Everything Flows OUP CORRECTED PROOF – FINAL, 2/5/2018, SPi OUP CORRECTED PROOF – FINAL, 2/5/2018, SPi Everything Flows Towards a Processual Philosophy of Biology Daniel J. Nicholson and John Dupre ́ 1 OUP CORRECTED PROOF – FINAL, 2/5/2018, SPi 3 Great Clarendon Street, Oxford, OX2 6DP, United Kingdom Oxford University Press is a department of the University of Oxford. It furthers the University ’ s objective of excellence in research, scholarship, and education by publishing worldwide. Oxford is a registered trade mark of Oxford University Press in the UK and in certain other countries © the several contributors 2018 The moral rights of the authors have been asserted First Edition published in 2018 Impression: 1 Some rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted, in any form or by any means, for commercial purposes, without the prior permission in writing of Oxford University Press, or as expressly permitted by law, by licence or under terms agreed with the appropriate reprographics rights organization. This is an open access publication, available online and distributed under the terms of a Creative Commons Attribution – Non Commercial – No Derivatives 4.0 International licence (CC BY-NC-ND 4.0), a copy of which is available at http://creativecommons.org/licenses/by-nc-nd/4.0/. Enquiries concerning reproduction outside the scope of this licence should be sent to the Rights Department, Oxford University Press, at the address above Published in the United States of America by Oxford University Press 198 Madison Avenue, New York, NY 10016, United States of America British Library Cataloguing in Publication Data Data available Library of Congress Control Number: 2017958461 ISBN 978 – 0 – 19 – 877963 – 6 Printed and bound by CPI Group (UK) Ltd, Croydon, CR0 4YY Links to third party websites are provided by Oxford in good faith and for information only. Oxford disclaims any responsibility for the materials contained in any third party website referenced in this work. OUP CORRECTED PROOF – FINAL, 2/5/2018, SPi Contents Acknowledgements vii Contributors ix Foreword xi Part I. Introduction 1. A Manifesto for a Processual Philosophy of Biology 3 John Dupre ́ and Daniel J. Nicholson Part II. Metaphysics 2. Processes and Precipitates 49 Peter Simons 3. Dispositionalism: A Dynamic Theory of Causation 61 Rani Lill Anjum and Stephen Mumford 4. Biological Processes: Criteria of Identity and Persistence 76 James DiFrisco 5. Genidentity and Biological Processes 96 Thomas Pradeu 6. Ontological Tools for the Process Turn in Biology: Some Basic Notions of General Process Theory 113 Johanna Seibt Part III. Organisms 7. Reconceptualizing the Organism: From Complex Machine to Flowing Stream 139 Daniel J. Nicholson 8. Objectcy and Agency: Towards a Methodological Vitalism 167 Denis M. Walsh 9. Symbiosis, Transient Biological Individuality, and Evolutionary Processes 186 Fre ́de ́ric Bouchard 10. From Organizations of Processes to Organisms and Other Biological Individuals 199 Argyris Arnellos OUP CORRECTED PROOF – FINAL, 2/5/2018, SPi Part IV. Development and Evolution 11. Developmental Systems Theory as a Process Theory 225 Paul Grif fi ths and Karola Stotz 12. Waddington ’ s Processual Epigenetics and the Debate over Cryptic Variability 246 Flavia Fabris 13. Capturing Processes: The Interplay of Modelling Strategies and Conceptual Understanding in Developmental Biology 264 Laura Nuño de la Rosa 14. Intersecting Processes Are Necessary Explanantia for Evolutionary Biology, but Challenge Retrodiction 283 Eric Bapteste and Gemma Anderson Part V. Implications and Applications 15. A Process Ontology for Macromolecular Biology 303 Stephan Guttinger 16. A Processual Perspective on Cancer 321 Marta Bertolaso and John Dupre ́ 17. Measuring the World: Olfaction as a Process Model of Perception 337 Ann-Sophie Barwich 18. Persons as Biological Processes: A Bio-Processual Way Out of the Personal Identity Dilemma 357 Anne Sophie Meincke Index 379 OUP CORRECTED PROOF – FINAL, 2/5/2018, SPi vi Acknowledgements The work leading to this volume is a central outcome of a grant from the European Research Council under the European Union ’ s Seventh Framework Programme (FP7/2007 – 2013)/ERC Grant Agreement 324186, on which JD was the Principal Investigator and DJN was a Research Fellow. We are very grateful to the ERC for its support. More speci fi cally, the majority of the papers herein originated at the workshop “ Process Philosophy of Biology ” , the fi rst major event funded by the grant, held in Exeter in November 2014. We would like to thank all the participants in that event, which marked the fi rst step on the road to this publication. We must also thank Stephan Guttinger and Anne Sophie Meincke, the other two Research Fellows on the project, who have been essential contributors to each stage of the development of the project, both intellectually and practically. Additionally, anyone who has run a large research project will know how important it is to have a capable administrator, and we have been very