With this manifesto, John Dupré systematically attacks the ideal of scientific unity by showing how its underlying assumptions are at odds with the central conclusions of science itself.

Controversies about optimality models and adaptationist methodologies have animated the discussions of evolutionary theory in recent years. The sociobiologists, following the lead of E. O. Wilson, have argued that if Darwinian natural selection can be reliably expected to produce the best possible type of organism - one that optimizes the value of its genetic contribution to future generations - then evolution becomes a powerfully predictive theory as well as an explanatory one. The enthusiastic claims of the sociobiologists for the predictability (...) and applicability that the optimalist approach engenders have been met with severe criticism by Richard C. Lewontin, Stephen Jay Gould, and other biologists and philosophers of biology. These original essays take up both sides of the controversy over the role of optimality models in evolutionary biology, providing a refreshingly insightful and balanced discussion of optimality issues by an interdisciplinary group of leading philosophers of biology, biologists, psychologists, anthropologists, and an economist. They focus on the current state of adaptationist and optimalist methodology in evolutionary theory, and on the possibility of extending such methodology to the human sciences, especially those of psychology and anthropology. Introduction / John Dupre -- Part 1. Methodological questions. Simple models of complex phenomena: the case of cultural evolution / Peter J. Richerson and Robert Boyd -- Natural selection and the null hypothesis / John Beatty -- Why not the best? / Philip Kitcher -- Part 2. Evolution and optimality. What is adaptationism? / Elliot Sober -- How to model evolution / John Maynard Smith -- Comments on Maynard Smith’s "How to Model Evolution" / Elliot Sober -- Reply to Sober / John Maynard Smith -- The shape of optimality / Richard C. Lewontin -- Part 3. Applications. Evolutionary ecology and the optimality assumption / John M. Emlen -- Optimality theory and behavior / John E.R. Staddon -- Part 4. Applications to human behavior. Optimization theory in anthropology: applications and critiques / Eric Alden Smith -- Evolution of a mesh between principles of the mind and regularities of the world / Roger N. Shepard -- From evolution to behavior: evolutionary psychology as the missing link / Leda Cosmides and John Tooby -- On the emotions as guarantors of threats and promises / Jack Hirschleifer -- Human kinds / John Dupre. (shrink)

This chapter argues that scientific and philosophical progress in our understanding of the living world requires that we abandon a metaphysics of things in favour of one centred on processes. We identify three main empirical motivations for adopting a process ontology in biology: metabolic turnover, life cycles, and ecological interdependence. We show how taking a processual stance in the philosophy of biology enables us to ground existing critiques of essentialism, reductionism, and mechanicism, all of which have traditionally been associated with (...) substance ontology. We illustrate the consequences of embracing an ontology of processes in biology by considering some of its implications for physiology, genetics, evolution, and medicine. And we attempt to locate the subsequent chapters of the book in relation to the position we defend. (shrink)

This Element is an introduction to the metaphysics of biology, a very general account of the nature of the living world. The first part of the Element addresses more traditionally philosophical questions - whether biological systems are reducible to the properties of their physical parts, causation and laws of nature, substantialist and processualist accounts of life, and the nature of biological kinds. The second half will offer an understanding of important biological entities, drawing on the earlier discussions. This division should (...) not be taken too seriously, however: the topics in both parts are deeply interconnected. Although this does not claim to be a scientific work, it does aim to be firmly grounded in our best scientific knowledge; it is an exercise in naturalistic metaphysics. Its most distinctive feature is that argues throughout for a view of living systems as processes rather than things or, in the technical philosophical sense, substances. (shrink)

We address three fundamental questions: What does it mean for an entity to be living? What is the role of inter-organismic collaboration in evolution? What is a biological individual? Our central argument is that life arises when lineage-forming entities collaborate in metabolism. By conceiving of metabolism as a collaborative process performed by functional wholes, which are associations of a variety of lineage-forming entities, we avoid the standard tension between reproduction and metabolism in discussions of life – a tension particularly evident (...) in discussions of whether viruses are alive. Our perspective assumes no sharp distinction between life and non-life, and does not equate life exclusively with cellular or organismal status. We reach this conclusion through an analysis of the capabilities of a spectrum of biological entities, in which we include the pivotal case of viruses as well as prions, plasmids, organelles, intracellular and extracellular symbionts, unicellular and multicellular life-forms. The usual criterion for classifying many of the entities of our continuum as non-living is autonomy. This emphasis on autonomy is problematic, however, because even paradigmatic biological individuals, such as large animals, are dependent on symbiotic associations with many other organisms. These composite individuals constitute the metabolic wholes on which selection acts. Finally, our account treats cooperation and competition not as polar opposites but as points on a continuum of collaboration. We suggest that competitive relations are a transitional state, with multi-lineage metabolic wholes eventually outcompeting selfish competitors, and that this process sometimes leads to the emergence of new types or levels of wholes. Our view of life as a continuum of variably structured collaborative systems leaves open the possibility that a variety of forms of organized matter – from chemical systems to ecosystems – might be usefully understood as living entities. (shrink)

