Contents

  1. Preface xi
  2.   1 Microbial Design 1
  3. How to Read; Theoretical Background; The Design of Metabolism
  4. PART 1: THEORETICAL BACKGROUND
  5.   2 Forces of Design 11
  6. What Is Fitness?; The Difficulty of Measuring Fitness
  7.   3 Comparison and Causality 17
  8. Comparative Predictions; Evolutionary Response versus Organismal Response; Fundamental Forces and Partial Causes; Causal Inference; Structure and Notation of Comparative Predictions; Recap and Goal
  9.   4 Brief Examples 29
  10. Metabolism and Growth Rate; Support by Empirical Test; Patch Lifespan and Microbial Cancer; Heterogeneity in Public Goods; Stage-Dependent Growth; Summary
  11.   5 Theory: Forces 43
  12. Tragedy of the Commons; Similarity Selection and Kin Selection; Tradeoffs and Marginal Values; Repression of Competition; Heterogeneity in Vigor and Public Goods; Demography and Reproductive Value; Stage-Dependent Traits in Life Cycle; The Three Measures of Value; Scaling of Time and Space; Variable Environments
  13.   6 Theory: Traits 83
  14. Nature of Traits; Modification of Traits; Origin of Traits
  15.   7 Theory: Control 95
  16. Error-Correcting Feedback and Robustness; Principles of Control; Error Correction and Signal Amplification; Robustness to Process Uncertainty; Responsiveness versus Homeostasis; Sensors; Control Tradeoffs
  17.   8 Studying Biological Design 115
  18. PART 2: THE DESIGN OF METABOLISM
  19.   9 Microbial Metabolism 121
  20. 10 Growth Rate 123
  21. Comparative Hypotheses in the Study of Design; Testing Comparative Predictions; Comparative Predictions about Growth Rate; Comparative Predictions about Tradeoffs
  22. 11 Thermodynamics: Biochemical Flux 141
  23. Entropy Production; Force and Resistance Determine Flux; Mechanisms of Metabolic Flux Control
  24. 12 Flux Modulation: Driving Force 155
  25. Near-Equilibrium Glycolysis; Overflow Metabolism: Mechanisms; Overflow Metabolism: Design Puzzles; Evolutionary Timescale; Alternative Glycolytic Pathways
  26. 13 Flux Modulation: Resistance 189
  27. Resistance Impedes Flux; Mechanisms to Alter Resistance and Flux; Genetic Drift; Challenges in Control Design; Problems of Flux Modulation; Limitations and Prospects
  28. 14 Variant Pathways 205
  29. Glycolytic Yield; Final Electron Acceptors; Weak Redox Gradients; Electron Flow between Cells; Alternative Carbon Sources; Hierarchical Usage of Complex Carbohydrates; Puzzles of Design
  30. 15 Tradeoffs 227
  31. Biophysical Constraints and Cellular Allocation; Exploration versus Exploitation versus Regulation; Thermodynamics and Biochemical Flux; Fitness Components and Life History; Warfare versus Productive Traits; Cooperative Traits; Timescale Tradeoffs; Bet-Hedging Tradeoffs; Control Tradeoffs; Summary
  32. 16 Predictions: Overflow Metabolism 253
  33. Comparative Predictions and Partial Causes; Background; Proteome Limitation; Membrane Space Limitation; Response to Environmental Challenge; Summary
  34. 17 Predictions: Diauxie, Electrons, Storage 291
  35. Switching between Food Sources; Distributed Electron Flux; Storage When Resources Fluctuate; Challenges in the Study of Design
  36. 18 Design Revisited 331
  37. References 333
  38. Index 369