| Preface |
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xiii | |
| Acknowledgments |
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xxiii | |
| 1 The planetary scope of biogenesis: the biosphere is the fourth geosphere |
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1 | (34) |
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1.1 A new way of being organized |
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1 | (5) |
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1.1.1 Life is a planetary process |
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2 | (3) |
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1.1.2 Drawing from many streams of science |
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5 | (1) |
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1.2 The organizing concept of geospheres |
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6 | (6) |
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1.2.1 The three traditional geospheres |
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7 | (1) |
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1.2.2 The interfaces between geospheres |
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8 | (2) |
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1.2.3 The biosphere is the fourth geosphere |
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10 | (2) |
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1.3 Summary of main arguments of the book |
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12 | (19) |
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1.3.1 An approach to theory that starts in the phenomenology of the biosphere |
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13 | (3) |
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1.3.2 Placing evolution in context |
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16 | (6) |
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1.3.3 Chance and necessity understood within the larger framework of phase transitions |
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22 | (6) |
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1.3.4 The emergence of the fourth geosphere and the opening of organic chemistry on Earth |
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28 | (3) |
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1.4 The origin of life and the organization of the biosphere |
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31 | (4) |
| 2 The organization of life on Earth today |
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35 | (38) |
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2.1 Many forms of order are fundamental in the biosphere |
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35 | (5) |
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2.1.1 Three conceptions of essentiality |
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37 | (1) |
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2.1.2 The major patterns that order the biosphere |
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37 | (3) |
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2.2 Ecosystems must become first-class citizens in biology |
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40 | (2) |
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2.2.1 No adequate concept of ecosystem identity in current biology |
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40 | (1) |
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2.2.2 Ecosystems are not super-organisms |
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41 | (1) |
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2.2.3 Ecological patterns can transcend the distinction between individual and community dynamics |
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42 | (1) |
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2.3 Bioenergetic and trophic classification of organism-level and ecosystem-level metabolisms |
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42 | (16) |
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2.3.1 Divergence and convergence: phylogenetic and typological classification schemes |
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43 | (2) |
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2.3.2 The leading typological distinctions among organisms |
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45 | (5) |
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2.3.3 Anabolism and catabolism: the fundamental dichotomy corresponding to the biochemical and ecological partitions |
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50 | (1) |
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2.3.4 Ecosystems, in aggregate function, are simpler and more universal than organisms |
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51 | (5) |
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2.3.5 Universality of the chart of intermediary metabolism |
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56 | (2) |
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2.4 Biochemical pathways are among the oldest fossils on Earth |
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58 | (2) |
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2.4.1 Evidence that currently bounds the oldest cellular life |
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58 | (1) |
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2.4.2 Disappearance of the rock record across the Hadean horizon |
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58 | (1) |
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2.4.3 Metabolism: fossil or Platonic form? |
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59 | (1) |
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2.5 The scales of living processes |
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60 | (6) |
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2.5.1 Scales of biochemistry |
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60 | (4) |
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2.5.2 Scales of physical organization |
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64 | (1) |
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2.5.3 Scales of information and control |
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64 | (2) |
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2.6 Diversity within the order that defines life: the spectrum from necessity to chance |
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66 | (4) |
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2.6.1 How contingency has been extrapolated from modern evolution to origins |
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67 | (1) |
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2.6.2 Natural selection for change and for conservation |
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68 | (1) |
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2.6.3 Different degrees of necessity for different layers |
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68 | (2) |
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2.7 Common patterns recapitulated at many levels |
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70 | (3) |
| 3 The geochemical context and embedding of the biosphere |
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73 | (97) |
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3.1 Order in the abiotic context for life |
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73 | (2) |
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3.1.1 Many points of contact between living and non-living energetics and order |
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74 | (1) |
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3.1.2 Barriers, timescales, and structure |
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75 | (1) |
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3.2 Activation energy and relaxation temperature regimes in abiotic chemistry and metabolism |
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75 | (2) |
