4 - Using complexity science to search for unity in the natural sciences  pp. 68-79

Using complexity science to search for unity in the natural sciences

By Eric J. Chaisson

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Nature writ large is a mess. Yet, underlying unities pervade the long and storied, albeit meandering, path from the early universe to civilization on Earth. Evolution is one of those unifiers, incorporating physical, biological, and cultural changes within a broad and inclusive cosmic-evolutionary scenario. Complexity is another such unifier, delineating the growth of structure, function, and diversity within and among galaxies, stars, planets, life, and society throughout natural history. This chapter summarizes a research agenda now underway not only to search for unity in Nature but also, potentially and more fundamentally, to quantify both unceasing evolution and increasing complexity by modeling energy, whose flows through non-equilibrium systems arguably grant opportunities for evolution to create even more complexity.

COSMIC EVOLUTION

Truth be told, I am a phenomenologist – neither a theorist studying Nature from first principles (I’m not smart enough) nor an experimentalist actually measuring things (although I used to). My current philosophy of approach aims to observe and characterize Nature thermodynamically, seeking to explicate a scientific worldview that chronicles systematically and sequentially the many varied changes that have occurred from the big bang to humankind on Earth. I call that epic worldview cosmic evolution.

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Reference Title: References

Reference Type: reference-list

Blount, Z. D. , Barrick, J. E. , Davidson, C. J. , & Lenski, R. E. (2012). Genomic analysis of a key innovation in an experimental Escherichia coli population. Nature, 489, 513–518, .
Dyson, F. J. (1971). Energy in the Universe. Scientific American, 225, Issue 3, pp. 50–59.
ENCODE Project Consortium , (2012). An integrated encyclopedia of DNA elements in the human genome. Nature, 489, 57–74.
Gibbs, J. (1881). From Gibbs's letter accepting the Rumford Medal (1881). Quoted in A. L. Mackay (1994). Dictionary of Scientific Quotations (London: Taylor & Francis).
Gregory, T. R. (2001). Coincidence, coevolution or causation? DNA content, cell size, and the C-value enigma. Biological Review, 76, 65–101.
Gould, S. J. (1996). Full House: The Spread of Excellence from Plato to Darwin. New York: Harmony Books.
Hazen, R. M. , Papineau, D. , Bleeker, W. et al. (2008). Mineral Evolution. Amer. Mineralogist, 93, 1693–1720.
Kelvin, W. T. (1883). The Six Gateways of Knowledge, Presidential Address to the Birmingham and Midland Institute, Birmingham (3 Oct 1883). In Popular Lectures and Addresses (1891), 1, 280.
Kleidon, A. (2012). How does the Earth system generate and maintain thermodynamic disequilibrium and what does it imply for the future of the planet? Phil. Trans. R. Soc A, 370, 1012–1040.
McShea, D. W. & Brandon, R. N. (2010). Biology's First Law. Chicago: University of Chicago Press.
Meysman, F. J. R. & Bruers, S. (2010). Ecosystem functioning and maximum entropy production: a quantitative test of hypotheses, Phil. Trans. R. Soc. B. 365, 1405–1416.
Ulanowicz, R. E. & Hannon, B. M. (1987). Life and the production of entropy. Proc. Royal Soc. London. Series B, Biological Sciences, 232, No. 1267, 181–192.

Reference Title: References

Reference Type: reference-list

Adams, F. C. & Laughlin, G. (2000). The Five Ages of the Universe: Inside the Physics of Eternity. New York: The Free Press.
Atkins, P. (1986). Time and dispersal: the second law. In Flood, R. & Lockwood, M. (eds.), The Nature of Time. Oxford: Blackwell.
Atkins, P. (2010). The Four Laws of Thermodynamics: a Very Short Introduction. Oxford: Oxford University Press.
Bekenstein, J. D. (1973). Black holes and entropy. Physical Review, D, 8: 2333–2350.
Bennett, C. H. (1988). Logical depth and physical complexity. In Herken, R. The Universal Turing Machine – a Half-Century Survey. USA: Oxford University Press, pp. 227–257.
Bousso, R. (2002). The holographic principle. Reviews of Modern Physics, 74 (3), 825–874.
Bruner, E. , Manzi, G. , & Arsuaga, J. L. (2003). Encephalization and allometric trajectories in the genus Homo: evidence from the Neandertal and modern lineages. PNAS, 100, 15335–15340.
Caldwell, R. R. , Kamionkowski, M. , & Weinberg, N. N. (2003). Phantom energy and cosmic doomsday. Phys. Rev. Lett., 91, 071301–1.
Chaitin, G. (1987). Information, Randomness and Incompleteness. Singapore: World Scientific.
Crick, F. (1982). Life Itself: Its Nature and Origin. New York: Simon & Schuster.
Darwin, C. (1863). Letter from Charles Darwin to J. D. Hooker. In Burkhardt, F. , Porter, D. , Deon, S. A. , Topham, J. R. , & Wilmot, S. (eds.), The Correspondence of Charles Darwin 1863. Reprint (2000) (11): 278. Cambridge: Cambridge University Press.
Davies, P. C. W. (1975). The Physics of Time Asymmetry. Berkeley: University of California Press.
Davies, P. C. W. (1977). The thermodynamic theory of black holes. Proc. Roy. Soc., A 353, 499.
Davies, P. C. W. (1988). Cosmological event horizons, entropy and quantum particles. Annales de l’Institut Henri Poincaré, 49, 3, 297.
Davies, P. C. W. (1994). The Last Three Minutes. London: Weidenfeld & Nicolson.
Davies, P. C. W. (2003). The Origin of Life. London: Penguin.
Davies, P. C. W. (2008). The Goldilocks Enigma: Why is the Universe Just Right for Life? London: Penguin.
Davies, P. C. W. (2010). The Eerie Silence: Are We Alone in the Universe? London: Penguin.
Davies, P. C. W. (2012). Epigenetics and top-down causation. Interface Focus, 2, 42–48.
Davies, P. C. W. & Davis T. M. (2003). How far can the generalized second law be generalized? Foundations of Physics, 32, 1877–1892.
Davies, P. C. W. , Davis, T. M. , & Lineweaver, C. H. (2003). Black hole versus cosmo-logical horizon entropy. Classical and Quantum Gravity, 20, 2753–2775.
Davies, P. C. W. & Lineweaver, C. H. (2005). Searching for a second sample of life on Earth. Astrobiology, 5, 154–172.
Davies, P. C. W. , Benner, S. A. , Cleland, C. E. , Lineweaver, C. H. , McKay, C. P. , & Wolfe-Simon, F. (2009). Signatures of a shadow biosphere. Astrobiology, 9, 241–249.
Davies, P. C. W. & Lineweaver, C. H. (2011). Cancer tumors as Metazoa 1.0: tapping genes of ancient ancestors. Physical Biology, 8, 1–7.
De Duve, C. (1995). Vital Dust. New York: Basic Books.
Dyson, F. J. (1979). Disturbing the Universe. New York: Harper & Row.
Egan, C. A. & Lineweaver, C. H. (2010). A larger estimate of the entropy of the Universe. Astrophysical Journal, 710, 1825–1834.
Goldenfeld, N. & Woese, C. (2011). Life is physics: evolution as a collective phenomenon far from equilibrium. Ann. Rev. Condens. Matter Phys., 2, 17.1–17.25.
Gould, S. J. (1996). Full House: the Spread of Excellence from Plato to Darwin. New York: Harmony Books.
Hanahan, D. & Weinberg, R. (2000). The hallmarks of cancer. Cell, 100, 57–70.
Hawking, S. W. (1971). Supermassive objects in astropysics. Phys. Rev. Lett., 26, 1344.
Hawking, S. W. (1975). Particle creation by black holes. Communications in Mathematical Physics, 43, 199–220.
Hawking, S. W. (1978). Space-time foam. Nucl. Phys., B, 144, 349.
Leibniz, G. W. (1697). Philosophical Writings. Translated (1997) by Morris, M. and Parkinson, G. H. R. Edited by Tuttle, C. E. Vermont: Everyman.
Lineweaver, C. H. & Egan, C. A. (2008). Life, gravity and the second law of thermodynamics. Physics of Life Reviews, 5, 225–242.
Lloyd, S. & Pagels, H. (1988). Complexity as thermodynamic depth. Ann. Phys., 188, 186.
Monod, J. (1972) Chance and Necessity. Translated by Wainhouse, A. London: Collins, p. 167.
Nandakumar, V. , Kelbauskas, L. , Johnson, R. , & Meldrum, D. (2010). Quantitative characterization of preneoplastic progression using single-cell computed tomography and three-dimensional karyometry. International Society for Advancement of Cytometry, 79A, 25–34.
Nitecki, M. H. (1989). Evolutionary Progress. Chicago: University of Chicago Press.
Paget, S. (1889). The distribution of secondary growths in cancer of the breast. Lancet, 133, 571–573.
Penrose, R. (1979). Singularities and time-asymmetry. In Hawking, S. W. & Israel, W. General Relativity: an Einstein Centenary Survey. New York: Cambridge University Press, pp. 581–638.
Russell, B. (1957). Why I Am Not a Christian. New York: Allen & Unwin.
Thompson, W. (1852). On a universal tendency in nature to the dissipation of mechanical energy. Proceedings of the Royal Society of Edinburgh, April 19, 1852.

