A Companion to the Philosophy

of Biology

Edited by

Sahotra Sarkar

and

Anya Plutynski

A Companion to the Philosophy of Biology

Blackwell Companions to Philosophy

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6. A Companion to Philosophy of Mind Edited by Samuel Guttenplan

7. A Companion to Metaphysics Edited by Jaegwon Kim and Ernest Sosa

8. A Companion to Philosophy of Law and Legal Theory

Edited by Dennis Patterson

9. A Companion to Philosophy of Religion Edited by Philip L. Quinn and Charles Taliaferro

10. A Companion to the Philosophy of Language Edited by Bob Hale and Crispin Wright

11. A Companion to World Philosophies Edited by Eliot Deutsch and Ron Bontekoe

12. A Companion to Continental Philosophy Edited by Simon Critchley and William Schroeder

13. A Companion to Feminist Philosophy Edited by Alison M. Jaggar and

Iris Marion Young

14. A Companion to Cognitive Science Edited by William Bechtel and George Graham

15. A Companion to Bioethics Edited by Helga Kuhse and Peter Singer

16. A Companion to the Philosophers Edited by Robert L. Arrington

17. A Companion to Business Ethics Edited by Robert E. Frederick

18. A Companion to the Philosophy of Science Edited by W. H. Newton-Smith

19. A Companion to Environmental Philosophy Edited by Dale Jamieson

20. A Companion to Analytic Philosophy Edited by A. P. Martinich and David Sosa

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24. A Companion to Philosophy in the Middle Ages

Edited by Jorge J. E. Gracia and Timothy B. Noone

25. A Companion to African-American Philosophy

Edited by Tommy L. Lott and John P. Pittman

26. A Companion to Applied Ethics Edited by R. G. Frey and

Christopher Heath Wellman

27. A Companion to the Philosophy of Education Edited by Randall Curren

28. A Companion to African Philosophy Edited by Kwasi Wiredu

29. A Companion to Heidegger Edited by Hubert L. Dreyfus and

Mark A. Wrathall

30. A Companion to Rationalism Edited by Alan Nelson

31. A Companion to Ancient Philosophy Edited by Mary Louise Gill and Pierre Pellegrin

32. A Companion to Pragmatism Edited by John R. Shook and Joseph Margolis

33. A Companion to Nietzsche Edited by Keith Ansell Pearson

34. A Companion to Socrates Edited by Sara Ahbel-Rappe and

Rachana Kamtekar

35. A Companion to Phenomenology and Existentialism

Edited by Hubert L. Dreyfus and Mark A. Wrathall

36. A Companion to Kant Edited by Graham Bird

37. A Companion to Plato Edited by Hugh H. Benson

38. A Companion to Descartes Edited by Janet Broughton and John Carriero

39. A Companion to the Philosophy of Biology Edited by Sahotra Sarkar and Anya Plutynski

Forthcoming

40. A Companion to Hume Edited by Elizabeth S. Radcliffe41. A Companion to Aristotle Edited by Georgios Anagnostopoulos

A Companion to the Philosophy

of Biology

Edited by

Sahotra Sarkar

and

Anya Plutynski

© 2008 by Blackwell Publishing Ltdexcept for editorial material and organization © 2008 by Sahotra Sarkar and Anya Plutynski

BLACKWELL PUBLISHING350 Main Street, Malden, MA 02148-5020, USA9600 Garsington Road, Oxford OX4 2DQ, UK550 Swanston Street, Carlton, Victoria 3053, Australia

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Library of Congress Cataloging-in-Publication Data

A companion to the philosophy of biology / edited by Sahotra Sarkar and Anya Plutynski. p. cm. – (Blackwell companions to philosophy ; 39) Includes bibliographical references and index. ISBN 978-1-4051-2572-7 (hardcover : alk. paper) 1. Biology–Philosophy. I. Sarkar, Sahotra. II. Plutynski, Anya.