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3.3 Stellar and planetary systems operate in a cascade of disequilibria |
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77 | (29) |
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3.3.1 The once young and now middle-aged Sun |
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77 | (5) |
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3.3.2 Disequilibria in the Earth are gated by a hierarchy of phases and associated diffusion timescales |
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82 | (24) |
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3.4 The restless chemical Earth |
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106 | (9) |
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3.4.1 Mafic and felsic: ocean basins and continental rafts |
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107 | (1) |
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3.4.2 Three origins of magmas |
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108 | (7) |
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3.5 The dynamics of crust formation at submarine spreading centers |
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115 | (25) |
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3.5.1 Melt formation and delivery at mid-ocean ridges |
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116 | (1) |
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3.5.2 Tension, pressure, brittleness, and continual fracturing |
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117 | (2) |
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3.5.3 Fractures, water invasion, buoyancy, and the structure of hydrothermal circulation systems |
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119 | (7) |
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3.5.4 Chemical changes of rock and water in basalt-hosted systems |
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126 | (5) |
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3.5.5 Serpentinization in peridotite-hosted hydrothermal systems |
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131 | (7) |
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3.5.6 Principles and parameters of hydrothermal alteration: a summary |
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138 | (2) |
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3.6 The parallel biosphere of chemotrophy on Earth |
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140 | (28) |
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3.6.1 The discovery of ecosystems on Earth that do not depend on photosynthetically fixed carbon |
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140 | (2) |
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3.6.2 The evidence for a deep (or at least subsurface), hot (or at least warm) biosphere |
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142 | (6) |
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3.6.3 The complex associations of temperature, chemistry, and microbial metabolisms |
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148 | (2) |
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3.6.4 Major classes of redox couples that power chemotrophic ecosystems today |
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150 | (5) |
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3.6.5 Why the chemotrophic biosphere has been proposed as a model for early life |
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155 | (2) |
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3.6.6 Differences between hydrothermal systems today and those in the Archean |
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157 | (10) |
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3.6.7 Feedback from the biosphere to surface mineralogy |
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167 | (1) |
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3.7 Expectations about the nature of life |
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168 | (2) |
| 4 The architecture and evolution of the metabolic substrate |
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170 | (103) |
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4.1 Metabolism between geochemistry and history |
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170 | (3) |
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4.2 Modularity in metabolism, and implications for the origin of life |
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173 | (5) |
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4.2.1 Modules and layers in metabolic architecture and function |
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173 | (1) |
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4.2.2 Reading through the evolutionary palimpsest |
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174 | (1) |
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4.2.3 Support for a progressive emergence of metabolism |
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175 | (1) |
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4.2.4 Feedbacks, and bringing geochemistry under organic control |
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175 | (1) |
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4.2.5 The direction of propagation of constraints: upward from metabolism to higher-level aggregate structures |
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176 | (2) |
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4.3 The core network of small metabolites |
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178 | (41) |
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4.3.1 The core in relation to anabolism and catabolism |
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180 | (2) |
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4.3.2 The core of the core |
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182 | (1) |
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4.3.3 Precursors in the citric acid cycle and the primary biosynthetic pathways |
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183 | (9) |
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4.3.4 One-carbon metabolism in relation to TCA and anabolism |
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192 | (4) |
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4.3.5 The universal covering network of autotrophic carbon fixation |
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196 | (4) |
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4.3.6 Description of the six fixation pathways |
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200 | (14) |
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4.3.7 Pathway alignments and redundant chemistry |
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214 | (2) |
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4.3.8 Distinctive initial reactions and conserved metal-center enzymes |
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216 | (1) |
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4.3.9 The striking lack of innovation in carbon fixation |
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217 | (2) |
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4.4 A reconstructed history of carbon fixation, and the role of innovation constraints in history |
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219 | (30) |
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4.4.1 Three reasons evolutionary reconstruction enters the problem of finding good models for early metabolism |
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219 | (2) |
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4.4.2 Phylogenetic reconstruction of functional networks |
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221 | (3) |
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4.4.3 Functional and comparative assignment of biosynthetic pathways in modern Glades |
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224 | (6) |
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4.4.4 A maximum-parsimony tree of autotrophic carbon-fixation networks |
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230 | (11) |