fortunate to have Chee Wong in that capacity. We are most grateful for her tireless contributions to the project ’ s management. Finally, we have had the privilege of inviting a very substantial number of colleagues from around the world to workshops, colloquia, and other kinds of collaborative research visits. We will not try to name them, if only because we would surely leave someone out, but we are grateful to them all. More even than is obvious from the many authors who have contributed to the volume, this is an output that has been in fl uenced by an extended international and interdisciplinary academic community. OUP CORRECTED PROOF – FINAL, 2/5/2018, SPi OUP CORRECTED PROOF – FINAL, 2/5/2018, SPi Contributors G A , Centre for the Study of Life Sciences (Egenis), University of Exeter, Exeter, UK R L A , Centre for Applied Philosophy of Science, School of Economics and Business, Norwegian University of Life Sciences, Ås, Norway A A , IAS-Research Centre for Life, Mind, and Society, Department of Logic and Philosophy of Science, University of the Basque Country, San Sebastián, Spain E B , Institute of Biology Paris-Seine, Sorbonne University, Paris, France A -S B , Center for Science and Society, Departments of the Bio- logical Sciences and Philosophy, Columbia University in the City of New York, New York, USA M B , Institute of Philosophy of Scienti fi c and Technological Practice, Campus Bio-Medico University of Rome, Rome, Italy F ́ ́ B , Department of Philosophy, University of Montreal, Montreal, Canada J D F , Konrad Lorenz Institute for Evolution and Cognition Research, Klosterneuburg, Austria J D ́, Centre for the Study of Life Sciences (Egenis), University of Exeter, Exeter, UK F F , Centre for the Study of Life Sciences (Egenis), University of Exeter, Exeter, UK P G , Department of Philosophy and Charles Perkins Centre, University of Sydney, Sydney, Australia S G , Centre for the Study of Life Sciences (Egenis), University of Exeter, Exeter, UK A S M , Centre for the Study of Life Sciences (Egenis), University of Exeter, Exeter, UK S M , Department of Philosophy, University of Durham, Durham, UK and Centre for Applied Philosophy of Science, School of Economics and Business, Norwegian University of Life Sciences, Ås, Norway D J. N , Centre for the Study of Life Sciences (Egenis), University of Exeter, Exeter, UK OUP CORRECTED PROOF – FINAL, 2/5/2018, SPi L N Ñ R , IAS-Research Centre for Life, Mind, and Society, Depart- ment of Logic and Philosophy of Science, University of the Basque Country, San Sebastián, Spain T P , Immunology Unit, CNRS and University of Bordeaux, Bordeaux, France J S , Department of Philosophy and the History of Ideas, University of Aarhus, Aarhus, Denmark P S , Department of Philosophy, Trinity College Dublin, Dublin, Ireland K S , Department of Philosophy, Macquarie University, Sydney, Australia D M. W , Department of Philosophy, Institute for the History and Philoso- phy of Science and Technology, Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada OUP CORRECTED PROOF – FINAL, 2/5/2018, SPi x Foreword [T]here is really no ‘ thing ’ in the world. — David Bohm (1999: 12) [O]ur mind has an irresistible tendency to consider the idea it most frequently uses to be the clearest. — Henri Bergson (1946: 214) There is a notable lack of substance, not in the writing you will fi nd in this book, I assure you, but out there in the domain of the living. Let ’ s face it: there is no thing in biology (or, as Bohm would have it, in the world). Things are abstractions from an ever-changing reality. Reality consists of a hierarchy of intertwined processes. If life is change, then the activities driving this change are what we must explain. Yet we lack concepts and experimental approaches for the study of the dynamic aspects of living systems. This severely limits the range of questions we ask, most of the time even without our realizing. The problem is so obvious it is rarely ever talked about. There are very few explicitly processual theories in biology today. As a practising biologist, I ’ ve always found this utterly baf fl ing and disappointing. We remain strangely fi xated on explanation in terms of static unchanging entities. The prime example of this substance fi xation in biology is our love affair with genes, those particulate agents of heredity and development. It is all too easy for biologists to slip into deterministic and preformationist language, where genes represent some sort of enduring essence of an ephemeral living body. As a result, the mysterious source of gene agency remains unexamined and unexplained. Another example is our insistence that proper ‘ mechanistic ’ explanations of living organisms must be formulated at the level of component molecules, which we take to be unchanging at the timescales relevant to the processes we study. James Ladyman and Don Ross (2007), in their book Every Thing Must Go , call this the metaphysics of ‘ microbangings ’ , small entities causing their effects by bumping into each other. Ladyman and Ross point out