Informed Generation: Physical origin and biological evolution of genetic codescript interpreters

Journal of Theoretical Biology

Volumn 257, Issue 3, 2009, Pages 345-358

  Wills, Peter R ^a  

^a NONE   (New Zealand)

Author keywords

Coding self organization; Genetic codescript; Genotype phenotype mapping; GRT system; Molecular sequence information

Indexed keywords

DNA;

GENOMICS; GENOTYPE; MAPPING; NATURAL SELECTION; PHENOTYPE;

ARTICLE; CATALYSIS; DNA SEQUENCE; EVOLUTION; GENE REPLICATION; GENOME; GENOTYPE PHENOTYPE CORRELATION; HUMAN; MOLECULAR BIOLOGY; NATURAL SELECTION; NONHUMAN; OPERON; PRIORITY JOURNAL; PROTEIN ASSEMBLY; THEORETICAL MODEL;

ANIMALS; EVOLUTION, MOLECULAR; GENETIC CODE; GENOTYPE; MODELS, GENETIC; PHENOTYPE; SELECTION, GENETIC; SYSTEMS BIOLOGY;

EID: 61449213821     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2008.12.030     Document Type: Article

References (111)

1. Amaral P.P., Dinger M.E., Mercer T.R., and Mattick J.S. The eukayotic genome as an RNA machine. Science 319 (2008) 1787-1788
2. Argollo de Menezes M., and Barabási A.-L. Fluctuations in network dynamics. Phys. Rev. Lett. 92 (2004) 028701
3. Argollo de Menezes M., and Barabási A.-L. Separating internal and external dynamics of complex systems. Phys. Rev. Lett. 93 (2004) 068701
4. Bains W. Many chemistries could be used to build living systems. Astrobiology 4 (2004) 137-167
5. Bak P. How Nature Works: The Science of Self-organized Criticality (1997), Oxford University Press, Oxford
6. Bedau M.A. The nature of life. In: Boden M. (Ed). The Philosophy of Artificial Life (1996), Oxford University Press, Oxford 332-357
7. Bedian V. The possible role of assignment catalysts in the origin of the genetic code. Origins Life 12 (1982) 181-204
8. Behe M. The Edge of Evolution: The Search for the Limits of Darwinism (2007), Free Press, New York
9. Bird A. Perceptions of epigenetics. Nature 447 (2007) 396-398
10. Blount Z.D., Borland C.Z., and Lenski R.E. Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli. Proc. Natl. Acad. Sci. USA 105 (2008) 7899-7906
11. Boogerd F.C., Bruggeman F.J., Hofmeyer J.S., and Westerhoff H.V. Systems Biology Philosophical Foundations (2007), Elsevier, Amsterdam
12. Copley S.D., Smith E., and Morowitz H.J. The origin of the RNA world: co-evolution of genes and metabolism. Bioorg. Chem. 35 (2007) 430-443
13. Crick F.H.C. On protein synthesis. Symp. Soc. Exp. Biol. 12 (1958) 138-163
14. Crick F.H.C. Central dogma of molecular biology. Nature 227 (1970) 561-563
15. Daley A.J., Girvin A., Kauffman S.A., Wills P.R., and Yamins D. Simulation of a chemical autonomous agent. Z. Phys. Chem. 216 (2002) 41-49
16. Dawkins R. The Selfish Gene (1976), Oxford University Press, Oxford
17. Dawkins R. The Blind Watchmaker (1986), Longman, Harlow
18. De Duve C. Singularities: Landmarks on the Pathways of Life (2005), Cambridge University Press, Cambridge
19. Delarue M. An asymmetric underlying rule in the assignment of codons: possible clue to a quick early evolution of the genetic code via successive binary choices. RNA 13 (2006) 161-169
20. Dembski W.A., and Ruse M. Debating Design: From Darwin to DNA (2004), Cambridge University Press, Cambridge
21. Edelmann J.B., and Denton M.J. The uniqueness of biological self-organization: challenging the Darwinian paradigm. Biol. Philos. 22 (2007) 579-601
22. Eigen M. Self-organization of Matter and the Evolution of Biological Macromolecules. Naturwiss 58 (1971) 465-523
23. Eigen M., and Schuster P. The Hypercycle (1979), Springer, Berlin
24. Eigen M., and Winkler-Oswatitsch R. Naturwiss 68 (1981) 282-292
25. Fernando C., and Rowe J. Natural selection in chemical evolution. J. Theor. Biol. 247 (2007) 152-167
26. Fernando C., and Rowe J. The origin of autonomous agents by natural selection. Biosystems 91 (2008) 355-373
