Venenivibrio. Licensed under CC  BY-SA 3.0 via Wikimedia Commons. http://commons.wikimedia.org/wiki/File:Venenivibrio.jpg#/media/File:Venenivibrio.jpg.
 Anabaena sperica2. Licensed under CC  BY-SA 3.0 via Wikimedia Commons. http://commons.wikimedia.org/wiki/File:Anabaena_sperica2.jpg#/ media/File:Anabaena_sperica2.jpg.
 Published under GNU free documentation license. http://en.wikipedia.org/wiki /GNU_Free_Documentation_License.
 Leopard africa, by JanErkamp at the English language Wikipedia. Licensed under CC  BY-SA 3.0 via Wikimedia Commons. http://commons.wikimedia.org/ wiki/File:Leopard_africa.jpg#/media/File:Leopard_africa.jpg.
 2006-10-25 Amanita muscaria crop, by Amanita_muscaria_3_vliegenzwammen _op_rij.jpg: Onderwijsgekderivative work: Ak ccm. This file was derived from: Amanita muscaria 3 vliegenzwammen op rij.jpg. Licensed under CC  BY-SA 3.0 nl via Wikimedia Commons. http://commons.wikimedia.org/wiki/File:2006 -10-25_Amanita_muscaria_crop.jpg#/media/File:2006-10-25_Amanita_muscaria_ crop.jpg.
 Licensed under CC .
 20090719 062218 ParameciumBursaria, by at en.wikipedia. Licensed under CC  BY-SA 3.0 via Wikimedia Commons. http://commons.wikimedia. org/wiki/File:20090719_062218_ParameciumBursaria.jpg#/media/File:200907.
 Global volcanism program, 2013. volcanoes of the world, v. 4.3.4. http://dx.doi.org /10.5479/si.GVP.VOTW4-2013, 2013.
 Length of the global plate boundary at 2.4 Ga. Geology, 18:58–61, 1990. and .
 Structure and Interpretation of Computer Programs. MIT Press, Cambridge, MA, second edition, 1996., , and .
 Sequence complexity in Darwinian evolution. Complexity, 8:49–56, 2002..
 Information theory in molecular biology. Phys. Life Rev., 1:3–22, 2004..
 A new look at the statistical model identification. IEEE Trans. Autom. Control, 19:716–723, 1974..
 The possible nutritional or detoxification role of the epibiotic bacteria of alvinellid polychaetes: review of current data. Symbiosis, 4:51–62, 1987., , and .
 Molecular Biology of the Cell. Garland Science, New York, fourth edition, 2002..
 Paul Boyer: bioenergetics and error. J. Hist. Biol., 35:149–172, 2002..
 Compositional controls on vent fluids from ultramafic-hosted hydrothermal systems at mid-ocean ridges: an experimental study at 400?C, 500 bars. Geochim. Cosmochim. Acta, 67:1531–1542, 2004. and
 Serpentinization and heat generation: constraints from Lost City and Rainbow hydrothermal systems. Geochim. Cosmochim. Acta, 68:1347–1354, 2004. and
 Nunes Amaral and Kent Baekgaard Lauritsen. Self-organized criticality in a rice-pile model. Phys. Rev. E, 54:R4512–R4515, 1996.
 Energetics of amino acid synthesis in hydrothermal ecosystems. Science, 281:1659–1662, 1998. and .
 Energetics of overall metablic reactions of thermophilic and hyperthermophilic archaea and bacteria. FEMS Microbiol. Rev., 25:175–243, 2001. and .
 The energetics of organic synthesis inside and outside the cell. Philos. Trans. R. Soc. London, Ser. B, 368:20120255, 2013., , , and .
 Energetics of chemolithoautotrophy in the hydrothermal system of Vulcano Island, southern Italy. Geobiology, 1:37–58, 2003., , , , and .
 Navigating the chemical space of HCN polymerization and hydrolysis: guiding graph grammars by mass spectrometry data. Entropy, 15:4066–4083, 2013., , , , , and .
 Maximizing output and recognizing autocatalysis in chemical reaction networks is NP-complete. J. Syst. Chem., 3:1, 2012., , , and .
 Inferring chemical reaction patterns using rule composition in graph grammars. J. Syst. Chem., 4:4:1–14, 2013., , , and .
 Generic strategies for chemical space exploration. Int. J. Comput. Biol. Drug Des., 7:225–258, 2014., , , and .
 In silico support for Eschenmoser's glyoxylate scenario. Isr. J. Chem., in review, 2015., , , and .
 New Theory of the Earth. Cambridge University Press, London, 2007..
 More is different. Science, New Series, 177:393–396, 1972..
 The Fischer–Tropsch Synthesis. Academic Press, New York, 1984..
 A novel oxcalosuccinate-forming enzyme involved in the reductive carboxylation of 2-oxoglutarate in Hydrogenobacter thermophilus TK-6. Mol. Microbiol., 62:748–759, 2006. and .
 Nondecarboxylating and decarboxylating isocitrate dehydrogenases: oxalosuccinate reductase as an ancestral form of isocitrate dehydrogenase. J. Bacteriol., 190:2050–2055, 2008. and .
 A novel biotin protein required for reductive carboxylation of 2-oxoglutarate by isocitrate dehydrogenase in Hydrogenobacter thermophilus TK-6. Mol. Microbiol., 51:791–798, 2004., , and .
 A novel enzyme, citryl-CoA lyase, catalysing the second step of the citrate cleavage reaction in Hydrogenobacter thermophilus TK-6. Mol. Microbiol., 52:763–770, 2004., , and .
 A novel enzyme, citryl-CoA synthetase, catalysing the first step of the citrate cleavage reaction in Hydrogenobacter thermophilus TK-6. Mol. Microbiol., 52:751–761, 2004., , and .
 History of Animals. Translated by D'ArcyWentworth Thompson. Clarendon Press, Oxford, 1910..
 An Introduction to Cybernetics. Chapman and Hall, London, 1956..
 Requisite variety and its implications for the control of complex systems. Cybernetica, 1:83–99, 1958..
 RNA folding and catalysis mediated by iron(II). PLoS ONE, 7:e38024, 2012., , , , , , , , , , , , , and .
 Strehler's theory of mortality and the second principle of thermodynamics. J. Gerontol., 23:196–200, 1968..
 Evolution of the solar ionizing flux. J. Geophys. Res., 102:1641–1651, 1997..
 1620.. Novum Organum.
 The New Organon. Michael Silverthorne and Lisa Jardine, editors. Cambridge University Press, London, 2000..
 The structure of T. aquaticus DNA polymerase III is distinct from eukaryotic replicative DNA polymerases. Cell, 126:893–904, 2006., , and .
 Self-organized criticality: an explanation of the 1/f noise. Phys. Rev. Lett., 59:381–384, 1987., , and .
 Self-organized criticality. Phys. Rev. A, 38:364–374, 1988., , and .
 Specificity and biological distribution of coenzyme M (2-mercaptoethanesulfonic acid). J. Bacteriol., 137:256–263, 1979. and .
 The many faces of vitamin B12: catalysis by cobalamin-dependent enzymes. Annu. Rev. Biochem., 72:209–247, 2003. and .
 Thermodynamic constraints shape the structure of carbon fixation pathways. Biochim. Biophys. Acta Bioenergetics, 1817(9):1646–1659, 2012., , , and .
 Organocatalysis lost: modern chemistry, ancient chemistry, and an unseen biosynthetic apparatus. Angew. Chem. Int. Ed., 47:42–47, 2008. III.
 Pyrophosphate synthesis in iron mineral films and membranessimulating prebiotic submarine hydrothermal precipitates. Geochim. Cosmochim. Acta, 128:1–12, 2014., , , , , , , , , and .
 The fuel cell model of abiogenesis: a new approach to origin-of-life simulations. Astrobiology, 14:254–270, 2014., , , , , , , , , , , and .
 The fermentative decomposition of purines by Clostridium acidi-urici and Clostridium cylindrosporum. J. Biol. Chem., 141(1):3–27, 1941. and .
 The path of carbon in photosynthesis XXI. The cyclic regeneration of carbon dioxide acceptor. J. Am. Chem. Soc., 76:1760–1770, 1954., , , , , and .
 An anaerobic-type a-ketoglutarate ferredoxin oxidoreductase completes the oxidative tricarboxylic acid cycle of Mycobacterium tuberculosis. PLoS Pathogens, 5:e1000662, 1–10, 2009., , , and
 Enzymes of the reductive citric acid cycle in the autotrophic eubacterium Aquifex pyrophilus and in the archaebacterium Thermoproteus neutrophilus. Arch. Microbiol., 160:306–311, 1993., , , , and .
 Les tourbillons cellulaires dans une nappe liquide. Rev. Gén. Sci. Pure Appl., 11:1261–1271, 1900..
 Metal centers in the anaerobic microbial metabolism of CO and CO2. Metallomics, 3:797–815, 2011., , , , and .
 Modern metabolism as a palimpsest of the RNA world. Proc. Natl. Acad. Sci. USA, 18:7054–7058, 1989., , and .
 Logical reversibility of computation. IBM J. Res. Dev., 17:525–532, 1973..
 The thermodynamics of computation – a review. Int. J. Theor. Phys., 21:905–940, 1982..
 Autotrophic carbon fixation in archaea. Nature Rev. Microbiol., 8:447–460, 2010., , , , , , , and .
 Graphs and Hypergraphs. North-Holland, Amsterdam, revised edition, 1973..
 Crystal structure of biotin synthase, an S-adenosylmethioninedependent radical enzyme. Science, 303(5654):76–79, 2004., , , , and .
 The Physical Basis of Life. Routledge & Kegan Paul, London, 1951..
 The Origin of Life, Weidenfeld and Nicolson, London, 1967., editor.
 Reduction of CO2 during serpentinization of olivine at 300°C and 500 bar. Geology, 24:351–354, 1996., , and
 Chemical weathering and controls on atmospheric O2 and CO2: fundamental principles were enunciated by J. J. Ebelmen in 1845. Geochim. Cosmochim. Acta, 60:1633–1637, 1996. and .
 The RNA world hypothesis: the worst theory of the early evolution of life (except for all the others). Biol. Direct, 7:23, 2012..
 Macroscopic fluctuation theory for stationary non equilibrium states. J. Stat. Phys., 107:635–675, 2002., , , , and .
 On the long-range correlations of thermodynamic systems out of equilibrium. arXiv:0705. 2996v1 [cond-mat.stat-mech], 2007., , , , and .
 Towards a nonequilibrium thermodynamics: a self-contained macroscopic description of driven diffusive systems. J. Stat. Phys., 135:857–872, 2009., , , , and .
 13C metabolic flux analysis identifies an unusual route for pyruvate dissimilation in mycobacteria which requires isocitrate lyase and carbon dioxide fixation. PLoS Pathogens, 7(7):e1002091, 07, 2011., , , , , , , , , and .
 Proc. Natl. Acad. Sci. USA, early edition:1–5, 2013., , , , , and . Nucleobases bind to and stabilize aggregates of a prebiotic amphiphile, providing a viable mechanism for the emergence of protocells.
 Fossils to Astrobiology, pages 275–295. Springer, New York, 2009.. Phylogenomic dating and the relative ancestry of prokaryotic metabolisms. In and , editors, From
 Molecular Mechanisms of Photosynthesis. Blackwell Science,Malden, MA, 2002..
 Vortices in high-temperature superconductors. Rev. Mod. Phys., 66:1125–1388, 1994., , , , and .
 Blondes in Venetian Paintings, the Nine-Banded Armadillo, and Other Essays in Biochemistry. Yale University Press, New Haven, CT, 1997..
 A hierarchical model for evolution of 23S ribosomal RNA. Nature, 457:977–980, 2009. and .
 Populäre Schriften. J. A. Barth, Leipzig, 1905. Re-issued F. Vieweg, Braunschweig, 1979..
 In Populäre Schriften, pages 25–50. J. A. Barth, Leipzig, 1905. Re-issued F. Vieweg, Braunschweig, 1979.. The second law of thermodynamics.
 Lateral gene transfer and the origins of prokaryotic groups. Annu. Rev. Genet., 37:283–328, 2003., , , , , , , and .
 Accounting for horizontal gene transfers explains conflicting hypotheses regarding the position of aquificales in the phylogeny of bacteria. BMC Evol. Biol., 8:272, 2008., , and .
 The ribosome challenge to the RNA world. J. Mol. Evol., 80:143–161, 2015., , and .
 Priscoan (4.00–4.03 Ga) orthogneisses from northwestern Canada. Contrib. Mineral Petrol., 134:3–16, 1999. and .
 New insights into the evolutionary history of biological nitrogen fixation. Frontiers Microbiol., 4:201, 2013. and .
 Coupling mechanisms in capture, transmission, and use of energy. Annu. Rev. Biochem., 46:955–1026, 1977..
 Computation of metabolic fluxes and efficiencies for biological carbon dioxide fixation. Metab. Eng., 13:150–158, 2011. and .
 The emergence and early evolution of biological carbon fixation. PLoS Comp. Biol., 8:e1002455, 2012. PMID: 22536150. and .
 The compositional and evolutionary logic of metabolism. Phys. Biol., 10:011001, 2013. PMID: 23234798. and .
 Metabolic evolution of a deep-branching hyperthermophilic chemoautotrophic bacterium. PLoS ONE, 9:e87950, 2014. and .
 Compilation, alignment, and phylogenetic relationships of DNA polymerases. Nucleic Acids Res., 21:787–802, 1993. and .
 Abiotic nitrogen reduction on the early Earth. Nature, 395:365–367, 1998., , , , , and
 Bifurcated ubihydroquinone oxidation in the cytochrome bc1 complex by proton-gated charge transfer. FEBS Lett., 387:1–6, 1996..
 Turnstiles and bifurcators: the disequilibrium converting engines that put metabolism on the road. Biochim. Biophys. Acta, 1827:62–78, 2013. and .
 Abundant transposases encoded by the metagenome of a hydrothermal chimney biofilm. ISME J., 1–5, 2009. and .
 Science and Information Theory. Dover Phoenix Editions,Mineola, NY, second edition, 2004..
 Macroecology. University of Chicago Press, Chicago, IL, 1995..
 Inorganic polyphosphate in the origin and survival of species. Proc. Natl. Acad. Sci. USA, 101:16085–16087, 2004. and .
 On the prebiotic potential of reduced oxidation state phosphorus: the H-phosphinate-pyruvate system. Chem. Commun., 46:3726–3728, 2010., , , , , and .
 A reverse Krebs cycle in photosynthesis: consensus at last. Photosynth. Res., 24:47–53, 1990. and .
 Energy conservation via electron bifurcating ferredoxin reduction and proton/Na+ translocating ferredoxin oxidation. Biochim. Biophys. Acta, 1827:94–113, 2013. and .
