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BK

First published

Cambridge : Cambridge University Press, 2016

xxiv, 677 stran : ilustrace (některé barevné), mapy ; 26 cm

ISBN 978-1-107-12188-1 (vázáno)

Obsahuje bibliografii na stranách 611-659, bibliografické odkazy a rejstřík

001459776

Contents // Preface // A chi o wl ed g m en t s // page xiii xxiii // 1 The planetary scope of biogenesis: the biosphere is the fourth geosphere // 1.1 A new way of being organized // 1.1.1 Life is a planetary process // 1.1.2 Drawing from many streams of science // 1.2 The organizing concept of geospheres // 1.2.1 The three traditional geospheres // 1.2.2 The interfaces between geospheres // 1.2.3 The biosphere is the fourth geosphere // 1.3 Summary of main arguments of the book // 1.3.1 An approach to theory that starts in the phenomenology of the biosphere // 1.3.2 Placing evolution in context // 1.3.3 Chance and necessity understood within the larger framework of phase transitions // 1.3.4 The emergence of the fourth geosphere and the opening of organic chemistry on Earth // 1.4 The origin of life and the organization of the biosphere // 2 // 5 // 6 // 7 // 8 10 12 // 13 // 16 // 22 // 28 // 31 // 2 The organization of life on Earth today 35 // 2.1 Many forms of order are fundamental in the biosphere 35 // 2.1.1 Three conceptions of essentiality 37 // 2.1.2 The major patterns that order the biosphere 37 // 2.2 Ecosystems must become first-class citizens in biology 40 // 2.2.1 No adequate concept of ecosystem identity in current biology 40 // 2.2.2 Ecosystems are not super-organisms 41 // 2.2.3 Ecological patterns can transcend the distinction between // individual and community dynamics 42 // v // VI // Contents // 2.3 Bioenergetic and trophic classification of organism-level

and // ecosystem-level metabolisms 42 // 2.3.1 Divergence and convergence: phylogenetic and typological classification // schemes 43 // 2.3.2 The leading typological distinctions among organisms 45 // 2.3.3 Anabolism and catabolism: the fundamental dichotomy // corresponding to the biochemical and ecological partitions 50 // 2.3.4 Ecosystems, in aggregate function, are simpler and more // universal than organisms 51 // 2.3.5 Universality of the chart of intermediary metabolism 56 // 2.4 Biochemical pathways are among the oldest fossils on Earth 58 // 2.4.1 Evidence that currently bounds the oldest cellular life 58 // 2.4.2 Disappearance of the rock record across the Hadean horizon 58 // 2.4.3 Metabolism: fossil or Platonic form? 59 // 2.5 The scales of living processes 60 // 2.5.1 Scales of biochemistry 60 // 2.5.2 Scales of physical organization 64 // 2.5.3 Scales of information and control 64 // 2.6 Diversity within the order that defines life: the spectrum from // necessity to chance 66 // 2.6.1 How contingency has been extrapolated from modern // evolution to origins 67 // 2.6.2 Natural selection for change and for conservation 68 // 2.6.3 Different degrees of necessity for different layers 68 // 2.7 Common patterns recapitulated at many levels 70 // 3 The geochemical context and embedding of the biosphere 73 // 3.1 Order in the abiotic context for life 73 // 3.1.1 Many points of contact between living and non-living // energetics and order 74 // 3.1.2 Barriers, timescales,

and structure 75 // 3.2 Activation energy and relaxation temperature regimes in abiotic // chemistry and metabolism 75 // 3.3 Stellar and planetary systems operate in a cascade of disequilibria 77 // 3.3.1 The once young and now middle-aged Sun 77 // 3.3.2 Disequilibria in the Earth are gated by a hierarchy of phases // and associated diffusion timescales 82 // 3.4 The restless chemical Earth 106 // 3.4.1 Mafic and felsic: ocean basins and continental rafts 107 // 3.4.2 Three origins of magmas 108 // Contents // vii // 3.5 The dynamics of crust formation at submarine spreading centers 115 // 3.5.1 Melt formation and delivery at mid-ocean ridges 116 // 3.5.2 Tension, pressure, brittleness, and continual fracturing 117 // 3.5.3 Fractures, water invasion, buoyancy, and the structure of // hydrothermal circulation systems 119 // 3.5.4 Chemical changes of rock and water in basalt-hosted systems 126 // 3.5.5 Serpentinization in peridotite-hosted hydrothermal systems 131 // 3.5.6 Principles and parameters of hydrothermal alteration: a summary 138 // 3.6 The parallel biosphere of chemotrophy on Earth 140 // 3.6.1 The discovery of ecosystems on Earth that do not depend on // photosynthetically fixed carbon 140 // 3.6.2 The evidence for a deep (or at least subsurface), hot (or at least // warm) biosphere 142 // 3.6.3 The complex associations of temperature, chemistry, and // microbial metabolisms 148 // 3.6.4 Major classes of redox couples that power chemotrophic // ecosystems today 150

