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9 - Emergent order in processes: the interplay of complexity, robustness, correlation, and hierarchy in the biosphere

from Part III - Biological complexity, evolution, and information

Published online by Cambridge University Press:  05 July 2013

By
Eric Smith
Edited by
Charles H. Lineweaver ,
Paul C. W. Davies  and
Michael Ruse
Charles H. Lineweaver
Affiliation:
Australian National University, Canberra
Paul C. W. Davies
Affiliation:
Arizona State University
Michael Ruse
Affiliation:
Florida State University
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Summary

A large part of the structure that is recognized and understood in the vacuum (Weinberg, 1995; Weinberg, 1996) and in condensed matter (Ma, 1976; Mahan, 1990; Goldenfeld, 1992) is the result of a hierarchy of phase transitions in either quantum-mechanical or thermodynamic systems. Each phase transition creates a form of long-range order among components of the system that in the absence of the phase transition could fluctuate independently. To the extent that the phase transitions are nested or sequential in order of decreasing energy or increasing spatial scale, both of which correlate with increasing age of the universe, the progression through the sequence and the accretion of additional forms of long-range order constitute a progression of complexity.

In this chapter I argue that phase transition continues to be the appropriate paradigm in which to understand the emergence of the biosphere on Earth, and that at least some universal patterns in life should be understood as what are called the order parameters (Goldenfeld, 1992) of one or more such transitions. The phase transitions that formed the biosphere, however, are dynamical transitions rather than equilibrium transitions, and this distinction requires a different class of thermodynamic descriptions and leads to some striking differences in gross phenomenology from what has become familiar from equilibrium systems.

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Chapter
Information
Complexity and the Arrow of Time , pp. 191 - 223
Publisher: Cambridge University Press
Print publication year: 2013

