Reasoning in Biological Discoveries: Essays on Mechanisms, Interfield Relations, and Anomaly Resolution (Cambridge Studies in Philosophy and Biology)

Reasoning In Biological Discoveries Brings Together A Series Of Essays, Which Focus On One Of The Most Heavily Debated Topics Of Scientific Discovery. Collected Together And Richly Illustrated, Darden's Essays Represent A Groundbreaking Foray Into One Of The Major Problems Facing Scientists And Philosophers Of Science. Divided Into Three Sections, The Essays Focus On Broad Themes, Notably Historical And Philosophical Issues At Play In Discussions Of Biological Mechanism; And The Problem Of Developing And Refining Reasoning Strategies, Including Interfield Relations And Anomaly Resolution. Darden Summarizes The Philosophy Of Discovery And Elaborates On The Role That Mechanisms Play In Biological Discovery. Throughout The Book, She Uses Historical Case Studies To Extract Advisory Reasoning Strategies For Discovery. Examples In Genetics, Molecular Biology, Biochemistry, Immunology, Neuroscience And Evolutionary Biology Reveal The Process Of Discovery In Action.--publisher's Website. Thinking About Mechanisms /with Peter Machamer And Carl F. Craver -- Discovering Mechanisma In Neurobiology: The Case Of Spatial Memory / With Carl F. Craver -- Strategies In The Interfield Discovery Of The Mechanism Of Protein Synthesis /with Carl F. Craver -- Relationsamong Fields: Mendelian, Cytological, And Molecular Mechanisms -- Interfield Theories /with Nancy Maull -- Theory Construction In Genetics / Relations Among Fields In The Evolutionary Synthesis / Selction Type Theories / With Joseph A. Cain -- Strategies For Anaomaly Resolution: Diagnosis And Redesign -- Exemplars, Abstractions And Anaomalies: Representations And Theory Change In Mendelian And Molecular Genetics -- Strategies For Anaomaly Resolution In The Case Of Adaptive Mutation -- Strategies For Discovering Mechanisms: Construction, Evaluation, Revision. Lindley Darden ; Illustrated By Darren Hudson Hick. Includes Bibliographical References (p. 313-335) And Index. Cover 1 Half-title 3 Series-title 5 Title 7 Copyright 8 Dedication 9 Contents 11 Long Contents 13 Introduction 13 Part I: Biological mechanisms 13 Chapter 1: Thinking About Mechanisms, with Peter Machamer and Carl F. Craver 13 Chapter 2: Discovering Mechanisms in Neurobiology: The Case of Spatial Memory with Carl F. Craver 13 Chapter 3: Strategies in the Interfield Discovery of the Mechanism of Protein Synthesis with Carl F. Craver 14 Chapter 4: Relations Among Fields: Mendelian, Cytological, and Molecular Mechanisms 14 Part II: Reasoning strategies: relating fields, resolving anomalies 14 Chapter 5: Interfield Theories with Nancy Maull 14 Chapter 6: Theory Construction in Genetics 15 Chapter 7: Relations Among Fields in the Evolutionary Synthesis 15 Chapter 8: Selection Type Theories with Joseph A. Cain 15 Chapter 9: Strategies for Anomaly Resolution: Diagnosis and Redesign 16 Chapter 10: Exemplars, Abstractions, and Anomalies: Representations and Theory Change in Mendelian and Molecular Genetics 16 Chapter 11: Strategies for Anomaly Resolution in the Case of Adaptive Mutation 16 Part III: Discovering mechanisms: construction, evaluation, revision 17 Chapter 12: Strategies for Discovering Mechanisms: Construction, Evaluation, Revision 17 List of Figures 19 List of Tables 21 Acknowledgments 23 Introduction 27 I Biological Mechanisms 37 