Punctuated equilibrium in statistical models of generalized coevolutionary resilience: How sudden ecosystem transitions can entrain both phenotype expression and darwinian selection

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 5121 LNBI, Issue , 2009, Pages 23-85

  Wallace, Rodrick ^a   Wallace, Deborah ^b  

^a NEW YORK STATE PSYCHIATRIC INSTITUTE   (United States)

^b Consumers Union ^*

Author keywords

[No Author keywords available]

Indexed keywords

ASYMPTOTIC LIMITS; CO-EVOLUTIONARY; COMMON DENOMINATORS; COMMUNICATION THEORY; DARWINIAN SELECTION; DYNAMICAL STRUCTURE; ECOSYSTEM RESILIENCE; EVOLUTIONARY TRANSITIONS; FREE ENERGY DENSITY; GENETIC DYNAMICS; GEOLOGIC TIME SCALE; IMMUNE FUNCTION; INFORMATION SOURCES; LARGE DEVIATIONS; MATHEMATICAL TREATMENTS; MESOSCALE; ONSAGER RELATIONS; PHENOTYPE EXPRESSION; PHYSICAL SYSTEMS; PUNCTUATED EQUILIBRIUM; RATE DISTORTIONS; SECOND ORDERS; SELECTION PRESSURES; STATISTICAL MODELS; STOCHASTIC DIFFERENTIAL EQUATIONS; TIME-SCALE; TOPOLOGICAL HYPOTHESIS;

BIOACTIVITY; BIOLOGY; DIFFERENTIAL EQUATIONS; ECOSYSTEMS; GENE EXPRESSION; INFORMATION THEORY;

PHASE TRANSITIONS;

EID: 67650305603     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-540-88765-2-2     Document Type: Conference Paper

References (99)