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References

Berg, I. A., Kockelkorn, D., Ramos-Vera, W. H., et al. (2010). Autotrophic carbon fixation in archaea. Nature Rev. Microbiol., 8, 447–460.CrossRefGoogle ScholarPubMed
Bertini, L., De Sole, A., Gabrielli, D., Jona-Lasinio, G., & Landim, C. (2009). Towards a nonequilibrium thermodynamics: a self-contained macroscopic description of driven diffusive systems. J. Stat. Phys., 135, 857–872.CrossRefGoogle Scholar
Boltzmann, L. (1905). Populate Schriften. Leipzig: J. A. Barth, re-issued Braunschweig: F. Vieweg, 1979.CrossRef
Braakman, R. & Smith, E. (2012). The emergence and early evolution of biological carbon fixation. PLoS Comp. Biol., 8, el002455.CrossRefGoogle ScholarPubMed
Braakman, R. & Smith, E. (2013). The compositional and evolutionary logic of metabolism. Physical Biology, 10, 011001, .
Brillouin, L. (2004). Science and Information Theory, second edn. Mineola, NY: Dover Phoenix Editions.Google Scholar
Brown, J. H., Gillooly, J. F., Allen, A. P., Savage, V. M., & West, G. B. (2004). Toward a metabolic theory of ecology. Ecology, 85, 1771–1789.CrossRefGoogle Scholar
Buss, L. W. (2007). The Evolution of Individuality. Princeton, NJ: Princeton University Press.Google Scholar
Chaitin, G. J. (1966). On the length of programs for computing finite binary sequences. J. Assoc. Comp. Machinery, 13, 547–569.CrossRefGoogle Scholar
Chaitin, G. J. (1990). Algorithmic Information Theory. New York: Cambridge University Press.Google Scholar
Chistoserdova, L., Kalyuzhnaya, M. G., & Lidstrom, M. E. (2009). The expanding world of methylotrophic metabolism. Ann. Rev. Microbiol., 63, 477–499.CrossRefGoogle ScholarPubMed
Claverie, J.-M. (2006). Viruses take center stage in cellular evolution. Genome Biol., 7, 110:1–5.CrossRefGoogle ScholarPubMed
Cody, G. D., Boctor, N. Z., Hazen, R. M., Brandeis, J. A., Morowitz, H. J., & Yoder, H. S. J. (2001). Geochemical roots of autotrophic carbon fixation: hydrothermal experiments in the system citric acid, h2O-(±FeS) (±NiS). Geochimica et Cosmochimica Ada., 65, 3557–3576.CrossRef
Copley, S. D., Smith, E., & Morowitz, H. J. (2005). A mechanism for the association of amino acids with their codons and the origin of the genetic code. Proc. Nat. Acad. Set. USA, 102, 4442–4447.CrossRefGoogle ScholarPubMed
Copley, S. D., Smith, E., & Morowitz, H. J. (2007). The origin of the RNA world: co-evolution of genes and metabolism. Bioorganic Chemistry, 35, 430–443.CrossRefGoogle ScholarPubMed
Copley, S. D., Smith, E., & Morowitz, H. J. (2010). The emergence of sparse metabolic networks. In Russel, M. (ed.), Abiogenesis and the origins of life. Cambridge, MA: Cosmo. Sci. Publishers, pp. 175–191.Google Scholar
Cover, T. M. & Thomas, J. A. (1991). Elements of Information Theory. New York: Wiley.CrossRefGoogle Scholar
Csete, M. & Doyle, J. (2004). Bow ties, metabolism and disease. Trends. Biotechnol., 22, 446–450.CrossRefGoogle ScholarPubMed
Doolittle, F. (2000). Uprooting the tree of life. Set. Am., 282, 90–95.Google ScholarPubMed
Dunne, J. A., Williams, R. J., Martinez, N. D., Wood, R. A., & Erwin, D. H. (2008). Compilation and network analyses of Cambrian food webs. PLoS Biology, 6 (4), e102, .CrossRefGoogle ScholarPubMed
Ellis, R. S. (1985). Entropy, Large Deviations, and Statistical Mechanics. New York: Springer-Verlag.CrossRefGoogle Scholar
Fermi, E. (1956). Thermodynamics. New York: Dover.Google Scholar
Fisher, R. A. (2000). The Genetical Theory of Natural Selection. London: Oxford University Press.Google Scholar
Forterre, P. (2010). Defining life: the virus viewpoint. Orig. Life Evol. Biosphere, 40, 151–160.CrossRefGoogle ScholarPubMed
Frank, S. A. (1997). The price equation, Fisher's fundamental theorem, kin selection, and causal analysis. Evolution, 51, 1712–1729.CrossRefGoogle ScholarPubMed
Freidlin, M. I. & Wentzell, A. D. (1998). Random Perturbations in Dynamical Systems, second edn. New York: Springer.CrossRefGoogle Scholar
Gell-Mann, M. (1994). The Quark and the Jaguar: Adventures in the Simple and the Complex. New York: Freeman.Google Scholar