This paper considers the applicability of standard accounts of causation to living systems. In particular it examines critically the increasing tendency to equate causal explanation with the identification of a mechanism. A range of differences between living systems and paradigm mechanisms are identified and discussed. While in principle it might be possible to accommodate an account of mechanism to these features, the attempt to do so risks reducing the idea of a mechanism to vacuity. It is proposed that the solution (...) to this problem requires the development of a philosophical account of process adequate to apply to living systems. (shrink)

In the context of scientists' reflections on genomics, we examine some fundamental issues in the emerging postgenomic discipline of systems biology. Systems biology is best understood as consisting of two streams. One, which we shall call ‘pragmatic systems biology’, emphasises large‐scale molecular interactions; the other, which we shall refer to as ‘systems‐theoretic biology’, emphasises system principles. Both are committed to mathematical modelling, and both lack a clear account of what biological systems are. We discuss the underlying issues in identifying systems (...) and how causality operates at different levels of organisation. We suggest that resolving such basic problems is a key task for successful systems biology, and that philosophers could contribute to its realisation. We conclude with an argument for more sociologically informed collaboration between scientists and philosophers. BioEssays 27:1270–1276, 2005. © 2005 Wiley Periodicals, Inc. (shrink)

The thesis of this paper is that our understanding of life, as reflected in the biological and medical sciences but also in our everyday transactions, has been hampered by an inappropriate metaphysics. The metaphysics that has dominated Western philosophy, and that currently shapes most understanding of life and the life sciences, sees the world as composed of things and their properties. While these things appear to undergo all kinds of changes, it has often been supposed that this amounts to no (...) more than a change in the spatial relations of their unchanging parts. From antiquity, however, there has been a rival to this view, the process ontology, associated in antiquity with the fragmentary surviving writings of Heraclitus. In the last century it has been especially associated with the work of the British metaphysician and logician, Alfred North Whitehead. For process ontology, what most fundamentally exists is change, or process. What we are tempted to think of as constant things are in reality merely temporary stabilities in this constant flux of change, eddies in the flux of process. My main claim in this paper will be that a metaphysics of this latter kind is the only kind adequate to making sense of the living world. After explaining in more detail, the differences between these ontological views, I shall illustrate the advantages of a process ontology with reference to the category of organism. Finally I shall explore some further implications of a process ontology for biology and for philosophy. (shrink)

John Dupré explores the ways in which we categorize animals, including humans, and comes to refreshingly radical conclusions. He opposes the idea that there is only one legitimate way of classifying things in the natural world, the 'scientific' way. The lesson we should learn from Darwin is to reject the idea that each organism has an essence that determines its necessary place in the unique hierarchy of things. Nature is not like that: it is not organized in a single system. (...) For instance, there is no universal principle by which organisms can be sorted into species. We are obliged to accept that different classificatory schemes are equally valid, and to take a pluralistic view of biology and the human sciences. These provocative and readable essays move on to discuss a set of contentious topics relating to human nature. To start with, Dupré argues that the concept of a universal human nature should be rejected. He questions the relevance of evolution to explanation of human behaviour, and casts doubt on the concept of normality in human behaviour. He shows that misunderstanding of biology and evolution has lead to widespread misconceptions about human sex and gender-in particular, about sexual behaviour and gender roles. The books concludes with a pair of essays about the differences between humans and animals, which may not be quite so clear-cut as we think. (shrink)

