Stigmergic gene transfer and emergence of universal coding

HFSP Journal

Volumn 3, Issue 5, 2009, Pages 317-327

  Prokopenko, Mikhail ^a   Polani, Daniel ^b   Chadwick, Matthew ^c  

^a CSIRO   (Australia)

^b UNIVERSITY OF HERTFORDSHIRE   (United Kingdom)

^c Meadow End   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 80051805397     PISSN: 19552068     EISSN: 1955205X     Source Type: Journal    
DOI: 10.2976/1.3175813     Document Type: Article

References (36)

1. Adami, C (1998). Introduction to Artificial Life, Springer, NewYork.
2. Barbieri, M (2003). The Organic Codes: An Introduction to Semantic Biology Cambridge University Press, Cambridge, UK.
3. Bialek, W, de Ruyter van Steveninck, RR, and Tishby, N (2006). "Efficient representation as a design principle for neural coding and computation." 2006 IEEE International Symposium on Information Theory, pp. 659-663.
4. Bonabeau, E, Theraulaz, G, Fourcassié, V, and Deneubourg, J-L (1998). "Phase-ordering kinetics of cemetery organization in ants." Phys. Rev. E 57(4), 4568-4571.
5. Crutchfield, JP (1990). "Information and its metric." Nonlinear Structures in Physical Systems-Pattern Formation, Chaos andWaves, L Lam and HC Morris, eds., pp 119-130, Springer, NewYork.
6. Eigen, M (1971). "Self-organization of matter and evolution of biological macromolecules." Naturwiss. 58(10), 465-523.
7. Grassé, PP (1959). "La reconstruction du nid et les coordinations interindividuelles chez bellicositermes na-talensis et cubitermes sp. La theorie de la stigmergie: essai d'interpretation des termites constructeurs." Insectes Soc. 6, 41-83.
8. Haken, H (1983). Synergetics, an Introduction: Nonequilibrium Phase Transitions and Self-Organization in Physics, Chemistry, and Biology, 3rd Ed., Springer, NewYork.
9. Hofstadter, DR (1989). Gödel, Escher, Bach: An Eternal Golden Braid, Vintage Books, NewYork.
10. Holland, O, and Melhuish, C (1999). "Stigmergy, self-organisation, and sorting in collective robotics." Artif. Life 5(2), 173-202.
11. Kauffman, SA (2000). Investigations, Oxford University Press, Oxford, UK.
12. Klyubin, A, Polani, D, and Nehaniv, C (2007). "Representations of space and time in the maximization of information flow in the perceptionaction loop." Neural Comput. 19(9), 2387-2432.
13. Laughlin, SB, Anderson, JC, Carroll, DC, and de Ruyter van Steveninck, RR (2000). "Coding efficiency and the metabolic cost of sensory and neural information." Information Theory and the Brain, R Baddeley, P Hancock, and P Földiák, eds., pp 41-61, Cambridge University Press, Cambridge, UK.
14. Laughlin, SB, de Ruyter van Steveninck, RR, and Anderson, JC (1998). "The metabolic cost of neural information." Nat. Neurosci. 1(1), 36-41.
15. Lizier, JT, Prokopenko, M, and Zomaya, AY (2008). "Local information transfer as a spatiotemporal filter for complex systems." Phys. Rev. E 77(2), 026110.
16. Lloyd, A (1995). "The coupled logistic map: a simple model for the effects of spatial heterogeneity on population dynamics." J. Theor. Biol. 173, 217-230.
17. MacKay, DJ, (2003). Information Theory, Inference, and Learning Algorithms, Cambridge University Press, Cambridge, UK.
18. Piraveenan, M, Polani, D, and Prokopenko, M (2007). "Emergence of genetic coding: an information-theoretic model." Advances in Artificial Life: 9th European Conf. on Artificial Life (ECAL-2007)-Lecture Notes in Artificial Intelligence, Vol. 4648, F Almeida e Costa, L Rocha, E Costa, I Harvey, and A Coutinho, eds., pp. 42-52, Springer.
19. Piraveenan, M, Prokopenko, M, and Zomaya, AY (2009). "Assortiveness and information in scale-free networks." Eur. Phys. J. B 67, 291-300.
20. Polani, D, Nehaniv, C, Martinetz, T, and Kim, JT (2006). "Relevant information in optimized persistence vs. progeny strategies." Artificial Life X: Proc., 10th Int. Conf. on the Simulation and Synthesis of Living Systems, L Rocha, L Yaeger, M Bedau, D Floreano, R Goldstone, and A Vespignani, eds., Bloomington, IN.
21. Polani, D, Prokopenko, MM, and Chadwick, M (2008). "Modelling stigmergic gene transfer." Artificial Life XI-Proc., 11th Int. Conf. on the Simulation and Synthesis of Living Systems, S Bullock, J Noble, R Watson, and M A Bedau, eds., pp. 490-497, MIT Press.
22. Prigogine, I (1980). From Being to Becoming: Time and Complexity in the Physical Sciences,W. H. Freeman & Co., San Francisco.
23. Prokopenko, M, Boschetti, F, and Ryan, A (2008). "An informationtheoretic primer on complexity, self-organisation and emergence." Complexity, http://www3.interscience.wiley.com/journal/121495010/abstract?CRETRY=1&SRETRY=0.
24. Prokopenko, M, Gerasimov, V, and Tanev, I (2006). "Evolving spatiotemporal coordination in a modular robotic system." From Animals to Animats 9: 9th Int. Conf. on the Simulation of Adaptive Behavior (SAB 2006)-Lecture Notes in Computer Science, Vol. 4095, S Nolfi, G Baldassarre, R Calabretta, J Hallam, D Marocco, J-A Meyer, and D Parisi, eds., 558-569, Springer.
25. Shannon, CE (1948a). "A mathematical theory of communication." Bell Syst. Tech. J. 27, 379-423.
26. Shannon, CE (1948b). "A mathematical theory of communication." Bell Syst. Tech. J. 27, 623-656.
27. Vetsigian, K, Woese, C, and Goldenfeld, N (2006). "Collective evolution and the genetic code." Proc. Natl. Acad. Sci. U.S.A. 103(28), 10696-10701.
28. Wagner, A (2005). Robustness and Evolvability in Living Systems, Princeton University Press, Princeton, NJ.
29. Wikipedia (2009). "Error threshold (evolution)." Wikipedia, The Free Encyclopedia (accessed May 18).
30. Woese, CR (1965). "On the evolution of the genetic code." Proc. Natl. Acad. Sci. U.S.A. 54, 1546-1552.
31. Woese, CR (1972). "The emergence of genetic organization." Exobiology, C Ponnamperuma, ed., pp. 301-341, North-Holland, Amsterdam, The Netherlands.
32. Woese, CR (1998). "The universal ancestor." Proc. Natl. Acad. Sci. U.S.A. 95, 6854-6859.
33. Woese, CR (2004). "A new biology for a new century." Microbiol. Mol. Biol. Rev. 68(2), 173-186.
34. Woese, CR and Fox, GE (1977). "The concept of cellular evolution." J. Mol. Evol. 10, 1-6.
35. Zurek, WH (1990a). "How to define complexity in physics, and why." Complexity, Entropy and the Physics of Information, Santa Fe Studies in the Sciences of Complexity, pp. 137-148, Addison-Wesley, Reading, MA.
36. Zurek, WH (1990b). "Valuable information." Complexity, Entropy and the Physics of Information, Santa Fe Studies in the Sciences of Complexity, pp. 193-197, Addison-Wesley, Reading, MA.