The Impact of the Paradigm of Complexity on the Foundational Frameworks of Biology and Cognitive Science

Philosophy of Complex Systems

Volumn , Issue , 2011, Pages 311-333

  Moreno, Alvaro ^a   Ruiz Mirazo, Kepa ^a   Barandiaran, Xabier ^b  

^a UNIVERSITY OF THE BASQUE COUNTRY UPV EHU   (Spain)

^b UNIVERSITY OF SUSSEX   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84884446849     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1016/B978-0-444-52076-0.50011-0     Document Type: Chapter

References (91)

1. Alberch P. Developmental constraints in evolutionary processes. Evolution and Development, Dahlen Conference, Springer 1982, Verlag, New York. J.T. Bonner (Ed.).
2. Argollo de Menezes M., Barabási A.L. Fluctuations in Network Dynamics. Physical Review Letters 2004, 92(2):028701.
3. Argollo de Menezes M., Barabási A.L. Separating Internal and External Dynamics of Complex Systems. Physical Review Letters 2004, 93(6):068701.
4. Barabási A.L., Albert R. Emergence of scaling in random networks. Science 1999, 286:509-512.
5. th International Conference on the Simulation and Synthesis of Living Systems (ALifeX) 2006, 513-519. MIT Press, Cambridge, MA. L.M. Rocha, L.S. Yaeger, M.A. Bedau, D. Floreano, R.L. Goldstone, A. Vespignani (Eds.).
6. Barandiaran X., Moreno A. On What Makes Certain Dynamical Systems Cognitive: A Minimally Cognitive Organization Program. Adaptive Behavior 2006, 14(2):171-185.
7. Modelling autonomy 2008, BioSystems, 91(1). X. Barandiaran, P. Ruiz-Mirazo (Eds.).
8. Bechtel W. Discovering Cell Mechanisms. The Creation of Modern Cell Biology 2006, Cambridge University Press, Cambridge.
9. Bechtel W. Mental Mechanisms: Philosophical Perspectives on Cognitive Neuroscience 2007, Erlbaum, NJ.
10. Bechtel W., Abrahamsen A. Explanation: A mechanist alternative. Studies in History and Philosophy of Biological and Biomedical Sciences 2005, 36:421-441.
11. Beer R.D. A dynamical systems perspective on agent-environment interaction. Artificial Intelligence 1995, 72:73-215.
12. Benner S.A., Sismour A.M. Synthetic Biology. Nat. Rev. Genet 2005, 6:533-542.
13. von Bertalanffy L. Problems of life: An evaluation of modern biological thought 1952, Watts & Co., London.
14. Block N. What is Functionalism?. Readings in the Philosophy of Psychology 1980, Harvard University Press, Cambridge MA. N. Block (Ed.).
15. Bray D., Matthew L., Lipkow K. The Chemotactic Behavior of Computer-Based Surrogate Bacteria. Current Biology 2007, 17:12-19.
16. Brooks R.A. Intelligence without representation. Artificial Intelligence Journal 1991, 47:139-160.
17. Brooks R.A. From Earwigs to Humans. Robotics and Autonomous Systems 1997, 20(2-4):291-304.
18. Christensen W. The evolutionary origins of volition. Distributed Cognition and the Will: Individual Volition and Social Context 2007, MIT Press, Cambridge MA. D. Spurrett, H. Kincaid, D. Ross, L. Stephens (Eds.).
19. Clark A. Being there. Putting Brain, Body, and World Together Again 1997, MIT Press, Cambridge, MA.
20. Collier J.D., Hooker C.A. Complexly organised dynamical systems. Open Systems and Information Dynamics 1999, 6(3):241-302.
21. Damasio A.R. Descartes' Error. Emotion, Reason and the Human Brain 1994, G. P. Putnam, New York.
22. Dawkins R. The Selfish Gene 1974, Oxford University Press, Oxford.
23. Edelman G.M., Gally J.A. Degeneracy and complexity in biology systems. Proc. Natl. Acad. Sci. USA 2001, 98:13763-13768.
24. Elman J.L., Bates E., Johnson M.H., Karmiloff-Smith A., Parisi D., Plunkett K. Rethinking innateness: a connectionist perspective on development 1996, MIT Press, Cambridge MA.
25. Elsasser W.M. Atom and organism 1966, Princeton Univ. Press, Princeton NJ.
26. The contribution of Artificial Life and the Sciences of Complexity to the Understanding of Autonomous Systems 2000, CC AI:Comunication and Cognition-Artificial Intelligence, 17(3-4). A. Etxeberria, A. Moreno, J. Umerez (Eds.).
27. Fodor J.A. The language of thought 1975, Thomas Crowell, New York.
