| Preface | |
| Pt. I | Scientific Discovery and Rationality | |
| Ch. 1 | Cognitive strategies and Scientific Discovery | 3 |
| 1 | Rationalizing Scientific Discovery | 3 |
| 2 | Procedural Rationality | 11 |
| Ch. 2 | Complex Systems and Mechanistic Explanations | 17 |
| 1 | Mechanistic Explanation | 17 |
| 2 | Decomposition and Localization | 23 |
| 3 | Hierarchy and Organization | 27 |
| 4 | Conclusion: Failure of Localization | 31 |
| Pt. II | Emerging Mechanisms | |
| Introduction | 35 |
| Ch. 3 | Identifying the Locus of Control | 39 |
| 1 | Introduction: Identifying System and Context | 39 |
| 2 | External Control: The Environment as a Control | 41 |
| 3 | Internal Control: The System as a Control | 47 |
| 4 | Fixing on a Locus of Control: The Cell in Respiration | 51 |
| 5 | Conclusion: Localization of Function | 59 |
| Ch. 4 | Direct Localization | 63 |
| 1 | Introduction: Relocating Control | 63 |
| 2 | Phrenology and Cerebral Localization | 65 |
| 3 | Competing Models of Cellular Respiration | 72 |
| 4 | Conclusion: Direct Localization and Competing Mechanisms | 88 |
| Ch. 5 | The Rejection of Mechanism | 93 |
| 1 | Introduction: Mechanism and Its Opponents | 93 |
| 2 | Flourens and the Integrity of the Nervous System | 95 |
| 3 | The Vitalist Opposition to Mechanistic Physiology | 99 |
| 4 | Conclusion: Settling for Descriptions | 113 |
| Pt. III | Elaborating Mechanisms | |
| Introduction | 119 |
| Ch. 6 | Complex Localization | 125 |
| 1 | Introduction: Constraints on Localization | 125 |
| 2 | Top-Down Constraints | 128 |
| 3 | Bottom-Up Constraints | 138 |
| 4 | Conclusion: The Rise and Decline of Decomposability | 145 |
| Ch. 7 | Integrated Mechanisms | 149 |
| 1 | Introduction: Replacing a Direct Localization | 149 |
| 2 | Direct Localization of Fermentation in Zymase | 153 |
| 3 | A Complex Linear Model of Fermentation | 156 |
| 4 | An Integrated System Responsible for Fermentation | 163 |
| 5 | Conclusion: The Discovery of Integration | 168 |
| Ch. 8 | Reconstituting the Phenomena | 173 |
| 1 | Introduction: Biochemical Genetics | 173 |
| 2 | Classical Genetics | 175 |
| 3 | Developmental Genetics | 181 |
| 4 | One Gene/One Enzyme | 188 |
| 5 | Conclusion: Reconstituting the Phenomena | 192 |
| Pt. IV | Emergent Mechanism | |
| Introduction | 199 |
| Ch. 9 | "Emergent" Phenomena in Interconnected Networks | 202 |
| 1 | Introduction: Dispensing with Modules | 202 |
| 2 | Hierarchical Control: Hughlings Jackson's Analysis of the Nervous System | 203 |
| 3 | Parallel Distributed Processing and Cognition | 210 |
| 4 | Distributed Mechanisms for Genomic Regulation | 223 |
| 5 | Conclusion: Mechanistic Explanations without Functional Decomposition and Localization | 227 |
| Ch. 10 | Constructing Causal Explanations | 230 |
| 1 | Decomposition and Localization in Perspective | 230 |
| 2 | Four Constraints on Development | 234 |
| 3 | Conclusion: Looking Forward | 243 |
| Notes | 245 |
| References | 257 |
| Index | 281 |