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v

Contents

List of Figures viii

List of Tables x

Notes on Contributors xi

Acknowledgments xvii

Introduction xviiiSahotra Sarkar and Anya Plutynski

Part I Molecular Biology and Genetics 1

1 Gene Concepts 3 Hans-Jörg Rheinberger and Staffan Müller-Wille

2 Biological Information 22 Stefan Artmann

3 Heredity and Heritability 40 Richard C. Lewontin

4 Genomics, Proteomics, and Beyond 58 Sahotra Sarkar

Part II Evolution 75

5 Darwinism and Neo-Darwinism 77 James G. Lennox

6 Systematics and Taxonomy 99 Marc Ereshefsky

7 Population Genetics 119 Christopher Stephens

8 The Units and Levels of Selection 138 Samir Okasha

contents

vi

9 Molecular Evolution 157 Michael R. Dietrich

10 Speciation and Macroevolution 169 Anya Plutynski

11 Adaptationism 186 Peter Godfrey-Smith and Jon F. Wilkins

Part III Developmental Biology 203

12 Phenotypic Plasticity and Reaction Norms 205 Jonathan M. Kaplan

13 Explaining the Ontogeny of Form: Philosophical Issues 223 Alan C. Love

14 Development and Evolution 248 Ron Amundson

Part IV Medicine 269

15 Self and Nonself 271 Moira Howes

16 Health and Disease 287 Dominic Murphy

Part V Ecology 299

17 Population Ecology 301 Mark Colyvan

18 Complexity, Diversity, and Stability 321 James Justus

19 Ecosystems 351 Kent A. Peacock

20 Biodiversity: Its Meaning and Value 368 Bryan G. Norton

Part VI Mind and Behavior 391

21 Ethology, Sociobiology, and Evolutionary Psychology 393 Paul E. Griffi ths

22 Cooperation 415 J. McKenzie Alexander

23 Language and Evolution 431 Derek Bickerton

contents

vii

Part VII Experimentation, Theory, and Themes 453

24 What is Life? 455 Mark A. Bedau

25 Experimentation 472 Marcel Weber

26 Laws and Theories 489 Marc Lange

27 Models 506 Jay Odenbaugh

28 Function and Teleology 525 Justin Garson

29 Reductionism in Biology 550 Alexander Rosenberg

Index 568

viii

Figures

Figure 2.1 Schematic diagram of a general communication system. 24Figure 3.1 Norms of reaction of eye size as a function of temperature

for three different genotypes of Drosophila melanogaster. 42Figure 3.2 Growth of clones of Achillea millefolium at three different

elevations. 43Figure 3.3 Four different models of the determination of phenotype. 45Figure 3.4 Hypothetical norms of reaction for two genotypes and

the phenotypic distribution resulting from variation in the environment and genetic variation. 55

Figure 6.1 Phylogenetic trees. 105Figure 6.2 Speciation by cladogenesis and anagenesis. 108Figure 6.3 A phylogenetic tree of lizards, snakes, crocodiles, and birds. 109Figure 6.4 Two cladograms of the same taxa. 111Figure 12.1 Phenotypic plasticity and reaction norms. 206Figure 12.2 Developmental sensitivity versus developmental conversion. 210Figure 12.3 A developmental reaction norm visualization of buffering. 216Figure 12.4 Developmental stability versus phenotypic plasticity. 217Figure 13.1 Different mechanisms of morphogenesis. 228Figure 15.1 A two signal model of T helper lymphocyte activation. 277Figure 15.2 Idiotypic interactions between antibodies. 279Figure 21.1 The “hydraulic model” of instinctual motivation. 395Figure 21.2 The Prisoner’s Dilemma. 401Figure 21.3 Two versions of the Wason card selection task, one an abstract

problem and the other a problem concerning social exchange. 403Figure 22.1 The Prisoner’s Dilemma payoffs. 416Figure 22.2 Reciprocity changes the Prisoner’s Dilemma into an

Assurance Game. 421Figure 22.3 The payoff matrix for cooperative behavior generated through

byproduct mutualism. 425Figure 22.4 The spatial prisoner’s dilemma illustrating the evolution

of stable cooperative regions. 427

ix

Figure 22.5 The spatial prisoner’s dilemma illustrating the evolution of stable cooperative regions. 427

Figure 22.6 The Spatial Prisoner’s Dilemma. 428

fi gures

x

Tables

Table 15.1 Some of the main cell types of the immune system. 273Table 18.1 Different concepts of ecological stability. 340Table 23.1 Incongruous properties of language and ACSs. 435

xi

Notes on Contributors

J. McKenzie Alexander is at the Department of Philosophy, Logic and Scientifi c Method at the London School of Economics and Political Science. His interests are in Evolutionary game theory, philosophy of social science, and rational choice theory. Recent publications include, “Follow the leader: local interactions with infl uence neigh-borhoods,” Philosophy of Science, 72, 86–113 (2005), “Random Boolean networks and evolutionary games,” Philosophy of Science, 70, 1289–1304 (2003),“Bargaining with neighbours: Is justice contagious?” (with Brian Skyrms), Journal of Philosophy, 96 (11), 588–98 (1999), and The Structural Evolution of Morality (Cambridge: Cambridge University Press, 2007).

Ron Amundson is Professor, Dept of Philosophy, University of Hawaii at Hilo. His research is in history and philosophy of biology, as well as bioethics and disability rights. Recent publications include: “Bioethics and disability rights: confl icting values and perspectives,” (with Shari Tresky) in press, and The Changing Role of the Embryo in Evolutionary Thought: Roots of Evo-Devo (Cambridge: Cambridge University Press, 2005).

Stefan Artmann is at the Institute of Philosophy, Friedrich-Schiller-University Jena. In 2007, he fi nished his postdoctoral thesis on the philosophy of structural sciences (such as information theory, cybernetics, and decision theory). He has published several papers on questions related to the application of information theory and semiotics to biological systems, e.g., “Artifi cial life as a structural science,” Philosophia naturalis, 40, 183–205 (2003), “Biosemiotics as a structural science: between the forms of life and the life of forms,” Journal of Biosemiotics, 1, 183–209 (2005), and “Computing codes versus interpreting life. Two alternative ways of synthesizing biological knowledge through semiotics,” in M. Barbieri (Ed.), Introduction to Biosemiotics (Dordrecht: Springer, 2007), pp. 209–33.