Reference Title: References

Reference Type: reference-list

Adami, C. (2002). What is complexity? BioEssays, 24, 12, 1085–1094.
Adami, C. , Ofria, C. , & Collier, T. C. (2000). Evolution of biological complexity. PNAS, 97, 9, 4463–4468.
Barrow, J. D. (1994). The Origin of the Universe. New York: Basic Books.
Barrow, J. D. (2011). Personal communication.
Bejan, A. (2006). Advanced Engineering Thermodynamics, 3rd edn. New York: Wiley.
Bennett, C. H. (1987). Demons, engines and the second law. Scientific American, Nov., pp. 108–116.
Bennett, C. H. (1988). Information, dissipation, and the definition of organization. In D. Pines (ed.), Emerging Syntheses in Science. Santa Fe: Addison-Wesley.
Bennett, C. H. (1994). Complexity in the Universe. In J. J. Halliwell , J. Perez-Mercader & W. H. Zurek (eds.), Physical Origins of Time Asymmetry. Cambridge: Cambridge University Press.
Carroll, S. (2010). From Eternity to Here: the Quest for the Ultimate Theory of Time. New York: Dutton, Penguin.
Chaisson, E. J. (2001). Cosmic Evolution: the Rise of Complexity in Nature. Cambridge: Harvard University Press.
Chaitin, G. (1987). Algorithmic Information Theory. Cambridge: Cambridge University Press.
Crutchfield, J. P. & Young, K. (1989). Inferring statistical complexity. Phys. Rev. Lett., 63, 105–108.
Davies, P. C. W. (1974). The Physics of Time Asymmetry. Berkeley: University California Press.
Davies, P. C. W. (1994). Stirring up trouble. In Zurek, W. H. , Perez-Mercader, J. , & Halliwell, J. J. (eds.), Physical Origins of Time Asymmetry. Cambridge: Cambridge University Press, pp. 119–130.
Deutsch, D. (1997). The Fabric of Reality. New York: Penguin, p. 179.
Dopita, M. A. , Krauss, L. M. , Sutherland, R. S. et al. (2011). Re-ionizing the Universe without stars. Astrophys. Space Sci., 335, 345–352.
Dyson, F. J. (1979). Time without end: physics and biology in an open Universe. Rev. Mod. Physics, 51, 447–460.
Egan, C. & Lineweaver, C. H. (2010). A larger entropy of the Universe. Astrophysical Journal, 710, 1825–1834.
Evans, D. & Searles, D. J. (1994). Equilibrium microstates which generate second law violating steady states. Physical Review, E, 50, 2, 1645–1648.
Frautschi, S. (1988). Entropy in an expanding Universe. In B. H. Weber , D. J. Depew & J. D. Smith (eds.), Entropy, Information, and Evolution: New Perspectives on Physical and Biological Evolution. Cambridge, MA: MIT Press, pp. 11–22.
Fullsack, M. (2011). Complexity and its observer: does complexity increase in the course of evolution? Paper presented at the 11th Congress of the Austrian Philosophical Society (OeGP), University of Vienna.
Gell-Mann, M. (1994). The Quark and the Jaguar: Adventures in the Simple and Complex. New York: W. H. Freeman.
Gell-Mann, M. (1995). What is complexity? Complexity, 1, no. 1.
Gell-Mann, M. & Lloyd, S. (2003). Effective complexity. In M. Gell-Mann & C. Tsallis (eds.), Nonextensive Entropy – Interdisciplinary Applications. USA: Oxford University Press, pp. 387–398.
Hazen, R. M. , Papineau, D. , Bleeker, W. et al. (2008). Mineral evolution. American Mineralogist, 93, 1693–1720.
Hazen, R. M. & Eldredge, N. (2010). Themes and variations in Complex systems. Elements, 6, 43–46.
Jaynes, E. T. (1989). Clearing up mysteries – the original goal. In J. Skilling (eds.), Maximum Entropy and Bayesian Methods. Dordrecht: Kluwer Academic Publishing, pp. 1–27.
Kauffman, S. (1995). At Home in the Universe: the Laws of Complexity. London: Penguin.
Kleidon, A. (2010). Life, hierarchy and the thermodynamics machinery of planet Earth. Physics of Life Reviews, .
Kleidon, A. (2012). How does the Earth system generate and maintain thermodynamic disequilibrium and what does it imply for the future of the planet? Phil. Trans. R. Soc A, 370, 1012–1040.
Kleidon, A. & Lorenz, R. D. (2005). Non-equilibrium Thermodynamics and the Production of Entropy: Life, Earth and Beyond. Heidelberg: Springer.
Kolb, E. W. & Turner, M. S. (1990). The Early Universe. New York: Addison-Wesley.
Krauss, L. & Starkman, G. (2000). Life, the Universe and nothing: life and death in an ever-expanding Universe. Astrophysical Journal, 531, 22–30.
Layzer, D. (1975). The arrow of time. Scientific American, 233, 6, 56–69.
Layzer, D. (1988). Growth of order in the Universe. In B. H. Weber , D. J. Depew and J. D. Smith (eds.), Entropy, Information, and Evolution: New Perspectives on Physical and Biological Evolution. Cambridge, MA: MIT Press, pp. 23–39.
Li, M. & Vitanyi, P. M. B. (2008). An Introduction to Kolmogorov Complexity and Its Applications. 3rd ed., New York: Springer.
Liddle, A. R. & Lyth, D. H. (2000). Cosmological Inflation and Large-Scale Structure. Cambridge: Cambridge University Press.
Lineweaver, C. H. (2001). An estimate of the age distribution of terrestrial planets in the Universe: quantifying metallicity as a selection effect. Icarus, 151, 307–313.
Lineweaver, C.H. (2010). Spreading the power: commentary on life, hierarchy, and the thermodynamic machinery of planet Earth by A. Kleidon. Phys. Life Rev., .
Lineweaver, C. H. & Egan, C. (2008). Life, gravity and the second law of thermodynamics. Physics of Life Reviews, 5, 225–242.
Lineweaver, C. H. & Egan, C. (2011). The initial low gravitational entropy of the Universe as the origin of design in nature. In R. Gordon , L. Stillwaggon-Swan & J. Seckbach (eds.), Origins of Design in Nature. Dordrecht: Springer, pp. 3–16.
Lloyd, S. (2001). Measures of complexity: a non-exhaustive list. IEEE Control Systems Magazine.
Lloyd, S. & Pagels, H. (1988). Complexity as thermodynamic depth. Annals of Physics, 188, 186–213.
Maxwell, J. C. (1888). Theory of Heat. London: Longmans, Green and Co.
McShea D. W. (2000). Functional complexity in organisms: parts as proxies. Biological Philosophy, 15, pp. 641–668.
McShea, D. W. & Brandon, R. N. (2010). Biology's First Law: the Tendency for Diversity and Complexity to Increase in Evolutionary Systems. Chicago: University of Chicago Press.
Penrose R. (1979). Singularities and time-asymmetry. In Hawking, S. W. & Israel, W. (eds), General Relativity: an Einstein Centenary Survey. Cambridge: Cambridge University Press, pp. 581–638.
Penrose R. (2004). The big bang and its thermodynamic legacy. In Road to Reality: a Complete Guide to the Laws of the Universe. London: Vintage Books, pp. 686–734. Plot used in Fig. 1, panel c, from A. Thomas (2009), .
Prigogine I. (1978). Time, structure and fluctuations. Science, 201, 777–85.
Quinn, H. R. & Nir, Y. (2008). The Mystery of the Missing Antimatter. Princeton: Princeton University Press.
Rubi, J. M. (2008). Does nature break the second law of thermodynamics? (also published as “The long arm of the second law”). Scientific American, November.
Sakharov, A. D. (1967). Violation of CP symmetry, C-asymmetry and baryon asymmetry of the Universe. JETP Letters, 5, 24–27.
Schneider, E. D. & Sagan, D. (2006). Into the Cool: Energy Flow, Thermodynamics, and Life. Chicago: University of Chicago Press.
Schrödinger, E. (1944). What is life? Cambridge: Cambridge University Press.
Smoot, G. F. , Bennett, C. L. , Kogut, A. et al. (1992). Structure in the COBE differential microwave radiometer first-year maps. Astrophysical Journal, 396, L1–5.
Spiegelman, S. (1971). An approach to the experimental analysis of precellular evolution. Quarterly Reviews of Biophysics, 4(2&3), 213–253.
Susskind, L. (1995) The world as a hologram. Journal of Mathematical Physics, 36, 6377–6396, arXiv:hep-th/9409089.
Szilard, L. (1929). Uber die Entropie verminderung in einem thermodynamischen System bei Eingriffen intelligenter wesen. Zeitschrift für Physik, 53, 840–856.
Traub, J. F. , Wasilkowsu, G. W. & Wozniakowski, H. (1983). Information, Uncertainty, Complexity. Reading, MA: Addison-Wesley.
Ulanowicz, R. E. & Hannon, B. M. (1987). Life and the production of entropy. Proc. Royal Soc. London. Series B, Biological Sciences, 232, No. 1267, 181–192.
Weaver, W. (1948). Science and complexity. American Scientist, 36, 536.
Weber, B. H. , Depew, D. J. , & Smith, J. D. (eds.) (1988). Entropy, Information, and Evolution: New Perspectives on Physical and Biological Evolution. Cambridge, MA: MIT Press.
Wicken, J. S. (1988). Thermodynamics, evolution, and emergence: ingredients for a new synthesis. In B. H. Weber , D. J. Depew & J. D. Smith (eds.), Entropy, Information, and Evolution: New Perspectives on Physical and Biological Evolution. Cambridge, MA: MIT Press, pp. 139–169.
Wilson E. O. (1992). The Diversity of Life. Cambridge: Harvard University Press, p. 9.
Zaikowski, L. & Friedrich, J. (eds.) (2008). Chemical Evolution across Space and Time: from the Big Bang to Prebiotic Chemistry. American Chemical Society Symposium Series. USA: Oxford University Press.
Zimdahl, W. & Pavon, D. (2001). Cosmological two-fluid thermodynamics. General Relativity and Gravitation, 33, 5, 791–804, arXiv:astro-ph/0005352v1.
Zurek, W. H. (1989). Thermodynamic cost of computation, algorithmic complexity and the information metric. Nature, 341, 119–124.

Reference Title: References

Reference Type: reference-list

Chaisson, E. J. (2001). Cosmic Evolution: the Rise of Complexity in Nature. Cambridge & London: Harvard University Press.
Chaisson, E. J. (2009a). Cosmic evolution – state of the science. In S. Dick and M. Lupisella (eds.). Cosmos & Culture. Washington: NASA Press.
Chaisson, E. J. (2009b). Exobiology and complexity. In R. Meyers (ed.). Encyclopedia of Complexity and Systems Science. Berlin: Springer.
Chaisson, E. J. (2011a). Energy rate density as a complexity metric and evolutionary driver. Complexity, 16, 27–40; .
Chaisson, E. J. (2011b). Energy rate density II: probing further a new complexity metric. Complexity, 17, 44–63; .
Neubauer, R. L. (2011). Evolution and the Emergent Self: the Rise of Complexity and Behavioral Versatility in Nature. New York: Columbia University Press.
Spier, F. (2011). Big History and the Future of Humanity. London: Wiley-Blackwell.