 Estimating the number of species in microbial diversity studies. Annu. Rev. Stat. Appl., 1:427–455, 2014., , and .
 Christopher Strachey – understanding programming languages. Higher-Order Symbolic Comput., 13:52, 2000..
 The Evolution of Individuality. Princeton University Press, Princeton, NJ, 2007..
 Marine siderophores and microbial iron mobilization. BioMetals, 18:369–374, 2005..
 Extreme genetic code optimality from a molecular dynamics calculation of amino acid polar requirement. Phys. Rev. E, 79:00901, 2009., , , and .
 Formation synthetique d'une substance sucree. Compt. Rend. Acad. Sci., 53:145–147, 1861..
 Evidence for basaltic Sr in midocean ridge-flank hydrothermal systems and implications for the global oceanic Sr isotope balance. Geochim. Cosmochim. Acta, 65:4141–4153, 2001., , , , and .
 The origin of modern metabolic networks inferred from phylogenemic analysis of protein architecture. Proc. Natl. Acad. Sci. USA, 104:9358–9363, 2007., , and .
 Structural phylogenomics retrodicts the origin of the genetic code and uncovers the evolutionary impact of protein flexibility. PLoS ONE, 8:e72225, 2013., , and .
 Genetic Takeover: and the Mineral Origins of Life. Cambridge University Press, Cambridge, 1982..
 Seven Clues to the Origin of Life – A Scientific Detective Story. Cambridge University Press, Cambridge, 1985..
115] Clay Minerals and the Origin of Life. Cambridge University Press, Cambridge, 1986. and , editors.
 Evidence of chemolithoautotrophy in the bacterial community associated with Alvinella pompehana, a hydrothermal vent polychaete. Appl. Environ. Microbiol., 69:5070–5078, 2003. and .
 Constraints on continental growth models from Nb/U ratios in the 3.5 Ga Barberton and other Archaean basalt-komatiite suites. Am. J. Sci., 303:319–351, 2003..
 Melting in an Archean mantle plume: heads it's basalts, tails it's komatiites. Nature, 339:697–699, 1989., , and .
 Reflections on the Motive Power of Fire, , editor. Dover, New York, 1960..
 The anthropic principle and the structure of the physical world. Nature, 278:605–612, 1979. and .
 The planetary air leak. Sci. Am., May:36–43, 2009. and .
 The RNA worlds in context. Cold Spring Harb. Perspect. Biol., 4:a006742, 2011..
 Crystal structures of the key anaerobic enzyme pyruvate: ferredoxin oxidoreductase, free and in complex with pyruvate. Nature Struct. Biol., 6:182–190, 1999., , , , , and .
 Algorithmic Information Theory. Cambridge University Press, New York, 1990..
 GtRNAdb: a database of transfer RNA genes detected in genomic sequence. Nucleic Acids Res., 37:D93–D97, 2008. and .
 A theory of the epigenesis of neuronal networks by selective stabilization of synapses. Proc. Natl. Acad. Sci. USA, 70:2974–2978, 1973., , and .
 Hydrothermal methane venting between 12°N and 26°N along the Mid-Atlantic ridge. J. Geophys. Res., 98:9625–9642, 1993. and .
 Amino acid biosynthesis in the spirochete leptospira: evidence for a novel pathway of isoleucine biosynthesis. J. Bacteriol., 117(1):203–211, 1974., , and .
 Treatise on the Astrolabe, Prologue, II 39–40. 1391..
 A macroscopic description of lipid bilayer phase transitions of mixed-chain phosphatidylcholines: chain-length and chain-asymmetry dependence. Biophys. J., 80:254–270, 2001., , and .
 Lethal mutagenesis in viruses and bacteria. Genetics, 183:639–650, 2009. and .
 Ribozyme catalysis of metabolism in the RNA world. Chem. Biodiv., 4:633–655, 2007., , and .
 Modularity of methylotrophy, revisited. Environ. Microbiol., 13(10):2603–2622, 2011..
 The expanding world of methylotrophic metabolism. Annu. Rev. Microbiol., 63:477–499, 2009., , and .
 C1 transfer enzymes and coenzymes linking methylotrophic bacteria and methanogenic archaea. Science, 281:99–102, 1998., , , and .
 Environmental genomics reveals a single-species ecosystem deep within earth. Science, 322:275–278, 2008., , , , , , , , , , , , , , , , , , , and .
 Production of cysteic acid, taurine and cystamine under primitive earth conditions. Nature, 210:628–629, 1966. and .
 Toward automatic reconstruction of a highly resolved tree of life. Science, 311:1283–1287, 2006., , , , , and .
 Modeling the signature of sulfur massindependent fractionation produced in the Archean atmosphere. Geochim. Cosmochim. Acta, 141:365–380, 2014., , , , , and .
 The Mechanical Theory of Heat, pages 215–250, Fourth Memoir. John van Voorst, London, 1865.. On the application of the theorem of the equivalence of transformations to interior work. In , editor,
 Viruses take center stage in cellular evolution. Genome Biol., 7:110, 2006..
 Principles of Stellar Evolution and Nucleosynthesis. University of Chicago Press, Chicago, IL, 1983..
 The nicotinamide biosynthetic pathway is a by-product of the RNA world. J. Mol. Evol., 52:73–77, 2001. and .
 Silicate-phosphate interactions in silicate glasses and melts: I. A multinuclear (27Al, 29Si, 31P) MAS NMR and ab initio chemical shielding (31P) study of phosphorus speciation in silicate glasses. Geochim. Cosmochim. Acta, 65:2395–2411, 2001., , , and .
 Assaying the catalytic potential of transition metal sulfides for abiotic carbon fixation. Geochim. Cosmochim. Acta, 68:2185–2196, 2004., , , , , and
 Primordial carbonylated iron-sulfur compounds and the synthesis of pyruvate. Science, 289:1337–1340, 2000., , , , , , and
 Geochemical roots of autotrophic carbon fixation: hydrothermal experiments in the system citric acid, H2O-(±FeS) (±NiS). Geochim. Cosmochim. Acta, 65:3557–3576, 2001., , , , , and
 Reflections on the clonal-selection theory. Nature Rev. Immunol., 7:823–830, 2007., , , , , and .
 Aspects of Symmetry. Cambridge University Press, Cambridge, 1985..
 The CMS Collaboration. Evidence for the direct decay of the 125 GeV Higgs boson to fermions. Nature Phys., 10:557–560, 2014.
 Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication. Microbiol. Rev., 45(2):316–354, 1981. and .
 Particle Physics and Cosmology. Wiley, New York, 1989., , and .
 Creative Commons. Attribution-noncommercial-sharealike 3.0 unported, April 2015. http://creativecommons.org/licenses/by-nc-sa/3.0/legalcode.
 Every good regulator of a system must be a model of that system. Int. J. Syst. Sci., 1:89–97, 1970. and .
 The Cell: A Molecular Approach. Sinauer Associates, Sunderland, MA, second edition, 2000..
 Detection and formation scenario of citric acid, pyruvic acid, and other possible metabolism precursors in carbonaceous meteorites. Proc. Natl. Acad. Sci. USA, 108:14015–14020, 2011., , , , and .
 Enzymes with extra talents: moonlighting functions and catalytic promiscuity. Curr. Opin. Chem. Biol., 7:265–272, 2003..
 A mechanism for the association of amino acids with their codons and the origin of the genetic code. Proc. Natl. Acad. Sci. USA, 102:4442–4447, 2005. PMID: 15764708., , and .
 The origin of the RNA world: co-evolution of genes and metabolism. Bioorg. Chem., 35:430–443, 2007. PMID: 17897696., , and .
 Plausible origins of homochirality in the amino acid catalyzed neogenesis of carbohydrates. Chem. Commun., 2005:2047–2049, 2005., , , , and .
 Submarine hydrothermal systems: a probable site for the origin of life. Oreg. State Univ. Sch. Oceanogr., 80-7:1–44, 1980., , and .
 Submarine thermal springs on the Galapagos rift. Science, 203:1073–1083, 1979., , , , , , , , , , and .
 Small players, large role: microbial influence on biogeochemical processes in pelagic aquatic ecosystems. Ecosystems, 5:105–121, 2002. and .
 Elements of Information Theory.Wiley, New York, 1991. and .
 Codon-antiodon pairing: the wobble hypothesis. J. Mol. Biol., 19:548–555, 1966..
 The origin of the genetic code. J. Mol. Biol., 38:367–379, 1968..
 Central dogma of molecular biology. Nature, 227:561–563, 1970..
 Life Itself: Its Origin and Nature. Simon and Schuster, New York, 1981..
 Directed panspermia. Icarus, 19:341–346, 1973. and .
 RNA virus error catastrophe: direct molecular test by using ribavirin. Proc. Natl. Acad. Sci. USA, 98:6895–6900, 2001., , and .
 Bow ties, metabolism and disease. Trends Biotechnol., 22:446–450, 2004. and .
 Estimating prokaryotic diversity and its limits. Proc. Natl. Acad. Sci. USA, 99:10494–10499, 2002., , and .
 An Introduction to Metabolic Pathways. Blackwell Scientific, Oxford, 1970. and .
 Formal Methods in Systems Biology, Lecture Notes in Computer Science, volume 5054, pages 103–122. Springer, Berlin, 2008., , , , and . Rule-based modelling, symmetries, refinements.
 The Biochemistry of Archaea, pages 1–24. Elsevier, Amsterdam, 1993.. Central metabolism of the archaea. In , , and , editors,
 Ni-Zn-[Fe4-S4] and Ni-Ni-[Fe4-S4] clusters in closed and open a subunits of acetyl-CoA synthase/carbon monoxide dehydrogenase. Nature Struct. Mol. Biol., 10(4):271–279, 2003., , , , , , and .
 On the Origin of Species. John Murray, London, 1859..
 The Life and Letters of Charles Darwin, including an Autobiographical Chapter, Vol. 3, , editor. John Murray, London, 1887..
 The Regulatory Genome: Gene Regulatory Networks in Development and Evolution. Academic Press, San Diego, CA, 2006..
 Gene regulatory networks and the evolution of animal body plans. Science, 311:796–800, 2006. and .
 The Selfish Gene. Oxford University Press, New York, 1976..
 Methane oxidation in deep-sea hydrothermal plumes of the Endeavour Segment of the Juan de Fuca Ridge. Deep-Sea Res., 40:1169–1186, 1993., , , and .
 Blueprint for a Cell. Neil Patterson, Burlington, NC, 1991..
 First Life: Discovering the Connections between Stars, Cells, and How Life Began. University of California Press, Los Angeles, CA, 2011..
 The Origins of Life. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 2011. and , editors.
 The complete genome of the hyperthermophilic bacterium Aquifex aeolicus. Nature, 392:353–358, 1998., , , , , , , , , , , , , , and .
 Generation of oligonucleotides under hydrothermal conditions by non-enzymatic polymerization. J. Mol. Evol., 78:251–262, 2014., , , and .
 The quantum event of oceanic crustal accretion: impacts of diking at mid-ocean ridges. Science, 281:222–230, 1998., , , , , , , and .
 The protein folds as platonic forms: new support for the pre-Darwinian conception of evolution by natural law. J. Theor. Biol., 219:325–342, 2002..
 Non equilibrium steady states: fluctuations and large deviations of the density and of the current. J. Stat. Mech., page P07023, 2007. arXiv:condmat/ 0703762v1..
 Tracing fluid-rock reaction and hydrothermal circulation at the Saldanha hydrothermal field. Chem. Geol., 273:168–179, 2010., , , , , , and .
 Calculations of the relative chemical stabilities of proteins as a function of temperature and redox chemistry in a hot spring. PLoS ONE, 6:e22782, 2011. and .
 The problem of the gene. Compt. Rend. Acad. Sci. Paris, 323:1139–1146, 2000..
 The in situ pH of hydrothermal fluids at midocean ridges. Earth Planet. Sci. Lett., 237:167–174, 2005., , , , , and .
 Sulfur-oxidizing bacterial endosymbionts: analysis of phylogeny and specificity by 16S rRNA sequences. J. Bacteriol., 170:2506–2510, 1988., , , , , , , and .
 Encyclopedia of Greco-Roman Mythology. ABC-Clio, New York, 1998..
 Crystal structure of a carbon monoxide dehydrogenase reveals a [Ni-4Fe- 5S] cluster. Science, 293:1281–1285, 2001., , , , and .
 Nothing in biology makes sense except in the light of evolution. Am. Biol. Teacher, 35:125–129, 1973..
 Second quantization representation for classical many-particle system. J. Phys. A, 9:1465–1478, 1976..
 Stochastic theory of diffusion-controlled reaction. J. Phys. A, 9:1479–1495, 1976..
 Using biogenic sulfur gases as remotely detectable biosignatures on anoxic planets. Astrobiology, 11:419–441, 2011., , , and .
 The fitness value of information. Oikos, 119:219–230, 2010., , and .
 Evolutionary Genomics and Systems Biology, pages 251–293. Wiley-Blackwell, Hoboken, NJ, 2010., , , , , , , and . Non-coding RNAs. In , editor,
 The Life and Letters of Herbert Spencer.D. Appleton, New York, 1908. Two volumes..
 Compilation and network analyses of Cambrian food webs. PLoS Biology, 6:e102, 2008., , , , and .
 Essentials of Stochastic Processes.Springer, New York, 1999..
 Large fluctuations and optimal paths in chemical kinetics. J. Chem. Phys., 100:5735–5750, 1994., , , and .
 An introductory lecture on political economy. Econ. J., 1(4):625–634..
 DNA-DNA solution hybridization studies of the bacterial symbionts of hydrothermal vent tube worms (Riftia pachyptila and Tevnia jerichonana). Appl. Environ. Microbiol., 57:1082–1088, 1991. and .
 Phasenumwandlungen im ueblichen und erweiterten Sinn, classifiziert nach den entsprechenden Singularitaeten des thermodynamischen Potentiales. Verh. K. Akad. Wet. Amsterdam, 36:153–157, 1933..
 Steps Toward Life.Oxford University Press, Oxford, 1992..
 From Strange Simplicity to Complex Familiarity.Oxford University Press, London, 2013..
 The hypercycle, Part A. The emergence of the hypercycle. Naturwissenschaften, 64:541–565, 1977. and .
 The hypercycle, Part C. The realistic hypercycle. Naturwissenschaften, 65:341–369, 1978. and .
 The plant-like C2 glycolate cycle and the bacterial-like glycerate pathway cooperate in phosphoglycolate metabolism in cyanobacteria. Plant Physiol., 142:333–342, 2006., , , , , , , , , and .
