John Dupre

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

Philip Kitcher's book begins with a familiar historical overview. In the 1940s and 50s a confident, optimistic vision of science was widely shared by philosophers and historians of science. The goal of science was to discover the truth about nature, and over the centuries science had advanced steadily towards that goal; science discerned the real kinds of things of which the world was composed and the causal relations between them; the methods of science were rational and its deliverances objective; and so on. Only where science failed in some of these respects was there any need to provide external, that is social, political, or individual, explanations of scientific belief. In the late 50s, and especially subsequent to Kuhn's classic, The Structure of Scientific Revolutions, all this started to change. Historians increasingly insisted that the development of science must be treated just like any other cultural process, which meant embedding the narrative of the growth of scientific knowledge fully in the social and political context in which it occurred. This suggested that the view of science as deriving from a uniquely rational process could no longer be sustained. And, notoriously, Kuhn argued that science could not be seen as cumulative across the most dramatic changes in scientific theory. Though philosophers have never given up entirely on the old optimistic picture ("Legend" as Kitcher refers to it), its influence has steadily waned. For various reasons philosophers have become increasingly concerned over whether one could believe scientific claims to be literally true. And influenced by Duhem's thesis, revived by Quine, that scientific theory must always be underdetermined by empirical evidence, they became more sympathetic to the possibility that scientific belief must be explained, at least in substantial part, by much more than the rational objective processes envisioned by Legend. These philosophical doubts existed in uneasy tension with more extreme tendencies toward thoroughgoing relativism or skepticism, and with the movement in the sociology of science to see the whole concern with truth and falsity as an irrelevant diversion.

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.

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.

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.

This paper will begin with some very broad and general considerations about the kind of biological entities we are. This exercise is motivated by the belief that the view of what we—multicellular eukaryotic organisms—are that is widely assumed by biologists, medical scientists and the general public, is an extremely limited one. It cannot be assumed a priori that a more sophisticated view will make a major difference to the science or practice of medicine, and there are areas of medicine to which it is probably largely irrelevant. However, in this case there are important implications for medicine, or so I shall argue. In particular, it enables us to appreciate fully the potential medical significance of some of the most exciting contemporary advances in general biology, in such fields as epigenetics, metagenomics, and systems biology; and part of this significance is that these advances have raised serious doubts about how we should understand the biological individuals that medicine is generally assumed to aim to treat

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.

Elliott Sober is among the leading contemporary contributors to the philosophy of biology. He also has an exceptional ability to explain difficult ideas clearly. He is therefore very well equipped to provide an accessible yet state-of-the-art introduction to the philosophy of biology, and in most respects this optimistic prognosis is justified by the present volume. Focussing on evolutionary biology, Sober provides a general overview of evolutionary theory; a chapter on creationism that serves as a vehicle for the discussion of the evidence for evolution; and chapters on fitness, the units of selection, adaptationism, systematics, and sociobiology. Sober displays a thorough mastery of both the biological issues and the recent philosophical controversies that have surrounded them, and the presentation is always lucid and free from unnecessary technicalities. Anyone not thoroughly conversant with contemporary discussions of evolutionary theory could learn from this book.

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.

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.

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.