Gell-Mann, M. & Lloyd, S. (1996). Information measures, effective complexity, and total information. Complexity, 2, 44–52.3.0.CO;2-X>CrossRefGoogle Scholar
Ghosh, K., Dill, K. A., Inamdar, M. M., Seitaridou, E. & Phillips, R. (2006). Teaching the principles of statistical dynamics. Am. J. Phys., 74, 123–133.CrossRefGoogle ScholarPubMed
Glasstone, S., Laidler, K. J., & Eyring, H. (1941). The Theory of Rate Processes. New York: Mc-Graw Hill.Google Scholar
Gluckheimer, J. & Holmes, P. (1988). Structurally stable heteroclinic cycles. Math. Proc. Cam. Phil. Soc., 103, 189–192.CrossRefGoogle Scholar
Goldenfeld, N. (1992). Lectures on Phase Transitions and the Renormalization Group. Boulder, CO: Westview Press.Google Scholar
Goldenfeld, N. & Woese, C. (2011). Life is physics: evolution as a collective phenomenon far from equilibrium. Ann. Rev. Cond. Matt. Phys. 2, 17.1–17.25, .CrossRefGoogle Scholar
Goldstein, H., Poole, C. P., & Safko, J. L. (2001). Classical Mechanics, third edn. New York: Addison Wesley.Google Scholar
Gould, S. J. (1989). Wonderful Life. New York: Norton.Google Scholar
Gould, S. J. (2002). The Structure of Evolutionary Theory. Cambridge, MA: Harvard University Press.Google Scholar
Gray, H. B. (1994). Chemical Bonds: an Introduction to Atomic and Molecular Structure. Sausalito, CA: University Science Press.Google Scholar
Hamilton, W. D. (1964a). The genetical evolution of social behavior. I. J. Theor. Biol., 7, 1–16.CrossRefGoogle Scholar
Hamilton, W. D. (1964b). The genetical evolution of social behavior, II. J. Theor. Biol., 7, 17–52.CrossRefGoogle Scholar
Hamilton, W. D. (1970). Selfish and spiteful behavior in an evolutionary model. Nature, 228, 1218–1220.CrossRefGoogle Scholar
Huber, C. & Wächtershäuser, G. (2000). Activated acetic acid by carbon fixation on (Fe, Ni)s under primordial conditions. Science, 276, 245–247.CrossRefGoogle Scholar
Hügler, M. & Seivert, S. M. (2011). Beyond the Calvin cycle: autotrophic carbon fixation in the ocean. Ann. Rev. Marine Sci., 3, 261–289.CrossRefGoogle ScholarPubMed
Hügler, M., Wirsen, C. O., Fuchs, G., Taylor, C. D., & Sievert, S. M. (2005). Evidence for autotrophic co2 fixation via the reductive tricarboxylic acid cycle by members of the ε subdivision of proteobacteria. J. Bacteriology, 187, 3020–3027.CrossRefGoogle ScholarPubMed
Jaynes, E. T. (1957a). Information theory and statistical mechanics. Phys. Rev., 106, 620–630. Reprinted in Rosenkrantz (1983).CrossRefGoogle Scholar
Jaynes, E. T. (1957b). Information theory and statistical mechanics. II. Phys. Rev., 108, 171–190. Reprinted in Rosenkrantz (1983).CrossRefGoogle Scholar
Jaynes, E. T. (1980). The minimum entropy production principle. Ann. Rev. Phys. Chem., 31, 579–601. Reprinted in Rosenkrantz (1983).CrossRefGoogle Scholar
Kittel, C. & Kroemer, H. (1980). Thermal Physics, second edn. New York: Freeman.Google Scholar
Kolmogorov, A. N. (1958). New metric invariant of transitive dynamical systems and endomorphisms of Pebesgue spaces. Doklady of Russian Academy of Sciences, 119, 861–864.Google Scholar
Kolmogorov, A. N. (1965). Three approaches to the definition of the quantity of information. Problems of Information Transmission, 1, 3–11.Google Scholar
Kondepudi, D. & Prigogine, I. (1998). Modern Thermodynamics: from Heat Engines to Dissipative Structures. New York: Wiley.Google Scholar
Koonin, E. V. & Martin, W. (2005). On the origin of genomes and cells within inorganic compartments. Trends Genet., 21, 647–654.CrossRefGoogle ScholarPubMed
Krakauer, D. C., Collins, J. P., Erwin, D. et al. (2011). The challenges and scope of theoretical biology. J. Theor. Biol., 276, 269–276.CrossRefGoogle ScholarPubMed
Lengeler, J. W., Drews, G., & Schlegel, H. G. (1999). Biology of the Prokaryotes. New York: Blackwell Science.Google Scholar
Lewontin, R. C. (1974). The Genetic Basis of Evolutionary Change. New York: Columbia University Press.Google Scholar
Li, M. & Vitányi, P. (2008). An Introduction to Kolmogorov Complexity and its Applications, third edn. Heidelberg: Springer.CrossRefGoogle Scholar
