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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 omnipresent 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 particularly , it addresses the question of whether epigeneticists explain differently —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 regulatory non-DNA factors that are taken to be causally responsible for realizing 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 WHAT IS EPIGENETICS? 2 ◂ 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. The 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 (fig. I.1). Moreover, both the highly ambitious Human Epigenome Project and the field’s own journal Epigenetics 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 qualitative changes. On the other hand, it should also highlight the need to investigate processes “above” the gene, as implied by the prefix epi, which means “over” or “upon.” More specifically, Waddington (1952b, vi) understood epiFIG . 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 “genetic (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. ▸ 3 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 epigenetics , 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, networklike 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 epigenetics 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 (transgenerational ) 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 that classical epigenetics 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-causeone -effect thinking popular during the rise of molecular biology. Moreover, as Patrick Murray, a...


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