1. Adami, C., Cerf, N.: Physical complexity of symbolic sequences. Physica D 137, 62-69 (2000)
2. Adami, C., Ofria, C., Collier, T.: Evolution of biological complexity. Proceedings of the National Academy of Sciences 97, 4463-4468 (2000) (Pubitemid 30238580)
3. Albert, R., Barabasi, A.: Statistical mechanics of complex networks. Reviews of Modern Physics 74, 47-97 (2002)
4. Ancel, L.: A quantitative model of the Simpson-Baldwin effect. Journal of Theoretical Biology 196, 197-209 (1999) (Pubitemid 29043824)
5. Ash, R.: Information Theory. Dover Publications, New York (1990)
6. Atlan, H., Cohen, I.: Immune information, self-organization and meaning. International Immunology 10, 711-717 (1998) (Pubitemid 28279473)
7. Auslander, L.: Differential Geometry. Harper and Row, New York (1967)
8. Avital, E., Jablonka, E.: Animal Traditions: Behavioral inheritance in evolution. Cambridge University Press, New York (2000)
9. Baker, M., Stock, J.: Signal transduction: networks and integrated circuits in bacterial cognition. Current Biology 17(4), R1021-R1024 (2007) (Pubitemid 350180462)
10. Barkow, J., Cosmides, L., Tooby, J. (eds.): The Adapted Mind: Biological Approaches to Mind and Culture. University of Toronto Press (1992)
11. Beck, C., Schlogl, F.: Thermodynamics of Chaotic Systems. Cambridge University Press, Cambridge (1995)
12. Binney, J., Dowrick, N., Fisher, A., Newman, M.: The theory of critical phenomena. Clarendon Press, Oxford (1986)
13. Bonner, J.: The evolution of culture in animals. Princeton University Press, Princeton (1980)
14. Burago, D., Burago, Y., Ivanov, S.: A Course in Metric Geometry. American Mathematical Society, Providence (2001)
15. Byrk, A., Raudenbusch, S.: Hierarchical Linear Models: Applications and Data Analysis Methods. Sage Publications, New York (2001)
16. Champagnat, N., Ferriere, R., Meleard, S.: Unifying evolutionary dynamics: From individual stochastic processes to macroscopic models. Theoretical Population Biology 69, 297-321 (2006)
17. Cohen, I.: The cognitive principle challenges clonal selection. Immunology Today 13, 441-444 (1992)
18. Cohen, I.: Tending Adam's Garden: Evolving the Cognitive Immune Self. Academic Press, New York (2000)
19. Cohen, I.: Immune system computation and the immunological homunculus. In: Nierstrasz, O., Whittle, J., Harel, D., Reggio, G. (eds.) MoDELS 2006. LNCS, vol.4199, pp. 499-512. Springer, Heidelberg (2006) (Pubitemid 44618580)
20. Cohen, I., Harel, D.: Explaining a complex living system: dynamics, multi-scaling and emergence. Journal of the Royal Society: Interface 4, 175-182 (2007) (Pubitemid 46513049)
21. Cover, T., Thomas, J.: Elements of Information Theory. John Wiley and Sons, New York (1991)
22. Dembo, A., Zeitouni, O.: Large Deviations: Techniques and Applications, 2nd edn. Springer, New York (1998)
23. Dercole, F., Ferriere, R., Gragnani, A., Rinaldi, S.: Coevolution of slow-fast populations: evolutionary sliding, evolutionary pseudo-equilibria and complex Red Queen dynamics. Proceedings of the Royal Society, B 273, 983-990 (2006) (Pubitemid 46768426)
24. Diekmann, U., Law, R.: The dynamical theory of coevolution: a derivation from stochastic ecological processes. Journal of Mathematical Biology 34, 579-612 (1996) (Pubitemid 126768843)
25. Dimitrov, A., Miller, J.: Neural coding and decoding: communication channels and quantization. Computation and Neural Systems 12, 441-472 (2001) (Pubitemid 33625157)
26. Dretske, F.: The explanatory role of information. Philosophical Transactions of the Royal Society A 349, 59-70 (1994)
27. Durham, W.: Coevolution: Genes, Culture, and Human Diversity. Stanford University Press, Palo Alto (1991)
28. Eldredge, N., Gould, S.: Punctuated equilibrium: an alternative to phyletic gradualism. In: Schopf, T. (ed.) Models in Paleobiology, pp. 82-115. Freeman, Cooper and Co., San Francisco (1972)
29. Eldredge, N.: Time Frames: The Rethinking of Darwinian Evolution and the Theory of Punctuated Equilibria. Simon and Schuster, New York (1985)
30. Emery, M.: Stochastic Calculus in Manifolds. Universitext series. Springer, New York (1989)
31. English, T.: Evaluation of evolutionary and genetic optimizers: no free lunch. In: Fogel, L., Angeline, P., Back, T. (eds.) Evolutionary Programming V: Proceedings of the Fifth Annual Conference on Evolutionary Programming, pp. 163-169. MIT Press, Cambridge (1996)
32. Fath, B., Cabezas, H., Pawlowski, C.: Regime changes in ecological systems: an information theory approach. Journal of Theoretical Biology 222, 517-530 (2003) (Pubitemid 36627375)
33. Feller,W.: An Introduction to Probability Theory and Its Applications. JohnWiley and Sons, New York (1971)
34. Feynman, R.: Feynman Lectures on Computation. Addison-Wesley, Reading (1996)
35. Fleming, R., Shoemaker, C.: Evaluating models for spruce budworm-forest management: comparing output with regional field data. Ecological Applications 2, 460-477 (1992) (Pubitemid 23399881)
