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'
14. Afterthoughts as foundations for Systems Biology