// 3.6.5 Why the chemotrophic biosphere has been proposed as a // model for early life 155 // 3.6.6 Differences between hydrothermal systems today and those in // the Archean 157 // 3.6.7 Feedback from the biosphere to surface mineralogy 167 // 3.7 Expectations about the nature of life 168 // 4 The architecture and evolution of the metabolic substrate 170 // 4.1 Metabolism between geochemistry and history 170 // 4.2 Modularity in metabolism, and implications for the origin of life 173 // 4.2.1 Modules and layers in metabolic architecture and function 173 // 4.2.2 Reading through the evolutionary palimpsest 174 // 4.2.3 Support for a progressive emergence of metabolism 175 // 4.2.4 Feedbacks, and bringing geochemistry under organic control 175 // 4.2.5 The direction of propagation of constraints: upward from // metabolism to higher-level aggregate structures 176 // 4.3 The core network of small metabolites 178 // 4.3.1 The core in relation to anabolism and catabolism 180 // 4.3.2 The core of the core 182 // 4.3.3 Precursors in the citric acid cycle and the primary biosynthetic // pathways 183 // 4.3.4 One-carbon metabolism in relation to TCA and anabolism 192 // 4.3.5 The universal covering network of autotrophic carbon fixation 196 // 4.3.6 Description of the six fixation pathways 200 // Contents // viii // 4.3.7 Pathway alignments and redundant chemistry 214 // 4.3.8 Distinctive initial reactions and conserved metal-center enzymes 216 // 4.3.9 The striking lack of innovation

in carbon fixation 217 // 4.4 A reconstructed history of carbon fixation, and the role of innovation // constraints in history 219 // 4.4.1 Three reasons evolutionary reconstruction enters the problem // of finding good models for early metabolism 219 // 4.4.2 Phylogenetic reconstruction of functional networks 221 // 4.4.3 Functional and comparative assignment of biosynthetic // pathways in modern clades 224 // 4.4.4 A maximum-parsimony tree of autotrophic carbon-fixation // networks 230 // 4.4.5 A reconstruction of Aquifex aeolicus and evidence for broad // patterns of evolutionary directionality 241 // 4.4.6 The rise of oxygen and the attending change in metabolism // and evolutionary dynamics 244 // 4.4.7 Chance and necessity for oxidative versus reductive TCA 248 // 4.5 Cofactors and the first layer of molecular-organic control 249 // 4.5.1 The intermediate position of cofactors, feedback, and the // emergence of metabolic control 249 // 4.5.2 Key cofactor classes for the earliest elaboration of // metabolism 253 // 4.5.3 The complex amino acids as cofactors 261 // 4.5.4 Situating cofactors within the elaboration of the // small-molecule metabolic substrate network 262 // 4.5.5 Roles of the elements and evolutionary convergences 264 // 4.6 Long-loop versus short-loop autocatalysis 268 // 4.7 Summary: continuities and gaps 269 // 4.8 Graphical appendix: definition of notations for chemical reaction // networks 270 // 4.8.1 Definition of graphic elements 271 // 5 Higher-level

