. The renewal of morphology hinges on homological correspondences and a homeostatic process is also the origin of serial and special homology. I will argue that special homology shows an evolutionary orientation insofar as it is a typically inter-specific character while serial homology is determined through an elementary usage of the categories of developmental morphology. (shrink)

This paper is a critical discussion of John Dupré's recent defence of promiscuous realism in Part 1 of his The Disorder of Things: Metaphysical Foundations of the Disunity of Science. It also discusses some more general issues in the philosophy of biology and science. Dupré's chief strategy of argumentation appeals to debates within the philosophy of biology, all of which concern the nature of species. While the strategy is well motivated, I argue that Dupré's challenge to essentialist and unificationist views (...) about natural kinds is not successful. One conclusion is that an integrative conception of species is a real alternative to Dupré's pluralism. (shrink)

This paper describes one complete and one ongoing empirical study in which philosophical analyses of the concept of the gene were operationalized and tested against questionnaire data obtained from working biologists to determine whether and when biologists conceive genes in the ways suggested. These studies throw light on how different gene concepts contribute to biological research. Their aim is not to arrive at one or more correct 'definitions' of the gene, but rather to map out the variation in the gene (...) concept and to explore its causes and its effects. (shrink)

It is common to defend the Homeostatic Property Cluster ( HPC ) view as a third way between conventionalism and essentialism about natural kinds ( Boyd , 1989, 1991, 1997, 1999; Griffiths , 1997, 1999; Keil , 2003; Kornblith , 1993; Wilson , 1999, 2005; Wilson , Barker , & Brigandt , forthcoming ). According to the HPC view, property clusters are not merely conventionally clustered together; the co-occurrence of properties in the cluster is sustained by a similarity generating ( (...) or homeostatic ) mechanism . I argue that conventional elements are involved partly but ineliminably in deciding which mechanisms define kinds , for deciding when two mechanisms are mechanisms of the same type, and for deciding where one particular mechanism ends and another begins. This intrusion of conventional perspective into the idea of a mechanism raises doubts as to whether the HPC view is sufficiently free of conventional elements to serve as an objective arbiter in scientific disputes about what the kinds of the special sciences should be. (shrink)

A scientific community cannot practice its trade without some set of received beliefs. These beliefs form the foundation of the "educational initiation that prepares and licenses the student for professional practice". The nature of the "rigorous and rigid" preparation helps ensure that the received beliefs are firmly fixed in the student's mind. Scientists take great pains to defend the assumption that scientists know what the world is like...To this end, "normal science" will often suppress novelties which undermine its foundations. Research (...) is therefore not about discovering the unknown, but rather "a strenuous and devoted attempt to force nature into the conceptual boxes supplied by professional education". (shrink)

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)

Thomas S. Kuhn's classic book is now available with a new index.

The article 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 objection that, according to current “species concepts,” species are relational is rejected. These concepts are primarily concerned with (...) what it is for a kind to be a species and throw little light on the essentialist issue of what it is for an organism to be a member of a particular kind. Finally, the article argues that this essentialism can accommodate features of Darwinism associated with variation and change. (shrink)

The historian Raphael Falk has described the gene as a ‘concept in tension’ (Falk 2000) – an idea pulled this way and that by the differing demands of different kinds of biological work. Several authors have suggested that in the light of contemporary molecular biology ‘gene’ is no more than a handy term which acquires a specific meaning only in a specific scientific context in which it occurs. Hence the best way to answer the question ‘what is a gene’, and (...) the only way to provide a truly philosophical answer to that question is to outline the diversity of conceptions of the gene and the reasons for this diversity. In this essay we draw on the extensive literature in the history of biology to explain how the concept has changed over time in response to the changing demands of the biosciences . Finally, we outline some of the conceptions of the gene current today. The seeds of change are implicit in many of those current conceptions and the future of the gene concept looks set to be at as turbulent as the past. (shrink)