Mark A. Bedau is Professor of Philosophy and Humanities at Reed College in Portland, Oregon. He is also Editor-in-Chief of the journal Artifi cial Life (MIT Press); co-founder of the European Center for Living Technology, a research institute in Venice, Italy, that

notes on contributors

xii

investigates theoretical and practical issues associated with living systems; and co-founder of ProtoLife SRL, a start-up company with the long-term aim of creating useful artifi cial cells. He has published and lectured around the world extensively on philo-sophical and scientifi c issues concerning emergence, evolution, life, mind, and the social and ethical implications of creating life from scratch.

Derek Bickerton is Professor Emeritus of Linguistics at the University of Hawaii. He is best known for his work on Creole languages, leading to the Language Bioprogram Hypothesis, and his subsequent work on the evolution of language. Among his books are Roots of Language, Language and Species, and Language and Human Behavior.

Mark Colyvan is Professor of Philosophy and Director of the Sydney Centre for The Foundations of Science at the University of Sydney in Sydney, Australia. He has pub-lished on the philosophy of mathematics, philosophy of science (especially ecology and conservation biology), philosophy of logic, and decision theory. His books include The Indispensability of Mathematics (OUP, 2001) and, with Lev Ginzburg, Ecological Orbits: How Planets Move and Populations Grow (OUP, 2004).

Michael R. Dietrich is an Associate Professor in the Department of Biology at Dartmouth College.

Marc Ereshefsky is Professor of Philosophy at the University of Calgary. He has written extensively on biological taxonomy and has published two books on the topic, The Poverty of the Linnaean Hierarchy and The Units of Evolution. His current research focuses on biological homology and its philosophical applications.

Justin Garson is a lecturer in Philosophy at the University of Texas at Austin. His interests are in the Philosophy of Science, with emphasis on the history and philosophy of neuroscience and psychiatry. He was one of the assistant editors of, and contributors to, The Philosophy of Science: An Encyclopedia (Routledge, 2005). Recent publications include “The introduction of information into neurobiology.” Philosophy of Science, 70, 926–36 (2003).

Peter Godfrey-Smith is Professor of Philosophy at Harvard University, but also spends time at the Philosophy Program, Research School of Social Sciences, The Australian National University. Godfrey-Smith’s primary research interests are in the philosophy of biology and philosophy of mind. He also has interests in other parts of philosophy of science, causation, and the philosophy of John Dewey. His books include: Complexity and the Function of Mind in Nature (Cambridge: Cambridge University Press, 1996) and Theory and Reality: An Introduction to the Philosophy of Science (Chicago: University of Chicago Press, 2003).

Paul E. Griffi ths is a philosopher of science with a focus on biology and psychology, and was educated at Cambridge and the Australian National University. He taught at Otago University in New Zealand and was later Director of the Unit for History and Philosophy of Science at the University of Sydney, before taking up a professorship in the Department of History and Philosophy of Science at the University of Pittsburgh.

notes on contributors

xiii

He returned to Australia in 2004, fi rst as an Australian Research Council Federation Fellow and then as University Professorial Research Fellow at the University of Sydney. He is a Fellow of the Australian Academy of the Humanities.

Moira Howes is Associate Professor of Philosophy at Trent University. She specializes in metaphysics, philosophy of science (especially immunology), and feminist epistemol-ogy. Her current research concerns immunological models of the human female repro-ductive tract.

James Justus wrote a dissertation on “The Stability-Diversity-Complexity Debate of Theoretical Community Ecology: A Philosophical Analysis” at the University of Texas, Austin. He has published in the journals Biology and Philosophy, Conservation Biology, and Philosophy of Science. Recent publications include “Qualitative scientifi c modeling and crop analysis,” Philosophy of Science (2005); and “Ecological and Lyapunov stabil-ity,” Philosophy of Science (2007). His interests outside the philosophy of science include the history of analytic philosophy, environmental philosophy, logic and philosophy of mathematics, formal epistemology, and bird watching.

Jonathan M. Kaplan, an Associate Professor of Philosophy at Oregon State University, specializes in the Philosophy of Biology, Philosophy of Science and Political Philosophy. In addition to various articles and book chapters, he has published two books, most recently Making Sense of Evolution: The Conceptual Foundations of Evolutionary Biology, co-authored with evolutionary biologist Massimo Pigliucci (Chicago: Chicago University Press, 2006).

Marc Lange is Professor of Philosophy at the University of North Carolina at Chapel Hill. He is the author of Natural Laws in Scientifi c Practice (Oxford, 2000), An Introduction to the Philosophy of Physics: Locality, Fields, Energy, and Mass (Blackwell, 2002), and Laws and Lawmakers (Oxford, forthcoming).

James Lennox is Professor at the Department of History and Philosophy of Science at the University of Pittsburgh. Research specialties include Ancient Greek philosophy, science and medicine, and Charles Darwin and Darwinism. Lennox has published essays on the philosophical and scientifi c thought of Plato, Aristotle, Theophrastus, Boyle, Spinoza, and Darwin, especially focused on scientifi c explanation, and particu-larly teleological explanation, in the biological sciences. He is author of Aristotle’s Philosophy of Biology (Cambridge 2000) and Aristotle on the Parts of Animals I–IV (Oxford, 2001), the fi rst English translation of this work since 1937. He is co-editor of Philosophical Issues in Aristotle’s Biology (Cambridge, 1987); Self-Motion from Aristotle to Newton (Princeton, 1995); and Concepts, Theories, and Rationality in the Biological Sciences (Pittsburgh and Konstanz, 1995).