1 Thinking About Mechanisms 39 1.1 Introduction 39 1.2 Mechanisms 40 1.3 Ontic status of mechanisms (ontic adequacy) 42 1.3.1 Activities and Causing 44 1.3.2 Activities and Laws 45 1.4 Example of a mechanism (descriptive adequacy) 46 1.4.1 Set-Up Conditions 48 1.4.2 Termination Conditions 50 1.4.3 Intermediate Activities 50 1.5 Hierarchies, bottoming out, mechanism schemata and sketches 51 1.5.1 Bottoming Out 52 1.5.2 An Historical Aside 53 1.5.3 Mechanism Schemata and Sketches 54 1.6 Case study: discovering the mechanism of protein synthesis 57 1.7 Activities, intelligibility, and explanation (epistemic adequacy) 60 1.8 Reduction 61 1.9 Conclusion 62 References 63 2 Discovering Mechanisms in Neurobiology: The Case of Spatial Memory 66 2.1 Introduction 66 2.2 Mechanisms and their organization 67 2.2.1 Mechanisms 67 2.2.2 Organization 67 2.2.3 Levels 71 2.3 Describing mechanisms 73 2.4 Constraints on the organization of mechanisms 74 2.4.1 Characterizing the Phenomenon 75 2.4.2 Componency Constraints 77 2.4.3 Spatial Constraints 78 2.4.4 Temporal Constraints 80 2.5 Experiments for testing hierarchical mechanisms 81 2.5.1 Bottom-Up Inhibitory Experiments 83 2.5.2 Top-Down Excitatory Experiments 84 2.5.3 Multilevel Experiments 85 2.6 Conclusion 87 References 88 3 Strategies in the Interfield Discovery of the Mechanism of Protein Synthesis 91 3.1 Introduction 91 3.2 Mechanisms, schemata, strategies 93 3.3 Discovering the mechanism of protein synthesis 1953–1965: biochemistry and molecular biology 94 3.3.1 Diagrams of 1953–1954 96 3.3.2 Molecular Biological Work: Three-Dimensional Structure 100 3.3.3 Draining the Biochemical Bog 100 3.3.4 Adaptor RNA and Soluble RNA to Transfer RNA 101 3.3.5 Anomalies for the Ribosome as Template 105 3.3.6 Rate Anomaly and Messenger RNA 106 3.3.7 Summary of Protein Synthesis Case 109 3.4 Strategies for discovering mechanisms 110 3.4.1 Productive Continuity 111 3.4.2 Schema Instantiation 112 3.4.3 Forward and Backward Chaining to Find Productive Continuity 114 3.4.4 Activity-Enabling Properties of Entities 115 3.4.5 Activity Consequences 117 3.4.6 Activity Signatures of Entities 118 3.4.7 Entity Signatures of Activities 118 3.5 Conclusion 119 References 119 4 Relations Among Fields: Mendelian, Cytological, and Molecular Mechanisms 124 4.1 Introduction 124 4.2 Tthe fields of mendelian genetics, molecular biology, and their neighbors 126 4.3 Previous work on the relations between mendelian genetics and molecular biology 129 4.4 Mechanisms, mechanism schemas, mechanism sketches 135 4.5 Historical developments: discovering hereditary mechanisms 138 4.6 Contemporary account of the relations among hereditary mechanisms 144 4.7 Conclusion 146 References 147 II Reasoning Strategies: Relating Fields, Resolving Anomalies 151 5 Interfield Theories 153 5.1 Introduction 153 5.2 The generation of interfield theories 158 5.3 The chromosome theory of mendelian heredity 161 5.4 The operon theory and theory of allosteric regulation 164 5.5 The function of interfield theories 169 5.6 Conclusion 169 References 172 6 Theory Construction in Genetics 175 References 193 7 Relations Among Fields in the Evolutionary Synthesis 196 7.1 Introduction 196 7.2 The synthetic theory 197 7.3 Other theories, other levels 199 7.4 The field of genetics 201 7.5 The synthetic theory versus interfield theories 204 7.6 Conclusion 206 References 206 8 Selection Type Theories 208 8.1 Introduction 208 8.2 