 The photorespiratory glycolate metabolism is essential for cyanobacteria and might have been conveyed endosymbiontically to plants. Proc. Natl. Acad. Sci. USA, 105(44):17199–17204, 2008., , , , , and .
 RNA-catalyzed RNA polymerization using nucleoside triphosphates. Nature, 382:373–376, 1996. and .
 Discovery of a new prokaryotic type I GTP cyclohydrolase family. J. Biol. Chem., 281:37586–37593, 2006., , , , , and .
 Linked magma ocean solidification and atmospheric growth for Earth and Mars. Earth Planet. Sci. Lett., 271:181–191, 2008..
 Formation of early water oceans on rocky planets. Astrophys. Space Sci., 332:359–364, 2011..
 Magma oceans in the inner solar system. Annu. Rev. Earth Planet. Sci., 40:113–139, 2012..
 Evolutionary dichotomy for rocky planets. Nature, 497:570–572, 2013..
 Experimental testing of theories of an early RNA world. Methods Enzymol, 224:646–664, 1993..
 Entropy, Large Deviations, and Statistical Mechanics.Springer-Verlag, New York, 1985..
 Functional RNAs exhibit tolerance for non-heritable 2′–5′ vs. 2′–5′ backbone heterogeneity. Nature Chem., 5:390–394, 2013., , and .
 Extinction: How Life on Earth Nearly Ended 250 Million Years Ago.Princeton University Press, Princeton, NJ, 2006..
 The evolution of hierarchical gene regulatory networks. Nature Rev. Genet., 10:141–148, 2009. and .
 The Cambrian Explosion: The Construction of Animal Biodiversity.Roberts and Company, Englewood, CO, 2013. and .
 The Cambrian conundrum: early divergence and later ecological success in the early history of animals. Science, 334:1091–1097, 2011., , , , , and .
 The Memoirs of Sherlock Holmes.Simon and Schuster, New York, 2014..
 On a hypothetical generational relationship between HCN and constituents of the reductive citric acid cycle. Chem. Biodivers., 4:554–573, 2007..
 Markov Processes: Characterization and Convergence.Wiley, New York, 1986. and .
 Nitrite-driven anaerobic methane oxidation by oxygenic bacteria. Nature, 464:543–548, 2010., , , , , , , , , , , , , , , , , , , , , , and .
 A new ferredoxin dependent carbon reduction cycle in photosynthetic bacterium. Proc. Natl. Acad. Sci. USA, 55:928–934, 1966., , and .
 Evolution of the nitrogen cycle and its influence on the biological sequestration of CO2 in the ocean. Nature, 387:272–275, 1997..
 The microbial engines that drive Earth's biogeochemical cycles. Science, 320:1034–1039, 2008., , and .
 Atmospheric influence of the Earth's earliest sulfur cycle. Science, 289:756–758, 2000., , and .
 Isotopic evidence for Mesoarchean anoxia and changing atmospheric sulphur chemistry. Nature, 449:706–709, 2007., , , , , , and .
 Observation of wavelength-sensitive mass-independent sulfur isotope effects during SO2 photolysis: implications for the early atmosphere. J. Geophys. Res., 106:32829–32839, 2001., , , and .
 Rates and equilibrium of CuA to heme a electron transfer in Paracoccus denitrificans cytochrome c oxidase. Biophys. J., 90:2131–2137, 2006., , , , and .
 Intramolecular electron transfer in cytochrome cd(1) nitrite reductase from Pseudomonas stutzeri; kinetics and thermodynamics. Biophys. Chem., 98:27–34, 2002., , , and .
 A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. Mol. Syst. Biol., 3:121:1–18, 2007., , , , , , , , and .
 Versuch einer theorie der ß-strahlen. i. Z. Phys., 88:161–177, 1934..
 Thermodynamics.Dover, New York, 1956..
 Mineral catalysis and prebiotic synthesis: montmorillonitecatalyzed formation of RNA. Elements, 1:145–149, 2005..
 An unusual photochemical re-arrangement in the synthesis of adenine from hydrogen cyanide. J. Am. Chem. Soc., 88:1074, 1966. and .
 Catalysis in prebiotic chemistry: application to the synthesis of RNA oligomers. Adv. Space Res., 33:100–105, 2004., , , , and .
 Studies in prebiotic synthesis: III. Synthesis of pyrimidines from cyanoacetylene and cyanate. J. Mol. Biol., 33:693–704, 1968., , and .
 The stepwise evolution of early life driven by energy conservation. Mol. Biol. Evol., 23:1286–1292, 2006. and .
 High-energy chemistry of formamide: a unified mechanism of nucleobase formation. Proc. Natl. Acad. Sci. USA, early edition:1412072111, 2014., , , , , , , and .
 The faint young sun problem. Rev. Geophys., 50:RG2006, 2012..
 Space-time approach to quantum electrodynamics. Phys. Rev., 76:769–789, 1949..
 A novel metabolic cycle catalyzes glucose oxidation and anaplerosis in hungry Escherichia coli. J. Biol. Chem., 278(47):46446–46451, 2003. and .
 The structures and physicochemical properties of organic cofactors in biocatalysis. J. Mol. Biol., 403:803–824, 2010., , , and .
 Spin Glasses.Cambridge University Press, New York, 1991. and .
 The Genetical Theory of Natural Selection.Oxford University Press, London, 2000..
 Phosphorus compounds of muscle and liver. Science, 70:381–382, 1929. and .
 Modeling ‘Evo-Devo’ with RNA. Bioessays, 24:1164–1177, 2002..
 Boundaries and Barriers, pages 56–116. Addison-Wesley, New York, 1996. and . The barrier of objects: from dynamical systems to bounded organizations. In and , editors,
 Beyond digital naturalism. Artificial Life, 1:211–227, 1994., , and .
 Structure-function relationships of anaerobic gas-processing metalloenzymes. Nature, 460:814–822, 2009., , , , and .
 Structure/function relationships of [NiFe]- and [FeFe]-hydrogenases. Chem. Rev., 107:4273–4303, 2007., , , and .
 Defining life: the virus viewpoint. Orig. Life Evol. Biosphere, 40:151–160, 2010..
 Geodiversity of hydrothermal processes along the Mid-Atlantic Ridge and ultramafic-hosted mineralization: a new type of oceanic Cu-Zn-Co- Au volcanogenic massive sulfide deposit. Geophys. Monogr. Ser., 188:321–367, 2010., , , , , , , , , , , , , and .
 Ancestral reconstruction of a pre-LUCA aminoacyltRNA synthetase ancestor supports the late addition of Trp to the genetic code. J. Mol. Evol., 80:171–185, 2015. and .
 Molecular evolution of aminoacyl tRNA synthetase proteins in the early history of life. Orig. Life Evol. Biosphere, 41:621–632, 2011., , , and .
 Hydrocarbons in hydrothermal vent fluids: the role of chrome-bearing catalysts. Science, 304:1002–1005, 2004. and .
 Chemical and isotopic constraints on water/rock interactions at the Lost City hydrothermal field, 30° N Mid-Atlantic Ridge. Geochim. Cosmochim. Acta, 72:5457–5474, 2008., , and .
 Origin and evolution of the ribosome. Cold Spring Harb. Perspect. Biol., 2:a003483, 2010..
 The Genetic Code and the Origin of Life, pages 92–105. Kluwer Academic/Plenum, New York, 2004. and . The evolutionary history of the ribosome. In , editor,
 The Genetic Code and the Origin of Life, pages 680–682. Kluwer Academic/Plenum, New York, 2004. and . The evolutionary history of the translation machinery. In , editor,
 Photorespiratory metabolism: genes, mutants, energetics, and redox signaling. Annu. Rev. Plant Biol., 60:455–484, 2009., , , and .
 The Price equation, Fisher's fundamental theorem, kin selection, and causal analysis. Evolution, 51:1712–1729, 1997..
 Fisher's fundamental theorem of natural selection. Trends Ecol. Evol., 7:92–95, 1992. and .
 Molecular configuration in sodium thymonucleate. Nature, 171:740–741, 1953. and .
 The genetic code is one in a million. J. Mol. Evol., 47:238–248, 1998. and .
 Early fixation of an optimal genetic code. Mol. Biol. Evol., 17:511–518, 2000., , , and .
 Random Perturbations in Dynamical Systems.Springer, New York, second edition, 1998. and .
 The redox state of Earth's mantle. Annu. Rev. Earth. Planet. Sci., 36:389–420, 2008. and .
 The Emergence of Life on Earth: A Historical and Scientific Overview.Rutgers University Press, New Brunswick, NJ, 2000..
 CO2 fixation in acetogenic bacteria: variations on a theme. FEMS Microbiol. Lett., 38:181–213, 1986..
 Alternative pathways of carbon dioxide fixation: insights into the early evolution of life?Annu. Rev. Microbiol., 65(1):631–658, 2011..
 Studies in prebiotic synthesis: VII. Solid-state synthesis of purine nucleosides. J. Mol. Evol., 1:249–257, 1972., , and .
 Fermentation of 4-aminobutyrate by Clostridium aminobytyricum: cloning of two genes involved in the formation and dehydration of 4-hydroxybutyryl-CoA. Arch. Microbiol., 174:189–199, 2000., , , , and .
 Occurrence of facultative anoxygenic photosynthesis among filamentous and unicellular cyanobacteria. J. Bacteriol., 129:623–629, 1977., , and .
 The Struggle for Existence.Williams and Wilkins, Baltimore, MD, 1934..
 The Private Science of Louis Pasteur.Princeton University Press, Princeton, NJ, 1995..
 The Quark and the Jaguar: Adventures in the Simple and the Complex.Freeman, New York, 1994..
 Information measures, effective complexity, and total information. Complexity, 2:44–52, 1996. and .
 Quantum electrodynamics at small distances. Phys. Rev., 95:1300–1312, 1954. and .
 Philosophy and the practice of Bayesian statistics. Br. J. Math. Stat. Psychol., 66:8–38, 2013. arXiv:1006.3868. and .
 Sodium ion cycling mediates energy coupling between complex I and ATP synthase. Proc. Natl. Acad. Sci. USA, 100:839–844, 2003., , and .
 Lie Algebras in Particle Physics.Perseus, New York, second edition, 1999..
 Crystallographic structure of the nitrogenase iron protein from Azotobacter vinelandii. Science, 257(5077):1653–1659, 1992., , , , , and .
 Cells, Embryos, and Evolution.Wiley, New York, 1997. and .
 The theory of facilitated variation. Proc. Natl. Acad. Sci. USA, 104:8582–8589, 2007. and .
 The RNA World.Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 2006., , and , editors.
 Peptidyl transfers in gramicidin S biosynthesis from enzyme-bound thioester intermediates. Proc. Natl. Acad. Sci. USA, 63:1335–1342, 1969., , and .
 Erratum: Peptidyl transfers in gramicidin S biosynthesis from enzyme-bound thioester intermediates. Proc. Natl. Acad. Sci. USA, 65:249, 1970., , and .
 Synthesis of novel citrate-based siderophores and siderophore-ß-lactam conjugates. Iron transport-mediated drug delivery systems. J. Org. Chem., 58:7652–7659, 1993. and .
 Teaching the principles of statistical dynamics. Am. J. Phys., 74:123–133, 2006., , , , and .
 The RNA world.Nature, 319:618, 1986..
 Thermodynamic Theory of Structure, Stability, and Fluctuations.Wiley, New York, 1971. and .
 The Theory of Rate Processes.McGraw Hill, New York, 1941., , and .
 Magnesium silicate perovskite and effect of iron oxidation state on its bulk sound velocity at the conditions of the lower mantle. Earth Planet. Sci. Lett., 393:182–186, 2014., , , , , , , and .
 Prokaryotic evolution in light of gene transfer. Mol. Biol. Evol., 19:2226–2238, 2002., , and .
 Lectures on Phase Transitions and the Renormalization Group.Westview Press, Boulder, CO, 1992..
 Life is physics: evolution as a collective phenomenon far from equilibrium. Annu. Rev. Condens. Matter Phys., 2:375–399, 2011. and .
 Classical Mechanics.Addison Wesley, New York, third edition, 2001., , and .
 On the nature of the function expressive of the law of human mortality, and on a new mode of determining the value of life contingencies. Philos. Trans. R. Soc. London, 115:513–585, 1825..
 Wonderful Life.Norton, New York, 1989..
 The Structure of Evolutionary Theory.Harvard University Press, Cambridge, MA, 2002..
 Exaptation – a missing term in the science of form. Paleobiology, 8:4–15, 1982. and .
 Chemical Bonds: An Introduction to Atomic and Molecular Structure.University Science Press, Sausalito, CA, 1994..
 The chemistry and catalysis of the water gas shift reaction. J. Catal., 67:90–102, 1981., , and .
 Characterization of an Fe2+-dependent archaeal-specific GTP cyclohydrolase, MptA, from Methanocaldococcus jannaschii. Biochemistry, 46:6658–6667, 2007., , , and .
 The aconitase family: three structural variations on a common theme. Trends Biochem. Sci., 22:3–6, 1997., , and .
 The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme. Cell, 35:849–857, 1983., , , , and .
 Differential Topology.Prentice Hall, New York, 1974. and .
 The hyperthermophilic bacterium Aquifex aeolicus: from respiratory pathways to extremely resistant enzymes and biotechnological applications. Adv. Microb. Physiol., 61:125–194, 2012., , , , , , , and .
 A membrane-bound multienzyme, hydrogen-oxidizing, and sulfur-reducing complex from the hyperthermophilic bacterium Aquifex aeolicus. J. Biol. Chem., 280:42004–42015, 2005., , , , , and .
 Phosphorus as a factor in the origin of life. Am. Sci., 43:479–489, 1955..
 Understanding nature's catalytic toolkit. Trends Biochem. Sci., 30:622–629, 2005. and .
 Studies in Social Psychology in World War II Volume IV: Measurement and Prediction, pages 60–90. Wiley, New York, 1950.. The basis for scalogram analysis. In , , , , , and , editors,
 Photo-production of lactate from glyoxylate: how minerals can facilitate energy storage in a prebiotic world. Chem. Commun., 46:2265–2267, 2010. and .
 Generelle Morphologie der Organismen. Allgemeine Grundzüge der organischen Form-Wissenschaft, Mechanisch begründet durch die von Charles Darwin reformirte Descendenz-Theorie.G. Reimer, Berlin, 1866..
 A quantitative measure of error minimization in the genetic code. J. Mol. Evol., 33:412–417, 1991. and .
 The origin of life. Rationalist Animal, page 148, 1929. Reprinted as ..
 The Origin of Life, pages 242–249. Weidenfeld and Nicolson, London, 1967.. The origin of life. In , editor,
 Electrochemistry.Wiley, New York, completely revised and updated edition, 2007., , and .
 Emergence of two types of terrestrial planet on solidification of magma ocean. Nature, 497:607–610, 2013., , and .
