The emergence of life. From chemical origins to synthetic biology

Preface page xi Acknowledgments xiii List of books on the origin of life xiv 1 Conceptual framework of research on the origin of life on Earth 1 Introduction 1 Determinism and contingency in the origin of life 4 Only one start – or many? 10 The anthropic principle, SETI, and the creationists 12 Questions for the reader 16 2 Approaches to the definitions of life 17 Introduction 17 A historical framework 19 The visit of the Green Man 23 Main operational approaches to the origin of life 26 I. The “prebiotic” RNA world 27 II. The compartmentalistic approach 29 III. The “prebiotic metabolism” approach 31 Concluding remarks 36 Questions for the reader 37 3 Selection in prebiotic chemistry: why this . . . and not that? 38 Introduction 38 From Oparin to Miller – and beyond 40 Other sources of organic molecules 46 Miller’s α-amino acids: why do they form? 50 Some notes on homochirality 52 Concluding remarks 56 Questions for the reader 58 4 The bottle neck: macromolecular sequences 59 Introduction 59 Proteins and nucleic acids are copolymers 60 The quest for macromolecular sequences 62 What about polynucleotides? 65 A grain of sand in the Sahara 68 The “never-born proteins” 70 A model for the aetiology of macromolecular sequences – and a testable one 72 Homochirality in chains 76 Chain chirality and chain growth 78 Concluding remarks 82 Questions for the reader 84 5 Self-organization 85 Introduction 85 Self-organization of simpler molecular systems 87 Self-organization and autocatalysis 91 Polymerization 93 Self-organization and kinetic control 95 Self-organization and breaking of symmetry 97 Complex biological systems 100 Self-organization and finality 105 Out-of-equilibrium self-organization 106 Concluding remarks 109 Questions for the reader 111 6 The notion of emergence 112 Introduction 112 A few simple examples 114 Emergence and reductionism 116 Deducibility and predictability 117 Downward causation 119 Emergence and non-linearity 120 Life as an emergent property 123 Concluding remarks 125 Questions for the reader 128 7 Self-replication and self-reproduction 129 Introduction 129 Self-replication and non-linearity 129 Myths and realities of self-replication 132 Self-replicating, enzyme-free chemical systems 133 One more step towards complexity 141 Self-reproducing micelles and vesicles 143 Concluding remarks 153 Questions for the reader 154 8 Autopoiesis: the logic of cellular life 155 Introduction 155 Historical background 156 Basic autopoiesis 157 Criteria of autopoiesis 159 What autopoiesis does not include 160 Chemical autopoiesis 162 Autopoiesis and cognition 164 Cognition and enaction 167 Necessary and sufficient? 169 One glance further up: from autopoiesis to the cognitive domain 172 Social autopoiesis 175 Autopoiesis and the chemoton: a comparison of the views of Ganti with those of Maturana and Varela 177 Concluding remarks 179 Questions for the reader 181 9 Compartments 182 Introduction 182 Surfactant aggregates 182 Aqueous micelles 187 Compartmentation in reverse micelles 189 Cubic phases 19