28. Fox Keller E. The century beyond the gene. J. Biosci 2005, 30:3-10.
29. Fox Keller E. Revisiting 'scale-free' networks. BioEssays 2005, 27:1060-1068.
30. Fox Keller E. The disappearance of function from 'self-organizing systems. Systems Biology: Philosophical Foundations 2007, 303-317. Elsevier, Ámsterdam. F. Boogerd, F. Bruggeman, J.-H. Hofmeyr, H.V. Westerhoff (Eds.).
31. Ganti T. The principles of life 1987, Oxford University Press, Oxford, 2003, (Rev. with notes, from 1971 and OMIKK English 1987, edns.).
32. Gell-Mann M. The quark and the jaguar 1994, Freeman and co., New York.
33. Goodwin B., Holder N., Wyllie C.C. Development and evolution 1983, Cambridge University Press, Cambridge.
34. Harold F. The way of the cell: molecules, organisms and the order of life 2001, Oxford University Press, Oxford.
35. Hartwell L.H., Hopfield J.J., Leibler S., Murray A.W. From molecular to modular cell biology. Nature 1999, 42(supp):c47-252.
36. Hempel C.G., Oppenheim P. Studies in the logic of explanation. Philosophy of Science 1948, 15:137-175.
37. Hopfield J.J. Neural networks and physical systems with emergent collective computational abilities. Proc. Natl. Acad. Sci 1982, 79:2554-2558.
38. Jacob F. Evolution as tinkering. Science 1977, 196:1161-1166.
39. Kauffman S. The origins of order: self-organization and selection in evolution 1993, Oxford Univ. Press, Oxford.
40. Kelso J.A.S. Dynamic patterns: The self-organization of brain and behavior 1995, MIT Press, Cambridge MA.
41. Krichmar J.L., Edelman G.M. Brain-based devices for the study of nervous systems and the development of intelligent machines. Artificial Life 2005, 11:63-77.
42. Laland K.N., Odling-Smee J., Feldman M.W. Evolutionary consequences of niche construction and their implications for ecology. Proc. Natl Acad. Sci. USA 1999, 96(18):10242-10247.
43. Langton C.G. Computation at the edge of chaos. Physica D 1990, 42:12-37.
44. Lewin R. Complexity: life at the edge of chaos 1992, MacMillan, New York.
45. Lewis E.B. Clusters of master control genes regulate the development of higher organisms. Journal of the American Medical Association 1992, 267:1524-1531.
46. Lewis M.D. Bridging emotion theory and neurobiology through dynamic systems modeling. Behavioral and Brain Sciences 2005, 169-194:28.
47. Lewontin R. The triple helix 2000, Harvard University Press, Harvard.
48. Li M., Vitányi P. An introduction to Kolmogorv complexity and its applications 1997, Springer, New York.
49. Mattick J.S. The hidden genetic program of complex organisms. Scientific American, *(Oct.) 2004, 61-67.
50. Merleau-Ponty M. The Structure of Behavior 1963, Dusquene University Press, Pittsburgh PA, Pittsburgh PA.
51. Mitchell M. Complex systems: Network thinking. Artificial Intelligence 2006, 170(18):1194-1212.
52. Montoya J.M., Solé R.V. Small world patterns in food webs. J. Theor. Biol 2002, 214:405-412.
53. Morange M. Histoire de la biologie moléculaire 2003, La Découverte, Paris.
54. Moreno A., Lasa A. From Basic Adaptivity to Early Mind. Evolution and Cognition 2003, 9(1):12-30.
55. Newell A. Physical Symbol Systems. Cognitive Science 1980, 4:135-183.
56. Nicolis G., Prigogine I. Self-organization in Non-equilibrium Systems 1977, Wiley, New York.
57. Nolfi S. Using emergent modularity to develop control systems for mobile robots. Adaptive Behavior 1997, 5(3-4):343-364.
58. Pask G. The Natural History of Networks. Self-organizing Systems 1960, 232-263. Pergamon Press, Oxford. M.C. Yovits, S. Cameron (Eds.).
59. Pastor-Satorras R., Vespignani A. Epidemic spreading in scale-free networks. Physical Review Letters 2001, 86(14):3200-3203.
60. Pattee H. The Physical Basis and Origin of Hierarchical Control. Hierarchy Theory. The Challenge of Complex Systems 1973, George Braziller, New York. H. Pattee (Ed.).
61. Polanyi M. Life's irreducible structure. Science 1968, 1308-1312:160.
62. Mind as motion: Explorations in the dynamics of cognition 1995, The MIT Press, Cambridge MA. R.F. Port, T. van Gelder (Eds.).