Richard C. Lewontin is Alexander Agassiz Research Professor at the Museum of Comparative Zoology, Harvard University. He is an evolutionary biologist, geneticist, and pioneer in the application of techniques from molecular biology to questions of genetic variation and evolution. He is the author of The Genetic Basis of Evolutionary

notes on contributors

xiv

Change and Biology as Ideology, and the co-author of The Dialectical Biologist (with Richard Levins) and Not in Our Genes (with Steven Rose and Leon Kamin).

Alan C. Love is Assistant Professor of Philosophy at the University of Minnesota. His current work focuses on the nature of conceptual change and explanation in the bio-logical sciences, specifi cally within the dynamic of the discipline of evolutionary devel-opmental biology, using a combination of historical and philosophical methodologies. Selected Publications include “Evolutionary morphology and evo-devo: hierarchy and novelty,” Theory in Biosciences, 124, 317–33 (2006), “Evolvability, dispositions, and intrinsicality,” Philosophy of Science, 70(5), 1015–27 (2003), and “Evolutionary mor-phology, innovation, and the synthesis of evolutionary and developmental biology”, Biology and Philosophy, 18, 309–45 (2003).

Staffan Müller-Wille received his PhD in Philosophy from the University of Bielefeld for his dissertation on Linnaeus’ taxonomy. He worked at the Max-Planck-Institute for the History of Science (Berlin) from 2000 to 2004 and is currently holding a post as Senior Research Fellow for Philosophy of Biology at the University of Exeter. He is author of the book Botanik und weltweiter Handel (1999) and has published articles on the history and epistemology of natural history, genetics, and anthropology.

Dominic Murphy is Assistant Professor of Philosophy at Caltech. He is the author of Psychiatry in the Scientifi c Image (MIT, 2006), as well as papers in the philosophy of mind and the philosophy of biology.

Bryan G. Norton is Professor in the School of Public Policy, Georgia Institute of Technology and author of Why Preserve Natural Variety? (Princeton University Press, 1987), Toward Unity Among Environmentalists (Oxford University Press, 1991), Searching for Sustainability (Cambridge University Press, 2003), and Sustainability: A Philosophy of Adaptive Ecosystem Management (University of Chicago Press, 2005). Norton has contributed to journals in several fi elds and has served on the Environmental Economics Advisory Committee of the US EPA Science Advisory Board, and two terms as a member of the Governing Board of the Society for Conservation Biology. His current research concentrates on sustainability theory and on spatio-temporal scaling of environmental problems. He was a member of the Board of Directors of Defenders of Wildlife from 1994 to 2005 and continues on their Science Advisory Board.

Jay Odenbaugh is a member of the Department of Philosophy and Environmental Studies Program at Lewis and Clark College. His main areas of research are in the phi-losophy of science (especially ecology and evolutionary biology) and environmental ethics. He is currently working on a book tentatively entitled On the Contrary: A Philosophical Examination of the Environmental Sciences and their Critics examining these issues especially in ecology, climatology, and environmental economics.

Samir Okasha received his doctorate from the University of Oxford in 1998 and is currently Reader in Philosophy of Science at the University of Bristol. He has published numerous research articles in journals such as Philosophy of Science, Evolution, British

notes on contributors

xv

Journal for the Philosophy of Science, Synthese, Biology and Philosophy, and others. He is currently completing a monograph on the units of selection debate to be published by Oxford University Press.

Kent A. Peacock is Associate Professor of Philosophy at the University of Lethbridge, Alberta, Canada. He has published in philosophy of physics and ecology, and is the editor of a text, Living With the Earth: An Introduction to Environmental Philosophy (Toronto: Harcourt Brace, 1996).

Anya Plutynski is an Assistant Professor of Philosophy at the University of Utah. Her research is in the history and philosophy of biology. She is the author of several recent articles and book chapters on the early synthesis and evolutionary explanation, in some of the following journals: Proceedings of the Philosophy of Science, British Journal of Philosophy of Science, Biology and Philosophy, and Biological Theory.

Hans-Jörg Rheinberger is Director at the Max Planck Institute for the History of Science in Berlin and a Scientifi c Member of the Max Planck Society. He studied philosophy (MA) and biology (PhD) at the University of Tübingen and the Free University of Berlin. He worked as a molecular biologist at the Max Planck Institute for Molecular Genetics in Berlin, and as a historian of science at the Univer-sities of Lübeck and Salzburg. Among his books are Toward a History of Epistemic Things (1997), Iterationen (2005), Epistemologie des Konkreten (2006) and Historische Epistemologie zur Einführung (2007). He is also a co-editor of The Concept of the Gene in Development and Evolution (2000), and The Mapping Cultures of Twentieth Century Genetics (2004).

Alex Rosenberg is the R. Taylor Cole Professor of Philosophy, and co-Director of the Center for Philosophy of Biology, Duke University. His interests focus on problems in metaphysics, mainly surrounding causality, the philosophy of social sciences, espe-cially economics, and most of all, the philosophy of biology, in particular the relation-ship between molecular, functional, and evolutionary biology. Recent publications include: Darwinian Reductionism: Or, How to Stop Worrying and Love Molecular Biology (University of Chicago, 2006).

