Skip to main content Accessibility help
The Origin and Nature of Life on Earth
  • Get access
    Check if you have access via personal or institutional login
  • Cited by 21
  • Export citation
  • Recommend to librarian
  • Buy the print book

Book description

Uniting the conceptual foundations of the physical sciences and biology, this groundbreaking multidisciplinary book explores the origin of life as a planetary process. Combining geology, geochemistry, biochemistry, microbiology, evolution and statistical physics to create an inclusive picture of the living state, the authors develop the argument that the emergence of life was a necessary cascade of non-equilibrium phase transitions that opened new channels for chemical energy flow on Earth. This full colour and logically structured book introduces the main areas of significance and provides a well-ordered and accessible introduction to multiple literatures outside the confines of disciplinary specializations, as well as including an extensive bibliography to provide context and further reading. For researchers, professionals entering the field or specialists looking for a coherent overview, this text brings together diverse perspectives to form a unified picture of the origin of life and the ongoing organization of the biosphere.


‘… the most significant book on the origin of life hitherto written.'

Walter Fontana - Harvard University, Massachusetts

‘This is a truly unusual work of scholarship, which offers both novel perspectives on a huge range of disciplines and a model of scientific synthesis. This is a remarkable, and remarkably impressive, book.'

Cosma Shalizi - Carnegie Mellon University

‘… an exceptionally important, highly original, unique scientific contribution …'

Elbert Branscomb - University of Illinois

'The Origin and Nature of Life on Earth reads more like a well-executed textbook, one that covers much of what you need to know to jump in and start researching the origins of life. … For physicists wishing to dive headfirst into the origin-of-life field, this book is a great place to start … the book is not merely a compendium of existing knowledge; it offers genuinely new perspectives. [The authors] turn scientists' conventional origin stories on their heads. Rather than focus strictly on the chemical origin of life, they regard life as a planetary process … they introduce the idea of life as a 'fourth geosphere' that complements the other three: the atmosphere, hydrosphere, and lithosphere. In so doing, they make the problem of the origin of life one that may be tractable for physicists, and they lay out a possible framework for how to do it.'

Sara I. Walker Source: Physics Today

'For those interested in an easy-to-follow introduction to this fascinating topic …'

Graham Godfrey Source: The Biologist

Refine List

Actions for selected content:

Select all | Deselect all
  • View selected items
  • Export citations
  • Download PDF (zip)
  • Send to Kindle
  • Send to Dropbox
  • Send to Google Drive

Save Search

You can save your searches here and later view and run them again in "My saved searches".

Please provide a title, maximum of 40 characters.