 The genetical evolution of social behavior IJ. Theor. Biol., 7:1–16, 1964..
 The genetical evolution of social behavior. II. J. Theor. Biol., 7:17–52, 1964..
 Selfish and spiteful behavior in an evolutionary model. Nature, 228:1218–1220, 1970..
 Expanding metabolic networks: scopes of compounds, robustness, and evolution. J. Mol. Evol., 61:498–512, 2005., , and .
 Lambda Calculi: A Guide for Computer Scientists.Oxford University Press, New York, 1994..
 Ribosomal history reveals origins of modern protein synthesis. PLoS ONE, 7:e32776, 2012. and .
 Molecular Genetics of Mycobacteria, ASM Press, Washington, DC, 2000. and , editors.
 SO2 photoexcitation mechanism links mass-independent sulfur isotopic fractionation in cryospheric sulfate to climate impacting volcanism. Proc. Natl. Acad. Sci. USA, 110:17656–17661, 2013., , , , , , and .
 Synthesis and fluorescence characterization of pteridine adenosine nucleoside analogs for DNA incorporation. Anal. Biochem., 298:231–240, 2001., , , and .
 Progress in Biological Chirality, Chapter 11, pages 137–151. Elsevier, New York, 2004.. Chiral crystal faces of common rock-forming minerals. In , , and , editors,
 Mineral surfaces and the prebiotic selection and organization of biomolecules (Presidential address to the Mineralogical Society of America). Am. Mineral., 91:1715–1729, 2006..
 Paleomineralogy of the Hadean eon: a preliminary species list. Am. J. Sci., 313:807–843, 2006..
 Hydrothermal reactions of pyruvic acid: synthesis, selection, and self-assembly of amphiphilic molecules. Orig. Life Evol. Biosphere, 37:143–152, 2007. and .
 Mineral evolution: mineralogy in the fourth dimension. Elements, 6:9–12, 2010. and .
 Mineral surfaces, geochemical complexities, and the origins of life. Cold Spring Harb. Perspect. Biol., 2:a002162, 2010. and .
 2015., , , , and . Mineral ecology: chance and necessity in the mineral diversity of terrestrial planets. Can. Mineral., in press,
 Mineral evolution. Am. Mineral., 93:1693–1720, 2008., , , , , , , and .
 Thiol:fumarate reductase (Tfr) from Methanobacterium thermoautotrophicum identification of the catalytic sites for fumarate reduction and thiol oxidation. Eur. J. Biochem., 253:292–299, 1998., , , and .
 Organic sulfur compounds resulting from the interaction of iron sulfide, hydrogen sulfide and carbon dioxide in an anaerobic aqueous environment. Orig. Life Evol. Biosphere, 26:131–150, 1996. and .
 Thermal generation of pteridines and flavines from amino acid mixtures. Angew. Chem. Int. Ed. Engl., 8:478–483, 1979., , and .
 Chemistry of star-forming regions. J. Phys. Chem., 109:4017–4029, 2005..
 Energy conservation via electron-transferring flavoprotein in anaerobic bacteria. J. Bacteriol., 190:784–791, 2008., , , and .
 Cellular differentiation and individuality in the ‘minor’ multicellular taxa. Biol. Rev., 88:844–861, 2013., , , and .
 The intramolecular facilitated hydrolytic rates of methyl-substituted succinanilic acids. J. Am. Chem. Soc., 88:3805–3808, 1966., , and .
 Synthesis of adenine from HCN tetramer and ammonium formate. Orig. Life Evol. Biosphere, 32:99–102, 2002. and .
 The Mechanical Theory of Heat.John van Voorst, London, 1865., editor.
 Evolution of photosynthesis. Annu. Rev. Plant Biol., 62:515–548, 2011. and .
 The Subseafloor Biosphere at Mid-Ocean Ridges, pages 13–24. American Geophysical Soceity, vol. 144, Washington DC, 2004. and . The upper temperature limit for life based on hyperthermophile culture experiments and field observations. In , , , , and , editors,
 Thermophilic and hyperthermophilic microorganisms in 3–30°C hydrothermal fluids following a deep-sea volcanic eruption. FEMS Microbiol. Ecol., 25:33–41, 1998., , and .
 Glasses as sources of condensed phosphates on the early earth. Geochem. Trans., 15:8, 2014..
 The rate of turnover of the adenosine triphosphate pool of Escherichia coli growing aerobically in simple defined media. Arch. Microbiol., 83:95–109, 1972., , and .
 Chloroflexus aurantiacus secretes 3-hydroxypropionate, a possible intermediate in the assimilation of CO2 and acetate. Arch. Microbiol., 151:252–256, 1989..
 Polyglucose synthesis in Chloroflexus aurantiacus studied by 13C-NMR. Evidence for acetate metabolism by a new metabolic pathway in autotrophically grown cells. Arch. Microbiol., 148:292–297, 1987. and .
 Constraints on Hadean geodynamics from mineral inclusions in >4 Ga zircons. Earth Planet. Sci. Lett., 298:367–376, 2010., , and .
 Detecting autocatalytic, self-sustaining sets in chemical reaction systems. J. Theor. Biol., 227:451–461, 2004. and .
 Required levels of catalysis for emergence of autocatalytic sets in models of chemical reaction systems. Int. J. Mol. Sci., 12:3085–3101, 2011., , and .
 The structure of autocatalytic sets: evolvability, enablement, and emergence. Acta Biotheor., 60:379–392, 2012. arXiv:1205.0584v2., , and .
 Abiogenic methane formation and isotopic fractionation under hydrothermal conditions. Science, 285:1055–1057, 1999. and .
 On the evolution of biochemical synthesis. Proc. Natl. Acad. Sci. USA, 31:153–157, 1945..
 Iron(II) plus RNA can catalyze electron transfer. Nature Chem., 5:525–528, 2013., , , , , , , , , , and .
 Peeling the onion: establishing a chronology of early ribosome evolution. Mol. Biol. Evol., 26:2415–2425, 2009., , , and .
 Statistical Mechanics.Wiley, New York, 1987..
 Mechanism for the coupling of ATP hydrolysis to the conversion of 5-formyltetrahydrofolate to 5,10-methenyltetrahydrofolate. J. Biol. Chem., 270(38):22296–22300, 1995. and .
 Synthesis of 35–40mers of RNA oligomers from unblocked monomers. A simple approach to the RNA world. Chem. Commun., 2003:1458–1459, 2003. and .
 ASD: a comprehensive database of allosteric proteins and modulators. Nucleic Acids Res., 39:D663–D669, 2011., , , , , , , , , , , , , , and .
 Activated acetic acid by carbon fixation on (Fe,Ni)S under primordial conditions. Science, 276:245–247, 1997. and .
 Primordial reductive amination revisited. Tetrahedron Lett., 44:1695–1697, 2003. and .
 A dicarboxylate/4-hydroxybutyrate autotrophic carbon assimilation cycle in the hyperthermophilic archaeum Ignicoccus hospitalis. Proc. Natl. Acad. Sci. USA, 105:7851–7856, 2008., , , , , , , and .
 Impact of cultureindependent studies on the emerging phylogenetic view of bacterial diversity. J. Bacteriol., 180:4765–4774, 1998., , and .
 Beyond the Calvin cycle: autotrophic carbon fixation in the ocean. Annu. Rev. Marine Sci., 3:261–289, 2011. and .
 Autotrophic CO2 fixation via the reductive tricarboxylic acid cycle in different lineages within the phylum Aquificae: evidence for two ways of citrate cleavage. Env. Microbiol., 9:81–92, 2007., , , , and .
 Variations in the S33, S34, and S33 contents of meteorites and their relation to chemical and nuclear effects. J. Geophys. Res., 70:3475–3484, 1965. and .
 Thermal and non-thermal escape mechanisms for terrestrial bodies. Planet. Space Sci., 30:773, 1982..
 Ribosome origins: the relative age of 23S rRNA domains. Orig. Life Evol. Biosphere, 36:421–429, 2006., , , and .
 Literature and Science.Ox Bow Press, Woodbridge, CT, 1991..
 Synthesis of cytidine ribonucleotides by stepwise assembly of the heterocycle on a sugar phosphate. ChemBioChem, 4:504–507, 2003., , , and .
 Comparative transcriptome analysis reveals vertebrate phylotipic period during organogenesis. Nature Commun., 2:248, 2011. and .
 Genetic regulatory mechanisms in the synthesis of proteins. J. Mol. Biol., 3:318–356, 1961. and .
 The fidelity of template-directed oligonucleotide ligation and the inevitability of polymerase function. Orig. Life Evol. Biosphere, 29:375–390, 1999. and .
 Information theory and statistical mechanics. Phys. Rev., 106:620–630, 1957. Reprinted in ..
 Information theory and statistical mechanics. II. Phys. Rev., 108:171–190, 1957. Reprinted in ..
 The minimum entropy production principle. Annu. Rev. Phys. Chem., 31:579–601, 1980..
 Probability Theory: The Logic of Science.Cambridge University Press, New York, 2003..
 Dynamical Theory of Gases.Cambridge University Press, London, fourth edition, 2009. Original edition, 1916..
 An invariant form for the prior probability in estimation problems. Proc. R. Soc. London, Ser. A, 186:453–461, 1946..
 Scientific Inference.Cambridge University Press, London, second edition, 1957..
 Excess 3He and 4He in Galapagos submarine hydrothermal waters. Nature, 272:156–158, 1978., , and .
 Enzyme recruitment in evolution of new function. Annu. Rev. Microbiol., 30:409–425, 1976..
 Detection of mantle plumes in the lower mantle by diffraction tomography: Hawaii. Earth Planet. Sci. Lett., 159:99–115, 1998. and .
 Theory and Applications of Satisfiability Testing, Lecture Notes in Computer Science, volume 3542, pages 199–210. Springer, New York, 2005., , and . From spin glasses to hard satisfiable formulas. In and , editors,
 Ionization of a critical adenosine residue in the Neurospora Varkud satellite ribozyme active site. Biochem., 42:4265–4276, 2003. and .
 Origins of Life: The Central Concepts, pages xi–xii. Jones and Bartlett, Boston, MA, 1994.. Foreword. In and , editors,
 Polymerisation in Bilayers. PhD Thesis, Technische Universiteit Eindhoven, 2000..
 The structural and biochemical foundations of thiamin biosynthesis. Annu. Rev. Biochem., 78(1):569–603, 2009., , and .
 Proton-coupled electron transfer in cytochrome oxidase. Chem. Rev., 110:7062–7081, 2010., , and .
 The dissociation constants of tetrahydrofolic acid. J. Biol. Chem., 241:5845–5850, 1966. and .
 Strongly Correlated Fermions and Bosons in Low-Dimensional Disordered Systems, pages 313–340. Springer-Verlag, Heidelberg, 2002.. Keldysh and Doi–Peliti techniques for out-of-equilibrium systems. In , , , and , editors,
 Purification of three aminotransferases from Hydrogenobacter thermophilus TK-6 – novel types of alanine or glycine aminotransferase: enzymes and catalysis. FEBS J., 277:1876–1885, 2010. PMID: 20214682., , , and .
 Eutectic phases in ice facilitate nonenzymatic nucleic acid synthesis. Astrobiology, 1:271–281, 2001., , and .
 The KEGG database. Novartis Found. Symp., 247:91–101, 2002. www.genome.ad.jp/kegg/..
 The MetaCyc database. Nucleic Acids Res., 30:59–61, 2002. http://ecocyc.org/ecocyc/metacyc.html., , , and .
 Nutrient fluxes to planktonic osmotrophs in the presence of fluid motion. Oceanogr. Marine Biol. Annu. Rev., 34:71–107, 1996. and .
 Motion of diatom chains in a steady shear flow. Limnol. Oceanogr., 43:1767–1773, 1998. and .
 Coupling of ferredoxin and heterodisulfide reduction via electron bifurcation in hydrogenotrophic methanogenic archaea. Proc. Natl. Acad. Sci. USA, 108:2981–2986, 2012., , , and .
 Climatic consequences of very high CO2 levels in the early Earth's atmosphere. Science, 234:1383–1385, 1986. and .
 Evolution of a habitable planet. Annu. Rev. Astron. Astrophys., 41:429–463, 2003. and .
 Atmosphere composition and climate on the early Earth. Philos. Trans. R. Soc. London, Ser. B, 361:1733–1742, 2006. and .
 Loss of water from Venus. I Hydrodynamic escape of hydrogen. Icarus, 53:479–508, 1983. and .
 Photochemistry of methane in the Earth's early atmosphere. Precambrian Res., 20:121–148, 1983., , and .
 A new parameterization of hydrous mantle melting. Geochem. Geophys. Geosyst., 4:1073, 2003. doi:10.1029/2002GC000433., , and .
 Autocatalytic sets of proteins. J. Theor. Biol., 119:1–24, 1986..
 Late Archean biospheric oxygenation and atmospheric evolution. Science, 317:1900–1903, 2007., , , , , , , , , and .
 High incidence of halotolerant bacteria in Pacific hydrothermal vent and pelagic environments. FEMS Microbiol. Ecol., 32:429–460, 2000. and .
 Horizontal gene transfer in eukaryotic evolution. Nature Rev. Genet., 9:605–628, 2008. and .
 From the mantle to microbes: the Lost City hydrothermal field. Oceanography, 18:32–45, 2005..
 Volcanoes, fluids, and life at mid-ocean ridge spreading centers. Annu. Rev. Earth Planet. Sci., 30:385–491, 2002., , and .
 the AT3-60 Shipboard Party. An off-axis hydrothermal vent field near the Mid-Atlantic Ridge at 30° N. Nature, 412:145–149, 2001., , , , , , , , , , , and
 A serpentinite-hosted ecosystem: the Lost City hydrothermal field. Science, 307:1428–1434, 2005., , , , , , , , , , , , , , , , , , , , , , , , , and .
 A Treatise on Probability.MacMillan, London, 1921..
 The Collected Writings of John Maynard Keynes: Volume 4, A Tract on Monetary Reform.Cambridge University Press, London, 2012..
 A coupled atmosphere-ecosystem model of the early Archean Earth. Geobiology, 3:53–76, 2005., , and .
 Enzyme promiscuity: a mechanistic and evolutionary perspective. Annu. Rev. Biochem., 79:471–505, 2010. and .
 Role of chemistry versus substrate binding in recruiting promiscuous enzyme functions. Biochemistry, 50:2683–2690, 2011., , , and .
 The glycine cleavage system: composition, reaction mechanism, and physiological significance. Mol. Cell. Biochem., 1:169–187, 1973..
 Energetic selection of topology in ferredoxins. PLoS Comp. Biol., 8:e1002463, 2012., , , , and .
