On the emergence of living systems

Biosemiotics

Volumn 2, Issue 3, 2009, Pages 343-359

  Weber, Bruce H ^a  

^a CALIFORNIA STATE UNIVERSITY   (United States)

Author keywords

Biogenesis; Biosemiosis; Complexity; Emergence; Natural organization; Origin of life

Indexed keywords

EID: 77949657190     PISSN: 18751342     EISSN: 18751350     Source Type: Journal    
DOI: 10.1007/s12304-009-9060-6     Document Type: Article

References (135)

1. Arrhenius, G., Sales, B., Mojzsis, S., & Lee, T. (1997). Entropy and charge in molecular evolution-the case of phosphate. Journal of Theoretical Biology, 187, 503-522.
2. Bachman, P. A., Luisi, P. L., & Lang, J. (1992). Autocatalytic self-replication micelles as modes for prebiotic structures. Science, 357, 57-58.
3. Bada, J. L. (2004). How life began on earth: a status report. Earth and Planetary Science Letters, 226, 1-15.
4. Bada, J. L., & Lazcano, A. (2003). Prebiotic soup-revisiting the Miller experiment. Science, 300, 745-746.
5. Baltscheffsky, M. & Baltscheffsky, H. (1992). Inorganic pyrophosphate and inorganic pyrophosphatases. Molecular Mechanisms in Bioenergetics, 331-348.
6. Bar-Yam, Y. (1997). Dynamics of complex systems. Reading: Perseus.
7. Barbieri, M. (2003). The organic codes: An introduction to semiotic biology. Cambridge: Cambridge University Press.
8. Barbieri, M. (ed). (2008). Introduction to biosemiotics: The new biological synthesis. Dordrecht: Springer.
9. Behe, M. J. (1996). Darwin's black box: The biochemical challenge to evolution. New York: The Free.
10. Benner, S. A., Ricardo, A., & Carrigan, M. A. (2004). Is there a common chemical model for life in the universe? Current Opinion in Chemical Biology, 8, 672-689.
11. Bernal, J. D. (1951). The physical basis of life. London: Routledge & Kegan Paul.
12. Bernal, J. D. (1967). The origin of life. Cleveland: World.
13. Bradley, W. L. (2004). Information, entropy, and the origin of life. In W. A. Dembski & M. Ruse (Eds.), Debating design: From Darwin to DNA. Cambridge: Cambridge University Press.
14. Brooks, D. R., & Wiley, E. O. (1986). Evolution as entropy: Toward a unified theory of biology. Chicago: University of Chicago Press.
15. Camazine, S., Deneubourg, J.-L., Franks, N. R., Sneyd, J., Theraulaz, G., & Bonabeau, E. (2001). Self-organization in biological systems. Princeton: Princeton University Press.
16. Carter, C. W., & Kraut, J. (1974). A proposed model for interaction of polypeptides with RNA. Proceedings of the National Academy of Science USA, 71, 283-287.
17. Casti, J. L. (1994). Complexification: Explaining a paradoxical world through the science of surprise. New York: Collins.
18. Cech, T. R. (1986). Bootstrapping model of the origin of life. BioSystems, 15, 209-219.
19. Cech, T. R. (1987). The chemistry of self-splicing RNA and RNA enzymes. Science, 236, 4360-4363.
20. Clayton, P. (2004). Mind & Emergence: From quantum to consciousness. Oxford: Oxford University Press.
21. Clayton, P. (2006). Biology, directionality, and God: Getting clear on the stakes for religion-science discussion. Theology and Science, 4, 121-127.
22. Conway Morris, S. (2003). Life's solutions: Inevitable humans in a lonely universe. Cambridge: Cambridge University Press.
23. Corning, P. A. (2002). The re-emergence of "emergence": a venerable concept in search of a theory. Complexity, 7(6), 18-30.
24. Corning, P. A. (2003). Nature's magic: Synergy in evolution and the fate of humankind. Cambridge: Cambridge University Press.
25. Darwin, C. (1859). On the origin of species by means of natural selection, or the preservation of favoured races in the struggle for life. London: John Murray. available also as a facsimile reprint (1964), with an introduction by Ernst Mayr, Cambridge, MA: Harvard University Press.
