Toward a Philosophy of Systems Biology

Abstract

Systems Biology: Philosophical Foundations is an insightful and timely book that fuses scientific and philosophical insights in a highly effective and mostly accessible manner. Numerous books address scientific aspects of the emerging and expansive field of systems biology (SB) but this is the first to deal specifically with its underlying philosophical issues. Contributors include life scientists as well as philosophers of science, who, besides introducing readers to the field, address topics ranging from the nature of explanation to the definition of life. Although the editors have divided the various chapters into three themes (SB Research Programmes, Theories and Models, and Organization), we found it helpful to group the contributions slightly differently and let certain chapters appear in more than one theme. Theme One consists of overviews, background, and characterizations of SB. Chapters 1, 2, 9, and 14 are prime expositions of these topics, which are rooted in an appreciation of the limitations of biochemical, molecular biological, and genomic approaches for the attainment of deep biological understanding. Chapter 9 (Krohs and Callebaut) sets out a clear and compelling “topography” of SB and its three roots, which are helpfully connected to top-down and bottom-up approaches. This description, along with the characterizations in Chs. 1 and 2, more accurately illuminates the variety of SB approaches than do earlier typological attempts (e.g., O’Malley and Dupre 2005). Theme Two—the bulk of the book—is concerned with the nature of system-level explanation and its implications for the philosophy of science. Chapter 1 in particular exposes the shortfalls of existing philosophy of science and biology— a view contested here only by Ch. 3 (Sulman)—and argues that mechanistic explanation trumps narrowly construed reductionist explanation. Mechanisms are discussed in accord with accounts that now dominate the philosophical literature. These favor explanations based on multilevel regularity producing mechanisms over mereologically or theoretically reductionist explanations (e.g., Bechtel and Richardson 1993; Machamer et al. 2000; Glennan 2002). The distinctive feature of such mechanistic explanations and their relevance for systems biology is that constitutive and interacting elements of the mechanism must be dealt with in their systemic context. Chapter 6 (Richardson and Stephan) expands on mechanistic explanations as highly detailed and dynamic redescriptions of system behaviors in terms of the context-dependent behaviors of their parts (see also Boogerd et al. 2005). These authors raise but do not resolve the questions of what exactly levels are and what the relationship is between organizational and explanatory levels. Chapter 2 (Westerhoff and Kell) extends the mechanism discussion to argue that emergent properties such as life are calculable, although the calculations involved relate necessarily to nonlinear interactions. In Ch. 7 Schaffner proposes a more abstract account of mechanisms that may capture “emergent simplifications” of systems (p. 155). Although it would have been good to see more systems-biologic interrogation of current philosophies of mechanism, the book makes it clear that a common orientation to mechanism is conducive to profitable engagement between biologists and philosophers of science. An associated general topic about which there is less consensus is the issue of what theories, models, and simulations are. The status of theories in biology is an issue raised in Ch. 2 (Westerhoff and Kell) and is one that recurs elsewhere in the book. Theories have often been troublesome entities in the philosophy of biology, due to the nature