[1] Venenivibrio. Licensed under CC [153] BY-SA 3.0 via Wikimedia Commons.
[2] Anabaena sperica2. Licensed under CC [153] BY-SA 3.0 via Wikimedia Commons. media/File:Anabaena_sperica2.jpg.
[3] Published under GNU free documentation license. /GNU_Free_Documentation_License.
[4] Leopard africa, by JanErkamp at the English language Wikipedia. Licensed under CC [153] BY-SA 3.0 via Wikimedia Commons. wiki/File:Leopard_africa.jpg#/media/File:Leopard_africa.jpg.
[5] 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 [153] BY-SA 3.0 nl via Wikimedia Commons. -10-25_Amanita_muscaria_crop.jpg#/media/File:2006-10-25_Amanita_muscaria_ crop.jpg.
[6] Licensed under CC [153].
[7] 20090719 062218 ParameciumBursaria, by Bob, Blaylock at en.wikipedia. Licensed under CC [153] BY-SA 3.0 via Wikimedia Commons. http://commons.wikimedia. org/wiki/File:20090719_062218_ParameciumBursaria.jpg#/media/File:200907.
[8] Global volcanism program, 2013. volcanoes of the world, v. 4.3.4. /10.5479/si.GVP.VOTW4-2013, 2013.
[9] Dallas, Abbot and William, Menke. Length of the global plate boundary at 2.4 Ga. Geology, 18:58–61, 1990.
[10] Harold, Abelson, Gerald Jay, Sussman, and Julie, Sussman. Structure and Interpretation of Computer Programs. MIT Press, Cambridge, MA, second edition, 1996.
[11] Christoph, Adami. Sequence complexity in Darwinian evolution. Complexity, 8:49–56, 2002.
[12] Christoph, Adami. Information theory in molecular biology. Phys. Life Rev., 1:3–22, 2004.
[13] Hirotugu, Akaike. A new look at the statistical model identification. IEEE Trans. Autom. Control, 19:716–723, 1974.
[14] A. M., Alayse-Danet, D., Debruyères, and F., Gaill. The possible nutritional or detoxification role of the epibiotic bacteria of alvinellid polychaetes: review of current data. Symbiosis, 4:51–62, 1987.
[15] Bruce, Alberts. Molecular Biology of the Cell. Garland Science, New York, fourth edition, 2002.
[16] Douglas, Allchin. Paul Boyer: bioenergetics and error. J. Hist. Biol., 35:149–172, 2002.
[17] Douglas E., Allen and W. E. Jr., SeyfriedCompositional 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.
[18] Douglas E., Allen and W. E. Jr., SeyfriedSerpentinization and heat generation: constraints from Lost City and Rainbow hydrothermal systems. Geochim. Cosmochim. Acta, 68:1347–1354, 2004.
[19] Luís, A.Nunes Amaral and Kent Baekgaard Lauritsen. Self-organized criticality in a rice-pile model. Phys. Rev. E, 54:R4512–R4515, 1996.
[20] J. P., Amend and E. L., Shock. Energetics of amino acid synthesis in hydrothermal ecosystems. Science, 281:1659–1662, 1998.
[21] Jan P., Amend and Everett L., Shock. Energetics of overall metablic reactions of thermophilic and hyperthermophilic archaea and bacteria. FEMS Microbiol. Rev., 25:175–243, 2001.
[22] Jan. P., Amend, Douglas E., LaRowe, Thomas M., McCollom, and Everett L., Shock. The energetics of organic synthesis inside and outside the cell. Philos. Trans. R. Soc. London, Ser. B, 368:20120255, 2013.
[23] Jan P., Amend, Karyn L., Rogers, Everett L., Shock, Sergio, Gurrieri, and Salvatore, Inguaggiato. Energetics of chemolithoautotrophy in the hydrothermal system of Vulcano Island, southern Italy. Geobiology, 1:37–58, 2003.
[24] Jakob L., Andersen, Tommy, Andersen, Christoph, Flamm, Martin M., Hanczyc, Daniel, Merkle, and Peter F., Stadler. Navigating the chemical space of HCN polymerization and hydrolysis: guiding graph grammars by mass spectrometry data. Entropy, 15:4066–4083, 2013.
[25] Jakob L., Andersen, Christoph, Flamm, Daniel, Merkle, and Peter F., Stadler. Maximizing output and recognizing autocatalysis in chemical reaction networks is NP-complete. J. Syst. Chem., 3:1, 2012.
[26] Jakob L., Andersen, Christoph, Flamm, Daniel, Merkle, and Peter F., Stadler. Inferring chemical reaction patterns using rule composition in graph grammars. J. Syst. Chem., 4:4:1–14, 2013.
[27] Jakob L., Andersen, Christoph, Flamm, Daniel, Merkle, and Peter F., Stadler. Generic strategies for chemical space exploration. Int. J. Comput. Biol. Drug Des., 7:225–258, 2014.
[28] Jakob L., Andersen, Christoph, Flamm, Daniel, Merkle, and Peter F., Stadler. In silico support for Eschenmoser's glyoxylate scenario. Isr. J. Chem., in review, 2015.
[29] Don L., Anderson. New Theory of the Earth. Cambridge University Press, London, 2007.
[30] P. W., Anderson. More is different. Science, New Series, 177:393–396, 1972.
[31] R. B., Anderson. The Fischer–Tropsch Synthesis. Academic Press, New York, 1984.
[32] Miho, Aoshima and Yasuo, Igarashi. A novel oxcalosuccinate-forming enzyme involved in the reductive carboxylation of 2-oxoglutarate in Hydrogenobacter thermophilus TK-6. Mol. Microbiol., 62:748–759, 2006.
[33] Miho, Aoshima and Yasuo, Igarashi. Nondecarboxylating and decarboxylating isocitrate dehydrogenases: oxalosuccinate reductase as an ancestral form of isocitrate dehydrogenase. J. Bacteriol., 190:2050–2055, 2008.
[34] Miho, Aoshima, Masaharu, Ishii, and Yasuo, Igarashi. 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.
[35] Miho, Aoshima, Masaharu, Ishii, and Yasuo, Igarashi. 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.
[36] Miho, Aoshima, Masaharu, Ishii, and Yasuo, Igarashi. 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.
[37] Aristotle, . History of Animals. Translated by D'ArcyWentworth Thompson. Clarendon Press, Oxford, 1910.
[38] William Ross, Ashby. An Introduction to Cybernetics. Chapman and Hall, London, 1956.
[39] W. Ross, Ashby. Requisite variety and its implications for the control of complex systems. Cybernetica, 1:83–99, 1958.
[40] Shreyas S., Athavale, Anton S., Petrov, Chiaolong, Hsiao, Derrick, Watkins, Caitlin D., Prickett, J. Jared, Gossett, Lively, Lie, Jessica C., Bowman, Eric, O-Neill, Chad R., Bernier, Nicholas V., Hud, Roger M., Wartell, Stephen C., Harvey, and Loren Dean, Williams. RNA folding and catalysis mediated by iron(II). PLoS ONE, 7:e38024, 2012.
[41] Henri, Atlan. Strehler's theory of mortality and the second principle of thermodynamics. J. Gerontol., 23:196–200, 1968.
[42] Thomas R., Ayers. Evolution of the solar ionizing flux. J. Geophys. Res., 102:1641–1651, 1997.
[43] Francis, Bacon. Novum Organum. 1620.
[44] Francis, Bacon. The New Organon. Michael Silverthorne and Lisa Jardine, editors. Cambridge University Press, London, 2000.
[45] Scott, Bailey, Richard A., Wing, and Thomas A., Steitz. The structure of T. aquaticus DNA polymerase III is distinct from eukaryotic replicative DNA polymerases. Cell, 126:893–904, 2006.
[46] Per, Bak, Chao, Tang, and Kurt, Wiesenfeld. Self-organized criticality: an explanation of the 1/f noise. Phys. Rev. Lett., 59:381–384, 1987.
[47] Per, Bak, Chao, Tang, and Kurt, Wiesenfeld. Self-organized criticality. Phys. Rev. A, 38:364–374, 1988.
[48] W. E., Balche and R. S., Wolfe. Specificity and biological distribution of coenzyme M (2-mercaptoethanesulfonic acid). J. Bacteriol., 137:256–263, 1979.
[49] Ruma, Banerjee and Stephen W., Ragsdale. The many faces of vitamin B12: catalysis by cobalamin-dependent enzymes. Annu. Rev. Biochem., 72:209–247, 2003.
[50] Arren, Bar-Even, Avi, Flamholz, Elad, Noor, and Ron, Milo. Thermodynamic constraints shape the structure of carbon fixation pathways. Biochim. Biophys. Acta Bioenergetics, 1817(9):1646–1659, 2012.
[51] Carlos F., Barbas III. Organocatalysis lost: modern chemistry, ancient chemistry, and an unseen biosynthetic apparatus. Angew. Chem. Int. Ed., 47:42–47, 2008.
[52] Laura M., Barge, Ivria J., Doloboff, Michael J., Russell, David, VanderVelde, Lauren M., White, Galen D., Stucky, Marc M., Baum, John, Zeytounian, Richard, Kidd, and Isik, Kanik. Pyrophosphate synthesis in iron mineral films and membranessimulating prebiotic submarine hydrothermal precipitates. Geochim. Cosmochim. Acta, 128:1–12, 2014.
[53] Laura M., Barge, Terence P., Kee, Ivria J., Doloboff, Joshua M. P., Hampton, Mohammed, Ismail, Mohamed, Ourkashanian, John, Zeytounian, Marc M., Baum, John A., Moss, Ghung-Kuang, Lin, Richard D., Kidd, and Isik, Kanik. The fuel cell model of abiogenesis: a new approach to origin-of-life simulations. Astrobiology, 14:254–270, 2014.
[54] H. A., Barker and J. V., Beck. The fermentative decomposition of purines by Clostridium acidi-urici and Clostridium cylindrosporum. J. Biol. Chem., 141(1):3–27, 1941.
[55] J. A., Bassham, A. A., Benson, L. D., Kay, A. Z., Harris, A., T.Wilson, and M., Calvin. The path of carbon in photosynthesis XXI. The cyclic regeneration of carbon dioxide acceptor. J. Am. Chem. Soc., 76:1760–1770, 1954.
[56] Anthony D., Baughn, Scott J., Garforth, Catherine, Vilchèze, and William R. Jr., JacobsAn anaerobic-type a-ketoglutarate ferredoxin oxidoreductase completes the oxidative tricarboxylic acid cycle of Mycobacterium tuberculosis. PLoS Pathogens, 5:e1000662, 1–10, 2009.
[57] Monika, Beh, Gerhard, Strauss, Robert, Huber, Karl-Otto, Stetter, and Georg, Fuchs. 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.
[58] Henri, Bénard. Les tourbillons cellulaires dans une nappe liquide. Rev. Gén. Sci. Pure Appl., 11:1261–1271, 1900.
[59] Gunes, Bender, Elizabeth, Pierce, Jeffrey A., Hill, Joseph E., Darty, and Stephen W., Ragsdale. Metal centers in the anaerobic microbial metabolism of CO and CO2. Metallomics, 3:797–815, 2011.
[60] Steven A., Benner, Andrew D., Ellington, and Andreas, Tauer.Modern metabolism as a palimpsest of the RNA world. Proc. Natl. Acad. Sci. USA, 18:7054–7058, 1989.
[61] Charles H., Bennett. Logical reversibility of computation. IBM J. Res. Dev., 17:525–532, 1973.
[62] Charles H., Bennett. The thermodynamics of computation – a review. Int. J. Theor. Phys., 21:905–940, 1982.
[63] Ivan A., Berg, Daniel, Kockelkorn, W. Hugo, Ramos-Vera, Rafael F., Say, Jan, Zarzycki, Michael, Hügler, Birgit E., Alber, and Georg, Fuchs. Autotrophic carbon fixation in archaea. Nature Rev. Microbiol., 8:447–460, 2010.
[64] Claude, Berge. Graphs and Hypergraphs. North-Holland, Amsterdam, revised edition, 1973.
[65] Frederick, Berkovitch, Yvain, Nicolet, Jason T., Wan, Joseph T., Jarrett, and Catherine L., Drennan. Crystal structure of biotin synthase, an S-adenosylmethioninedependent radical enzyme. Science, 303(5654):76–79, 2004.
[66] J. D., Bernal. The Physical Basis of Life. Routledge & Kegan Paul, London, 1951.
[67] J. D., Bernal, editor. The Origin of Life, Weidenfeld and Nicolson, London, 1967.
[68] Michael E., Berndt, Douglas E., Allen, and William E. Jr., SeyfriedReduction of CO2 during serpentinization of olivine at 300°C and 500 bar. Geology, 24:351–354, 1996.
[69] R. A., Berner and K. A., Maasch. 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.
[70] Harold S., Bernhardt. The RNA world hypothesis: the worst theory of the early evolution of life (except for all the others). Biol. Direct, 7:23, 2012.
[71] L., Bertini, A., De Sole, D., Gabrielli, G., Jona-Lasinio, and C., Landim. Macroscopic fluctuation theory for stationary non equilibrium states. J. Stat. Phys., 107:635–675, 2002.
[72] L., Bertini, A., De Sole, D., Gabrielli, G., Jona-Lasinio, and C., Landim. On the long-range correlations of thermodynamic systems out of equilibrium. arXiv:0705. 2996v1 [cond-mat.stat-mech], 2007.
[73] L., Bertini, A., De Sole, D., Gabrielli, G., Jona-Lasinio, and C., Landim. Towards a nonequilibrium thermodynamics: a self-contained macroscopic description of driven diffusive systems. J. Stat. Phys., 135:857–872, 2009.
[74] Dany J. V., Beste, Bhushan, Bonde, Nathaniel, Hawkins, Jane L., Ward, Michael H., Beale, Stephan, Noack, Katharina, Nöh, Nicholas J., Kruger, R. George, Ratcliffe, and Johnjoe, McFadden. 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.
[75] Roy A., Black, Matthew C., Blosser, Benjamin L., Stottrup, Ravi, Tavakley, David W., Deamer, and Sarah L., Keller. Nucleobases bind to and stabilize aggregates of a prebiotic amphiphile, providing a viable mechanism for the emergence of protocells. Proc. Natl. Acad. Sci. USA, early edition:1–5, 2013.
[76] Carrine E., Blank. Phylogenomic dating and the relative ancestry of prokaryotic metabolisms. In J., Seckbach and M., Walsh, editors, From Fossils to Astrobiology, pages 275–295. Springer, New York, 2009.
[77] Robert E., Blankenship. Molecular Mechanisms of Photosynthesis. Blackwell Science,Malden, MA, 2002.
[78] G., Blatter, M. V., Feigel'man, V. B., Geshkenbein, A. I., Larkin, and V. M., Vinokur. Vortices in high-temperature superconductors. Rev. Mod. Phys., 66:1125–1388, 1994.
[79] Konrad, Bloch. Blondes in Venetian Paintings, the Nine-Banded Armadillo, and Other Essays in Biochemistry. Yale University Press, New Haven, CT, 1997.
[80] Konstantin, Bokov and Sergey V., Steinberg. A hierarchical model for evolution of 23S ribosomal RNA. Nature, 457:977–980, 2009.
[81] Ludwig, Boltzmann. Populäre Schriften. J. A. Barth, Leipzig, 1905. Re-issued F. Vieweg, Braunschweig, 1979.
[82] Ludwig, Boltzmann. The second law of thermodynamics. In Populäre Schriften, pages 25–50. J. A. Barth, Leipzig, 1905. Re-issued F. Vieweg, Braunschweig, 1979.
[83] Yan, Boucher, Christophe J., Douady, R., Thane Papke, David A., Walsh, Mary Ellen R., Boudreau, Camilla L., Nesbø, Rebecca J., Case, and W. Ford, Doolittle. Lateral gene transfer and the origins of prokaryotic groups. Annu. Rev. Genet., 37:283–328, 2003.
[84] Bastien, Boussau, Laurent, Guéguen, and Manolo, Gouy. Accounting for horizontal gene transfers explains conflicting hypotheses regarding the position of aquificales in the phylogeny of bacteria. BMC Evol. Biol., 8:272, 2008.
[85] Jessica C., Bowman, Nicholas V., Hud, and Loren Dean, Williams. The ribosome challenge to the RNA world. J. Mol. Evol., 80:143–161, 2015.
[86] Samuel A., Bowring and Ian S., Williams. Priscoan (4.00–4.03 Ga) orthogneisses from northwestern Canada. Contrib. Mineral Petrol., 134:3–16, 1999.
[87] Eric S., Boyd and John W., Peters. New insights into the evolutionary history of biological nitrogen fixation. Frontiers Microbiol., 4:201, 2013.
[88] Paul, Boyer. Coupling mechanisms in capture, transmission, and use of energy. Annu. Rev. Biochem., 46:955–1026, 1977.
[89] Nanette R., Boyle and John A., Morgan. Computation of metabolic fluxes and efficiencies for biological carbon dioxide fixation. Metab. Eng., 13:150–158, 2011.
[90] Rogier, Braakman and Eric, Smith. The emergence and early evolution of biological carbon fixation. PLoS Comp. Biol., 8:e1002455, 2012. PMID: 22536150.
[91] Rogier, Braakman and Eric, Smith. The compositional and evolutionary logic of metabolism. Phys. Biol., 10:011001, 2013. PMID: 23234798.
[92] Rogier, Braakman and Eric, Smith. Metabolic evolution of a deep-branching hyperthermophilic chemoautotrophic bacterium. PLoS ONE, 9:e87950, 2014.
[93] Dan K., Braithwaite and Junetsu, Ito. Compilation, alignment, and phylogenetic relationships of DNA polymerases. Nucleic Acids Res., 21:787–802, 1993.
[94] Jay A., Brandes, Nabil Z., Boctor, George D., Cody, Benjamin A., Cooper, Robert M., Hazen, and Hatten S. Jr., YoderAbiotic nitrogen reduction on the early Earth. Nature, 395:365–367, 1998.
[95] Ullrich, Brandt. Bifurcated ubihydroquinone oxidation in the cytochrome bc1 complex by proton-gated charge transfer. FEBS Lett., 387:1–6, 1996.
[96] Elbert, Branscomb and Michael J., Russell. Turnstiles and bifurcators: the disequilibrium converting engines that put metabolism on the road. Biochim. Biophys. Acta, 1827:62–78, 2013.
[97] William J., Brazelton and John A., Baross. Abundant transposases encoded by the metagenome of a hydrothermal chimney biofilm. ISME J., 1–5, 2009.
[98] Leon, Brillouin. Science and Information Theory. Dover Phoenix Editions,Mineola, NY, second edition, 2004.
[99] James H., Brown. Macroecology. University of Chicago Press, Chicago, IL, 1995.
[100] Michael R. W., Brown and Arthur, Kornberg. Inorganic polyphosphate in the origin and survival of species. Proc. Natl. Acad. Sci. USA, 101:16085–16087, 2004.
[101] David E., Bryant, Katie E. R., Marriott, Stuart A., Macgregor, Colin, Kilner, Matthew A., Pasek, and Terence P., Kee. On the prebiotic potential of reduced oxidation state phosphorus: the H-phosphinate-pyruvate system. Chem. Commun., 46:3726–3728, 2010.
[102] Bob B., Buchanan and Daniel I., Arnon. A reverse Krebs cycle in photosynthesis: consensus at last. Photosynth. Res., 24:47–53, 1990.
[103] Wolfgang, Buckel and Rudolf K., Thauer. Energy conservation via electron bifurcating ferredoxin reduction and proton/Na+ translocating ferredoxin oxidation. Biochim. Biophys. Acta, 1827:94–113, 2013.
[104] John, Bunge, Amy, Willis, and Fiona, Walsh. Estimating the number of species in microbial diversity studies. Annu. Rev. Stat. Appl., 1:427–455, 2014.
[105] Rod, Burstall. Christopher Strachey – understanding programming languages. Higher-Order Symbolic Comput., 13:52, 2000.
[106] Leo W., Buss. The Evolution of Individuality. Princeton University Press, Princeton, NJ, 2007.
[107] Alison, Butler. Marine siderophores and microbial iron mobilization. BioMetals, 18:369–374, 2005.
[108] Thomas, Butler, Nigel, Goldenfeld, Damien, Mathew, and Zaida, Luthey-Schulten. Extreme genetic code optimality from a molecular dynamics calculation of amino acid polar requirement. Phys. Rev. E, 79:00901, 2009.
[109] A., Butlerow. Formation synthetique d'une substance sucree. Compt. Rend. Acad. Sci., 53:145–147, 1861.
[110] David A., Butterfield, Bruce K., Nelson, Geoffrey, Wheat, Michael, Mottl, and Kevin K., Roe. 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.
[111] Gustavo, Caetano-Anollés, Hee Shin, Kim, and Jay E., Mittenthal. The origin of modern metabolic networks inferred from phylogenemic analysis of protein architecture. Proc. Natl. Acad. Sci. USA, 104:9358–9363, 2007.
[112] Gustavo, Caetano-Anollés, Minglei, Wang, and Derek, Caetano-Anollés. Structural phylogenomics retrodicts the origin of the genetic code and uncovers the evolutionary impact of protein flexibility. PLoS ONE, 8:e72225, 2013.
[113] A. G., Cairns-Smith. Genetic Takeover: and the Mineral Origins of Life. Cambridge University Press, Cambridge, 1982.
[114] A. G., Cairns-Smith. Seven Clues to the Origin of Life – A Scientific Detective Story. Cambridge University Press, Cambridge, 1985.
115] A. G., Cairns-Smith and H., Hartman, editors. Clay Minerals and the Origin of Life. Cambridge University Press, Cambridge, 1986.
[116] Barbara J., Campbell and S. Craig, Cary. Evidence of chemolithoautotrophy in the bacterial community associated with Alvinella pompehana, a hydrothermal vent polychaete. Appl. Environ. Microbiol., 69:5070–5078, 2003.
[117] Ian H., Campbell. 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.
[118] I. H., Campbell, R.W., Griffiths, and R. I., Hill. Melting in an Archean mantle plume: heads it's basalts, tails it's komatiites. Nature, 339:697–699, 1989.
[119] Sadi, Carnot. Reflections on the Motive Power of Fire, E., Mendoza, editor. Dover, New York, 1960.
[120] B. J., Carr and M. J., Rees. The anthropic principle and the structure of the physical world. Nature, 278:605–612, 1979.
[121] David C., Catling and Kevin J., Zahnle. The planetary air leak. Sci. Am., May:36–43, 2009.
[122] Thomas R., Cech. The RNA worlds in context. Cold Spring Harb. Perspect. Biol., 4:a006742, 2011.
[123] E., Chabrière, M. H., Charon, A., Volbeda, L., Pieulle, E. C., Hatchikian, and J. C., Fontecilla-Camps. Crystal structures of the key anaerobic enzyme pyruvate: ferredoxin oxidoreductase, free and in complex with pyruvate. Nature Struct. Biol., 6:182–190, 1999.
[124] Gregory J., Chaitin. Algorithmic Information Theory. Cambridge University Press, New York, 1990.
[125] Patricia P., Chan and Todd M., Lowe. GtRNAdb: a database of transfer RNA genes detected in genomic sequence. Nucleic Acids Res., 37:D93–D97, 2008.
[126] Jean-Pierre, Changeux, Philippe, Courrége, and Antoine, Danchin. A theory of the epigenesis of neuronal networks by selective stabilization of synapses. Proc. Natl. Acad. Sci. USA, 70:2974–2978, 1973.
[127] Jean-Luc, Charlou and Jean-Pierre, Donval. Hydrothermal methane venting between 12°N and 26°N along the Mid-Atlantic ridge. J. Geophys. Res., 98:9625–9642, 1993.
[128] Nyles W., Charon, Russell C., Johnson, and David, Peterson. Amino acid biosynthesis in the spirochete leptospira: evidence for a novel pathway of isoleucine biosynthesis. J. Bacteriol., 117(1):203–211, 1974.