that this view is outdated and inconsistent with the dynamic view of the world given to us by modern physics. Our fi xation on static things leads to fallacious patterns of reasoning, within biology and elsewhere. The French process philosopher Henri Bergson alluded to this in the quote above, while Alfred North Whitehead (1925: 52) put it more explicitly by calling it ‘ the fallacy of misplaced concreteness ’ . This consists in the unwarranted rei fi cation of objects, which become fundamental and replace the underlying dynamic reality in our thinking. This fallacy is deeply engrained in our cognitive habits. From a very early stage of development, we learn to distinguish objects, to isolate them from their context. Cognitive linguists George Lakoff and Mark Johnson (1980: 30 – 2) have suggested that this re fl ects a tacit commitment to a doctrine of ‘ containment ’ : we treat the world as a container of objects that change properties or location and interact with one another. Each object is in turn a container with smaller objects OUP CORRECTED PROOF – FINAL, 2/5/2018, SPi inside, and so on. This doctrine is fundamental to our thinking; it forms the basis of set theory and relational logic. It is very deeply rooted in our human nature: all western languages share it, even ancient ones. To identify an object as a container, we must establish its boundaries as precisely as possible. Where and when does it begin? Where and when does it end? We instinctively crave for clear and rigorous answers to such questions. However, modern science suggests that reality is simply not like that. The world is full of fuzzy boundaries. Seemingly unchanging entities keep on emerging and decaying if we consider them over a long enough time span. Moreover, it is impos- sible to say precisely when they truly become what they are and when they cease to be themselves. Or where they begin and where they end. This problem of identi fi cation and individuation is beautifully illustrated by the ancient Greek thought experiment about the ship of Theseus. According to the legend, the ship was preserved by the Athenians for centuries upon Theseus ’ return from his journeys. In the process, each plank of the hull was replaced when it started to rot, until none of the original planks was left. Just as in our own bodies, the substance that makes up the ship is constantly replaced. Does this mean that the ship changes over time, or does it remain the same? As this conundrum illustrates, we need criteria for recognizing, individuating, and classifying processes. We need more accurate and adequate thinking tools that let go of the abstraction of the object. In short, we need to transcend the limitations of substance-based thinking. This is what the book you have in your hands sets out to do. This is not armchair philosophy, nor is it an exercise in speculative system building. This book outlines a processual research agenda for theoretical biology with direct and wide-ranging implications for practicing biologists. It connects to speci fi c areas of inquiry, such as cancer genetics, evolutionary theory, developmental biology, and the neuroscience of olfaction. It is written in a language that makes it accessible not just to philosophers but also to experimentalists. And, perhaps most importantly, it challenges many of the substance-based assumptions that hamper progress in speci fi c domains. These fundamental assumptions about the world shape the research questions we pursue and the explanations we accept as satisfactory. Unfortunately, modern scienti fi c curricula have long forgotten to teach students about these hidden aspects of science. Even worse, the format of scienti fi c meetings and papers is designed deliberately to sweep these philosophical foundations under the rug. They have become invisible, barred from the conscious attention of many researchers. In ignorance of their own metaphysical assumptions, scientists are falling back on naïve, often neopositivist preconceptions that severely constrain their thinking and keep their minds closed to the possibility of unconsidered alternatives. This is a terrible shame. If this book succeeds in doing only one thing, I hope that it will be to ignite a lively and public discussion among researchers in the life sciences about our underlying philosophical worldviews and their limitations. My own scienti fi c trajectory has been inspired and shaped, in an absolutely crucial way, by such philosophical considerations. As a child, I was very strongly committed, both emotionally and intellectually, to a view of static preservation. I am writing these words while on vacation in my hometown of Tschiertschen, a small mountain village in the Swiss Alps. I can assure you that there is a strong and deeply ingrained resistance to change in rural Swiss society. Like many of my country people, I also wished to preserve the beauty of the mountain environment I grew up in and the OUP CORRECTED PROOF – FINAL, 2/5/2018, SPi xii wealth and orderliness of its society. It seemed perfect