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4.4.5 A reconstruction of Aquifex aeolicus and evidence for broad patterns of evolutionary directionality |
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241 | (3) |
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4.4.6 The rise of oxygen and the attending change in metabolism and evolutionary dynamics |
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244 | (4) |
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4.4.7 Chance and necessity for oxidative versus reductive TCA |
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248 | (1) |
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4.5 Cofactors and the first layer of molecular-organic control |
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249 | (19) |
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4.5.1 The intermediate position of cofactors, feedback, and the emergence of metabolic control |
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249 | (4) |
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4.5.2 Key cofactor classes for the earliest elaboration of metabolism |
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253 | (8) |
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4.5.3 The complex amino acids as cofactors |
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261 | (1) |
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4.5.4 Situating cofactors within the elaboration of the small-molecule metabolic substrate network |
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262 | (2) |
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4.5.5 Roles of the elements and evolutionary convergences |
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264 | (4) |
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4.6 Long-loop versus short-loop autocatalysis |
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268 | (1) |
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4.7 Summary: continuities and gaps |
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269 | (1) |
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4.8 Graphical appendix: definition of notations for chemical reaction networks |
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270 | (3) |
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4.8.1 Definition of graphic elements |
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271 | (2) |
| 5 Higher-level structures and the recapitulation of metabolic order |
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273 | (67) |
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5.1 Coupled subsystems and shared patterns |
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273 | (4) |
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5.1.1 Shared boundaries: correlation is not causation |
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274 | (1) |
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5.1.2 Different kinds of modularity have changed in different directions under evolution |
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275 | (2) |
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5.2 Metabolic order recapitulated in higher-level aggregate structures |
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277 | (1) |
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5.3 Order in the genetic code: fossils of the emergence of translation? |
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278 | (44) |
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5.3.1 Context for the code: the watershed of the emergence of translation |
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283 | (2) |
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5.3.2 The modern translation system could be a firewall |
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285 | (2) |
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5.3.3 What kinds of information does a pattern contain, and how much? |
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287 | (3) |
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5.3.4 Part of the order in the code is order in the amino acid inventory |
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290 | (1) |
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5.3.5 Four major forms of metabolic order in the code |
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291 | (11) |
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302 | (4) |
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5.3.7 Accounting for order |
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306 | (13) |
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5.3.8 A proposal for three phases in the emergence of translation |
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319 | (3) |
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5.4 The essential role of bioenergetics in both emergence and control |
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322 | (9) |
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5.4.1 Energy conservation, energy carriers, and entropy |
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323 | (2) |
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5.4.2 Three energy buses: reductants, phosphates, and protons |
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325 | (3) |
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5.4.3 The cellular energy triangle |
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328 | (2) |
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5.4.4 Geochemical context for emergence of redox and phosphate energy systems |
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330 | (1) |
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5.5 The three problems solved, by cellularization |
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331 | (6) |
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5.5.1 Distinct functions performed by distinct subsystems |
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332 | (1) |
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5.5.2 An exercise in transversality |
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333 | (4) |
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5.6 The partial integration of molecular replication with cellular metabolism |
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337 | (1) |
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5.7 Cellular life is a confederacy |
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338 | (2) |
| 6 The emergence of a biosphere from geochemistry |
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340 | (84) |
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6.1 From universals to a path of biogenesis |
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340 | (15) |
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6.1.1 On empiricism and theory: evaluating highly incomplete scenarios |
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341 | (3) |
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6.1.2 The functions versus the systems chemistry of RNA |
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344 | (5) |
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6.1.3 An emergent identity for metabolism or the emergence of a control paradigm? |
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349 | (6) |
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6.2 Planetary disequilibria and the departure toward biochemistry |
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355 | (15) |
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6.2.1 The partitioning role of the abiotic geospheres |
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356 | (3) |
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6.2.2 Species that bridge geosphere boundaries to form the great arcs of planetary chemical disequilibrium |
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359 | (7) |
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6.2.3 Mineral-hosted hydrothermal systems are pivotal in the sense that they are key focusing centers for chemical disequilibria |