27. Füchslin R.M., and McCaskill J.S. Evolutionary self-organization of cell-free genetic coding. Proc. Natl. Acad. Sci. USA 98 (2001) 9185-9190
28. Gánti T. The Principles of Life (2003), Oxford University Press, Oxford
29. Gatenby R.A., and Frieden B.R. Information theory in living systems, methods, applications, and challenges. Bull. Math. Biol. 69 (2007) 635-657
30. In: Gesteland R.F., Cech T., and Atkins J.F. (Eds). The RNA World. third ed (2006), Cold Spring Harbor Laboratory Press
31. Glansdorff P., and Prigogine I. Thermodynamic Theory of Structure, Stability and Fluctuations (1971), Wiley-Interscience, London
32. Goldenberg N., and Woese C. Biology's next revolution. Nature 445 (2007) 369
33. Hoffmann G.W. On the origin of the genetic code and the stability of the translation apparatus. J. Mol. Biol. 86 (1974) 349-362
34. Hodgson G.M., and Knudsen T. Information, complexity and generative replication. Biol. Philos. 23 (2008) 47-65
35. Hopkin M. UK set to reverse stance on research with chimeras. Nature Medicine 13 (2007) 890-891
36. Johannes F., Colot V., and Jansen C. Epigenome dynamics: a quantitative genetics perspective. Nature Rev. Genet. 9 (2008) 883-980
37. Jordan I.K., Katz L.S., Denver D.R., and Streelman J.T. Natural selection governs local, but not global, evolutionary gene coexpression networks in Caenorhabditis elegans. BMC Syst. Biol. 2 (2008) 96
38. Kauffman B.B., Yang Q., Mettetal J.T., and van Oudenaarden A. Heritable stochastic switching revealed by single-cell genealogy. PLoS Biol. 5 (2007) 1973-1980
39. Kauffman S.A. Autocatalytic sets of proteins. J. Theor. Biol. 119 (1986) 1-24
40. Kauffman S.A. The Origins of Order (1993), Oxford University Press, Oxford
41. Kauffman S.A. At Home in the Universe (1995), Oxford University Press, Oxford
42. Kauffman S.A. Investigations (2000), Oxford University Press, Oxford
43. Keller L. Levels of Selection in Evolution (1999), Princeton University Press, Princeton, NJ
44. Kirschner M., and Gerhart J. Evolvability. Proc. Nat. Acad. Sci. USA 95 (1998) 8420-8427
45. Kornberg A. The universal language. Biotechnology 5 (1987) 520
46. In: Kornberg W. (Ed). DNA: The Master Molecule (1983), Avery, New York
47. Kunin V., Goldovsky L., Darzentas N., and Ouzounis C.A. The net of life: reconstructing the microbial phylogenetic network. Genome Res. 15 (2005) 954-959
48. Lartigue C., Glass J.I., Alperovich N., Pieper R., Parmar P.P., Hutchison III C.A., Smith H.O.J., and Venter C. Genome transplantation in bacteria: changing one species to another. Science 317 (2007) 632-638
49. Lenski R.E., Rose M.R., Simpson S.C., and Tadler S.C. Long-term experimental evolution in Escherichia coli. I. Adaptation and divergence during 2,000 generations. Am. Nat. 138 (1991) 1315-1341
50. Lenski R.E., and Travisano M. Dynamics of adaptation and diversification: a 10,000-generation experiment with bacterial populations. Proc. Nat. Acad. Sci. USA 91 (1994) 6808-6814
51. Luscombe N.M., Badu M.M., Yu H., Snyder M., Teichmann S.A., and Gerstein M. Genomic analysis of regulatory network dynamics reveals large topological changes. Nature 431 (2004) 308-312
52. Markowitz S., Drummond A., Nieselt K., and Wills P.R. Simulation model of prebiotic evolution of genetic coding. In: Rocha L.M., Bedau M., Floreano D., Goldstone R., Vespignani A., and Yaeger L. (Eds). Artificial Life X (2006), MIT Press, Cambridge 152-157
53. Maynard Smith J., and Szathmáry E. The Major Transitions in Evolution (1995), Oxford University Press, Oxford
54. McMullin B. John von Neumann and the evolutionary growth of complexity: looking backward, looking forward. Artif. Life 6 (2001) 347-361
55. Michod R.E. Darwinian Dynamics: Evolutionary Transitions in Fitness and Individuality (1999), Princeton University Press, Princeton, NJ