[129] Geoffrey, Chaucer. Treatise on the Astrolabe, Prologue, II 39–40. 1391.
[130] Lubin, Chen, Michael L., Johnson, and Rodney L., Biltonen. A macroscopic description of lipid bilayer phase transitions of mixed-chain phosphatidylcholines: chain-length and chain-asymmetry dependence. Biophys. J., 80:254–270, 2001.
[131] Peiqiu, Chen and Eugene I., Shakhnovich. Lethal mutagenesis in viruses and bacteria. Genetics, 183:639–650, 2009.
[132] Xi, Chen, Na, Li, and Andrew D., Ellington. Ribozyme catalysis of metabolism in the RNA world. Chem. Biodiv., 4:633–655, 2007.
[133] Ludmila, Chistoserdova. Modularity of methylotrophy, revisited. Environ. Microbiol., 13(10):2603–2622, 2011.
[134] L., Chistoserdova, M. G., Kalyuzhnaya, and M. E., Lidstrom. The expanding world of methylotrophic metabolism. Annu. Rev. Microbiol., 63:477–499, 2009.
[135] Ludmila, Chistoserdova, Julia A., Vorholt, Rudolf K., Thauer, and Mary E., Lidstrom. C1 transfer enzymes and coenzymes linking methylotrophic bacteria and methanogenic archaea. Science, 281:99–102, 1998.
[136] Dylan, Chivian, Eoin L., Brodie, Eric J., Alm, David E., Culley, Paramvir S., Dehal, Todd Z., DeSantis, Thomas M., Gihring, Alla, Lapidus, Li-Hung, Lin, Stephen R., Lowry, Duane P., Moser, Paul M., Richardson, Gordon, Southam, Greg, Wanger, Lisa M., Pratt, Gary L., Andersen, Terry C., Hazen, Fred J., Brockman, Adam P., Arkin, and Tullis C., Onstott. Environmental genomics reveals a single-species ecosystem deep within earth. Science, 322:275–278, 2008.
[137] Ahmed S. U., Choughuley and Richard M., Lemmon. Production of cysteic acid, taurine and cystamine under primitive earth conditions. Nature, 210:628–629, 1966.
[138] Francesca D., Ciccarelli, Tobias, Doerks, Christian von, Mering, Christopher J., Creevey, Berend, Snel, and Peer, Bork. Toward automatic reconstruction of a highly resolved tree of life. Science, 311:1283–1287, 2006.
[139] Mark W., Claire, James F., Jasting, Shawn D., Domagal-Goldman, Eva E., Stüeken, Roger, Buick, and Victoria S., Meadows. Modeling the signature of sulfur massindependent fractionation produced in the Archean atmosphere. Geochim. Cosmochim. Acta, 141:365–380, 2014.
[140] R., Clausius. On the application of the theorem of the equivalence of transformations to interior work. In T. Archer, Hirst, editor, The Mechanical Theory of Heat, pages 215–250, Fourth Memoir. John van Voorst, London, 1865.
[141] Jean-Michel, Claverie. Viruses take center stage in cellular evolution. Genome Biol., 7:110, 2006.
[142] Donald D., Clayton. Principles of Stellar Evolution and Nucleosynthesis. University of Chicago Press, Chicago, IL, 1983.
[143] H. James, Cleaves and Stanley L., Miller. The nicotinamide biosynthetic pathway is a by-product of the RNA world. J. Mol. Evol., 52:73–77, 2001.
[144] George D., Cody, Bjorn, Mysen, Gotthard, Sághi-Szabó, and John A., Tosell. 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.
[145] G. D., Cody, N. Z., Boctor, J. A., Brandes, T. E., Filley, R. M., Hazen, and H. S. Jr., YoderAssaying the catalytic potential of transition metal sulfides for abiotic carbon fixation. Geochim. Cosmochim. Acta, 68:2185–2196, 2004.
[146] George D., Cody, Nabil Z., Boctor, Timothy R., Filley, Robert M., Hazen, James H., Scott, Anurag, Sharma, and Hatten S. Jr., YoderPrimordial carbonylated iron-sulfur compounds and the synthesis of pyruvate. Science, 289:1337–1340, 2000.
[147] G. D., Cody, N. Z., Boctor, R. M., Hazen, J. A., Brandes, H. J., Morowitz, and H. S. Jr., YoderGeochemical roots of autotrophic carbon fixation: hydrothermal experiments in the system citric acid, H2O-(±FeS) (±NiS). Geochim. Cosmochim. Acta, 65:3557–3576, 2001.
[148] Melvin, Cohn, N. Av, Mitchison, William E., Paul, Arthur M., Silverstein, David W., Talmage, and Martin, Weigert. Reflections on the clonal-selection theory. Nature Rev. Immunol., 7:823–830, 2007.
[149] Sidney, Coleman. Aspects of Symmetry. Cambridge University Press, Cambridge, 1985.
[150] The CMS Collaboration. Evidence for the direct decay of the 125 GeV Higgs boson to fermions. Nature Phys., 10:557–560, 2014.
[151] Matthew D., Collins and Dorothy, Jones. Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication. Microbiol. Rev., 45(2):316–354, 1981.
[152] P. D. B., Collins, A. D., Martin, and E. J., Squires. Particle Physics and Cosmology. Wiley, New York, 1989.
[153] Creative Commons. Attribution-noncommercial-sharealike 3.0 unported, April 2015.
[154] R. C., Conant and W. R., Ashby. Every good regulator of a system must be a model of that system. Int. J. Syst. Sci., 1:89–97, 1970.
[155] Geoffrey M., Cooper. The Cell: A Molecular Approach. Sinauer Associates, Sunderland, MA, second edition, 2000.
[156] George, Cooper, Chris, Reed, Dang, Nguyen, Malika, Carter, and Yi, Wang. 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.
[157] Shelley D., Copley. Enzymes with extra talents: moonlighting functions and catalytic promiscuity. Curr. Opin. Chem. Biol., 7:265–272, 2003.
[158] Shelley D., Copley, Eric, Smith, and Harold J., Morowitz. 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.
[159] Shelley D., Copley, Eric, Smith, and Harold J., Morowitz. The origin of the RNA world: co-evolution of genes and metabolism. Bioorg. Chem., 35:430–443, 2007. PMID: 17897696.
[160] Armando, Córdova, Magnus, Engqvist, Ismail, Ibrahem, Jesús, Casas, and Henrik, Sunden. Plausible origins of homochirality in the amino acid catalyzed neogenesis of carbohydrates. Chem. Commun., 2005:2047–2049, 2005.
[161] John B., Corliss, John A., Baross, and Sarah E., Hoffman. Submarine hydrothermal systems: a probable site for the origin of life. Oreg. State Univ. Sch. Oceanogr., 80-7:1–44, 1980.
[162] J. B., Corliss, J., Dymond, L. I., Gordon, J. M., Edmond, R. P. von, Herzen, R. D., Ballard, K., Green, D., Williams, A., Bainbridge, K., Crane, and T. H.van, Andel. Submarine thermal springs on the Galapagos rift. Science, 203:1073–1083, 1979.
[163] James B., Cotner and Bopaiah A., Biddanda. Small players, large role: microbial influence on biogeochemical processes in pelagic aquatic ecosystems. Ecosystems, 5:105–121, 2002.
[164] Thomas M., Cover and Joy A., Thomas. Elements of Information Theory.Wiley, New York, 1991.
[165] F. H. C., Crick. Codon-antiodon pairing: the wobble hypothesis. J. Mol. Biol., 19:548–555, 1966.
[166] F. H. C., Crick. The origin of the genetic code. J. Mol. Biol., 38:367–379, 1968.
[167] Francis, Crick. Central dogma of molecular biology. Nature, 227:561–563, 1970.
[168] Francis, Crick. Life Itself: Its Origin and Nature. Simon and Schuster, New York, 1981.
[169] F. H. C., Crick and L. E., Orgel. Directed panspermia. Icarus, 19:341–346, 1973.
[170] Shane, Crotty, Craig E., Cameron, and Raul, Andino. RNA virus error catastrophe: direct molecular test by using ribavirin. Proc. Natl. Acad. Sci. USA, 98:6895–6900, 2001.
[171] Marie, Csete and John, Doyle. Bow ties, metabolism and disease. Trends Biotechnol., 22:446–450, 2004.
[172] Thomas P., Curtis, William T., Sloan, and Jack W., Scannell. Estimating prokaryotic diversity and its limits. Proc. Natl. Acad. Sci. USA, 99:10494–10499, 2002.
[173] S., Dagley and Donald E., Nicholson. An Introduction to Metabolic Pathways. Blackwell Scientific, Oxford, 1970.
[174] Vincent, Danos, Jérôme, Feret, Walter, Fontana, Russell, Harmer, and Jean, Krivine. Rule-based modelling, symmetries, refinements. Formal Methods in Systems Biology, Lecture Notes in Computer Science, volume 5054, pages 103–122. Springer, Berlin, 2008.
[175] M. J., Danson. Central metabolism of the archaea. In M., Kates, D. J., Kushner, and A. T., Matheson, editors, The Biochemistry of Archaea, pages 1–24. Elsevier, Amsterdam, 1993.
[176] Claudine, Darnault, Anne, Volbeda, Eun Jin, Kim, Pierre, Legrand, Xavier, Vernede, Paul A., Lindahl, and Juan C., Fontecilla-Camps. 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.
[177] Charles, Darwin. On the Origin of Species. John Murray, London, 1859.
[178] Charles, Darwin. The Life and Letters of Charles Darwin, including an Autobiographical Chapter, Vol. 3, Francis, Darwin, editor. John Murray, London, 1887.
[179] Eric H., Davidson. The Regulatory Genome: Gene Regulatory Networks in Development and Evolution. Academic Press, San Diego, CA, 2006.
[180] Eric H., Davidson and Douglas H., Erwin. Gene regulatory networks and the evolution of animal body plans. Science, 311:796–800, 2006.
[181] Richard C., Dawkins. The Selfish Gene. Oxford University Press, New York, 1976.
[182] M. A de, Angelis, M. D., Lilley, E. J., Olson, and J. A., Baross. Methane oxidation in deep-sea hydrothermal plumes of the Endeavour Segment of the Juan de Fuca Ridge. Deep-Sea Res., 40:1169–1186, 1993.
[183] Christian de, Duve. Blueprint for a Cell. Neil Patterson, Burlington, NC, 1991.
[184] David, Deamer. First Life: Discovering the Connections between Stars, Cells, and How Life Began. University of California Press, Los Angeles, CA, 2011.
[185] David, Deamer and Jack W., Szostak, editors. The Origins of Life. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 2011.
[186] Gerard, Deckert, Patrick V., Warren, Terry, Gaasterland, William G., Young, Anna L., Lenox, David E., Graham, Ross, Overbeek, Marjory A., Snead, Martin, Keller, Monette, Aujay, Robert, Huber, Robert A., Feldman, Jay M., Short, Gary J., Olsen, and Ronald V., Swanson. The complete genome of the hyperthermophilic bacterium Aquifex aeolicus. Nature, 392:353–358, 1998.
[187] Veronica, DeGuzman, Wenonah, Vercoutere, Hossein, Shenasa, and David, Deamer. Generation of oligonucleotides under hydrothermal conditions by non-enzymatic polymerization. J. Mol. Evol., 78:251–262, 2014.
[188] J. R., Delaney, D. S., Kelley, M. D., Lilley, D. A., Butterfield, J. A., Baross, W. S. D., Wilcock, R. W., Embley, and M., Summit. The quantum event of oceanic crustal accretion: impacts of diking at mid-ocean ridges. Science, 281:222–230, 1998.
[189] Michael, Denton. 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.
[190] Bernard, Derrida. Non equilibrium steady states: fluctuations and large deviations of the density and of the current. J. Stat. Mech., page P07023, 2007. arXiv:condmat/ 0703762v1.
[191] Á. S., Dias, R. A., Mills, I. Ribiero da, Costa, R., Costa, R. N., Taylor, M. J., Cooper, and F. J. A. S., Barriga. Tracing fluid-rock reaction and hydrothermal circulation at the Saldanha hydrothermal field. Chem. Geol., 273:168–179, 2010.
[192] Jeffrey M., Dick and Everett L., Shock. 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.
[193] Michael R., Dietric. The problem of the gene. Compt. Rend. Acad. Sci. Paris, 323:1139–1146, 2000.
[194] Kang, Ding, William E. Jr., Seyfried, Zhong, Zhang, Margaret K., Tivey, Karen L., Von Damm, and Albert M., Bradley. The in situ pH of hydrothermal fluids at midocean ridges. Earth Planet. Sci. Lett., 237:167–174, 2005.
[195] D. L., Distel, D. J., Lane, G. J., Olsen, S. J., Giovannoni, B., Pace, N. R., Pace, D. A., Stahl, and H., Felbeck. Sulfur-oxidizing bacterial endosymbionts: analysis of phylogeny and specificity by 16S rRNA sequences. J. Bacteriol., 170:2506–2510, 1988.
[196] Mike, Dixon-Kennedy. Encyclopedia of Greco-Roman Mythology. ABC-Clio, New York, 1998.
[197] Holger, Dobbek, Vitali, Svetlitchnyi, Lothar, Gremer, Robert, Huber, and Ortwin, Meyer. Crystal structure of a carbon monoxide dehydrogenase reveals a [Ni-4Fe- 5S] cluster. Science, 293:1281–1285, 2001.
[198] Theodosius, Dobzhansky. Nothing in biology makes sense except in the light of evolution. Am. Biol. Teacher, 35:125–129, 1973.
[199] M., Doi. Second quantization representation for classical many-particle system. J. Phys. A, 9:1465–1478, 1976.
[200] M., Doi. Stochastic theory of diffusion-controlled reaction. J. Phys. A, 9:1479–1495, 1976.
[201] Shawn D., Domagal-Goldman, Victoria S., Meadows, Mark W., Claire, and James F., Kasting. Using biogenic sulfur gases as remotely detectable biosignatures on anoxic planets. Astrobiology, 11:419–441, 2011.
[202] Matina C., Donaldson-Matasci, Carl T., Bergstrom, and Michael, Lachmann. The fitness value of information. Oikos, 119:219–230, 2010.
[203] Alexander, Donath, Sven, Findei, Jana, Hertel, Manja, Marz, Wolfgang, Otto, Christine, Schulz, Peter F., Stadler, and Stefan, Wirth. Non-coding RNAs. In Gustavo, Caetano- Anollés, editor, Evolutionary Genomics and Systems Biology, pages 251–293. Wiley-Blackwell, Hoboken, NJ, 2010.
[204] David, Duncan. The Life and Letters of Herbert Spencer.D. Appleton, New York, 1908. Two volumes.
[205] Jennifer A., Dunne, Richard J., Williams, Neo D., Martinez, Rachel A., Wood, and Douglas H., Erwin. Compilation and network analyses of Cambrian food webs. PLoS Biology, 6:e102, 2008.
[206] Rick, Durrett. Essentials of Stochastic Processes.Springer, New York, 1999.
[207] M. I., Dykman, Eugenia, Mori, John, Ross, and P. M., Hunt. Large fluctuations and optimal paths in chemical kinetics. J. Chem. Phys., 100:5735–5750, 1994.
[208] F. Y., Edgeworth. An introductory lecture on political economy. Econ. J., 1(4):625–634.
[209] Deeanne B., Edwards and Douglas C., Nelson. 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.
[210] P., Ehrenfest. Phasenumwandlungen im ueblichen und erweiterten Sinn, classifiziert nach den entsprechenden Singularitaeten des thermodynamischen Potentiales. Verh. K. Akad. Wet. Amsterdam, 36:153–157, 1933.
[211] Manfred, Eigen. Steps Toward Life.Oxford University Press, Oxford, 1992.
[212] Manfred, Eigen. From Strange Simplicity to Complex Familiarity.Oxford University Press, London, 2013.
[213] Manfred, Eigen and Peter, Schuster. The hypercycle, Part A. The emergence of the hypercycle. Naturwissenschaften, 64:541–565, 1977.
[214] Manfred, Eigen and Peter, Schuster. The hypercycle, Part C. The realistic hypercycle. Naturwissenschaften, 65:341–369, 1978.
[215] Marion, Eisenhut, Shira, Kahlon, Dirk, Hasse, Ralph, Ewald, Judy, Lieman-Hurwitz, Teruo, Ogawa, Wolfgang, Ruth, Hermann, Bauwe, Aaron, Kaplan, and Martin, Hagemann. The plant-like C2 glycolate cycle and the bacterial-like glycerate pathway cooperate in phosphoglycolate metabolism in cyanobacteria. Plant Physiol., 142:333–342, 2006.
[216] Marion, Eisenhut, Wolfgang, Ruth, Maya, Haimovich, Hermann, Bauwe, Aaron, Kaplan, and Martin, Hagemann. 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.
[217] Eric H., Ekland and David P., Bartel. RNA-catalyzed RNA polymerization using nucleoside triphosphates. Nature, 382:373–376, 1996.
[218] Basma El, Yacoubi, Shilah, Bonnett, Jessica N., Anderson, A., Swairjo Manal, Dirk, Iwata-Reuyl, and Valérie de, Crécy-Lagard. Discovery of a new prokaryotic type I GTP cyclohydrolase family. J. Biol. Chem., 281:37586–37593, 2006.
[219] Linda T., Elkins-Tanton. Linked magma ocean solidification and atmospheric growth for Earth and Mars. Earth Planet. Sci. Lett., 271:181–191, 2008.
[220] Linda T., Elkins-Tanton. Formation of early water oceans on rocky planets. Astrophys. Space Sci., 332:359–364, 2011.
[221] Linda T., Elkins-Tanton. Magma oceans in the inner solar system. Annu. Rev. Earth Planet. Sci., 40:113–139, 2012.
[222] Linda T., Elkins-Tanton. Evolutionary dichotomy for rocky planets. Nature, 497:570–572, 2013.
[223] Andrew D., Ellington. Experimental testing of theories of an early RNA world. Methods Enzymol, 224:646–664, 1993.
[224] Richard S., Ellis. Entropy, Large Deviations, and Statistical Mechanics.Springer-Verlag, New York, 1985.
[225] Aaron E., Engelhart, Matthew W., Powner, and Jack W., Szostak. Functional RNAs exhibit tolerance for non-heritable 2′–5′ vs. 2′–5′ backbone heterogeneity. Nature Chem., 5:390–394, 2013.
[226] Douglas H., Erwin. Extinction: How Life on Earth Nearly Ended 250 Million Years Ago.Princeton University Press, Princeton, NJ, 2006.
[227] Douglas H., Erwin and Eric H., Davidson. The evolution of hierarchical gene regulatory networks. Nature Rev. Genet., 10:141–148, 2009.
[228] Douglas H., Erwin and James W., Valentine. The Cambrian Explosion: The Construction of Animal Biodiversity.Roberts and Company, Englewood, CO, 2013.
[229] Douglas H., Erwin, Marc, Laflamme, Sarah M., Tweedt, Erik A., Sperling, Davide, Pisani, and Kevin J., Peterson. The Cambrian conundrum: early divergence and later ecological success in the early history of animals. Science, 334:1091–1097, 2011.
[230] Arthur Conan, Doyle. The Memoirs of Sherlock Holmes.Simon and Schuster, New York, 2014.
[231] Albert, Eschenmoser. On a hypothetical generational relationship between HCN and constituents of the reductive citric acid cycle. Chem. Biodivers., 4:554–573, 2007.
[232] Stewart N., Ethier and Thomas G., Kurtz. Markov Processes: Characterization and Convergence.Wiley, New York, 1986.
[233] Katharina F., Ettwig, Margaret K., Butler, Denis, Le Paslier, Eric, Pelletier, Sophie, Mangenot, Marcel M. M., Kuypers, Frank, Schreiber, Bas E., Dutilh, Johannes, Zedelius, Dirk de, Beer, Jolein, Gloerich, Hans J. C. T., Wessels, Theo van, Alen, Francisca, Luesken, Ming L. van de, Wu, Katinka T., Pas-Schoonen, Huub J. M., Op den Camp, Eva M., Janssen-Megens, Kees-Jan, Francoijs, Henk, Stunnenberg, Jean, Weissenbach, Mike S. M., Jetten, and Marc, Strous. Nitrite-driven anaerobic methane oxidation by oxygenic bacteria. Nature, 464:543–548, 2010.
[234] M. C. W., Evans, B. B., Buchanan, and D. I., Arnon. A new ferredoxin dependent carbon reduction cycle in photosynthetic bacterium. Proc. Natl. Acad. Sci. USA, 55:928–934, 1966.
[235] Paul G., Falkowski. Evolution of the nitrogen cycle and its influence on the biological sequestration of CO2 in the ocean. Nature, 387:272–275, 1997.
[236] Paul G., Falkowski, Tom, Fenchel, and Edward F., Delong. The microbial engines that drive Earth's biogeochemical cycles. Science, 320:1034–1039, 2008.
[237] James, Farquhar, Huiming, Bao, and Mark, Thiemens. Atmospheric influence of the Earth's earliest sulfur cycle. Science, 289:756–758, 2000.
[238] James, Farquhar, Marc, Peters, David T., Johnston, Harald, Strauss, Andrew, Masterson, Uwe, Wiechert, and Alan J., Kaufman. Isotopic evidence for Mesoarchean anoxia and changing atmospheric sulphur chemistry. Nature, 449:706–709, 2007.
[239] James, Farquhar, Joel, Savarino, Sabine, Airieau, and Mark H., Thiemes. Observation of wavelength-sensitive mass-independent sulfur isotope effects during SO2 photolysis: implications for the early atmosphere. J. Geophys. Res., 106:32829–32839, 2001.
[240] Ole, Farver, Ernst, Greil, Bernd, Luwig, Hartmut, Michel, and Israel, Pecht. Rates and equilibrium of CuA to heme a electron transfer in Paracoccus denitrificans cytochrome c oxidase. Biophys. J., 90:2131–2137, 2006.
[241] Ole, Farver, Peter M. H., Kroneck, Walter G., Zumft, and Israel, Pecht. Intramolecular electron transfer in cytochrome cd(1) nitrite reductase from Pseudomonas stutzeri; kinetics and thermodynamics. Biophys. Chem., 98:27–34, 2002.
[242] Adam M., Feist, Christopher S., Henry, Jennifer L., Reed, Markus, Krummenacker, Andrew, R. Joyce, Peter D., Karp, Linda J., Broadmelt, Vassily, Hatzimanikatis, and Berhard O., Palsson. 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.
[243] E., Fermi. Versuch einer theorie der ß-strahlen. i. Z. Phys., 88:161–177, 1934.
[244] Enrico, Fermi. Thermodynamics.Dover, New York, 1956.
[245] James P., Ferris. Mineral catalysis and prebiotic synthesis: montmorillonitecatalyzed formation of RNA. Elements, 1:145–149, 2005.
[246] J. P., Ferris and L. E., Orgel. An unusual photochemical re-arrangement in the synthesis of adenine from hydrogen cyanide. J. Am. Chem. Soc., 88:1074, 1966.
[247] J. P., Ferris, P. C., Joshi, K.-J., Wang, S., Miyakawa, and W., Huang. Catalysis in prebiotic chemistry: application to the synthesis of RNA oligomers. Adv. Space Res., 33:100–105, 2004.
[248] James P., Ferris, Robert A., Sanchez, and Leslie E., Orgel. Studies in prebiotic synthesis: III. Synthesis of pyrimidines from cyanoacetylene and cyanate. J. Mol. Biol., 33:693–704, 1968.
[249] James G., Ferry and Christopher H., House. The stepwise evolution of early life driven by energy conservation. Mol. Biol. Evol., 23:1286–1292, 2006.
