The methodologies of systems biology

In this book on philosophical aspects of systems biology, this chapter summarizes the philosophical status of a variety of sciences. Biology, physics and molecular biology offer particular contrast here. It is contended that philosophy 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 themselves 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 discussions with philosophers of science about how new and unique the philosophical foundations of systems biology are or should be.