Biology Reference
In-Depth Information
14
Afterthoughts as foundations for systems biology
Fred C. Boogerd, Frank J. Bruggeman, Jan-Hendrik S. Hofmeyr and
Hans V. Westerhoff
This topic on the Philosophical Foundations of Systems Biology is the first of its
kind. Several topics on systems biology have been published or will be published
soon. Some of these are text books aimed at teaching and as introductory
texts (Kitano, 2001; Klipp et al., 2005; Alon 2006; Palsson, 2006), others were
multiauthored volumes reporting on systems biology progress (Kitano, 2001;
Kholodenko & Westerhoff, 2004; Kriete & Eils, 2006; Szallasi et al., 2006),
and one focused on the definition of what systems biology is (Alberghina &
Westerhoff, 2005). None of them deals extensively with the philosophical issues
related to and underlying systems biology. For a long time, there have been
a number of treatises on the philosophy of biology (Schaffner, 1994; Hull &
Ruse, 1998; Sterelny & Griffith, 1999; Sober, 1999; Weber, 2005). Many of
these emphasized that biology differs from physics and chemistry because of its
perspectives of evolution and function. Earlier the importance of systems and
the whole were emphasized (Wiener, 1965; Von Bertalanffy, 1976; Savageau,
1976; Atkinson, 1977; Reich & Selkov, 1981).
This topic we have in front of us is special because it came after the genomics
revolution, at a time when frustrations are accumulating on the lack of delivery
of promises by molecular biology and gene sequencing alone. Perhaps this is
a time where the thrust of one paradigm runs out, and where a new science
paradigm is taking over, in a process that is not always smooth and accompanied
by strong reactions by proponents of the earlier paradigms (Kuhn, 1996). Tradi-
tionally, treatises on the philosophy of science have come in the aftermath of the
development of new sciences. An early treatise of the structure (cf. Nagel, 1979)
