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Above the Gene, Beyond Biology ABOVE THE GENE, BEYOND BIOLOGY ABOVE THE GENE, BEYOND BIOLOGY TOWARD A PHILOSOPHY OF EPIGENETICS JAN BAEDKE University of Pittsburgh Press Published by the University of Pittsburgh Press, Pittsburgh, Pa., 15260 Copyright © 2018, University of Pittsburgh Press All rights reserved Manufactured in the United States of America Printed on acid-free paper 10 9 8 7 6 5 4 3 2 1 Cataloging-in-Publication data is available from the Library of Congress ISBN 13: 978-0-8229-4521-5 Cover art: (foreground) Line drawing adaptation of the epigenetic landscape into an ontogenetic landscape for locomotion, from E. Thelen and L. B. Smith, “Dynamic Systems Theories,” in Handbook of Child Psychology, 5th ed., vol. 1, edited by W. Da- mon and R. M. Lerner (New York: Wiley, 1998); (background) original art courtesy of DNA Art Gallery LLC. Cover design by Joel W. Coggins For A, U, and J, my epigenotype ”Epigenetics.” The science concerned with the causal analysis of development. CONRAD HAL WADDINGTON, 1952 I suppose the process of acceptance will pass through the usual four stages: 1. This is worthless nonsense, 2. This is an interesting, but perverse, point of view, 3. This is true, but quite unimportant, 4. I always said so. JOHN BURDON SANDERSON HALDANE, 1963 CONTENTS Acknowledgments xi INTRODUCTION. WHAT IS EPIGENETICS? 1 1. HOW EPIGENETICS DEALS WITH BIOLOGICAL COMPLEXITY 13 2. CHALLENGES OF EPIGENETICS IN LIGHT OF THE EXTENDED EVOLUTIONARY SYNTHESIS 41 3. CAUSAL EXPLANATION 90 4. MECHANISTIC EXPLANATION 129 5. ASSESSING THE EXPLANATORY POWER OF EPIGENETICS 168 CONCLUSION. A PHILOSOPHY OF EPIGENETICS 201 Notes 217 References 245 Index 301 ACKNOWLEDGMENTS . try with a little help from my friends THE BEATLES, 1967 I AM GRATEFUL TO a number of people who have helped in writing this book. Their intellectual, material, and emotional support is deeply appreciated. I benefited from exciting exchanges on causality, mechanisms, and sci- entific explanation, as well as on past and present epigenetics, with Mas- simo Pigliucci, Eva Jablonka, Siobhan F. Guerrero Mc Manus, Jani Raerinne, James DiFrisco, and Maurizio Meloni. In addition, I am very thankful to Daniel Brooks, Frank Paris, Kirsten Schmidt, Melinda B. Fagan, Fridolin Gross, Maria Kronfeldner, and Marcel Weber for making constructive com- ments on ideas presented in this book. I am especially grateful to Helmut Pulte and Christina Brandt for their comprehensive and valuable com- ments, as well as their kind advice and support. This book was written in different places. I would like to thank the Phi- losophy of Science Group (Helsinki University), including Petri Ylikoski and Jaakko Kuorikoski, the Biolosophy Group (Bielefeld University), the ACKNOWLEDGMENTS PhiBio Group (Metropolitan Autonomous University, Mexico City), and the members of the Centre for the Study of Life Sciences (Egenis, University of Exeter), including Daniel Nicholson, John Dupré, and Thijs van Stigt, who commented on several ideas initially presented in the form of confer- ence papers. The research behind this book was supported by the German Research Foundation (DFG), the Foundation Mercator, the Ruhr Univer- sity Research School, the Heinrich Hertz Foundation, and the German Aca- demic Exchange Service (DAAD). Many thanks to Dusa McDuff for sharing with me translations of Rus- sian papers originally prepared for her father, C. H. Waddington. Also, as a non-native speaker of English, I am especially grateful to Daniel Brooks and Maureen Creamer Bemko, who made this book readable and possibly enjoyable by editing my “German-style” English. At the University of Pitts- burgh Press, I thank Abby Collier for her support and enthusiasm for the project and for making this such an enjoyable process. Also, I am grateful for the comprehensive comments of the reviewers, which were insightful and very helpful in correcting omissions and clarifying arguments. Finally, I owe an immeasurable debt to Ulla Quadbeck-Baedke and Jochen Baedke for supporting this project a long time before it actually began, as well as to Abigail Nieves Delgado for making me think and smile every single day since I met her. xii ◂ ABOVE THE GENE, BEYOND BIOLOGY INTRODUCTION WHAT IS EPIGENETICS? The potential is staggering. The age of epigenetics has arrived. TIME, JANUARY 2010 THIS BOOK IS ABOUT how biologists in the booming field of epigenetics explain living systems. It directly responds to an idea seemingly omnipres- ent in the academic and non-academic world: the view that epigenetics imposes a major theoretical shift on modern biology by invoking previously neglected phenomena and new levels of biological complexity. More par- ticularly, it addresses the question of whether epigeneticists explain differ- ently—both from how other