Towards an evolutionary theory of the origin of life based on kinetics and thermodynamics

Open Biology

Volumn 3, Issue NOV, 2013, Pages

  Pascal, Robert ^a   Pross, Addy ^b   Sutherland, John D ^c  

^a UNIVERSITÉ DE MONTPELLIER   (France)

^b BEN GURION UNIVERSITY OF THE NEGEV   (Israel)

^c MRC LABORATORY OF MOLECULAR BIOLOGY   (United Kingdom)

Author keywords

Abiogenesis; Dynamic kinetic stability; Irreversibility; Metabolism; Origin of life; Systems chemistry

Indexed keywords

ABIOGENESIS; BIOGENESIS; CHEMICAL STRUCTURE; DYNAMIC KINETIC STABILITY; EVOLUTION; IRREVERSIBILITY; KINETICS; METABOLISM; MOLECULAR EVOLUTION; REVIEW; SYSTEMS CHEMISTRY; THERMODYNAMICS;

ABIOGENESIS; DYNAMIC KINETIC STABILITY; IRREVERSIBILITY; METABOLISM; ORIGIN OF LIFE; SYSTEMS CHEMISTRY;

BIOGENESIS; BIOLOGICAL EVOLUTION; EVOLUTION, MOLECULAR; KINETICS; MODELS, MOLECULAR; THERMODYNAMICS;

EID: 84894432265     PISSN: None     EISSN: 20462441     Source Type: Journal    
DOI: 10.1098/rsob.130156     Document Type: Article

References (68)