Reference Title: References

Reference Type: reference-list

Abbott, E. A. (1992). Flatland: a Romance in Many Dimensions (1884). New York: Dover.
Aguirre, A. , Tegmark, M. , & Layzer, D. (2010). Born in an infinite universe: a cosmological interpretation of quantum mechanics. arXiv:1008.1066.
Albrecht, A. & Sorbo, L. (2004). Can the universe afford inflation? Phys. Rev. D., 70, 063528.
Bennett, C. H. (1985). Dissipation, information, computational complexity and the definition of organization. In D. Pines (ed.), Emerging Syntheses in Science. Redwood City CA: Addison-Wesley, pp. 215–233.
Bennett, C. H. (1990). How to define complexity in physics, and why. In W. H. Zurek (ed.) Complexity, Entropy and the Physics of Information. Redwood City CA: Addison-Wesley, pp. 137–148.
Birrell, N. D. & Davies, P. C. W. (1982). Quantum Fields in Curved Space. Cambridge: Cambridge University Press.
Bousso, R. & Susskind, L. (2011). The multiverse interpretation of quantum mechanics. arXiv:1105.3796.
Chaitin, G. J. (1987). Algorithmic Information Theory. Cambridge: Cambridge University Press.
Cover, T. M. & Thomas, J. A. (1991). Elements of Information Theory. New York: Wiley.
Davies, P. C. W. (1974). The Physics of Time Asymmetry. Berkeley: University of California Press.
Dyson, L. , Kleban, M. , & Susskind, L. (2002). Disturbing implications of a cosmological constant. J. High. Ener. Phys., 0210, 011.
Gell-Mann, M. & Hartle, J. B. (1993). Classical equations for quantum systems. Phys. Rev. D, 47, 3345–3382.
Griffiths, R. (2002). Consistent Quantum Theory. Cambridge: Cambridge University Press.
Guth, A. H. (1981). Inflationary universe: a possible solution to the horizon and flatness problems. Phys. Rev. D, 23, 347–356.
Kolmogorov, A. N. (1965). Three approaches to the quantitative definition of information. Prob. Inf. Trans. 1, 1–11.
Li, M. & Vitanyi, P. (2008). An Introduction to Kolmogorov Complexity and Its Applications, 2nd edn. New York: Springer-Verlag.
Liddle, A. R. & Lyth, D. H. (2000). Cosmological Inflation and Large-Scale Structure. Cambridge: Cambridge University Press.
Linde, A. D. (1986a). Eternally existing self-reproducing chaotic inflationary universe. Phys. Lett. B, 175, 395–400.
Linde, A. D. (1986b). Eternal chaotic inflation. Mod. Phys. Lett. A, 1, 81.
Linde, A. (2007). Sinks in the landscape, Boltzmann brains, and the cosmological constant problem. J. Cos. Astr. Phys., 0701, 022.
Lloyd, S. (1993). Quantum computers and uncomputability. Phys. Rev. Lett. 71, 943–946.
Lloyd, S. (1995). Almost any quantum logic gate is universal. Phys. Rev. Lett., 75, 346–349.
Lloyd, S. (1996). Universal quantum simulators. Science, 273, 1073–1078.
Lloyd, S. (1997). Universe as quantum computer. Complexity, 3/1, 32–35.
Lloyd, S. (2000). Ultimate physical limits to computation. Nature, 406, 1047–1054.
Lloyd, S. (2002). Computational capacity of the universe. Phys. Rev. Lett., 88, 237901.
Lloyd, S. (2006). Programming the Universe. New York: Knopf.
Lloyd, S. & Pagels, H. (1988). Complexity as thermodynamic depth. Ann. Phys., 188, 186–213.
Margolus, N. (1984). Physics-like models of computation. Physica D, 10, 81–95.
Margolus, N. & Levitin, L. B. (1998). The maximum speed of dynamical evolution. Physica D, 120, 188–195.
Messiah, A. (1999). Quantum Mechanics. New York: Dover.
Mukhanov, V. (2005). Physical Foundations of Cosmology. Cambridge: Cambridge University Press.
Newton, I. (1687). Philosophiae Naturalis Principia Mathematica. London: Royal Society.
Nielsen, M. A. , Chuang, I. L. (2000). Quantum Computation and Quantum Information, Cambridge: Cambridge University Press.
Nomura, Y. (2011). Physical theories, eternal inflation, and the quantum universe. arXiv:1104.2324.
Omnés, R. (1994). The Interpretation of Quantum Mechanics. Princeton: Princeton University Press.
Papadimitriou, C. H. & Lewis, H. (1982). Elements of the Theory of Computation. Englewood Cliffs: Prentice-Hall.
Peres, A. (2002). Quantum Theory: Concepts and Methods. New York: Kluwer.
Perlmutter, S. , Alderling, G. , Goldhaber, G. et al. (1999). Measurements of omega and lambda from 42 high-redshift supernovae. Astro. Journal, 517, 565–586.
Riess, A. , Filippeuko, A. V. , Challis, P. et al. (1998). Observational evidence from supernovae for an accelerating Universe and a cosmological constant. Astro. Journal, 116, 1009–1038.
Schmidhuber, J. (1997). A computer scientist's view of life, the universe, and everything. In C. Freksa (ed.). Foundations of Computer Science: Potential – Theory – Cognition, Lecture Notes in Computer Science. New York: Springer, pp. 201–208.
Solomonoff, R. J. (1964). A formal theory of inductive inference, Part I. Inf. Control, 7, 1–22. A formal theory of inductive inference, Part II. Inf. Control, 7, 224–254.
Starobinsky, A. A. (1982). Dynamics of phase transition in the new inflationary universe scenario and generation of perturbations. Phys. Lett. B, 117, 175–178.
Susskind, L. (2007). The anthropic landscape of string theory. In B. Carr (ed.), Universe or Multiverse. Cambridge: Cambridge University Press.
Tegmark, M. (1998). Is ‘the theory of everything’ merely the ultimate ensemble theory? Ann. Phys., 270, 1–51.
Tegmark, M. (2007). The multiverse hierarchy. In B. Carr (ed.), Universe or Multiverse. Cambridge: Cambridge University Press.
Tegmark, M. (2008). The mathematical universe. Found. Phys., 38, 101–150.
Tegmark, M. , Strauss, M. A. , Blanton, M. R. et al. (2004). Cosmological parameters from SDSS and WMAP. Phys. Rev. D, 69, 103501.
Turing, A. M. (1937). On computable numbers, with an application to the Entscheidungsproblem, Proc. Lond. Math. Soc., 2, 42, 230–265. Turing, A. M. (1937). On computable numbers, with an application to the Entscheidungsproblem: a correction. Proc. Lond. Math. Soc., 2, 43, 544–546.
Vilenkin, A. (1994). Topological inflation. Phys. Rev. Lett., 72, 3137–3140.
Weinberg, S. (2008). Cosmology. Oxford: Oxford University Press.
Wolfram, S. (1986). Theory and Applications of Cellular Automata, Advanced series on complex systems 1. Singapore: World Scientific.
Zurek, W. H. (1989). Algorithmic randomness and physical entropy. Phys. Rev. A, 40, 4731–4751.
Zurek, W. H. (1991). Decoherence and the transition from quantum to classical. Phys. Today, 44, 36–44.

Reference Title: References

Reference Type: reference-list

Adib, A. , Gleiser, M. , & Almeida, C. (2002). Long-lived oscillons from asymmetric bubbles. Physical Review D, 66, 085011.
Amin, M. A. & Shirokoff, D. (2010). Flat-top oscillons in an expanding Universe. Physical Review D, 81, 011602.
Amin, M. A. , Easther, R. , Finkel, H. , Flauger, R. & Hertzberg, M. P. (2012). Oscillons after inflation. Physical Review Letters, 108, 241302.
Bogolubsky, I. L. & Makhankov, V. G. (1976). J. Exp. Theor. Phys. Lett., 24, 12 [Pis'ma Zh. Eksp. Teor. Fiz., 24, 15].
Copeland, E. J. , Gleiser, M. , & Muller, H.-R. (1995). Oscillons: resonant configurations during bubble collapse. Physical Review D, 52, 1920.
Crawford, C. & Riecke, H. (1999). Oscillon-type structures and their interaction in a Swift–Hohenberg Model. Physica D, 129, 83.
Cross, M. C. & Hohenberg, P. C. (1993). Pattern formation outside of equilibrium. Reviews of Modern Physics, 65, 851.
Dyson, F. (1984). Origins of Life. Cambridge, UK: Cambridge University Press.
Farhi, E. , Graham, N. , Guth, A. H. et al. (2008). Emergence of oscillons in an expand background. Physical Review D, 77, 085019.
Flach, S. & Willis, C. R. (1998). Discrete breathers. Physics Reports, 295, 181.
Fodor, G. , Forgács, P. , Grandclément, P. & Rácz, I. (2006). Oscillons and quasibreathers in the phi4 Klein–Gordon model. Physical Review D, 74, 124003.
Gleiser, M. (1994). Pseudo-stable bubbles. Physical Review D, 49, 2978.
Gleiser, M. (2004). The problem of the 3 origins: cosmos, life, and mind. In J. Barrow , P. C. W. Davies & C. Harper, Jr. (eds.), Science and Ultimate Reality: a Celebration of John A. Wheeler's Vision. Cambridge, UK: Cambridge University Press.
Gleiser, M. & Haas, R. (1996). Oscillons in a hot heat bath. Physical Review D, 54, 1626.
Gleiser, M. & Howell, R. (2003). Resonant emergence of local and global spatiotemporal order in a nonlinear field mode. Physical Review E, 68, 065203(RC).
Gleiser, M. & Sicilia, D. (2008). An analytic characterization of oscillons: their energy, radius, frequency, and lifetime. Physical Review Letters, 101, 011602.
Gleiser, M. & Sicilia, D. (2009). General theory of oscillon dynamics. Physical Review D, 80, 125037.
Gleiser, M. & Sornborger, A. (2000). Long-lived localized configurations in small lattices: application to oscillons. Physical Review E, 62, 1368.
Gleiser, M. & Stamatopoulos, N. (2012a). Entropic measure for localized energy configurations: kinks, bounces, and bubbles. Physics Letters B, 713, 304.
Gleiser, M. & Stamatopoulos, N. (2012b). Information content of spontaneous symmetry breaking. Physical Review D, 86, 045004.
Gleiser, M. & Thorarinson, J. (2007). A phase transition in U(1) configuration space: oscillons as remnants of vortex–antivortex annihilation. Physical Review D, 76, 041701(R).
Gleiser, M. & Thorarinson, J. (2009a). A class of nonperturbative configurations in Abelian-Higgs models: complexity from dynamical symmetry breaking. Physical Review D, 79, 025016.
Gleiser, M. & Walker, S. I. (2009b). Toward homochiral protocells in noncatalytic peptide systems. Origins of Life and Evolution of Biospheres, 39, 479.
Graham, N. & Stamatopoulos, N. (2006). Unnatural oscillon lifetimes in an expanding background. Physics Letters B, 639, 541.
Gunton, J. D. (1999). Journal of Statistical Physics, 95, 903.
Gunton, J. D. , San Miguel, M. , & Sahni, P. S. (1983). The dynamic of first-order phase transitions. In C. Domb & J. L. Lebowitz (eds.), Phase Transitions and Critical Phenomena, vol. 8. London: Academic Press.
Hertzberg, M. P. (2010). Quantum radiation of oscillons. Physical Review D, 82, 045022.
Hindmarsh, M. & Salmi, P. (2006). Numerical investigations of oscillons in 2 dimensions. Physical Review D, 74, 105005.
Hindmarsh, M. & Salmi, P. (2008). Oscillons and domain walls. Physical Review, D, 77, 105025.
Honda, E. & Choptuik, M. (2002). Fine structure of oscillons in the spherically-symmetric phi4 Klein–Gordon model. Physical Review D, 68, 084037.
Infeld, E. & Rowlands G. (2000). Nonlinear Waves, Solitons and Chaos. Cambridge, UK: Cambridge University Press.
Jeong, S.-O. & Moon, H.-T. (1999). Nucleation of oscillons. Physical Review E, 59, 850.
Kauffman, F. (1993). The Origins of Order: Self-Organization and Selection in Evolution. Oxford, UK: Oxford University Press.
Landau, L. D. & Lifshitz, E. M. (1976). Mechanics. Oxford, UK: Pergamon Press.
Langer, J. S. (1992). An Introduction to the Kinetics of First Order Phase Transitions. In C. Godrèche (ed.), Solids Far from Equilibrium. Cambridge, UK: Cambridge University Press.
Lee, T. D. & Pang, Y. (1992). Nontopological solitons. Physics Reports, 221, 251.
Lineweaver, C. H. & Egan, C. A. (2008). Life, gravity, and the second law of thermodynamics. Physics of Life Reviews, 5, 225.
Melo, F. , Umbanhowar, P. & Swinney, H. (1994). Transition to parametric wave patterns in a vertically oscillated granular layer. Physical Review Letters, 72, 172.
Prigogine, I. (1978). Time, structure, and fluctuations. Science, 201, 777.
Prigogine, I. (1980). From Being to Becoming. New York: WH Freeman.
Rajamaran, R. (1987). Solitons and Instantons. Amsterdam: North-Holland.
Scott, A. C. (2007). The Nonlinear Universe: Chaos, Emergence, Life. Berlin: Springer-Verlag.
Shats, M. , Xia, H. & Punzmann, H. (2012). Parametrically excited water surface ripples as ensembles of solitons. Physical Review Letters, 108, 034502.
Stenflo, L. & Yu, M. Y. (2007). Oscillons and standing wave patterns. Physica Scripta, 76 C1.
Tsimring, L. S. & Aranson, I. S. (1997). Localized and cellular patterns in a vibrated granular layer. Physical Review Letters, 79, 213.
Umbanhowar, P. , Melo, F. & Swinney, H. (1996). Localized excitations in a vertically vibrated granular layer. Nature, 382, 793.
Umurhan, O. M. , Tao, L. , & Spiegel, E. A. (1998). Stellar oscillons. Annals of New York Academy of Sciences, 867, 298.
Walgraef, D. (1997) Spatiotemporal Pattern Formation. New York: Springer.

