Biology Reference
In-Depth Information
2
The methodologies of systems biology
Hans V. Westerhoff and Douglas B. Kell
SUMMARY
In this topic on philosophical aspects of systems biology, this chapter sum-
marizes the philosophical status of a variety of sciences. Biology, physics and
molecular biology offer particular contrast here. It is contended that philos-
ophy and methodology should be determined substantially by the degree of
complexity of the system under study. Some of the new experimental methods
that have made systems biology possible are summarized. Research strategies
that claim to be systems biology yet approach the topic in different ways are
described. Inductive reasoning and the development and exploitation of suitable
technologies are important parts of the systems biology agenda but are not them-
selves hypothesis-dependent science. A new methodology for systems biology
is sketched that spirals in an iterative manner between experiments and theory
but makes inherent use of mathematics in ways that are new to the life sciences.
It is shown that the construction of a computer replica of parts of living systems
has become possible and that the 'silicon cell' strategy enables the calculation
of emergent properties. This may then serve as a basis for subsequent discus-
sions with philosophers of science about how new and unique the philosophical
foundations of systems biology are or should be.
1. THE METHODOLOGY AND PHILOSOPHICAL FOUNDATIONS
OF THE VARIOUS SCIENCES
1.1. Physics
According to classical philosophy of science (e.g. Carnap, 1966; Nagel, 1961),
science advances by an iteration between the world of mental constructs (ideas,
