Contents // Acknowledgments page xii // Introduction 1 // 1 The Enduring Legacy of Aristotle: The Battle over Life as // Self-Organization or (Genetic-Based) Reproduction 8 // 1.1 Overview 8 // 1.2 Aristotle on the Nature of Life: Nutrition Versus Reproduction 10 // 1.3 Classical Mechanism about Life: From Optimism to Quiet // Desperation 15 // 1.4 Darwin to the Rescue? 18 // 1.5 Here We Go Again: Aristotelian Roots of Contemporary // Accounts of the Nature and Origin(s) of Life 21 // 1.5.1 Metabolism-Based Versus Evolution-Based Definitions // of the Nature of Life 22 // 1.5.2 Metabolism-First Versus Genes-First Theories // of the Origin(s) of Life 25 // 1.6 Concluding Thoughts 29 // 2 Why Life Cannot Be Defined 33 // 2.1 Overview 33 // 2.2 Popular Definitions of Life 36 // 2.2.1 Thermodynamic Definitions 36 // 2.2.2 Metabolic Definitions 37 // 2.2.3 Evolutionär)’ Definitions 40 // 2.2.4 Defining Life as Self-Organized Complexity 43 // 2.3 The Problem with Definitions 45 // 2.3.1 Logical Character of Definition 45 // 2.3.2 Limits of Definition 50 // x // Contents // 2.3.3 Diagnosing ihe Problem: A Defective Theory of Meaning // and Reference 53 // 2.3.4 Why Natural Kinds Cannot Be “Defined” 55 // 2.3.5 Is life an Exception to the Rule? 59 // 2.4 Concluding Thoughts 61 // 3 What Is a Scientific Theory? 63 // 3.1 Overview 63 // 3.2 The Syntactic Conception of Scientific Theories 65 // 3.3 The Semantic Conception of Scientific Theories 68 // 3.4 Scientific Theories and Definitions
73 // 3.4.1 Scientific Theories Do Not “Define” Natural Kinds 74 // 3.4.2 Nonstandard Definitions Do Not “Define” Scientific // Theories 76 // 3.5 Concluding Thoughts 79 // 4 How Scientific Theories Develop 82 // 4.1 Overview 82 // 4.2 How Scientifically Fruitful Ontologies Develop: Content Matters 84 // 4.3 The Goldilocks Level of Abstraction 88 // 4.4 The Threat Posed by Premature Commitment to Ontologies 93 // 4.5 The Monist (Versus Pluralist) Stance 98 // 4.6 Concluding Thoughts 102 // 5 Challenges for a Universal Theory of Life 105 // 5.1 Overview 105 // 5.2 The Magnitude of the A = l Problem of Biology 107 // 5.3 Microbes: The Most Representative and Least Well Understood // Form of Earth Life 114 // 5.3.1 Planet of the Microbes 115 // 5.3.2 A Brief History of Misunderstandings and Surprises 118 // 5.4 The Problem of Contingencies and the Origin(s) of Life 120 // 5.4.1 A Plague of Contingencies (on Both the SM World and the // RNA World) 123 // 5.4.2 The Origin Versus Nature Problem 127 // 5.5 Concluding Thoughts 130 // 6 Rethinking the Traditional Paradigm for Life: Lessons from the World // of Microbes 132 // 6.1 Overview 132 // 6.2 Evolution Viewed Through the Lens of the Microbial World 133 // 6.2.1 The Concept of a Biological Species and the Tree of Life 134 // Contents xi // 6.2.2 Is Lamarck Hiding in the Shadows? 138 // 6.3 The Living Individual Viewed Through the Lens of the // Microbial World 143 // 6.3.1 Is the Host-Microbiome Complex (Holobiont) // a Living
Thing? 146 // 6.3.2 Biofilms: Aggregates of Cells or Living Individuals? 149 // 6.3.3 Could Rock-Powered Ecosystems Be Living Things? 155 // 6.4 Concluding Thoughts 159 // 7 Artificial Life: Could ALife Solve the N =1 Problem? 161 // 7.1 Overview 161 // 7.2 Soft ALife: Digital Organisms? 161 // 7.3 Hard ALife: Living Robots? 164 // 7.4 Synthetic Biology: Creating Novel Life in the Laboratory? 167 // 7.5 Concluding Thoughts 170 // 8 Searching for Extraterrestrial Life Without a Definition or Universal // Theory of Life 172 // 8.1 Overview 172 // 8.2 A Case Study: The Viking Missions to Mars 172 // 8.3 The Role of Anomalies in Scientific Discovery’ 176 // 8.4 Searching for Anomalies Using Tentative (Versus Defining) // Criteria 184 // 8.5 Concluding Thoughts 193 // 9 A Shadow Biosphere: Alien Microbes on Earth? 195 // 9.1 Overview 195 // 9.2 How Scientifically Plausible Is a Shadow Biosphere? 196 // 9.2.1 Did Life Originate Only Once on Earth? 197 // 9.2.2 Could the Present-Day Earth Be Host to a Shadow // Biosphere? 201 // 9.3 If They Exist, Why Have We Not Found Them? 206 // 9.3.1 Limitations to Microscopy 206 // 9.3.2 Limitations to Cultivation 207 // 9.3.3 Limitations to Metagenomic Methods 208 // 9.4 Potentially Biological Anomalies: Have We Already // Encountered Them ? 211 // 9.5 Concluding Thoughts 215 // Conclusion 217 // References 220 // Index 243