to me as it was. Thinking this through, however, I became aware of the suffocating dread of such a vision. This was a very visceral realization. Everything that is beautiful and exciting about the moun- tains I love has its basis in the dynamical processes that shape them: eon-long upheaval and erosion, the wild torrents so much appreciated by the Romantics, the unpredictability of the weather, and a tradition of tough high-altitude life, fl exibly adapting to ever-changing and harsh environmental conditions. To me, static pres- ervation, a freezing of the current state, no matter how precious, kills all that is beautiful, all that is exciting. The illusion of stability is just that: an illusion, and a perilous one at that. This realization was itself a slow and gradual process, not a sudden epiphany. And it has guided my journey of exploration ever since. It guided me during my undergraduate training as a geneticist, which occurred in a staunchly reductionist molecular biology research environment. I suffered from the strongly antiphilosophical attitude around me, but was not able to express my dissatisfaction explicitly and convincingly. I wish I had known more about process thinking back then, to give my doubts and qualms focus and rigor. Who knows if this would have changed anything, as most of my colleagues didn ’ t even feel that there was a problem. Worse still, they thought that molecular biologists didn ’ t need any philosophy at all, since they were dealing with hard empirical facts! It didn ’ t help to point out that this is itself a philosophical statement. In fact, nowadays scientists often use the term ‘ philosophical ’ in a derogatory manner, to describe questions that may or may not be interesting, but are de fi nitely not answerable given our current state of research. Science, it is believed, will increasingly replace philosophy by making such questions answerable. This attitude has always bothered me. It creates a kind of intellectual monoculture that focuses only on the lowest-hanging fruit: the motto of science as the art of the feasible, taken to an unhealthy extreme. Everybody around me was obsessed with the same question: how to decode the logic of gene expression during development by studying the regulatory sequences on the DNA that are thought to implement this logic. I felt that my colleagues ascribed an almost magical agency to those sequences. The central idea was (and to a large extent still is) that there is some sort of ‘ code ’ that can be read out of the DNA and that will result in a particular pattern in the embryo at some stage of development. Everybody was looking for the genetic program formed by this code: preformationist thinking par excellence! And yet very few people seemed to believe that their underlying assump- tions were problematic and warranted philosophical scrutiny. When I looked for postgraduate advisors, I deliberately sought out (and was lucky to fi nd) a number of exceptions to this widespread rule of wilful, self-imposed philosophical ignorance. The most eclectic of these was Brian Goodwin, an unorthodox and open-minded thinker if there ever was one. Brian brought me into contact with process thought in the form of Husserl ’ s and Merleau-Ponty ’ s classic phenomenology, as well as with his own theory of biological structuralism (e.g. Webster and Goodwin 1996). On the one hand, I found these views tremendously fascinating and inspiring, funda- mentally altering and refocusing my thinking about ways of becoming in embryology. But on the other, I felt that these approaches were a bit vague and detached from current experimental practices. Luckily, around the same time I learned the mathematical and conceptual tools of dynamical systems theory from Brian, Nick Monk, and my doctoral supervisor, John Reinitz. These tools could be combined in a powerful way with OUP CORRECTED PROOF – FINAL, 2/5/2018, SPi xiii quantitative experimental work to study the processes of pattern formation. During this stage of my career my interests decidedly moved away from the molecular details and the substance-based approach of molecular developmental genetics. This ended up causing a string of problems that I didn ’ t anticipate at the time but which are obvious to explain with the bene fi t of hindsight. Many of my applications for postdoctoral fellowships, and then for grants that might fund my newly estab- lished independent research group, were rejected. Papers came back from journals too, often unread or with strange, uninformative, and even hostile reviews. It wasn ’ t only that the editors and referees thought that my research was fl awed. They didn ’ t fi nd it interesting at all, and mostly didn ’ t even make an effort to understand the question. It took me a while to realize that the problem I had wasn ’ t scienti fi c but philosophical! Sadly, scienti fi c reviewers are often so stuck in the habits and tradi- tions of their fi eld that they can ’ t think of research being worthwhile if it does not neatly fi t into one of their familiar