56. Morowitz H.J. Energy Flow in Biology (1968), Academic Press, New York
57. Morowitz H.J. Beginnings of Cellular Life: Metabolism Recapitulates Biogenesis (1992), Yale University Press, New Haven
58. Munteanu A., Attolini C.S.-O., Rasmussen S., Ziock H., and Solé R.V. Generic Darwinian selection in catalytic protocell assemblies. Philos. Trans. R. Soc. B 362 (2007) 1847-1855
59. Munteanu A., and Solé R.V. Phenotypic diversity and chaos in a minimal cell model. J. Theor. Biol. 240 (2006) 434-442
60. Nacher J.C., Ochiai T., and Akutsu T. On the relation between fluctuation, and scaling-law in gene expression time series from yeast to human. Mod. Phys. Lett. B 19 (2005) 1169-1177
61. Newman S.J. Developmental mechanisms: putting genes in their place. J. Biosci. 27 (2002) 97-104
62. Nieselt-Struwe K., and Wills P.R. The emergence of genetic coding in physical systems. J. Theor. Biol. 187 (1997) 1-14
63. Ochiaia T., Nachera J.C., and Akutsua T. Emergence of the self-similar property in gene expression dynamics. Phys. A 382 (2007) 739-752
64. O'Donoghue P., and Luthey-Schulten Z. On the evolution of structure in aminoacyl-tRNA synthetases. Microbiol. Mol. Biol. Rev. 67 (2003) 550-573
65. Olasagastia F., Moreno A., Peretó J., and Morán F. Energetically plausible model of a self-maintaining protocellular system. Bull. Math. Biol. 69 (2007) 1423-1445
66. Okasha S. Evolution and Levels of Selection (2006), Oxford University Press, Oxford
67. Orgel L.E. Prebiotic chemistry and the origin of the RNA World. Crit. Rev. Biochem. Mol. Biol. 39 (2004) 99-123
68. Pattee H.H. Evolving self-reference: matter, symbols and semantic closure. Comm. Cogn. Artif. Intell. 12 (1995) 9-27
69. Prigogine, I., Defay, R., 1954. Chemical Thermodynamics. Everett, D.H., (Trans.), 1962. Longmans, London.
70. Prigogine I., and Nicolis G. Biological order, structure and instabilities. Q.. Rev. Biophys. 4 (1971) 107-148
71. Rodin S.N., and Rodin A.S. Partitioning of aminoacyl-tRNA synthetases in two classes could have been encoded in a strand-symmetric RNA world. DNA Cell Biol. 25 (2006) 617-626
72. Ruiz-Mirazo K., Umerez J., and Moreno A. Enabling conditions for 'open-ended evolution'. Biol. Philos. 23 (2008) 67-85
73. Ruse M. Darwinism and its Discontents (2006), Cambridge University Press, Cambridge
74. Sakar S. A note on frequency dependence and the levels/units of selection. Biol. Philos. 23 (2008) 217-228
75. Samal A., and Jain S. The regulatory network of E. coli metabolism as a Boolean dynamical system exhibits both homeostasis and flexibility of response. BMC Syst. Biol. 2 (2008) 21
76. Schneider E.D., and Kay J.J. Life as a manifestation of the second law of thermodynamics. Math. Comp. Modelling 19 (1994) 25-48
77. Schrödinger E. What is Life? (1944), Cambridge University Press, Cambridge
78. Smith E. Thermodynamics of natural selection I: energy flow and the limits on organization. J. Theor. Biol. 252 (2008) 185-197
79. Smith E. Thermodynamics of natural selection II: chemical Carnot cycles. J. Theor. Biol. 252 (2008) 198-212
80. Smith E. Thermodynamics of natural selection III: Landauer's principle in computation and chemistry. J. Theor. Biol. 252 (2008) 213-220
81. Szathmáry E., Santos M., and Fernando C. Evolutionary potential and requirements for minimal protocells. Top. Curr. Chem. 259 (2005) 167-211
82. Szathmáry E. Coevolution of metabolic networks and membranes: the scenario of progressive sequestration. Philos. Trans. R. Soc. London B 362 (2006) 1781-1787
83. Szejka A., Mihaljev T., and Drossel B. The phase diagram of random threshold networks. New J. Phys. 10 (2008) 063009
84. Tessier P.M., and Linsquist S. Prion recognition elements govern nucleation, strain specificity and species barriers. Nature 447 (2007) 556-562
