Introducing Dynamics into the Field of Biosemiotics: A Formal Account with Examples from Language and Immunology

Biosemiotics

Volumn 4, Issue 1, 2011, Pages 5-24

  de Beule, Joachim ^a,b   Hovig, Eivind ^c,d   Benson, Mikael ^e  

^a VRIJE UNIVERSITEIT BRUSSEL   (Belgium)

^b UNIVERSITÉ LIBRE DE BRUXELLES   (Belgium)

^c OSLO UNIVERSITY HOSPITAL   (Norway)

^d UNIVERSITY OF OSLO   (Norway)

^e QUEEN SILVIA CHILDREN'S HOSPITAL   (Sweden)

Author keywords

Artificial chemistry; Mathematical modeling; Organic codes; Semiotic dynamics

Indexed keywords

EID: 79953164593     PISSN: 18751342     EISSN: 18751350     Source Type: Journal    
DOI: 10.1007/s12304-010-9101-1     Document Type: Article

References (54)

1. Alberts, B., Johnson, A., Lewis, J., Raff, M., Roberts, K., & Walters, P. (2002). Molecular Biology of the Cell (4th ed.). New York: Garland science.
2. Barbieri, M. (2008). Biosemiotics: a new understanding of life. Naturwissenschaften, 95(7), 577-599.
3. Baronchelli, A., Loreto, V., & Steels, L. (2008). In-depth analysis of the naming game dynamics: the homogeneous mixing case. International Journal of Modern Physics C, 19(5), 785-812.
4. Benson, M., Adner, M., & Cardell, L. O. (2001). Cytokines and cytokine receptors in allergic rhinitis: how do they relate to the th2 hypothesis in allergy? Clinical and Experimental Allergy, 31, 361-367.
5. Benson, M., Carlsson, L., Guillot, G., Jernas, M., Langston, M. A., Rudemo, M., et al. (2006). A network-based analysis of allergen-challenged cd4+ t cells from patients with allergic rhinitis. Genes and Immunity, 7, 514-521.
6. Burnet, F. M. (1959). The clonal selection theory of acquired immunity. Cambridge: Cambridge University Press.
7. Catutto, C., Loreto, V., & Pietronero, L. (2007). Semiotic dynamics and collaborative tagging. Proceedings of the National Academy of Sciences, 104(5), 1461-1464.
8. Chomsky, N. (1977). Language and responsibility. New York: The New Press.
9. Conradi, C., Saez-Rodriguez, J., Gilles, E. D., & Raisch, J. (2006). Chemical reaction network theory: A tool for systems biology. In Proceedings of the 5th MATHMOD: 5th Vienna Symposium on Mathematical Modelling.
10. Craciun, G., & Feinberg, M. (2006). Multiple equilibria in complex chemical reaction networks: extensions to entrapped species models. Systems Biology, 153(4), 179-186.
11. Croft, W. (2005). Logical and typological arguments for radical construction grammar. In J. O. Ostman & M. Fried (Eds.), Construction grammars: Cognitive grounding and theoretical extensions. Amsterdam: Benjamin.
12. De Beule, J. (2008). The emergence of compositionality, hierarchy and recursion in peer-to-peer interactions. In A. D. M. Smith, K. Smith, & R. Ferrer i Cancho (Eds.), Proceedings of the 7th International Conference on the Evolution of Language (pp. 75-82). World Scientific.
13. De Beule, J. (2009). A chemical model of the naming game. In Proceedings of the 10th European Conference on Artificial Life. LNCS. Springer.
14. De Beule, J., & Steels, L. (2005). Hierarchy in fluid construction grammar. In U. Furbach (Ed.), Proceedings of KI-2005, volume 3698 of Lecture Notes in AI (pp. 1-15). Berlin: Springer-Verlag.
15. De Beule, J., De Vylder, B., & Belpaemem, T. (2006). A cross-situational learning algorithm for damping homonymy in the guessing game. In L. M. Rocha, et al. (Eds.), Artificial Life X (pp. 466-472). MIT.