 Structural models for the metal centers in the nitrogenase molybdenum-iron protein. Science, 257(5077):1677–1682, 1992. and .
 Three serendipitous pathways in E. coli can bypass a block in pyridoxal-5′-phosphate synthesis. Mol. Syst. Biol., 6:436:1–13, 2010., , , , and .
 General models of multilocus evolution. Genetics, 161:1727–1750, 2002., , and .
 Evolvability. Proc. Natl. Acad. Sci. USA, 95(15):8420–8427, 1998. and .
 Thermal Physics.Freeman, New York, second edition, 1980. and .
 Selection, history and chemistry: the three faces of the genetic code. Trends Biochem. Sci., 24:241–247, 1999., , and .
 Rewiring the keyboard: evolvability of the genetic code. Nature. Rev. Genet., 2:49–58, 2001., , and .
 Life on a Young Planet.Princeton University Press, Princeton, NJ, 2003..
 Curie–Weiss magnet – a simple model of phase transition. Eur. J. Phys., 34:1555–1573, 2013., , and .
 The Phases of Quantum Chromodynamics: From Confinement to Extreme Environments.Cambridge University Press, Cambridge, 2004. and .
 New metric invariant of transitive dynamical systems and endomorphisms of Lebesgue spaces. Dokl. Akad. Nauk SSSR, 119:861–864, 1958..
 Entropy per unit time as a metric invariant of automorphism. Dokl. Akad. Nauk SSSR, 124:754–755, 1959..
 On tables of random numbers. Sankhyā Ser. A, 25:369–375, 1963. Reprinted in ..
 On tables of random numbers. Theor. Comput. Sci., 207:387–395, 1998..
 Modern Thermodynamics: From Heat Engines to Dissipative Structures.Wiley, New York, 1998. and .
 On the origin of genomes and cells within inorganic compartments. Trends Genet., 21:647–654, 2005. and .
 Initiation and evolution of plate tectonics on Earth: theories and observations. Annu. Rev. Earth Planet. Sci., 41:117–151, 2013..
 Inorganic polyphosphate: a molecule of many functions. Annu. Rev. Biochem., 68:89–125, 1999., , and .
 Redundancy, antiredundancy, and the robustness of genomes. Proc. Natl. Acad. Sci. USA, 99:1405–1409, 2002. and .
 The role of citric acid in intermediate metabolism in animal tissues. Enzymologia, 4:148–156, 1937. and .
 The stochastic behavior of a molecular switching circuit with feedback. Biol. Direct, 2:13, 2007. PMID: 17540019., , , and .
 Self-splicing RNA: autoexcision and autocyclization of the ribosomal RNA intervening sequence of Tetrahymena. Cell, 31:147–157, 1982., , , , , and .
 The Structure of Scientific Revolutions.University of Chicago Press, Chicago, IL, 1962..
 Electron tunneling paths in proteins. Science, 236:1647–1652, 2000. and .
 Biochemistry of inorganic polyphosphates. Rev. Physiol. Biochem. Pharmacol., 73:131–158, 1975..
 The Biochemistry of Inorganic Polyphosphates.Wiley, New York, second edition, 2004., , and .
 Hydrothermal Fe fluxes during the Precambrian: effect of low oceanic sulfate concentrations and low hydrostatic pressure on the composition of black smokers. Earth Planet. Sci. Lett., 235:654–662, 2005. and .
 Inferring clocks when lacking rocks: the variable rates of molecular evolution in bacteria. Biol. Direct, 4:35, 2009. and .
 Long-range interacting Systems, Chapter 2. Oxford University Press, Oxford, 2010.. Six out of equilibrium lectures. In , , and , editors,
 Biogenesis: Theories of Life's Origin.Oxford University Press, London, 1999..
 Philosophie Zoologique ou Exposition des Considérations Relatives à l'Histoire Naturelle des Animaux.Cambridge University Press, London, 2011. Original edition, 1809..
 Theory of phase transformations. Zh. Eksp. Teor. Fiz., 7:19–32, 1937..
 Irreversibility and heat generation in the computing process. IBM J. Res. Dev., 3:183–191, 1961..
 Power, Sex, Suicide: Mitochondria and the Meaning of Life.Oxford University Press, Oxford, 2005..
 Why are cells powered by proton gradients?Nature Ed., 3:18, 2010..
 The energetics of genome complexity. Nature, 467:929–934, 2010. and .
 The origin of membrane bioenergetics. Cell, 151:1406–1416, 2012. and .
 How did LUCA make a living? Chemiosmosis in the origin of life. Bioessays, 32:271–280, 2010., , and .
 Energy, genes, and evolution: introduction to an evolutionary synthesis. Philos. Trans. R. Soc. London, Ser. B, 368:1–5, 2013., , , and .
 Elevated concentrations of formate, acetate, and dissolved organic carbon found at the Lost City hydrothermal field. Geochim. Cosmochim. Acta, 74:941–952, 2010., , , , and .
 Mantle melting beneath mid-ocean ridges. Oceanography, 20:78–89, 2007. and .
 Mémoire sur la probabilité des causes par les évènements. Mém. Acad. Sci. Paris, 6:621–656, 1774..
 Mémoire sur les approximations des formules qui sont fonctions de très grands nombres et sur leur application aux probabilités. Mém. Acad. R. Sci. Paris, année 1809:353–415, 1810..
 Magnetotactic bacteria, magnetosomes and their application. Microbiol. Res., 167:507–519, 2012., , , , , and .
 Biology of the Prokaryotes.Blackwell Science, New York, 1999., , and .
 The units of selection. Annu. Rev. Ecol. System., 1:1–18, 1970..
 The Genetic Basis of Evolutionary Change.Columbia University Press, New York, 1974..
 Coupled ferredoxin and crotonyl coenzyme A (CoA) reduction with NADH catalyzed by the butyryl-CoA dehydrogenase/Etf complex from Clostridium kluyveri. J. Bacteriol., 190:843–850, 2008., , , , , and .
 An Introduction to Kolmogorov Complexity and its Applications.Springer, Heidelberg, third edition, 2008. and .
 The constancy of upper mantle fO2 through time inferred from V/Sc ratios in basalts. Earth Planet. Sci. Lett., 228:483–493, 2004. and .
 Long-term sustainability of a high-energy, low-diversity crustal biome. Science, 314:479–482, 2006., , , , , , , , , , , , , and .
 Self-sustained replication of an RNA enzyme. Science, 323:1229–1232, 2009. and .
 Nonlinear dynamics: jamming is not just cool any more. Nature, 396:21–22, 1998. and .
 Transcriptome dynamics of Deinococcus radiodurans recovering from ionizing radiation. Proc. Natl. Acad. Sci. USA, 100:4191–4196, 2003., , , , , , , , , , , , , , and .
 Incorporation of C14 from carbon dioxide into sugar phosphates, carboxylic acids, and amino acids by Clostridium thermoaceticum. J. Bacteriol., 89:1055–1064, 1965. and .
 Total synthesis of acetate from CO2. I. CO-methylcobyric acid and CO-(methyl)-5-methoxybenzimidazolylcobamide as intermediates with Clostridium thermoaceticum. Biochemistry, 4:2771–2780, 1965., , and .
 The Structure and Confirmation of Evolutionary Theory.Princeton University Press, Princeton, NJ, 1994..
 The mechanism of aconitase: 1.8 Å resolution crystal structure of the S642A:citrate complex. Protein Sci., 8:2655–2662, 1999., , , and .
 Early evolution of the biotin-dependent carboxylase family. BMC Evol. Biol., 11:232:1–22, 2011. and .
 From Suns to Life: a Chronological Approach to the History of Life on Earth, pages 171–174. Springer, Dordrecht, 2006., , and . Origin and evolution of compartments. In , , , , , , and , editors,
 Gaia: A New Look at Life on Earth.Oxford University Press, London, 2000..
 Geologic evidence for Archean atmospheric and climatic CO2, CH4, and O2 with an overriding tectonic control. Geology, 36:493–496, 2004. and .
 Seafloor hydrothermal systems. J. Geophys. Res., 100:327–352, 1995., , and .
 U–Th systematics and 230Th ages of carbonate chimneys at the Lost City hydrothermal field. Geochim. Cosmochim. Acta, 75:1869–1888, 2011., , , , and .
 Emergence of Life: From Chemical Origins to Synthetic Biology.Cambridge University Press, London, 2006.. The
 Lipid vesicles as possible intermediates in the origin of life. Curr. Op. Colloids Interface Sci., 4:33–39, 1999., , and .
 Helium, heat, and the generation of hydrothermal event plumes at mid-ocean ridges. Earth Planet. Sci. Lett., 171:343–350, 1999., , and .
 Rapid growth at deep-sea vents. Nature, 371:663–664, 1994., , , , , , and .
 Lipid phases: structure and structural transitions. Annu. Rev. Phys. Chem., 25:79–94, 1974. and .
 Modern Theory of Critical Phenomena.Perseus, New York, 1976..
 Folates and Pterins, vol. 1: Chemistry and Biochemistry of Folates, pages 255–306. John Wiley & Sons, New York, 1984.. Biogenesis and interconversion of substituted tetrahydrofolates. In and , editors,
 The advent and development of organocatalysis. Nature, 455:304–308, 2008..
 Tetrahydrofolate and tetrahydromethanopterin compared: functionally distinct carriers in C1 metabolism. Biochem. J., 350:609–629, 2000..
 Effect of focusing and caustics on exit phenomena in systems lacking detailed balance. Phys. Rev. Lett., 71:1783–1786, 1993. and .
 Oscillatory behavior of the rate of escape through an unstable limit cycle. Phys. Rev. Lett., 77:4860–4863, 1996. and .
 Stop asking why there's anything. Erkenntnis, 77:51–63, 2012..
 An Essay on the Principle of Population.Cosimo, New York, 2007. Original edition, 1798..
 HCN polymers characterized by SSNMR: solid state reaction of crystalline tetramer (diaminomaleonitrile). J. Chem. Phys., 130:134504, 2009. and .
 The basic reproductive ratio of life. J. Theor. Biol., 263:317–327, 2010., , and .
 The role of sufficiency and of estimation in thermodynamics. Ann. Math. Stat., 33:1021–1038, 1962..
 Geology, age and origin of supracrustal rocks at Akilia, West Greenland. Am. J. Sci., 306:303–366, 2006., , and .
 Five Kingdoms: An Illustrated Guide to the Phyla of Life on Earth.W. H. Freeman, New York, 1998. and .
 Physiological proteomics of the uncultured endosymbiont of Riftia pachyptila. Science, 315:247–250, 2007., , , , , , , , , , , and .
 Mineralogy, geochemistry, and Nd isotope composition of the Rainbow hydrothermal field, Mid-Atlantic Ridge. Miner. Deposita, 41:52–67, 2006., , , and .
 On theory in ecology. BioScience, 64(8):701–710, 2014., , , , , , , , , , , , , , , and .
 Statistical dynamics of classical systems. Phys. Rev. A, 8:423–437, 1973., , and .
 Hydrogen, metals, bifurcating electrons, and proton gradients: the early evolution of biological energy conservation. FEBS Lett., 586:485–493, 2012..
 On the origin of cells: an hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells. Philos. Trans. R. Soc. London, Ser. B, 358:27–85, 2003. and .
 On the origin of biochemistry at an alkaline hydrothermal vent. Philos. Trans. R. Soc. London, Ser. B, 362:1887–1926, 2007. and .
 Hydrothermal vents and the origin of life. Nature Rev. Microbiol., 6:805–814, 2008., , , and .
 Energy at life's origin. Science, 344:1092–1093, 2014., , and .
 Crystal structure of 4-hydroxybutyryl-CoA dehydratase: radical catalysis involving a [4Fe-4S] cluster and flavin. Proc. Natl. Acad. Sci. USA, 101(44):15645–15649, 2004., , , , and .
 Hydrogen cyanide polymers, comets and the origin of life. Faraday Discuss., 133:393–401, 2006. and .
 The evolution of controlled multitasked gene networks: the role of introns and other noncoding RNAs in the development of complex organisms. Mol. Biol. Evol., 18:1611–1630, 2004. and .
 The uses of quantum field theory in diffusion-limited reactions. Rev. Mod. Phys, 70:979–1001, 1998. and .
 Autopoietic self-reproducing vesicles: a simplified kinetic model. J. Phys. Chem., 100:16600–16607, 1998. and .
 Where are we? Cold Spring Harbor Symp. Quant. Biol., 24:1–14, 1959..
 The Growth of Biological Thought: Diversity, Evolution, and Inheritance.Harvard University Press, Cambridge, MA, 1985..
 A natural system of organisms. Nature, 348:491, 1990..
 More natural classification. Nature, 353:122, 1991..
 The objects of selection. Proc. Natl. Acad. Sci. USA, 94:2091–2094, 1997..
 Two empires or three?Proc. Natl. Acad. Sci. USA, 95:9720–9723, 1998..
 Earth's Deep Mantle: Structure, Composition, and Evolution, pages 219–240. American Geophysical Union, Washington, DC, 2005.. Mantle oxidation state and oxygen fugacity: constraints on mantle chemistry, structure, and dynamics. In , , , and , editors,
 Hydrothermal and oceanic pH conditions of possible relevance to the origin of life. Orig. Life Evol. Biosphere, 24:19–41, 1994., , , and .
 Methanogenesis as a potential source of chemical energy for primary biomass production by autotrophic organisms in hydrothermal systems on Europa. J. Geophys. Res., 104:30729–30742, 1999..
 Laboratory simulations of abiotic hydrocarbon formation in Earth's deep subsurface. Rev. Mineral. Geochem., 75:467–494, 2013..
 A reassessment of the potential for reduction of dissolved CO2 to hydrocarbons during serpentinization of olivine. Geochim. Cosmochim. Acta, 65:3769–3778, 2001. and .
 Carbon isotope composition of organic compounds produced by abiotic synthesis under hydrothermal conditions. Earth Planet. Sci. Lett., 243:74–84, 2006. and .
 Geochemical constraints on chemolithoautotrophic metabolism by microorganisms in seafloor hydrothermal systems. Geochim. Cosmochim. Acta, 61:4375–4391, 1997. and .
 The influence of carbon source on abiotic organic synthesis and carbon isotope fractionation under hydrothermal conditions. Geochim. Cosmochim. Acta, 74:2717–2740, 2010., , , and .
 The composition of the Earth. Chem. Geol., 120:223–253, 1995. and .
 Formaldehyde as a probe of DNA structure. I. Reaction with exocyclic amino groups of DNA bases. Biochemistry, 14:1281–1296, 1975. and .
 In search of an RNA replicase ribozyme. Chem. Biol., 10:5–14, 2003. and .
 The possible origin and persistence of life on Enceladus and detection of biomarkers in the plume. Astrobiology, 8:909–919, 2008., , , , and .
