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6
Mechanism and mechanical explanation in
systems biology 1
Robert C. Richardson and Achim Stephan
SUMMARY
Mechanistic explanations in cell biology provide a strong case for systems biol-
ogy; for systems biology involves explaining the properties of cells in terms of
the properties and interactions of their molecular constituents. Mechanistic expla-
nations are, essentially, more detailed redescriptions and dynamic explanations
of system behavior, which treat cells (or organisms) as complex biochemical
systems. As an illustration, we apply this approach to the regulation of diauxic
growth of Escherichia coli and the involvement of the lac operon. We dis-
cuss when properties manifested by mechanisms can be considered emergent
properties, and contrast mechanistic explanations with properly reductionistic
explanations.
1 This work began in March 2005, at the Hanse Institute for Advanced Study (HWK) at Delmenhorst
(Germany), in collaboration with Fred Boogerd and Frank Bruggeman. The HWK was a remarkable envi-
ronment, and we acknowledge their support as the prime movers of this paper. The work continued at the
University of Osnabrück in the summer of 2005. In many ways, Boogerd and Bruggeman deserve to be
coauthors of this paper. We certainly would not, and could not, have done this work without our four-way
collaboration. We do intend to develop another paper with them in which these themes are worked out in
a more satisfactory way. RCR also would like to thank the Taft Faculty Committee at the University of
Cincinnati for supporting the project.
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