[250] Martin, Ferus, David, Nesvorný, Jiří, Šponer, Petr, Kubelík, Regina, Michalčíková, Violetta, Shestivská, Judit D., Šponer, and Svatopluk, Civiš. High-energy chemistry of formamide: a unified mechanism of nucleobase formation. Proc. Natl. Acad. Sci. USA, early edition:1412072111, 2014.
[251] Georg, Feulner. The faint young sun problem. Rev. Geophys., 50:RG2006, 2012.
[252] Richard P., Feynman. Space-time approach to quantum electrodynamics. Phys. Rev., 76:769–789, 1949.
[253] Eliane, Fischer and Uwe, Sauer. A novel metabolic cycle catalyzes glucose oxidation and anaplerosis in hungry Escherichia coli. J. Biol. Chem., 278(47):46446–46451, 2003.
[254] Julia D., Fischer, Gemma L., Holliday, Syed A., Rahman, and Janet M., Thornton. The structures and physicochemical properties of organic cofactors in biocatalysis. J. Mol. Biol., 403:803–824, 2010.
[255] K. H., Fischer and J. A., Hertz. Spin Glasses.Cambridge University Press, New York, 1991.
[256] R. A., Fisher. The Genetical Theory of Natural Selection.Oxford University Press, London, 2000.
[257] Cyrus H., Fiske and Y., Subbarow. Phosphorus compounds of muscle and liver. Science, 70:381–382, 1929.
[258] W., Fontana. Modeling ‘Evo-Devo’ with RNA. Bioessays, 24:1164–1177, 2002.
[259] Walter, Fontana and Leo W., Buss. The barrier of objects: from dynamical systems to bounded organizations. In John, Casti and Anders, Karlqvist, editors, Boundaries and Barriers, pages 56–116. Addison-Wesley, New York, 1996.
[260] Walter, Fontana, Günter, Wagner, and Leo W., Buss. Beyond digital naturalism. Artificial Life, 1:211–227, 1994.
[261] Juan C., Fontecilla-Camps, Patricia, Amara, Christine, Cavazza, Yvain, Nicolet, and Anne, Volbeda. Structure-function relationships of anaerobic gas-processing metalloenzymes. Nature, 460:814–822, 2009.
[262] Juan C., Fontecilla-Camps, Anne, Volbeda, Christine, Cavazza, and Yvain, Nicolet. Structure/function relationships of [NiFe]- and [FeFe]-hydrogenases. Chem. Rev., 107:4273–4303, 2007.
[263] Patrick, Forterre. Defining life: the virus viewpoint. Orig. Life Evol. Biosphere, 40:151–160, 2010.
[264] Yves, Fouquet, Pierre, Camboun, Joël, Etoubleau, Jean Luc, Charlou, Hélène, Ondréas, Fernando J. A. S., Barriga, Georgy, Cherkashov, Tatiana, Semkova, Irina, Poroshina, M., Bohn, Jean Pierre, Donval, Katell, Henry, Pamela, Murphy, and Olivier, Rouxel. 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.
[265] G. P., Fournier and E. J., Alm. 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.
[266] Gregory P., Fournier, Cheryl P., Andam, Eric J., Alm, and J., Peter Gogarten. Molecular evolution of aminoacyl tRNA synthetase proteins in the early history of life. Orig. Life Evol. Biosphere, 41:621–632, 2011.
[267] Dionysis I., Foustoukos and William E., Seyfried Jr. Hydrocarbons in hydrothermal vent fluids: the role of chrome-bearing catalysts. Science, 304:1002–1005, 2004.
[268] Dionysis I., Foustoukos, Ivan P., Savov, and David R., Janecky. 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.
[269] George E., Fox. Origin and evolution of the ribosome. Cold Spring Harb. Perspect. Biol., 2:a003483, 2010.
[270] George E., Fox and Ashwinikumar K., Naik. The evolutionary history of the ribosome. In Lluís Ribas de, Pouplana, editor, The Genetic Code and the Origin of Life, pages 92–105. Kluwer Academic/Plenum, New York, 2004.
[271] George E., Fox and Ashwinikumar K., Naik. The evolutionary history of the translation machinery. In Lluís Ribas de, Pouplana, editor, The Genetic Code and the Origin of Life, pages 680–682. Kluwer Academic/Plenum, New York, 2004.
[272] Christine H., Foyer, Arnold J., Bloom, Guillaume, Queval, and Graham, Noctor. Photorespiratory metabolism: genes, mutants, energetics, and redox signaling. Annu. Rev. Plant Biol., 60:455–484, 2009.
[273] Steven A., Frank. The Price equation, Fisher's fundamental theorem, kin selection, and causal analysis. Evolution, 51:1712–1729, 1997.
[274] Steven A., Frank and Montgomery, Slatkin. Fisher's fundamental theorem of natural selection. Trends Ecol. Evol., 7:92–95, 1992.
[275] Rosalind E., Franklin and R. G., Gosling. Molecular configuration in sodium thymonucleate. Nature, 171:740–741, 1953.
[276] Steven J., Freeland and Laurence D., Hurst. The genetic code is one in a million. J. Mol. Evol., 47:238–248, 1998.
[277] Steven J., Freeland, Robin D., Knight, Laura F., Landweber, and Laurence D., Hurst. Early fixation of an optimal genetic code. Mol. Biol. Evol., 17:511–518, 2000.
[278] M. I., Freidlin and A. D., Wentzell. Random Perturbations in Dynamical Systems.Springer, New York, second edition, 1998.
[279] Daniel J., Frost and Catherine A., McCammon. The redox state of Earth's mantle. Annu. Rev. Earth. Planet. Sci., 36:389–420, 2008.
[280] Iris, Fry. The Emergence of Life on Earth: A Historical and Scientific Overview.Rutgers University Press, New Brunswick, NJ, 2000.
[281] Georg, Fuchs. CO2 fixation in acetogenic bacteria: variations on a theme. FEMS Microbiol. Lett., 38:181–213, 1986.
[282] Georg, Fuchs. Alternative pathways of carbon dioxide fixation: insights into the early evolution of life?Annu. Rev. Microbiol., 65(1):631–658, 2011.
[283] W. D., Fuller, R. A., Sanchez, and L. E., Orgel. Studies in prebiotic synthesis: VII. Solid-state synthesis of purine nucleosides. J. Mol. Evol., 1:249–257, 1972.
[284] Astrid, Gerhardt, Irfan, Çinkaya, Dietmar, Linder, Gjalt, Hulsman, and Wolfgang, Buckel. 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.
[285] S., Garlick, A., Oren, and E., Padan. Occurrence of facultative anoxygenic photosynthesis among filamentous and unicellular cyanobacteria. J. Bacteriol., 129:623–629, 1977.
[286] G. F., Gause. The Struggle for Existence.Williams and Wilkins, Baltimore, MD, 1934.
[287] Gerald L., Geison. The Private Science of Louis Pasteur.Princeton University Press, Princeton, NJ, 1995.
[288] Murray, Gell-Mann. The Quark and the Jaguar: Adventures in the Simple and the Complex.Freeman, New York, 1994.
[289] Murray, Gell-Mann and Seth, Lloyd. Information measures, effective complexity, and total information. Complexity, 2:44–52, 1996.
[290] Murray, Gell-Mann and Francis, Low. Quantum electrodynamics at small distances. Phys. Rev., 95:1300–1312, 1954.
[291] Andrew, Gelman and Cosma, Rohilla Shalizi. Philosophy and the practice of Bayesian statistics. Br. J. Math. Stat. Psychol., 66:8–38, 2013. arXiv:1006.3868.
[292] Anja C., Gemperli, Peter, Dimroth, and Julia, Steuber. Sodium ion cycling mediates energy coupling between complex I and ATP synthase. Proc. Natl. Acad. Sci. USA, 100:839–844, 2003.
[293] Howard, Georgi. Lie Algebras in Particle Physics.Perseus, New York, second edition, 1999.
[294] M. M., Georgiadis, H., Komiya, P., Chakrabarti, D., Woo, J. J., Kornuc, and D. C., Rees. Crystallographic structure of the nitrogenase iron protein from Azotobacter vinelandii. Science, 257(5077):1653–1659, 1992.
[295] John, Gerhart and Marc, Kirschner. Cells, Embryos, and Evolution.Wiley, New York, 1997.
[296] John, Gerhart and Marc, Kirschner. The theory of facilitated variation. Proc. Natl. Acad. Sci. USA, 104:8582–8589, 2007.
[297] Raymond F., Gesteland, Thomas R., Cech, and John F., Atkins, editors. The RNA World.Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 2006.
[298] Wieland, Gevers, Horst, Kleinkauf, and Fritz, Lipmann. Peptidyl transfers in gramicidin S biosynthesis from enzyme-bound thioester intermediates. Proc. Natl. Acad. Sci. USA, 63:1335–1342, 1969.
[299] Wieland, Gevers, Horst, Kleinkauf, and Fritz, Lipmann. Erratum: Peptidyl transfers in gramicidin S biosynthesis from enzyme-bound thioester intermediates. Proc. Natl. Acad. Sci. USA, 65:249, 1970.
[300] Arun, Ghosh and Marvin J., Miller. Synthesis of novel citrate-based siderophores and siderophore-ß-lactam conjugates. Iron transport-mediated drug delivery systems. J. Org. Chem., 58:7652–7659, 1993.
[301] Kingshuk, Ghosh, Ken A., Dill, Mandar M., Inamdar, Effrosyni, Seitaridou, and Rob, Phillips. Teaching the principles of statistical dynamics. Am. J. Phys., 74:123–133, 2006.
[302] Walter, Gilbert. The RNA world.Nature, 319:618, 1986.
[303] P., Glansdorff and I., Prigogine. Thermodynamic Theory of Structure, Stability, and Fluctuations.Wiley, New York, 1971.
[304] S., Glasstone, K. J., Laidler, and H., Eyring. The Theory of Rate Processes.McGraw Hill, New York, 1941.
[305] K., Glazyrin, T., Boffa Ballaran, D. J., Frost, C., McCammon, A., Kantor, M., Merlini, M., Hanfland, and L., Dubrovinsky. 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.
[306] J., Peter Gogarten, W., Ford Doolittle, and Jeffrey G., Lawrence. Prokaryotic evolution in light of gene transfer. Mol. Biol. Evol., 19:2226–2238, 2002.
[307] Nigel, Goldenfeld. Lectures on Phase Transitions and the Renormalization Group.Westview Press, Boulder, CO, 1992.
[308] Nigel, Goldenfeld and Carl, Woese. Life is physics: evolution as a collective phenomenon far from equilibrium. Annu. Rev. Condens. Matter Phys., 2:375–399, 2011.
[309] Herbert, Goldstein, Charles P., Poole, and John L., Safko. Classical Mechanics.Addison Wesley, New York, third edition, 2001.
[310] Benjamin, Gompertz. 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.
[311] Stephen Jay, Gould. Wonderful Life.Norton, New York, 1989.
[312] Stephen Jay, Gould. The Structure of Evolutionary Theory.Harvard University Press, Cambridge, MA, 2002.
[313] Stephen Jay, Gould and Elisabeth S., Vrba. Exaptation – a missing term in the science of form. Paleobiology, 8:4–15, 1982.
[314] Harry B., Gray. Chemical Bonds: An Introduction to Atomic and Molecular Structure.University Science Press, Sausalito, CA, 1994.
[315] D. C., Grenoble, M. M., Estadt, and D. F., Ollis. The chemistry and catalysis of the water gas shift reaction. J. Catal., 67:90–102, 1981.
[316] Laura L., Grochowski, Huimin, Xu, Kabo, Leung, and Robert H., White. Characterization of an Fe2+-dependent archaeal-specific GTP cyclohydrolase, MptA, from Methanocaldococcus jannaschii. Biochemistry, 46:6658–6667, 2007.
[317] Megan J., Gruer, Peter J., Artymiuk, and John R., Guest. The aconitase family: three structural variations on a common theme. Trends Biochem. Sci., 22:3–6, 1997.
[318] C., Guerrier-Takada, K., Gardiner, T., Marsh, N., Pace, and S., Altman. The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme. Cell, 35:849–857, 1983.
[319] Victor, Guillemin and Alan, Pollack. Differential Topology.Prentice Hall, New York, 1974.
[320] Marianne, Guiral, Laurence, Prunetti, Clément, Aussignargues, Alexandre, Ciaccafava, Pascale, Infossi, Marianne, Llbert, Elisabeth, Lojou, and Marie-Thérèse, Giudici-Orticoni. The hyperthermophilic bacterium Aquifex aeolicus: from respiratory pathways to extremely resistant enzymes and biotechnological applications. Adv. Microb. Physiol., 61:125–194, 2012.
[321] Marianne, Guiral, Pascale, Tron, Corinne, Aubert, Alexandre, Gloter, Chantal, Iobbi-Nivol, and Marie-Thérès, Giuici-Orticoni. A membrane-bound multienzyme, hydrogen-oxidizing, and sulfur-reducing complex from the hyperthermophilic bacterium Aquifex aeolicus. J. Biol. Chem., 280:42004–42015, 2005.
[322] Addison, Gulick. Phosphorus as a factor in the origin of life. Am. Sci., 43:479–489, 1955.
[323] Alex, Gutteridge and Janet M., Thornton. Understanding nature's catalytic toolkit. Trends Biochem. Sci., 30:622–629, 2005.
[324] Louis, Guttman. The basis for scalogram analysis. In Samuel A., Stouffer, Louis, Guttman, Edward A., Suchman, Paul F., Lazarsfeld, Shirley A., Star, and John A., Clausen, editors, Studies in Social Psychology in World War II Volume IV: Measurement and Prediction, pages 60–90. Wiley, New York, 1950.
[325] Marcelo I., Guzman and Scot T., Martin. Photo-production of lactate from glyoxylate: how minerals can facilitate energy storage in a prebiotic world. Chem. Commun., 46:2265–2267, 2010.
[326] Ernst, Haeckel. Generelle Morphologie der Organismen. Allgemeine Grundzüge der organischen Form-Wissenschaft, Mechanisch begründet durch die von Charles Darwin reformirte Descendenz-Theorie.G. Reimer, Berlin, 1866.
[327] David, Haig and Laurence D., Hurst. A quantitative measure of error minimization in the genetic code. J. Mol. Evol., 33:412–417, 1991.
[328] J. B. S., Haldane. The origin of life. Rationalist Animal, page 148, 1929. Reprinted as [329].
[329] J. B. S., Haldane. The origin of life. In J. D., Bernal, editor, The Origin of Life, pages 242–249. Weidenfeld and Nicolson, London, 1967.
[330] Carl H., Hamann, Andrew, Hamnett, and Wolf, Vielstich. Electrochemistry.Wiley, New York, completely revised and updated edition, 2007.
[331] Keiko, Hamano, Yutaka, Abe, and Hidenori, Genda. Emergence of two types of terrestrial planet on solidification of magma ocean. Nature, 497:607–610, 2013.
[332] William D., Hamilton. The genetical evolution of social behavior IJ. Theor. Biol., 7:1–16, 1964.
[333] William D., Hamilton. The genetical evolution of social behavior. II. J. Theor. Biol., 7:17–52, 1964.
[334] William D., Hamilton. Selfish and spiteful behavior in an evolutionary model. Nature, 228:1218–1220, 1970.
[335] Thomas, Handorf, Oliver, Ebenhöh, and Reinhart, Heinrich. Expanding metabolic networks: scopes of compounds, robustness, and evolution. J. Mol. Evol., 61:498–512, 2005.
[336] Chris, Hankin. Lambda Calculi: A Guide for Computer Scientists.Oxford University Press, New York, 1994.
[337] Ajith, Harish and Gustavo, Caetano-Anollés. Ribosomal history reveals origins of modern protein synthesis. PLoS ONE, 7:e32776, 2012.
[338] G. F., Hatfull and W. R. Jr., Jacobs, editors. Molecular Genetics of Mycobacteria, ASM Press, Washington, DC, 2000.
[339] Shuhei, Hattori, Johan A., Schmidt, Matthew S., Johnson, Sebastian O., Danielache, Akinori, Yamada, Yuichiro, Ueno, and Naohiro, Yoshida. 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.
[340] Mary E., Hawkins, Wolfgang, Pfleiderer, Oliver, Jungmann, and Frank M., Balis. Synthesis and fluorescence characterization of pteridine adenosine nucleoside analogs for DNA incorporation. Anal. Biochem., 298:231–240, 2001.
[341] Robert M., Hazen. Chiral crystal faces of common rock-forming minerals. In G., Palyi, C., Zucchi, and L., Cagglioti, editors, Progress in Biological Chirality, Chapter 11, pages 137–151. Elsevier, New York, 2004.
[342] Robert M., Hazen. Mineral surfaces and the prebiotic selection and organization of biomolecules (Presidential address to the Mineralogical Society of America). Am. Mineral., 91:1715–1729, 2006.
[343] Robert M., Hazen. Paleomineralogy of the Hadean eon: a preliminary species list. Am. J. Sci., 313:807–843, 2006.
[344] Robert M., Hazen and David W., Deamer. Hydrothermal reactions of pyruvic acid: synthesis, selection, and self-assembly of amphiphilic molecules. Orig. Life Evol. Biosphere, 37:143–152, 2007.
[345] Robert M., Hazen and John M., Ferry. Mineral evolution: mineralogy in the fourth dimension. Elements, 6:9–12, 2010.
[346] Robert M., Hazen and Dimitri A., Sverjensky. Mineral surfaces, geochemical complexities, and the origins of life. Cold Spring Harb. Perspect. Biol., 2:a002162, 2010.
[347] Robert M., Hazen, Edward S., Grew, Robert T., Downs, Joshua, Golden, and Grethe, Hystad. Mineral ecology: chance and necessity in the mineral diversity of terrestrial planets. Can. Mineral., in press, 2015.
[348] Robert M., Hazen, Dominic, Papineau, Wouter, Bleeker, Robert T., Downs, John M., Ferry, Timothy J., McCoy, Dimitri A., Sverjensky, and Heixiong, Yang. Mineral evolution. Am. Mineral., 93:1693–1720, 2008.
[349] Steffen, Heim, Andreas, Künkel, Rudolf K., Thauer, and Reiner, Hedderich. 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.
[350] Wolfgang, Heinen and Anne Marie, Lauwers. 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.
[351] Bettina, Heinz, Walter, Ried, and Klaus, Dose. Thermal generation of pteridines and flavines from amino acid mixtures. Angew. Chem. Int. Ed. Engl., 8:478–483, 1979.
[352] Eric, Herbst. Chemistry of star-forming regions. J. Phys. Chem., 109:4017–4029, 2005.
[353] Gloria, Herrmann, Elamparithi, Jayamani, Galina, Mai, and Wolfgang, Buckel. Energy conservation via electron-transferring flavoprotein in anaerobic bacteria. J. Bacteriol., 190:784–791, 2008.
[354] Matthew D., Herron, Armin, Rashidi, Deborah E., Shelton, and William W., Driscoll. Cellular differentiation and individuality in the ‘minor’ multicellular taxa. Biol. Rev., 88:844–861, 2013.
[355] Takeru, Higuchi, Lennart, Eberson, and Allen K., Herd. The intramolecular facilitated hydrolytic rates of methyl-substituted succinanilic acids. J. Am. Chem. Soc., 88:3805–3808, 1966.
[356] A., Hill and L. E., Orgel. Synthesis of adenine from HCN tetramer and ammonium formate. Orig. Life Evol. Biosphere, 32:99–102, 2002.
[357] T., Archer Hirst, editor. The Mechanical Theory of Heat.John van Voorst, London, 1865.
[358] Martin F., Hohmann-Marriott and Robert E., Blankenship. Evolution of photosynthesis. Annu. Rev. Plant Biol., 62:515–548, 2011.
[359] James F., Holden and Roy M., Daniel. The upper temperature limit for life based on hyperthermophile culture experiments and field observations. In William S. D., Wilcock, Edward F., DeLong, Deborah S., Kelley, John A., Baross, and S., Craig Cary, editors, The Subseafloor Biosphere at Mid-Ocean Ridges, pages 13–24. American Geophysical Soceity, vol. 144, Washington DC, 2004.
[360] James F., Holden, Melanie, Summit, and John A., Baross. Thermophilic and hyperthermophilic microorganisms in 3–30°C hydrothermal fluids following a deep-sea volcanic eruption. FEMS Microbiol. Ecol., 25:33–41, 1998.
[361] Nils G., Holm. Glasses as sources of condensed phosphates on the early earth. Geochem. Trans., 15:8, 2014.
[362] W. H., Holmes, I. D., Hamilton, and A. G., Robertson. The rate of turnover of the adenosine triphosphate pool of Escherichia coli growing aerobically in simple defined media. Arch. Microbiol., 83:95–109, 1972.
[363] Helge, Holo. Chloroflexus aurantiacus secretes 3-hydroxypropionate, a possible intermediate in the assimilation of CO2 and acetate. Arch. Microbiol., 151:252–256, 1989.
[364] H., Holo and D., Grace. 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.
[365] Michelle D., Hopkins, T., Mark Harrison, and Craig E., Manning. Constraints on Hadean geodynamics from mineral inclusions in >4 Ga zircons. Earth Planet. Sci. Lett., 298:367–376, 2010.
[366] Wim, Hordijk and Mike, Steel. Detecting autocatalytic, self-sustaining sets in chemical reaction systems. J. Theor. Biol., 227:451–461, 2004.
[367] Wim, Hordijk, Stuart A., Kauffman, and Mike, Steel. Required levels of catalysis for emergence of autocatalytic sets in models of chemical reaction systems. Int. J. Mol. Sci., 12:3085–3101, 2011.
[368] Wim, Hordijk, Mike, Steel, and Stuart, Kauffman. The structure of autocatalytic sets: evolvability, enablement, and emergence. Acta Biotheor., 60:379–392, 2012. arXiv:1205.0584v2.
[369] Juske, Horita and Michael E., Berndt. Abiogenic methane formation and isotopic fractionation under hydrothermal conditions. Science, 285:1055–1057, 1999.
[370] N. H., Horowitz. On the evolution of biochemical synthesis. Proc. Natl. Acad. Sci. USA, 31:153–157, 1945.
[371] Chiaolong, Hsiao, I.-Chun, Chou, C., Denise Okafor, Jessica C., Bowman, Eric B., O'Neill, Shreyas S., Athavale, Anton S., Petrov, Nicholas V., Hud, Roger M., Wartell, Stephen C., Harvey, and Loren Dean, Williams. Iron(II) plus RNA can catalyze electron transfer. Nature Chem., 5:525–528, 2013.
[372] Chiaolong, Hsiao, Srividya, Mohan, Benson K., Kalahar, and Loren Dean, Williams. Peeling the onion: establishing a chronology of early ribosome evolution. Mol. Biol. Evol., 26:2415–2425, 2009.
[373] Kerson, Huang. Statistical Mechanics.Wiley, New York, 1987.
[374] Teng, Huang and Verne, Schirch. 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.
[375] Wenhua, Huang and James P., Ferris. Synthesis of 35–40mers of RNA oligomers from unblocked monomers. A simple approach to the RNA world. Chem. Commun., 2003:1458–1459, 2003.
[376] Zhimin, Huang, Liang, Zhu, Yan, Cao, Geng, Wu, Xinyi, Liu, Yingyi, Chen, Qi, Wang, Ting, Shi, Yaxue, Zhao, Yuefei, Wang, Weihua, Li, Yixue, Li, Haifeng, Chen, Chen, Guoqiang, and Jian, Zhang. ASD: a comprehensive database of allosteric proteins and modulators. Nucleic Acids Res., 39:D663–D669, 2011.
