History, Philosophy and Theory of the Life Sciences Sara Green Editor Philosophy of Systems Biology Perspectives from Scientists and Philosophers History, Philosophy and Theory of the Life Sciences Editors Charles T. Wolfe, Ghent University, Belgium Philippe Huneman, IHPST (CNRS/Université Paris I Panthéon-Sorbonne), France Thomas A.C. Reydon, Leibniz Universität Hannover, Germany Editorial Board Marshall Abrams (University of Alabama at Birmingham) Andre Ariew (Missouri) Minus van Baalen (UPMC, Paris) Domenico Bertoloni Meli (Indiana) Richard Burian (Virginia Tech) Pietro Corsi (EHESS, Paris) François Duchesneau (Université de Montréal) John Dupré (Exeter) Paul Farber (Oregon State) Lisa Gannett (Saint Mary’s University, Halifax) Andy Gardner (Oxford) Paul Griffi ths (Sydney) Jean Gayon (IHPST, Paris) Guido Giglioni (Warburg Institute, London) Thomas Heams (INRA, AgroParisTech, Paris) James Lennox (Pittsburgh) Annick Lesne (CNRS, UPMC, Paris) Tim Lewens (Cambridge) Edouard Machery (Pittsburgh) Alexandre Métraux (Archives Poincaré, Nancy) Hans Metz (Leiden) Roberta Millstein (Davis) Staffan Müller-Wille (Exeter) Dominic Murphy (Sydney) François Munoz (Université Montpellier 2) Stuart Newman (New York Medical College) Frederik Nijhout (Duke) Samir Okasha (Bristol) Susan Oyama (CUNY) Kevin Padian (Berkeley) David Queller (Washington University, St Louis) Stéphane Schmitt (SPHERE, CNRS, Paris) Phillip Sloan (Notre Dame) Jacqueline Sullivan (Western University, London, ON) Giuseppe Testa (IFOM-IEA, Milano) J. Scott Turner (Syracuse) Denis Walsh (Toronto) Marcel Weber (Geneva) More information about this series at http://www.springer.com/series/8916 Sara Green Editor Philosophy of Systems Biology Perspectives from Scientists and Philosophers Editor Sara Green Department of Science Education University of Copenhagen Copenhagen, Denmark ISSN 2211-1948 ISSN 2211-1956 (electronic) History, Philosophy and Theory of the Life Sciences ISBN 978-3-319-46999-7 ISBN 978-3-319-47000-9 (eBook) DOI 10.1007/978-3-319-47000-9 Library of Congress Control Number: 2016959572 © Springer International Publishing AG 2017 This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. The publisher, the authors and the editors are safe to assume that the advice and information in this book are believed to be true and accurate at the date of publication. Neither the publisher nor the authors or the editors give a warranty, express or implied, with respect to the material contained herein or for any errors or omissions that may have been made. Printed on acid-free paper This Springer imprint is published by Springer Nature The registered company is Springer International Publishing AG The registered company address is: Gewerbestrasse 11, 6330 Cham, Switzerland Preface Do you want to know what scientists and philosophers really think? You will not find that in the typical journal paper or even conference talk. If you are lucky enough to be able to sit down with them at a pub, they may open up to you. But most of us are not so lucky. The intention with this volume is to offer an alternative to the typi- cal academic publications by providing a format for scholars to freely express their personal opinions and tell their story. I have asked a selection of systems biologists and philosophers to address the same set of questions designed to probe their approaches, aspirations, interests, and frustrations in an informal manner. I hope that the volume at the same time can serve as an introduction to philosophy of sys- tems biology and as a source of insight to what motivates people engaged in systems biology or its philosophy. Moreover, I hope it can serve as a starting point for dis- cussions of the implications of systems biology for philosophy, science, and society. Of course, if you want to pursue the dialogue beyond these initial statements, it is up to you to engage the scholars in discussions about questions you most care about. The emergence of and research within systems biology reveal the depth of the fascinating and overwhelming challenge of understanding biological complexity. While the problem of biological complexity unites systems biology research, the strategies pursued to deal with this challenge are diverse. The wish to compile a selection of viewpoints on philosophy of systems biology in this volume is in part inspired by my own fascination (and frustration) with the difficulty of coming to grips with what systems biology is as I was pursuing my PhD project on the philoso- phy of systems biology. As I worked my way through much of the literature in and about systems biology, and asked practicing scientists what systems biology is all about, I realized that there are many different views on what systems biology is or should be. These differences should not only be regarded as signs that systems biol- ogy is a new, and perhaps immature, approach in development. Rather, the diverse views on the significant aspects of and future directions for systems biology reflect how many different scientific traditions come together and impact what it means to do biological research. I have come to see these differences, whether revealed through heated scientific disagreements or through subtle methodological diversities, v vi Preface as a rich source for philosophical insights into the characteristics of epistemic cul- tures and scientific worldviews of practicing scientists. This volume is therefore motivated by an interest in getting insight into the aspects of systems biology which prominent scholars take to be its most salient features and to give them the chance to freely express their views on the scope, aim, and future directions of systems biology. The contributions of this volume are not intended as review articles but as per- sonal perspectives on the philosophical implications of systems biology in response to five questions (listed below). I have left it open to the authors whether they wanted to answer all questions or a subset and whether they wanted to present their view- points as separate answers to the questions or as an essay. The questions addressed in this volume are as follows: – How and why were you initially drawn to systems biology? – How do you view the relation between philosophy and systems biology, and (how) can these fields inform each other? – What do you consider the most neglected topics and/or contributions in the late twentieth-century (philosophy of) biology? – What have been the most significant advances in systems biology? – What do you consider the most important problems in (philosophy of) systems biology, and what are the prospects for progress in this respect? To serve the intended purpose for this volume, I found it important to address practicing scientists as well as philosophers. Since my intention has been to open up these discussions for debate, the following introduction is mainly written as a guide to the philosophical questions raised in discussions in and about systems biology, by pointing to various viewpoints and topics discussed in this volume. After each con- tribution, there will be a short list of suggested readings for each author for readers interested in learning more about the work of specific contributors. Acknowledgements I am grateful that so many prominent scholars accepted the invitation to provide their perspectives, and I would like to thank them all for their insightful and thought- provoking answers. I also thank the authors for useful feedback on the introductory chapter and inputs on various choices in the editing process. Sadly, one of the contributors, Eric Davidson, passed away in September 2015. Eric Davidson will be remembered as a key figure in systems biology as well as developmental biology due to his pioneering and groundbreaking investigation of gene regulatory networks. While editing the volume, I have benefitted from support by the Centre for Science Studies (Aarhus University), the Center for Philosophy of Science (University of Pittsburgh), and the Department of Science Education (University of Copenhagen). I thank two anonymous reviewers for useful feedback on the whole book, Maria Serban and Mette Skau for their help and support, and the staff and editors at Springer for professional handling and production of the book. The copy-editing of the volume has been financially supported by Lillian and Dan Finks Fund. Sara Green vii Contents 1 Introduction to Philosophy of Systems Biology .................................... 1 Sara Green 2 Systems Biology: Negotiating Between Holism and Reductionism.................................................................................... 25 William Bechtel 3 A System Approach to Cancer. From Things to Relations .................. 37 Marta Bertolaso 4 Systems Biology in the Broad Sense ...................................................... 49 Fred C. Boogerd