36. Forlenza, M., Baum, A.: Psychosocial influences on cancer progression: alternative cellular and molecular mechanisms. Current Opinion in Psychiatry 13, 639-645 (2000) (Pubitemid 30834650)
37. Franzosi, R., Pettini, M.: Theorem on the origin of phase transitions. Physical Review Letters 92, 060601 (2004)
38. Fredlin, M., Wentzell, A.: Random Perturbations of Dynamical Systems. Springer, New York (1998)
39. Glazebrook, J.,Wallace, R.: Rate distortion manifolds as model spaces for cognitive information (submitted, 2007)
40. Goubault, E.: Some geometric perspectives in concurrency theory. Homology, Homotopy, and Applications 5, 95-136 (2003) (Pubitemid 40660008)
41. Goubault, E., Raussen, M.: Dihomotopy as a tool in state space analysis. In: Rajsbaum, S. (ed.) LATIN 2002. LNCS, vol.2286, pp. 16-37. Springer, Heidelberg (2002)
42. Gould, S.: The Structure of Evolutionary Theory. Harvard University Press, Cambridge (2002)
43. Grossman, Z.: Round 3. Seminars in Immunology 12, 313-318 (2000)
44. Gunderson, L.: Ecological resilience - in theory and application. Annual Reviews of Ecological Systematics 31, 425-439 (2000)
45. Gunderson, L.: Personal communication (2007)
46. Hartl, D., Clark, A.: Principles of Population Genetics. Sinaur Associates, Sunderland (1997)
47. Holling, C.: Resilience and stability of ecological systems. Annual Reviews of Ecological Systematics 4, 1-23 (1973)
48. Holling, C.: Cross-scale morphology, geometry and dynamics of ecosystems. Ecological Monographs 41, 1-50 (1992) (Pubitemid 23399177)
49. Jimenez-Montano, M.: Formal languages and theoretical molecular biology. In: Goodwin, B., Saunders, P. (eds.) Theoretical Biology: Epigenetic an Evolutionary Order in Complex Systems. Edinburgh University Press (1989)
50. Kastner, M.: Phase transitions and configuration space topology (2006) (ArXiv preprint cond-mat/0703401)
51. Khinchin, A.: Mathematical Foundations of Information Theory. Dover Publications, New York (1957)
52. Laland, K., Odling-Smee, F., Feldman, M.: Evolutionary consequences of niche construction and their implications for ecology. Proceedings of the National Academy of Sciences 96, 10242-10247 (1999) (Pubitemid 29422543)
53. Lee, J.: Introduction to Topological Manifolds. Springer, New York (2000)
54. Levin, S.: Ecology in theory and application. In: Levin, S., Hallam, T., Gross, L. (eds.) Applied Mathematical Ecology biomathematics Texts, vol.18. Springer, New York (1989)
55. Lewontin, R.: Biology as Ideology: The Doctrine of DNA. Harper Collins, New York (1993)
56. Lewontin, R.: The Triple Helix: gene, organism, and environment. Harvard University Press (2000)
57. Liao, J., Biscolo, R., Yang, Y., My Tran, L., Sabatti, C., Roychowdhury, V.: Network component analysis: Reconstruction of regulatory signals in biological systems. Proceedings of the National Academy of Sciences 100, 15522-15527 (2003) (Pubitemid 38021022)
58. Liu, Y., Ringner, M.: Revealing signaling pathway deregulation by using gene expression signatures and regulatory motif analysis. Genome Biology 8, R77 (2007) (Pubitemid 351902764)
59. Luchinsky, D.: On the nature of large fluctuations in equilibrium systems: observations of an optimal force. Journal of Physics A 30, L577-L583 (1997) (Pubitemid 127373994)
60. Matsumoto, Y.: An Introduction to Morse Theory, Translations of Mathematical Monographs, vol.208. American Mathematical Society (2002)
61. Michel, L., Mozrymas, J.: Application of Morse Theory to the symmetry breaking in the Landau theory of the second order phase transition. In: Kramer, P., Rieckers, A. (eds.) Group Theoretical Methods in Physics: Sixth International Colloquium. Lecture Notes in Physics, vol.79, pp. 447-461. Springer, New York (1977)
62. Milnor, J.: Morse Theory. Annals of Mathematical Studies, vol.51. Princeton University Press, Princeton (1963)
63. Nunney, L.: Lineage selection and the evolution of multistage carcinogenesis. Proceedings of the London Royal Society B 266, 493-498 (1999) (Pubitemid 29110179)
64. Odling-Smee, F., Laland, K., Feldman, M.: Niche construction. The American Naturalist 147, 641-648 (1996) (Pubitemid 26476371)
65. Ofria, C., Adami, C., Collier, T.: Selective pressures on genomes in molecular evolution. Journal of Theoretical Biology 222, 477-483 (2003) (Pubitemid 36627371)
66. Onsager, L., Machlup, S.: Fluctuations and irreversible processes. Physical Review 91, 1505-1512 (1953)
67. O'Nuallain, S.: Code and context in gene expression, cognition, and consciousness. In: Barbieri, M., Hoffmeyer, J. (eds.) Biosemiotics: The codes of life. Springer, New York (2008)
68. Pettini, M.: Geometry and Topology in Hamiltonian Dynamics and Statistical Mechanics. Springer, New York (2007)
69. Pettini, M., Franzosi, R., Spinelli, L.: Topology and phase transitions I. Preliminary results. Nuclear Physics B 782, 189-218 (2007)
