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NOTES INTRODUCTION 1. For a historical overview of the different roles the gene played in twentiethcentury biology, see the work by Rheinberger et al. (2015). For the disappointing results of the so-called Human Genome Project, see chapter 1. 2. Throughout this book the terms “dependency (relation)” and “relation (ship)” are used interchangeably. They can refer to a (degree of) connectedness between the properties of entities (e.g., DNA, cells, organisms) or events (e.g., transcription, mitosis, reproduction) in the world. For example, these dependencies can be said to be causal (see chap. 3) or constitutive (see chap. 4). In addition, the terms above are also used to describe explanatory dependencies or relations expressed, for example, in a model, equation, generalization , law, and so forth, between an explanandum (a phenomenon that is to be explained) and an explanans (usually sentences or equations that should explain the phenomenon). 3. For example, model organisms may be considered exemplary of higher taxons (Bolker 2009; Ankeny and Leonelli 2011). Due to this feature they can facilitate surrogate reasoning and extrapolation in contrastive explanation. 218 ◂ 4. For further historical “stimuli” (and also some sociological and anthropological ones), see the conclusion of this book. 1. HOW EPIGENETICS DEALS WITH BIOLOGICAL COMPLEXITY 1. For early studies in philosophy of biology, see, for example, the works of Schaffner (1967a, 1967b, 1969), Wimsatt (1974, 1976), and Hull (1974). For an even longer tradition of philosophy of biology starting in the early twentieth century, see the concluding chapter in this book. 2. Far-from-equilibrium open systems, like organisms, have to work against the second law of thermodynamics, which says heat cannot be perfectly transformed into work. Thus, it holds that the amount of free energy is constantly decreasing while entropy (as a measure for the amount of dissipated energy) is constantly increasing. Against this tendency the organization of open systems allows them to import matter rich in free energy to stay at a low entropy state far from equilibrium, for example, in organisms at a state far from death (Schrödinger 1944). Note that also some nonliving systems, such as flames, are far from-equilibrium open systems (Nicolis and Prigogine 1977). 3. Among these authors, abstraction refers to the amount of detail omitted from an explanation. In what follows, I treat abstraction as following this line of thought (see esp. chap. 3). I do not address the idea, prominent especially in the history of empiricism, that properties, concepts, and numbers result from abstraction from concrete instances (i.e., they are abstract objects). Moreover , abstraction should be distinguished from idealization, which describes the idea as including in a model assumptions that are known to be false with respect to a given phenomenon (see Jones 2005). 4. A gene’s genomic context may be understood as the network of regulatory genes involved in regulating the expression of the particular gene, for example, through coding for repressor and activator proteins or microRNAs (Jacob and Monod 1959; He and Hannon 2004). The latter may modulate gene activity on the posttranscriptional level. 5. For Waddington’s research and biographical writings, see, for example, works by Robertson (1977), Hall (1992), S. Gilbert (2000, 2012), Slack (2002), Van Speybroeck (2002), and Peterson (2011, 2016). 6. Notice that canalization is, in fact, not the exact opposite of phenotypic plasticity , since, on the molecular level, developmental robustness of a trait can NOTES TO PAGES 12–22 ▸ 219 be understood as a product of the plastic responses of developmental processes compensating for environmental or genetic variation. Thus, both concepts are relative to the level of description chosen. 7. On the history of the notion of epigenetics, see, for example, works by Wu and Morris (2001), Jablonka and Lamb (2002), Van Speybroeck (2002), Holliday (2002, 2006), Haig (2004, 2012), Ptashne (2007), and Deichmann (2016a). 8. For example, Wu and Morris (2001, 1104) define epigenetics as “the study of changes in gene function that are mitotically and/or meiotically heritable and that do not entail a change in DNA sequence.” On definitions of epigenetics in the 1980s and 1990s, see especially the work of Jablonka and Lamb (2002, 86–88). 9. For a more detailed discussion of these regulatory epigenetic processes involved in development and heredity, see works by Jablonka and Lamb (2005, 2010) and Lamm (2014). 10. For the ecological-evolutionary dimension of epigenetics, see also a special issue in Genetics Research International (for editorial, see Schrey et al. 2012) and chapter 2 in this volume. 11. In other words...


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