Stepping beyond the Newtonian Paradigm in Biology

Towards an Integrable Model of Life: Accelerating Discovery in the Biological Foundations of Science


The INBIOSA project brings together a group of experts across many disciplines who believe that science requires a revolutionary transformative step in order to address many of the vexing challenges presented by the world. It is INBIOSA’s purpose to enable the focused collaboration of an interdisciplinary community of original thinkers.


Living System Category Theory Class Identity Living Entity Local Logic 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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  1. Abramsky, S.: Semantics of Interaction: an introduction to Game Semantics. In: Dybjer, P., Pitts, A. (eds.) Proceedings of the 1996 CLiCS Summer School, Isaac Newton Institute, pp. 1–31. Cambridge University Press (1997)Google Scholar
  2. Abramsky, S., Coecke, B.: A categorical semantics of quantum protocols. In: Proc. of the 19th IEEE Conf. on Logic in Computer Science (LiCS 2004). IEEE Computer Science Press (2004),
  3. Arianhod, R.: Einstein’s Heroes: Imagining the World through the Language of Mathematics. Oxford University Press (2006) ISBN-10: 0195308905; ISBN-13: 978-0195308907Google Scholar
  4. Arleo, A., Gerstner, W.: Spatial cognition and neuro-mimetic navigation: a model of hippocampal place cell activity. Biol. Cybern. 83, 287–299 (2000)CrossRefGoogle Scholar
  5. Auffray, C., Nottale, L.: Scale relativity and integrative systems biology. 1. Founding principles and scale laws. Prog. Biophys. Mol. Biol. 97, 79–114 (2008)CrossRefGoogle Scholar
  6. Ball, P.: The Dawn of Quantum Biology. Nature 474, 272–274 (2011)CrossRefGoogle Scholar
  7. Barabási, A.-L., Albert, R.: Emergence of scaling in random networks. Science 286, 509–512 (1999)MathSciNetCrossRefGoogle Scholar
  8. Barrett, A.B., Seth, A.K.: Practical measures of integrated information for time-series data. PLoS Comput. Biol. 7(1), e1001052 (2011)MathSciNetCrossRefGoogle Scholar
  9. Bateson, G.: Steps to an Ecology of Mind. The University of Chicago Press, Chicago (1972) ISBN 0226-03905-6Google Scholar
  10. Bastiani(-Ehresmann), A., Ehresmann, C.: Categories of sketched structures, Cahiers Top. et Géom. Dif. XIII(2) (1972)Google Scholar
  11. Bateson, G.: Mind and Nature: a Necessary Unity. Hampton Press (2002) ISBN: 1572734345Google Scholar
  12. Bressler, S.L.: The Formation of Global Neurocognitive State. Springer, Heidelberg (2007)Google Scholar
  13. Burgess, N., Recce, M., O’Keefe, J.: A model of hippocampal function. Neural Netw. 7, 1065–1081 (1994)zbMATHCrossRefGoogle Scholar
  14. Cardelli, L.: Brane calculi. In: Computational Methods in Systems Biology, pp. 257–280 (2005)Google Scholar
  15. Cardelli, L.: Bitonal membrane systems. Theoretical Computer Science 404(1-2) (2008)Google Scholar
  16. Carroll, S.B.: Endless Forms Most Beautiful: The New Science of Evo Devo. WW Norton, New York (2005)Google Scholar
  17. Case, J.: A Note on Degrees of Self-Describing Turing Machines. Journal of the A.C.M. 18(3), 329–338 (1971)MathSciNetzbMATHGoogle Scholar
  18. Chaisson, E.J.: Cosmic Evolution: The Rise of Complexity in Nature. Harvard University Press (2002) ISBN-10: 0674009878; ISBN-13: 978-0674009875Google Scholar
  19. Chaitin, G.J.: Meta Math: The Quest for Omega. Vintage (2006) ISBN-10: 1400077974; ISBN-13: 978-1400077977Google Scholar
