Introduction -- 1. Towards philosophical foundations of Systems Biology: Introduction -- Research programs of Systems Biology -- 2. The methodologies of Systems Biology -- 3. Methodology is Philosophy -- 4. How can we understand metabolism? -- 5. On Building Reliable Pictures with Unreliable Data: an Evolutionary and Developmental Coda for the New Systems Biology? -- Theory / models -- 6. Mechanism and mechanical explanation in cell biology -- 7. Theories, Models, and Equations in Systems Biology -- 8. All models are wrong ... some more than others -- 9. Data without models merging with models without data -- Organization in biological systems -- 10. The biochemical factory that autonomously fabricates itself: a systems-biological view of the living cell -- 11. A systemic approach to the origin of biological organization -- 12. Organization and biological mechanisms: organized to maintain autonomy -- 13. The disappearance of function from 'self-organizing systems' -- Conclusion -- 14. Afterthoughts as foundations for Systems Biology.

Publisher description: Systems biology is a vigorous and expanding discipline, in many ways a successor to genomics and perhaps unprecedented in its combination of biology with a great many other sciences, from physics to ecology, from mathematics to medicine, and from philosophy to chemistry. Studying the philosophical foundations of systems biology may resolve a longer standing issue, i.e., the extent to which Biology is entitled to its own scientific foundations rather than being dominated by existing philosophies.