Ljungdahl, L., Irion, E., & Wood, H. G. (1965). Total sunthesis of acetate from CO2. I co-methylcobyric acid and co-(methyl)-5-methoxybenzimidazolylcobamide as intermediates with Clostridium thermoaceticum. Biochemistry, 4, 2771–2780.CrossRefGoogle Scholar
Luisi, P. L. (2006), The Emergence of Life: from Chemical Origins to Synthetic Biology. London: Cambridge University Press.CrossRefGoogle Scholar
Ma, S.-K. (1976). Modern Theory of Critical Phenomena. New York: Perseus.Google Scholar
MacKenzie, R. E. (1984). Biogenesis and interconversion of substituted tetrahydrofolates. In Blakely, R. L. & Benkovic, S. J. (eds.), Folates and Pterins, vol. 1: Chemistry and Biochemistry of Folates. New York: John Wiley & Sons, pp. 255–306.
Maden, B. E. H. (2000). Tetrahydrofolate and tetrahydromethanopterin compared: functionally distinct carriers in C1 metabolism. Biochem. J., 350, 609–629.CrossRefGoogle ScholarPubMed
Mahan, G. D. (1990). Many-particle Physics, second edn. New York: Plenum.CrossRefGoogle Scholar
Martin, W. & Russell, M. J. (2003). 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. Roy. Soc. London, 358B, 27–85.Google Scholar
Martin, W. & Russell, M. J. (2006). On the origin of biochemistry at an alkaline hydrothermal vent. Phil. Trans. Roy. Soc. B, , 1–39.Google Scholar
Martin, W., Baross, J., Kelley, D., & Russell, M. J. (2008). Hydrothermal vents and the origin of life. Nature Rev. Microbiol., 6, 805–814.CrossRefGoogle ScholarPubMed
Mézard, M., Parisi, G., Sourias, N., Toulouse, G., & Virasoro, M. (1984). Nature of the spin-glass phase, Phys. Rev. Lett., 52, 1156–1159.CrossRefGoogle Scholar
Morowitz, H. J. (1992). Beginnings of Cellular Life. New Haven, CT: Yale University Press.Google Scholar
Morowitz, H. J. & Smith, E. (2007). Energy flow and the organization of life. Complexity, 13, 51–59. SFI preprint # 06-08-029.CrossRefGoogle Scholar
Morowitz, H. J., Srinivasan, V., & Smith, E. (2010). Ligand field theory and the origin of life as an emergent feature of the periodic table of elements. Biol. Bull., 219, 1–6.CrossRefGoogle ScholarPubMed
Nowak, M. A. & Ohtsuki, H. (2008). Prevolutionary dynamics and the origin of evolution. Proc. Nat. Acad. Set. USA, 105, 14924–14927.CrossRefGoogle Scholar
Odling-Smee, F. J., Laland, K. N., & Feldman, M. W. (2003). Niche Construction: the Neglected Process in Evolution. Princeton, NJ: Princeton University Press.Google Scholar
Onsager, L. (1931a). Reciprocal relations in irreversible processes. I. Phys. Rev., 37, 405–426.CrossRefGoogle Scholar
Onsager, L. (1931b). Reciprocal relations in irreversible processes. II. Phys. Rev., 38, 2265–2279.CrossRefGoogle Scholar
Peretó, J., López-García, P., & Moreira, D. (2004). Ancestral lipid biosynthesis and early membrane evolution. Trends Biochem. Sci., 29, 469–477.CrossRefGoogle ScholarPubMed
Puigbo, P., Wolf, Y., & Koonin, E. (2009). Search for a “Tree of Life” in the thicket of the phylogenetic forest, Journal of Biology, 8, 59, .Google Scholar
Quastler, H. (1964). The Emergence of Biological Organization. New Haven, CT: Yale University Press.Google Scholar
Riehl, W. J., Krapivsky, P. L., Redner, S., & Segrè, D. (2010). Signatures of arithmetic simplicity in metabolic network architecture. Biol., 6 (4), e100725, .CrossRefGoogle Scholar
Rissanen, J. (1989). Stochastic Complexity in Statistical Inquiry. Teaneck, NJ: World Scientific.Google Scholar
Rodrigues, J. a. F. M. & Wagner, A. (2009). Evolutionary plasticity and innovations in complex metabolic reaction networks. PLoS Computational Biology, 5, el000613:l-11.Google Scholar
Rosenkrantz, R. D. (ed.) (1983), Jaynes, E. T.: Papers on Probability, Statistics and Statistical Physics. Dordrecht, Holland: D. Reidel.CrossRef
Russell, M. J. & Hall, A. J. (1997). The emergence of life from iron monosulphide bubbles at a submarine hydrothermal redox and ph front. J. Geol. Soc. London, 154, 377–402.CrossRefGoogle Scholar
Russell, M. J. & Hall, A. J. (2006). The onset and early evolution of life. Geol. Soc. Am. Memoir, 198, 1–32.Google Scholar
Russell, M. J. & Martin, W. (2004). The rocky roots of the acetyl-coa pathway. Trends Biochem. Sci., 29, 358–363.CrossRefGoogle ScholarPubMed