16. De Vylder, B. (2006). Coordinated communication, a dynamical systems perspective. In Proceedings of the European Conference on Complex Systems.
17. De Vylder, B. (2007). The evolution of conventions in multi-agent systems. PhD thesis, VUB Artificial Intelligence Lab.
18. Di Giulio, M. (2000). The late stage of genetic code structuring took place at a high temperature. Gene, 261, 189195.
19. Dittrich, P., Ziegler, J., & Banzhaf, W. (2001). Artificial chemistries-a review. Artificial Life, 7, 225-275.
20. Eigen, M. (1971). Selforganization of matter and the evolution of biological macro-molecules. Naturwissenschaften, 58, 465523.
21. Flajnik, M. F., & Kasahara, M. (2010). Origin and evolution of the adaptive immune system: genetic events and selective pressures. Nature Reviews. Genetics, 11, 47-59.
22. Georgescu, C., Longabaugh, W. J., Scripture-Adams, D. D., David-Fung, E. S., Yui, M. A., Zarnegar, M. A., et al. (2008). A gene regulatory network armature for T lymphocyte specification. Proceedings of the National Academy of Sciences of the United States of America, 105(51), 20100-20105.
23. Goldberg, A. (1995). Constructions: A Construction grammar approach to argument structure. Chicago: University of Chicago Press.
24. Gorlich, D., & Dittrich, P. (2009). Identifying molecular organic codes in reaction networks. In Proceedings of the 10th European Conference on Artificial Life. LNCS. Springer.
25. Gunawardena, J. (2003). Chemical reaction network theory for in-silico biologists. Available from www. jeremy-gunawardena. com.
26. Gutfraind, A., & Kempf, A. (2008). Error-reducing structure of the genetic code indicates code origin in non-thermophile organisms. Origins of Life and Evolution of the Biosphere, 38, 7585.
27. Jerne, N. K. (1955). The natural selection theory of antibody formation. Proceedings of the National Academy of Sciences of the United States of America, 41, 849-857.
28. Jerne, N. K. (1985). The generative grammar of the immune system. Bioscience Reports, 5(6), 439-451. Nobel Lecture Note.
29. Jestin, A. L., & Kempf, A. (2009). Optimization models and the structure of the genetic code. Journal of Molecular Evolution, 69, 452457.
30. Johnson, M. (1987). The body in the mind: The bodily basis of meaning, imagination and reason. University of Chicago.
31. Kruizinga, R. C., Bestebroer, J., Berghuis, P., de Haas, C. J., Links, T. P., de Vries, E. G., et al. (2009). Role of chemokines and their receptors in cancer. Current Pharmaceutical Design, 15, 3396-3416.
32. Kuppers, B. O. (1990). Information and the origin of life. Cambridge: MIT.
33. Lakoff, G. (1987). Women, fire, and dangerous things: What categories reveal about the mind. Chicago: University of Chicago Press.
34. Lu, T. X., Munitz, A., & Rothenberg, M. E. (2009). Microrna-21 is up-regulated in allergic airway inflammation and regulates il-12p35 expression. Journal of Immunology, 182, 4994-5000.
35. Maynard-Smith, J., & Szathmary, E. (1995). The major transitions in evolution. Morgan-Freeman.
36. Mendoza, L. (2006). A network model for the control of the differentiation process in Th cells. Biosystems, 84(2), 101-114.
37. Mobini, R., Andersson, B. A., Erjeflt, J., Hahn-Zoric, M., Langston, M. A., Perkins, A. D., et al. (2009). Module-based analytical strategy to identify novel disease-associated genes shows an inhibitory role for interleukin 7 receptor 23 in allergic inflammation. BMC Syst Biol, 3-19.
38. Smith, K., Kirby, S., & Brighton, H. (2003). Iterated learning: a framework for the emergence of language. Artificial Life, 9(4), 3710386.
