Sober Elliott,2024-The Philosophy of Evolutionary Theory Concepts Inferences and Probabilities

List of Figures page x
List of Tables xiii
Preface xv
Acknowledgments xviii
1 A Darwinian Introduction 1
1.1 Common Ancestry 1
1.2 Species 3
1.3 Evolution 3
1.4 Divergence and Opportunism 5
1.5 Selection – Natural, Artificial, Sexual, and Bi-leveled 6
1.6 Heredity 9
1.7 Gradualism 12
1.8 Mutation 13
1.9 Was Darwin “Illogical”? 14
2 Fitness and Natural Selection 16
2.1 Malthusian Struggle and Competition 16
2.2 Fitness 19
2.3 Fitness Refined 23
2.4 Estimating Fitnesses 27
2.5 Type and Token 30
2.6 Trait Fitnesses Are Averages 31
2.7 Fitness ≠ Advantageousness 32
2.8 Improvement in Fitness 35
2.9 The Groups Above, the Genes Below 38
3 Units of Selection 39
3.1 Darwin on Altruism and Group Selection 39
3.2 Simpson’s Paradox 42
Contents
viii Contents
3.3 The Problem of Origination 46
3.4 The Evolution of Altruism and Selfishness in Groups of Size 2 48
3.5 Fortuitous Group Benefits and the Definition of a Group 52
3.6 Reciprocal Altruism 55
3.7 Inclusive Fitness, Then and Now 58
3.8 Community Selection 60
3.9 Group Selection without Altruism 62
3.10 A Third Unit of Selection – Intragenomic Conflict 64
3.11 Species Selection and Cultural Group Selection 67
3.12 Reductionism 69
3.13 Two Conventionalisms 71
4 Common Ancestry 77
4.1 Darwin on Common Ancestry 77
4.2 What Is Ancestry? 79
4.3 The Law of Likelihood 81
4.4 When Common Ancestry Has the Higher Likelihood 88
4.5 Matches Sometimes Provide Evidence Against a Common Cause 93
4.6 Matches and Strength of Evidence 94
4.7 Hypothetico-Deductivism 98
4.8 Mismatches 99
4.9 Correlations to the Rescue? 101
4.10 Concluding Comments 108
5 Drift 110
5.1 The Extinction of Family Names 111
5.2 Strict Neutrality 114
5.3 The Molecular Clock 117
5.4 Null Hypotheses 119
5.5 Alternatives to the Strictly Neutral Theory 125
5.6 When Drift and Selection Both Affect a Trait’s Evolution 127
5.7 Drift as Cause and Process 131
5.8 Selection, Drift, and Domination 134
6 Mutation 141
6.1 Darwin and Asa Gray 141
6.2 Two Experiments 144
6.3 The Evolution of Mutation Rates 149
6.4 Darwin’s Gradualism 152
6.5 Fisher’s Geometric Argument 155
Contents ix
6.6 From One Mutation to a Sequence of Mutations 161
6.7 Genome-Wide Association Studies 164
6.8 Concluding Comments 164
7 Taxa and Genealogy 167
7.1 Darwin’s Hope 167
7.2 Ranks and Hierarchy 168
7.3 Three Systematic Philosophies 169
7.4 Taxa Are Tokens, Not Types 175
7.5 Essentialism 176
7.6 The Taxonomic Status of Ancestors 179
7.7 Species 180
7.8 Race 182
7.9 Inferring Phylogenies 190
7.10 Inferring the Character States of Ancestors 196
7.11 Why Use Likelihood to Evaluate Cladistic Parsimony? 200
7.12 Statistical Consistency 202
8 Adaptationism 206
8.1 Darwin’s Formulation 206
8.2 What Is Adaptationism? 210
8.3 How Genetics Can Get in the Way 213
8.4 Ancestral Influence (aka “Phylogenetic Inertia”) 217
8.5 Optimality Models 221
8.6 The Chronological-Order Test of Adaptation Hypotheses 225
8.7 Testability and Research Programs 227
9 Big-Picture Questions 230
9.1 Are There Laws of Evolution? 230
9.2 Determinism, Indeterminism, and Objective Probabilities 235
9.3 Must Micro-indeterminism Percolate Up? 239
9.4 Objective Interpretations of Probability 240
9.5 Contingency, Inevitability, and Sensitivity to Initial Conditions 244
9.6 Evolution and Information Loss 249
References 258
Index 281