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366 | (2) |
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6.2.4 The alkaline hydrothermal vents model |
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368 | (2) |
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6.3 Stages in the emergence of the small-molecule network |
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370 | (19) |
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6.3.1 Carbon reduction and the first C-C bonds |
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371 | (13) |
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6.3.2 rTCA: the potential for self-amplification realized and the first strong selection of the metabolic precursors |
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384 | (3) |
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6.3.3 Reductive amination of a-ketones and the path to amino acids |
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387 | (1) |
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6.3.4 A network of sugar phosphates and aldol reactions |
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388 | (1) |
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6.4 The early organic feedbacks |
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389 | (11) |
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391 | (5) |
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6.4.2 Cyclohydrolase reactions: purine nucleotides and folates |
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396 | (2) |
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6.4.3 Thiamin-like chemistry: lifting rTCA off the rocks |
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398 | (1) |
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6.4.4 Biotin: uses in rTCA and in fatty acid synthesis |
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399 | (1) |
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399 | (1) |
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6.5 Selection of monomers for chirality |
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400 | (3) |
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6.5.1 Degree of enantiomeric selection at different scales |
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400 | (1) |
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6.5.2 Mechanisms and contexts for stereoselectivity |
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401 | (1) |
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6.5.3 The redundancy of biochemical processes simplifies the problem of chiral selection |
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402 | (1) |
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6.6 The oligomer world and molecular replication |
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403 | (6) |
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6.6.1 Increased need for dehydrating ligation reactions |
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404 | (1) |
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6.6.2 Coupling of surfaces and polymerization |
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405 | (2) |
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6.6.3 Distinguishing the source of selection from the emergence of memory in a ribozyme-catalyzed era |
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407 | (2) |
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6.7 Transitions to cellular encapsulation in lipids |
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409 | (4) |
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6.7.1 Contexts that separate the aggregate transformation into independent steps |
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412 | (1) |
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6.8 The advent of the ribosome |
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413 | (7) |
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6.8.1 The core and evolution of catalysis |
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414 | (2) |
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6.8.2 Catalytic RNA and iron |
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416 | (1) |
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6.8.3 The origin of translation and the three-base reading frame |
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417 | (2) |
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6.8.4 Reliable translation and the birth of phylogeny |
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419 | (1) |
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6.9 The major biogeochemical transitions in the evolutionary era |
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420 | (1) |
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6.10 Tentative conclusions: the limits of narrative and the way forward |
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421 | (3) |
| 7 The phase transition paradigm for emergence |
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424 | (115) |
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7.1 Theory in the origin of life |
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424 | (3) |
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7.1.1 What does a phase transition framing add to the search for relevant environments and relevant chemistry? |
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426 | (1) |
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7.2 Arriving at the need for a phase transition paradigm |
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427 | (9) |
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7.2.1 Why there is something instead of nothing |
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428 | (2) |
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7.2.2 Selecting pattern from chaos in organosynthesis |
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430 | (1) |
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7.2.3 The phase transition paradigm |
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431 | (1) |
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7.2.4 Developing the stability perspective |
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432 | (3) |
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7.2.5 A chapter of primers |
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435 | (1) |
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7.3 Large deviations and the nature of thermodynamic limits |
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436 | (16) |
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7.3.1 The combinatorics of large numbers and simplified fluctuation-probability distributions |
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437 | (2) |
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7.3.2 Interacting systems and classical thermodynamics |
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439 | (7) |
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7.3.3 Statistical roles of state variables |
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446 | (5) |
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7.3.4 Phase transitions and order parameters |
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451 | (1) |
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7.4 Phase transitions in equilibrium systems |
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452 | (34) |
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7.4.1 Worked example: the Curie-Weiss phase transition |
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452 | (14) |
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7.4.2 Reduction, emergence, and prediction |
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466 | (2) |
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7.4.3 Unpredictability and long-range order |
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468 | (3) |
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7.4.4 The hierarchy of matter |
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471 | (8) |
