Martin Döring Imme Petersen Anne Brüninghaus Regine Kollek Contextualizing Systems Biology Presuppositions and Implications of a New Approach in Biology Contextualizing Systems Biology Martin Döring • Imme Petersen Anne Brüninghaus • Regine Kollek Contextualizing Systems Biology Presuppositions and Implications of a New Approach in Biology Martin Döring Imme Petersen University of Hamburg University of Hamburg Hamburg , Germany Hamburg , Germany Anne Brüninghaus Regine Kollek University of Hamburg University of Hamburg Hamburg , Germany Hamburg , Germany ISBN 978-3-319-17105-0 ISBN 978-3-319-17106-7 (eBook) DOI 10.1007/978-3-319-17106-7 Library of Congress Control Number: 2015944085 Springer Cham Heidelberg New York Dordrecht London © Springer International Publishing Switzerland 2015 This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifi cally the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfi lms 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 specifi c 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 Springer International Publishing AG Switzerland is part of Springer Science+Business Media (www.springer.com) Pref ace This book explores the development of systems biology as a new approach to life. It is based on an empirical social study of science and analyzes the epistemic pre- conditions, infrastructural requirements, innovative potentials, and policy implica- tions of emerging and expanding concepts and practices of systems biology. In conducting the research that provided the basis for this publication we were inter- ested not only in systems biology’s capacity to give rise to a better understanding of complex biological entities such as cells or organisms but also in its cognitive, social, and policy framings and contexts. The results of the study show that systems biology is as complex as its objects of research, and that it also is an interdisciplin- ary enterprise which will most likely have a profound impact on our perception of life as well as on science itself. The overall aim of this book is to contribute to a better understanding of the implications nestling in the current shift in molecular biology towards a systems- oriented perspective for science and society. It was written for specialists of differ- ent academic disciplines as well as for experts coming from nonacademic fi elds. Talking about experts from academia, we do not only think about those from biol- ogy, informatics, physics or other natural sciences, or medicine but also think about scholars from the social and cultural studies of science, from history and philosophy of science, or from linguistics. And when we talk about experts from nonacademic fi elds, we mean anyone interested in scientifi c developments such as systems biology coming from science policy, science administration, or the media reporting about science. It is our mission to make science, its presuppositions and preconditions, as well as its implications, as transparent and accountable as possible. Therefore we tried—and we hope succeeded—to use a language that makes a complex, but v vi Preface nevertheless highly topical and important subject accessible to all of those who are interested in a more than superfi cial understanding of science and of how it shapes and is shaped by us, by society, and by culture. Hamburg, Germany Martin Döring Imme Petersen Anne Brüninghaus Regine Kollek Acknowledgments The study presented here and the research conducted would not have been possible without the participation of the many individuals who encouraged and supported our work. We are extremely grateful to all of them. First of all, we would like to thank scientists active in systems biology as well as experts from politics, adminis- tration, and the media, who were available for interviews and patiently answered our questions. Furthermore, we also thank the participants of the feedback- workshops at Charité Universitätsmedizin in Berlin and Technische Universität Braunschweig in Spring 2014 for open and inspiring discussions. The work presented here was conducted in the context of the research project Towards a holistic conception of life ? Epistemic presumptions and socio - cultural implications of systems biology (THCL; www.thcl.de ), which was funded by the German Federal Ministry of Education and Research (BMBF) (May 2010 to July 2014). THCL was part in the funding line Ethical, Legal, and Social Aspects of Genome Research (ELSA-GEN). We would like to thank Marina Schindel, Detlef Böcking, and Anja Heintze at Deutsches Zentrum für Luft- und Raumfahrt (DLR) for taking care of all administrative and fi nancial issues and providing help when- ever necessary. THCL was carried out by the Research Centre for Biotechnology, Society and the Environment (FSP BIOGUM)—Research Group Medicine and Neurosciences at Universität Hamburg. The principle investigator of the project was Regine Kollek. Martin Döring (May 2010 to September 2012) and Imme Petersen (October 2012 to July 2014) were responsible for managing the project. Anne Brüninghaus, Martin Döring, and Imme Petersen conducted the empirical research presented in this book. Most of it was done in Germany, but partially also in Austria. This resulted inter alia in a comparative analysis of media representations of systems biology in Austria and Germany, which is included in this book. Part of the project was carried out in cooperation with Karen Kastenhofer and Helge Torgersen at the Institute for Technology Assessment (ITA) at the Österreichische Akademie der Wissenschaften in Vienna. However, this book presents the results of the research group at BIOGUM whereas the results of our cooperating partners at ITA have been published elsewhere. The close and continuous exchange with Karen Kastenhofer and Helge Torgersen vii viii Acknowledgments and the joint meetings and discussions in Vienna and Hamburg were extremely inspiring and fruitful; we thank both of them for this wonderful cooperation. We also would like to express our gratitude to those of our former colleagues who cooperated with us in the course of the EU project ACGT — Advancing Clinico - Genomic Clinical Trials on Cancer in the 6th Framework Program and who agreed to participate in the interviews for the case study reported in this book. In particular, we would like to thank Georgios Stamatakos (Institute of Communication and Computer Systems, National Technical University of Athens) for advice and assistance in under- standing the function of the oncosimulator and for proofreading Sect. 4.2 . The project was expertly advised by a scientifi c board whose members were Paul Martin (Department of Sociological Studies, University of Sheffi eld), Roger Strand (Centre for the Study of the Sciences and the Humanities, University of Bergen), Hans Westerhoff (Centre for Integrative Systems Biology, University of Manchester), and Ana Cãno-Delgado (Centre for Research in Agricultural Genomics, Barcelona). We would like to thank all of them for advice and support and for participating in the inspiring project workshop on Different Forms of Life ? Comparative Perspectives on Systems and Synthetic Biology on January 19–20, 2012 in Hamburg. The interviews were transcribed by Rita Stark (Köln) and Angela Wiedl (East Aurora), and the translation of German interview citations was done by Sandra H. Lustig (Hamburg). Many thanks to all of them for their work! Last, but not least, we want to give thanks to our colleagues at the FSP BIOGUM, especially to Birgit Sonntag for giving excellent organizational and administrative support as well as for taking care of a constant supply of coffee, tea, and biscuits during long meetings and workshops and Moritz Hettrich for arranging the literature, formatting, and proof- reading the manuscript. Contents 1 Understanding Systems Biology: A Place for Social Science Analysis ....................................................................... 1 Regine Kollek , Imme Petersen , Anne Brüninghaus , and Martin Döring 2 Basic Concepts of Systems Biology as Seen Through Systems Biologists’ Eyes: Metaphorical Imagination and Epistemic Presuppositions ................................................................ 27 Martin Döring , Regine Kollek , Anne Brüninghaus , and Imme Petersen 3 Systems-Oriented Approaches in Biology: System Biologist’s Narratives of Present, Past, and Future .................. 119 Martin Döring , Anne Brüninghaus , Regine Kollek , and Imme Petersen 4 Systems Biology, Information Technology, and Cancer Research ................................................................................ 147 Imme Petersen , Regine Kollek , Anne Brüninghaus , and Martin