Sahotra Sarkar is Professor of Integrative Biology, Geography and the Environment, and Philosophy at the University of Texas at Austin. His research is in history and philosophy of science, formal epistemology, philosophy of biology, and conservation biology. Recent books include Doubting Darwin? Creationist Designs on Evolution (Blackwell, 2007), Biodiversity and Environmental Philosophy: An Introduction (Cambridge, 2005), and Molecular Models of Life (MIT, 2005).

Christopher Stephens is Assistant Professor of Philosophy at University of British Columbia. Dr Stephens specializes in philosophy of biology, philosophy of science, and epistemology. Recent publications include “Modelling reciprocal altruism,” British Journal for the Philosophy of Science (1996) and “When is it selectively advantageous to have true beliefs?” Philosophical Studies (2001). His current research interests include

notes on contributors

xvi

drift and chance in evolutionary biology, the evolution of rationality, and the relation-ship between prudential and epistemic rationality.

Marcel Weber received an MSc in molecular biology from the University of Basel, a PhD in philosophy at the University of Konstanz, and a Habilitation in philosophy at the University of Hannover. He is currently Swiss National Science Foundation Professor of Philosophy of Science at the University of Basel. His books include Philosophy of Experimental Biology (Cambridge University Press, 2005) and Die Architektur der Synthese: Entstehung und Philosophie der modernen Evolutionstheorie (Walter de Gruyter, Berlin, 1998).

Jon F. Wilkins is Research Professor at the Santa Fe Institute. His research interests include coalescent theory, genomic imprinting, human demographic history, altruism, and cultural evolution. Recent publications include: “Gene genealogies in a continuous habitat: a separation of timescales approach,” Genetics, 168, 2227–44 (2004); (with J. Wakeley) “The coalescent in a continuous, fi nite, linear population,” Genetics, 161, 873–88 (2002); “Genomic imprinting and methylation: epigenetic canalization and confl ict,” Trends Genet., 21, 356–65 (2005); and (with D. Haig) “What good is genomic imprinting: the function of parent-specifi c gene expression,” Nat. Rev. Genet., 4, 359–68 (2003).

xvii

Acknowledgments

The editors gratefully acknowledge all the contributors and the editors at Blackwell, especially Jeff Dean, for their efforts in completing this volume.

xviii

Introduction

sahotra sarkar and anya plutynski

There are many different ways to do the philosophy of biology. At one end of a spectrum of possibilities would be works of general philosophical interest drawing on biological examples for illustration and support. At the other end would be works that deal only with conceptual and methodological issues that arise within the practice of biology. The strategy of this book is closer to the second way of approaching the subject. It aims to provide overviews of philosophical issues as they arise in a variety of areas of con-temporary biology. Traditionally, evolution has been the focus of most philosophical attention. While it surely remains true that “nothing in biology makes sense except in light of evolution” (Dobzhansky, 1973), this tradition within the philosophy of biology is myopic insofar as it ignores much – if not most – of the work in contemporary biology. Intended primarily for students and beginning scholars, this book takes a wider per-spective and addresses philosophical questions arising in molecular biology, develop-mental biology, immunology, ecology, and theories of mind and behavior. It also explores general themes in the philosophy of biology, for instance, the role of laws and theories, reductionism, and experimentation. In this respect, this book aims to break new ground in the philosophy of biology. Before we turn to what is new, let us briefl y look at the background from which contemporary philosophy of biology emerged.

1. Background

When the logical empiricists reoriented the direction of philosophy of science in the 1920s and 1930s, the loci of their attention were mathematics (and within it, almost entirely mathematical logic) and physics (initially relativity theory, later also quantum mechanics). This not only set the agenda, but also the tone, for the philosophy of science. The relatively simple axiomatic structures of relativity theory and quantum mechanics – or, at least, how professional philosophers conceived those fi elds – became the yardstick of comparison for other disciplines. If these other disciplines were found to be less general in their intended domain, to be using different criteria of rigor (that is, using techniques different from the type of mathematics used in mathematical logic), or simply different, they were presumed to be wanting. This applied not only to biology

xix

or chemistry (or, for that matter, the social sciences) but even to other areas of physics. Biology thus suffered from a not always benign neglect throughout this period.

Yet, in spite of this limited attention, if the sophistication of the discussion is used as a standard, biology fared much better during the early decades of the logical empiricist regime (that is, from 1925 to 1945) than during the next 20 years. This is not only because many biologists – including Driesch (1929), J. S. Haldane (1929, 1931), Hogben (1930), and J. B. S. Haldane (1936, 1939) – explicitly debated philosophical positions, in particular, the relative roles of reductionism and holism in biology, during those decades. These debates within the biological community helped the development of philosophy of biology, but there were also signifi cant attempts by philosophers to come to terms with the exciting developments that had taken place in biology, particu-larly in genetics and evolution, during the fi rst three decades of the twentieth century. Woodger (1929) produced an exploration of traditional philosophical problems in biology, such as vitalism and mechanism, as well as a theory of biological explanation. In 1937 he went on to attempt to axiomatize parts of genetics.1 By 1952 Woodger (1952) had clearly articulated what, after independent formulation and elaboration by Nagel (1949, 1951, 1961), became the standard model of theory reduction.2 Nagel used this model in an attempt to explicate mechanistic explanation in biology. Less successfully, he attempted to provide a defl ationary account of teleological explanation in biology (Nagel, 1961, 1977).

