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.