1. Darwin C. 1859 On the origin of species, p. 484. Cambridge, MA: Harvard University Press.
2. Woese CR. 2002 On the evolution of cells. Proc. Natl Acad. Sci. USA 99, 8742-8747. (doi:10.1073/pnas. 132266999) (Pubitemid 34693630)
3. Pross A, Pascal R. 2013 The origin of life: what we know, what we can know, what we will never know. Open Biol. 3, 120190. (doi:10. 1098/rsob.120190)
4. Kindermann M, Stahl I, Reimold M, Pankau WM, von Kiedrowski G. 2005 Systems chemistry: kinetic and computational analysis of a nearly exponential organic replicator. Angew. Chem. Int. Ed. 44, 6750-6755. (doi:10.1002/anie. 200501527) (Pubitemid 41532228)
5. Ludlow RF, Otto S. 2008 Systems chemistry. Chem. Soc. Rev. 37, 101-108. (doi:10.1039/b611921m)
6. von Kiedrowski G, Otto S, Herdewijn P. 2010 Welcome home, systems chemists! J. Syst. Chem. 1, 1. (doi:10.1186/1759-2208-1-1)
7. Schrodinger E. 1944 What is life. Cambridge, UK: Cambridge University Press.
8. Watson JD, Crick FHC. 1953 Molecular structure of nucleic acids: a molecular structure for deoxyribose nucleic acid. Nature 171, 737-738. (doi:10.1038/ 171737a0)
9. Monod J. 1970 Le hasard et la necessite: Essai sur la philosophie naturelle de la biologie moderne. Paris, France: Editions du Seuil.
10. Morowitz HJ. 1992 Beginnings of cellular life: metabolism recapitulates biogenesis. New Haven, CT: Yale University Press.
11. Bruylants G, Bartik K, Reisse J. 2011 Prebiotic chemistry: a fuzzy field. C. R. Chim. 14, 388-391. (doi:10.1016/j.crci.2010.04.002)
12. Bruylants G, Bartik K, Reisse J. 2010 Is it useful to have a clear-cut definition of life? On the use of fuzzy logic in prebiotic chemistry. Orig. Life Evol. Biosph. 40, 137-143. (doi:10.1007/s11084-010- 9192-3)
13. Ruiz-Mirazo K, Pereto J, Moreno A. 2004 A universal definition of life: autonomy and open-ended evolution. Orig. Life Evol. Biosph. 34, 323-346. (doi:10.1023/B:ORIG.0000016440.53346.dc) (Pubitemid 38362076)
14. Popa R. 2004 Between necessity and probability: searching for the definition and origin of life. Heidelberg, Germany: Springer.
15. Tirard S, Morange M, Lazcano A. 2010 The definition of life: a brief history of an elusive scientific endeavor. Astrobiology 10, 1003-1009. (doi:10.1089/ast.2010.0535)
16. Pross A, Khodorkovsky V. 2004 Extending the concept of kinetic stability: toward a paradigm for life. J. Phys. Org. Chem. 17, 312-316. (doi:10.1002/ poc.729)
17. Pross A. 2005 Stability in chemistry and biology: life as a kinetic state of matter. Pure Appl. Chem. 77, 1905-1921. (doi:10.1351/pac200577111905) (Pubitemid 41746293)
18. Pross A. 2008 How can a chemical system act purposefully? Bridging between life and non-life. J. Phys. Org. Chem. 21, 724-730. (doi:10.1002/ poc.1382)
19. Pross A. 2009 Seeking the chemical roots of Darwinism: bridging between chemistry and biology. Chem. Eur. J. 15, 8374-8381. (doi:10.1002/chem.200900805)
20. Pross A. 2011 Toward a general theory of evolution: extending Darwinian theory to inanimate matter. J. Syst. Chem. 2, 1. (doi:10.1186/1759-2208-2-1)
21. Pross A. 2012 What is life? How chemistry becomes biology. Oxford, UK: Oxford University Press.
22. Wagner N, Pross A. 2011 The nature of stability in replicating systems. Entropy 13, 518-527. (doi:10.3390/e13020518)
23. Eigen M, Schuster P. 1977 The hypercycle, a principle of natural self-organization part A emergence of the hypercycle. Naturwissenschaften 64, 541-565. (doi:10.1007/BF00450633) (Pubitemid 8215838)
24. von Kiedrowski G. 1986 A self-replicating hexadeoxynucleotide. Angew. Chem. Int. Ed. 25, 932-935. (doi:10.1002/anie.198609322)
25. Szathmary E, Gladkih I. 1989 Sub-exponential growth and coexistence of non-enzymatically replicating templates. J. Theor. Biol. 138, 55-58. (doi:10.1016/S0022-5193(89)80177-8) (Pubitemid 19142926)
26. Lifson S. 1997 On the crucial stages in the origin of animate matter. J. Mol. Evol. 44, 1-8. (doi:10.1007/PL00006115) (Pubitemid 27030430)
27. Eigen M. 1971 Selforganisation of matter and the evolution of biological macromolecules. Naturwissenschaften 58, 465-523. (doi:10.1007/ BF00623322)
28. Nicolis G, Prigogine I. 1977 Self-organization in nonequilibrium system: from dissipative structures to order through fluctuations. New York, NY: Wiley.
29. Wu M, Higgs PG. 2009 Origin of self-replicating biopolymers: autocatalytic feedback. Can jump-start the RNA world. J. Mol. Evol. 69, 541-554. (doi:10. 1007/s00239-009-9276-8)
30. Zachar I, Szathmary E. 2010 A new replicator: a theoretical framework for analysing replication. BMC Biol. 8, 21. (doi:10.1186/1741-7007-8-21)
31. Kauffman SA. 1993 The origin of order: selforganization and selection in evolution. Oxford, UK: Oxford University Press.
32. Szathmary E. 2013 On the propagation of a conceptual error concerning hypercycles and cooperation. J. Syst. Chem. 4, 1. (doi:10.1186/ 1759-2208-4-1)
33. Plasson R, Brandenburg A, Jullien L, Bersini H. 2011 Autocatalyses. J. Phys. Chem. A 115, 8073-8085. (doi:10.1021/jp110079p)
34. Sievers D, von Kiedrowski G. 1994 Self-replication of complementary nucleotide-based oligomers. Nature 369, 221-224. (doi:10.1038/369221a0) (Pubitemid 24154798)
35. Lee DH, Granja JR, Martinez JA, Severin K, Ghadiri MR. 1996 A self-replicating peptide. Nature 382, 525-528. (doi:10.1038/382525a0) (Pubitemid 26260690)