biologists explain their phenomena and from how philosophers of science usually conceptualize biological explanations. Today, epigenetics is usually described as the investigation of regula- tory non-DNA factors that are taken to be causally responsible for realiz- ing genetic information. These factors are addressed not only to explain developmental phenomena, like phenotypic plasticity or, more specifically, cancer, schizophrenia, obesity, alcoholism, and aging, but also to aid in the search for successful associated medical applications, like stem cell therapy INTRODUCTION and cloning. In addition, epigenetic factors are highlighted in investigations of heredity phenomena, like disease etiology and sex-linked inheritance patterns, and in studies of the role of development in evolution. In short, epigenetics is currently one of the hottest topics in biology. Th e number of paper titles containing the word “epigenetic(s)” has increased more than tenfold since 2000, thus gradually chipping away at the predominance of genetics (fi g. I. 1). Moreover, both the highly ambitious Human Epigenome Project and the fi eld’s own journalEpigenetics have been launched since 2000. However, despite its current topicality, the term “epigenetics” is anything but new. It was introduced by the prominent British embryologist Conrad Hal Waddington back in the 1940s. According to Waddington, epigenetics should, on the one hand, refer to the Aristotelian theory of epigenesis, which understands development as consisting of both gradual and qualita- tive changes. On the other hand, it should also highlight the need to inves- tigate processes “above” the gene, as implied by the prefi x epi, which means “over” or “upon.” More specifi cally, Waddington (1952b, vi) understood epi- FIG. I.1. Relative frequency of articles with the word “epigenetic(s)” in their title (using ISI Web of Knowledge, 1950 to 2015). A frequency index of 1 means there is one title including the word “epigenetic(s)” for every one hundred titles including “genet- ic(s).” In total numbers, until the year 2000 there are fewer than one hundred articles for each year, and in 2015 there are more than twenty-four hundred. 2 ◂ INTRODUCTION genetics as the “science concerned with the causal analysis of development,” especially the causal role of networks of interacting genes and how these networks bring phenotypes into being. If we compare Waddington’s classical epigenetics and contemporary epi- genetics, we find a few general views that seem to have survived over the decades. First, both Waddington’s epigenetics as well as substantial parts of its modern counterpart investigate development in a systemic, network- like manner. Waddington called this environmentally sensitive network of interactions the “epigenotype”—a web of processes that jointly gives rise to the phenotype. This network view currently reappears in epigenetic studies, such as the Human Epigenome Project, in which researchers seek not to “genotype” humans but to “epigenotype” them (i.e., to screen their whole epigenome). Second, epigenetics remains closely linked to study of causal analysis. For example, in the mission statement of the journal Epigenetics, the editors define contemporary epigenetics as the field that “studies heritable changes in gene expression caused by mechanisms others [sic] than the modification of the DNA sequence” (Epigenetics 2017). In other words, while classical epi- genetics was focused on the causal role of genes, many modern epigeneticists investigate how nongenetic changes are caused (e.g., through environmental influences) and how they lead to developmental and hereditary (transgen- erational) effects. Thus, despite the fact that the causal factors of interest might have changed over the decades, from genes to everything but or, as one might now rightfully say, everything above—genes, the cornerstones of epigenetics’ causality-based research program seem to have survived. These general similarities should not convey the view thatclassical epi- genetics was a success story. Figure I.1 clearly shows that it was not. In fact, until today almost no concepts and central ideas of the original field were picked up by mainstream biology. This is unsurprising, since Waddington’s systemic view was not considered in line with the reductionist one-cause- one-effect thinking popular during the rise of molecular biology. Moreover, as Patrick Murray, a colleague of Waddington in the early 1930s, once noted, reading Waddington’s books is like “wading through mud up to the armpits” (quoted in Hall 1992, 116). As a consequence, not only Waddington’s view of the complex dynamics between gene interaction and development but also his attempt to unite genetics, embryology, and evolutionary theory were largely forgotten.
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