structures and the recapitulation of metabolic order 273 // 5.1 Coupled subsystems and shared patterns 273 // 5.1.1 Shared boundaries: correlation is not causation 274 // 5.1.2 Different kinds of modularity have changed in different // directions under evolution 275 // 5.2 Metabolic order recapitulated in higher-level aggregate structures 277 // 5.3 Order in the genetic code: fossils of the emergence of translation? 278 // 5.3.1 Context for the code: the watershed of the emergence of // translation 283 // 5.3.2 The modern translation system could be a firewall 285 // Contents // ix // 5.3.3 What kinds of information does a pattern contain, and // how much? 287 // 5.3.4 Part of the order in the code is order in the amino acid inventory 290 // 5.3.5 Four major forms of metabolic order in the code 291 // 5.3.6 Rule combinations 302 // 5.3.7 Accounting for order 306 // 5.3.8 A proposal for three phases in the emergence of translation 319 // 5.4 The essential role of bioenergetics in both emergence and control 322 // 5.4.1 Energy conservation, energy carriers, and entropy 323 // 5.4.2 Three energy buses: reductants, phosphates, and protons 325 // 5.4.3 The cellular energy triangle 328 // 5.4.4 Geochemical context for emergence of redox and phosphate // energy systems 330 // 5.5 The three problems solved by cellularization 331 // 5.5.1 Distinct functions performed by distinct subsystems 332 // 5.5.2 An exercise in transversality 333 // 5.6 The partial integration of molecular replication

with cellular metabolism 337 // 5.7 Cellular life is a confederacy 338 // 6 The emergence of a biosphere from geochemistry 340 // 6.1 From universal to a path of biogenesis 340 // 6.1.1 On empiricism and theory: evaluating highly incomplete // scenarios 341 // 6.1.2 The functions versus the systems chemistry of RNA 344 // 6.1.3 An emergent identity for metabolism or the emergence of a // control paradigm? 349 // 6.2 Planetary disequilibria and the departure toward biochemistry 355 // 6.2.1 The partitioning role of the abiotic geospheres 356 // 6.2.2 Species that bridge geosphere boundaries to form the great // arcs of planetary chemical disequilibrium 359 // 6.2.3 Mineral-hosted hydrothermal systems are pivotal in the sense // that they are key focusing centers for chemical disequilibria 366 // 6.2.4 The alkaline hydrothermal vents model 368 // 6.3 Stages in the emergence of the small-molecule network 370 // 6.3.1 Carbon reduction and the first C—C bonds 371 // 6.3.2 rTCA: the potential for self-amplification realized and the first // strong selection of the metabolic precursors 384 // 6.3.3 Reductive amination of a-ketones and the path to amino acids 387 // 6.3.4 A network of sugar phosphates and aldol reactions 388 // 6.4 The early organic feedbacks 389 // 6.4.1 C—N heterocycles 391 // 6.4.2 Cyclohydrolase reactions: purine nucleotides and folates 396 // x Contents // 6.4.3 Thiamin-like chemistry: lifting rTCA off the rocks 398 // 6.4.4 Biotin: uses in rTCA and in fatty

acid synthesis 399 // 6.4.5 Alkyl thiols 399 // 6.5 Selection of monomers for chirality 400 // 6.5.1 Degree of enantiomeric selection at different scales 400 // 6.5.2 Mechanisms and contexts for stereoselectivity 401 // 6.5.3 The redundancy of biochemical processes simplifies the // problem of chiral selection 402 // 6.6 The oligomer world and molecular replication 403 // 6.6.1 Increased need for dehydrating ligation reactions 404 // 6.6.2 Coupling of surfaces and polymerization 405 // 6.6.3 Distinguishing the source of selection from the emergence of // memory in a ribozyme-catalyzed era 407 // 6.7 Transitions to cellular encapsulation in lipids 409 // 6.7.1 Contexts that separate the aggregate transformation into // independent steps 412 // 6.8 The advent of the ribosome 413 // 6.8.1 The core and evolution of catalysis 414 // 6.8.2 Catalytic RNA and iron 416 // 6.8.3 The origin of translation and the three-base reading frame 417 // 6.8.4 Reliable translation and the birth of phylogeny 419 // 6.9 The major biogeochemical transitions in the evolutionary era 420 // 6.10 Tentative conclusions: the limits of narrative and the way forward 421 // 7 The phase transition paradigm for emergence 424 // 7.1 Theory in the origin of life 424 // 7.1.1 What does a phase transition framing add to the search for // relevant environments and relevant chemistry? 426 // 7.2 Arriving at the need for a phase transition paradigm 427 // 7.2.1 Why there is something instead of nothing 428 // 7.2.2 Selecting