[377] Claudia, Huber and Günter, Wächtershäuser. Activated acetic acid by carbon fixation on (Fe,Ni)S under primordial conditions. Science, 276:245–247, 1997.
[378] Claudia, Huber and Günter, Wächtershäuser. Primordial reductive amination revisited. Tetrahedron Lett., 44:1695–1697, 2003.
[379] Harald, Huber, Martin, Gallenberger, Ulrike, Jahn, Eva, Eylert, Ivan A., Berg, Daniel, Kockelkorn, Wolfgang, Eisenreich, and Georg, Fuchs. A dicarboxylate/4-hydroxybutyrate autotrophic carbon assimilation cycle in the hyperthermophilic archaeum Ignicoccus hospitalis. Proc. Natl. Acad. Sci. USA, 105:7851–7856, 2008.
[380] Philip, Hugenholtz, Brett M., Goebel, and Norman R., Pace. Impact of cultureindependent studies on the emerging phylogenetic view of bacterial diversity. J. Bacteriol., 180:4765–4774, 1998.
[381] Michael, Hügler and S. M., Seivert. Beyond the Calvin cycle: autotrophic carbon fixation in the ocean. Annu. Rev. Marine Sci., 3:261–289, 2011.
[382] Michael, Hügler, Harald, Huber, Stephen J., Molyneaux, Costantino, Vetriani, and Stefan M., Seivert. 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.
[383] J. R., Hulston and H. G., Thode. 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.
[384] Donald M., Hunten. Thermal and non-thermal escape mechanisms for terrestrial bodies. Planet. Space Sci., 30:773, 1982.
[385] James, Hury, Uma, Nagaswamy, Maia, Larios-Sanz, and George E., Fox. Ribosome origins: the relative age of 23S rRNA domains. Orig. Life Evol. Biosphere, 36:421–429, 2006.
[386] Aldous, Huxley. Literature and Science.Ox Bow Press, Woodbridge, CT, 1991.
[387] Abdul-Aziz, Ingar, Richard W. A., Luke, Barry R., Hayter, and John D., Sutherland. Synthesis of cytidine ribonucleotides by stepwise assembly of the heterocycle on a sugar phosphate. ChemBioChem, 4:504–507, 2003.
[388] Naoki, Irie and Shigeru, Kuratani. Comparative transcriptome analysis reveals vertebrate phylotipic period during organogenesis. Nature Commun., 2:248, 2011.
[389] F., Jacob and J., Monod. Genetic regulatory mechanisms in the synthesis of proteins. J. Mol. Biol., 3:318–356, 1961.
[390] Kenneth D., James and Andrew D., Ellington. The fidelity of template-directed oligonucleotide ligation and the inevitability of polymerase function. Orig. Life Evol. Biosphere, 29:375–390, 1999.
[391] E. T., Jaynes. Information theory and statistical mechanics. Phys. Rev., 106:620–630, 1957. Reprinted in [680].
[392] E. T., Jaynes. Information theory and statistical mechanics. II. Phys. Rev., 108:171–190, 1957. Reprinted in [680].
[393] E. T., Jaynes. The minimum entropy production principle. Annu. Rev. Phys. Chem., 31:579–601, 1980.
[394] E. T., Jaynes. Probability Theory: The Logic of Science.Cambridge University Press, New York, 2003.
[395] James, Jeans. Dynamical Theory of Gases.Cambridge University Press, London, fourth edition, 2009. Original edition, 1916.
[396] Harold, Jeffreys. An invariant form for the prior probability in estimation problems. Proc. R. Soc. London, Ser. A, 186:453–461, 1946.
[397] Harold, Jeffreys. Scientific Inference.Cambridge University Press, London, second edition, 1957.
[398] W. J., Jenkins, J. M., Edmond, and J. B., Corliss. Excess 3He and 4He in Galapagos submarine hydrothermal waters. Nature, 272:156–158, 1978.
[399] Roy A., Jensen. Enzyme recruitment in evolution of new function. Annu. Rev. Microbiol., 30:409–425, 1976.
[400] Ying, Ji and Henri-Claude, Nataf. Detection of mantle plumes in the lower mantle by diffraction tomography: Hawaii. Earth Planet. Sci. Lett., 159:99–115, 1998.
[401] Haixia, Jia, Cris, Moore, and Bart, Selman. From spin glasses to hard satisfiable formulas. In Holger H., Hoos and David G., Mitchell, editors, Theory and Applications of Satisfiability Testing, Lecture Notes in Computer Science, volume 3542, pages 199–210. Springer, New York, 2005.
[402] Fatima D., Jones and Scott A., Strobel. Ionization of a critical adenosine residue in the Neurospora Varkud satellite ribozyme active site. Biochem., 42:4265–4276, 2003.
[403] Gerald F., Joyce. Foreword. In David W., Deamer and Gail R., Fleischaker, editors, Origins of Life: The Central Concepts, pages xi–xii. Jones and Bartlett, Boston, MA, 1994.
[404] Martin, Jung. Polymerisation in Bilayers. PhD Thesis, Technische Universiteit Eindhoven, 2000.
[405] Christopher T., Jurgenson, Tadhg P., Begley, and Steven E., Ealick. The structural and biochemical foundations of thiamin biosynthesis. Annu. Rev. Biochem., 78(1):569–603, 2009.
[406] Ville R. I., Kaila, Michael I., Verkhovsky, and Mårten, Wikström. Proton-coupled electron transfer in cytochrome oxidase. Chem. Rev., 110:7062–7081, 2010.
[407] Roland G., Kallen and William P., Jencks. The dissociation constants of tetrahydrofolic acid. J. Biol. Chem., 241:5845–5850, 1966.
[408] Alex, Kamenev. Keldysh and Doi–Peliti techniques for out-of-equilibrium systems. In I. V., Lerner, B. L, Althsuler, V. I., Fal′ko, and T., Giamarchi, editors, Strongly Correlated Fermions and Bosons in Low-Dimensional Disordered Systems, pages 313–340. Springer-Verlag, Heidelberg, 2002.
[409] Masafumi, Kameya, Hiroyuki, Arai, Masaharu, Ishii, and Yasuo, Igarashi. 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.
[410] Anastassia, Kanavarioti, Pierre-Alain, Monnard, and David W., Deamer. Eutectic phases in ice facilitate nonenzymatic nucleic acid synthesis. Astrobiology, 1:271–281, 2001.
[411] M., Kanehisa. The KEGG database. Novartis Found. Symp., 247:91–101, 2002.
[412] Peter D., Karp, Monica, Riley, Suzanne M., Paley, and Alida, Pellegrini-Toole. The MetaCyc database. Nucleic Acids Res., 30:59–61, 2002.
[413] L., Karp-Boss and P. A., Jumars. Nutrient fluxes to planktonic osmotrophs in the presence of fluid motion. Oceanogr. Marine Biol. Annu. Rev., 34:71–107, 1996.
[414] Lee, Karp-Boss and Peter A., Jumars. Motion of diatom chains in a steady shear flow. Limnol. Oceanogr., 43:1767–1773, 1998.
[415] Anne-Kristin, Kaster, Johanna, Moll, Kristian, Parey, and Rudolf K., Thauer. Coupling of ferredoxin and heterodisulfide reduction via electron bifurcation in hydrogenotrophic methanogenic archaea. Proc. Natl. Acad. Sci. USA, 108:2981–2986, 2012.
[416] J. F., Kasting and T. P., Ackerman. Climatic consequences of very high CO2 levels in the early Earth's atmosphere. Science, 234:1383–1385, 1986.
[417] James F., Kasting and David, Catling. Evolution of a habitable planet. Annu. Rev. Astron. Astrophys., 41:429–463, 2003.
[418] James F., Kasting and M., Tazewell Howard. Atmosphere composition and climate on the early Earth. Philos. Trans. R. Soc. London, Ser. B, 361:1733–1742, 2006.
[419] James F., Kasting and James B., Pollack. Loss of water from Venus. I Hydrodynamic escape of hydrogen. Icarus, 53:479–508, 1983.
[420] J. F., Kasting, K. J., Zahnle, and J. C. G., Walker. Photochemistry of methane in the Earth's early atmosphere. Precambrian Res., 20:121–148, 1983.
[421] Richard F., Katz, Marc, Spiegelman, and Charles H., Langmuir. A new parameterization of hydrous mantle melting. Geochem. Geophys. Geosyst., 4:1073, 2003. doi:10.1029/2002GC000433.
[422] Stuart A., Kauffman. Autocatalytic sets of proteins. J. Theor. Biol., 119:1–24, 1986.
[423] Alan J., Kaufman, David T., Johnston, James, Farquhar, Andrew L., Masterson, Timothy W., Lyons, Steve, Bates, Ariel D., Anbar, Gail L., Arnold, Jessica, Garvin, and Roger, Buick. Late Archean biospheric oxygenation and atmospheric evolution. Science, 317:1900–1903, 2007.
[424] Jonathan Z., Kaye and John A., Baross. High incidence of halotolerant bacteria in Pacific hydrothermal vent and pelagic environments. FEMS Microbiol. Ecol., 32:429–460, 2000.
[425] Patrick J., Keeling and Jeffrey D., Palmer. Horizontal gene transfer in eukaryotic evolution. Nature Rev. Genet., 9:605–628, 2008.
[426] Deborah S., Kelley. From the mantle to microbes: the Lost City hydrothermal field. Oceanography, 18:32–45, 2005.
[427] Deborah S., Kelley, John A., Baross, and John R., Delaney. Volcanoes, fluids, and life at mid-ocean ridge spreading centers. Annu. Rev. Earth Planet. Sci., 30:385–491, 2002.
[428] Deborah S., Kelley, Jeffrey A., Karson, Donna K., Blackman, Gretchen L., Früh-Green, David A, Butterfield, Marvin D., Lilley, Eric J., Olson, Matthew O., Schrenk, Kevin K., Roe, Geoff T., Lebon, Pete, Rivizzigno, 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.
[429] Deborah S., Kelley, Jeffrey A., Karson, Gretchen L., Früh-Green, Dana R., Yoerger, Timothy M., Shank, David A., Butterfield, John M., Hayes, Matthew O., Schrenk, Eric J., Olson, Giora, Proskurowski, Mike, Jakuba, Al, Bradley, Ben, Larson, Kristin, Ludwig, Deborah, Glickson, Kate, Buckman, Alexander S., Bradley, William J., Brazelton, Kevin, Roe, Mitch J., Elend, Ad'elie, Delacour, Stefano M., Bernasconi, Marvin D., Lilley, John A., Baross, Roger E., Summons, and Sean P., Sylva. A serpentinite-hosted ecosystem: the Lost City hydrothermal field. Science, 307:1428–1434, 2005.
[430] J. M., Keynes. A Treatise on Probability.MacMillan, London, 1921.
[431] John Maynard, Keynes. The Collected Writings of John Maynard Keynes: Volume 4, A Tract on Monetary Reform.Cambridge University Press, London, 2012.
[432] P., Kharecha, J., Kasting, and J., Seifert. A coupled atmosphere-ecosystem model of the early Archean Earth. Geobiology, 3:53–76, 2005.
[433] Olga, Khersonsky and Dan S., Tawfik. Enzyme promiscuity: a mechanistic and evolutionary perspective. Annu. Rev. Biochem., 79:471–505, 2010.
[434] Olga, Khersonsky, Sergey, Malitsky, Ilana, Rogachev, and Dan S., Tawfik. Role of chemistry versus substrate binding in recruiting promiscuous enzyme functions. Biochemistry, 50:2683–2690, 2011.
[435] Goro, Kikuchi. The glycine cleavage system: composition, reaction mechanism, and physiological significance. Mol. Cell. Biochem., 1:169–187, 1973.
[436] J., Dongun Kim, Augustina, Rodriguez-Granillo, David A., Case, Vikas, Nanda, and Paul G., Falkowski. Energetic selection of topology in ferredoxins. PLoS Comp. Biol., 8:e1002463, 2012.
[437] Jonsun, Kim and D. C., Rees. Structural models for the metal centers in the nitrogenase molybdenum-iron protein. Science, 257(5077):1677–1682, 1992.
[438] Juhan, Kim, Jamie P., Kershner, Yehor, Novikov, Richard K., Shoemaker, and Shelley D., Copley. Three serendipitous pathways in E. coli can bypass a block in pyridoxal-5′-phosphate synthesis. Mol. Syst. Biol., 6:436:1–13, 2010.
[439] Mark, Kirkpatrick, Toby, Johnson, and Nick, Barton. General models of multilocus evolution. Genetics, 161:1727–1750, 2002.
[440] Marc, Kirschner and John, Gerhart. Evolvability. Proc. Natl. Acad. Sci. USA, 95(15):8420–8427, 1998.
[441] Charles, Kittel and Herbert, Kroemer. Thermal Physics.Freeman, New York, second edition, 1980.
[442] Robin D., Knight, Steven J., Freeland, and Laura F., Landweber. Selection, history and chemistry: the three faces of the genetic code. Trends Biochem. Sci., 24:241–247, 1999.
[443] Robin D., Knight, Steven J., Freeland, and Laura F., Landweber. Rewiring the keyboard: evolvability of the genetic code. Nature. Rev. Genet., 2:49–58, 2001.
[444] Andrew H., Knoll. Life on a Young Planet.Princeton University Press, Princeton, NJ, 2003.
[445] Martin, Kochmański, Tadeusz, Paszkiewicz, and Slawomir, Wolski. Curie–Weiss magnet – a simple model of phase transition. Eur. J. Phys., 34:1555–1573, 2013.
[446] John B., Kogut and Mikhail A., Stephanov. The Phases of Quantum Chromodynamics: From Confinement to Extreme Environments.Cambridge University Press, Cambridge, 2004.
[447] A. N., Kolmogorov. New metric invariant of transitive dynamical systems and endomorphisms of Lebesgue spaces. Dokl. Akad. Nauk SSSR, 119:861–864, 1958.
[448] A. N., Kolmogorov. Entropy per unit time as a metric invariant of automorphism. Dokl. Akad. Nauk SSSR, 124:754–755, 1959.
[449] Andrey, Kolmogorov. On tables of random numbers. Sankhyā Ser. A, 25:369–375, 1963. Reprinted in [450].
[450] Andrey, Kolmogorov. On tables of random numbers. Theor. Comput. Sci., 207:387–395, 1998.
[451] Dilip, Kondepudi and Ilya, Prigogine. Modern Thermodynamics: From Heat Engines to Dissipative Structures.Wiley, New York, 1998.
[452] Eugene V., Koonin and William, Martin. On the origin of genomes and cells within inorganic compartments. Trends Genet., 21:647–654, 2005.
[453] Jun, Korenaga. Initiation and evolution of plate tectonics on Earth: theories and observations. Annu. Rev. Earth Planet. Sci., 41:117–151, 2013.
[454] Arthur, Kornberg, Narayana N., Rao, and Dana, Ault-Riché. Inorganic polyphosphate: a molecule of many functions. Annu. Rev. Biochem., 68:89–125, 1999.
[455] David C., Krakauer and Joshua B., Plotkin. Redundancy, antiredundancy, and the robustness of genomes. Proc. Natl. Acad. Sci. USA, 99:1405–1409, 2002.
[456] H. A., Krebs and W. A., Johnson. The role of citric acid in intermediate metabolism in animal tissues. Enzymologia, 4:148–156, 1937.
[457] Supriya, Krishnamurthy, Eric, Smith, David C., Krakauer, and Walter, Fontana. The stochastic behavior of a molecular switching circuit with feedback. Biol. Direct, 2:13, 2007. PMID: 17540019.
[458] K., Kruger, P. J., Grabowski, A. J., Zaug, J., Sands, D. E., Gottschling, and T. R., Cech. Self-splicing RNA: autoexcision and autocyclization of the ribosomal RNA intervening sequence of Tetrahymena. Cell, 31:147–157, 1982.
[459] Thomas S., Kuhn. The Structure of Scientific Revolutions.University of Chicago Press, Chicago, IL, 1962.
[460] A., Kuki and P. G., Wolynes. Electron tunneling paths in proteins. Science, 236:1647–1652, 2000.
[461] I. S., Kulaev. Biochemistry of inorganic polyphosphates. Rev. Physiol. Biochem. Pharmacol., 73:131–158, 1975.
[462] I. S., Kulaev, V. M., Vagabov, and T. V., Kulakovskaya. The Biochemistry of Inorganic Polyphosphates.Wiley, New York, second edition, 2004.
[463] Lee R., Kump and William E. Jr, Seyfried. 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.
[464] Chi-Horng, Kuo and Howard, Ochman. Inferring clocks when lacking rocks: the variable rates of molecular evolution in bacteria. Biol. Direct, 4:35, 2009.
[465] Jorge, Kurchan. Six out of equilibrium lectures. In Thierry, Dauxois, Stefano, Ruffo, and Leticia F., Cugliandolo, editors, Long-range interacting Systems, Chapter 2. Oxford University Press, Oxford, 2010.
[466] Noam, Lahav. Biogenesis: Theories of Life's Origin.Oxford University Press, London, 1999.
[467] Jean-Baptiste, Lamarck. Philosophie Zoologique ou Exposition des Considérations Relatives à l'Histoire Naturelle des Animaux.Cambridge University Press, London, 2011. Original edition, 1809.
[468] L. D., Landau. Theory of phase transformations. Zh. Eksp. Teor. Fiz., 7:19–32, 1937.
[469] R., Landauer. Irreversibility and heat generation in the computing process. IBM J. Res. Dev., 3:183–191, 1961.
[470] Nick, Lane. Power, Sex, Suicide: Mitochondria and the Meaning of Life.Oxford University Press, Oxford, 2005.
[471] Nick, Lane. Why are cells powered by proton gradients?Nature Ed., 3:18, 2010.
[472] Nick, Lane and William, Martin. The energetics of genome complexity. Nature, 467:929–934, 2010.
[473] Nick, Lane and William F., Martin. The origin of membrane bioenergetics. Cell, 151:1406–1416, 2012.
[474] Nick, Lane, John F., Allen, and William, Martin. How did LUCA make a living? Chemiosmosis in the origin of life. Bioessays, 32:271–280, 2010.
[475] Nick, Lane, William F., Martin, John A., Raven, and John F., Allen. Energy, genes, and evolution: introduction to an evolutionary synthesis. Philos. Trans. R. Soc. London, Ser. B, 368:1–5, 2013.
[476] Susan Q., Lang, David A., Butterfield, Mitch, Schulte, Deborah S., Kelley, and Marvin D., Lilley. Elevated concentrations of formate, acetate, and dissolved organic carbon found at the Lost City hydrothermal field. Geochim. Cosmochim. Acta, 74:941–952, 2010.
[477] Charles H., Langmuir and Donald W., Forsyth. Mantle melting beneath mid-ocean ridges. Oceanography, 20:78–89, 2007.
[478] Pierre Simon, Laplace. Mémoire sur la probabilité des causes par les évènements. Mém. Acad. Sci. Paris, 6:621–656, 1774.
[479] Pierre Simon, Laplace. 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.
[480] Yanm, Lei, Shuang, Zhang, Peng, Chen, Hetao, Liu, Huanhuan, Yin, and Hongyu, Li. Magnetotactic bacteria, magnetosomes and their application. Microbiol. Res., 167:507–519, 2012.
[481] Joseph W., Lengeler, Gerhart, Drews, and Hans G., Schlegel. Biology of the Prokaryotes.Blackwell Science, New York, 1999.
[482] Richard C., Lewontin. The units of selection. Annu. Rev. Ecol. System., 1:1–18, 1970.
[483] Richard C., Lewontin. The Genetic Basis of Evolutionary Change.Columbia University Press, New York, 1974.
[484] Fuli, Li, Julia, Hinderberger, Henning, Seedorf, Jin, Zhang, Wolfgang, Buckel, and Rudolf K., Thauer. 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.
[485] Ming, Li and Paul, Vitányi. An Introduction to Kolmogorov Complexity and its Applications.Springer, Heidelberg, third edition, 2008.
[486] Zheng-Xue, Anser Li and Cin-Ty, Aeolus Lee. The constancy of upper mantle fO2 through time inferred from V/Sc ratios in basalts. Earth Planet. Sci. Lett., 228:483–493, 2004.
[487] Li-Hung, Lin, Pei-Ling, Wang, Douglas, Rumble, Johanna, Lippmann-Pipke, Erik, Boice, Lisa M., Pratt, Barbara Sherwood, Lollar, Eoin L., Brodie, Terry C., Hazen, Gary L., Andersen, Todd Z., DeSantis, Duane P., Moser, Dave, Kershaw, and T. C., Onstott. Long-term sustainability of a high-energy, low-diversity crustal biome. Science, 314:479–482, 2006.
[488] Tracy A., Lincoln and Gerald F., Joyce. Self-sustained replication of an RNA enzyme. Science, 323:1229–1232, 2009.
[489] Andrea J., Liu and Sidney R., Nagel. Nonlinear dynamics: jamming is not just cool any more. Nature, 396:21–22, 1998.
[490] Yongqing, Liu, Jizhong, Zhou, Marina V., Omelchenko, Alex S., Beliaev, Amudhan, Venkateswaran, Julia, Stair, Liyou, Wu, Dorothea K., Thompson, Dong, Xu, Igor B., Rogozin, Elena K., Gaidamakova, Min, Zhai, Kira S., Makarova, Eugene V., Koonin, and Michael J., Daly. Transcriptome dynamics of Deinococcus radiodurans recovering from ionizing radiation. Proc. Natl. Acad. Sci. USA, 100:4191–4196, 2003.
[491] L., Ljungdahl and H. G., Wood. Incorporation of C14 from carbon dioxide into sugar phosphates, carboxylic acids, and amino acids by Clostridium thermoaceticum. J. Bacteriol., 89:1055–1064, 1965.
[492] L., Ljungdahl, E., Irion, and H. G., Wood. 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.
[493] Elisabeth A., Lloyd. The Structure and Confirmation of Evolutionary Theory.Princeton University Press, Princeton, NJ, 1994.
[494] S. J., Lloyd, H., Lauble, G. S., Prasad, and C. D., Stout. The mechanism of aconitase: 1.8 Å resolution crystal structure of the S642A:citrate complex. Protein Sci., 8:2655–2662, 1999.
[495] Jonathan, Lombard and David, Moreira. Early evolution of the biotin-dependent carboxylase family. BMC Evol. Biol., 11:232:1–22, 2011.
[496] Purificación, López-García, David, Moreira, and Juli, Peretó. Origin and evolution of compartments. In Muriel, Gargaud, Phillippe, Claeys, Purificación, López-García, Hervé, Martin, Thierry, Montmerle, Robert, Pascal, and Jacques, Reisse, editors, From Suns to Life: a Chronological Approach to the History of Life on Earth, pages 171–174. Springer, Dordrecht, 2006.
[497] James, Lovelock. Gaia: A New Look at Life on Earth.Oxford University Press, London, 2000.
[498] Donald R., Lowe and Michael M., Tice. Geologic evidence for Archean atmospheric and climatic CO2, CH4, and O2 with an overriding tectonic control. Geology, 36:493–496, 2004.
[499] Robert P., Lowell, Peter A., Rona, and Richard P., Von Herzen. Seafloor hydrothermal systems. J. Geophys. Res., 100:327–352, 1995.
[500] Kristin A., Ludwig, Chuan-Chou, Shen, Deborah S., Kelley, Hai, Cheng, and R., Lawrence Edwards. U–Th systematics and 230Th ages of carbonate chimneys at the Lost City hydrothermal field. Geochim. Cosmochim. Acta, 75:1869–1888, 2011.
[501] Pier Luigi, Luisi. The Emergence of Life: From Chemical Origins to Synthetic Biology.Cambridge University Press, London, 2006.
