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)

Philosophers and historians of biology have argued that genes are conceptualized differently in different fields of biology and that these differences influence both the conduct of research and the interpretation of research by audiences outside the field in which the research was conducted. In this paper we report the results of a questionnaire study of how genes are conceptualized by biological scientists at the University of Sydney, Australia. The results provide tentative support for some hypotheses about conceptual differences between different (...) fields of biological research. (shrink)

No question in theoretical biology has been more perennially controversial or perplexing than "What is a species?" Recent advances in phylogenetic theory have called into question traditional views of species and spawned many concepts that are currently competing for general acceptance. Once the subject of esoteric intellectual exercises, the "species problem" has emerged as a critically important aspect of global environmental concerns. Completion of an inventory of biodiversity, success in conservation, predictive knowledge about life on earth, management of material resources, (...) formulation of scientifically credible public policy and law, and more depend upon our adoption of the "right" species concept. Quentin D. Wheeler and Rudolf Meier present a debate among top systematic biology theorists to consider the strengths and weaknesses of five competing concepts. Debaters include (1) Ernst Mayr (Biological Species Concept), (2) Rudolf Meier and Rainer Willmann (Hennigian species concept), (3) Brent Mishler and Edward Theriot (one version of the Phylogenetic Species Concept), (4) Quentin Wheeler and Norman Platnick (a competing version of the Phylogenetic Species Concept), and (5) E. O. Wiley and Richard Mayden (the Evolutionary Species Concept). Each author or pair of authors contributes three essays to the debate: first, a position paper with an opening argument for their respective concept of species; second, a counterpoint view of the weakness of competing concepts; and, finally, a rebuttal of the attacks made by other authors. This unique and lively debate format makes the comparative advantages and disadvantages of competing species concepts clear and accessible in a single book for the first time, bringing to light numerous controversies in phylogenetic theory, taxonomy, and philosophy of science that are important to a wide audience. Species Concepts and Phylogenetic Theory will meet a need among scientists, conservationists, policy-makers, and students of biology for an explicit, critical evaluation of a large and complex literature on species. An important reference for professionals, the book will prove especially useful in classrooms and discussion groups where students may find a concise, lucid entrée to one of the most complex questions facing science and society. (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)

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)

I argue that there are at least four different ways in which the term ‘function’ is used in connection with the study of living organisms, namely: function as activity, function as biological role, function as biological advantage, and function as selected effect. Notion refers to what an item does by itself; refers to the contribution of an item or activity to a complex activity or capacity of an organism; refers to the value for the organism of an item having a (...) certain character rather than another; refers to the way in which a trait acquired and has maintained its current share in the population. The recognition of a separate notion of function as biological advantage solves the problem of the indeterminate reference situation that has been raised against a counterfactual analysis of function, and emphasizes the importance of counterfactual comparison in the explanatory practice of organismal biology. This reveals a neglected problem in the philosophy of biology, namely that of accounting for the insights provided by counterfactual comparison. (shrink)

After the discovery of the structure of DNA in 1953, scientists working in molecular biology embraced reductionism—the theory that all complex systems can be understood in terms of their components. Reductionism, however, has been widely resisted by both nonmolecular biologists and scientists working outside the field of biology. Many of these antireductionists, nevertheless, embrace the notion of physicalism—the idea that all biological processes are physical in nature. How, Alexander Rosenberg asks, can these self-proclaimed physicalists also be antireductionists? With clarity and (...) wit, Darwinian Reductionism navigates this difficult and seemingly intractable dualism with convincing analysis and timely evidence. In the spirit of the few distinguished biologists who accept reductionism—E. O. Wilson, Francis Crick, Jacques Monod, James Watson, and Richard Dawkins—Rosenberg provides a philosophically sophisticated defense of reductionism and applies it to molecular developmental biology and the theory of natural selection, ultimately proving that the physicalist must also be a reductionist. (shrink)

This notice provides a critical discussion of some of the issues from Alex Rosenberg’s Darwinian Reductionism, in particular proper functions and the relationship of proximate and ultimate biology, developmental programs and genocentrism, biological laws, the principle of natural selection as a fundamental law, genetic determinism, and the definition of “reductionism.”.