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7.4.5 Parallels in matter and life: the product space of chemical reactions |
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479 | (2) |
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481 | (5) |
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7.5 The (large-deviations!) theory of asymptotically reliable error correction |
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486 | (15) |
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7.5.1 Information theory as a mirror on thermodynamics |
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487 | (1) |
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7.5.2 The large-deviations theory of optimal error correction |
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488 | (1) |
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7.5.3 Transmission channel models |
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489 | (2) |
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7.5.4 Capacity and error probability |
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491 | (5) |
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7.5.5 Error correction and molecular recognition in an energetic system |
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496 | (3) |
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7.5.6 The theory of optimal error correction is thermodynamic |
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499 | (1) |
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7.5.7 One signal or many? |
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500 | (1) |
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7.6 Phase transitions in non-equilibrium systems |
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501 | (24) |
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7.6.1 On the equilibrium entropy and living systems |
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502 | (7) |
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7.6.2 Ensembles of processes and of histories |
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509 | (1) |
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7.6.3 Phase transfer catalysis |
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510 | (1) |
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7.6.4 A first-order, non-equilibrium, phase transition in the context of autocatalysis |
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511 | (9) |
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7.6.5 The lightning strike analogy |
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520 | (4) |
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7.6.6 Conclusion: the frontier in the study of collective and cooperative effects |
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524 | (1) |
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7.7 Technical appendix: non-equilibrium large-deviations formulae |
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525 | (14) |
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7.7.1 Master equation for the one-variable model of autocatalysis |
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526 | (1) |
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7.7.2 Ordinary power-series generating function and Liouville equation |
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527 | (4) |
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7.7.3 Escape trajectories and effective potential for non-equilibrium phases |
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531 | (3) |
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7.7.4 Gaussian fluctuations about stationary-path backgrounds |
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534 | (5) |
| 8 Reconceptualizing the nature of the living state |
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539 | (69) |
|
8.1 Bringing the phase transition paradigm to life |
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539 | (15) |
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8.1.1 Necessary order in the face of pervasive disturbance |
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542 | (2) |
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8.1.2 The role of phase transitions in hierarchical complex systems |
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544 | (5) |
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8.1.3 How uniqueness becomes a foundation for diversity |
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549 | (3) |
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8.1.4 Beyond origins to the nature of the living state |
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552 | (2) |
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8.2 Metabolic layering as a form of modular architecture |
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554 | (15) |
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8.2.1 Herbert Simon's arguments that modularity is prerequisite to hierarchical complexity |
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554 | (4) |
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8.2.2 The modularity argument in a dynamical setting |
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558 | (1) |
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8.2.3 Error correction from regression to ordered thermal states |
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558 | (1) |
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8.2.4 The universal metabolic chart as an order parameter |
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559 | (2) |
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8.2.5 The use of order parameters in induction |
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561 | (5) |
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8.2.6 Control systems and requisite variety |
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566 | (2) |
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8.2.7 Biology designs using order parameters |
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568 | (1) |
|
8.3 The emergence of individuality |
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|
569 | (18) |
|
8.3.1 Darwinian evolution is predicated on individuality |
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570 | (2) |
|
8.3.2 How unique solutions give rise to conditions that support diversity |
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572 | (3) |
|
8.3.3 The nature of individual identity |
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575 | (5) |
|
8.3.4 Individuality within the structure of evolutionary theory |
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580 | (4) |
|
8.3.5 The ecosystem as community and as entity |
|
|
584 | (2) |
|
8.3.6 Why material simplicity precedes complexity in the phase transition paradigm |
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586 | (1) |
|
8.4 The nature of the living state |
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587 | (10) |
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8.4.1 Replicators: a distinction but not a definition |
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589 | (2) |
|
8.4.2 Life is defined by participation in the biosphere |
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591 | (1) |
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8.4.3 Covalent chemistry flux and other order parameters |
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|
591 | (2) |
|
8.4.4 The importance of being chemical |
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593 | (4) |
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8.5 The error-correcting hierarchy of the biosphere |
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|
597 | (11) |
|
8.5.1 The main relation: a general trade-off among stability, complexity, and correlation length |
|
|
597 | (1) |
|
8.5.2 Simple and complex phase transitions |
|
|
598 | (3) |
|
8.5.3 Living matter as active data |
|
|
601 | (5) |
|
8.5.4 Patterns and entities in the biosphere |
|
|
606 | (2) |
| Epilogue |
|
608 | (3) |
| References |
|
611 | (49) |
| Index |
|
660 | |