categories. This is when process thinking itself became a central and fi xed part of my research agenda. Publishing our philosophical arguments has allowed me not only to detect weaknesses and fi nd a better grounding for my own thinking, but also to better explain why I do what I do to my colleagues. And slowly I ’ m beginning to see an effect. Over the last decades I ’ ve been happy to observe interest shifting towards dynamical systems modelling in developmental biology. Reviewers who state that ‘ nothing can ever be learned from a model ’ still exist, but have become exceedingly rare these days. In fact they appear to be a species on the verge of extinction. An increasing number of my colleagues have overcome the scepticism they initially exhibited and now tolerate, or even actively support, the processual research agenda a small minority of us have been pursuing for years. This recent trend is tremendously encouraging. Quite clearly, the time is ripe for more process thinking, not only in developmental biology but across the life sciences. This is why I am so excited about the collection of essays in this book. It is an important and timely endeavour. I hope it will inspire young biologists in particular to open their minds, to widen their intellectual horizons, and to adopt new philo- sophical perspectives. I also hope it encourages them to ask radically new questions, build new conceptual frameworks and theories, and develop new experimental approaches that directly address the fundamentally processual nature of living systems. Enjoy the read! I certainly did. Johannes Jaeger Associate Researcher Complexity Science Hub Vienna Klosterneuburg, Austria, 16 August 2017 References Bergson, H. (1946). The Creative Mind. New York: Philosophical Library. Bohm, D. and Biederman, C. (1999). Bohm-Biederman Correspondence , vol. 1: Creativity and Science. London: Routledge. OUP CORRECTED PROOF – FINAL, 2/5/2018, SPi xiv Ladyman, J. and Ross, D. (2007). Every Thing Must Go: Metaphysics Naturalized. Oxford: Oxford University Press. Lakoff, G. and Johnson, M. (1980). Metaphors We Live By. Chicago, IL: University of Chicago Press. Webster, G. and Goodwin, B. (1996). Form and Transformation: Generative and Relational Principles in Biology. Cambridge: Cambridge University Press. Whitehead, A. N. (1925). Science and the Modern World. New York: Macmillan. OUP CORRECTED PROOF – FINAL, 2/5/2018, SPi xv OUP CORRECTED PROOF – FINAL, 2/5/2018, SPi P A R T I Introduction OUP CORRECTED PROOF – FINAL, 5/5/2018, SPi OUP CORRECTED PROOF – FINAL, 5/5/2018, SPi 1 A Manifesto for a Processual Philosophy of Biology John Dupré and Daniel J. Nicholson 1. Introduction This book is a venture in the metaphysics of science, the exploration of the most basic features of the world implied or presupposed by science. One of its main aims is to demonstrate the fundamental importance of such an investigation. Getting this very general picture right makes a real difference to whether we do the science well and understand properly what it tells us. The particular metaphysical thesis that motiv- ates this book is that the world — at least insofar as living beings are concerned — is made up not of substantial particles or things, as philosophers have overwhelmingly supposed, but of processes. It is dynamic through and through. This thesis, we believe, has profound consequences. More speci fi cally, we propose that the living world is a hierarchy of processes, stabilized and actively maintained at different timescales. We can think of this hierarchy in broadly mereological terms: molecules, cells, organs, organisms, popu- lations, and so on. Although the members of this hierarchy are usually thought of as things, we contend that they are more appropriately understood as processes. A question that arises for any process, as we shall discuss in more detail below, is what enables it to persist. The processes in this hierarchy not only compose one another but also provide conditions for the persistence of other members, both larger and smaller. So, if we take for example a liver, we see that it provides enabling conditions for the persistence of the organism of which it is a part, but also for the hepatocytes that compose it. Outside a very specialized laboratory, a hepatocyte can persist only in a liver. And reciprocally, in order to persist, a liver requires both an organism in which it resides, and hepatocytes of which it is composed. A key point is that these reciprocal dependencies are not merely structural, but are also grounded in activity. A hepatocyte sustains a liver, and a liver sustains an organism, by doing things. This ultimately underlies our insistence on seeing such seemingly substantial entities as cells, organs, and organisms as processes. These processes — which have so often been taken for things, or substances — themselves engage in more familiar-sounding processes such as metabolism, devel- opment, and evolution; processes that, again, often provide the explanations for the OUP CORRECTED PROOF – FINAL, 5/5/2018, SPi