 Characterization of the plasma membrane of Mycoplasma Laidlawii. Biochim. Biophys. Acta, 219:114–122, 1970., , , and .
 Moby-Dick; or, The Whale.Modern Library, New York, 1992..
 Experiments on plant hybridization. J. R. Hortic. Soc., 26:1–32, 1901. English translation..
 Prebiotic chemistry in eutectic solutions at the water-ice matrix. Chem. Soc. Rev., 41:5404–5415, 2012. and .
 2014. www.geol.umd.edu/~jmerck/geol212/lectures/13.html.. Volcanism I: sources and composition of magma. GEOL212: planetary geology lecture notes,
 Spin Glass Theory and Beyond.World Scientific, Singapore, 1987., , and .
 Production of amino acids under possible primitive Earth conditions. Science, 117:528–529, 1953..
 The thermodynamics of the Krebs cycle and related compounds. J. Phys. Chem. Ref. Data, 19:1049–1073, 1990. and .
 Coupling of phosphorylation to electron and hydrogen transfer by a chemi-osmotic type of mechanism. Nature, 191:144–148, 1961..
 Evidence of life on Earth before 3,800 million years ago. Nature, 384:55–59, 1996., , , , , and .
 Chance and Necessity.Knopf, New York, 1971..
 Allosteric proteins and cellular control systems. J. Mol. Biol., 6(4):306–329, 1963., , and .
 Encyclopedia of Astrobiology, pages 749–754. Springer, Berlin, 2011. and . Hertzsprung–Russell diagram.
 Evolution of Precambrian crust from strontium isotopic evidence. Nature, 254:395–398, 1975..
 The Nature of Computation.Oxford University Press, London, 2011. and .
 How many species are there on earth and in the ocean. PLoS Biol., 9:e1001127, 2011., , , , and .
 Darwin's multicellularity: from neurotrophic theories and cell competition to fitness fingerprints. Curr. Opin. Cell Biol., 31:16–22, 2014. and .
 Convection plumes in the lower mantle. Nature, 230:42–43, 1971..
 Proton semiconductors and energy transduction in biological systems. Am. J. Physiol., 235:R99–R114, 1978..
 Energy Flow in Biology.Ox Bow Press, Woodbridge, CT, 1979..
 Foundations of Bioenergetics.Academic Press, New York, 1987..
 Beginnings of Cellular Life. Yale University Press, New Haven, CT, 1992..
 Phenetics, a born-again science. Complexity, 8:12–13, 2003..
 The origin of intermediary metabolism. Proc. Natl. Acad. Sci. USA, 97:7704–7708, 2000., , , and .
 Chain-length dependence of lipid bilayer properties near the liquid crystal to gel transition. Biophys. J., 63:18–27, 1992., , and .
 Chemistry of alpha aminonitriles: aldomerization of glycolaldehyde phosphate to racemic hexose 2,4,6-triphosphates and (in presence of formaldehyde) racemic pentose 2,4-diphosphates: rac-allose 2,4,6-triphosphate and racemic ribose 2,4-diphosphate are the main reaction products. Helv. Chim. Acta, 73:1410–1468, 1990., , , , , and .
 4-hydroxybutyryl-CoA dehydratase from Clostridium aminobutyricum: characterization of FAD and iron–sulfur clusters involved in an overall non-redox reaction. Biochemistry, 35(36):11710–11718, 1996., , , and .
 The past and present of the sodium energetics: may the sodium-motive force be with you. Biochim. Biophys. Acta, 1777:985–992, 2008., , and .
 Co-evolution of primordial membranes and membrane proteins. Trends. Biochem. Sci., 34:206–215, 2009., , and .
 Evolutionary primacy of sodium bioenergetics. Biol. Direct, 3:13, 2008., , , , and .
 The relation of recombination to mutational advance. Mutat. Res., 1:1–9, 1964..
 Effects of wavelength of light and pulse magnetism on different magnetoreception systems in a migratory bird. Aust. J. Zool., 45:189–198, 1997., , , and .
 An experimental study of phosphorus and aluminosilicate speciation in and partitioning between aqueous fluids and silicate melts determined in-situ at high temperature and pressure. Am. Mineral. 96:1636–1649, 2011..
 Silicate-phosphate interactions in silicate glasses and melts: II. Quantitative, high-temperature structure of P-bearing alkali aluminosilicate melts. Geochim. Cosmochim. Acta, 65:2413–2431, 2001. and .
 Theory of the main lipid bilayer phase transition. Annu. Rev. Phys. Chem., 31:157–195, 1980..
 General acidbase catalysis in the mechanism of a hepatitis delta virus ribozyme. Science, 287:1493–1497, 2000., , and .
 Lehninger Principles of Biochemistry.W. H. Freeman, New York, fourth edition, 2004. and .
 Formation of H2 and CH4 by weathering of olivine at temperatures between 30 and 70°C. Geochem. Trans., 12:6:1–10, 2011., , , , and .
 The “strong” RNA World hypothesis: fifty years old. Astrobiology, 13:391–403, 2013., , and .
 The Will to Power.C. G. Naumann, Leipzig, 1901..
 RNA tertiary interactions in the large ribosomal subunit: the A-minor motif. Proc. Natl. Acad. Sci. USA, 98:4899–4903, 2001., , , , and .
 Hydrothermal focusingof chemical and chemiosmotic energy, supported by delivery of catalytic Fe, Ni, Mo/W, Co, S and Se, forced life to emerge. J. Mol. Evol., 69:481–498, 2009. and .
 Beating the acetyl coenzyme A-pathway to the origin of life. Philos. Trans. R. Soc. London, Ser. B, 368:20120258, 2013. and .
 Photosynthesis: from Light to the Biosphere, vol. 1, pages 945–950. Kluwer Academic Press, Dordrecht, 1995., , , and . From naptho- to benzoquinones – (r)evolutionary reorganizations of electron transfer chains. In , editor,
 The RNA World, pages 137–156. Cold Spring Harbor Laboratory Press, Plainview, New York, 1993.. On the origin of the ribosome: co-evolution of sub-domains of tRNA and rRNA. In and , editors,
 The RNA World, pages 197–219. Cold Spring Harbor Laboratory Press, Plainview, New York, 1999.. On the origin of the ribosome: co-evolution of sub-domains of tRNA and rRNA. In and , editors,
 Reactivity landscape of pyruvate unde r simulated hydrothermal vent conditions. Proc. Natl. Acad. Sci. USA, 110:13283–13288, 2013. and .
 Prevolutionary dynamics and the origin of evolution. Proc. Natl. Acad. Sci. USA, 105:14924–14927, 2008. and .
 Eoarchaean crustal growth in West Greenland (Itsaq Gneiss Complex) and in northeastern China (Anshan area): review and synthesis. Earth Accret. Syst. Space Time, 318:127–154, 2009., , , , and .
 A bacterial kind of aging. PLoS Genet., 3:2355–2357, 2007..
 Catalytic promiscuity and the evolution of new enzymatic activities. Chem. Biol., 6:R91–R105, 1999. and .
 Niche Construction: The Neglected Process in Evolution. Princeton University Press, Princeton, NJ, 2003., , and .
 Time's speed regulator: the optimum efficiency for maximum output in physical and biological systems. Am. Sci., 43:331–343, 1955. and .
 Modern Control Engineering. Prentice-Hall, New York, fifth edition, 2010..
 Ribosomal RNA: a key to phylogeny. FASEB J., 7:113–123, 1993. and .
 Neodymium-142 evidence for Hadean mafic crust. Science, 321:1828–1831, 2008., , , and .
 Reciprocal relations in irreversible processes. I. Phys. Rev., 37:405–426, 1931..
 Reciprocal relations in irreversible processes. II. Phys. Rev., 38:2265–2279, 1931..
 Fluctuations and irreversible processes. Phys. Rev., 91:1505, 1953. and .
 Proiskhozhdenie zhizy. Moskovski Rabochii, Moscow, 1924. In Russian..
 The Origin of Life, pages 199–234. Weidenfeld and Nicolson, London, 1967.. The origin of life. In , editor,
 Microbial life at high salt concentration: phylogenetic and metabolic diversity. Saline Syst., 4:2:1–13, 2008..
 Prebiotic chemistry and the origin of the RNA world. Crit. Rev. Biochem. Mol. Biol., 39:99–123, 2004..
 The implausibility of metabolic cycles on the early Earth. PLoS Biology, 6:e18, 2008..
 Mechanisms of synthesis of adenine from hydrogen cyanide under possible primitive Earth conditions. Nature, 191:1193–1194, 1961..
 Synthesis of adenine from ammonium cyanide. Biochem. Biophys. Res. Commun., 2:407–412, 1960. and .
 Synthesis of purines under possible primitive Earth conditions I: adenine from hydrogen cyanide. Arch. Biochem. Biophys., 94:217–227, 1961. and .
 Synthesis of purines under possible primitive Earth conditions II: purine intermediates from hydrogen cyanide. Arch. Biochem. Biophys., 96:293–313, 1962. and .
 Million-fold acceleration of a Diels–Alder reaction due to combined Lewis acid and micellar catalysis in water. J. Am. Chem. Soc., 120:9517–9525, 1998., , and .
 Prebiotic synthesis of polypeptides by heterogeneous polycondensation of amino-acid adenylates. Nature, 228:636–639, 1970., , and .
 Systems Biology. Cambridge University Press, Cambridge, MA, 2006..
 Prebiotic synthesis of methionine and other sulfur-containing organic compounds on the primitive Earth: a contemporary reassessment based on an unpublished 1958 Stanley Miller experiment. Orig. Life Evol. Biosphere, 41:201–212, 2011., , , , , , and .
 Towards an evolutionary theory of the origin of life based on kinetics and thermodynamics. Open Biol., 3:130156, 2013., , and .
 Aqueous corrosion of phosphide minerals from iron meteorites: a highly reactive source of prebiotic phosphorus on the surface of the early Earth. Astrobiology, 5:515–535, 2005. and .
 Evidence for reactive reduced phosphorus species in the early Archean ocean. Proc. Natl. Acad. Sci. USA, 110:10089–11194, 2013., , , , and .
 Redox chemistry in the phosphorus biogeochemical cycle. Proc. Natl. Acad. Sci. USA, 43:15468–15473, 2014., , and .
 Mass-independent fractionation of sulfur isotopes in Archean sediments: strong evidence for an anoxic Archean atmosphere. Astrobiology, 2:27–41, 2002. and .
 UV shielding of NH3 and O2 by organic hazes in the Archean atmosphere. J. Geophys. Res., 106:23267–23287, 2001., , and .
 Mystery of the volcanic massindependent sulfur isotope fractionation signature in the Antarctic ice core. J. Geophys. Res., 32:L12816, 2005., , and .
 Path-integral approach to birth-death processes on a lattice. J. Phys. (Paris), 46:1469, 1985..
 Renormalization of fluctuation effects in a + a → a reaction. J. Phys. A, 19:L365, 1986..
 Out of fuzzy chemistry: from prebiotic chemistry to metabolic networks. Chem. Soc. Rev., 41:5394–5403, 2012..
 The geological setting of the ultramafic-hosted Logatchev hydrothermal field (14°45′N, Mid - AtlanticRidge) and its influence on massive sulfide formation. Lithos, 112:40–56, 2009., , , , , , and .
 Secondary structure and domain architecture of the 23S and 5S rRNAs. Nucleic Acids Res., 14:7522–7535, 2013., , , , , , , , , , , , , and .
 Evolution of the ribosome at atomic resolution. Proc. Natl. Acad. Sci. USA, 2014., , , , , , , , , , , and .
 Deep subsurface microbial biomass and community structure in Witwatersrand basin mines. Geomicrobiol. J., 23:431–442, 2006., , , , and .
 Stochastic path integral formulation of full counting statistics. Phys. Rev. Lett., 90:206801, 2003., , , and .
 Prebiotic amino acids as asymmetric catalysts. Science, 303:1151, 2004. and .
 Thermodynamic functions of hydration of hydrocarbons at 298.15 K and 0.1 MPa. Geochim. Cosmochim. Acta, 64:439–468, 2000. and .
 An ancient pathway combining carbon dioxide fixation with the generation and utilization of a sodium iongradient for ATP synthesis. PLoS ONE, 7:e33439, 2012., , , , , , , , , , , , , and .
 The origin and early evolution of membrane channels. Astrobiology, 5:1–17, 2005., , and .
 Membrane peptides and their role in protobiological evolution. Orig. Life Evol. Biosphere, 33:173–197, 2003., , and .
 Renormalization group and effective lagrangians. Nucl. Phys. B, 231:269–295, 1984..
 The path from the RNA world. J. Mol. Evol., 46:1–17, 1998., , and .
 Logik der Forschung. Julius Springer Verlag, Vienna, 1935..
 The Logic of Scientific Discovery. Hutchinson, London, 1959. Translation of ..
 Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions. Nature, 459:239–242, 2009., , and .
 The origins of nucleotides. SYNLETT, 14:1956–1964, 2011., , and .
 The principles of maximum entropy and maximum caliber in statistical physics. Rev. Mod. Phys, 85:1115–1141, 2013., , , and .
 Fisher's ‘fundamental theorem’ made clear. Ann. Hum. Genet., 36:129–140, 1972..
 Abiogenic hydrocarbon production at Lost City hydrothermal field. Science, 319:604–607, 2008., , , , , , , and .
 The Origins of Theoretical Population Genetics. University of Chicago Press, Chicago, IL, 2001..
 Life at low Reynolds number. Am. J. Phys., 45:3–11, 1973..
 The Emergence of Biological Organization. Yale University Press, New Haven, CT, 1964..
 Statistical Analysis withR. Packt Publishing, Birmingham, 2010..
 Reconstitution of purple membrane vesicles catalyzing light-driven proton uptake and adenosine triphosphate formation. J. Biol. Chem., 249:662–663, 1974. and .
 Characterization of two pterin derivatives isolated from Methanoculleus thermophilicum. Eur. J. Biochem., 200:783–787, 1991., , , , and .
 Structural characterization of tatiopterin, a novel pterin isolated from Methanogenium tationis. Biofactors, 2:117–122, 1989., , , , , and .
 Enzymology of the Wood–Ljungdahl pathway of acetogenesis. Ann. N Y Acad. Sci., 1125:129–136, 2008..
 Nickel-containing carbon monoxide dehydrogenase/acetyl-CoA synthase. Chem. Rev., 96:2515–2540, 1996. and .
 Enzymology of the acetyl-CoA pathway of CO2 fixation. Crit. Rev. Biochem. Mol. Biol., 26:261–300, 1991. and .