[502] Pier Luigi, Luisi, Peter, Walde, and Thomas, Oberholzer. Lipid vesicles as possible intermediates in the origin of life. Curr. Op. Colloids Interface Sci., 4:33–39, 1999.
[503] John E., Lupton, Edward T., Baker, and Gary J., Massoth. Helium, heat, and the generation of hydrothermal event plumes at mid-ocean ridges. Earth Planet. Sci. Lett., 171:343–350, 1999.
[504] Richard A., Lutz, Timothy M., Shank, Daniel J., Fornari, Rachel M., Haymon, Marvin D., Lilley, Karen L., Von Damm, and Daniel, Desbruyeres. Rapid growth at deep-sea vents. Nature, 371:663–664, 1994.
[505] Vittorio, Luzzati and A., Tardieu. Lipid phases: structure and structural transitions. Annu. Rev. Phys. Chem., 25:79–94, 1974.
[506] Shang-Keng, Ma. Modern Theory of Critical Phenomena.Perseus, New York, 1976.
[507] Robert E., MacKenzie. Biogenesis and interconversion of substituted tetrahydrofolates. In Raymond L., Blakely and Stephen J., Benkovic, editors, Folates and Pterins, vol. 1: Chemistry and Biochemistry of Folates, pages 255–306. John Wiley & Sons, New York, 1984.
[508] David W. C., MacMillan. The advent and development of organocatalysis. Nature, 455:304–308, 2008.
[509] B. Edward, H. Maden. Tetrahydrofolate and tetrahydromethanopterin compared: functionally distinct carriers in C1 metabolism. Biochem. J., 350:609–629, 2000.
[510] Robert S., Maier and D. L., Stein. Effect of focusing and caustics on exit phenomena in systems lacking detailed balance. Phys. Rev. Lett., 71:1783–1786, 1993.
[511] Robert S., Maier and D. L., Stein. Oscillatory behavior of the rate of escape through an unstable limit cycle. Phys. Rev. Lett., 77:4860–4863, 1996.
[512] Stephen, Maitzen. Stop asking why there's anything. Erkenntnis, 77:51–63, 2012.
[513] Thomas Robert, Malthus. An Essay on the Principle of Population.Cosimo, New York, 2007. Original edition, 1798.
[514] I., Mamajanov and J., Herzfeld. HCN polymers characterized by SSNMR: solid state reaction of crystalline tetramer (diaminomaleonitrile). J. Chem. Phys., 130:134504, 2009.
[515] Michael L., Manapat, Irene A., Chen, and Martin A., Nowak. The basic reproductive ratio of life. J. Theor. Biol., 263:317–327, 2010.
[516] Benoit, Mandelbrot. The role of sufficiency and of estimation in thermodynamics. Ann. Math. Stat., 33:1021–1038, 1962.
[517] Craig E., Manning, Stephen J., Mojzsis, and T., Mark Harrison. Geology, age and origin of supracrustal rocks at Akilia, West Greenland. Am. J. Sci., 306:303–366, 2006.
[518] Lynn, Margulis and Karlene V., Schwartz. Five Kingdoms: An Illustrated Guide to the Phyla of Life on Earth.W. H. Freeman, New York, 1998.
[519] Stephanie, Markert, Cordelia, Arndt, Horst, Felbeck, Dörte, Becher, Stefan M., Sievert, Michael, Hügler, Dirk, Albrecht, Julie, Robidart, Shellie, Bench, Robert A., Feldman, Michael, Hecker, and Thomas, Schweder. Physiological proteomics of the uncultured endosymbiont of Riftia pachyptila. Science, 315:247–250, 2007.
[520] Ana Filipa A., Marques, Fernando J. A. S., Barriga, Valerie, Chavagnac, and Yves, Fouquet. Mineralogy, geochemistry, and Nd isotope composition of the Rainbow hydrothermal field, Mid-Atlantic Ridge. Miner. Deposita, 41:52–67, 2006.
[521] Pablo A., Marquet, Andrew P., Allen, James H., Brown, Jennifer A., Dunne, Brian J., Enquist, James F., Gillooly, Patricia A., Gowaty, Jessica L., Green, John, Harte, Steve P., Hubbell, James, O'Dwyer, Jordan G., Okie, Annette, Ostling, Mark, Ritchie, David, Storch, and Geoffrey B., West. On theory in ecology. BioScience, 64(8):701–710, 2014.
[522] P. C., Martin, E. D., Siggia, and H. A., Rose. Statistical dynamics of classical systems. Phys. Rev. A, 8:423–437, 1973.
[523] William F., Martin. Hydrogen, metals, bifurcating electrons, and proton gradients: the early evolution of biological energy conservation. FEBS Lett., 586:485–493, 2012.
[524] William, Martin and Michael J., Russell. 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.
[525] William, Martin and Michael J., Russell. On the origin of biochemistry at an alkaline hydrothermal vent. Philos. Trans. R. Soc. London, Ser. B, 362:1887–1926, 2007.
[526] William, Martin, John, Baross, Deborah, Kelley, and Michael J., Russell. Hydrothermal vents and the origin of life. Nature Rev. Microbiol., 6:805–814, 2008.
[527] William F., Martin, Filipa L., Fousa, and Nick, Lane. Energy at life's origin. Science, 344:1092–1093, 2014.
[528] Berta M., Martins, Holger, Dobbek, Irfan, Cinkaya, Wolfgang, Buckel, and Albrecht, Messerschmidt. 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.
[529] C. N., Matthews and R. D., Minnard. Hydrogen cyanide polymers, comets and the origin of life. Faraday Discuss., 133:393–401, 2006.
[530] John S., Mattick and Michael J., Gagen. 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.
[531] Daniel C., Mattis and M., Lawrence Glasser. The uses of quantum field theory in diffusion-limited reactions. Rev. Mod. Phys, 70:979–1001, 1998.
[532] Fabio, Mavelli and Pier L., Luisi. Autopoietic self-reproducing vesicles: a simplified kinetic model. J. Phys. Chem., 100:16600–16607, 1998.
[533] Ernst, Mayr. Where are we? Cold Spring Harbor Symp. Quant. Biol., 24:1–14, 1959.
[534] Ernst, Mayr. The Growth of Biological Thought: Diversity, Evolution, and Inheritance.Harvard University Press, Cambridge, MA, 1985.
[535] Ernst, Mayr. A natural system of organisms. Nature, 348:491, 1990.
[536] Ernst, Mayr. More natural classification. Nature, 353:122, 1991.
[537] Ernst, Mayr. The objects of selection. Proc. Natl. Acad. Sci. USA, 94:2091–2094, 1997.
[538] Ernst, Mayr. Two empires or three?Proc. Natl. Acad. Sci. USA, 95:9720–9723, 1998.
[539] Catherine A., McCammon. Mantle oxidation state and oxygen fugacity: constraints on mantle chemistry, structure, and dynamics. In R. D., Van Der Hilst, J. D., Bass, J., Mates, and J., Trampert, editors, Earth's Deep Mantle: Structure, Composition, and Evolution, pages 219–240. American Geophysical Union, Washington, DC, 2005.
[540] Gordon, McCleod, Christopher, McKeown, Allan J., Hall, and Michael J., Russell. Hydrothermal and oceanic pH conditions of possible relevance to the origin of life. Orig. Life Evol. Biosphere, 24:19–41, 1994.
[541] Thomas M., McCollom. 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.
[542] Thomas M., McCollom. Laboratory simulations of abiotic hydrocarbon formation in Earth's deep subsurface. Rev. Mineral. Geochem., 75:467–494, 2013.
[543] Thomas M., McCollom and Jeffrey S., Seewald. A reassessment of the potential for reduction of dissolved CO2 to hydrocarbons during serpentinization of olivine. Geochim. Cosmochim. Acta, 65:3769–3778, 2001.
[544] Thomas M., McCollom and Jeffrey S., Seewald. Carbon isotope composition of organic compounds produced by abiotic synthesis under hydrothermal conditions. Earth Planet. Sci. Lett., 243:74–84, 2006.
[545] Thomas M., McCollom and Everett L., Shock. Geochemical constraints on chemolithoautotrophic metabolism by microorganisms in seafloor hydrothermal systems. Geochim. Cosmochim. Acta, 61:4375–4391, 1997.
[546] Thomas M., McCollom, Barbara Sherwood, Lollar, Georges, Lacrampe-Couloume, and Jeffrey S., Seewald. The influence of carbon source on abiotic organic synthesis and carbon isotope fractionation under hydrothermal conditions. Geochim. Cosmochim. Acta, 74:2717–2740, 2010.
[547] W. F., McDonough and S.-S., Sun. The composition of the Earth. Chem. Geol., 120:223–253, 1995.
[548] James D., McGhee and Peter H., von Hippel. Formaldehyde as a probe of DNA structure. I. Reaction with exocyclic amino groups of DNA bases. Biochemistry, 14:1281–1296, 1975.
[549] Kathleen E., McGinness and Gerald F., Joyce. In search of an RNA replicase ribozyme. Chem. Biol., 10:5–14, 2003.
[550] Christopher P., McKay, Carolyn C., Porco, Travis, Altheide, Wanda L., Davis, and Timothy A., Kral. The possible origin and persistence of life on Enceladus and detection of biomarkers in the plume. Astrobiology, 8:909–919, 2008.
[551] Donald L., Melchior, Harold J., Morowitz, Julian M., Sturtevant, and Tian Yow, Tsong. Characterization of the plasma membrane of Mycoplasma Laidlawii. Biochim. Biophys. Acta, 219:114–122, 1970.
[552] Herman, Melville. Moby-Dick; or, The Whale.Modern Library, New York, 1992.
[553] Gregor, Mendel. Experiments on plant hybridization. J. R. Hortic. Soc., 26:1–32, 1901. English translation.
[554] César, Menor-Salván and Margarita R., Marin-Yaseli. Prebiotic chemistry in eutectic solutions at the water-ice matrix. Chem. Soc. Rev., 41:5404–5415, 2012.
[555] John W., Merck. Volcanism I: sources and composition of magma. GEOL212: planetary geology lecture notes, 2014.
[556] Marc, Mezard, Giorgio, Parisi, and Miguel Angel, Virasoro. Spin Glass Theory and Beyond.World Scientific, Singapore, 1987.
[557] S. L., Miller. Production of amino acids under possible primitive Earth conditions. Science, 117:528–529, 1953.
[558] S. L., Miller and D., Smith-Magowan. The thermodynamics of the Krebs cycle and related compounds. J. Phys. Chem. Ref. Data, 19:1049–1073, 1990.
[559] Peter, Mitchell. Coupling of phosphorylation to electron and hydrogen transfer by a chemi-osmotic type of mechanism. Nature, 191:144–148, 1961.
[560] S. J., Mojzsis, G., Arrhenius, K. D., McKeegan, T. M., Harrison, A. P., Nutman, and C. R. L., Friend. Evidence of life on Earth before 3,800 million years ago. Nature, 384:55–59, 1996.
[561] Jacques, Monod. Chance and Necessity.Knopf, New York, 1971.
[562] Jacques, Monod, Jean-Pierre, Changeux, and Francois, Jacob. Allosteric proteins and cellular control systems. J. Mol. Biol., 6(4):306–329, 1963.
[563] Thierry, Montmerle and Sylvia, Exström. Hertzsprung–Russell diagram. Encyclopedia of Astrobiology, pages 749–754. Springer, Berlin, 2011.
[564] S., Moorbath. Evolution of Precambrian crust from strontium isotopic evidence. Nature, 254:395–398, 1975.
[565] Cristopher, Moore and Stephan, Mertens. The Nature of Computation.Oxford University Press, London, 2011.
[566] Camilo, Mora, Derek P., Titensor, Sina, Adl, Alistair G. B., Simpson, and Boris, Worm. How many species are there on earth and in the ocean. PLoS Biol., 9:e1001127, 2011.
[567] Eduardo, Moreno and Christa, Rhiner. Darwin's multicellularity: from neurotrophic theories and cell competition to fitness fingerprints. Curr. Opin. Cell Biol., 31:16–22, 2014.
[568] W. J., Morgan. Convection plumes in the lower mantle. Nature, 230:42–43, 1971.
[569] Harold J., Morowitz. Proton semiconductors and energy transduction in biological systems. Am. J. Physiol., 235:R99–R114, 1978.
[570] Harold J., Morowitz. Energy Flow in Biology.Ox Bow Press, Woodbridge, CT, 1979.
[571] Harold J., Morowitz. Foundations of Bioenergetics.Academic Press, New York, 1987.
[572] Harold J., Morowitz. Beginnings of Cellular Life. Yale University Press, New Haven, CT, 1992.
[573] Harold J., Morowitz. Phenetics, a born-again science. Complexity, 8:12–13, 2003.
[574] H. J., Morowitz, J. D., Kostelnik, J., Yang, and G. D., Cody. The origin of intermediary metabolism. Proc. Natl. Acad. Sci. USA, 97:7704–7708, 2000.
[575] Michael R., Morrow, John P., Whitehead, and Dalian, Lu. Chain-length dependence of lipid bilayer properties near the liquid crystal to gel transition. Biophys. J., 63:18–27, 1992.
[576] Daniel, Mueller, Stefan, Pitsch, Atsushi, Kittaka, Ernst, Wagner, Claude E., Wintner, and Albert, Eschenmoser. 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.
[577] Ute, Müh, Irfan, Cinkaya, Simon P. J., Albracht, and Wolfgang, Buckel. 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.
[578] Armen Y., Mulkidjanian, Pavel, Dibrov, and Michael Y., Galperin. The past and present of the sodium energetics: may the sodium-motive force be with you. Biochim. Biophys. Acta, 1777:985–992, 2008.
[579] Armen Y., Mulkidjanian, Michael Y., Galperin, and Eugene V., Koonin. Co-evolution of primordial membranes and membrane proteins. Trends. Biochem. Sci., 34:206–215, 2009.
[580] Armen Y., Mulkidjanian, Michael Y., Galperin, Kira S., Makarova, Yuri I., Wolf, and Eugene V., Koonin. Evolutionary primacy of sodium bioenergetics. Biol. Direct, 3:13, 2008.
[581] H. J., Muller. The relation of recombination to mutational advance. Mutat. Res., 1:1–9, 1964.
[582] Ursula, Munro, John A., Munro, John B., Phillips, and Wolfgang, Wiltschko. Effects of wavelength of light and pulse magnetism on different magnetoreception systems in a migratory bird. Aust. J. Zool., 45:189–198, 1997.
[583] Bjorn O., Mysen. 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.
[584] Bjorn O., Mysen and George D., Cody. 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.
[585] John F., Nagle. Theory of the main lipid bilayer phase transition. Annu. Rev. Phys. Chem., 31:157–195, 1980.
[586] Shu-ichi, Nakano, Durga M., Chadalavada, and Philip C., Bevilacqua. General acidbase catalysis in the mechanism of a hepatitis delta virus ribozyme. Science, 287:1493–1497, 2000.
[587] David L., Nelson and Michael M., Cox. Lehninger Principles of Biochemistry.W. H. Freeman, New York, fourth edition, 2004.
[588] Anna, Neubeck, Nguyen Thanh, Duc, David, Bastviken, Patrick, Crill, and Nils G., Holm. Formation of H2 and CH4 by weathering of olivine at temperatures between 30 and 70°C. Geochem. Trans., 12:6:1–10, 2011.
[589] Marc, Neveu, Hyo-Joong, Kim, and Steven A., Benner. The “strong” RNA World hypothesis: fifty years old. Astrobiology, 13:391–403, 2013.
[590] Friedrich, Nietzsche. The Will to Power.C. G. Naumann, Leipzig, 1901.
[591] Poul, Nissen, Joseph A., Ippolito, Nenad, Ban, Peter B., Moore, and Thomas A., Steitz. RNA tertiary interactions in the large ribosomal subunit: the A-minor motif. Proc. Natl. Acad. Sci. USA, 98:4899–4903, 2001.
[592] Wolfgang, Nitschke and Michael J., Russell. 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.
[593] Wolfgang, Nitschke and Michael J., Russell. Beating the acetyl coenzyme A-pathway to the origin of life. Philos. Trans. R. Soc. London, Ser. B, 368:20120258, 2013.
[594] W., Nitscke, D. M., Kramer, A., Riedel, and U., Liebl. From naptho- to benzoquinones – (r)evolutionary reorganizations of electron transfer chains. In P., Mathis, editor, Photosynthesis: from Light to the Biosphere, vol. 1, pages 945–950. Kluwer Academic Press, Dordrecht, 1995.
[595] Harry F., Noller. On the origin of the ribosome: co-evolution of sub-domains of tRNA and rRNA. In Raymond F., Gesteland and John F., Atkins, editors, The RNA World, pages 137–156. Cold Spring Harbor Laboratory Press, Plainview, New York, 1993.
[596] Harry F., Noller. On the origin of the ribosome: co-evolution of sub-domains of tRNA and rRNA. In Raymond F., Gesteland and John F., Atkins, editors, The RNA World, pages 197–219. Cold Spring Harbor Laboratory Press, Plainview, New York, 1999.
[597] Yehor, Novikov and Shelley D., Copley. Reactivity landscape of pyruvate unde r simulated hydrothermal vent conditions. Proc. Natl. Acad. Sci. USA, 110:13283–13288, 2013.
[598] Martin A., Nowak and Hisashi, Ohtsuki. Prevolutionary dynamics and the origin of evolution. Proc. Natl. Acad. Sci. USA, 105:14924–14927, 2008.
[599] Allen P., Nutman, Vickie C., Benett, Clark. R. L., Friend, Frances, Jenner, and Yusheng, Wan. 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.
[600] Thomas, Nyström. A bacterial kind of aging. PLoS Genet., 3:2355–2357, 2007.
[601] Patrick J., O'Brien and Daniel, Herschlag. Catalytic promiscuity and the evolution of new enzymatic activities. Chem. Biol., 6:R91–R105, 1999.
[602] F. John, Odling-Smee, Kevin N., Laland, and Marcus W., Feldman. Niche Construction: The Neglected Process in Evolution. Princeton University Press, Princeton, NJ, 2003.
[603] Howard T., Odum and Richard C., Pinkerton. Time's speed regulator: the optimum efficiency for maximum output in physical and biological systems. Am. Sci., 43:331–343, 1955.
[604] Katsuhiko, Ogata. Modern Control Engineering. Prentice-Hall, New York, fifth edition, 2010.
[605] Gary J., Olsen and Carl R., Woese. Ribosomal RNA: a key to phylogeny. FASEB J., 7:113–123, 1993.
[606] Jonathan, O'Neil, Richard W., Carlson, Don, Francis, and Ross K., Stevenson. Neodymium-142 evidence for Hadean mafic crust. Science, 321:1828–1831, 2008.
[607] Lars, Onsager. Reciprocal relations in irreversible processes. I. Phys. Rev., 37:405–426, 1931.
[608] Lars, Onsager. Reciprocal relations in irreversible processes. II. Phys. Rev., 38:2265–2279, 1931.
[609] L., Onsager and S., Machlup. Fluctuations and irreversible processes. Phys. Rev., 91:1505, 1953.
[610] A. I., Oparin. Proiskhozhdenie zhizy. Moskovski Rabochii, Moscow, 1924. In Russian.
[611] Alexander I., Oparin. The origin of life. In J. D., Bernal, editor, The Origin of Life, pages 199–234. Weidenfeld and Nicolson, London, 1967.
[612] Aharon, Oren. Microbial life at high salt concentration: phylogenetic and metabolic diversity. Saline Syst., 4:2:1–13, 2008.
[613] Leslie E., Orgel. Prebiotic chemistry and the origin of the RNA world. Crit. Rev. Biochem. Mol. Biol., 39:99–123, 2004.
[614] Leslie E., Orgel. The implausibility of metabolic cycles on the early Earth. PLoS Biology, 6:e18, 2008.
[615] J., Oró. Mechanisms of synthesis of adenine from hydrogen cyanide under possible primitive Earth conditions. Nature, 191:1193–1194, 1961.
[616] J., Oró and A., Kimball. Synthesis of adenine from ammonium cyanide. Biochem. Biophys. Res. Commun., 2:407–412, 1960.
[617] J., Oró and A., Kimball. Synthesis of purines under possible primitive Earth conditions I: adenine from hydrogen cyanide. Arch. Biochem. Biophys., 94:217–227, 1961.
[618] J., Oró and A., Kimball. Synthesis of purines under possible primitive Earth conditions II: purine intermediates from hydrogen cyanide. Arch. Biochem. Biophys., 96:293–313, 1962.
[619] Sijbren, Otto, Jan B. F. N., Engberts, and Jan C. T., Kwak. 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.
[620] M., Paecht-Horowitz, J., Berger, and A., Katchalsky. Prebiotic synthesis of polypeptides by heterogeneous polycondensation of amino-acid adenylates. Nature, 228:636–639, 1970.
[621] Bernhard O., Palsson. Systems Biology. Cambridge University Press, Cambridge, MA, 2006.
[622] Eric T., Parker, H. James, Cleaves, Michael P., Callahan, Jason P., Dworkin, Daniel P., Glavin, Antonio, Lazcano, and Jeffrey L., Bada. 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.
[623] Robert, Pascal, Addy, Pross, and John D., Sutherland. Towards an evolutionary theory of the origin of life based on kinetics and thermodynamics. Open Biol., 3:130156, 2013.
[624] Matthew A., Pasek and Dante S., Lauretta. 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.
[625] Matthew A., Paseka, Jelte P., Harnmeijerb, Roger, Buick, Maheen, Gulla, and Zachary, Atlas. Evidence for reactive reduced phosphorus species in the early Archean ocean. Proc. Natl. Acad. Sci. USA, 110:10089–11194, 2013.
[626] Matthew A., Pasek, Jacqueline M., Sampson, and Zachary, Atlas. Redox chemistry in the phosphorus biogeochemical cycle. Proc. Natl. Acad. Sci. USA, 43:15468–15473, 2014.
[627] A. A., Pavlov and J. F., Kasting. Mass-independent fractionation of sulfur isotopes in Archean sediments: strong evidence for an anoxic Archean atmosphere. Astrobiology, 2:27–41, 2002.
[628] Alexander A., Pavlov, Lisa L., Brown, and James F., Kasting. UV shielding of NH3 and O2 by organic hazes in the Archean atmosphere. J. Geophys. Res., 106:23267–23287, 2001.
[629] A. A., Pavlov, M. J., Mills, and O. B., Toon. Mystery of the volcanic massindependent sulfur isotope fractionation signature in the Antarctic ice core. J. Geophys. Res., 32:L12816, 2005.
[630] L., Peliti. Path-integral approach to birth-death processes on a lattice. J. Phys. (Paris), 46:1469, 1985.
[631] L., Peliti. Renormalization of fluctuation effects in a + a → a reaction. J. Phys. A, 19:L365, 1986.
[632] Juli, Peretó. Out of fuzzy chemistry: from prebiotic chemistry to metabolic networks. Chem. Soc. Rev., 41:5394–5403, 2012.
[633] S., Petersen, K., Kuhn, T., Kuhn, N., Augustin, R., Hékinian, L., Franz, and C., Borowski. 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.
[634] Anton S., Petrov, Chad R., Bernier, Eli, Hershkovitz, Yuzhen, Xue, Chris C., Waterbury, Chiaolong, Hsiao, Victor G., Stepanov, Eric A., Gaucher, Martha A., Grover, Steven C., Harvey, Nicholas V., Hud, Roger M., Wartell, George E., Fox, and Loren D., Williams. Secondary structure and domain architecture of the 23S and 5S rRNAs. Nucleic Acids Res., 14:7522–7535, 2013.