pattern from chaos in organosynthesis 430 // 7.2.3 The phase transition paradigm 431 // 7.2.4 Developing the stability perspective 432 // 7.2.5 A chapter of primers 435 // 7.3 Large deviations and the nature of thermodynamic limits 436 // 7.3.1 The combinatorics of large numbers and simplified // fluctuation-probability distributions 437 // 7.3.2 Interacting systems and classical thermodynamics 439 // 7.3.3 Statistical roles of state variables 446 // 7.3.4 Phase transitions and order parameters 451 // 7.4 Phase transitions in equilibrium systems 452 // 7.4.1 Worked example: the Curie-Weiss phase transition 452 // Contents x i // 7.4.2 Reduction, emergence, and prediction 466 // 7.4.3 Unpredictability and long-range order 468 // 7.4.4 The hierarchy of matter 471 // 7.4.5 Parallels in matter and life: the product space of chemical // reactions 479 // 7.4.6 Oil and water 481 // 7.5 The (large-deviations!) theory of asymptotically reliable error // correction 486 // 7.5.1 Information theory as a mirror on thermodynamics 487 // 7.5.2 The large-deviations theory of optimal error correction 488 // 7.5.3 Transmission channel models 489 // 7.5.4 Capacity and error probability 491 // 7.5.5 Error correction and molecular recognition in an energetic // system 496 // 7.5.6 The theory of optimal error correction is thermodynamic 499 // 7.5.7 One signal or many? 500 // 7.6 Phase transitions in non-equilibrium systems 501 // 7.6.1 On the equilibrium entropy and living systems 502 // 7.6.2 Ensembles

of processes and of histories 509 // 7.6.3 Phase transfer catalysis 510 // 7.6.4 A first-order, non-equilibrium, phase transition in the context // of autocatalysis 511 // 7.6.5 The lightning strike analogy 520 // 7.6.6 Conclusion: the frontier in the study of collective and // cooperative effects 524 // 7.7 Technical appendix: non-equilibrium large-deviations formulae 525 // 7.7.1 Master equation for the one-variable model of autocatalysis 526 // 7.7.2 Ordinary power-series generating function and Liouville // equation 527 // 7.7.3 Escape trajectories and effective potential for non-equilibrium // phases 531 // 7.7.4 Gaussian fluctuations about stationary-path backgrounds 534 // 8 Reconceptualizing the nature of the living state 539 // 8.1 Bringing the phase transition paradigm to life 539 // 8.1.1 Necessary order in the face of pervasive disturbance 542 // 8.1.2 The role of phase transitions in hierarchical complex systems 544 // 8.1.3 How uniqueness becomes a foundation for diversity 549 // 8.1.4 Beyond origins to the nature of the living state 552 // 8.2 Metabolic layering as a form of modular architecture 554 // 8.2.1 Herbert Simon’s arguments that modularity is prerequisite to // hierarchical complexity 554 // Contents // xii // 8.2.2 The modularity argument in a dynamical setting 558 // 8.2.3 Error correction from regression to ordered thermal states 558 // 8.2.4 The universal metabolic chart as an order parameter 559 // 8.2.5 The use of order parameters in induction

561 // 8.2.6 Control systems and requisite variety 566 // 8.2.7 Biology designs using order parameters 568 // 8.3 The emergence of individuality 569 // 8.3.1 Darwinian evolution is predicated on individuality 570 // 8.3.2 How unique solutions give rise to conditions that // support diversity 572 // 8.3.3 The nature of individual identity 575 // 8.3.4 Individuality within the structure of evolutionary theory 580 // 8.3.5 The ecosystem as community and as entity 584 // 8.3.6 Why material simplicity precedes complexity in the phase // transition paradigm 586 // 8.4 The nature of the living state 587 // 8.4.1 Replicators: a distinction but not a definition 589 // 8.4.2 Life is defined by participation in the biosphere 591 // 8.4.3 Covalent chemistry flux and other order parameters 591 // 8.4.4 The importance of being chemical 593 // 8.5 The error-correcting hierarchy of the biosphere 597 // 8.5.1 The main relation: a general trade-off among stability, // complexity, and correlation length 597 // 8.5.2 Simple and complex phase transitions 598 // 8.5.3 Living matter as active data 601 // 8.5.4 Patterns and entities in the biosphere 606 // Epilogue 608 // References 61 1 // Index 660