 Properties of purified carbon monoxide dehydrogenase from Clostridium thermoaceticum, a nickel, iron-sulfur protein. J. Biol. Chem., 258(4):2364–2369, 1983., , , , and .
 Effect of substituents of alloxazine derivatives on the selectivity and affinity for adenine in AP-sitecontaining DNA duplexes. Org. Biomol. Chem., 8:4949–4959, 2010., , , , , , , and .
 Geochemistry. University of Chicago Press, Chicago, IL, 1950. and .
 The natural history of nitrogen fixation. Mol. Biol. Evol., 21:541–554, 2004., , , and .
 The origin of methanethiol in midocean ridge hydrothermal fluids. Proc. Natl. Acad. Sci. USA, 111:5474–5479, 2014., , and .
 Introduction to Statistics: Fundamental Concepts and Procedures of Data Analysis. SAGE publications, Washington DC, 2014..
 Merging genomes with geochemistry in hydrothermal ecosystems. Science, 296:1077–1082, 2002. and .
 2005. www.geo.umass.edu/courses/ geo321/Lecture.. Mantle melting and origin of basaltic magma. Notes: GEO-321. Igneous & Metamorphic Petrology, March
 International Astronomical Union Symposium No. 264, 2009, pages 3–18. Cambridge University Press, Cambridge, 2010.. The sun and stars as the primary energy input in planetary atmospheres. In , , and , editors, Proc.
 Borate minerals stabilize ribose. Science, 303:196, 2004., , , and .
 Signatures of arithmetic simplicity in metabolic network architecture. PLoS Comput. Biol., 6:e1000725, 2010., , , and .
 Trophic ecology of Rimicaris exoculata: a combined lipid abundance stable isotope approach. Mar. Biol., 133:495–499, 1999., , , and .
 Stochastic Complexity in Statistical Inquiry. World Scientific, Teaneck, NJ, 1989..
 The origins of the RNA world. Cold Spring Harb. Perspect. Biol., 4:a003608, 2010. and .
 The structural basis of ribozymecatalyzed RNA assembly. Science, 315:1549–1553, 2007. and .
 Evolutionary plasticity and innovations in complex metabolic reaction networks. PLoS Comput. Biol., 5:e1000613:1–11, 2009. and .
 Kinetic and mechanistic analysis of nonenzymatic, template-directed oligoribonucleotide ligation. J. Am. Chem. Soc., 118:3332–3339, 1996., , and .
 Nonenzymatic, templatedirected ligation of oligoribonucleotides is highly regioselective for the formation of 3′–5′ phosphodiester bonds. J. Am. Chem. Soc., 118:3340–3344, 1996., , and .
 Papers on Probability, Statistics and Statistical Physics. D. Reidel, Dordrecht, 1983., editor. :
 Structure and mechanism of DNA polymerases. Adv. Protein Chem., 71:401–440, 2005. and .
 A History of Western Philosophy. Simon & Schuster, New York, 1967..
 Downward-excavating hydrothermal cells and Irish-type ore deposits: importance of an underlying thick Caledonian prism. Trans. Inst. Min. Metall., B87:168–171, 1978..
 Mining, metallurgy and the origin of life. Miner. Indust. Int., 1009:4–8, 1993..
 First life. Am. Sci., 94:32–39, 2006..
 The alkaline solution to the emergence of life: energy, entropy, and early evolution. Acta Biotheor., 55:133–179, 2007..
 The emergence of life from iron monosulphide bubbles at a submarine hydrothermal redox and pH front. J. Geol. Soc. London, 154:377–402, 1997. and .
 The onset and early evolution of life. Geol. Soc. Am. Memoir, 198:1–32, 2006. and .
 The rocky roots of the acetyl-CoA pathway. Trends Biochem. Sci., 29:358–363, 2004. and .
 The drive to life on wet and icy worlds. Astrobiology, 14:308–343, 2014., , , , , , , , , , , , , and .
 On the emergence of life via catalytic iron-sulphide membranes. Terra Nova, 5:343–347, 1993., , and .
 On hydrothermal convection systems and the emergence of life. Econ. Geol., 100:419–438, 2005., , , and .
 Submarine hot springs and the origin of life. Nature, 336:117, 1988., , , and .
 Serpentinization as a source of energy at the origin of life. Geobiology, 8:355–371, 2010., , and .
 Evolution of aldolase. Fed. Proc., 23:1248–1257, 1964..
 The early faint young sun paradox: organic shielding of ultraviolet-labile greenhouse gases. Science, 276:1217–1221, 1997. and .
 Earth and Mars: evolution of atmospheres and surface temperatures. Science, New Series, 177:52–56, 1972. and .
 From the one-carbon amide formamide to RNA all the steps are prebiotically possible. Biochimie, 94:1451–1456, 2012., , , , and .
 Materials for the onset: a story of necessity and chance. Frontiers Biosci., 18:1275–1289, 2013., , , , and .
 Codon Evolution: Mechanisms and Models, pages 258–270, Oxford University Press, New York, 2012. and . Structural and molecular features of non-standard genetic codes. In . and , editors,
 Genetic evidence identifying the true gluconeogenic fructose-1,6-bisphosphatase in Thermococcus kodakaraensis and other hyperthermophiles. J. Bacteriol., 186:5799–5807, 2004., , , , , and .
 Hot mantle upwelling across the 660 beneath Yellowstone. Earth Planet. Sci. Lett., 331:224–236, 2012., , , and .
 Carbon dioxide photolysis from 150 to 210 nm: singlet and triplet channel dynamics, UV-spectrum, and isotope effects. Proc. Natl. Acad. Sci. USA, 110:17691–17696, 2013., , and .
 High molecular diversity of extraterrestrial organic matter in Murchisonmeteorite revealed 40 years after its fall. Proc. Natl. Acad. Sci. USA, 107:2763–2768, 2010., , , , , , , , and .
 Theory of molecular machines I: channel capacity of molecular machines. J. Theor. Biol., 148:83–123, 1991..
 Theory of molecular machines II: energy dissipation from molecular machines. J. Theor. Biol., 148:125–137, 1991..
 Menaquinone as a pool quinone in a purple bacterium. Proc. Natl. Acad. Sci. USA, 106:8549–8554, 2005., , , , , , and .
 Microfossils of the early Archaean apex chert: new evidence of the antiquity of life. Science, 260:640–646, 1993..
 Emulsions, Foams, and Suspensions: Fundamentals and Applications. Wiley, New York, 2005..
 Incidence and diversity of microorganisms within the walls of an active deep-sea sulfide chimney. Appl. Environ. Microbiol., 69:3580–3592, 2003., , , and .
 What is Life? The Physical Aspect of the Living Cell. Cambridge University Press, New York, 1992..
 Serpentinization and its implications for life on the early Earth and Mars. Astrobiology, 6:364–376, 2006., , , and .
 The iron-hydrogenase of Thermotoga maritima utilizes ferredoxin and NADH synergistically: a new perspective on anaerobic hydrogen production. J. Bacteriol., 191:4451–4457, 2009. and .
 The naphthoquinol oxidizing cytochrome bc1 complex of the hyperthermophilic knallgasbacterium Aquifex aeolicus: properties and phylogenetic relationships. Biochemistry, 42:10800–10808, 2003., , , , , , , , , and .
 Phosphorus in prebiotic chemistry. Philos. Trans. R. Soc. London, Ser. B, 361:1743–1749, 2006..
 Estimating the dimension of a model. Ann. Stat., 6:461–464, 1978..
 Serpentinization and carbon sequestration: a study of two ancient peridotite-hosted hydrothermal systems. Chem. Geol., 351:115–133, 2013., , , , and .
 Toward catalytically active oligonucleotides: synthesis of a flavin nucleotide and its incorporation into DNA. Org. Lett., 2:1415–1418, 2000. and .
 The Mystery of Consciousness. New York Review of Books, New York, 1997..
 The genome of Clostridium kluyveri, a strict anaerobe with unique metabolic features. Proc. Natl. Acad. Sci. USA, 105:2128–2133, 2008., , , , , , , , , , , , and .
 Compositional genomes: prebiotic information transfer in mutually catalytic noncovalent assemblies. Proc. Natl. Acad. Sci. USA, 97:4112–4117, 2000., , and .
 Graded autocatalysis replication domain (GARD): kinetic analysis of self-replication in mutually catalytic sets. Orig. Life Evol. Biosphere, 28:501–514, 1998., , , and .
 The molecular roots of compositional inheritance. J. Theor. Biol., 213:481–491, 2001., , , and .
 Why I am not an objective Bayesian: some reflections prompted by Rosenkrantz. Theory Decision, 11:413–440, 1979..
 Foundations of Statistical Inference, pages 259–287. Reidel, Boston, MA, 1987.. Entropy and uncertainty. In and , editors,
 Evidence that NiNi acetyl-CoA synthase is active and that the CuNi enzyme is not. Biochemistry, 43(13):3944–3955, 2004., , , , , , , and .
 Seafloor Hydrothermal Systems: Physical, Chemical, Biological, and Geological Interactions, pages 248–272. Geophysical Monograph. American Geophysical Union, Washington, DC, 1995. and . Phase equilibria in subseafloor hydrothermal systems: a review of the role of redox, temperature, pH and dissolved Cl on the chemistry of hot spring fluids at mid-ocean ridges. In , , , and , editors,
 Phase equilibria constraints on the chemistry of hot spring fluids at mid-ocean ridges. Geochim. Cosmochim. Acta, 55:3559–3580, 1991., , and .
 Dynamics of Bayesian updating with dependent data and misspecified models. Electron. J. Stat., 3:1039–1074, 2009..
 Temporal and spatial patterns of biological community development at nascent deep-sea hydrothermal vents (9°50′N, East Pacific Rise). Deep-Sea Res. II, 45:465–515, 1998., , , , , and .
 Communication in the presence of noise. Proc. IEEE, 86:447–457, 1949..
 The Mathematical Theory of Communication. University of Illinois Press, Urbana, IL, 1949. and .
 Small molecule interactions were central to the origin of life. Q. Rev. Biol., 81:105–125, 2006..
 In situ diamond-anvil cell observations of methanogenesis at high pressures and temperatures. Energy Fuels, 23:5572–5579, 2009., , and .
 Structural insights into the effects of 2′–5′ linkages on the RNA duplex. Proc. Natl. Acad. Sci. USA, 111:3050–3055, 2014., , , , , and .
 Estimated minimal divergence times of the major bacterial and archaeal phyla. Geomicrobiol. J., 20:1–14, 2003., , and .
 Unravelling abiogenic and biogenic sources of methane in the Earth's deep subsurface. Chem. Geol., 226:328–339, 2006., , , , , , , and .
 Abiogenic formation of gaseous alkanes in the Earth's crust as a minor source of global hydrocarbon reservoirs. Nature, 416:522–524, 2002., , , , and .
 high-temperature hydrothermal fluids in the early Archean ocean. Precambrian Res., 182:230–238, 2010., , , , and . ,
 Depth variation of carbon and oxygen isotopes of calcites in Archean altered upper oceanic crust: implications for the CO2 flux from ocean to oceanic crust in the Archean. Earth Planet. Sci. Lett., 321:64–73, 2012., , , , , , , , , , , and .
 Decrease of seawater CO2 concentration in the Late Archean: an implication from 2.6 Ga seafloor hydrothermal alteration. Precambrian Res., 236:59–64, 2013., , , , , , , and .
 Reactions between basalt and CO2-rich seawater at 250 and 350?C, 500 bars: implications for CO2 sequestration into the modern oceanic crust and the composition of hydrothermal vent fluid in the CO2-rich early ocean. Chem. Geol., 359:1–9, 2013., , , , , and .
 The case for a neoproterozoic oxygenation event: chemical evidence and biological consequences. GSA Today, 21:4–11, 2011. and .
 Tryptophan-accelerated electron flow through proteins. Science, 320:1760–1762, 2008., , , , , , , , , , , , and .
 Calculation of the thermodynamic and transport properties of aqueous species at high pressures and temperatures: standard partial molal properties of organic species. Geochim. Cosmochim. Acta, 54:915–945, 1990. and .
 Organic synthesis during fluid mixing in hydrothermal systems. J. Geophys. Res., 103:28513–28527, 1998. and .
 Calculation of the thermodynamic and transport properties of aqueous species at high pressures and temperatures: Standard partial molal properties of inorganic neutral species. Geochim. Cosmochim. Acta, 53:2157–2183, 1989., , and .
 Quantifying inorganic sources of geochemical energy in hydrothermal ecosystems, Yellowstone National Park, USA. Geochim. Cosmochim. Acta, 74:4005–4043, 2010., , , , , and .
 Thermophiles: The Keys to Molecular Evolution and the Origin of Life, pages 59–76. Taylor and Francis, London, 1998., , and . The emergence of metabolism from within hydrothermal systems. In and , editors,
 Life's Origin: the Beginnings of Biological Evolution. University of California Press, Berkeley, CA, 2002., editor.
 Phenotypic correlates of genomic DNA content in unicellular eukaryotes. Am. Nat., 122:26–44, 1983., , , and .
 Atmospheric erosion induced by oblique impacts. Meteoritics Planet. Sci., 44:1095–1105, 2009..
 Archaeal fructose-1,6-bisphosphate aldolases constitute a new family of archaeal type class I aldolase. J. Biol. Chem., 276:28710–28718, 2001., , , , , , and .
 The architecture of complexity. Proc. Am. Philos. Soc., 106:467–482, 1962..
 Hierarchy Theory: The Challenge of Complex Systems, pages 3–27. George Braziller, New York, 1973.. The organization of complex systems. In , editor,
 The Sciences of the Artificial. MIT Press, Cambridge, MA, third edition, 1996..
 Membrane organization and lipid rafts. Cold Spring Harb. Perspect. Biol., 3:a004697, 2011. and .
 On the notion of entropy of a dynamical system. Dokl. Akad. Nauk SSSR, 124:768–771, 1959..
 Universal geometric theory of mesoscopic stochastic pumps and reversible ratchets. Phys. Rev. Lett., 99:220408, 2007. and .
 H2-rich fluids from serpentinization: geochemical and biotic implications. Proc. Natl. Acad. Sci. USA, 101:12818–12823, 2004., , , , and .
 Abiotic ammonium formation in the presence of Ni-Fe metals and alloys and its implications for the Hadean nitrogen cycle. Geochem. Trans., 9:5, 2008., , , , and .
 Self-organization from structural refrigeration.Phys. Rev. E, 68:046114, 2003..
 Thermodynamic dual structure of linearly dissipative driven systems. Phys. Rev. E, 72:36130, 2005..
 Thermodynamics of natural selection I: energy and entropy flows through non-equilibrium ensembles. J. Theor. Biol., 252:185–197, 2008..
 Thermodynamics of natural selection II: chemical Carnot cycles. J. Theor. Biol., 252:198–212, 2008..
