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)

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)

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.

This paper attacks the perennial philosophical and scientific quest for a simple and unified vision of the world. Without denying the attraction of this vision, I argue that such a goal often seriously distorts our understanding of complex phenomena. The argument is illustrated with reference to simplistic attempts to provide extremely general views of biology, and especially of human nature, through the theory of evolution. Although that theory is a fundamental ingredient of our scientific world view, it provides only one (...) of a number of perspectives that are required for an understanding of biology in general, and human behaviour in paticular. The argument is connected to the replacement of views of science in terms of universal laws with views that emphasise ranges of models more locally suited to specific phenomena. (shrink)

This collection of essays explores the metaphysical thesis that the living world is not made up of substantial particles or things, as has often been assumed, but is rather constituted by processes. The biological domain is organised as an interdependent hierarchy of processes, which are stabilised and actively maintained at different timescales. Even entities that intuitively appear to be paradigms of things, such as organisms, are actually better understood as processes. Unlike previous attempts to articulate processual views of biology, which (...) have tended to use Alfred North Whitehead’s panpsychist metaphysics as a foundation, this book takes a naturalistic approach to metaphysics. It submits that the main motivations for replacing an ontology of substances with one of processes are to be found in the empirical findings of science. Biology provides compelling reasons for thinking that the living realm is fundamentally dynamic, and that the existence of things is always conditional on the existence of processes. The phenomenon of life cries out for theories that prioritise processes over things, and it suggests that the central explanandum of biology is not change but rather stability, or more precisely, stability attained through constant change. This edited volume brings together philosophers of science and metaphysicians interested in exploring the consequences of a processual philosophy of biology. The contributors draw on an extremely wide range of biological case studies, and employ a process perspective to cast new light on a number of traditional philosophical problems, such as identity, persistence, and individuality. (shrink)

In an earlier paper (Dupré 1984), I criticized a thesis sometimes defended by theorists of probabilistic causality, namely, that a probabilistic cause must raise the probability of its effect in every possible set of causally relevant background conditions (the "contextual unanimity thesis"). I also suggested that a more promising analysis of probabilistic causality might be sought in terms of statistical relevance in a fair sample. Ellery Eells (1987) has defended the contextual unanimity thesis against my objections, and also raised (...) objections of his own to my positive claims. In this paper I defend and amplify both my objections to the contextual unanimity thesis and my constructive suggestion. (shrink)

Much scientific thinking and thinking about science involves assumptions that there is a deep and pervasive order to the world that it is the business of science to disclose. A paradigmatic statement of such a view can be found in a widely discussed paper by a prominent economist, Milton Friedman (a paper which will be discussed in more detail shortly): A fundamental hypothesis of science is that appearances are deceptive and that there is a way of looking at or interpreting (...) or organizing the evidence that will reveal superficially disconnected and diverse phenomena to be manifestations of a more fundamental and relatively simple structure. (1953/1984, p.231) On the other hand, the person sometimes described as the father of modern science, Francis Bacon, wrote: The human understanding is of its own nature prone to suppose the existence of more order and regularity in the world than it finds. And though there be many things in nature which are singular and unmatched, yet it devises for them conjugates and relatives which do not exist. (1620/1960, p. 50). (shrink)

John Dupre warns that our understanding of human nature is being distorted by two faulty and harmful forms of pseudo-scientific thinking. Not just in the academic world but in everyday life, we find one set of experts who seek to explain the ends at which humans aim in terms of evolutionary theory, while the other set uses economic models to give rules of how we act to achieve those ends. Dupre demonstrates that these theorists' explanations do not work and (...) that, if taken seriously, their theories tend to have dangerous social and political consequences. For these reasons, it is important to resist scientism: an exaggerated conception of what science can be expected to do for us. Dupre restores sanity to the study of human nature by pointing the way to a proper understanding of humans in the societies that are our natural and necessary environments. Anyone interested in science and human life will enjoy this book--unless they are its targets. (shrink)

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)

John Dupr explores recent revolutionary developments in biology and considers their relevance for our understanding of human nature and society. He reveals how the advance of genetic science is changing our view of the constituents of life, and shows how an understanding of microbiology will overturn standard assumptions about the living world.

John Dupré explores recent revolutionary developments in biology and considers their relevance for our understanding of human nature and human society. Epigenetics and related areas of molecular biology have eroded the exceptional status of the gene and presented the genome as fully interactive with the rest of the cell. Developmental systems theory provides a space for a vision of evolution that takes full account of the fundamental importance of developmental processes. Dupré shows the importance of microbiology for (...) a proper understanding of the living world, and reveals how it subverts such basic biological assumptions as the organisation of biological kinds on a branching tree of life, and the simple traditional conception of the biological organism. (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)

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)

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)

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)

This book is a collection of essays by a leading philosopher of biology and spans his career over almost the last twenty years. Most of the topics that have been of concern to philosophers of biology in this period are touched on to some extent, and the collection of these essays in a convenient volume will certainly be welcomed by everyone working in this field. The essays are arranged chronologically, and divided into three sections. Although the chapters in the first (...) section have substantial interconnections, being involved with fundamental conceptual issues in evolutionary theory, on the whole there is not much attempt to tie the book into anything more than a sequence of independent essays. The later sections, moreover, cover a quite diverse range of topics. The whole is neither more nor less than the sum of the parts. For. (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)

Analytic metaphysics has recently discovered biology as a means of grounding metaphysical theories. This has resulted in long-standing metaphysical puzzles, such as the problems of personal identity and material constitution, being increasingly addressed by appeal to a biological understanding of identity. This development within metaphysics is in significant tension with the growing tendency amongst philosophers of biology to regard biological identity as a deep puzzle in its own right, especially following recent advances in our understanding of symbiosis, the evolution of (...) multi-cellular organisms and the inherently dynamical character of living systems. Moreover, and building on these biological insights, the broadly substance ontological framework of metaphysical theories of biological identity appears problematic to a growing number of philosophers of biology who invoke process ontology instead. This volume addresses this tension, exploring to what extent it can be dissolved. For this purpose, the volume presents the first selection of essays exclusively focused on biological identity and written by experts in metaphysics, the philosophy of biology and biology. The resulting cross-disciplinary dialogue paves the way for a convincing account of biological identity that is both metaphysically constructive and scientifically informed, and will be of interest to metaphysicians, philosophers of biology and theoretical biologists. (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)

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)

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)

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)

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.

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)

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)