Chapter 1: Towards philosophical foundations of Systems Biology: introduction

Chapter 2: The methodologies of systems biology

Chapter 3: Methodology is Philosophy

Chapter 4: How can we understand metabolism?

Chapter 5: On building reliable pictures with unreliable data: An evolutionary and developmental coda for the new systems biology

Chapter 6: Mechanism and mechanical explanation in systems biology

Chapter 7: Theories, models, and equations in systems biology

Chapter 8: All models are wrong: … some more than others

Chapter 9: Data without models merging with models without data

Chapter 10: The biochemical factory that autonomously fabricates itself: A systems biological view of the living cell

Chapter 11: A systemic approach to the origin of biological organization

Chapter 12: Biological mechanisms: organized to maintain autonomy

Chapter 13: The disappearance of function from ‘self-organizing systems’

Chapter 14: Afterthoughts as foundations for systems biology

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