This paper investigates what molecular biology has done for our understanding of the gene. I base a new account of the gene concept of classical genetics on the classical dogma that gene differences cause phenotypic differences. Although contemporary biologists often think of genes in terms of this concept, molecular biology provides a second way to understand genes. I clarify this second way by articulating a molecular gene concept. This concept unifies our understanding of the molecular basis of a wide variety (...) of phenomena, including the phenomena that classical genetics explains in terms of gene differences causing phenotypic differences. (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)

Philosophical discussions of biological classification have failed to recognise the central role of homology in the classification of biological parts and processes. One reason for this is a misunderstanding of the relationship between judgments of homology and the core explanatory theories of biology. The textbook characterisation of homology as identity by descent is commonly regarded as a definition. I suggest instead that it is one of several attempts to explain the phenomena of homology. Twenty years ago the ‘new experimentalist’ movement (...) in philosophy of science drew attention to the fact that many experimental phenomena have a ‘life of their own’: the conviction that they are real is not dependent on the theories used to characterise and explain them. I suggest that something similar can be true of descriptive phenomena, and that many homologies are phenomena of this kind. As a result the descriptive biology of form and function has a life of its own—a degree of epistemological independence from the theories that explain form and function. I also suggest that the two major ‘homology concepts’ in contemporary biology, usually seen as two competing definitions, are in reality complementary elements of the biological explanation of homology. (shrink)

We outline three very different concepts of the gene—instrumental, nominal, and postgenomic. The instrumental gene has a critical role in the construction and interpretation of experiments in which the relationship between genotype and phenotype is explored via hybridization between organisms or directly between nucleic acid molecules. It also plays an important theoretical role in the foundations of disciplines such as quantitative genetics and population genetics. The nominal gene is a critical practical tool, allowing stable communication between bioscientists in a wide (...) range of fields grounded in well-defined sequences of nucleotides, but this concept does not embody major theoretical insights into genome structure or function. The post-genomic gene embodies the continuing project of understanding how genome structure supports genome function, but with a deflationary picture of the gene as a structural unit. This final concept of the gene poses a significant challenge to conventional assumptions about the relationship between genome structure and function, and between genotype and phenotype. (shrink)

Philosophical discussions of species have focused on multicellular, sexual animals and have often neglected to consider unicellular organisms like bacteria. This article begins to fill this gap by considering what species concepts, if any, apply neatly to the bacterial world. First, I argue that the biological species concept cannot be applied to bacteria because of the variable rates of genetic transfer between populations, depending in part on which gene type is prioritized. Second, I present a critique of phylogenetic bacterial species, (...) arguing that phylogenetic bacterial classification requires a questionable metaphysical commitment to the existence of essential genes. I conclude by considering how microbiologists have dealt with these biological complexities by using more pragmatic and not exclusively evolutionary accounts of species. I argue that this pragmatism is not borne of laziness but rather of the substantial conceptual problems in classifying bacteria based on any evolutionary standard. (shrink)

Philosophy of science has always been an integral part of philosophy, and since the beginning of the 20h century it has developed its own structure and its fair share of technical vocabulary and problems. Philosophy of Science A-Z gives you concise, accurate and illuminating accounts of key positions, concepts, arguments and figures in the philosophy of science. It helps you to understand the current debates, explains their historical development and connects them with broader philosophical issues. It presupposes little prior knowledge (...) of philosophy of science and is equally useful to students coming to the subject for the first time and for more advanced scholars who need to look up particular terms or figures. You will find illuminating explanations, careful analysis, relevant examples, open problems and precise arguments. Philosophy of science is a flourishing discipline and Philosophy of Science A-Z is a practical and imaginative way into and through it. (shrink)

