Biology Reference
In-Depth Information
development,
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in particular molecular biology, (gen)omics and, most recently,
systems biology. This volume is a most welcome first attempt to correct this bias.
However, we should be aware from the outset that articulating a full-fledged
philosophy of systems biology will be a formidable task indeed. The challenge
is for a community of philosophers with the necessary critical mass to learn to
collaborate with systems biologists (who will have to accept them as 'partners'
of some kind!) and master the relevant technical literature, which is quickly
growing, in sufficient detail. This cannot be expected to happen overnight. But
the challenge is certainly a seducing one. A cursory look at the literature in
this burgeoning field
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suffices to conclude that with a few notable exceptions,
systems biology remains largely uninformed of the results of contemporary
philosophy of science, although many of the issues - e.g., data- vs. hypothesis-
or theory-driven research, reduction or emergence, realism vs. simplification or
idealization regarding models and theories, mere aggregates vs. systems - cry
out for philosophical analysis. The good news for philosophers is that they will
not have to start from scratch: many if not most of the relevant issues will not
take them by surprise as they will already be more or less familiar from other
contexts (cf. Boogerd et al., 2005; O'Malley & Dupré, 2005).
Obvious first questions for philosophers to ask about systems biology con-
cern its 'topography.' It is generally accepted that systems biology not only
has several roots, but also consists of two branches: 'bottom-up' and 'top-
down' systems biology. After a preliminary sketch of the layout of the field
(Section 2) and a survey of its main roots - models of metabolic and signaling
pathways (Section 3), biological cybernetics and mathematical systems analysis
(Section 4), and 'omics' (Section 5) - our main concern will be to reconstruct
the theoretical links between the different branches of systems biology in order
to present the current structure of the field (Sections 6 and 7). In addition, we
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Development and application of scientific results in general are 'messy' areas that have traditionally been
disregarded by philosophers (and the scientists echoing them) operating under the Platonist/Cartesian illusion
that 'pure' - i.e., physical (see, e.g., Kitano, 2002b) and ultimately mathematical - foundations are to be
privileged; see Wimsatt (in press) for a forceful rebuttal. More generally, it would seem that the philosophy of a
field like systems biology, which relies heavily on massive data acquisition and has 'emergence' written on its
banner, could benefit from adopting an account of explanation and unification that centers on “cooperation and
communication among theoretical and phenomenological equals, rather than on imperialism and competition
for primacy and fundamentality, which reduces or replaces one theory by another or trivializes one explanandum
as epiphenomenal to another” (Griesemer, 2006, p. 5). In this vein, we interpret the search for 'foundations'
suggested in the title of this volume as a search for conceptual filiations (resulting, hopefully, in conceptual
clarification) rather than for epistemic priority.
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Including the rhetoric of promise that accompanies its incipient stage, which is often much more daring than
one would expect after the disillusionment that followed the announcement of the results of the Human Genome
Project (see, e.g., Lewontin, 1997; Newman, 2003). To guarantee their empirical adequacy, philosophical
reflections on systems biology will soon have to be complemented by both professional historical research into
its antecedents and investigations of the social, institutional, and economic framing of the field by researchers
in science, technology, and society studies.