85. Timoféeff-Ressovsky N.W., Zimmer K.G., and Delbrück M. Über die Natur der Genmutation und der Genstruktur. Nachr. Ges. Wiss. Göttingen, Fachgruppe VI N. F 1 (1935) 189-245
86. Toussaint, M., 2003a. The evolution of genetic representations and modular adaptation. Dissertation zur Erlangung des Grades eines Doktors der Naturwissenschaften in der Fakultät für Physik und Astronomie der Ruhr-Universität Bochum.
87. Toussaint, M., 2003b. On the evolution of phenotypic exploration distributions. In: De Jong, K.A., Poli, R., Rowe J. (Eds.), Foundations of Genetic Algorithms 2003 (FOGA 7) Morgan Kaufmann, pp. 169-182.
88. Toussaint M., and von Seelen W. Complex adaptation and system structure. BioSystems 90 (2007) 769-782
89. Toussaint O., and Schneider E.D. The thermodynamics and evolution of complexity in biological systems. Comp. Biochem. Physiol. A 120 (1998) 3-9
90. Turing A.M. On computable numbers, with an application to the Entschei-dungsproblem. Proc. London Math. Soc. 42 (1936) 230-265
91. Turing A.M. The chemical basis of morphogenesis. Philos. Trans. R. Soc. B (London) 237 (1952) 37-72
92. Vetsigian K., Woese C., and Goldenfeld N. Collective evolution and the genetic code. Proc. Natl. Acad. Sci. USA 103 (2006) 10696-10701
93. Von Neumann J. In: Burks A.W. (Ed). Theory of Self-Reproducing Automata (1949), University of Illinois Press, Urbana 29-87
94. Wagner A. Robustness and Evolvability in Living Systems (2005), Princeton University Press, Princeton, NJ
95. Wagner A. Gene networks and natural selection: Is there a network biology?. In: Pagel M., and Pomiankowski A. (Eds). Evolutionary Genomics and Proteomics (2007), Sinauer Associates, Sunderland, MA
96. Wagner A. Robustness and evolvability: a paradox resolved. Proc. R. Soc. B 275 (2008) 91-100
97. Watson J.D., and Crick F.H.C. Genetical implications of the structure of deoxyribonucleic acid. Nature 171 (1953) 964-967
98. Weber B.H., Depew D.J., Dyke C., Salthe S.N., Schneider E.D., Ulanowicz R.E., and Wicken J.S. Evolution in thermodynamic perspective: an ecological approach. Biol. Philos. 4 (1989) 373-405
99. West-Eberhard M.J. Developmental Plasticity and Evolution (2003), Oxford University Press, Oxford
100. Wills P.R. Scrapie, ribosomal proteins and biological information. J. Theor. Biol. 122 (1986) 157-178
101. Wills P.R. Quantitative constraints on mechanisms of replication for information-carrying prions. Prog. Clin. Biol. Res. 317 (1989) 669-677
102. Wills P.R. Self-organisation of genetic coding. J. Theor. Biol. 162 (1993) 267-287
103. Wills P.R. Does information acquire meaning naturally?. Ber. Bunsenges. Phys. Chem. 98 (1994) 1129-1134
104. Wills P.R. Autocatalysis, information and coding. BioSystems 60 (2001) 49-57
105. Wills P.R. Stepwise evolution of molecular biological coding. In: Pollack J., Bedau M., Husbands P., Ikegami T., and Watson R.A. (Eds). Artificial Life IX (2004), MIT Press, Cambridge 51-56
106. Wills P.R., Marshall J.M., and Smith P.J. Genetic information and self-organised criticality. Europhys. Lett. 68 (2004) 901-907
107. Wills, P.R., Henderson, L., 2000. Self-organisation and information-carrying capacity of collectively autocatalytic sets of polymers: ligation systems. In: Bar-Yam, Y. (Ed.), Unifying Themes in Complex Systems: Proceedings of the First International Conference on Complex Systems (Perseus Books) pp. 613-623.
108. Woese C.R. On the evolution of the genetic code. Proc. Natl. Acad. Sci. USA. 54 (1965) 1546-1552
109. Woese C.R. A new biology for a new century. Microbiol. Mol. Biol. Rev. 68 (2004) 173-186
110. Woese C.R., Olsen G.J., Ibba M., and Soll D. Aminoacyl-tRNA synthetases, the genetic code, and the evolutionary process. Microbiol. Mol. Biol. Rev. 64 (2000) 202-236
111. Wiley E.O., and Brooks D.R. Victims of history: a non-equilibrium approach to evolution. Syst. Zool. 31 (1982) 1-24