Reference Title: References

Reference Type: reference-list

Adamowicz, S. J. , Purvis, A. , & Wills, M.A. (2008). Increasing morphological complexity in multiple parallel lineages of the Crustacea. Proc. Natl. Acad. Sci. USA, 105, 4786–4791.
Aruga, J. , Odaka, Y. S. , Kamiya, A. , & Furuya, H. (2007). Dicyema Pax6 and Zic: tool-kit genes in a highly simplified bilaterian. BMC Evol. Biol., 7, art. 201.
Badger, M. R. , Hanson, D. , & Price, G. D. (2002). Evolution and diversity of CO2 concentrating mechanisms in cyanobacteria. Functional Plant Biol., 29, 161–173.
Bertolino, E. , Reimund, B. , Wildt-Perinic, D. , & Clerc, R. G. (1995). A novel homeobox protein which recognizes a TGT core and functionally interferes with a retinoid-responsive motif. J. Biological Chem., 270, 31178–31188.
Burkhardt, P. , Stegmann, C. M. , Cooper, B. et al. (2011). Primordial neurosecretory apparatus identified in the choanoflagellate Monosiga brevicollis. Proc. Natl. Acad. Sci. USA, 108, 15264–15269.
Christin, P.-A. , Weinreich, D. M. , & Besnard, G. (2010). Causes and evolutionary significance of genetic convergence. Trends Genetics, 26, 400–405.
Cnotka, J. , Güntürkün, O. , Rehkämper, G. , Gray, R. D. , & Hunt, G. R. (2008). Extraordinary large brains in tool-using New Caledonian crows (Corvus moneduloides). Neurosci. Letters, 433, 241–245.
Conway Morris, S. (2003). Life's Solution: Inevitable Humans in a Lonely Universe. Cambridge: Cambridge University Press.
Conway Morris, S. (2010a). The predictability of evolution: glimpses into a post-Darwinian world. Naturwissenschaften, 96, 1313–1337.
Conway Morris, S. (2010b). Evolution: like any other science it is predictable. Phil. Trans. R. Soc. Lond. B., 365, 133–145.
Conway Morris, S. (2010c). Aliens at home? EMBO Rep., 11, 563.
Conway Morris, S. (2011a). Consider the octopus. EMBO Rep., 12, 182.
Conway Morris, S. (2011b). Predicting what extraterrestrials will be like: and preparing for the worst. Phil. Trans. R. Soc. Lond. A., 369, 555–571.
Conway Morris, S. (2011c). Complexity: the ultimate frontier? EMBO Reports, 12, 481–482.
Crespi, B. J. (2001). The evolution of social behavior in microorganisms. Trends Ecology Evol., 16, 178–183.
Derelle, R. , Lopez, P. , Le Guyader, H. , & Manuel, M. (2007). Homeodomain proteins belong to the ancestral molecular toolkit of eukaryotes. Evol. Dev., 9, 212–219.
Ellis, R. J. (1979). The most abundant protein in the world. Trends Biochem. Sci., 4, 241–244.
Elsasser, W. M. (1998). Reflections on a Theory of Organisms: Holism in Biology. Baltimore: John Hopkins University Press.
Evans, D. R. & Sanson, G. D. (2003). The tooth of perfection: functional and spatial constraints on mammalian tooth shape. Biol. J. Linn. Soc., 78, 173–191.
Fanenbruck, M. & Harzsch, S. (2005). A brain atlas of Godzilliognomus frondosus Yager, 1989 (Remipedia, Godzilliidae) and comparison with the brain of Speleonectes tulumensis Yager, 1987 (Remipedia, Speleonectidiae): implications for arthropod relationships. Arthropod Struct. Dev., 34, 343–378.
Farrell, B. D. , Sequeira, A. S. , O’Meara, B. C. , Normark, B. B. , Chung, J. H. , & Jordal, B. H. (2001). The evolution of agriculture in beetles (Curculionidae: Scolytinae and Platypodinae). Evolution, 55, 2011–2027.
Fraser, C. M. , Gocayne, J. D. , White, O. et al. (1995). The minimal gene complement of Mycoplasma genitalium. Science, 270, 397–403.
Fritz-Laylin, L. K. , Prochnik, S. E. , Ginger, M. L. et al. (2010). The genome of Naegleria gruberi illuminates early eukaryotic versatility. Cell, 140, 631–642.
Furuya, H. & Tsuneki, K. (2003). Biology of dicyemid mesozoans. Zool. Sci., 20, 519–532.
Gehring, W. J. (2005). New perspectives on eye development and the evolution of eyes and photoreceptors. J. Heredity, 96, 171–184.
Graumann, P. L. (2007). Cytoskeletal elements in bacteria. Ann. Review Microbiol., 61, 589–618.
Harcet, M. , Roller, M. , Ćetković, H. et al. (2010). Demosponge EST sequencing reveals a complex genetic toolkit of the simplest metazoans. Mol. Biol. Evol., 27, 2747–2756.
Haring, E. , Däubl, B. , Pinsker, W. , Kryukov, A. , & Gamauf, A. (2012). Genetic divergences and intraspecific variation in corvids of the genus Corvus (Aves: Passeriformes: Corvidae) – a first survey based on museum specimens. J. Zoological Systematics Evolutionary Research, 50, 230–246.
Hata, H. & Kato, M. (2006). A novel obligate cultivation mutualism between damselfish and Polysiphonia algae. Biol. Lett., 2, 593–596.
Heanue, T. A. , Reshef, R. , Davis, R. J. et al. (1999). Synergistic regulation of vertebrate muscle development by Dach2, Eya2, and Six1, homologs of genes required for Drosophila eye formation. Genes Dev., 13, 3231–3243.
Heino, J. (2007). The collagen family members as cell adhesion receptors. BioEssays, 29, 1001–1010.
Hochberg, F. G. (1982). The “kidneys” of cephalopods: a unique habitat for parasites. Malacologia, 23, 121–134.
Hofmann, M. A. (2001). Brain evolution in hominids: are we at the end of the road? In D. Falk & K. R. Gibson (eds.), Evolutionary anatomy of the primate cerebral cortex, pp. 113–127. Cambridge: Cambridge University Press.
Kant, S. , Bagaria, D. , & Ramakumar, S. (2002). Putative homeodomain proteins identified in prokaryotes based on pattern and sequence similarity. Biochem. Biophys. Res. Comm., 299, 229–232.
Keim, C. N. F. , Abreu, F. , Lins, U. , Lins de Barros, H. , & Farina, M. (2004). Cell organization and ultrastructure of a magnetotactic multicellular organism. J. Struct. Biol., 145, 254–262.
Kent, M. L. , Andree, K. B. , Bartholoew, J. L. et al. (2001). Recent advances in our knowledge of the Myxozoa. J. Eukaryotic Microbiol., 48, 395–413.
King, N. , Westbrook, M. J. , Young, S. L. et al. (2008). The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans. Nature, 451, 783–788.
Kloepper, T. H. , Kienle, C. N. , & Fasshauer, D. (2007). An elaborate classification of SNARE proteins sheds light on the conservation of the eukaryotic endomembrane system. Mol. Biol. Cell, 18, 3463–3471.
Kloepper, T. H. , Kienle, C. N. , & Fasshauer, D. (2008). SNAREing the basis of multicellularity: consequences of protein family expansion during evolution. Mol. Biol. Evol., 25, 2055–2068.
Kozmik, Z. (2008). The role of Pax genes in eye evolution. Brain Research Bull., 75, 335–339.
Kozmik, Z. , Daube, M. , Frei, E. et al. (2003). Role of Pax genes in eye evolution: a cnidarian PaxB gene uniting Pax2 and Pax6 functions. Dev. Cell, 5, 773–785.
Kozmik, Z. , Swamynathan, S. K. , Ruzickova, J. et al. (2008). Cubozoan crystallins: evidence for convergent evolution of pax regulatory sequences. Evol. Dev., 10, 52–61.
Kuch, U. , Müller, J. , Mödden, C. , & Mebs, D. (2006). Snake fangs from the Lower Miocene of Germany: evolutionary stability of perfect weapons. Naturwissenschaften, 98, 84–87.
Laughlin, S. B. , van Steveninck, R. R. de R. , & Anderson, J. C. (1998). The metabolic cost of neural information. Nature Neuroscience, 1, 36–41.
Li, Q. , Chen, Y. , & Yang, F. (2004). Identification of a collagen-like protein gene from white spot syndrome virus. Archives Virology, 149, 215–223.
Lüttge, U. (2004). Ecophysiology of crassulacean acid metabolism (CAM). Annals Botany, 93, 629–652.
McShea, D. W. (1998). Possible largest-scale trends in organismal evolution: eight ‘live hypotheses’. Annu. Rev. Ecol. Systematics, 29, 293–318.
McShea, D. W. (2002). A complexity drain on cells in the evolution of multicellularity. Evolution, 56, 441–452.
Macklem, P. T. (2008). Emergent phenomenon and the secrets of life. J. Applied Physiol., 104, 1844–1846.
Marino, L. , McShea, D. W. , & Uhen, M. D. (2004). Origin and evolution of large brains in toothed whales. Anatomical Record, 281A, 1247–1256.
Mineta, K. , Nakazawa, M. , Cebrià, F. , Ikeo, K. , Agata, K. , & Gojobori, T. (2003). Original and evolutionary process of the CNS elucidated by comparative genomics analysis of planarian ESTs. Proc. Natl. Acad. Sci. USA, 100, 7666–7671.
Mongodin, E. F. , Nelson, K. E. , Dougherty, S. et al. (2005). The genome of Salinibacter ruber: convergence and gene exchange among hyperhalophilic bacteria and archaea. Proc. Natl. Acad. Sci. USA, 102, 18147–18152.
Nickel, M. (2010). Evolutionary emergence of synaptic nervous systems: what can we learn from the non-synaptic, nerveless Porifera? Invertebrate Biol., 129, 1–16.
Pecoits, E. , Konhauser, K. O. , Aubet, R. R. et al. (2012). Bilaterian burrows and grazing behavior at >585 million years ago. Science, 336, 1693–1696.
Penrose, R. (1994). Shadows of the Mind: a Search for the Missing Science of Consciousness. Oxford: Oxford University Press.
Piraino, S. , Zega, G. , Di Benedetto, C. et al. (2011). Complex neural architecture in the diploblastic larva of Clava multicornis (Hydrozoa, Cnidaria). J. Comparative Neurology, 519, 1931–1951.
Puigbò, P. , Passamontes, A. , & Garcia-Vallve, S. (2008). Gaining and losing the thermophilic adaptation in prokaryotes. Trends Genetics, 24, 10–14.
Putnam, N. H. , Srivastava, M. , Hellsten, U. et al. (2007). Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization. Science, 317, 86–94.
Royo, J. L. , Maesto, I. , Irimia, M. et al. (2011). Transphyletic conservation of developmental regulatory state in animal evolution. Proc. Natl. Acad. Sci. USA, 108, 14186–14191.
Ryan, T. J. & Grant, S. G. N. (2009). The origin and evolution of synapses. Nature Reviews. Neurosci., 10, 701–712.
Sage, R. F. (2004). The evolution of C4 photosynthesis. New Phytol., 161, 341–370.
Salthe, S. N. (2008). Natural selection in relation to complexity. Artificial Life, 14, 363–374.
Schultz, T. R. & Brady, R. (2008). Major evolutionary transitions in ant agriculture. Proc. Natl. Acad. Sci. USA, 105, 5435–5440.
Setiawan, J. , Roccatagliata, V. , Fedele, D. et al. (2012). Planetary companions around the metal-poor star HIP 11952. Astronomy Astrophysics, 540, A141.
Srivastava, M. , Simakov, O. , Chapman, J. et al. (2010). The Amphimedon queenslandica genome and the evolution of animal complexity. Nature, 466, 720–726.
Tcherkez, G. G. B. , Farquhar, G. D. , & Andrews, T. J. (2006). Despite slow catalysis and confused substrate specificity all ribulose bisphosphate carboxylases may be nearly perfectly optimized. Proc. Natl. Acad. Sci. USA, 103, 7246–7251.
Thompson , D’Arcy, W. (1942). On Growth and Form. Cambridge: Cambridge University Press.
Valentine, J. W. (2000). Two genomic paths to the evolution of complexity in bodyplans. Paleobiology, 26, 513–519.
Waller, L. N. , Stump, N. J. , Fox, K. F. et al. (2005). Identification of a second collagen-like glycoprotein produced by Bacillus anthracis and demonstration of associated spore-specific sugars. J. Bacteriol., 187, 4592–4597.
Wang, C.-S. & St. Leger, R. J. (2006). A collagenous protective coat enables Metarhizium anisopliae to evade insect immune responses. Proc. Natl. Acad. Sci. USA, 103, 6647–6652.
Wickstead, B. , Gull, K. , & Richards, T. A. (2010). Patterns of kinesin evolution reveal a complex ancestral eukaryote with a multifunctional cytoskeleton. BMC Evolutionary Biol., 10, art. 110.
Zollikofer, C. P. E. , Ponco de Léon, M. S. , Lieberman, D. E. et al. (2005). Virtual cranial reconstruction of Sahelanthropus tchadensis. Nature, 434, 755–759.