36. Lincoln TA, Joyce GF. 2009 Self-sustained replication of an RNA enzyme. Science 323, 1229-1232. (doi:10.1126/science.1167856)
37. Vaidya N, Manapat M, Chen I, Xulvi-Brunet R, Hayden E, Lehman N. 2012 Spontaneous network formation among cooperative RNA replicators. Nature 491, 72-77. (doi:10.1038/nature11549)
38. Pross A. 2013 The evolutionary origin of biological function and complexity. J. Mol. Evol. 76, 185-191. (doi:10.1007/s00239-013-9556-1)
39. Eschenmoser A. 1994 Chemistry of potentially prebiological natural products. Orig. Life Evol. Biosph. 24, 389-423. (doi:10.1007/BF01582017)
40. Eschenmoser A. 2007 Question 1: commentary referring to the statement 'the origin of life can be traced back to the origin of kinetic control' and the question 'do you agree with this statement; and how would you envisage the prebiotic evolutionary bridge between thermodynamic and kinetic control?' Stated in 1.1. Orig. Life Evol. Biosph. 37, 309-314. (doi:10.1007/ s11084-007-9102-5)
41. Eschenmoser A. 2011 Etiology of potentially primordial biomolecular structures: from vitamin B12 to the nucleic acids and an inquiry into the chemistry of life's origin: a retrospective. Angew. Chem. Int. Ed. 50, 12 412-12 472. (doi:10.1002/ anie.201103672)
42. Pascal R. 2012 Suitable energetic conditions for dynamic chemical complexity and the living state. J. Syst. Chem. 3, 3. (doi:10.1186/1759-2208-3- 3)
43. Pascal R. 2013 Life, metabolism and energy. In Astrochemistry and astrobiology: physical chemistry in action (eds IWL Smith, CS Cockell, S Leach), pp. 243-269. Berlin, Germany: Springer.
44. Pascal R, Boiteau L. 2011 Energy flows, metabolism, and translation. Phil. Trans. R. Soc. B 366, 2949-2958. (doi:10.1098/rstb.2011.0135)
45. Lineweaver CH, Chopra A. 2012 The habitability of our earth and other earths: astrophysical, geochemical, geophysical, and biological limits on planet habitability. Annu. Rev. Earth Planet. Sci. 40, 597-623. (doi:10.1146/annurev- earth-042711- 105531)
46. Mitchell P. 1961 Coupling of phosphorylation to electron and hydrogen transfer by a chemi-osmotic type of mechanism. Nature 191, 144-148. (doi:10. 1038/191144a0)
47. Dibrova D, Chudetsky M, Galperin M, Koonin E, Mulkidjanian A. 2012 The role of energy in the emergence of biology from chemistry. Orig. Life Evol. Biosph. 42, 459-468. (doi:10.1007/ s11084-012-9308-z)
48. Lotka A. 1922 Contribution to the energetics of evolution. Proc. Natl Acad. Sci. USA 8, 147-151. (doi:10.1073/pnas.8.6.147)
49. Lotka A. 1925 Elements of physical biology, p. 357. Baltimore, MD: Willams & Wilkins Co.
50. Kondepudi D, Prigogine I. 1998 Modern thermodynamics: from heat engines to dissipative structures. Chichester, UK: Wiley.
51. Grandy Jr WT. 2008 Entropy and the time evolution of macroscopic systems. Oxford, UK: Oxford University Press.
52. Martin O, Horvath JE. 2013 Biological evolution of replicator systems: towards a quantitative approach. Orig. Life Evol. Biosph. 43, 151-160. (doi:10.1007/ s11084-013-9327-4)
53. Kauffman SA. 2000 Investigations. Oxford, UK: Oxford University Press.
54. Mossio M, Moreno A. 2010 Organisational closure in biological organisms. Hist. Philos. Life Sci. 32, 269-288.
55. Baum RM. 2013 The chemistry of life. Chem. Eng. News 91, 38-39.
56. Ganti T. 2003 The principles of life. Oxford, UK: Oxford University Press.
57. Lazcano A. 2010 Which way to life? Orig. Life Evol. Biosph. 40, 161-167. (doi:10.1007/s11084-010- 9195-0)
58. de Duve C. 1995 Vital dust: life as a cosmic imperative. New York, NY: Basic Books.
59. Pereto J. 2011 Origin and evolution of metabolisms. In Origins and evolution of life: an astrobiological perspective (eds M Gargaud, P Lopez-Garc?a, H Martin), ch. 18, pp. 270-287. Cambridge, UK: Cambridge University Press.
60. Pereto J. 2012 Out of fuzzy chemistry: from prebiotic chemistry to metabolic networks. Chem. Soc. Rev. 41, 5394-5403. (doi:10.1039/ c2cs35054h)
61. Pereto J, Velasco A, Becerra A, Lazcano A. 1999 Comparative biochemistry of CO2 fixation and the evolution of autotrophy. Int. Microbiol. 2, 3-10. (Pubitemid 129771320)
62. Morowitz HJ, Kostelnik JD, Yang J, Cody GD. 2000 The origin of intermediate metabolism. Proc. Natl Acad. Sci. USA 97, 7704-7708. (doi:10.1073/pnas. 110153997)
63. Wachtershauser G. 1988 Before enzymes and templates: theory of surface metabolism. Microbiol. Rev. 52, 452-484.
64. Huber C, Kraus F, Hanzlik M, Eisenreich W, Wachtershauser G. 2012 Elements of metabolic evolution. Chem. Eur. J. 18, 2063-2080. (doi:10.1002/chem.201102914)
65. Martin W, Russell MJ. 2003 On the origins of cells: a hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells. Phil. Trans. R. Soc. Lond. B 358, 59-85. (doi:10.1098/rstb.2002.1183) (Pubitemid 36178219)
66. Eschenmoser A. 2007 On a hypothetical generational relationship between HCN and constituents of the reductive citric acid cycle. Chem. Biodivers. 4, 554-573. (doi:10.1002/cbdv. 200790050) (Pubitemid 46930024)
67. Ritson D, Sutherland JD. 2012 Prebiotic synthesis of simple sugars by photoredox systems chemistry. Nat. Chem. 4, 895-899. (doi:10.1038/NCHEM.1467)
68. Ritson DJ, Sutherland JD. 2013 Synthesis of aldehydic ribonucleotide and amino acid precursors by photoredox chemistry. Angew. Chem. Int. Ed. 52, 5845-5847. (doi:10.1002/anie.201300321)