26. Davies, P. (1998). Teleology without teleology: Purpose through emergent complexity. In R. J. Russell, W. R. Stoeger & F. J. Ayala (Eds.), Evolutionary and molecular biology: Scientific perspectives on divine action (pp. 151-162). Vatican City: Vatican Observatory.
27. Davies, P. (1999). The fifth miracle: The search for the origin and meaning of life. New York: Simon & Schuster.
28. Davies, P. (2004). Emergent complexity, teleology, and the arrow of time. In W. A. Dembski & M. Ruse (Eds.), Debating design: From Darwin to DNA (pp. 191-209). Cambridge: Cambridge University Press.
29. Dawkins, R. (1976). The selfish gene. Oxford: Oxford University Press.
30. Dawkins, R. (1989). The selfish gene: New edition. Oxford: Oxford University Press.
31. Deacon, T. W. (2003). The hierarchic logic of emergence: untangling the interdependence of evolution and self-organization. In B. H. Weber & D. J. Depew (Eds.), Evolution and learning: The Baldwin effect reconsidered (pp. 273-308). Cambridge: MIT.
32. Deacon, T. W. (2006). Reciprocal linkage between self-organizing processes is sufficient for self-reproduction and evolvability. Biological Theory, 1(2), 1-14.
33. Deamer, D. W. (1992). Polycyclic aromatic hydrocarbons: Primitive pigment systems in the prebiotic environment. Advances in Space Research, 12, 1-4.
34. Deamer, D. W., & Pashley, R. M. (1989). Amphiphilic components of the Murchison carbonaceious chondrite: Surface properties and membrane formation. Origin of Life and Evolution of the Biosphere, 19, 21-38.
35. Deamer, D. W., Dworkin, J. P., Sandford, S. A., Bernstein, M. P., & Allamandola, L. J. (2002). The first cell membranes. Astrobiology, 2, 371-381.
36. Dembski, W. A. (1998). The design inference: Eliminating chance through small probabilities. Cambridge: Cambridge University Press.
37. Depew, D. J., & Weber, B. H. (1995). Darwinism evolving: Systems dynamics and the genealogy of natural selection. Cambridge: MIT.
38. Desmond, A. (1989). The politics of evolution. Chicago: Chicago University Press.
39. Dewar, R. (2003). Information theory explanation of the fluctuation theorem, maximum entropy production and self-organized criticality in non-equilibrium stationary states. Journal of Physics A: Mathematical and General, 36, 631-641.
40. Fox, S. W. (1965). Simulated natural experiments in spontaneous organization of morphological units from proteins. In S. W. Fox (Ed.), The origins of prebiological systems and their molecular matrices (pp. 361-382). New York: Academic Press.
41. Fox, R. F. (1982). Biological energy transduction: The Oroboros. New York: Wiley.
42. Fox, R. F. (1988). Energy and the evolution of life. New York: Freeman.
43. Fox, R. F. (1997). The origins of life: What one needs to know. Zygon, 32, 393-406.
44. Fry, I. (2000). The emergence of life on earth: A historical and scientific overview. New Brunswick: Rutgers University Press.
45. Gesteland, R. F., & Atkins, J. F. (1993). The RNA world: The nature of modern RNA suggests a prebiotic RNA world. Cold Spring Harbor: Cold Spring Harbor.
46. Haldane, J. B. S. (1929). The origin of life. In J. D. Bernal (Ed.), Rationalist animal, reprinted in The origin of life (pp. 242-249). Cleveland: World.
47. Harper, C. L., Jr. (2005). What does a slug know about Mozart? Introducing the ontological multiverse. In C. L. Harper Jr. (Ed.), Spiritual information. Philadelphia and London: Templeton Foundation.
48. Hoffmeyer, J. (2009). Biosemiotics: An examination into the signs of life and the life of signs. Scranton: University of Scranton Press.
49. Imai, E., et al. (1999). Elongation of oligopeptides in a simulated submarine hydrothermal system. Science, 283, 831-833.
50. Joyce, G. F., & Orgel, L. E. (1993). Prospects for understanding the origin of the RNA world. In R. F. Gesteland & J. F. Atkins (Eds.), The RNA World (pp. 1-25). Cold Spring Harbor: Cold Spring Harbor.
51. Kauffman, S. A. (1993). The origins of order: Self-organization and selection in evolution. New York: Oxford University Press.