Reference Title: References

Reference Type: reference-list

Askenasy, G. & Wagner, N. (2009). Symmetry and order in systems chemistry. The Journal of Chemical Physics, 130, 164907–164911S.
Hordijk, W. & Steel, M. (2004). Detecting autocatalytic, self-sustaining sets in chemical reaction systems. Journal of Theoretical Biology, 227, no. 4, 451–461.
Hordijk, W. , Steel, M. , & Kauffman, S. (2012). The structure of autocatalytic sets: evolvability, enablement and emergence. Acta Biotheoretica, 60, 379–392. Physics ArXiv 1205.0584v2.
Kant, I. (2000). The Critique of Judgment. Translated by J. H. Bernard . New York: Prometheus Books.
Kauffman, S. (1969). Metabolic stability and epigenesis in randomly constructed genetic nets. Journal of Theoretical Biology, 22, 437–467.
Kauffman, S. (1971). Cellular homeostasis, epigenesis and replication in randomly aggregated macromolecular systems. Journal of Cybernetics, 1, 71–96.
Kauffman, S. (1986). Autocatalytic sets of proteins. Journal of Theoretical Biology, 119, 1–24.
Kauffman, S. (1993). The Origins of Order: Self-organization and Selection in Evolution. New York: Oxford University Press.
Kauffman, S. (2000). Investigations. New York: Oxford University Press.
Kauffman, S. & Clayton, P. (2006). On emergence, agency, and organization. Phil-osophy and Biology, 21, 501–521.
Lam, M. & Joyce, G. (2009). Autocatalytic aptazymes: ligand-dependent exponential amplification of RNA. Nature Biotechnology, 37, 288–292.
Longo, G. , Montevil, M. , & Kauffman, S. (2012). No entailing laws, but enablement in the evolution of the biosphere. In Proceedings of the Fourteenth International Conference on Genetic and Evolutionary Computation Conference Companion, pp. 1379–1392. , Physics ArXiv 1201.2069v1 (Jan. 10, 2012), pp. 1–19.
Luisi, P. L. , Mavelli, F. , Rasi, S. , & Stano, P. (2004). A possible route to prebiotic vesicle reproduction. Artifical Life, 10, no. 3, 297–308.
Monod, J. (1995). Chance and Necessity: an Essay on the Natural Philosophy of Modern Biology. New York: Alfred A. Knopf.
Mossel, E. & Steel, M. (2005). Random biochemical networks: the probability of self-sustaining autocatalysis. Journal of Theoretical Biology, 233, 3, 327–336.
Piel, K. T. (2012). Emotion: a self-regulatory sense. Biophysical Psychological Review, 2 (in press, ).
von Kiedrowski, G. (1986). A self-replicating hexadesoxynucleotide. Angewandte Chemie. International Edition in English, 25, 982–912.