  20. Chaitin, G.J.: Thinking about Gödel and Turing: Essays on Complexity, 1970-2007. World Scientific Pub. Co. (2007) ISBN-10: 9812708952; ISBN-13: 978-9812708953Google Scholar
  21. Chaitin, G.J.: Life as Evolving Software (2011),
  22. Chargaff, E.: Heraclitean Fire: Sketches from a Life Before Nature, 1st edn. Rockefeller University Press (1978) ISBN-10: 0874700299; ISBN-13: 978-0874700299Google Scholar
  23. Church, A.: A Formulation of the Simple Theory of Types. Journal of Symbolic Logic 5 (1940)Google Scholar
  24. Clarck, A.: A Theory of Sentience. Oxford University Press (2000) ISBN-10: 0198238517; ISBN-13: 978-0198238515Google Scholar
  25. Coecke, B.: Quantum Picturalism. Contemporary Physics 51, 59–83 (2010), CrossRefGoogle Scholar
  26. Collier, J.: Organized Complexity: Properties, Models and the Limits of Understanding (2004),
  27. Collini, E., Wong, C.Y., Wilk, K.E., Curmi, P.M.G., Brumer, P., Scholes, G.D.: Coherently wired light-harvesting in photosynthetic marine algae at ambient temperature. Nature 463(7281), 644–647 (2010)CrossRefGoogle Scholar
  28. Conrad, M.: Quantum molecular computing: The self-assembly model. Int. J. of Quantum Chemistry 44(sup. 19), 125–143 (1992), (Article first published online: October 19, 1992)
  29. Cottam, R., Ranson, W., Vounckx, R.: A diffuse biosemiotic model for cell-to-tissue computational closure. BioSystems 55, 159–171 (2000)CrossRefGoogle Scholar
  30. Cottam, R., Ranson, W., Vounckx, R.: Autocreative Hierarchy II: Dynamics - Self-Organization, Emergence and Level-Changing. In: Hexmoor, H. (ed.) International Conference on Integration of Knowledge Intensive Multi-Agent Systems, pp. 766–773. IEEE, Piscataway (2003)Google Scholar
  31. Cottam, R., Ranson, W., Vounckx, R.: Autocreative hierarchy I: structure – ecosystemic dependence and autonomy. SEED Journal 4, 24–41 (2004)Google Scholar
  32. Cottam, R., Ranson, W., Vounckx, R.: Life and Simple Systems. Systems Research and Behavioral Science. Syst. Res. 22, 413–430 (2005),, doi:10.1002/sres.716CrossRefGoogle Scholar
  33. Cottam, R., Ranson, W., Vounckx, R.: Living in hyperscale: internalization as a search for unification. In: Wilby, J., Allen, J.K., Loureiro-Koechlin, C. (eds.) Proceedings of the 50th Annual Meeting of the International Society for the Systems Sciences, paper #2006-362, pp. 1–22. ISSS, Asilomar (2006)Google Scholar
  34. Csermely, P.: Weak Links. Stabilizers of Complex Systems from Proteins to Social Networks. Springer, Heidelberg (2006)Google Scholar
  35. Damasio, A.: Descartes’ Error: Emotion, Reason, and the Human Brain. Penguin (2005) ISBN-10: 014303622X; ISBN-13: 978-0143036227Google Scholar
  36. Deacon, T.W.: Incomplete Nature: How Mind Emerged from Matter. W. W. Norton & Company (2011) ISBN-10: 0393049914; ISBN-13: 978-0393049916Google Scholar
  37. Donald, M.: The Virtues of Rigorous Interdisciplinarity. In: Lucariello, J.M., Hudson, J.A., Fivush, R., Bauer, P.J. (eds.) The Development of the Mediated Mind, ch. 12. Lawrence Erlbaum Associates (2004)Google Scholar
  38. Dressler, G.R.: The Cellular Basis of Kidney Development. Annu. Rev. Cell Dev. Biol. 22, 509–529 (2006)CrossRefGoogle Scholar
  39. Edelman, G.M.: Neural Darwinism: The Theory of Neuronal Group Selection. Basic Books (1987) ISBN-10: 0465049346; ISBN-13: 978-0465049349Google Scholar