52. Kauffman, S. A. (2000). Investigations. New York: Oxford University Press.
53. Kauffman, S. A. (2004). Autonomous agents. In J. D. Barrow, P. C. W. Davies & C. L. Harper Jr. (Eds.), Science and ultimate reality: Quantum theory, cosmology and complexity. Philadelphia and London: Templeton Foundation.
54. Kleidon, A., & Lorenz, R. D. (2005). Non-equilibrium thermodynamics and the production of entropy: Life, earth, and beyond. Heidelberg: Springer Verlag.
55. Krüppers, B.-O. (1990). Information and the origin of life. Cambridge MA: MIT Press.
56. Kumar, J. K., & Oliver, J. S. (2002). Proximity effects in monolayer films: Kinetic analysis of amide bond formation in the air-water interface using proton NMR spectroscopy. Journal of the American Chemical Society, 124, 11307-11314.
57. Lahav, N. (1999). Biogenesis: Theories of life's origin. New York: Oxford University Press.
58. Lal, A. K. (2008). Origin of life. Astrophysics Space Science, 317, 267-278.
59. Lane, N. (2006). Power, sex, suicide: Mitochondria and the meaning of life. Oxford: Oxford University Press.
60. Laughlin, R. B. (2005). A different universe: Reinventing physics from the bottom down. New York: Basic Books.
61. Leman, L., Orgel, L., & Ghadiri, M. R. (2004). Carbonylsulfide-mediated prebiotic formation of peptides. Science, 306, 283-286.
62. Liebman, S. A., Pesce-Rodriguez, R. A., & Matthews, C. N. (1995). Organic analysis of hydrogen cyanide polymers: Prebiotic and extraterrestrial chemistry. Advances in Space Research, 15(3), 71-80.
63. Luisi, P. I. (2006). The emergence of life: From chemical origins to synthetic biology. Cambridge: Cambridge University Press.
64. Lurquin, P. F. (2003). The origins of life and the universe. New York: Columbia University Press.
65. Martin, W., & Russell, M. T. (2003). On the origin of cells: A hypothesis for evolutionary transitions from abiotic geochemistry to chemoautotropic prokaryotes, and from prokaryotes to nucleated cells. Philosophical Transactions of the Royal Society of London (Series B), 358, 59-85.
66. Matthews, C. N., & Moser, R. E. (1967). Peptide synthesis from hydrogen cyanide and water. Nature, 215, 1230-1234.
67. Meyer, S. C. (2003). DNA and the origin of life: Information, specification, and explanation. In J. H. Campbell & S. C. Meyer (Eds.), Darwinism, design, and public education (pp. 223-285). Lansing: Michigan State University Press.
68. Meyer, S. C. (2004). The origin of biological information and the higher taxonomic categories. Proceedings of the Biological Society of Washington, 117(2), 213-239.
69. Meyer, S. C. (2009). Signature in the Cell: DNA and the Evidence for Intelligent Design. New York: Harper One.
70. Miller, S. L. (1953). A production of amino acids under possible primitive earth conditions. Science, 117, 528-529.
71. Miller, K. B. (2003). Common descent, transitional forms, and the fossil record, in Perspectives on an Evolving Creation (pp. 152-181). Grand Rapids: Eerdmans.
72. Minard, R. D., Hatcher, P. G., Gourley, R. C., & Matthews, C. N. (1998). Structural investigations of hydrogen cyanide polymers: new insights using TMAH thermochemolysis/GC-MS. Origins of Life and Evolution of the Biosphere, 28, 461-473.
73. Mitchell, P. D. (1961). Coupling of phosphorylation to electron and hydrogen transfer by a chemiosmotic type of mechanism. Nature, 191, 144-148.
74. Morowitz, H. J. (1992). Beginnings of cellular life: Metabolism recapitulates biogenesis. New Haven: Yale University Press.
75. Morowitz, H. J. (2002). The emergence of everything: How the world became complex. New York: Oxford University Press.
76. Morowitz, H., Deamer, D. W., & Smith, T. (1991). Biogeneisis as an evolutionary process. Journal of Molecular Evolution, 33, 207-208.
77. Oparin, A. I. (1924). Proiskhozhdenie zhizy. Moscow: Moskovski Rabochii.