Reference Title: References

Reference Type: reference-list

Berg, I. A. , Kockelkorn, D. , Ramos-Vera, W. H. , et al. (2010). Autotrophic carbon fixation in archaea. Nature Rev. Microbiol., 8, 447–460.
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.
Boltzmann, L. (1905). Populate Schriften. Leipzig: J. A. Barth, re-issued Braunschweig: F. Vieweg, 1979.
Braakman, R. & Smith, E. (2012). The emergence and early evolution of biological carbon fixation. PLoS Comp. Biol., 8, el002455.
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.
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.
Buss, L. W. (2007). The Evolution of Individuality. Princeton, NJ: Princeton University Press.
Chaitin, G. J. (1966). On the length of programs for computing finite binary sequences. J. Assoc. Comp. Machinery, 13, 547–569.
Chaitin, G. J. (1990). Algorithmic Information Theory. New York: Cambridge University Press.
Chistoserdova, L. , Kalyuzhnaya, M. G. , & Lidstrom, M. E. (2009). The expanding world of methylotrophic metabolism. Ann. Rev. Microbiol., 63, 477–499.
Claverie, J.-M. (2006). Viruses take center stage in cellular evolution. Genome Biol., 7, 110:1–5.
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.
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.
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.
Copley, S. D. , Smith, E. , & Morowitz, H. J. (2010). The emergence of sparse metabolic networks. In M. Russel (ed.), Abiogenesis and the origins of life. Cambridge, MA: Cosmo. Sci. Publishers, pp. 175–191.
Cover, T. M. & Thomas, J. A. (1991). Elements of Information Theory. New York: Wiley.
Csete, M. & Doyle, J. (2004). Bow ties, metabolism and disease. Trends. Biotechnol., 22, 446–450.
Doolittle, F. (2000). Uprooting the tree of life. Set. Am., 282, 90–95.
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, .
Ellis, R. S. (1985). Entropy, Large Deviations, and Statistical Mechanics. New York: Springer-Verlag.
Fermi, E. (1956). Thermodynamics. New York: Dover.
Fisher, R. A. (2000). The Genetical Theory of Natural Selection. London: Oxford University Press.
Forterre, P. (2010). Defining life: the virus viewpoint. Orig. Life Evol. Biosphere, 40, 151–160.
Frank, S. A. (1997). The price equation, Fisher's fundamental theorem, kin selection, and causal analysis. Evolution, 51, 1712–1729.
Freidlin, M. I. & Wentzell, A. D. (1998). Random Perturbations in Dynamical Systems, second edn. New York: Springer.
Gell-Mann, M. (1994). The Quark and the Jaguar: Adventures in the Simple and the Complex. New York: Freeman.
Gell-Mann, M. & Lloyd, S. (1996). Information measures, effective complexity, and total information. Complexity, 2, 44–52.
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.
Glasstone, S. , Laidler, K. J. , & Eyring, H. (1941). The Theory of Rate Processes. New York: Mc-Graw Hill.
Gluckheimer, J. & Holmes, P. (1988). Structurally stable heteroclinic cycles. Math. Proc. Cam. Phil. Soc., 103, 189–192.
Goldenfeld, N. (1992). Lectures on Phase Transitions and the Renormalization Group. Boulder, CO: Westview Press.
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, .
Goldstein, H. , Poole, C. P. , & Safko, J. L. (2001). Classical Mechanics, third edn. New York: Addison Wesley.
Gould, S. J. (1989). Wonderful Life. New York: Norton.
Gould, S. J. (2002). The Structure of Evolutionary Theory. Cambridge, MA: Harvard University Press.
Gray, H. B. (1994). Chemical Bonds: an Introduction to Atomic and Molecular Structure. Sausalito, CA: University Science Press.
Hamilton, W. D. (1964a). The genetical evolution of social behavior. I. J. Theor. Biol., 7, 1–16.
Hamilton, W. D. (1964b). The genetical evolution of social behavior, II. J. Theor. Biol., 7, 17–52.
Hamilton, W. D. (1970). Selfish and spiteful behavior in an evolutionary model. Nature, 228, 1218–1220.
Huber, C. & Wächtershäuser, G. (2000). Activated acetic acid by carbon fixation on (Fe, Ni)s under primordial conditions. Science, 276, 245–247.
Hügler, M. & Seivert, S. M. (2011). Beyond the Calvin cycle: autotrophic carbon fixation in the ocean. Ann. Rev. Marine Sci., 3, 261–289.
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.
Jaynes, E. T. (1957a). Information theory and statistical mechanics. Phys. Rev., 106, 620–630. Reprinted in Rosenkrantz (1983).
Jaynes, E. T. (1957b). Information theory and statistical mechanics. II. Phys. Rev., 108, 171–190. Reprinted in Rosenkrantz (1983).
Jaynes, E. T. (1980). The minimum entropy production principle. Ann. Rev. Phys. Chem., 31, 579–601. Reprinted in Rosenkrantz (1983).
Kittel, C. & Kroemer, H. (1980). Thermal Physics, second edn. New York: Freeman.
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.
Kolmogorov, A. N. (1965). Three approaches to the definition of the quantity of information. Problems of Information Transmission, 1, 3–11.
Kondepudi, D. & Prigogine, I. (1998). Modern Thermodynamics: from Heat Engines to Dissipative Structures. New York: Wiley.
Koonin, E. V. & Martin, W. (2005). On the origin of genomes and cells within inorganic compartments. Trends Genet., 21, 647–654.
Krakauer, D. C. , Collins, J. P. , Erwin, D. et al. (2011). The challenges and scope of theoretical biology. J. Theor. Biol., 276, 269–276.
Lengeler, J. W. , Drews, G. , & Schlegel, H. G. (1999). Biology of the Prokaryotes. New York: Blackwell Science.
Lewontin, R. C. (1974). The Genetic Basis of Evolutionary Change. New York: Columbia University Press.
Li, M. & Vitányi, P. (2008). An Introduction to Kolmogorov Complexity and its Applications, third edn. Heidelberg: Springer.
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.
Luisi, P. L. (2006), The Emergence of Life: from Chemical Origins to Synthetic Biology. London: Cambridge University Press.
Ma, S.-K. (1976). Modern Theory of Critical Phenomena. New York: Perseus.
MacKenzie, R. E. (1984). Biogenesis and interconversion of substituted tetrahydrofolates. In R. L. Blakely & S. J. Benkovic (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.
Mahan, G. D. (1990). Many-particle Physics, second edn. New York: Plenum.
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.
Martin, W. & Russell, M. J. (2006). On the origin of biochemistry at an alkaline hydrothermal vent. Phil. Trans. Roy. Soc. B, , 1–39.
Martin, W. , Baross, J. , Kelley, D. , & Russell, M. J. (2008). Hydrothermal vents and the origin of life. Nature Rev. Microbiol., 6, 805–814.
Mézard, M. , Parisi, G. , Sourias, N. , Toulouse, G. , & Virasoro, M. (1984). Nature of the spin-glass phase, Phys. Rev. Lett., 52, 1156–1159.
Morowitz, H. J. (1992). Beginnings of Cellular Life. New Haven, CT: Yale University Press.
Morowitz, H. J. & Smith, E. (2007). Energy flow and the organization of life. Complexity, 13, 51–59. SFI preprint # 06-08-029.
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.
Nowak, M. A. & Ohtsuki, H. (2008). Prevolutionary dynamics and the origin of evolution. Proc. Nat. Acad. Set. USA, 105, 14924–14927.
Odling-Smee, F. J. , Laland, K. N. , & Feldman, M. W. (2003). Niche Construction: the Neglected Process in Evolution. Princeton, NJ: Princeton University Press.
Onsager, L. (1931a). Reciprocal relations in irreversible processes. I. Phys. Rev., 37, 405–426.
Onsager, L. (1931b). Reciprocal relations in irreversible processes. II. Phys. Rev., 38, 2265–2279.
Peretó, J. , López-García, P. , & Moreira, D. (2004). Ancestral lipid biosynthesis and early membrane evolution. Trends Biochem. Sci., 29, 469–477.
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, .
Quastler, H. (1964). The Emergence of Biological Organization. New Haven, CT: Yale University Press.
Riehl, W. J. , Krapivsky, P. L. , Redner, S. , & Segrè, D. (2010). Signatures of arithmetic simplicity in metabolic network architecture. Biol., 6 (4), e100725, .
Rissanen, J. (1989). Stochastic Complexity in Statistical Inquiry. Teaneck, NJ: World Scientific.
Rodrigues, J. a. F. M. & Wagner, A. (2009). Evolutionary plasticity and innovations in complex metabolic reaction networks. PLoS Computational Biology, 5, el000613:l-11.
Rosenkrantz, R. D. (ed.) (1983), Jaynes, E. T.: Papers on Probability, Statistics and Statistical Physics. Dordrecht, Holland: D. Reidel.
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.
Russell, M. J. & Hall, A. J. (2006). The onset and early evolution of life. Geol. Soc. Am. Memoir, 198, 1–32.
Russell, M. J. & Martin, W. (2004). The rocky roots of the acetyl-coa pathway. Trends Biochem. Sci., 29, 358–363.
Schrödinger, E. (1992). What is Life?: the Physical Aspect of the Living Cell. New York: Cambridge University Press.
Sherrington, D. (2010). Physics and complexity. Phil. Trans.R. Soc. A, 368, 1175–1189.
Simon, H. A. (1962). The architecture of complexity. Proc. Am. Phil. Soc., 106, 467–482.
Simon, H. A. (1973). The organization of complex systems. H. H. Pattee (ed.), Hierarchy Theory: the Challenge of Complex Systems. New York: George Braziller, pp. 3–27.
Sinai, Y. G. (1959). On the notion of entropy of a dynamical system. Doklady of Russian Academy of Sciences, 124, 768–771.
Smith, E. (1998). Carnot's theorem as Noether's theorem for thermoacoustic engines. Phys. Rev. E, 58, 2818–2832.
Smith, E. (1999). Statistical mechanics of self-driven Carnot cycles. Phys. Rev. E, 60, 3633–3645.
Smith, E. (2003). Self-organization from structural refrigeration. Phys. Rev. E, 68, 046114. SFI preprint # 03-05-032.
Smith, E. (2005). Thermodynamic dual structure of linearly dissipative driven systems. Phys. Rev. E, 72, 36130. SFI preprint # 05-08-033.
Smith, E. (2008a). Thermodynamics of natural selection I: Energy and entropy flows through non-equilibrium ensembles. J. Theor. Biol., 252, 2, 185–197.
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. .
Smith, E. & Morowitz, H. J. (2004). Universality in intermediary metabolism. Proc. Nat. Acad. Set. USA, 101, 13168–13173. SFI preprint # 04-07-024.
Smith, E. & Morowitz, H. J. (2010). The autotrophic origins paradigm and small-molecule organocatalysis. Orig. Life Evol. Biosphere, 40, 397–402.
Srinivasan, V. & Morowitz, H. J. (2009a). Analysis of the intermediary metabolism of a reductive chemoautotroph. Biol. Bulletin, 217, 222–232.
Srinivasan, V. & Morowitz, H. J. (2009b). The canonical network of autotrophic intermediary metabolism: minimal metabolome of a reductive chemoautotroph. Biol. Bulletin, 216, 126–130.
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.
Stryer, L. (1981). Biochemistry, second edn. San Francisco, CA: Freeman.
Touchette, H. (2009). The large deviation approach to statistical mechanics. Phys. Rep., 478, 1–69. arxiv:0804.0327.
Vetsigian, K. , Woese, C. , & Goldenfeld, N. (2006). Collective evolution and the genetic code. Proc. Nat. Acad. Set. USA, 103, 10696–10701.
Wächtershäuser, G. (1988). Before enzymes and templates: a theory of surface metabolism. Microbiol. Rev., 52, 452–484.
Wächtershäuser, G. (1990). Evolution of the first metabolic cycles. Proc. Nat. Acad. Set. USA, 87, 200–204.
Weinberg, S. (1995). The Quantum Theory of Fields, Vol. I: Foundations. New York: Cambridge.
Weinberg, S. (1996). The Quantum Theory of Fields, Vol. II: Modern applications. New York: Cambridge.
Wilson, K. G. & Kogut, J. (1974). The renormalization group and the ε expansion. Phys. Rep., Phys. Lett., 12C, 75–200.
Woese, C. R. (1987). Bacterial evolution. Microbiol. Rev., 51, 221–271.
Woese, C. R. (2000). Interpreting the universal phylogenetic tree. Proc. Nat. Acad. Set. USA, 97, 8392–8396.
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.

Reference Title: References

Reference Type: reference-list

Adami, C. , Ofria C. , & Collier, T. (2000). Evolution of biological complexity. Proc. Nat. Acad. Sci., 6, 363–376.
Barnsley, M. & Hurd, L. (1993). Fractal Image Compression. A. K. Boca Raton, FL: Peters/CRC Press.
Carroll, S. (2001). Chance and necessity: the evolution of morphological complexity and diversity. Nature, 409, 1102–1109.
Davies, P. (2006). The Origin of Life. London: Penguin.
Eigen, M. (2000). Natural selection: a phase transition? Biophysical Chemistry, 85, 101–123.
Faerna, J. M. (1997). Mondrian Harry N. New York: Abrams.
Farmelo, G. (2011). The Strangest Man. The Hidden Life of Paul Dirac, Mystic of the Atom. New York: Basic Books (AZ).
Gell-Mann, M. (1995). The Quark and the Jaguar. Adventures in the Simple and the Complex. New York: St. Martin's Griffin.
Gillespie, J. (2004). Population Genetics: a Concise Guide. Baltimore: JHU Press.
Gould, S. (2002). The Structure of Evolutionary Theory. Cambridge, MA: Harvard University Press.
Keynes, J. M. (1923). A Tract on Monetary Reform. Amherst, NY: Reprinted by Prometheus Books (April 2000).
Krakauer, D. C. (2011). Darwinian demons, evolutionary complexity, and information maximization. Chaos, 41, 037110–037110-12.
McShea, D. W. (1991). Complexity and evolution: what everybody knows. Biology and Philosophy, 6, 303–324.
Mehra, J. & Rechenberg, H. (2000). The Historical Development of Quantum Theory. New York: Springer.
Nowak, M. A. (2006). Evolutionary Dynamics: Exploring the Equations of Life. Cambridge, MA: Belknap Press.
Ruse, M. (2009). Monad to Man. The Concept of Progress in Evolutionary Biology. Cambridge, MA: Harvard University Press.
Ruse, M. & Travis, J. (2009). Evolution. The First Four Billion Years. Cambridge, MA: Belknap Press.
Smith, J. M. & Szathmary, E. (1999). The Origins of Life. From the Birth of Life to the Origin of Language. New York: Oxford University Press.
Zhang, J. (2009). Adaptive learning via selectionism and Bayesianism, Part I: Connection between the two. Neural Networks, 22(3) (April): 220228. .