63. Prescott T.J. Forced moves or good tricks in design space? Landmarks in the evolution of neural mechanisms for action selection. Adaptive Behavior 2007, 15(1):9-31.
64. Rachevsky N. Mathematical biophysics: Physico-mathematical foundations of biology 1938, Dover Publications, New York.
65. Ravesz E., Somera A.L., Mongru D.A., Oltvai Z.N, Barabassi A.L. Hierarchical Organization of Modularity in Metabolic Networks. Science 2002, 1551-1555:297.
66. Rosen R., Life itself : A comprehensive inquiry into the nature, origin and fabrication of life 1991, Columbia Univ. Press, New York.
67. Ruiz-Mirazo K., Moreno A. Basic Autonomy as a fundamental step in the synthesis of life. Artificial Life 2004, 10(3):235-259.
68. Ruiz-Mirazo K., Umerez J., Moreno A. Enabling conditions for'open-ended evolution. Biology and Philosophy 2007, 23(1):67-85.
69. Rumelhart D.E., McClelland J.L. Parallel Distributed Processing: Explorations in the Microstructure of Cognition 1986, 1. the PDP Research Group, Foundations. MIT Press, Cambridge Mass.
70. Schrödinger E. What is life? The physical aspect of the living cell 1944, Cambridge Univ. Press, Cambridge.
71. Skarda C.A., Freeman W.J. How brains make chaos in order to make sense of the world. Behavioral and Brain Sciences 1987, 10:161-195.
72. Simon H.A. The Architecture of Complexity. Proceedings of the American Philosophical Society 1962, 106:467-482. Reprinted in H. A. Simon, The Sciences of the Artificial, 193-229, 1969.
73. Solé R.V., Salazar I., Garcia-Fernandez J. Common Pattern Formation, Modularity and Phase Transitions in a Gene Network Model of Morphogenesis. Physica A 2002, 305:640-647.
74. Solé R.V., Ferrer R., Montoya J.M., Valverde S. Selection, Tinkering and Emergence in Complex Networks. Complexity 2002, 8:20-33.
75. Solé R.V., Munteanu A., Rodriguez-Caso C., Macía J. Synthetic protocell biology: from reproduction to computation. Phil. Trans. Roy. Soc. Lond. B 2007, 1727-1739:362.
76. Sporns O., Tononi G., Kotter R. The human connectome: A structural description of the human brain. PLoS Comput Biol 2005, 1(4):e42.
77. Sporns O., Tononi G., Edelman G.M. Theoretical neuroanatomy: relating anatomical and functional connectivity in graphs and cortical connection matrices. Cereb. Cortex 2000, 10:127-141.
78. Steels L. Towards a theory of emergent functionality. Simulation of Adaptive Behavior 1991, 451-461. MIT Press, Cambridge MA. J. Meyer, R. Wilson (Eds.).
79. Strogatz S.H. Exploring complex networks. Nature 2001, 410:268-277.
80. Thelen E., Smith L.B. A dynamic systems approach to the development of cognition and action 1994, Bradford Books/ MIT Press, Cambridge MA.
81. Tononi G., Sporns O., Edelman G.M. Measures of degeneracy and redundancy in biological networks. Proc. Natl. Acad. Sci. USA 1999, 96:3257-3262.
82. Tsuda I. Toward an interpretation of dynamic neural activity in terms of chaotic dynamical systems. Behavioral and Brain Sciences 2001, 24(5):793-847.
83. Turing A.M. The chemical basis of morphogenesis. Philos. Trans. R. Soc. Lond. B 1952, 237:37-72.
84. van Gulick R. Who's in Charge Here? And Who's Doing All the Work?. Mental Causation 1993, 233-256. Clarendon Press, Oxford. J. Heil, A.R. Mele (Eds.).
85. Waddington C.H. The strategy of the genes 1957, Macmillan, London.
86. Wagner A., Fell D. The small world inside large metabolic networks. Proc. R. Soc. Lond. B 2001, 268:1803-1810.
87. Waldrop M.M. Complexity: The emerging science at the edge of order and chaos 1992, Simon & Schuster, New York.
88. Weaver W. Science and Complexity. American Scientist 1948, 36(4):536-544. (Reprinted in G. J. Klir. Facets of System Science, 449-456, 1991.).
89. Weisbuch G. Networks of automata and biological organization. Journal of Theoretical Biology 1986, 121:255-267.
90. Wolfram S. Theory and applications of cellular automata 1986, World Scientific, Singapore.
91. Self-organizing systems the emergence of order 1987, Plenum Press, New York. F.E. Yates (Ed.).