The current widespread belief that taxonomic methods used before Darwin were essentialist is ill-founded. The essentialist method developed by followers of Plato and Aristotle required definitions to state properties that are always present. Polythetic groups do not obey that requirement, whatever may have been the ontological beliefs of the taxonomist recognizing such groups. Two distinct methods of forming higher taxa, by chaining and by examplar, were widely used in the period between Linnaeus and Darwin, and both generated polythetic groups. Philosopher (...) William Whewell congratulated pre-Darwinian taxonomists for not adhering to the rigid ideal of definition used in the mathematical sciences. What he called the method of types is here called the method of exemplars because typology has been equated with essentialism, whereas the use of a type species as the reference point or prototype for a higher category was a practice inconsistent with essentialism. The story that the essentialism of philosophers dominated the development of systematics may prove to be a myth. (shrink)

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)

The theory and practice of contemporary comparative biology and phylogeny reconstruction (systematics) emphasizes algorithmic aspects but neglects a concern for the evidence. The character data used in systematics to formulate hypotheses of relationships in many ways constitute a black box, subject to uncritical assessment and social influence. Concerned that such a state of affairs leaves systematics and the phylogenetic theories it generates severely underdetermined, we investigate the nature of the criteria of homology and their application to character conceptualization in the (...) context of transformationist and generative paradigms. Noting the potential for indeterminacy in character conceptualization, we conclude that character congruence (the coherence of character statements) relative to a hierarchy is a necessary, but not a sufficient, condition for phylogeny reconstruction. Specifically, it is insufficient due to the lack of causal grounding of character hypotheses. Conceptualizing characters as homeostatic property cluster natural kinds is in accordance with the empirical practice of systematists. It also accounts for the lack of sharpness in character conceptualization, yet requires character identification and re-identification to be tied to causal processes. (shrink)

A long-standing debate has dominated systematic biology and the ontological commitments made by its theories. The debate has contrasted individuals and the part – whole relationship with classes and the membership relation. This essay proposes to conceptualize the hierarchy of higher taxa is terms of a hierarchy of homeostatic property cluster natural kinds (biological species remain largely excluded from the present discussion). The reference of natural kind terms that apply to supraspecific taxa is initially fixed descriptively; the extension of those (...) natural kind terms is subsequently established by empirical investigation. In that sense, classification precedes generalization, and description provides guidance to empirical investigation. The reconstruction of a hierarchy of (homeostatic property cluster) natural kinds is discussed in the light of cladistic methods of phylogeny reconstruction. (shrink)

I defend a view of the species category, pluralistic realism, which is designed to do justice to the insights of many different groups of systematists. After arguing that species are sets and not individuals, I proceed to outline briefly some defects of the biological species concept. I draw the general moral that similar shortcomings arise for other popular views of the nature of species. These shortcomings arise because the legitimate interests of biology are diverse, and these diverse interests are reflected (...) in different legitimate approaches to the classification of organisms. In the final section, I show briefly how the pluralistic approach can help to illuminate some areas of biological and philosophical dispute. (shrink)

Biological species have been treated traditionally as spatiotemporally unrestricted classes. If they are to perform the function which they do in the evolutionary process, they must be spatiotemporally localized individuals, historical entities. Reinterpreting biological species as historical entities solves several important anomalies in biology, in philosophy of biology, and within philosophy itself. It also has important implications for any attempt to present an "evolutionary" analysis of science and for sciences such as anthropology which are devoted to the study of single (...) species. (shrink)

Darwinists classify biological traits either by their ancestry (homology) or by their adaptive role. Only the latter can provide traditional natural kinds, but only the former is practicable. Process structuralists exploit this embarrassment to argue for non-Darwinian classifications in terms of underlying developmental mechanisms. This new taxonomy will also explain phylogenetic inertia and developmental constraint. I argue that Darwinian homologies are natural kinds despite having historical essences and being spatio-temporally restricted. Furthermore, process structuralist explanations of biological form require an unwarranted (...) assumption about the space of developmental possibility. (shrink)

Species pluralism gives us reason to doubt the existence of the species category. The problem is not that species concepts are chosen according to our interests or that pluralism and the desire for hierarchical classifications are incompatible. The problem is that the various taxa we call 'species' lack a common unifying feature.