Reference Title: References

Reference Type: reference-list

Adams, M. , Dogic, Z. , Keller, S. , & Fraden, S. (1998). Entropically driven microphase transitions in mixtures of colloidal rods and spheres. Nature, 393, 349–352.
Asakura, S. & Oosawa, F. (1958). J. Polym. Sci., 33, 183.
Brillouin, L. (1953). Negentropy principle of information. Journal of Applied Physics, 24, 1152–1163.
Brillouin, L. (1962). Science and Information Theory. New York: Academic Press.
Carroll, S. (2001). Chance and necessity: the evolution of morphological complexity and diversity. Nature, 409, 1102–1109.
Cover, T. & Thomas, J. (1991). Elements of Information Theory. New York: Wiley-Interscience.
Crocker, J. C. , Matteo, J. A. , Dinsmore, A. D. , & Yodh, A. G. (1999). Entropie attraction and repulsion in binary colloids probed with a line optical tweezer. Physical Review Letters, 82, 4352–4355. .
Götzelmann, B. , Evans, R. , & Dietrich, S. (1998). Depletion forces in fluids. Phys. Rev. E, 57, 6785–6800. .
Grandy, W. T., J. (2008). Entropy and the Time Evolution of Macroscopic Systems. Oxford: Oxford University Press.
Gray, M. W. , Luke, J. , Archibald, J. M. , Keeling, P. J. , & Doolittle, W. F. (2010). Irremediable complexity? Science, 330(6006), 920–921.
Grinstein, G. & Linsker, R. (2007). Comments on a derivation and application of the ‘maximum entropy production’ principle. J. Phys. A: Math. Theor., 40, 971720.
Grosse, I. , Bernaola-Galvan, P. , Carpena, P. , Roman-Roldan, R. , Oliver, J. , & Stanley, H. E. (2002). Analysis of symbolic sequences using the Jensen–Shannon divergence measure. Phys. Rev. E, 65, 041905.
Ho, M. (1994). What is negentropy? Modern Trends in BioThermoKinetics, 3, 50–61.
Kauffman, S. A. (1995). At Home in the Universe: the Search for the Laws of Self-Organization and Complexity. New York: Oxford University Press.
Krakauer, D. (2011). Darwinian demons, evolutionary complexity, and information maximization. Chaos. 21, 037110, .
Lebon, G. , Jou, D. , & Casas-Vazquez, J. (2008). Understanding Non-equilibrium Thermodynamics: Foundations, Applications, Frontiers. New York: Springer-Verlag.
Mackay, D. (2003). Information Theory, Inference, and Learning Algorithms. Cambridge: Cambridge University Press.
Mahulikar, S. & Herwig, H. (2009). Exact thermodynamic principles for dynamic order existence and evolution in chaos. Chaos, Solitons and Fractals, 41, 1939–1948.
Marenduzzo, D. , Finan, K. , & Cook, P. (2006). The depletion attraction: an underappreciated force driving cellular organization. Journal of Cell Biology, 5, 681–686.
Martyushev, L. & Seleznev, V. (2006). Maximum entropy production principle in physics, chemistry and biology. Physics Reports, 426, 1–45.
McShea, D. (1991). Complexity and evolution: what everybody knows. Biology and Philosophy, 6, 303–324.
Morowitz, H. (1968). Energy Flow in Biology. Waltham, MA: Academic Press.
Morowitz, H. & Smith, E. (2007). Energy flow and the organization of life. Complexity, 13, 51–59.
Onsager, L. (1931a). Reciprocal relations in irreversible processes: 1. Physical Review, 37, 405.
Onsager, L. (1931b). Reciprocal relations in irreversible processes: 2. Physical Review, 38, 2265.
Paltridge, G. (1979). Climate and thermodynamic systems of maximum dissipation. Nature, 279, 5714.
Parrott, L. (2010). Measuring ecological complexity. Ecological Indicators, 10(6), 1069–1076.
Prigogine, I. (1945). Moderation et transformations irreversibles des systemes ouverts. Bulletin de la Classe des Sciences, Académie Royale de Belgique, 31, 600–606.
Proulx, R. & Parrott, L. (2008). Measures of structural complexity in digital images for monitoring the ecological signature of an old-growth forest ecosystem. Ecological Indicators, 8(3), 270–284.
Schrödinger, E. (1944). What is Life? Cambridge: Cambridge University Press.
Smith, E. (2008a). Thermodynamics of natural selection i: Energy flow and the limits on organization. Journal of Theoretical Biology, 252(2), 185–197.
Smith, E. (2008b). Thermodynamics of natural selection ii: Chemical carnot cycles. Journal of Theoretical Biology, 252(2), 198–212.
Smith, E. (2008c). Thermodynamics of natural selection iii: Landauer's principle in computation and chemistry. Journal of Theoretical Biology, 252(2), 213–220.
Smith, J. M. (1970). Time in the evolutionary process. Studium Generale, 23, 266–272.
Stanley, M. H. R. , Amaral, L. A. N. , Buldyrev, S. Y. et al. (1996). Scaling behaviour in the growth of companies. Nature, 379, 804–806.
Verma, R. , Crocker, J. C. , Lubensky, T. C. , & Yodh, A. G. (1998). Entropie colloidal interactions in concentrated dna solutions. Physics Review Letters, 81, 4004–4007, .
Wolpert, D. (2012). How to salvage Shannon entropy as a complexity measure. Submitted.
Wolpert, D. H. & Macready, W. (2000). Self-dissimilarity: an empirically observable measure of complexity. In Y. Bar-Yam (ed.), Unifying Themes in Complex Systems. New York: Perseus Books, pp. 626–643.
Wolpert, D. H. & Macready, W. (2004). Self-dissimilarity as a high dimensional complexity measure. In Y. Bar-Yam (ed.), Proceedings of the Fifth International Conference on Complex Systems. New York: Perseus Books.
Wolpert, D. H. & Macready, W. (2007). Using self-dissimilarity to quantify complexity. Complexity, 12, 77–85.

Reference Title: References

Reference Type: reference-list

Barrett, P. H. , Gautrey, P. J. , Herbert, S. , Kohn, D. , & Smith, S. (eds.) (1987). Charles Darwin's Notebooks, 1836–1844. Ithaca, NY: Cornell University Press.
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.
Darwin, C. (1861). Origin of Species (Third Edition). London: John Murray.
Darwin, C. (1985). The Correspondence of Charles Darwin. Cambridge: Cambridge University Press.
Dawkins, R. (1986). The Blind Watchmaker. New York, NY: Norton.
Dawkins, R. (1989). The evolution of evolvability. In C. G. Langton (ed.), Artificial Life. 201–20. Redwood City, CA.: Addison-Wesley.
Dawkins, R. (1992). Progress. In E. F. Keller & E. Lloyd (eds.), Keywords in Evolutionary Biology. 263–272. Cambridge, MA: Harvard University Press.
Dawkins, R. (1997). Human chauvinism: review of Full House by Stephen Jay Gould. Evolution 51, 3, 1015–1020.
Dawkins, R. (2003). A Devil's Chaplain: Reflections on Hope, Lies, Science and Love. Boston and New York: Houghton Mifflin.
Dawkins, R. & Krebs, J. R. (1979). Arms races between and within species. Proceedings of the Royal Society of London, B, 205, 489–511.
Fisher, R. A. (1930). The Genetical Theory of Natural Selection. Oxford: Oxford University Press.
Ford, E. B. (1931). Mendelism and Evolution. London: Methuen.
Goodwin, B. (2001). How the Leopard Changed its Spots, Second Edition. Princeton: Princeton University Press.
Gould, S. J. (1996). Full House: the Spread of Excellence from Plato to Darwin. New York, NY: Paragon.
Gray, J. L. (1894). Letters of Asa Gray. Boston: Houghton, Mifflin.
Gregory, T. R. (2001). Coincidence, coevolution, or causation? DNA content, cell size, and the C-value enigma. Biological Reviews, 76, 65–101.
Huxley, J. S. (1912). The Individual in the Animal Kingdom. Cambridge: Cambridge University Press.
Jerison, H. (1973). Evolution of the Brain and Intelligence. New York, NY: Academic Press.
Kauffman, S. A. (1995). At Home in the Universe: the Search for the Laws of Self-Organization and Complexity. New York: Oxford University Press.
McShea, D. & Brandon, R. (2010). Biology's First Law: the Tendency for Diversity and Complexity to Increase in Evolutionary Systems. Chicago: University of Chicago Press.
Maynard Smith, J. & Szathmary, E. (1995). The Major Transitions in Evolution. New York: Oxford University Press.
Provine, W. B. (1971). The Origins of Theoretical Population Genetics. Chicago: University of Chicago Press.
Provine, W. B. (1986). Sewall Wright and Evolutionary Biology. Chicago: University of Chicago Press.
Richards, R. J. (1987). Darwin and the Emergence of Evolutionary Theories of Mind and Behavior. Chicago: University of Chicago Press.
Ruse, M. (1980). Charles Darwin and group selection. Annals of Science, 37, 615–630.
Ruse, M. (1996). Monad to Man: the Concept of Progress in Evolutionary Biology. Cambridge, MA: Harvard University Press.
Ruse, M. (1999). The Darwinian Revolution: Science Red in Tooth and Claw. Second edn. Chicago: University of Chicago Press.
Ruse, M. (2004). Adaptive landscapes and dynamic equilibrium: the Spencerian contribution to twentieth-century American evolutionary biology. In A. Lustig , R. J. Richards , & M. Ruse (eds.), Darwinian Heresies, 131–50. Cambridge: Cambridge University Press.
Ruse, M. (2006). Darwinism and its Discontents. Cambridge: Cambridge University Press.
Ruse, M. (2013a). The Cambridge Encyclopedia of Darwin and Evolution. Cambridge: Cambridge University Press.
Ruse, M. (2013b). Gaia in Context: Plato to Pagans. Chicago: University of Chicago Press.
Spencer, H. (1852). A theory of population, deduced from the general law of animal fertility. Westminster Review, 1, 468–501.
Spencer, H. (1857). Progress: its law and cause. Westminster Review, LXVII, 244–267.
Spencer, H. (1862). First Principles. London: Williams and Norgate.
Spencer, H. 1864. Principles of Biology. London: Williams and Norgate.
Thompson, D. W. (1917). On Growth and Form. Cambridge: Cambridge University Press.
Whewell, W. (1840). The Philosophy of the Inductive Sciences. London: Parker.
Wright, S. (1931). Evolution in Mendelian populations. Genetics, 16, 97–159.
Wright, S. (1932). The roles of mutation, inbreeding, crossbreeding and selection in evolution. Proceedings of the Sixth International Congress of Genetics, 1, 356–66.