39. Smith, K., Smith, A., Blythe, R., & Vogt, P. (2006). Cross-situational learning, a mathematical approach. In P. Vogt, Y. Sugita, E. Tuci, & C. Nehaniv (Eds.), Proceedings of the Emergence and Evolution of Linguistic Communication. Springer.
40. Smits, H. H., van Rietschoten, J. G., Hilkens, C. M., Sayilir, R., Stiekema, F., Kapsenberg, M. L., et al. (2001). Il-12-induced reversal of human th2 cells is accompanied by full restoration of il-12 responsiveness and loss of gata-3 expression. European Journal of Immunology, 31, 10551065.
41. Steels, L. (2000). Language as a complex adaptive system. M. Schoenauer, K. Deb, G. Rudolph, X. Yao, E. Lutton, J. J. Merelo, et al. (Eds.), Proceedings of Parallel Problem Solving from Nature VI, Lecture Notes in Computer Science. Berlin: Springer.
42. Steels, L., & De Beule, J. (2006). A (very) brief introduction to fluid construction grammar. In Third International Workshop on Scalable Natural Language Understanding. New York City.
43. Steels, L., & Kaplan, F. (1999). Collective learning and semiotic dynamics. In D. Floreane, J.-D. Nicoud, & F. Mondada (Eds.), Advances in Artificial Life, Proceedings of ECAL'99, volume 1674 of Lecture Notes in Computer Science.
44. Steels, L., & Kaplan, F. (1999b). Bootstrapping grounded word semantics. In T. Briscoe (Ed.), Linguistic evolution through language acquisition: formal and computational models (pp. 53-73). Cambridge: Cambridge University Press.
45. Steels, L., & Szathmary, E. (2008). Replicator dynamics of language processing. In A. D. M. Smith, K. Smith, & R. Ferrer i Cancho (Eds.), The Evolution of Language: Proceedings of the 7th International Conference. Singapore: World Scientific.
46. Steels, L., & Wellens, P. (2006). How grammar emerges to dampen combinatorial search in parsing. In P. Vogt, et al. (Eds.), Symbol Grounding and Beyond: Proceedings of the Third International Workshop on the Emergence and Evolution of Linguistic Communication (pp. 76-88). Springer.
47. Szathmary, E. (2006). The origin of replicators and reproducers. Philosophical Transactions of the Royal Society of London. B, 361(1474), 1761-1776.
48. Takeuchi, N. (2010). Evolutionary dynamics of RNA-like replicators-a bioinformatic approach to the origin of life. PhD thesis, Utrecht University.
49. The Five Graces Group (2008). Language is a complex adaptive system. DOI: SFI-WP 08-12-047, SFI Working Papers.
50. Vincent, M. E., Liu, W., Haney, E. B., & Ismagilov, R. F. (2010). Microfluidic stochastic confinement enhances analysis of rare cells by isolating cells and creating high density environments for control of diffusible signals. Chemical Society Reviews, 39, 974-984. doi: 10. 1039/b917851a.
51. Viola, A., Molon, B., & Contento, R. L. (2008). Chemokines: coded messages for T-cell missions. Frontiers in Bioscience, 13, 6341-6353.
52. Wang, H., Barrenas, F., Bruhn, S., Mobini, R., & Benson, M. (2009). Increased ifn-gamma activity in seasonal allergic rhinitis is decreased by treatment with corticosteroids. Journal of Allergy and Clinical Immunology, 124, 1360-1362.
53. Yates, A., Callarda, R., & Stark, J. (2004). Combining cytokine signalling with t-bet and gata-3 regulation in th1 and th2 differentiation: a model for cellular decission making. Journal of Theoretical Biology, 231, 181-196.
54. Zhou, W., & Ouyang, M. (2003). The function of gata-3 in Th1 and Th2 differentiation. Immunologic Research, 28, 2537.