This paper takes up the cause of species pluralism. An argument for species pluralism is provided and standard monist objections to pluralism are answered. A new form of species pluralism is developed and shown to be an improvement over previous forms. This paper also offers a general foundation on which to base a pluralistic approach to biological classification.

This paper explains the metaphysical implications of the view that species are individuals (SAI). I first clarify SAI in light of the separate distinctions between individuals and classes, particulars and universals, and abstract and concrete things. I then show why the standard arguments given in defense of SAI are not compelling. Nonetheless, the ontological status of species is linked to the traditional "species problem," in that certain species concepts do entail that species are individuals. I develop the idea that species (...) names are rigid designators and show how this provides additional motivation for SAI. (shrink)

Paul E. Griffiths argues that most research on the emotions has been as misguided as Aristotelian efforts to study "superlunary objects" - objects...

The question of whether biologists should continue to use the Linnaean hierarchy has been a hotly debated issue. Invented before the introduction of evolutionary theory, Linnaeus's system of classifying organisms is based on outdated theoretical assumptions, and is thought to be unable to provide accurate biological classifications. Marc Ereshefsky argues that biologists should abandon the Linnaean system and adopt an alternative that is more in line with evolutionary theory. He traces the evolution of the Linnaean hierarchy from its introduction to (...) the present. He illustrates how the continued use of this system hampers our ability to classify the organic world, and then goes on to make specific recommendations for a post-Linnaean method of classification. Accessible to a wide range of readers by providing introductory chapters to the philosophy of classification and the taxonomy of biology, the book will interest both scholars and students of biology and the philosophy of science. (shrink)

Genes and the Agents of Life undertakes to rethink the place of the individual in the biological sciences, drawing parallels with the cognitive and social sciences. Genes, organisms, and species are all agents of life but how are each of these conceptualized within genetics, developmental biology, evolutionary biology, and systematics? The 2005 book includes highly accessible discussions of genetic encoding, species and natural kinds, and pluralism above the levels of selection, drawing on work from across the biological sciences. The book (...) is a companion to the author's Boundaries of the Mind (2004), also available from Cambridge, where the focus is the cognitive sciences. The book will appeal to a broad range of professionals and students in philosophy, biology, and the history of science. You can download the table of contents and the first chapter here. (shrink)

A historical and critical analysis of the concept of the gene that attempts to provide new perspectives and metaphors for the transformation of biology and its philosophy.

The paper describes the change from molecular genetics to postgenomic biology. It focuses on phenomena in the regulation of gene expression that provide a break with the central dogma, according to which sequence specificity for a gene product must be template derived. In its place we find what is called here ‘constitutive molecular epigenesis’. Its three classes of phenomena, which I call sequence ‘activation’, ‘selection’ and ‘creation’, are exemplified by processes such as transcriptional activation, alternative cis- and trans-splicing, and RNA (...) editing. These phenomena support the following main theses of the paper: 1. Other molecular resources share the causal role of ‘genes’: the ‘causal specificity’ for the linear sequence of any gene product is distributed between the coding sequence, cis-acting sequences, trans-acting factors, environmental signals, and the contingent history of the cell (the cellular code) (thesis of distributed causal specificity). 2. These multiple and overlapping processing and targeting mechanisms amplify the repertoire of RNA and protein products specified through the eukaryotic genome, expanding the possibilities specified by the literal code of DNA (thesis of genetic underdeterminism). 3. These mechanisms of gene expression change the focus of postgenomic research from single molecules and their molecular, biochemical and intrinsic function to their cellular, constituent, component or contextual function due to their recruitment and organization in complex cellular networks. In other words, all agents involved in the regulation of gene expression, including DNA, must interact with other agents to achieve full specificity, which is imposed by regulated recruitment and combinatorial control (theses of regulated recruitment and of system analysis). I conclude from these three main theses that the complexity of higher organisms lies not in its number of genes but in the flexibility, versatility and reactivity of its whole genome. (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)

An account of inductive inference is presented which addresses both its epistemological and metaphysical dimensions. It is argued that inductive knowledge is possible by virtue of the fit between our innate psychological capacities and the causal structure of the world.