Schrödinger, E. (1992). What is Life?: the Physical Aspect of the Living Cell. New York: Cambridge University Press.CrossRefGoogle Scholar
Sherrington, D. (2010). Physics and complexity. Phil. Trans.R. Soc. A, 368, 1175–1189.CrossRefGoogle ScholarPubMed
Simon, H. A. (1962). The architecture of complexity. Proc. Am. Phil. Soc., 106, 467–482.Google Scholar
Simon, H. A. (1973). The organization of complex systems. Pattee, H. H. (ed.), Hierarchy Theory: the Challenge of Complex Systems. New York: George Braziller, pp. 3–27.Google Scholar
Sinai, Y. G. (1959). On the notion of entropy of a dynamical system. Doklady of Russian Academy of Sciences, 124, 768–771.Google Scholar
Smith, E. (1998). Carnot's theorem as Noether's theorem for thermoacoustic engines. Phys. Rev. E, 58, 2818–2832.CrossRefGoogle Scholar
Smith, E. (1999). Statistical mechanics of self-driven Carnot cycles. Phys. Rev. E, 60, 3633–3645.CrossRefGoogle ScholarPubMed
Smith, E. (2003). Self-organization from structural refrigeration. Phys. Rev. E, 68, 046114. SFI preprint # 03-05-032.CrossRefGoogle ScholarPubMed
Smith, E. (2005). Thermodynamic dual structure of linearly dissipative driven systems. Phys. Rev. E, 72, 36130. SFI preprint # 05-08-033.CrossRefGoogle Scholar
Smith, E. (2008a). Thermodynamics of natural selection I: Energy and entropy flows through non-equilibrium ensembles. J. Theor. Biol., 252, 2, 185–197.Google Scholar
Smith, E. (2008b). Thermodynamics of natural selection II: Chemical Carnot cycles. J. Theor. Biol., 252, 2, 198–212.
Smith, E. (2011). Large-deviation principles, stochastic effective actions, path entropies, and the structure and meaning of thermodynamic descriptions. Rep. Prog. Phys., 74, 046601. .CrossRefGoogle Scholar
Smith, E. & Morowitz, H. J. (2004). Universality in intermediary metabolism. Proc. Nat. Acad. Set. USA, 101, 13168–13173. SFI preprint # 04-07-024.CrossRefGoogle ScholarPubMed
Smith, E. & Morowitz, H. J. (2010). The autotrophic origins paradigm and small-molecule organocatalysis. Orig. Life Evol. Biosphere, 40, 397–402.Google Scholar
Srinivasan, V. & Morowitz, H. J. (2009a). Analysis of the intermediary metabolism of a reductive chemoautotroph. Biol. Bulletin, 217, 222–232.CrossRefGoogle ScholarPubMed
Srinivasan, V. & Morowitz, H. J. (2009b). The canonical network of autotrophic intermediary metabolism: minimal metabolome of a reductive chemoautotroph. Biol. Bulletin, 216, 126–130.CrossRefGoogle ScholarPubMed
Stock, G., Chosh, K., & Dill, K. A. (2009). Maximum caliber: a variational approach applied to two-state dynamics. J. Chem. Phys., 128, 194192:1–12.Google Scholar
Stryer, L. (1981). Biochemistry, second edn. San Francisco, CA: Freeman.Google Scholar
Touchette, H. (2009). The large deviation approach to statistical mechanics. Phys. Rep., 478, 1–69. arxiv:0804.0327.CrossRefGoogle Scholar
Vetsigian, K., Woese, C., & Goldenfeld, N. (2006). Collective evolution and the genetic code. Proc. Nat. Acad. Set. USA, 103, 10696–10701.CrossRefGoogle ScholarPubMed
Wächtershäuser, G. (1988). Before enzymes and templates: a theory of surface metabolism. Microbiol. Rev., 52, 452–484.Google ScholarPubMed
Wächtershäuser, G. (1990). Evolution of the first metabolic cycles. Proc. Nat. Acad. Set. USA, 87, 200–204.CrossRefGoogle ScholarPubMed
Weinberg, S. (1995). The Quantum Theory of Fields, Vol. I: Foundations. New York: Cambridge.CrossRefGoogle Scholar
Weinberg, S. (1996). The Quantum Theory of Fields, Vol. II: Modern applications. New York: Cambridge.CrossRefGoogle Scholar
Wilson, K. G. & Kogut, J. (1974). The renormalization group and the ε expansion. Phys. Rep., Phys. Lett., 12C, 75–200.Google Scholar
Woese, C. R. (1987). Bacterial evolution. Microbiol. Rev., 51, 221–271.Google ScholarPubMed
Woese, C. R. (2000). Interpreting the universal phylogenetic tree. Proc. Nat. Acad. Set. USA, 97, 8392–8396.CrossRefGoogle ScholarPubMed
Wu, D., Ghosh, K., Inamdar, M. et al. (2009). Trajectory approach to two-state kinetics of single particles on sculpted energy landscapes. Phys. Rev. Lett., 103, 050603: 1–4.CrossRefGoogle ScholarPubMed

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