  40. Edelman, G., Tononi, G.: A Universe Of Consciousness How Matter Becomes Imagination. Basic Books (2001) ISBN-10: 0465013775; ISBN-13: 978-0465013777Google Scholar
  41. Ehresmann, C.: Trends toward the unity of mathematics. In: Cahiers de Topologie et Géométrie Différentielle Catégoriques, vol. 8, Exp. No. 1, pp. 1–7 (1966)Google Scholar
  42. Ehresmann, A.C., Vanbremeersch, J.-P.: Hierarchical Evolutive Systems: A mathemati-cal model for complex systems. Bull. of Math. Bio. 49(1), 13–50 (1987)MathSciNetzbMATHGoogle Scholar
  43. Ehresmann, A.C., Vanbremeersch, J.-P.: Hierarchical Evolutive Systems. In: Manikopoulos (ed.) Proc. 8th International Conference of Cybernetics and Systems, vol. 1, pp. 320–327. The NIJT Press, New York (1990)Google Scholar
  44. Ehresmann, A.C., Vanbremeersch, J.-P.: Emergence Processes up to Consciousness Using the Multiplicity Principle and Quantum Physics. In: ALP. Conference Proceedings, vol. 627, pp. 221–233 (2002); Dubois, D. (ed.) CASYS (2001)Google Scholar
  45. Ehresmann, A.C., Vanbremeersch, J.-P.: Memory Evolutive Systems: Hierarchy, Emergence, Cognition. Elsevier Science (2007) ISBN-10: 0444522441; ISBN-13: 978-0444522443Google Scholar
  46. Ehresmann, A.C., Vanbremeersch, J.-P.: MENS a mathematical model for cognitive systems. Journal of Mind Theory (2), 129–180 (2009)Google Scholar
  47. Ehresmann, A.C., Vanbremeersch, J.-P.: Analysis of Complex Events in Memory Evolutive Systems. In: Cezon, M., Wolfsthal, Y. (eds.) ServiceWave 2010 Workshops. LNCS, vol. 6569, pp. 153–159. Springer, Heidelberg (2011)CrossRefGoogle Scholar
  48. Ehresmann, A.C.: MENS: From Neurons to Higher Mental Processes up to Consciousness. In: Simeonov, P.L., Smith, L.S., Ehresmann, A.C. (eds.) Integral Biomathics: Tracing the Road to Reality, vol. 106, pp. 35–36. Springer, Heidelberg (2012)Google Scholar
  49. Ehresmann, A.C., Simeonov, P.L.: WLIMES, The Wandering LIMES: Towards a Theoretical Framework for Wandering Logic Intelligence Memory Evolutive Systems. In: Simeonov, P.L., Smith, L.S., Ehresmann, A.C. (eds.) Integral Biomathics: Tracing the Road to Reality, vol. 106, pp. 117–138. Springer, Heidelberg (2012)Google Scholar
  50. Einstein, A., Podolsky, B., Rosen, N.: Can Quantum-Mechanical Description of Physical Reality Be Considered Complete? Phys. Rev. 47(10), 777–780 (1935), doi:10.1103/PhysRev.47.777zbMATHCrossRefGoogle Scholar
  51. Elsasser, M.W.: A form of logic suited for biology. In: Rosen, R. (ed.) Progress in Theoretical Biology, vol. 6, pp. 23–62. Academic Press, New York (1981)Google Scholar
  52. Embechts, P.: Selfsimilar Processes (Princeton Series in Applied Mathematics). Princeton University Press (2002) ISBN 978-0691096278Google Scholar
  53. Engel, G.S., Calhoun, T.R., Read, E.L., Ahn, T.K., Mancal, T., Cheng, Y.-C., Blankenship, R.E., Fleming, G.R.: Evidence for Wavelike Energy Transfer Through Quantum Coherence in Photosynthetic Complexes. Nature 446, 782–786 (2007)CrossRefGoogle Scholar
  54. Everett III, H.: On the Foundations of Quantum Mechanics. Ph.D. Thesis, Princeton University (1957a)Google Scholar
  55. Everett III, H.: ”Relative State” Formulation of Quantum Mechanics. Review of Modern Physics 29, 454–462 (1957b); reprinted in: Wheeler, J.A., Zurek, W.H. (eds.): Quantum Theory and Measurement, pp. 315–323. Princeton University Press, Princeton (1983) (page numbers refer to the reprint)Google Scholar