Standard microbial evolutionary ontology is organized according to a nested hierarchy of entities at various levels of biological organization. It typically detects and defines these entities in relation to the most stable aspects of evolutionary processes, by identifying lineages evolving by a process of vertical inheritance from an ancestral entity. However, recent advances in microbiology indicate that such an ontology has important limitations. The various dynamics detected within microbiological systems reveal that a focus on the most stable entities (or features (...) of entities) over time inevitably underestimates the extent and nature of microbial diversity. These dynamics are not the outcome of the process of vertical descent alone. Other processes, often involving causal interactions between entities from distinct levels of biological organisation, or operating at different time scales, are responsible not only for the destabilisation of pre-existing entities, but also for the emergence and stabilisation of novel entities in the microbial world. In this article we consider microbial entities as more or less stabilised functional wholes, and sketch a network-based ontology that can represent a diverse set of processes including, for example, as well as phylogenetic relations, interactions that stabilise or destabilise the interacting entities, spatial relations, ecological connections, and genetic exchanges. We use this pluralistic framework for evaluating (i) the existing ontological assumptions in evolution (e.g. whether currently recognized entities are adequate for understanding the causes of change and stabilisation in the microbial world), and (ii) for identifying hidden ontological kinds, essentially invisible from within a more limited perspective. We propose to recognize additional classes of entities that provide new insights into the structure of the microbial world, namely “processually equivalent” entities, “processually versatile” entities, and “stabilized” entities. (shrink)

This paper considers the applicability of standard accounts of causation to living systems. In particular it examines critically the increasing tendency to equate causal explanation with the identification of a mechanism. A range of differences between living systems and paradigm mechanisms are identified and discussed. While in principle it might be possible to accommodate an account of mechanism to these features, the attempt to do so risks reducing the idea of a mechanism to vacuity. It is proposed that the solution (...) to this problem requires the development of a philosophical account of process adequate to apply to living systems. (shrink)

This paper considers the applicability of standard accounts of causation to living systems. In particular it examines critically the increasing tendency to equate causal explanation with the identification of a mechanism. A range of differences between living systems and paradigm mechanisms are identified and discussed. While in principle it might be possible to accommodate an account of mechanism to these features, the attempt to do so risks reducing the idea of a mechanism to vacuity. It is proposed that the solution (...) to this problem requires the development of a philosophical account of process adequate to apply to living systems. (shrink)

It has increasingly been recognised that units of biological classification cannot be identified with the units of evolution. After briefly defending the necessity of this distinction I argue, contrary to the prevailing orthodoxy, that species should be treated as the fundamental units of classification and not, therefore, as units of evolution. This perspective fits well with the increasing tendency to reject the search for a monistic basis of classification and embrace a pluralistic and pragmatic account of the species category. It (...) also provides a diagnosis of the paradoxical but popular idea that species are individuals: Species are not individuals, but the units of evolution are. (shrink)

This paper briefly describes process metaphysics, and argues that it is better suited for describing life than the more standard thing, or substance, metaphysics. It then explores the implications of process metaphysics for conceptualizing evolution. After explaining what it is for an organism to be a process, the paper takes up the Hull/Ghiselin thesis of species as individuals and explores the conditions under which a species or lineage could constitute an individual process. It is argued that only sexual species satisfy (...) these conditions, and that within sexual species the degree of organization varies. This, in turn, has important implications for species' evolvability. One important moral is that evolution will work differently in different biological domains. (shrink)

Whether we live in a world of autonomous things, or a world of interconnected processes in constant flux, is an ancient philosophical debate. Modern biology provides decisive reasons for embracing the latter view. How does one understand the practices and outputs of science in such a dynamic, ever-changing world - and particularly in an emergency situation such as the COVID-19 pandemic, where scientific knowledge has been regarded as bedrock for decisive social interventions? We argue that key to answering this question (...) is to consider the role of the activity of reification within the research process. Reification consists in the identification of more or less stable features of the flux, and treating these as constituting stable things. As we illustrate with reference to biological and biomedical research on COVID-19, reification is a necessary component of any process of inquiry and comes in at least two forms: means reification, when researchers create objects meant to capture features of the world, or phenomena, in order to be able to study them; and target reification, when researchers infer an understanding of phenomena from an investigation of the epistemic objects created to study them. We note that both objects and phenomena are dynamic processes and argue that have no reason to assume that changes in objects and phenomena track one another. We conclude that failure to acknowledge these forms of reification and their epistemic role in scientific inquiry can have dire consequences for how the resulting knowledge is interpreted and used. (shrink)