I argue that there are at least four different ways in which the term ‘function’ is used in connection with the study of living organisms, namely: function as activity, function as biological role, function as biological advantage, and function as selected effect. Notion refers to what an item does by itself; refers to the contribution of an item or activity to a complex activity or capacity of an organism; refers to the value for the organism of an item having a (...) certain character rather than another; refers to the way in which a trait acquired and has maintained its current share in the population. The recognition of a separate notion of function as biological advantage solves the problem of the indeterminate reference situation that has been raised against a counterfactual analysis of function, and emphasizes the importance of counterfactual comparison in the explanatory practice of organismal biology. This reveals a neglected problem in the philosophy of biology, namely that of accounting for the insights provided by counterfactual comparison. (shrink)

This paper reviews the debate on the notion of biological function and on functional explanation as this takes place in philosophy. It describes the different perspectives, issues, intuitions, theories and arguments that have emerged. The author shows that the debate has been too heavily influenced by the concerns of a naturalistic philosophy of mind and argues that in order to improve our understanding of biology the attention should be shifted from the study of intuitions to the study of the actual (...) practice of biological inquiry. (shrink)

“Functional homology” appears regularly in different areas of biological research and yet it is apparently a contradiction in terms—homology concerns identity of structure regardless of form and function. I argue that despite this conceptual tension there is a legitimate conception of ‘homology of function’, which can be recovered by utilizing a distinction from pre-Darwinian physiology (use versus activity) to identify an appropriate meaning of ‘function’. This account is directly applicable to molecular developmental biology and shares a connection to the theme (...) of hierarchy in homology. I situate ‘homology of function’ within existing definitions and criteria for structural assessments of homology, and introduce a criterion of ‘organization’ for judging function homologues, which focuses on hierarchically interconnected interdependencies (similar to relative position and connection for skeletal elements in structural homology). This analysis of biological concepts has at least three broad philosophical consequences: (1) it provides the grounds for the study of behavior and psychological categories as homologues; (2) it demonstrates that philosophers who take selected effect function as primary effectively ignore large portions of comparative, structural, and experimental research, thereby misconstruing biological reasoning and knowledge; and, (3) it underwrites causal generalizations, which illuminates inferences made from model organisms in experimental biology. (shrink)

Philosophers and historians of biology have argued that genes are conceptualized differently in different fields of biology and that these differences influence both the conduct of research and the interpretation of research by audiences outside the field in which the research was conducted. In this paper we report the results of a questionnaire study of how genes are conceptualized by biological scientists at the University of Sydney, Australia. The results provide tentative support for some hypotheses about conceptual differences between different (...) fields of biological research. (shrink)

Present-day thought on the notion of species is troubled by a mistaken understanding of the nature of the issue: while the species problem is commonly understood as concerning the epistemology and ontology of one single scientific concept, I argue that in fact there are multiple distinct concepts at stake. An approach to the species problem is presented that interprets the term ‘species’ as the placeholder for four distinct scientific concepts, each having its own role in biological theory, and an explanation (...) is given of the concepts involved. To illustrate how these concepts are commonly conflated, two widely accepted ideas on species are criticized: species individualism and species pluralism. I argue that by failing to distinguish between the four concepts and their particular roles in contemporary biological theory, these ideas stand in the way of a final resolution of the species problem. (shrink)

There is an interesting parallel between two debates in different domains of contemporary analytic philosophy. One is the endurantism– perdurantism, or three-dimensionalism vs. four-dimensionalism, debate in analytic metaphysics. The other is the debate on the species problem in philosophy of biology. In this paper I attempt to cross-fertilize these debates with the aim of exploiting some of the potential that the two debates have to advance each other. I address two issues. First, I explore what the case of species implies (...) regarding the feasibility of particular positions in the endurantism– perdurantism debate. I argue that the case of species casts doubt on the recent claim that three-dimensionalism and four-dimensionalism are equivalent descriptions of the same underlying reality. Second, and conversely, I examine whether the metaphysical worry about three-dimensionalism and four-dimensionalism can help us to better understand the nature of biological species. I show that analyzing the thesis that species are individuals against the background of the endurantism– perdurantism debate allows us to explicate two different ways in which this thesis can be interpreted. (shrink)