70. Pielou, E.C.: Mathematical Ecology. John Wiley and Sons, New York (1977)
71. Podolsky, S., Tauber, A.: The generation of diversity: Clonal selection theory and the rise of molecular biology. Harvard University Press (1998)
72. Pratt, V.: Modeling concurrency with geometry. In: Proceedings of the 18th ACM SIGPLAN-SIGACT Symposium on Principles of Programming Languages, pp. 311-322 (1991)
73. Priami, C.: Computational thinking in biology. In: Priami, C. (ed.) Transactions on Computational Systems Biology VIII. LNCS (LNBI), vol.4780, pp. 63-76. Springer, Heidelberg (2007) (Pubitemid 351152110)
74. Ricotta, C.: Additive partition of parametric information and its associated â- diversity measure. Acta Biotheoretica 51, 91-100 (2003) (Pubitemid 36820972)
75. Ridley, M.: Evolution, 2nd edn. Blackwell Science/Oxford University Press (1996)
76. Rojdestvensky, I., Cottam, M.: Mapping of statistical physics to information theory with applications to biological systems. Journal of Theoretical Biology 202, 43-54 (2000) (Pubitemid 30079554)
77. Sayyed-Ahmad, A., Tuncay, K., Ortoleva, P.: Transcriptional regulatory network refinement and quantification through kinetic modeling, gene expression microarray data and information theory. BMC Bioinformatics 8, 20 (2007) (Pubitemid 46243417)
78. Shirkov, D., Kovalev, V.: The Bogoliubov renormalization group and solution symmetry in mathematical physics. Physics Reports 352, 219-249 (2001) (Pubitemid 33668082)
79. Soyer, O., Salathe, M., Bonhoeffer, S.: Signal transduction networks: Topology, response and biochemical processes. Journal of Theoretical Biology 238, 416-425 (2006) (Pubitemid 41828441)
80. Tauber, A.: Conceptual shifts in immunology: Comments on the 'two-way paradigm'. Theoretical Medicine and Bioethics 19, 457-473 (1998) (Pubitemid 29038121)
81. Volney, W., Fleming, R.: Spruce budworm (Choristoneura spp.) biotype reactions to forest and climate characteristics. Global Change Biology 13, 1630-1643 (2007) (Pubitemid 47232217)
82. Waddington, C.: Epilogue. In:Waddington, C. (ed.) Towards a Theoretical Biology: Essays. Aldine-Atherton, Chicago (1972)
83. Wallace, R.,Wallace, R.G.: Psychopathica Automatorum: A cognitive neuroscience perspective on highly parallel computation and its dysfunctions (to appear, 2008)
84. Wallace, R., Fullilove, M.T.: Collective Consciousness and its Discontents: Institutional Distributed Cognition, Racial Policy and Public Health in the United States. Springer, New York (2008)
85. Wallace, R., Wallace, R.G.: Information theory, scaling laws and the thermodynamics of evolution. Journal of Theoretical Biology 192, 545-559 (1998) (Pubitemid 28349645)
86. Wallace, R., Wallace, R.G.: Organisms, organizations, and interactions: an information theory approach to biocultural evolution. BioSystems 51, 101-119 (1999) (Pubitemid 29347097)
87. Wallace, R., Wallace, R.G.: Immune cognition and vaccine strategy: beyond genomics. Microbes and Infection 4, 521-527 (2002) (Pubitemid 34270689)
88. Wallace, R.,Wallace, D.,Wallace, R.G.: Toward cultural oncology: the evolutionary information dynamics of cancer. Open Systems and Information Dynamics 10, 159-181 (2003) (Pubitemid 39063827)
89. Wallace, R.: Language and coherent neural amplification in hierarchical systems: renormalization and the dual information source of a generalized stochastic resonance. International Journal of Bifurcation and Chaos 10, 493-502 (2000)
90. Wallace, R.: Immune cognition and vaccine strategy: pathogenic challenge and ecological resilience. Open Systems and Information Dynamics 9, 51-83 (2002)
91. Wallace, R.: Adaptation, punctuation and rate distortion: non-cognitive 'learning plateaus' in evolutionary process. Acta Biotheoretica 50, 101-116 (2002)
92. Wallace, R.: Consciousness: A Mathematical Treatment of the Global Neuronal Workspace Model. Springer, New York (2005)
93. Wallace, R.: A global workspace perspective on mental disorders. Theoretical Biology and Medical Modelling 2, 49 (2005) (Pubitemid 43155071)
94. Whitham, T.: A framework for community and ecosystem genetics: from genes to ecosystems. Nature Reviews: genetics 7, 510-523 (2006) (Pubitemid 43943569)
95. Wilson, K.: Renormalization group and critical phenomena. I Renormalization group and the Kadanoff scaling picture. Physical Review B 4, 3174-3183 (1971)
96. Wymer, C.: Structural nonlinear continuous-time models in econometrics. Macroeconomic Dynamics 1, 518-548 (1997) (Pubitemid 127647802)
97. Zhu, R., Riberio, A., Salahub, D., Kauffman, S.: Studying genetic regulatory networks at the molecular level: Delayed reaction stochastic models. Journal of Theoretical Biology 246, 725-745 (2007) (Pubitemid 46719259)
98. Zurek, W.: Cosomological experiments in superfluid helium? Nature 317, 505-508 (1985)
99. Zurek, W.: Shards of broken symmetry. Nature 382, 296-298 (1996)