Arguably, until at least the 1960s, philosophers provided less philosophical insight about biology than theoretically oriented biologists. In the case of mechanistic explana-tion, for instance, as far as substantive biological questions are concerned, Nagel achieved little more than Hogben (1930). All he did was translate the simplest bio-logical questions into the logical empiricists’ framework and presumed that the result showed what was philosophically interesting about biology. Following the standard twentieth-century philosophical tradition, Nagel’s writings on biology contributed little that scientists, even philosophically oriented biologists, found valuable. Nagel also displayed a strange refusal to follow contemporary developments in biology: between 1949 and 1961 he saw no reason to temper his bleak assessment of the state of mech-anistic/reductionist explanation in biology – the events of 1953 either completely slipped by him, or failed to impress him. The Structure of Science from 1961 has several sections devoted to reductionism in biology but makes no mention of the double helix or, for that matter, any other development in molecular biology that had raised the potential for successful reduction in biology to an entirely different level (Nagel, 1961).

In the philosophy of biology, during the late 1950s and early 1960s only two notable exceptions stand out, Beckner’s The Biological Way of Thought and, especially, Goudge’s The Ascent of Life, the latter being a scientifi cally fairly sophisticated philo-sophical exploration of evolutionary theory (Beckner, 1959; Goudge, 1961; see also

1 Woodger (1937), under the sway of operationalism and skepticism about theoretical entities, attempted an axiomatization of genetics without “gene” as a term; Carnap (1958) developed some of Woodger’s formal treatment in more interesting ways.

2 For a history, see Sarkar (1989).

introduction

xx

Scriven, 1959). The situation changed for the better in the late 1960s and 1970s. Hull (1965, 1967, 1968) began to explore the conceptual structure of evolutionary biology. Wimsatt (1971, 1972) provided a detailed analysis of teleological explanation (and biological “feedback”), drawing extensively on contemporary work in theoretical biology. In a series of papers, Schaffner (1967a, b, 1969, 1976) began to argue the case for reductionism in molecular genetics while Hull (1972, 1974, 1976, 1981) questioned Schaffner’s assessment. Ruse (1976) and Wimsatt (1976) were among those who joined this debate. A consensus emerged against reductionism (provided that reduction was construed in the fashion inherited from Nagel and the logical empir-icists). Philosophy of biology also played its part, though rather late, in the rejection of logical empiricism in the 1960s and 1970s.

Since the early 1970s, the philosophy of biology has had a continuous and increas-ingly prominent presence in the philosophy of science. Occasional abuse of biology by philosophers has continued – as late as 1974, Popper would claim that Darwinism is not a scientifi c enterprise (Popper, 1974). Over the years, however, philosophy of biology has contributed to the development of the various alternatives to logical empir-icism, including scientifi c realism, the semantic view of theories, and, in particular, naturalistic epistemology. Within the general context of the philosophy of biology, the last of these programs has been particularly natural and fecund presumably because philosophers of biology, because of their engagement with biology, are more likely than other philosophers to analyze how humans are evolutionarily produced, constrained, and challenged, as biological organisms. In fact, barring a very few exceptions, there is consensus among philosophers of biology of the great value of the naturalized per-spective in philosophy where “naturalism” is very narrowly construed purely in evo-lutionary terms. Moreover, philosophers of biology have quite routinely begun to practice biology. If philosophy is to be done in continuity with science, as Quine once urged, no area in philosophy has followed that dictum more systematically than the philosophy of biology.

In the late 1970s, philosophy of biology became almost exclusively concerned with evolutionary theory. In some ways, this focus was productive; core philosophical ques-tions were addressed about the foundations of evolutionary theory. For instance, Hull (1965a, b; see also Sober, 1988), advanced a discussion of different schools of phylo-genetic analyses that has subsequently developed a rich literature on the method-ological commitments of different schools of thought in systematics and phylogenetics. Philosophers including Wimsatt (1980), Brandon (1982), and Sober (1984) produced useful analyses of what constitutes the units of selection, while several prominent biologists, including Lewontin (1970) and Maynard Smith (1976), made important philosophical contributions. Sober’s 1984 book, The Nature of Selection, advanced a clear analysis of the nature of laws and the structure of evolutionary theory, and par-ticularly clarifi ed related questions about the units-of-selection debate. Another 1984 book of equal merit was Flew’s (1984) Darwinian Evolution. However, the almost exclu-sive focus on evolution in much of the literature of the late 1970s and 80 s arguably hurt the development of the discipline. Many of the philosophical writings on biology from this period remained inattentive to molecular biology where, for better or for worse, most of biological research had become concentrated. Kitcher (1982, 1984) and Rosenberg (1985), however, are notable exceptions. Kitcher (1982) gave a thoughtful

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analysis of the transformation of biology after 1953, as well as a critical discussion of gene concepts (Kitcher, 1984), and Rosenberg (1985) advanced a perspective that treated genetics and molecular biology as being central to biology.