Species in biology are traditionally perceived as kinds of organisms about which explanatory and predictive generalizations can be made, and biologists commonly use species in this manner. This perception of species is, however, in stark contrast with the currently accepted view that species are not kinds or classes at all, but individuals. In this paper I investigate the conditions under which the two views of species might be held simultaneously. Specifically, I ask whether upon acceptance of an ontology of species (...) as diachronic segments of the tree of life species can perform the epistemic role of kinds of organisms to which explanatory and predictive generalizations apply. I show that, for species-level segments of the tree of life, several requirements have to be met before the performance of this epistemic role is possible, and I argue that these requirements can be met by defining species according to the Composite Species Concept proposed by Kornet and McAllister in the 1990s. (shrink)

Recent molecular biology has seen the development of genomics as a successor to traditional genetics. This paper offers an overview of the structure, epistemology, and history of contemporary genomics. A particular focus is on the question to what extent the genome contains, or is composed of, anything that corresponds to traditional conceptions of genes. It is concluded that the only interpretation of genes that has much contemporary scientific relevance is what is described as the "developmental defect" gene concept. However, developmental (...) defect genes typically only correspond to general areas of the genome and not to precise chemical structures . The parts of the genome to be identified for an account of the processes of normal development are highly diverse, little correlated with traditional genes, and act in ways that are highly dependent on the cellular and higher level environment. Despite its historical development out of genetics, genomics represents a radically different kind of scientific project. (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)

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.

Despite the traditional focus on metaphysical issues in discussions of natural kinds in biology, epistemological considerations are at least as important. By revisiting the debate as to whether taxa are kinds or individuals, I argue that both accounts are metaphysically compatible, but that one or the other approach can be pragmatically preferable depending on the epistemic context. Recent objections against construing species as homeostatic property cluster kinds are also addressed. The second part of the paper broadens the perspective by considering (...) homologues as another example of natural kinds, comparing them with analogues as functionally defined kinds. Given that there are various types of natural kinds, I discuss the different theoretical purposes served by diverse kind concepts, suggesting that there is no clear-cut distinction between natural kinds and other kinds, such as functional kinds. Rather than attempting to offer a unique metaphysical account of ‘natural’ kind, a more fruitful approach consists in the epistemological study of how different natural kind concepts are employed in scientific reasoning. (shrink)

Following Mayr (1961) evolutionary biologists often maintain that the hallmark of biology is its evolutionary perspective. In this view, biologists distinguish themselves from other natural scientists by their emphasis on why-questions. Why-questions are legitimate in biology but not in other natural sciences because of the selective character of the process by means of which living objects acquire their characteristics. For that reason, why-questions should be answered in terms of natural selection. Functional biology is seen as a reductionist science that applies (...) physics and chemistry to answer how-questions but lacks a biological point of view of its own. In this paper I dispute this image of functional biology. A close look at the kinds of issues studied in biology and at the way in which these issues are studied shows that functional biology employs a distinctive biological perspective that is not rooted in selection. This functional perspective is characterized by its concern with the requirements of the life-state and the way in which these are met. (shrink)

. Recent molecular biology has seen the development of genomics as a successor to traditional genetics. This paper offers an overview of the structure, epistemology, and history of contemporary genomics. A particular focus is on the question to what extent the genome contains, or is composed of anything that corresponds to traditional conceptions of genes. It is concluded that the only interpretation of genes that has much contemporary scientific relevance is what is described as the “developmental defect” gene concept. However, (...) developmental defect genes typically only correspond to general areas of the genome and not to precise chemical structures. The parts of the genome to be identified for an account of the processes of normal development are highly diverse, little correlated with traditional genes, and act in ways that are highly dependent on the cellular and higher level environment. Despite its historical development out of genetics, genomics represents a radically different kind of scientific project. (shrink)