[635] Anton S., Petrov, Chad R., Bernier, Chiaolong, Hsiao, Ashlyn M., Norris, Nicholas A., Kovacs, Chris C., Waterbury, Victor G., Stepanov, Stephen C., Harvey, George E., Fox, Roger M., Wartell, Nicholas V., Hud, and Loren D., Williams. Evolution of the ribosome at atomic resolution. Proc. Natl. Acad. Sci. USA, 2014.
[636] Susan M., Pfiffner, James M., Cantu, Amanda, Smithgall, Aaron D., Peacock, and David C., White. Deep subsurface microbial biomass and community structure in Witwatersrand basin mines. Geomicrobiol. J., 23:431–442, 2006.
[637] S., Pilgram, A. N., Jordan, E. V., Sukhorukov, and M., Büttiker. Stochastic path integral formulation of full counting statistics. Phys. Rev. Lett., 90:206801, 2003.
[638] Sandra, Pizzarello and Arthur L., Weber. Prebiotic amino acids as asymmetric catalysts. Science, 303:1151, 2004.
[639] Andrey V., Plyasunov and Everett L., Shock. Thermodynamic functions of hydration of hydrocarbons at 298.15 K and 0.1 MPa. Geochim. Cosmochim. Acta, 64:439–468, 2000.
[640] Anja, Poehlein, Silke, Schmidt, Anne-Kristin, Kaster, Meike, Goenrich, John, Vollmers, Andrea, Thürmer, Johannes, Bertsch, Kai, Schuchmann, Birgit, Voigt, Michael, Hecker, Rolf, Daniel, Rudolf K., Thauer, Gerhard, Gottschalk, and Volker, Müller. An ancient pathway combining carbon dioxide fixation with the generation and utilization of a sodium iongradient for ATP synthesis. PLoS ONE, 7:e33439, 2012.
[641] Andrew, Pohorille, Karl, Schweighofer, and Michael A., Wilson. The origin and early evolution of membrane channels. Astrobiology, 5:1–17, 2005.
[642] Andrew, Pohorille, Michael A., Wilson, and Christophe, Chipot. Membrane peptides and their role in protobiological evolution. Orig. Life Evol. Biosphere, 33:173–197, 2003.
[643] Joseph G., Polchinski. Renormalization group and effective lagrangians. Nucl. Phys. B, 231:269–295, 1984.
[644] Anthony M., Poole, Daniel C., Jeffares, and David, Penny. The path from the RNA world. J. Mol. Evol., 46:1–17, 1998.
[645] Karl R., Popper. Logik der Forschung. Julius Springer Verlag, Vienna, 1935.
[646] Karl R., Popper. The Logic of Scientific Discovery. Hutchinson, London, 1959. Translation of [645].
[647] Matthew W., Powner, Béatrice, Gerland, and John D., Sutherland. Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions. Nature, 459:239–242, 2009.
[648] Matthew W., Powner, John D., Sutherland, and Jack W., Szostak. The origins of nucleotides. SYNLETT, 14:1956–1964, 2011.
[649] Steve, Pressé, Kingshuk, Ghosh, Julian, Lee, and Ken A., Dill. The principles of maximum entropy and maximum caliber in statistical physics. Rev. Mod. Phys, 85:1115–1141, 2013.
[650] G. R., Price. Fisher's ‘fundamental theorem’ made clear. Ann. Hum. Genet., 36:129–140, 1972.
[651] Giora, Proskurowski, Marvin D., Lilley, Jeffery S., Seewald, Gretchen L., Früh-Green, Eric J., Olson, John E., Lupton, Sean P., Sylva, and Deborah S., Kelley. Abiogenic hydrocarbon production at Lost City hydrothermal field. Science, 319:604–607, 2008.
[652] William B., Provine. The Origins of Theoretical Population Genetics. University of Chicago Press, Chicago, IL, 2001.
[653] E. M., Purcell. Life at low Reynolds number. Am. J. Phys., 45:3–11, 1973.
[654] Henry, Quastler. The Emergence of Biological Organization. Yale University Press, New Haven, CT, 1964.
[655] John M., Quick. Statistical Analysis withR. Packt Publishing, Birmingham, 2010.
[656] Efraim, Racker and Walther, Stoeckenius. Reconstitution of purple membrane vesicles catalyzing light-driven proton uptake and adenosine triphosphate formation. J. Biol. Chem., 249:662–663, 1974.
[657] Petronella C., Raemakers-Franken, Roy, Bongaerts, Roel, Fokkens, Chris van der, Drift, and Godfried D., Vogels. Characterization of two pterin derivatives isolated from Methanoculleus thermophilicum. Eur. J. Biochem., 200:783–787, 1991.
[658] Petronella C., Raemakers-Franken, Frank G., Voncken, Jaap, Korteland, Jan T., Keltjens, Chris van der, Drift, and Godfried D., Vogels. Structural characterization of tatiopterin, a novel pterin isolated from Methanogenium tationis. Biofactors, 2:117–122, 1989.
[659] Stephen W., Ragsdale. Enzymology of the Wood–Ljungdahl pathway of acetogenesis. Ann. N Y Acad. Sci., 1125:129–136, 2008.
[660] Stephen W., Ragsdale and Manoj, Kumar. Nickel-containing carbon monoxide dehydrogenase/acetyl-CoA synthase. Chem. Rev., 96:2515–2540, 1996.
[661] Stephen W., Ragsdale and Harland G., Wood. Enzymology of the acetyl-CoA pathway of CO2 fixation. Crit. Rev. Biochem. Mol. Biol., 26:261–300, 1991.
[662] S.W., Ragsdale, J. E., Clark, L. G., Ljungdahl, L. L., Lundie, and H. L., Drake. Properties of purified carbon monoxide dehydrogenase from Clostridium thermoaceticum, a nickel, iron-sulfur protein. J. Biol. Chem., 258(4):2364–2369, 1983.
[663] Burki, Rajendar, Arivazhagan, Rajendran, Zhiqiang, Ye, Erko, Kanai, Yusuke, Sato, Seiichi, Nishizawa, Marek, Sikorski, and Norio, Teramae. 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.
[664] Kalervo, Rankama and Thure Georg, Sahama. Geochemistry. University of Chicago Press, Chicago, IL, 1950.
[665] Jason, Raymond, Janet L., Seifert, Christopher R., Staples, and Robert E., Blankenship. The natural history of nitrogen fixation. Mol. Biol. Evol., 21:541–554, 2004.
[666] Eoghan P., Reeves, Jill M., McDermott, and Jeffrey S., Seewald. The origin of methanethiol in midocean ridge hydrothermal fluids. Proc. Natl. Acad. Sci. USA, 111:5474–5479, 2014.
[667] Howard M., Reid. Introduction to Statistics: Fundamental Concepts and Procedures of Data Analysis. SAGE publications, Washington DC, 2014.
[668] Anna-Louise, Reysenbach and Everett, Shock. Merging genomes with geochemistry in hydrothermal ecosystems. Science, 296:1077–1082, 2002.
[669] J. M., Rhodes. Mantle melting and origin of basaltic magma. Notes: GEO-321. Igneous & Metamorphic Petrology, March 2005. geo321/Lecture.
[670] Ignasi, Ribas. The sun and stars as the primary energy input in planetary atmospheres. In A. G., Kosovichev, A. H., Andrei, and J.-P., Rozelot, editors, Proc. International Astronomical Union Symposium No. 264, 2009, pages 3–18. Cambridge University Press, Cambridge, 2010.
[671] A., Ricardo, M. A., Carrigan, A. N., Olcott, and S. A., Benner. Borate minerals stabilize ribose. Science, 303:196, 2004.
[672] William J., Riehl, Paul L., Krapivsky, Sidney, Redner, and Daniel, Segrè. Signatures of arithmetic simplicity in metabolic network architecture. PLoS Comput. Biol., 6:e1000725, 2010.
[673] G., Rieley, C. L., Van Dover, D. B., Hedrick, and G., Eglinton. Trophic ecology of Rimicaris exoculata: a combined lipid abundance stable isotope approach. Mar. Biol., 133:495–499, 1999.
[674] Jorma, Rissanen. Stochastic Complexity in Statistical Inquiry. World Scientific, Teaneck, NJ, 1989.
[675] Michael P., Robertson and Gerald F., Joyce. The origins of the RNA world. Cold Spring Harb. Perspect. Biol., 4:a003608, 2010.
[676] Michael P., Robertson and William G., Scott. The structural basis of ribozymecatalyzed RNA assembly. Science, 315:1549–1553, 2007.
[677] João F., Matias Rodrigues and Andreas, Wagner. Evolutionary plasticity and innovations in complex metabolic reaction networks. PLoS Comput. Biol., 5:e1000613:1–11, 2009.
[678] Rajat, Rohatgi, David P., Bartel, and Jack W., Szostak. Kinetic and mechanistic analysis of nonenzymatic, template-directed oligoribonucleotide ligation. J. Am. Chem. Soc., 118:3332–3339, 1996.
[679] Rajat, Rohatgi, David P., Bartel, and Jack W., Szostak. Nonenzymatic, templatedirected ligation of oligoribonucleotides is highly regioselective for the formation of 3′–5′ phosphodiester bonds. J. Am. Chem. Soc., 118:3340–3344, 1996.
[680] R. D., Rosenkrantz, editor. Jaynes, E. T.: Papers on Probability, Statistics and Statistical Physics. D. Reidel, Dordrecht, 1983.
[681] Paul J., Rothwell and Gabriel, Waksman. Structure and mechanism of DNA polymerases. Adv. Protein Chem., 71:401–440, 2005.
[682] Bertand, Russell. A History of Western Philosophy. Simon & Schuster, New York, 1967.
[683] Michael J., Russell. Downward-excavating hydrothermal cells and Irish-type ore deposits: importance of an underlying thick Caledonian prism. Trans. Inst. Min. Metall., B87:168–171, 1978.
[684] Michael J., Russell. Mining, metallurgy and the origin of life. Miner. Indust. Int., 1009:4–8, 1993.
[685] Michael J., Russell. First life. Am. Sci., 94:32–39, 2006.
[686] Michael J., Russell. The alkaline solution to the emergence of life: energy, entropy, and early evolution. Acta Biotheor., 55:133–179, 2007.
[687] Michael J., Russell and A. J., Hall. The emergence of life from iron monosulphide bubbles at a submarine hydrothermal redox and pH front. J. Geol. Soc. London, 154:377–402, 1997.
[688] Michael J., Russell and Allan J., Hall. The onset and early evolution of life. Geol. Soc. Am. Memoir, 198:1–32, 2006.
[689] Michael J., Russell and William, Martin. The rocky roots of the acetyl-CoA pathway. Trends Biochem. Sci., 29:358–363, 2004.
[690] Michael J., Russell, Laura M., Barge, Rohit, Bhartia, Dylan, Bocanegra, Paul J., Bracher, Elbert, Branscomb, Richard, Kidd, Shawn, McGlynn, David H., Meier,Wolfgang, Nitschke, Takazo, Shibuya, Steve, Vance, Lauren, White, and Isik, Kanik. The drive to life on wet and icy worlds. Astrobiology, 14:308–343, 2014.
[691] Michael J., Russell, Roy M., Daniel, and Allan J., Hall. On the emergence of life via catalytic iron-sulphide membranes. Terra Nova, 5:343–347, 1993.
[692] Michael J., Russell, Allan J., Hall, Adrian J., Boyce, and Anthony E., Fallick. On hydrothermal convection systems and the emergence of life. Econ. Geol., 100:419–438, 2005.
[693] M. J., Russell, A. J., Hall, A. G., Cairns-Smith, and P. S., Braterman. Submarine hot springs and the origin of life. Nature, 336:117, 1988.
[694] M. J., Russell, A. J., Hall, and W., Martin. Serpentinization as a source of energy at the origin of life. Geobiology, 8:355–371, 2010.
[695] W. J., Rutter. Evolution of aldolase. Fed. Proc., 23:1248–1257, 1964.
[696] Carl, Sagan and Christopher, Chyba. The early faint young sun paradox: organic shielding of ultraviolet-labile greenhouse gases. Science, 276:1217–1221, 1997.
[697] Carl, Sagan and George, Mullen. Earth and Mars: evolution of atmospheres and surface temperatures. Science, New Series, 177:52–56, 1972.
[698] Raffaele, Saladino, Giorgia, Botta, Samanta, Pino, Giovanna, Costanzo, and Ernesto Di, Mauro. From the one-carbon amide formamide to RNA all the steps are prebiotically possible. Biochimie, 94:1451–1456, 2012.
[699] Raffaele, Saladino, Giorgia, Botta, Samanta, Pino, Giovanna, Costanzo, and Ernesto Di, Mauro. Materials for the onset: a story of necessity and chance. Frontiers Biosci., 18:1275–1289, 2013.
[700] Maria do, Céu Santos and Manuel A. S., Santos. Structural and molecular features of non-standard genetic codes. In Gina, M. Cannarozzi, and Adrian, Schneider, editors, Codon Evolution: Mechanisms and Models, pages 258–270, Oxford University Press, New York, 2012.
[701] Takaaki, Sato, Hiroyuki, Imanaka, Naeem, Rashid, Toshiaki, Fukui, Haruyuki, Atomi, and Tadayuki, Imanaka. Genetic evidence identifying the true gluconeogenic fructose-1,6-bisphosphatase in Thermococcus kodakaraensis and other hyperthermophiles. J. Bacteriol., 186:5799–5807, 2004.
[702] Brandon, Schmandt, Kenneth, Dueker, Eugene, Humphreys, and Steven, Hansen. Hot mantle upwelling across the 660 beneath Yellowstone. Earth Planet. Sci. Lett., 331:224–236, 2012.
[703] Johan A., Schmidt, Matthew S., Johnson, and Reinhard, Schinke. 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.
[704] Philippe, Schmitt-Kopplin, Zelimir, Gabelica, Régis D., Gougeon, Agnes, Fekete, Basem, Kanawati, Mourad, Harir, Istvan, Gebefuegi, Gerhard, Eckel, and Norbert, Hertkorn. High molecular diversity of extraterrestrial organic matter in Murchisonmeteorite revealed 40 years after its fall. Proc. Natl. Acad. Sci. USA, 107:2763–2768, 2010.
[705] Thomas D., Schneider. Theory of molecular machines I: channel capacity of molecular machines. J. Theor. Biol., 148:83–123, 1991.
[706] Thomas D., Schneider. Theory of molecular machines II: energy dissipation from molecular machines. J. Theor. Biol., 148:125–137, 1991.
[707] Barbara, Schoepp-Cothenet, Clément, Lieutaud, Frauke, Baymann, André, Verméglio, Thorsten, Friedrich, David M., Kramer, and Wolfgang, Nitschke. Menaquinone as a pool quinone in a purple bacterium. Proc. Natl. Acad. Sci. USA, 106:8549–8554, 2005.
[708] J. William, Schopf. Microfossils of the early Archaean apex chert: new evidence of the antiquity of life. Science, 260:640–646, 1993.
[709] Laurier L., Schramm. Emulsions, Foams, and Suspensions: Fundamentals and Applications. Wiley, New York, 2005.
[710] Matthew O., Schrenk, John R., Kelley, Deborah S., anf Delaney, and John A., Baross. Incidence and diversity of microorganisms within the walls of an active deep-sea sulfide chimney. Appl. Environ. Microbiol., 69:3580–3592, 2003.
[711] E., Schrödinger. What is Life? The Physical Aspect of the Living Cell. Cambridge University Press, New York, 1992.
[712] Mitch, Schulte, David, Blake, Tori, Hoehler, and Thomas, McCollom. Serpentinization and its implications for life on the early Earth and Mars. Astrobiology, 6:364–376, 2006.
[713] Gerrit J., Schut and Michael W. W., Adams. The iron-hydrogenase of Thermotoga maritima utilizes ferredoxin and NADH synergistically: a new perspective on anaerobic hydrogen production. J. Bacteriol., 191:4451–4457, 2009.
[714] Michael, Schutz, Barbara, Schoepp-Cothenet, Elisabeth, Lojou, Mireille, Woodstra, Doris, Lexa, Pascale, Tron, Alain, Dolla, Marie-Claire, Durand, Karl Otto, Stetter, and Frauke, Baymann. The naphthoquinol oxidizing cytochrome bc1 complex of the hyperthermophilic knallgasbacterium Aquifex aeolicus: properties and phylogenetic relationships. Biochemistry, 42:10800–10808, 2003.
[715] Alan W., Schwartz. Phosphorus in prebiotic chemistry. Philos. Trans. R. Soc. London, Ser. B, 361:1743–1749, 2006.
[716] Gideon E., Schwarz. Estimating the dimension of a model. Ann. Stat., 6:461–464, 1978.
[717] Esther M., Schwarzenbach, Gretchen L., Früh-Green, Stefano M., Bernasconi, Jeffrey C., Alt, and Alessio, Plas. Serpentinization and carbon sequestration: a study of two ancient peridotite-hosted hydrothermal systems. Chem. Geol., 351:115–133, 2013.
[718] Anja, Schwögler and Thomas, Carell. Toward catalytically active oligonucleotides: synthesis of a flavin nucleotide and its incorporation into DNA. Org. Lett., 2:1415–1418, 2000.
[719] John R., Searle. The Mystery of Consciousness. New York Review of Books, New York, 1997.
[720] Henning, Seedorf, W. Florian, Fricke, Birgit, Veith, HolgerBr, üggemann, Heiko, Liesegang, Axel, Strittmatter, Marcus, Miethke, Wolfgang, Buckel, Julia, Hinderberger, Fuli, Li, Christoph, Hagemeier, Rudolf K., Thauer, and Gerhard, Gottschalk. The genome of Clostridium kluyveri, a strict anaerobe with unique metabolic features. Proc. Natl. Acad. Sci. USA, 105:2128–2133, 2008.
[721] Daniel, Segré, Dafna, Ben-Ali, and Doron, Lancet. Compositional genomes: prebiotic information transfer in mutually catalytic noncovalent assemblies. Proc. Natl. Acad. Sci. USA, 97:4112–4117, 2000.
[722] Daniel, Segré, Doron, Lancet, Ora, Kedem, and Yitzhak, Pilpel. Graded autocatalysis replication domain (GARD): kinetic analysis of self-replication in mutually catalytic sets. Orig. Life Evol. Biosphere, 28:501–514, 1998.
[723] Daniel, Segré, Barak, Shenhav, Ron, Kafri, and Doron, Lancet. The molecular roots of compositional inheritance. J. Theor. Biol., 213:481–491, 2001.
[724] Teddy, Seidenfeld. Why I am not an objective Bayesian: some reflections prompted by Rosenkrantz. Theory Decision, 11:413–440, 1979.
[725] Teddy, Seidenfeld. Entropy and uncertainty. In I. B., MacNeill and G. J., Umphrey, editors, Foundations of Statistical Inference, pages 259–287. Reidel, Boston, MA, 1987.
[726] Javier, Seravalli, Yuming, Xiao, Weiwei, Gu, Stephen P., Cramer, William E., Antholine, Vladimir, Krymov, Gary J., Gerfen, and Stephen W., Ragsdale. Evidence that NiNi acetyl-CoA synthase is active and that the CuNi enzyme is not. Biochemistry, 43(13):3944–3955, 2004.
[727] W. E. Jr., Seyfried and Kang, Ding. 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 Susan E., Humphris, Robert A., Zierenberg, Lauren S., Mullineaux, and Richard E., Thomson, editors, Seafloor Hydrothermal Systems: Physical, Chemical, Biological, and Geological Interactions, pages 248–272. Geophysical Monograph. American Geophysical Union, Washington, DC, 1995.
[728] W. E. Jr., Seyfried, Kang, Ding, and M. E., Berndt. Phase equilibria constraints on the chemistry of hot spring fluids at mid-ocean ridges. Geochim. Cosmochim. Acta, 55:3559–3580, 1991.
[729] Cosma Rohilla, Shalizi. Dynamics of Bayesian updating with dependent data and misspecified models. Electron. J. Stat., 3:1039–1074, 2009.
[730] Timothy M., Shank, Daniel J., Fornari, Karen L., Von Damm, Marvin D., Lilley, Rachel M., Haymon, and Richard A., Lutz. 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.
[731] Claude E., Shannon. Communication in the presence of noise. Proc. IEEE, 86:447–457, 1949.
[732] Claude Elwood, Shannon and Warren, Weaver. The Mathematical Theory of Communication. University of Illinois Press, Urbana, IL, 1949.
[733] Robert, Shapiro. Small molecule interactions were central to the origin of life. Q. Rev. Biol., 81:105–125, 2006.
[734] Anurag, Sharma, George D., Cody, and Russell J., Hemley. In situ diamond-anvil cell observations of methanogenesis at high pressures and temperatures. Energy Fuels, 23:5572–5579, 2009.
[735] Jia, Sheng, Li, Li, Aaron E., Engelhart, Jianhua, Gan, Jiawei, Wang, and Jack W., Szostak. Structural insights into the effects of 2′–5′ linkages on the RNA duplex. Proc. Natl. Acad. Sci. USA, 111:3050–3055, 2014.
[736] Peter P., Sheridan, Katherine H., Freeman, and Jean E., Brenchley. Estimated minimal divergence times of the major bacterial and archaeal phyla. Geomicrobiol. J., 20:1–14, 2003.
[737] B. Sherwood, Lollar, G., Lacrampe-Couloume, G. F., Slater, J., Ward, D. P., Moser, T. M., Gihring, L.-H., Lin, and T. C., Onstott. Unravelling abiogenic and biogenic sources of methane in the Earth's deep subsurface. Chem. Geol., 226:328–339, 2006.
[738] B. Sherwood, Lollar, T. D., Westgate, J. A., Ward, G. F., Slater, and G., Lacrampe-Couloume. Abiogenic formation of gaseous alkanes in the Earth's crust as a minor source of global hydrocarbon reservoirs. Nature, 416:522–524, 2002.
[739] Takazo, Shibuya, Tsuyoshi, Komiya, Kentaro, Nakamura, Ken, Takai, and Shigenori, Maruyama. Highly, alkaline, high-temperature hydrothermal fluids in the early Archean ocean. Precambrian Res., 182:230–238, 2010.
[740] Takazo, Shibuya, Miyuki, Tahata, Kouki, Kitajima, Yuichiro, Ueno, Tsuyoshi, Komiya, Shinji, Yamamoto, Motoko, Igisu, Masaru, Terabayashi, Yusuke, Sawaki, Ken, Takai, Naohiro, Yoshida, and Shigenori, Maruyama. 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.
[741] Takazo, Shibuya, Miyuki, Tahata, Yuichiro, Ueno, Tsuyoshi, Komiya, Ken, Takai, Naohiro, Yoshida, Shigenori, Maruyama, and Micheal J., Russell. Decrease of seawater CO2 concentration in the Late Archean: an implication from 2.6 Ga seafloor hydrothermal alteration. Precambrian Res., 236:59–64, 2013.
[742] Takazo, Shibuya, Motoko, Yoshizaki, Yuka, Masaki, Katsuhiko, Suzuki, Ken, Takai, and Michael J., Russell. 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.
[743] Graham, Shields-Zhou and Lawrence, Och. The case for a neoproterozoic oxygenation event: chemical evidence and biological consequences. GSA Today, 21:4–11, 2011.
[744] Cristal, Shih, Anna Katrine, Museth, Malin, Abrahamsson, Ana Maria, Blanco-Rodriguez, Angel J., Di Bilio, Jawahar, Sudhamsu, Brian R., Crane, Kate L., Ronayne, Mike Jr., Towrie, Antonn, Vlček, John H., Richards, Jay R., Winkler, and Harry B., Gray. Tryptophan-accelerated electron flow through proteins. Science, 320:1760–1762, 2008.
[745] Everett L., Shock and Harold C., Helgeson. 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.