78. Oparin, A. I. (1938). The origin of life. London: Macmillan.
79. Orgel, L. E. (1968). Evolution of the genetic apparatus. Journal of Molecular Biology, 38, 381-393.
80. Orgel, L. W. (1992). Molecular replication. Nature, 358, 203-209.
81. Oró, J. (1961). Mechanism of synthesis of adenine from hydrogen cyanice under possible primitive earth conditions. Nature, 191, 1193-1194.
82. Ourisson, G., & Nakatani, Y. (1994). The terpenoid theory of the origin of cellular life: the evolution of terpenoics do cholesterol. Current Biology, 1, 11-23.
83. Pagels, H. R. (1988). The dreams of reason: The computer and the rise of the sciences of complexity. New York: Simon and Schuster.
84. Peacocke, A. R. (1983). An introduction to the physical chemistry of biological organization. Oxford: Oxford University Press.
85. Powner, M. W., Gerland, B., & Sutherland, J. D. (2009). Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions. Nature, 459, 239-242.
86. Prebble, J., & Weber, B. H. (2003). Wandering in the gardens of the mind: Peter Mitchell and the making of Glynn. New York: Oxford University Press.
87. Prigogine, I. (1962). Introduction to non-equilibrium thermodynamics. New York: Wiley Interscience.
88. Prigogine, I. (1980). From being to becoming: Time and complexity in the physical sciences. New York: Freeman.
89. Prigogine, I. (1997). The end of certainty: Time, chaos, and the new laws of nature. New York: The Free.
90. Prigogine, I., & Stengers, I. (1984). Order out of chaos: Man's new dialogue with nature. New York: Bantam.
91. Royce, J. (1904). Herbert Spencer: An estimate and review. New York: Collier.
92. Ruse, M. (2006). Darwinism and its discontents. New York: Cambridge University Press.
93. Schneider, E., & Sagan, D. (2005). Into the cool: Energy flow, thermodynamics, and life. Chicago: University of Chicago Press.
94. Schopf, J. W. (1983). Earth's earliest biosphere: Its origin and evolution. Princeton: Princeton University Press.
95. Schwartz, A. W. (1997). Speculation on the RNA precursor problem. Journal of Theoretical Biology, 187, 523-527.
96. Scott, E. C. (2004). Evolution vs. creationism: An introduction. Westport: Greenwood.
97. Silberstein, M. (2002). Reduction, emergence and explanation. In P. Machamer & M. Silberstein (Eds.), The Blackwell guide to the philosophy of science (pp. 80-107). Malden: Blackwell.
98. Spencer, H. (1864). The principles of biology. London: Williams and Norgate.
99. Stewart, I. (2003). The second law of gravitics and the fourth law of thermodynamics. In N. H. Gregerson (Ed.), From complexity to life: On the emergence of life and meaning. Cambridge MA: Harvard University Press.
100. Strick, J. E. (2000). Sparks of life: Darwinism and the Victorian debates over spontaneous generation. Cambridge: Harvard University Press.
101. Swenson, R. (1989). Emergent attractors and the law of maximum entropy production: foundations to a theory of general evolution. Systems Research, 6, 187-197.
102. Szostak, J. W. (2009). Systems chemistry on early earth. Nature, 459, 171-172.
103. Taylor, M. C. (2003). The moment of complexity: Emerging network cultures. Chicago: University of Chicago Press.
104. Ulanowicz, R. E. (1997). Ecology the ascendant perspective. New York: Columbia University Press.
105. Ulanowicz, R. E. (2002). Ecology, a dialog between the quick and the dead. Emergence, 4(1), 34-52.
106. Ulanowicz, R. E. (2004). Ecosystem dynamics: a natural middle. Theology and Science, 2(2), 231-253.
107. Ulanowicz, R. E. (2009). A third window: Natural life beyond Newton and Darwin. West Conshohochen: Templeton Foundation.
108. Wächterhäuser, G. (1988a). Before enzymes and templates: theory of Surface Metabolism. Microbiological Reviews, 52, 452-484.
109. Wächterhäuser, G. (1988b). Pyrite formation, the first energy source for life: a hypothesis. Systematic and Applied Microbiology, 10, 207-210.