Given this state of the fi eld, it is easy to understand the molecular biologists’ lack of concern for philosophical critiques of their enterprise. This lack of concern was par-ticularly noticeable during the debates over the initiation of the Human Genome Project in the late 1980s and early 1990s, a debate on which philosophers, unlike historians and social scientists, had no perceptible infl uence. (A notable exception to these gener-alizations is neurobiology which has always received considerable philosophical attention though usually in the context of the philosophy of mind.)

Since the early 1990s, in a very welcome development, philosophical writing on biology has extended its scope to cover many areas within biology beyond evolutionary theory.3 There has been much recent interest in ecology, molecular and developmental biology. There has also fi nally been some attention to the role of experimentation in biology. In particular, Rheinberger (1993, 1997) has pioneered the use of techniques from the continental tradition of philosophy in the analysis of experimentation in molecular biology. Philosophers of biology have usually also paid ample attention to the history of biology. With intellectual and technical history gradually falling out of fashion in the professional history of science, philosophers of biology have done much to keep the history of the science of biology alive in contemporary research. This book refl ects all these trends.

2. Structure of the Companion

Most of biology today is molecular biology, and the Companion begins with a section on molecular biology and genetics (“Molecular Biology and Genetics”). Rheinberger and Müller-Wille (“Gene Concepts”) provide a historical review the various ways in which genes have been conceptualized, and how these have changed from the period of clas-sical genetics to the post-genomic era in which we now fi nd ourselves. Artmann (“Biological Information”) explores the troubled question of whether and how biologi-cal information is susceptible to precise, quantitative measurement, an issue that has been hotly debated by philosophers (Godfrey-Smith, 2004; Sarkar, 2005). Contrary to many philosophers (Sarkar, 1996), he argues that there is more to informational talk in biology than mere metaphor.

Lewontin (“Heredity and Heritability”) provides a philosophically sophisticated account of how classical genetics views heredity and adds a critique of the much-abused concept of heritability. Sarkar (“Genomics, Proteomics, and Beyond”) specu-lates on where the study of heredity and development is going in the wake of the massive whole-genome sequencing projects. Both Lewontin and Sarkar emphasize the limitations of a gene-centered view of biology and argue for a more developmentally oriented approach to understanding the emergence of phenotypes.

The next section (“Evolution”) turns to a number of classic issues addressed in the philosophy of biology, as well as some issues that have not perhaps received the atten-

3 The textbook by Sterelny and Griffi ths (1999) is indicative of this trend.

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tion they deserved. Reconciling Darwin’s own views with the various ways in which “Darwinism” has been understood during the last 130 years has been a challenge for biologists, historians, and philosophers of biology. Lennox (“Darwinism and Neo-Darwinism”) identifi es the core principles of Darwin’s original theory, and traces their empirical and conceptual development through the evolutionary synthesis, arguing that there is a meaningful set of commitments one can identify as “Darwinian.” A further classic problem in evolutionary biology is how species should be defi ned and classifi ed. Ereshefsky (“Systematics and Taxonomy”) analyzes a variety of controversies that have arisen among biologists and philosophers of biology about the nature of species and their classifi cation, ultimately defending a pluralist view of how species should be defi ned.

Population genetics has typically been viewed as the theoretical core of evolutionary biology. Stephens (“Population Genetics”) recounts the history of the origins of popula-tion genetics, and reviews central debates in the history of the theory. He also considers a number of conceptual issues about representation and explanation that arise in the context of theoretical population genetics. Okasha (“Units and Levels of Selection”) reviews the conceptual as well as empirical issues at stake in the debate over the units and levels of selection and gives a history of the debate from Darwin to the present day. He shows how this debate is tied to concerns about the evolution of altruism, the plau-sibility of group and kin selection, species selection and macroevolution, and concludes with a review of multilevel selection theory. Dietrich (“Molecular Evolution”) describes the rise of the neutral theory of molecular evolution, and discusses how debates over drift versus selection in molecular evolution are exemplary of relative signifi cance debates in biology.

One area that has received relatively little attention in philosophy of biology is the relationship between micro- and macro-evolution, and in particular, issues surround-ing how hypotheses about change at and above the species level are tested. Plutynski (“Speciation and Macroevolution”) addresses this question, and reviews recent empir-ical and theoretical work on speciation, the punctuated equilibrium debate, and questions about the disparity and evolvability. Finally, Godfrey-Smith and Wilkins (“Adaptationism”) trace the history of the debate over “adaptationist” thinking, nicely demarcating different senses of adaptationism: empirical, explanatory, and method-ological. In conclusion, they suggest a resolution to some of the controversy by illustrat-ing how various alternatives might be resolved through careful attention to the grain at which evolutionary processes are being described.