[746] Everett L., Shock and Mitchell D., Schulte. Organic synthesis during fluid mixing in hydrothermal systems. J. Geophys. Res., 103:28513–28527, 1998.
[747] Everett L., Shock, Harold C., Helgeson, and Dimitry A., Sverjensky. 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.
[748] Everett L., Shock, Melanie, Holland, D Arcy, Meyer-Dombard, Jan P., Amend, G. R., Osburn, and Tobias P., Fischer. Quantifying inorganic sources of geochemical energy in hydrothermal ecosystems, Yellowstone National Park, USA. Geochim. Cosmochim. Acta, 74:4005–4043, 2010.
[749] Everett L., Shock, Thomas, McCollom, and Mitchell D., Schulte. The emergence of metabolism from within hydrothermal systems. In Juergen, Wiegel and Michael W. W., Adams, editors, Thermophiles: The Keys to Molecular Evolution and the Origin of Life, pages 59–76. Taylor and Francis, London, 1998.
[750] J. William, Shopf, editor. Life's Origin: the Beginnings of Biological Evolution. University of California Press, Berkeley, CA, 2002.
[751] Brian J., Shuter, J. E., Thomas, William D., Taylor, and A. M., Zimmerman. Phenotypic correlates of genomic DNA content in unicellular eukaryotes. Am. Nat., 122:26–44, 1983.
[752] V., Shuvalov. Atmospheric erosion induced by oblique impacts. Meteoritics Planet. Sci., 44:1095–1105, 2009.
[753] Bettina, Siebers, Henner, Brinkmann, Christine, Dörr, Britta, Tjaden, Hauke, Lilie, John van der, Oost, and Corné H., Verhees. Archaeal fructose-1,6-bisphosphate aldolases constitute a new family of archaeal type class I aldolase. J. Biol. Chem., 276:28710–28718, 2001.
[754] Herbert A., Simon. The architecture of complexity. Proc. Am. Philos. Soc., 106:467–482, 1962.
[755] Herbert A., Simon. The organization of complex systems. In Howard H., Pattee, editor, Hierarchy Theory: The Challenge of Complex Systems, pages 3–27. George Braziller, New York, 1973.
[756] Herbert A., Simon. The Sciences of the Artificial. MIT Press, Cambridge, MA, third edition, 1996.
[757] Kai, Simons and Julio L., Sampaio. Membrane organization and lipid rafts. Cold Spring Harb. Perspect. Biol., 3:a004697, 2011.
[758] Y., Sinai. On the notion of entropy of a dynamical system. Dokl. Akad. Nauk SSSR, 124:768–771, 1959.
[759] N. A., Sinitsyn and Ilya, Nemenman. Universal geometric theory of mesoscopic stochastic pumps and reversible ratchets. Phys. Rev. Lett., 99:220408, 2007.
[760] N. H., Sleep, A., Meibom, Th., Fridriksson, R. G., Coleman, and D. K., Bird. H2-rich fluids from serpentinization: geochemical and biotic implications. Proc. Natl. Acad. Sci. USA, 101:12818–12823, 2004.
[761] Alexander, Smirnov, Douglas, Hausner, Richard, Laffers, Daniel R., Strongin, and Martin A. A., Schoonen. 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.
[762] Eric, Smith. Self-organization from structural refrigeration.Phys. Rev. E, 68:046114, 2003.
[763] Eric, Smith. Thermodynamic dual structure of linearly dissipative driven systems. Phys. Rev. E, 72:36130, 2005.
[764] Eric, Smith. Thermodynamics of natural selection I: energy and entropy flows through non-equilibrium ensembles. J. Theor. Biol., 252:185–197, 2008.
[765] Eric, Smith. Thermodynamics of natural selection II: chemical Carnot cycles. J. Theor. Biol., 252:198–212, 2008.
[766] Eric, Smith. Thermodynamics of natural selection III: Landauer's principle in chemistry and computation. J. Theor. Biol., 252:213–220, 2008.
[767] Eric, Smith. Large-deviation principles, stochastic effective actions, path entropies, and the structure and meaning of thermodynamic descriptions. Rep. Prog. Phys., 74:046601, 2011.
[768] Eric, Smith and Supriya, Krishnamurthy. Symmetry and Collective Fluctuations in Evolutionary Games. IOP Press, Bristol, 2015.
[769] Eric, Smith and Harold J., Morowitz. Universality in intermediary metabolism. Proc. Natl. Acad. Sci. USA, 101:13168–13173, 2004.
[770] Eric, Smith, Supriya, Krishnamurthy, Walter, Fontana, and David C., Krakauer. Nonequilibrium phase transitions in biomolecular signal transduction. Phys. Rev. E, 84:051917, 2011.
[771] Lee, Smolin. The Life of the Cosmos. Phoenix, London, 1997.
[772] Theodore P., Snow and Benjamin J., McCall. Diffuse atomic and molecular clouds. Annu. Rev. Astron. Astrophys., 44:367–414, 2006.
[773] Filipa L., Sousa and William F., Martin. Biochemical fossils of the ancient transition from geoenergetics to bioenergetics in prokaryotic one carbon compound metabolism. Biochem. Biophys. Acta, 1837:964–981, 2014.
[774] Roger W., Sperry. Mind, brain and humanist values. In John R., Platt, editor, New Views on the Nature of Man, pages 71–92. University of Chicago Press, Chicago, IL, 1965.
[775] Alexander S., Spirin. Energetics and dynamics of the protein synthesizing machinery. In Horst, Kleinkauf, Hans von, Dören, and Lothar, Jaenicke, editors, The Roots of Modern Biochemistry: Fritz Lippmann's Squiggle and its Consequences, pages 511–533. Walter de Gruyter, Berlin, 1988.
[776] Vijayasarathy, Srinivasan and Harold J., Morowitz. Analysis of the intermediary metabolism of a reductive chemoautotroph. Biol. Bull., 217:222–232, 2009.
[777] Vijayasarathy, Srinivasan and Harold J., Morowitz. The canonical network of autotrophic intermediary metabolism: minimal metabolome of a reductive chemoautotroph. Biol. Bull., 216:126–130, 2009.
[778] P. F., Stadler, S. J., Prohaska, C. V., Forst, and D. C., Krakauer. Defining genes: a computational framework. Theory Biosci., 128:165–170, 2009.
[779] Robert W., Sterner and James J., Elser. Ecological Stoichiometry: The Biology of Elements from Molecules to the Biosphere. Princeton University Press, Princeton, NJ, 2002.
[780] Patrick, Stover and Verne, Schirch. The metabolic role of leucovorin. Trends Biochem. Sci., 18(3):102–106, 1993.
[781] William E., Strawderman. Sufficient statistics: theoretical background. Wiley Stats- Ref, 2014.
[782] Bernard L., Strehler and Albert S., Mildvan. General theory of mortality and aging. Science, 132:14–21, 1960.
[783] Lubert, Stryer. Biochemistry. Freeman, San Francisco, CA, second edition, 1981.
[784] David P., Summers and Sherwood, Chang. Prebiotic ammonia from reduction of nitrite by iron(II) on the early Earth. Nature, 365:630–633, 1993.
[785] Melanie, Summit and John A., Baross. Thermophilic subseafloor microorganisms from the 1996 North Gorda Ridge eruption. Deep-Sea Res. II, 45:2751–2766, 1998.
[786] Melanie, Summit and John A., Baross. A novel microbial habitat in the mid-ocean ridge subsurface. Proc. Natl. Acad. Sci. USA, 98:2158–1263, 2001.
[787] Roger E., Summons, Linda L., Jahnke, Janet M., Hope, and Graham A., Logan. 2-methylhopanoids as biomarkers for cyanobacterial oxygenic photosynthesis. Nature, 400:554–557, 1999.
[788] Shunryu, Suzuki. Zen Mind, Beginner's Mind. Weatherhill, New York, 1973.
[789] Vitali, Svetlitchnyi, Holger, Dobbek, Wolfram, Meyer-Klaucke, Thomas, Meins, Bärbel, Thiele, Piero, Römer, Robert, Huber, and Ortwin, Meyer. 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.
[790] Eörs, Szathmáry and John Maynard, Smith. The Major Transitions in Evolution. Oxford University Press, London, 1995.
[791] Jack W., Szostak. The eightfold path to non-enzymatic RNA replication. J. Syst. Chem., 3:2, 2012.
[792] F. A., Tabita. Research on carbon dioxide fixation in photosynthetic microorganisms (1971–present). Photosynth. Res., 80:315–332, 2004.
[793] F. A., Tabita, T. E., Hanson, H., Li, S., Satagopan, J., Singh, and S., Chan. Function, structure, and evolution of the RubisCO-like proteins and their RubisCO homologs. Microbiol. Mol. Biol. Rev., 71:576–599, 2007.
[794] Ken, Takai, Tetsushi, Komatsu, Fumio, Inagaki, and Koki, Horikoshi. Distribution of archaea in a black smoker chimney structure. Appl. Env. Microbiol., 67:3618, 2001.
[795] Ken, Takai, Duane P., Moser, Tullis C., Onstott, Nico, Spoelstra, Susan M., Pfiffner, Alice, Dohnalkova, and Jim K., Fredrickson. 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.
[796] Dan S., Tawfik. Messy biology and the origins of evolutionary innovation. Nature Chem. Biol., 6:692–696, 2010.
[797] F. J. R., Taylor and D., Coates. The code within the codons. Biosystems, 22:177–187, 1989.
[798] Maureen E., Taylor and Kurt, Drickamer. Introduction to Glycobiology. Oxford University Press, London, third edition, 2011.
[799] Robin, Teufel, Johannes W., Jung, Daniel, Kockelkorn, Birgit E., Alber, and Georg, Fuchs. 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.
[800] Rudolf K., Thauer, Kurt, Jungermann, and Karl, Decker. Energy conservation in chemotrophic anaerobic bacteria. Bacteriol. Rev., 41:100–180, 1977.
[801] Rudolf K., Thauer, Anne-Kristin, Kaster, Henning, Seedorf, Wolfgang, Buckel, and Reiner, Hedderich. Methanogenic archaea: ecologically relevant differences in energy conservation. Nature Rev. Microbiol., 6:579–591, 2008.
[802] D'Arcy Wentworth, Thompson. On Growth and Form. Dover, New York, complete revised edition, 1992.
[803] G., Thompson, M. K., Tivey, and S. E., Humphris. 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.
[804] Feng, Tian, Owen B., Toon, Alexander A., Pavlov, and H. De, Sterck. Transonic hydrodynamic escape of hydrogen from extrasolar planetary atmospheres. Astrophys. J., 621:1049–1060, 2005.
[805] Jing, Tian, Ruslana, Bryk, Manabu, Itoh, Makoto, Suematsu, and Carl, Nathan. Variant tricarboxylic acid cycle in Mycobacterium tuberculosis: identification of a-ketoglutarate decarboxylase. Proc. Natl. Acad. Sci. USA, 102:10670–10675, 2005.
[806] Michael, Tinkham. Introduction to Superconductivity. Dover, New York, second edition, 2004.
[807] Margaret, Tivey. How to build a black smoker chimney. Oceanus, 41, 1998.
[808] Margaret Kingston, Tivey. Generation of seafloor hydrothermal vent fluid and associated mineral deposits. Oceanography, 20:50–65, 2007.
[809] Margaret Kingston, Tivey, Debra S., Stakes, Terri L., Cook, Mark D., Hannington, and Sven, Petersen. 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.
[810] Count Lyof N., Tolstoy. Anna Karénina. Thomas Y. Crowell, New York, 1914. Translated by Nathan Haskell Dole.
[811] Hugo, Touchette. The large deviation approach to statistical mechanics. phys. rep., 478:1–69, 2009.
[812] Edward N., Trifonov. The triplet code from first principles. J. Biomol. Struct. Dyn., 22:1–11, 2004.
[813] Rebecca M., Turk, Nataliya V., Chumachenko, and Michael, Yarus. Multiple traslational products from a five-nucleotide ribozyme. Proc. Natl. Acad. Sci. USA, 107:4585–4589, 2010.
[814] Yuichiro, Ueno, Matthew S., Johnson, Sebastian O., Danielache, Carsten, Eskebjerg, Antra, Pandey, and Naohiro, Yoshida. Geological sulfur isotopes indicate elevated OCS in the Archean atmosphere, solving faint young sun paradox. Proc. Natl. Acad. Sci. USA, 106:14784–14789, 2009.
[815] Yuichiro, Ueno, Shuhei, Ono, Douglas, Rumble, and Shigenori, Maruyama. 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.
[816] Jos, Uffink. Can the maximum entropy principle be explained as a consistency requirement? Studies Hist. Philos. Mod. Phys., 26B:223–261, 1995.
[817] Jos, Uffink. The constraint rule of the maximum entropy principle. Studies Hist. Philos. Mod. Phys., 27:47–79, 1996.
[818] H. Edwin, Umbarger and Barbara, Brown. Threonine deamination in Escherichia coli II: evidence for two L-threonine deaminases. J. Bacteriol., 73(1):105–112, 1957.
[819] The UniProt Consortium. Ongoing and future developments at the universal protein resource. Nucleic Acids Res., 39(suppl 1):D214–D219, 2011.
[820] D. A., Usher and A. H., McHale. Hydrolytic stability of helical RNA: a selective advantage for the natural 3′,5′- bond. Proc. Natl. Acad. Sci. USA, 73:1149–1153, 1976.
[821] M. F., Utter and H. G., Wood. Mechanisms of fixation of carbon dioxide by heterotrophs and autotrophs. Adv. Enzymol. Relat. Areas Mol. Biol., 12:41–151, 1951.
[822] Kaimars, Vafiya. Duality, Bosonic Particle Systems and Some Exactly Solvable Models of Non-Equilibrium. PhD Thesis, Universiteit Leiden, 2011.
[823] Nilesh, Vaidya, Michael L., Manapar, Irene A., Chen, Ramon, Xulvi-Brunet, Eric J., Hayden, and Niles, Lehman. Spontaneous network formation among coperative RNA replicators. Nature, 491:72–77, 2012.
[824] Patrick van, Beelen, Joannes F. A., Labro, Jan T., Keltjens, Wim J., Geertz, Godfried D., Vogels, Wim H., Laarhoven, Wim, Guijt, and A. G., Haasnoot. Derivatives of methanopterin, a coenzyme involved in methanogenesis. Eur. J. Biochem., 139:359–365, 1984.
[825] Cindy Lee, Van Dover and Brian, Fry. Microorganisms as food resources at deep-sea hydrothermal vents. Limnol. Oceanogr., 39:51–57, 1994.
[826] David A., Vanko and Debra S., Stakes. Fluids in oceanic layer 3: evidence from veined rocks, hole 735B, Southwest Indian Ridge. In Richard P., Von Herzen, Jeff, Fox, Amanda, Palmer-Julson, and Paul T., Robinson, editors, Proceedings of the Oceanic Drilling Program, Scientific Results, Vol. 118, pages 181–215. Texas A & M University, Houston, TX, 1991.
[827] Gabriele, Varani and William H., McClain. 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.
[828] Vera, Vasas, Eörs, Szathmary, and Mauros, Santos. 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.
[829] Krassimir, Vassilev, Marina, Dimitrova, and Sevdalina, Turmanova. Catalytic activity of histidine-metal complexes in oxidation reactions. Synth. React. Inorg. Met.-org. Nano-met. Chem., 43:243–249, 2013.
[830] J. Craig, Venter, Karin, Remington, John F., Heidelberg, Aaron L., Halpern, Doug, Rusch, Jonathan A., Eisen, Dongying, Wu, Ian, Paulsen, Karen E., Nelson, William, Nelson, Derrick E., Fouts, Samuel, Levy, Anthony H., Knap, Michael W., Lomas, Ken, Nealson, Owen, White, Jeremy, Peterson, Jeff, Hoffman, Rachel, Parsons, Holly, Baden-Tillson, Cynthia, Pfannkoch, Yu-Hui, Rogers, and Hamilton O., Smith. Environmental genome shotgun sequencing of the Sargasso Sea. Science, 304:66–74, 2004.
[831] Sergio, Verdú. Fifty years of Shannon theory. IEEE Trans. Inf. Theory, 44:2057–2078, 1998.
[832] Vladimir I., Vernadsky. Geochemistry and the Biosphere. Synergetic Press, Santa Fe, NM, 2007.
[833] Kalin, Vetsigian, Carl, Woese, and Nigel, Goldenfeld. Collective evolution and the genetic code. Proc. Natl. Acad. Sci. USA, 103:10696–10701, 2006.
[834] Ann M., Vickery and H., Jay Melosh. Atmospheric erosion and impactor retention in large impacts with application to mass extinctions. In V. L., Sharpton and P. D., Ward, editors, Global Catastrophes in Earth History, pages 289–300. Geological Society of America, Boulder, CO, 1990.
[835] Alexander V., Vlassov, Sergei A., Kazakov, Brian H., Johnston, and Laura F., Landweber. The RNA world on ice: a new scenario for the emergence of RNA information. J. Mol. Evol., 61:264–273, 2005.
[836] Alexey N., Volkov, Robert E., Johnson, Orenthal J., Tucker, and Justin T., Erwin. Thermally-driven atmospheric escape: transition from hydrodynamic to Jeans escape. Astrophys. J. Lett., 729:L24, 2011.
[837] K. L., von Damm. Seafloor hydrothermal activity: black smoker chemistry and chimneys. Annu. Rev. Earth Planet. Sci., 18:173–204, 1990.
[838] J., von Neumann. Probabilistic logics and the synthesis of reliable organisms from unreliable components. Automata Stud., 34:43–98, 1956.
[839] Diter von, Wettstein, Simon, Gough, and C. Gaminis, Kannangara. Chlorophyll biosynthesis. Plant Cell Online, 7(7):1039–1057, 1995.
[840] Julia A., Vorholt, Ludmila, Chistoserdova, Sergei M., Stolyar, Rudolf K., Thauer, and Mary E., Lidstrom. Distribution of tetrahydromethanopterin-dependent enzymes in methylotrophic bacteria and phylogeny of methenyl tetrahydromethanopterin cyclohydrolases. J. Bacteriol., 181:5750–5757, 1999.
[841] Julia M., Vraspir and Alison, Butler. Chemistry of marine ligands and siderophores. Annu. Rev. Marine Sci., 1:43–63, 2009.
[842] L. J., Waber and H. G., Wood. Mechanism of acetate synthesis from CO2 by Clostridium acidi-urici. J. Bacteriol., 140(2):468–478, 1979.
[843] Günter, Wächtershäuser. Before enzymes and templates: a theory of surface metabolism. Microbiol. Rev., 52:452–484, 1988.
[844] Günter, Wächtershäuser. Pyrite formation, the first energy source for life: a hypothesis. Syst. Appl. Microbiol., 10:207–210, 1988.
[845] Günter, Wächtershäuser. Evolution of the first metabolic cycles. Proc. Natl. Acad. Sci. USA, 87:200–204, 1990.
[846] C. H., Waddington. Canalization of development and the inheritance of acquired characters. Nature, 150:563–565, 1942.
[847] H., Wakamatsu, Y., Yamada, T., Saito, I., Kumashiro, and T., Takenishi. Synthesis of adenine by oligomerization of hydrogen cyanide. J. Org. Chem., 31:2035–2036, 1966.
[848] George, Wald. Life in the second and third periods: or why phosphorus and sulfur for high-energy bonds. In M., Kasha and B., Pullman, editors, Horizons in Biochemistry, pages 127–142. Academic Press, New York, 1962.
[849] P., Walde, R., Wick, M., Fresta, A., Mangone, and P. L., Luisi. Autopoietic selfreproduction of fatty acid vesicles. J. Am. Chem. Soc., 116:11649–11654, 1994.
[850] Sara Imari, Walker, Martha A., Grover, and Nicholas V., Hud. Universal sequence replication, reversible polymerization and early functional biopolymers: a model for the initiation of prebiotic sequence evolution. PLoS ONE, 7:e34166, 2012.
[851] Shuning, Wang, Haiyan, Huang, Johanna, Moll, and Rudolf K., Thauer. 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.
[852] Shinya, Watanabe, Michael, Zimmermann, Michael B., Goodwin, Uwe, Sauer, Clifton E., Barry 3rd, and Helena I., Boshoff. Fumarate reductase activity maintains an energized membrane in anaerobic Mycobacterium tuberculosis. PLoS Pathogens, 7:e1002287, 2011.
[853] J. D., Watson and F. H. C., Crick. A structure for deoxyribose nucleic acid. Nature, 171:737–738, 1953.
[854] James D., Watson, Tania A., Baker, Stephen P., Bell, Alexander, Gann, Michael, Levine, and Richard, Losick. Molecular Biology of the Gene. Pearson, New York, seventh edition, 2014.
[855] Duncan J., Watts. Everything is Obvious: How Common Sense Fails Us. Crown Business, New York, 2012.
[856] Arthur L., Weber. Energy from redox disproportionation of sugar carbon drives biotic and abiotic synthesis. J. Mol. Evol., 44:354–360, 1997.
[857] Arthur L., Weber. Sugars as the optimal biosynthetic carbon substrate of aqueous life throughout the universe. Orig. Life Evol. Biosphere, 30:33–43, 2000.
[858] Arthur L., Weber. 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.
[859] Arthur L., Weber. 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.
[860] Arthur L., Weber and Sandra, Pizzarello. The peptide-catalyzed stereospecific synthesis of tetroses: a possible model for prebiotic molecular evolution. Proc. Natl. Acad. Sci. USA, 103:12713–12717, 2006.
[861] Steven, Weinberg. Phenomenological Lagrangians. Physica A, 96:327–340, 1979.
[862] Steven, Weinberg. The First Three Minutes.Basic Books, New York, second edition, 1993.
[863] Steven, Weinberg. The Quantum Theory of Fields, Vol. I: Foundations.Cambridge University Press, Cambridge, 1995.
[864] P. P., Weiner, editor. Leibniz Selections.Charles Scribner, New York, 1951.
[865] Joshua S., Weinger, K. Mark, Parnell, Silke, Dorner, Rachel, Green, and Scott A., Strobel. Substrate-assisted catalysis of peptide bond formation by the ribosome. Nature Struct. Mol. Biol., 11:1101–1106, 2004.
[866] Pierre, Weiss. L'hypothèse du champ moléculaire et la propriété ferromagnétique. J. Phys. Theor. Appl., 6:661–690, 1907.
[867] Geoffrey B., West and James H., Brown. 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.
[868] Geoffrey B., West, James H., Brown, and Brian J., Enquist. A general model for ontogenetic growth. Nature, 413:628–631, 2001.
[869] Geoffrey B., West, William H., Woodruff, and James H., Brown. Allometric scaling of metabolic rate from molecules and mitochondria to cells and mammals. Proc. Natl. Acad. Sci. USA, 99:2473–2478, 2002.
[870] Frank H., Westheimer. Why nature chose phosphates. Science, 235:1173–1178, 1987.
[871] Laura Reiser, Wetzel and Everett L., Shock. Distinguishing ultramafic-from basalthosted submarine hydrothermal systems by comparing vent fluid compositions. J. Geophys. Res., 105:8319–8340, 2000.
[872] Harold B., White. Coenzymes as fossils of an earlier metabolic state. J. Mol. Evol.,