Reference Title: References

Reference Type: reference-list

Arthur, B. (1994). Increasing Returns and Path-Dependence in the Economy. Ann Arbor: Michigan University Press.
Arthur, B. (2009). The Nature of Technology. New York: Macmillan.
Arthur, W. (1997). The Origin of Animal Body Plans: a Study in Evolutionary Developmental Biology. Cambridge: Cambridge University Press.
Azevedo, R. , Lohaus, R. , Srinavasan, S. , Dang, K. , & Burch, C. (2006). Sexual reproduction selects for robustness and negative epistasis in artificial gene networks. Nature, 440/2, 87–90.
Bonner, J. T. (1965). Size and Cycle. Princeton: Princeton University Press.
Boyd, R. & Richerson, P. (1985). Culture and the Evolutionary Process. Chicago: University of Chicago Press.
Britten, R. J. (1986). Rates of DNA sequence evolution differ between taxonomic groups. Science, 231, 1393–1398.
Campbell, D. T. (1974). Evolutionary epistemology. In P. A. Schilpp (ed.), The Philosophy of Karl Popper, II. LaSalle, IL: Open Court, 413–463.
Caporael, L. (1995). Sociality: coordinating bodies, minds and groups. Psycoloquy, 6(01), Group Selection (1)..
Caporael, L. (1997). The evolution of truly social cognition: the core configuration model. Personality and Social Psychology Review, 1, 276–298.
Caporael, L. , Griesemer, J. , & Wimsatt, W. (eds.) (2013). Developing Scaffolding in Evolution, Cognition and Culture. Cambridge, MA: MIT Press.
Glassman, R. B. & Wimsatt, W. C. (1984). Evolutionary advantages and limitations of early plasticity. In R. Almli and S. Finger (eds.). Early Brain Damage, volume I, Academic Press, 35–58.
Griesemer, J. R. (2000). Development, culture and the units of inheritance. Philosophy of Science, 67, (Proceed) S348–S368.
Hounshell, D. A. (1984). From the American System to Mass Production, 1800–1932: The Development of Manufacturing Technology in the United States. Baltimore: The Johns Hopkins Press.
Kauffman, S. A. (1985). Self-organization, selective adaptation and its limits: a new pattern of inference in evolution and development. In D. J. Depew & Bruce H. Weber (eds.). Evolution at a Crossroads: the New Biology and the New Philosophy of Science. Cambridge, MA: MIT press.
Kauffman, S. (1993). The Origins of Order. Oxford: Oxford University Press.
Kirchner, M. & Gerhart, J. (2005). The Plausibility of Life: Resolving Darwin's Dilemma. New York: W. J. Norton.
Lewontin, R. C. (1970). The units of selection. Annual Review of Ecology and Systematics, 1, 1–18.
Livnat, A. , Papadimution, C. , Dashhoft, J. , & Feldman, M. V. (2008). A mixability theory for the role of sex in evolution. PNAS, 105, 19803–19808.
Lynch M. , Burger, R. , & Gabriel, W. (1993). The mutational meltdown in asexual populations. Journal of Heredity, 84: 339–344.
Mackie, G. (1996). Ending footbinding and fibulation: a convention account. American Sociological Review, 61, 999–1017.
Maynard Smith, J. & Szathmary, E. (1995). The Major Transitions in Evolution. Oxford: Oxford University Press.
Morange, M. (2000). Molecular Biology, a Short History. Cambridge, MA: Harvard University Press.
Morowitz, H. (1992). The Origins of Cellular Life. New Haven: Yale University Press.
Newman, S. & Bhat, R. (2009). Dynamical patterning modules: a “pattern language” for development and evolution of multicellular form. Int. J. Dev. Biol., 53, 693–705.
Raff, R. (1996). The Shape of Life: Genes, Development and the Evolution of Animal Form. Chicago: University of Chicago Press.
Rasmussen, N. (1987). A new model of developmental constraints as applied to the Drosophila system. J. Theoretical Biology, 127, 3, 271–301.
Riedl, R. (1978). Order in Living Organisms: a Systems Analysis of Evolution. New York: J. H. Wiley (translation of German original, 1975).
Sander, K. (1983). The evolution of patterning mechanisms: cleanings from insect embryogenesis and spermatogenesis. In B. C. Goodwin , N. Holder , & C. C. Wylie (eds.). Development and Evolution, pp. 137–159. Cambridge: Cambridge University Press.
Schank, J. C. , Wimsatt, W. C. (1988). Generative entrenchment and evolution. In A. Fine and P. K. Machamer (eds.). PSA-1986, volume II. East Lansing: The Philosophy of Science Association, pp. 33–60.
Schank, J. C. & Wimsatt, W. C. (2001). Evolvability: adaptation, and modularity. In R. Singh , K. Krimbas , D. Paul and J. Beatty . (eds.). Thinking about Evolution: Historical, Philosophical and Political Perspectives: Festschrift for Richard Lewontin. Cambridge: Cambridge University Press.
Simon, H. A. (1955). A behavioral theory of rational choice. Quarterly Journal of Economics, 69, 99–118.
Simon, H. A. (1962). The Architecture of Complexity. Philadelphia: American Philosophical Society, reprinted in The Sciences of the Artificial, 3rd. edn. (1996). Cambridge, MA: MIT Press.
Sterelny, K. (2012). The Evolved Apprentice. 2008 Jean Nicod lectures (expanded). Cambridge: MIT Press.
Szathmary, E. & Maynard Smith, J. (1997). From replicators to reproducers: the first major transitions leading to life. Journal of Theoretical Biology, 187, 555–571.
Wagner, A. (2005). Robustness and Evolvability in Living Systems. Princeton: Princeton University Press.
Williams, G. C. (1966). Adaptation and Natural Selection. Princeton: Princeton University Press.
Wilson, R. & Clark, A. (2009). How to situate cognition: letting nature take its course. In M. Aydede and P. Robbins (eds.). The Cambridge Handbook of Situated Cognition. London: Blackwell, pp. 55–77.
Wimsatt, B. (2013). Scaffolding a career. In L. Caporael , J. Griesemer , and W. Wimsatt (eds.). Developing Scaffolds in Evolution, Culture and Cognition. Cambridge, MA: MIT Press.
Wimsatt, W. C. (1980). Randomness and perceived-randomness in evolutionary biology. Synthese, 43, 287–329.
Wimsatt, W. C. (1981a). Robustness, reliability, and multiple-determination. In M. Brewer & B. Collins (eds.). Scientific Inquiry and the Social Sciences. San Francisco: Jossey-Bass, pp. 124–163. Reprinted as chapter 4 in Wimsatt (2007a).
Wimsatt, W. C. (1981b). Units of selection and the structure of the multi-level genome. In P. D. Asquith and R. N. Giere (eds.). PSA-1980, vol. 2. Lansing, MI: The Philosophy of Science Association, 122–183.
Wimsatt, W. C. (1986). Developmental constraints, generative entrenchment, and the innate-acquired distinction. In P. W. Bechtel (ed.) Integrating Scientific Disciplines. Dordrecht: Martinus-Nijhoff, pp. 185–208.
Wimsatt, W. (1991). Taming the dimensions – visualizations in science. In M. Forbes , L. Wessels , & A. Fine (eds.). PSA-1990, vol. 2. East Lancing, The Philosophy of Science Association, pp. 111–135.
Wimsatt, W. C. (1999). Genes, memes, and cultural inheritance. Biology and Philosophy, special issue on influence of R. C. Lewontin, 14, 279–310.
Wimsatt, W. C. (2001). The generative entrenchment approach to evolving systems. In S. Oyama , R. Gray , & P. Griffiths (eds.). Cycles of Contingency: Developmental Systems and Evolution. Cambridge, MA: MIT Press, 219–238.
Wimsatt, W. C. (2006a). Inconsistencies, optimization and satisficing – steps towards a philosophy for limited beings: commentary on Russell Hardin. In C. Engel & L. Daston (eds.). Is There Value in Inconsistency? Common Goods: Law, Politics, Economics, vol. 15,Baden-Baden, Germany: Nomos Verlagsgesellschaft, pp. 201–220.
Wimsatt, W. C. (2006b). Optimization, consistency, and kluged adaptations: can maximization survive? Comment on Kachalnik et al., In C. Engel & L. Daston (eds.). Is There Value in Inconsistency? Common Goods: Law, Politics, Economics, vol. 15, Baden-Baden, Germany: Nomos Verlagsgesellschaft, pp. 399–420.
Wimsatt, W. C. (2007a). Re-Engineering Philosophy for Limited Beings: Piecewise Approximations to Reality. Cambridge, MA: Harvard University Press.
Wimsatt, W. C. (2007b). On building reliable pictures with unreliable data: an evolutionary and developmental coda for the new systems biology. In F. C. Boogerd , F. J. Bruggeman , J.-H. S. Hofmeyer , & H. V. Westerhoff , (eds.). Systems Biology: Philosophical Foundations. Amsterdam: Reed-Elsevier, pp. 103–120.
Wimsatt, W. C. (2007c). Echoes of Haeckel? Re-entrenching development in evolution. In J. Maienschein and M. Laubichler (eds.). Evolution and Development, Cambridge, MA: MIT Press, pp. 309–355.
Wimsatt, W. C. (2010). Memetics does not provide a useful way of understanding cultural evolution: a developmental perspective (paired with Susan Blackmore arguing for memetics). In F. Ayala & R. Arp (eds.). Current Controversies in Philosophy of Biology. London: Blackwell, 273–291.
Wimsatt, W. C. (2013a). Entrenchment as a theoretical tool in evolutionary developmental biology. In A. C. Love (ed.). Conceptual Change in Biology: Scientific and Philosophical Perspectives on Evolution and Development. Berlin: Springer (Boston Studies in Philosophy of Science).
Wimsatt, W. C. (2013b). Evolution and the stability of functional architectures Philipe Huneman (ed.), CNRS Conference on Function and Teleology. Cambridge, MA: MIT Press.
Wimsatt, W. C. & Griesemer, J. R. (2007). Reproducing entrenchments to scaffold culture: the central role of development in cultural evolution. In R. Sansom & R. Brandon (eds.). Integrating Evolution and Development: from Theory to Practice. Cambridge, MA: MIT Press, pp. 228–323.
Wimsatt, W. C. & Schank, J. C. (1988). Two constraints on the evolution of complex adaptations and the means for their avoidance. In M. Nitecki . (ed.), Evolutionary Progress. East Lansing, MI: University of Chicago Press, 231–273.
Wimsatt, W. C. & Schank, J. C. (2004). Generative entrenchment, modularity and evolvability: when genic selection meets the whole organism. In G. Schlosser and G. Wagner (eds.). Modularity in Evolution and Development. Chicago: University of Chicago Press, pp. 359–394.
Woese, C. (2002). On the evolution of cells. PNAS, 99(13), 8742–8747.

Reference Title: References

Reference Type: reference-list

Auyang, S. (1998). Foundations of complex-system theories Economics, Evolutionary Biology, and Statistical Physics. Cambridge: Cambridge University Press.
Clayton, P. (1989). Explanation from Physics to Theology: an Essay in Rationality and Religion. New Haven, CT: Yale University Press.
Clayton, P. (2009). In Quest of Freedom: The Emergence of Spirit in the Natural World. Göttingen: Vandenhoeck & Ruprecht.
Dilthey, W. (2010). Understanding the Human World. In R. A. Makkreel & F. Rodi . (eds.), Wilhelm Dilthey, selected Works, II. Princeton, NJ: Princeton University Press.
Durham, W. H. (1991). Coevolution: Genes, Culture, and Human Diversity. Stanford: Stanford University Press.
Hoffmeyer, J. (2008). Biosemiotics: an Examination into the Signs of Life and the Life of Signs, trans. J. Hoffmeyer & D. Favareau . Scranton: University of Scranton Press.
Joslyn, C. (2000). Levels of control and closure in complex semiotic systems. In J. Chandler & G. van de Vijver (eds.), Closure: Emergent Organizations and their Dynamics. Annals of the New York Academy of Science Series, Volume 901. New York: New York Academy of Sciences, 67–74.
Kauffman, S. & Clayton, P. (2006). On emergence, agency, and organization. Philosophy and Biology, 21, 501–21.
Lemke, J. (2000). Opening up closure: semiotics across scales. In J. Chandler & G. van de Vijver . (eds.), Closure: Emergent Organizations and their Dynamics, Annals of the New York Academy of Science Series, Volume 901. New York: New York Academy of Sciences, 100–111.
Lindlof, T. R. (2008). Idiographic vs nomothetic science. In W. Donsbach (ed.), The International Encyclopedia of Communication, .
Nagel, E. (1961). The Structure of Science: Problems in the Logic of Scientific Explanation. London: Routledge and Kegan Paul.
Palsson, B. (2006). Systems Biology: Properties of Reconstructed Networks. Cambridge: Cambridge University Press.
Wilson, E. O. (1998). Consilience: the Unity of Knowledge. New York: Knopf.