Metagenomics is an emerging microbial systems science that is based on the large-scale analysis of the DNA of microbial communities in their natural environments. Studies of metagenomes are revealing the vast scope of biodiversity in a wide range of environments, as well as new functional capacities of individual cells and communities, and the complex evolutionary relationships between them. Our examination of this science focuses on the ontological implications of these studies of metagenomes and metaorganisms, and what they mean for common (...) sense and philosophical understandings of multicellularity, individuality and organism. We show how metagenomics requires us to think in different ways about what human beings are and what their relation to the microbial world is. Metagenomics could also transform the way in which evolutionary processes are understood, with the most basic relationship between cells from both similar and different organisms being far more cooperative and less antagonistic than is widely assumed. In addition to raising fundamental questions about biological ontology, metagenomics generates possibilities for powerful technologies addressed to issues of climate, health and conservation. We conclude with reflections about process-oriented versus entity-oriented analysis in light of current trends towards systems approaches. (shrink)

Most discussion of the unity of science has concerned what might be called vertical relations between theories: the reducibility of biology to chemistry, or chemistry to physics, and so on. In this paper I shall be concerned rather with horizontal relations, that is to say, with theories of different kinds that deal with objects at the same structural level. Whereas the former, vertical, conception of unity through reduction has come under a good deal of criticism recently (see, e.g., Dupré 1993), (...) horizontal unity has generally been conceded to be an important goal. The most pressing questions about horizontal unification arise in the study of human behavior. Numerous sciences including psychology, economics, anthropology, sociology, and parts of biology, attempt to provide explanations of human behavior. It is possible that some of these sciences may be able to coexist peacefully or even cooperatively. However things do not always go so smoothly, and at least two approaches to human behavior, those deriving from economics and evolutionary biology, often involve clearly imperialist tendencies. Devotees of these approaches are inclined to claim that they are in possession not just of one useful perspective on human behavior, but of the key that will open doors to the understanding of ever wider areas of human behavior. In this paper I shall consider some areas in which economic and evolutionary imperialists are currently staking claims. It is of particular interest to look at situations where two the two imperialist programs are staking the same claim, but limitations of space force me to focus here mainly on economics, and my remarks on evolutionary imperialism will be cursory. As well as some specific insights into the particular strategies of these scientific programs, I hope that my discussion will throw some more general light on the limits of such general theoretical strategies and, thereby, I shall suggest some motivations for adhering to a horizontal pluralism of science that matches the vertical pluralism advocated by anti-reductionists. (shrink)

Although molecular biology has meant different things at different times, the term is often associated with a tendency to view cellular causation as conforming to simple linear schemas in which macro-scale effects are specified by micro-scale structures. The early achievements of molecular biologists were important for the formation of such an outlook, one to which the discovery of recombinant DNA techniques, and a number of other findings, gave new life even after the complexity of genotype–phenotype
relations had become apparent. Against this (...) background we outline how a range of scientific developments and conceptual considerations can be regarded as enabling and perhaps necessitating contemporary systems approaches. We suggest that philosophical ideas have a valuable part to play in making sense of complex scientific and disciplinary issues. (shrink)

The traditional home for the concept of a natural kind in biology is of course taxonomy, the sorting of organisms into a nested hierarchy of kinds. Many taxonomists and most philosophers of biology now deny that it is possible to sort organisms into natural kinds. Many do not think that biological taxonomy sorts them into kinds at all, but rather identifies them as parts of historical individuals. But at any rate if the species, genera and so on of biological taxonomy (...) are kinds at all, there are various respects in which they fall short of the traditional requirements of naturalness. The members of biological taxa lack essential properties that make them members of a particular kind: any properties specific enough to belong only to members of the kind cannot be assumed to belong to all members of the kind. And if there are laws applying to members of biological taxa they are laws of very minor and local importance and, in view of the preceding point, at best probabilistic. (shrink)

This chapter defends a pluralistic view of science: the various projects of enquiry that fall under the general rubric of science share neither a methodology nor a subject matter. Ontologically, it is argued that sciences need have nothing in common beyond an antipathy to the supernatural. Epistemically one central virtue is defended, empiricism, meaning just that scientific knowledge must ultimately be answerable to experience. Prima facie science is as diverse as the world it studies; and rejection of this prima facie (...) diversity in favour of a spurious aspiration to unity is grounded in a priori assumption not experience. Disunity, however, does not mean disconnectedness, and the connections between different areas of knowledge are an important theme in the book. (shrink)