The concept of an abstraction 209 8.3 The process of natural selection 212 A. Preconditions for Natural Selection 212 B. Selective Interaction 214 C. Effect 217 D. and E. Longer-Range Effects 217 8.4 Abstraction for natural selection 218 A. Preconditions 218 B. Interaction 218 C. Effect 219 D. Longer-Range Effect 219 E. Even Longer-Range Effect 219 8.5 Clonal selection theory for antibody formation 221 A. Preconditions 222 B. Interaction 223 C. Effect 223 D. Longer-Range Effect 223 E. Even Longer-Range Effect 223 8.6 Selection theories for brain function 223 A. Preconditions 225 B. Interaction 225 C. Effect 225 D. Longer-Range Effect 225 E. Even Longer-Range Effect 225 8.7 Conclusion 227 References 230 9 Strategies for Anomaly Resolution: Diagnosis and Redesign 233 9.1 Introduction 233 9.2 Previous work on anomalies 236 9.3 Strategies for anomaly resolution 237 9.3.1 Confirm Anomalous Data or Problem 238 9.3.2 Localize the Anomaly 238 9.3.3 Alternative Ways of Removing an Anomaly 240 9.3.4 Assessing the Hypotheses to Resolve the Anomaly 243 9.3.5 Unresolved Anomalies 243 9.4 Representation and implementation of anomaly resolution in genetics 244 9.4.1 Representation of a Scientific Theory 244 9.4.2 Anomaly Resolution: Localization 247 9.4.3 Extensions to the Current Implementation 249 9.5 Conclusion 251 References 251 10 Exemplars, Abstractions, and Anomalies: Representations and Theory Change in Mendelian and Molecular Genetics 255 10.1 Introduction 255 10.2 Exemplars, abstractions, and diagrams 256 10.3 Anomalies and theory change 259 10.4 Mendelian genetics and linkage anomalies 261 10.5 Molecular genetics and reverse transcriptase 262 10.6 Conclusion 270 References 271 11 Strategies for Anomaly Resolution in the Case of Adaptive Mutation 274 11.1 Introduction 274 11.2 “The origin of mutants” (cairns, overbaugh, and miller 1988) 275 11.3 For what was directed mutation an anomaly? 278 11.4 Theoretical perspectives in responses to anomalies 281 11.5 Adequacy of the empirical evidence for adaptive mutation 282 11.6 Proposed mechanisms for adaptive mutation 284 11.7 Implications for strategies for anomaly resolution 287 11.8 Conclusion 290 References 290 III Discovering Mechanisms: Construction, Evaluation, Revision 295 12 Strategies for Discovering Mechanisms: Construction, Evaluation, Revision 297 12.1 Introduction 297 12.2 Characterization of mechanisms 299 12.3 Strategies for construction 310 12.3.1 Schema Instantiation 310 12.3.2 Modular Subassembly 312 12.3.3 Forward/Backward Chaining 313 12.4 Strategies for evaluation: how possibly to how plausibly to how actually 315 12.4.1 Evaluating and Improving Sketches 317 12.4.2 Evaluation Strategies for Assessing Possibility/Plausibility 318 12.4.3 Consideration of Rivals as an Evaluative Strategy 320 12.4.4 Experimental Strategies for Discovering How Actually the Mechanism Operates 321 12.4.5 Strategies for Finding Scope 323 12.4.6 Strategies for Evaluating Context 324 12.4.7 Comparison to Previous Work on Strategies for Theory Evaluation 325 12.5 Strategies for revision 327 12.6 Conclusion 332 References 334 Bibliography 339 Index 363 Reasoning in Biological Discoveries brings together a series of essays written and co-written by Lindley Darden which focus on one of the most heavily debated topics of scientific discovery today. Darden summarizes the philosophy of discovery and elaborates the role that mechanisms play in biological discovery