The section on “Developmental Biology” contains three important contributions. Kaplan (“Phenotypic Plasticity and Reaction Norms”) returns to the question of the relation between genotype and phenotype, already explored earlier by Lewontin. Once again the emphasis is on the complexity of this relation, which was largely ignored in classical genetics. Much of modern evolutionary theory was formulated at the geno-typic level, ignoring the complexities of organismic development. The received view is that development can be put in a “black box” and phenotypic change tracked by recording changes at the genotypic level. However, it has long been recognized that, eventually, to understand the evolution of phenotypes, we must understand how devel-opmental mechanisms have evolved. The past decade has seen a lot of excitement in evolutionary developmental biology, which many biologists now hold as fi nally

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successfully integrating evolutionary biology and studies of development. Amundson (“Development and Evolution”) puts these studies in historical perspective, analyzing the long, sometimes idiosyncratic, and largely unsuccessful past attempts to integrate the two disciplines. It is an open question whether the near future will be much differ-ent from the past. In “Explaining the Ontogeny of Form: Philosophical Issues,” Love provides a survey of issues surrounding the explanation of the ontogeny of form. He provides a philosophical framework for approaching different kinds of explanations in developmental biology, and addresses a variety of related epistemological and onto-logical issues; among them: representation, explanation, typology, individuality, model systems, and research heuristics.

The next section (“Medicine”) takes up the relatively underexplored fi eld of health and disease. One area that has received relatively little attention among philosophers of biology is immunology. Howes (“Self and Nonself”) considers how philosophers can play a critical role in analyzing the conceptual foundations and empirical justifi cations of different models of self and nonself deployed in immunology. Murphy (“Health and Disease”) considers “objectivist,” “constructivist,” and “revisionist” perspectives on health and disease, and focuses his discussion on the role of norms in judgments con-cerning mental illness.

The “Ecology” section summarizes much of the recent work on the philosophy of ecology, another area of the philosophy of biology that is receiving increased attention in recent years. Perhaps the most theoretically mature part of ecology is population ecology, and Colyvan (“Population Ecology”) summarizes the philosophical work on the subject, showing how this is a fertile area to explore questions such as the role of laws and theories in biology. Justus (“Complexity, Diversity, and Stability”) turns to a central issue in community ecology, whether there is any relation between diversity and stability. He shows how the concepts of diversity and stability (and, also, though to a lesser extent, complexity) can be interpreted in a variety of inconsistent ways, making it almost impossible to answer this question.

In the context of our increasing concern for the environment, Peacock (“Ecosystems”) describes recent thinking on ecosystems, including work done within science, and philosophically intriguing ideas at the fringe of science such as the Gaia hypothesis. Turning to conservation biology, Norton (“Biodiversity and Conservation”) shows how the concept of biodiversity is both descriptive (capturing some feature of habitats) and normative (refl ecting the values people have which make them want to preserve nature). He also embeds philosophical discussions of biodiversity in the context of environmental policy.

The next section turns to mental and cultural life (“Mind and Behavior”), about which there is perhaps more scientifi c controversy than in any other area explored in depth by philosophers of biology. Griffi ths (“Ethology, Sociobiology, and Evolutionary Psychology”) gives a historical analysis that shows the deep connection between mid-twentieth-century ethology, human sociobiology, and contemporary Evolutionary Psychology. He notes that, while there is no reason to doubt that mental features are results of biological and cultural evolution, the research program of contemporary “Evolutionary Psychology” makes many controversial assumptions that should be scrutinized carefully. Alexander (“Cooperation”) takes up recent approaches to the evolution of cooperative behavior including the many applications of game theory.

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Finally, Bickerton (“Communication and Language”) explores what we do and do not know about the emergence and evolution of human language and notes both the analogies and disanalogies between language and animal communication systems.

The fi nal section (“Experimentation, Theory, and Themes”) takes up a variety of general issues in the philosophy of biology, ranging from metaphysical issues about how to defi ne life, or whether there are biological laws, to epistemological issues about how biologists investigate the living world. Bedau (“What is Life?”) explores the variety of attempts to set out conditions for “life,” and discusses how and why this question has become especially pressing with recent research into artifi cial life. Weber (“Experimentation”) analyzes the special diffi culties and characteristics of experimental work in biology. He considers the roles of model organisms, the limitations and advan-tages of laboratory work in biology, and the nature of evidence and objectivity in the biological sciences.

Many philosophers hold that biology is not at all like physics insofar as there are no “laws” of biology; however, Lange (“Is Biology Like Physics?”) argues to the contrary. He considers the objection that laws of biology are not exceptionless and non-acciden-tal, and argues, using a number of different examples, that lawful generalizations are an integral part of evolutionary biology. While it is uncontroversial that models and modeling are central to empirical and theoretical work in all branches of biology, phi-losophers do not agree on what a “model” is. Odenbaugh (“Models”) reviews philo-sophical work on models, starting with the logical empiricists, explaining the subtle differences between the syntactic and semantic view of theories, and discusses a variety of historical and recent work on models and metaphors, and models as “mediators” between theory and data in the biological sciences.

It is hard to imagine biology without talk of functions but there is little philosophical agreement on what a function is. Garson (“Function and Teleology”) gives a compre-hensive review of the philosophical literature on functions, from etiological to conse-quentialist theories of function, and concludes with a defense of pluralist and context-dependent approaches to assignments of function. Yet another contentious issue in philosophy of biology has been the claim whether biological facts are reducible to molecular chemical or physical facts. Rosenberg (“Reductionism in Biology”) takes a radical stance on this question, arguing that while the reducibility of theories, as the logical empiricists understood it, is implausible, generalizations in functional biology can and should be reduced, in the sense of being “completed, corrected, made more precise or otherwise deepened” by “fundamental explanations in molecular biology.”

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Part I

Molecular Biology and Genetics