Humans are a kind of animal, and it is a natural and sensible idea that the way to understand what it is for a human person to persist over time is to reflect on what it is for an animal to persist. This paper accepts this strategy. However, especially in the light of a range of recent biological findings, the persistence of animals turns out to be much more problematic than is generally supposed. The main philosophical premise of the paper (...) is that living systems generally are best treated as processes rather than things. These processes prove to be so complexly intertwined and interdependent, that there is no unique, objective way of distinguishing the individuals from which they are composed. For this reason the animalist perspective, it is argued, problematizes as much as it resolves the problem of personal identity. Traditional concerns with responsibility and reactive attitudes provide an intelligible and defensible motivation for distinguishing the individuals we standardly assume as the explanandum in these discussions. But, from a biological point of view, the underlying individualism is a contingent perspective, as much justified by these concerns as providing an objective grounding for them. (shrink)

Processes produce changes: rivers erode their banks and thunderstorms cause floods. If I am right that organisms are a kind of process, then the causally efficacious behaviours of organisms are also examples of processes producing change. In this paper I shall try to articulate a view of how we should think of causation within a broadly processual ontology of the living world. Specifically, I shall argue that causation, at least in a central class of cases, is the interaction of processes, (...) that such causation is the exercise of a capacity inherent in that process and, negatively, that causation should not be understood as the instantiation of universal laws. The approach I describe has substantial similarities with the process causality articulated by Wesley Salmon and Phil Dowe for physical causation, making it plausible that the basic approach can be applied equally to the non-living world. It is an approach that builds at crucial points on the criticisms of determinism and universal causality famously articulated by Elizabeth Anscombe. (shrink)

Viruses have been virtually absent from philosophy of biology. In this editorial introduction, we explain why we think viruses are philosophically important. We focus on six issues, and we show how they relate to classic questions of philosophy of biology and even general philosophy.

Understanding how scientific activities use naming stories to achieve disciplinary status is important not only for insight into the past, but for evaluating current claims that new disciplines are emerging. In order to gain a historical understanding of how new disciplines develop in relation to these baptismal narratives, we compare two recently formed disciplines, systems biology and genomics, with two earlier related life sciences, genetics and molecular biology. These four disciplines span the twentieth century, a period in which the processes (...) of disciplinary demarcation fundamentally changed from those characteristic of the nineteenth century. We outline how the establishment of each discipline relies upon an interplay of factors that include paradigmatic achievements, technological innovation, and social formations. Our focus, however, is the baptism stories that give the new discipline a founding narrative and articulate core problems, general approaches and constitutive methods. The highly plastic process of achieving disciplinary identity is further marked by the openness of disciplinary definition, tension between technological possibilities and the ways in which scientific issues are conceived and approached, synthesis of reductive and integrative strategies, and complex social interactions. The importance – albeit highly variable – of naming stories in these four cases indicates the scope for future studies that focus on failed disciplines or competing names. Further attention to disciplinary histories could, we suggest, give us richer insight into scientific development. (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)

Charles Darwin transformed our understanding of the universe and our place in it with his development of the theory of evolution. 150 years later, we are still puzzling over the implications. John Dupr presents a lucid, witty introduction to evolution and what it means for our view of humanity, the natural world, and religion. He explains the right and the wrong ways to understand evolution: in the latter category fall most of the claims of evolutionary psychology, of which Dupr gives (...) a withering critique. He shows why the theory of evolution is one of the most important scientific ideas of all time, but makes clear that it can't explain everything - contrary to widespread popular belief, it has very little to tell us about the details of human nature and human behaviour, such as language, culture, and sexuality. Anyone who is interested in understanding what the theory of evolution can and can't do will find Darwin's Legacy a compelling and enjoyable introduction. (shrink)

Systems biology is the rapidly growing and heavily funded successor science to genomics. Its mission is to integrate extensive bodies of molecular data into a detailed mathematical understanding of all life processes, with an ultimate view to their prediction and control. Despite its high profile and widespread practice, there has so far been almost no bioethical attention paid to systems biology and its potential social consequences. We outline some of systems biology's most important socioethical issues by contrasting the concept of (...) systems as dynamic processes against the common static interpretation of genomes. New issues arise around systems biology's capacities for in silico testing, changing cultural understandings of life, synthetic biology, and commercialization. We advocate an interdisciplinary and interactive approach that integrates social and philosophical analysis and engages closely with the science. Overall, we argue that systems biology socioethics could stimulate new ways of thinking about socioethical studies of life sciences. (shrink)