110. Wächterhäuser, G. (1992). Groundworks for an evolutioinary biochemistry: the iron-sulfur world. Progress in Biophysics and Molecular Biology, 58, 85-201.
111. Wächterhäuser, G. (1997). The origin of life and its methodological challenge. Journal of Theoretical Biology, 187, 483-494.
112. Waldrup, M. M. (1992). Complexity: The emerging science at the edge of order and chaos. New York: Simon and Schuster.
113. Watson, J. D., & Crick, F. C. (1953). Molecular structure of nucleic acids: a structure for deoxyribose nucleic acid. Nature, 171, 737-738.
114. Weber, B. H. (1998). Emergence of life and biological selection from the perspective of complex systems dynamics. In G. van de Vijver, S. N. Salthe & M. Delpos (Eds.), Evolutionary systems: Biological and epistemological perspectives on selection and self-organization (pp. 59-66). Kluwer: Dordrecht.
115. Weber, B. H. (2000). Closure in the emergence and evolution of life. Annals of the New York Academy of Sciences, 901, 132-138.
116. Weber, B. H. (2007). Emergence of life. Zygon, 42, 837-856.
117. Weber, B. H. (2009). Design and its discontents. Synthese (in press).
118. Weber, B. H., & Depew, D. J. (1996). Natural selection and self-organization: dynamical models as clues to a new evolutionary synthesis. Biology and Philosophy, 11, 33-65.
119. Weber, B. H., & Deacon, T. (2000). Thermodynamic cycles, developmental systems, and emergence. Cybernetics and Human Knowing, 7, 21-43.
120. Weber, B. H., & Depew, D. J. (2004). Darwinism, design and complex systems dynamics. In W. A. Dembski & M. Ruse (Eds.), Debating design: From Darwin to DNA (pp. 173-190). Cambridge: Cambridge University Press.
121. Weber, B. H., & Prebble, J. N. (2006). An issue of originality and priority: The correspondence and theories of oxidative phosphorylation of Peter Mitchell and Robert J. P. Williams, 1961-1980. Journal of the History of Biology, 39, 125-163.
122. Westheimer, F. H. (1987). Why nature chose phosphates. Science, 235, 1173-1178.
123. Wicken, J. S. (1987). Evolution, information and thermodynamics: Extending the Darwinian program. New York: Oxford University Press.
124. Williams, R. J. P. (1961). Possible functions of chains of catalysts. Journal of Theoretical Biology, 1, 1-17.
125. Williams, R. J. P., & Fraústo da Silva, J. R. R. (1996). The natural selection of the elements. Oxford: Oxford University Press.
126. Williams, R. J. P., & Fraústo da Silva, J. R. R. (1999). Bringing chemistry to life: From matter to man. Oxford: Oxford University Press.
127. Williams, R. J. P., & Frausto da Silva, J. R. R. (2003). Evolution was chemically constrained. Journal of Theoretical Biology, 220, 323-343.
128. Williams, R. J. P., & Frausto da Silva, J. R. R. (2006). The chemistry of evolution. Amsterdam: Elsevier.
129. Williams, R. J. P., & Frausto, J. R. R. (2008). Evolution revisited by inorganic chemists. In J. D. Barrow, S. Conway Morris, S. J. Freeland & C. L. Harper Jr. (Eds.), Fitness of the cosmos for life: Biochemistry and fine-tuning (pp. 456-489). Cambridge: Cambridge University Press.
130. Wills, C., & Bada, J. (2000). The spark of life: Darwin and the primeval soup. Cambridge: Perseus.
131. Wilson, T. J., & Lilley, D. M. (2009). The evolution of ribozyme chemistry. Science, 323, 1436-1438.
132. Wilson, C., & Szostak, J. W. (1995). In vitro evolution of a self-replicating ribozyme. Nature, 374, 777-782.
133. Woese, C. (1967). The evolution of the genetic code. In The genetic code (pp. 179-195). New York: Harper & Row.
134. Yamagata, Y., & Inomata, K. (1997). Condensation of glycylglycine to oligoclycines with trimetaphosphate in aqueous solution. Origins of Life and Evolution of the Biosphere, 27, 339-344.
135. Yockey, H. P. (2005). Information theory, evolution, and the origin of life. Cambridge: Cambridge University Press.