A formal approach to evolution as self-referential language

BioSystems

Volumn 106, Issue 1, 2011, Pages 36-44

  Wallace, Rodrick ^a  

^a NEW YORK STATE PSYCHIATRIC INSTITUTE   (United States)

Author keywords

Evolution; Groupoid; Information theory; Large deviations; Morse function; Punctuation; Renormalization

Indexed keywords

GENE EXPRESSION; LANGUAGE; METHODOLOGY; NUMERICAL MODEL; RIVER BANK;

ARTICLE; BIOLOGICAL PHENOMENA AND FUNCTIONS CONCERNING THE ENTIRE ORGANISM; EVOLUTION; EVOLUTION TRANSITION; HUMAN; KADANOFF THEORY; LANGUAGE; MEDICAL INFORMATION; NETWORK INFORMATION THEORY; NONHUMAN; PHASE TRANSITION; RIPARIAN ECOSYSTEM; SELF REFERENTIAL LANGUAGE; THEORY;

EID: 80052394780     PISSN: 03032647     EISSN: 18728324     Source Type: Journal    
DOI: 10.1016/j.biosystems.2011.06.003     Document Type: Article

References (39)

1. Ash R. Information Theory 1990, Dover, New York.
2. Bennett C. Logical depth and physical complexity. The Universal Turing Machine: A Half-Century Survey 1988, 227-257. Oxford University Press. R. Herkin (Ed.).
3. Brown R. From groups to groupoids: a brief survey. Bulletin of the London Mathematical Society 1987, 19:113-134.
4. Canfield D., Rosing M., Bjerrum C. Early anaerobic metabolisms. Philosophical Transactions of the Royal Society B 2006, 361:1819-1836.
5. Cannas Da Silva A., Weinstein A. Geometric Models for Noncommutative Algebras 1999, American Mathematical Society, Providence, RI.
6. Champagnat N., Ferriere R., Meleard S. Unifying evolutionary dynamics: from individual stochastic process to macroscopic models. Theoretical Population Biology 2006, 69:297-321.
7. Cover T., Thomas J. Elements of Information Theory 2006, John Wiley and Sons, New York. 2nd edition.
8. Dembo A., Zeitouni O. Large Deviations and Applications 1998, Springer, New York. 2nd edition.
9. El Gamal, A., Kim, Y., 2010. Lecture Notes on Network Information Theory. arXiv:1001.3404v4.
10. Eldredge N., Gould S. Punctuated equilibrium: an alternative to pyletic gradualism. Models in Paleobiology 1972, Freeman Cooper and Co., San Francisco. T. Schopf (Ed.).
11. Emery M. Stochastic Calculus in Manifolds, Universititext series 1989, Springer, New York.
12. Feynman R. Lectures on Computation 2000, Westview Press, New York.
13. Gabora L., Aerts D. Evolution as context-driven actualization of potential: toward an interdisciplinary theory of change of state. Interdisciplinary Science Reviews 2005, 30:69-88.
14. Gabora L., Aerts D. A cross-disciplinary framework for the description of contextually mediated change. Electronic Journal of Theoretical Physics 2007, 4:1-22.
15. Goldenfeld, N., Woese, C., 2010. Life is physics: evolution as a collective phenomenon far from equilibrium. ArXiv:1011.4125v1 [q-bio.PE].
16. Goldenfeld, N., 2010. Personal communication.
17. Golubitsky M., Stewart I. Nonlinear dynamics and networks: the groupoid formalism. Bulletin of the American Mathematical Society 2006, 43:305-364.
18. Kastner, M., 2006. Phase transitions and configuration space topology. ArXiv cond-mat/0703401.
19. Khinchin A. Mathematical Foundations of Information Theory 1957, Dover, New York.
20. Landau L., Lifshitz L. Statistical Physics, 3rd edition, Part 1 2007, Elsevier, New York.
21. Langton C. Life at the edge of chaos. Artificial Live II 1992, Addison-Wesley, Reading, MA. C. Langton, C. Taylor, J. Farmer, S. Rasmussen (Eds.).
22. Matsumoto Y. An Introduction to Morse Theory. Translations of Mathematical Monographs, vol. 208 2002, American Mathematical Society.
23. Milnor J. Morse Theory. Annals of Mathematical Studies, vol. 51 1963, Princeton University Press.
24. Odling-Smee F., Laland K., Feldman M. Niche Construction: The Neglected Process in Evolution 2003, Princeton University Press, Princeton, NJ.
25. Pettini M. Geometry and Topology in Hamiltonian Dynamics and Statistical Mechanics 2007, Springer, New York.
26. Pielou E. Mathematical Ecology 1977, John Wiley and Sons, New York.
27. Roca C., Cuesta J., Sanchez A. Evolutionary game theory: temporal and spatial effects beyond replicator dynamics. Physicsl of Life Reviews 2009, 6:208-249.
28. Sereno M. Four analogies between biological and cultural/linguistic evolution. Journal of Theoretical Biology 1991, 151:467-507.
29. Shannon C. Two-way communication channels. Proceedings of the 4th Berkeley Symposium in Mathematical Statistics and Proability, vol. 1 1961, University of California Press, pp. 611-644.
30. Taylor P., Jonker L. Evolutionarily stable strategies and game dynamcs. Mathematical Biosciences 1978, 40:145-156.
31. Von Neumann J. Theory of Self-reproducing Automata 1966, University of Illinois Press.
32. Wallace R., Wallace D. Code, context, and epigenetic catalysis in gene expression. Transactions on Computational Systems Biology XI, LNBI 2009, 5750:283-334.
33. Wallace R. Consciousness: A Mathematical Treatment of the Global Neuronal Workspace Model 2005, Springer, New York.
34. Wallace R. Metabolic constraints on the eukaryotic transition. Origins of Life and Evolution of Biospheres 2009, 38:165-176.
35. Wallace R. Expanding the modern synthesis. Comptes Rendus Biologies 2010, 333:701-709.
36. Wallace, R., 2010b. Expanding the modern synthesis II: formal perspectives on the inherent role of niche construction in fitness. http://precedings.nature.com/documents/5059/version/2.
37. Wallace R. Structure and dynamics of the 'protein folding code' inferred using Tlusty's topological rate distortion approach. BioSystems 2011, 103:18-26.
38. Weinstein A. Groupoids: unifying internal and external symmetry. Notices of the American Mathematical Association 1996, 43:744-752.
39. Wilson K. Renormalization group and critical phenomena. I. Renormalization group and the Kadanoff scaling picture. Physical Review B 1971, 4:3174-3183.