 Thermodynamics of natural selection III: Landauer's principle in chemistry and computation. J. Theor. Biol., 252:213–220, 2008..
 Large-deviation principles, stochastic effective actions, path entropies, and the structure and meaning of thermodynamic descriptions. Rep. Prog. Phys., 74:046601, 2011..
 Symmetry and Collective Fluctuations in Evolutionary Games. IOP Press, Bristol, 2015. and .
 Universality in intermediary metabolism. Proc. Natl. Acad. Sci. USA, 101:13168–13173, 2004. and .
 Nonequilibrium phase transitions in biomolecular signal transduction. Phys. Rev. E, 84:051917, 2011., , , and .
 The Life of the Cosmos. Phoenix, London, 1997..
 Diffuse atomic and molecular clouds. Annu. Rev. Astron. Astrophys., 44:367–414, 2006. and .
 Biochemical fossils of the ancient transition from geoenergetics to bioenergetics in prokaryotic one carbon compound metabolism. Biochem. Biophys. Acta, 1837:964–981, 2014. and .
 New Views on the Nature of Man, pages 71–92. University of Chicago Press, Chicago, IL, 1965.. Mind, brain and humanist values. In , editor,
 The Roots of Modern Biochemistry: Fritz Lippmann's Squiggle and its Consequences, pages 511–533. Walter de Gruyter, Berlin, 1988.. Energetics and dynamics of the protein synthesizing machinery. In , , and , editors,
 Analysis of the intermediary metabolism of a reductive chemoautotroph. Biol. Bull., 217:222–232, 2009. and .
 The canonical network of autotrophic intermediary metabolism: minimal metabolome of a reductive chemoautotroph. Biol. Bull., 216:126–130, 2009. and .
 Defining genes: a computational framework. Theory Biosci., 128:165–170, 2009., , , and .
 Ecological Stoichiometry: The Biology of Elements from Molecules to the Biosphere. Princeton University Press, Princeton, NJ, 2002. and .
 The metabolic role of leucovorin. Trends Biochem. Sci., 18(3):102–106, 1993. and .
 Sufficient statistics: theoretical background. Wiley Stats- Ref, 2014..
 General theory of mortality and aging. Science, 132:14–21, 1960. and .
 Biochemistry. Freeman, San Francisco, CA, second edition, 1981..
 Nature, 365:630–633, 1993. and . Prebiotic ammonia from reduction of nitrite by iron(II) on the early Earth.
 Thermophilic subseafloor microorganisms from the 1996 North Gorda Ridge eruption. Deep-Sea Res. II, 45:2751–2766, 1998. and .
 A novel microbial habitat in the mid-ocean ridge subsurface. Proc. Natl. Acad. Sci. USA, 98:2158–1263, 2001. and .
 2-methylhopanoids as biomarkers for cyanobacterial oxygenic photosynthesis. Nature, 400:554–557, 1999., , , and .
 Zen Mind, Beginner's Mind. Weatherhill, New York, 1973..
 A functionalNi-Ni-[4Fe-4S] cluster in the monomeric acetyl-CoA synthase from Carboxydothermus hydrogenoformans. Proc. Natl. Acad. Sci. USA, 101(2):446–451, 2004., , , , , , , and .
 The Major Transitions in Evolution. Oxford University Press, London, 1995. and .
 The eightfold path to non-enzymatic RNA replication. J. Syst. Chem., 3:2, 2012..
 Research on carbon dioxide fixation in photosynthetic microorganisms (1971–present). Photosynth. Res., 80:315–332, 2004..
 Function, structure, and evolution of the RubisCO-like proteins and their RubisCO homologs. Microbiol. Mol. Biol. Rev., 71:576–599, 2007., , , , , and .
 Distribution of archaea in a black smoker chimney structure. Appl. Env. Microbiol., 67:3618, 2001., , , and .
 Alkaliphilus transvaalensis gen. nov., sp. nov., an extremely alkaliphilic bacterium isolated from a deep South African gold mine. Int. J. Syst. Evol. Microbiol., 51:1245–1256, 2001., , , , , , and .
 Messy biology and the origins of evolutionary innovation. Nature Chem. Biol., 6:692–696, 2010..
 The code within the codons. Biosystems, 22:177–187, 1989. and .
 Introduction to Glycobiology. Oxford University Press, London, third edition, 2011. and .
 3-Hydroxypropionyl-coenzyme A dehydratase and acroloyl-coenzyme A reductase, enzymes of the autotrophic 3-hydroxypropionate/4-hydroxybutyrate cycle in the Sulfolobales. J. Bacteriol., 191:4572–4581, 2009., , , , and .
 Energy conservation in chemotrophic anaerobic bacteria. Bacteriol. Rev., 41:100–180, 1977., , and .
 Methanogenic archaea: ecologically relevant differences in energy conservation. Nature Rev. Microbiol., 6:579–591, 2008., , , , and .
 On Growth and Form. Dover, New York, complete revised edition, 1992..
 Deducing patterns of fluid flow and mixing within the TAG active hydrothermal mound using mineralogical and geochemical data. J. Geophys. Res., 100:12527–12555, 1995., , and .
 Transonic hydrodynamic escape of hydrogen from extrasolar planetary atmospheres. Astrophys. J., 621:1049–1060, 2005., , , and .
 Variant tricarboxylic acid cycle in Mycobacterium tuberculosis: identification of a-ketoglutarate decarboxylase. Proc. Natl. Acad. Sci. USA, 102:10670–10675, 2005., , , , and .
 Introduction to Superconductivity. Dover, New York, second edition, 2004..
 How to build a black smoker chimney. Oceanus, 41, 1998..
 Generation of seafloor hydrothermal vent fluid and associated mineral deposits. Oceanography, 20:50–65, 2007..
 A model for growth of steep-sided vent structures on the Endeavour Segment of the Juan de Fuca Ridge: results of a petrologic and geochemical study. J. Geophys. Res., 104:22859–22883, 1999., , , , and .
 Count Lyof Anna Karénina. Thomas Y. Crowell, New York, 1914. Translated by Nathan Haskell Dole..
 The large deviation approach to statistical mechanics. phys. rep., 478:1–69, 2009..
 The triplet code from first principles. J. Biomol. Struct. Dyn., 22:1–11, 2004..
 Multiple traslational products from a five-nucleotide ribozyme. Proc. Natl. Acad. Sci. USA, 107:4585–4589, 2010., , and .
 Geological sulfur isotopes indicate elevated OCS in the Archean atmosphere, solving faint young sun paradox. Proc. Natl. Acad. Sci. USA, 106:14784–14789, 2009., , , , , and .
 Quadruple sulfur isotope analysis of ca. 3.5 Ga Dresser Formation: new evidence for microbial sulfate reduction in the early Archean. Geochim. Cosmochim. Acta, 72:5675–5691, 2008., , , and .
 Can the maximum entropy principle be explained as a consistency requirement? Studies Hist. Philos. Mod. Phys., 26B:223–261, 1995..
 The constraint rule of the maximum entropy principle. Studies Hist. Philos. Mod. Phys., 27:47–79, 1996..
 Threonine deamination in Escherichia coli II: evidence for two L-threonine deaminases. J. Bacteriol., 73(1):105–112, 1957. and .
 The UniProt Consortium. Ongoing and future developments at the universal protein resource. Nucleic Acids Res., 39(suppl 1):D214–D219, 2011.
 Hydrolytic stability of helical RNA: a selective advantage for the natural 3′,5′- bond. Proc. Natl. Acad. Sci. USA, 73:1149–1153, 1976. and .
 Mechanisms of fixation of carbon dioxide by heterotrophs and autotrophs. Adv. Enzymol. Relat. Areas Mol. Biol., 12:41–151, 1951. and .
 2011.. Duality, Bosonic Particle Systems and Some Exactly Solvable Models of Non-Equilibrium. PhD Thesis, Universiteit Leiden,
 Spontaneous network formation among coperative RNA replicators. Nature, 491:72–77, 2012., , , , , and .
 Derivatives of methanopterin, a coenzyme involved in methanogenesis. Eur. J. Biochem., 139:359–365, 1984., , , , , , , and .
 Microorganisms as food resources at deep-sea hydrothermal vents. Limnol. Oceanogr., 39:51–57, 1994. and .
 Proceedings of the Oceanic Drilling Program, Scientific Results, Vol. 118, pages 181–215. Texas A & M University, Houston, TX, 1991. and . Fluids in oceanic layer 3: evidence from veined rocks, hole 735B, Southwest Indian Ridge. In , , , and , editors,
 The G-U wobble base pair: a fundamental building block of RNA structure crucial to RNA function in diverse biological systems. EMBO Rep., 1:18–23, 2000. and .
 Lack of evolvability in selfsustaining autocatalytic networks: a constraint on metabolism-first path to the origin of life. Proc. Natl. Acad. Sci. USA, 107:1470–1475, 2010., , and .
 Catalytic activity of histidine-metal complexes in oxidation reactions. Synth. React. Inorg. Met.-org. Nano-met. Chem., 43:243–249, 2013., , and .
 Environmental genome shotgun sequencing of the Sargasso Sea. Science, 304:66–74, 2004., , , , , , , , , , , , , , , , , , , , , , and .
 Fifty years of Shannon theory. IEEE Trans. Inf. Theory, 44:2057–2078, 1998..
 Geochemistry and the Biosphere. Synergetic Press, Santa Fe, NM, 2007..
 Collective evolution and the genetic code. Proc. Natl. Acad. Sci. USA, 103:10696–10701, 2006., , and .
 Global Catastrophes in Earth History, pages 289–300. Geological Society of America, Boulder, CO, 1990. and . Atmospheric erosion and impactor retention in large impacts with application to mass extinctions. In and , editors,
 The RNA world on ice: a new scenario for the emergence of RNA information. J. Mol. Evol., 61:264–273, 2005., , , and .
 Thermally-driven atmospheric escape: transition from hydrodynamic to Jeans escape. Astrophys. J. Lett., 729:L24, 2011., , , and .
 Seafloor hydrothermal activity: black smoker chemistry and chimneys. Annu. Rev. Earth Planet. Sci., 18:173–204, 1990..
 Probabilistic logics and the synthesis of reliable organisms from unreliable components. Automata Stud., 34:43–98, 1956..
 Chlorophyll biosynthesis. Plant Cell Online, 7(7):1039–1057, 1995., , and .
 Distribution of tetrahydromethanopterin-dependent enzymes in methylotrophic bacteria and phylogeny of methenyl tetrahydromethanopterin cyclohydrolases. J. Bacteriol., 181:5750–5757, 1999., , , , and .
 Chemistry of marine ligands and siderophores. Annu. Rev. Marine Sci., 1:43–63, 2009. and .
 Mechanism of acetate synthesis from CO2 by Clostridium acidi-urici. J. Bacteriol., 140(2):468–478, 1979. and .
 Before enzymes and templates: a theory of surface metabolism. Microbiol. Rev., 52:452–484, 1988..
 Pyrite formation, the first energy source for life: a hypothesis. Syst. Appl. Microbiol., 10:207–210, 1988..
 Evolution of the first metabolic cycles. Proc. Natl. Acad. Sci. USA, 87:200–204, 1990..
 Canalization of development and the inheritance of acquired characters. Nature, 150:563–565, 1942..
 Synthesis of adenine by oligomerization of hydrogen cyanide. J. Org. Chem., 31:2035–2036, 1966., , , , and .
 Horizons in Biochemistry, pages 127–142. Academic Press, New York, 1962.. Life in the second and third periods: or why phosphorus and sulfur for high-energy bonds. In and , editors,
 Autopoietic selfreproduction of fatty acid vesicles. J. Am. Chem. Soc., 116:11649–11654, 1994., , , , and .
 Universal sequence replication, reversible polymerization and early functional biopolymers: a model for the initiation of prebiotic sequence evolution. PLoS ONE, 7:e34166, 2012., , and .
 NADP+ reduction with reduced ferredoxin and NADP+ reduction with NADH are coupled via an electron-bifurcating enzyme complex in Clostridium kluyveri. J. Bacteriol., 192:5115–5123, 2010., , , and .
 Fumarate reductase activity maintains an energized membrane in anaerobic Mycobacterium tuberculosis. PLoS Pathogens, 7:e1002287, 2011., , , , 3rd, and .
 A structure for deoxyribose nucleic acid. Nature, 171:737–738, 1953. and .
 Molecular Biology of the Gene. Pearson, New York, seventh edition, 2014., , , , , and .
 Everything is Obvious: How Common Sense Fails Us. Crown Business, New York, 2012..
 Energy from redox disproportionation of sugar carbon drives biotic and abiotic synthesis. J. Mol. Evol., 44:354–360, 1997..
 Sugars as the optimal biosynthetic carbon substrate of aqueous life throughout the universe. Orig. Life Evol. Biosphere, 30:33–43, 2000..
 Chemical constraints governing the origin of metabolism: the thermodynamic landscape of carbon group transformations under mild aqueous conditions. Orig. Life Evol. Biosphere, 32:333–357, 2002..
 Kinetics of organic transformations under mild aqueous conditions: implications for the origin of life and its metabolism. Orig. Life Evol. Biosphere, 34:473–495, 2004..
 The peptide-catalyzed stereospecific synthesis of tetroses: a possible model for prebiotic molecular evolution. Proc. Natl. Acad. Sci. USA, 103:12713–12717, 2006. and .
 Phenomenological Lagrangians. Physica A, 96:327–340, 1979..
 The First Three Minutes.Basic Books, New York, second edition, 1993..
 The Quantum Theory of Fields, Vol. I: Foundations.Cambridge University Press, Cambridge, 1995..
 Leibniz Selections.Charles Scribner, New York, 1951., editor.
 Substrate-assisted catalysis of peptide bond formation by the ribosome. Nature Struct. Mol. Biol., 11:1101–1106, 2004., , , , and .
 L'hypothèse du champ moléculaire et la propriété ferromagnétique. J. Phys. Theor. Appl., 6:661–690, 1907..
 The origin of allometric scaling laws in biology from genomes to ecosystems: towards a quantitative unifying theory of biological structure and organization. J. Exp. Biol., 208:1575–1592, 2005. and .
 A general model for ontogenetic growth. Nature, 413:628–631, 2001., , and .
 Allometric scaling of metabolic rate from molecules and mitochondria to cells and mammals. Proc. Natl. Acad. Sci. USA, 99:2473–2478, 2002., , and .
 Why nature chose phosphates. Science, 235:1173–1178, 1987..
 Distinguishing ultramafic-from basalthosted submarine hydrothermal systems by comparing vent fluid compositions. J. Geophys. Res., 105:8319–8340, 2000. and .
 Coenzymes as fossils of an earlier metabolic state. J. Mol. Evol., .