  56. Everett III., H.: The Theory of the Universal Wave Function. In: DeWitt, B.S., Graham, N. (eds.) The Many-Worlds Interpretation of Quantum Mechanics, pp. 3–140. Princeton University Press, Princeton (1973), (May 20, 2011) (University of California, Irvine Libraries. Irvine, California 92623-9557,
  57. Expert, et al.: Self-similar correlation function in brain resting-state fMRI, arXiv:1003.3682 (2010),
  58. Fasching, G.: Verlorene Wirklichkeiten: Über die ungewollte Erosion unseres Denkraumes durch Naturwissenschaft und Technik. Springer, Heidelberg (1996) ISBN-10: 3211828974; ISBN-13: 978-3211828977Google Scholar
  59. Fasching, G.: Phänomene der Wirklichkeit. Springer, Wien (2000) ISBN-10: 3211834591; ISBN-13: 978-3211834596Google Scholar
  60. Fasching, G.: Illusion der Wirklichkeit: Wie ein Vorurteil die Realität erfindet. Springer, Heidelberg (2003) ISBN-10: 3211403744; ISBN-13: 978-3211403747Google Scholar
  61. Fiorillo, C.D.: A New Approach to the Information in Neural Systems. In: Simeonov, P.L., Smith, L.S., Ehresmann, A.C. (eds.) Integral Biomathics: Tracing the Road to Reality, vol. 106, pp. 37–48. Springer, Heidelberg (2012)Google Scholar
  62. Fodor, J.A., Piattelli-Palmarini, M.: What Darwin Got Wrong. Profile Books (2010) ISBN-10: 9781846682193; ISBN-13: 978-1846682193Google Scholar
  63. Fogel, L.J.: Artificial Intelligence through Simulated Evolution. John Wiley & Sons Inc., New York (1966) ISBN-10: 0471265160; ISBN-13: 978-0471265160Google Scholar
  64. Fredkin, E.: Digital Mechanics, Physica D, pp. 254–270. North Holland (1990)Google Scholar
  65. Fredkin, E.: A New Cosmogony. In: Proc. of the IEEE Physics of Computation Workshop, October 2-4 (1992)
  66. Freeman, W.J.: Neurodynamics: An Exploration in Mesoscopic Brain Dynamics. Springer, Heidelberg (2000)zbMATHCrossRefGoogle Scholar
  67. Freeman, W.J.: Scale-free Neocortical Dynamics. Scholarpedia 2(2), 1357 (2007),, doi:10.4249/scholarpedia.1357CrossRefGoogle Scholar
  68. Frohlich, H.: The extraordinary dielectric properties of biological materials and the action of enzymes. Proc. Natl. Acad. Sci. 72(11), 4211–4215 (1975)CrossRefGoogle Scholar
  69. Fuster, J.M.: Cortex and Mind: Unifying Cognition. Oxford University Press (2005) ISBN-10: 019530084X; ISBN-13: 978-0195300840Google Scholar
  70. Gare, A.: Approaches To The Question ‘What Is Life?’: Reconciling Theoretical Biology With Philosophical Biology. Cosmos and History: The Journal of Natural and Social Philosophy 4(1-2) (2008),
  71. Gauger, E.M., Rieper, E., Morton, J.J.L., Benjamin, S.C., Vedral, V.: Sustained Quantum Coherence and Entanglement in the Avian Compass. Phys. Rev. Lett. 106, 040503 (2011)CrossRefGoogle Scholar
  72. Georgiev, D.: Photons Do Collapse In the Retina Not in the Brain Cortex: Evidence from Visual Illusions. NeuroQuantology 9(2), 206–230 (2011), Google Scholar
  73. Ghosh, S., Rosenbaum, T.F., Aeppli, G., Coppersmith, S.N.: Entangled Quantum State of Magnetic Dipoles. Nature 425, 48–51 (2003)CrossRefGoogle Scholar
  74. Glowacki, E.D., Leonat, L., Voss, G., Bodea, M., Bozkurt, Z., Irimia-Vladu, M., Bauer, S., Sariciftci, N.S.: Natural and Nature-Inspired Semiconductors for Organic Electronics. In: Proc. of SPIE, vol. 8118, pp. 81180M1–81180M9 (2011)Google Scholar
  75. Gillispie, C.C.: Pierre-Simon Laplace, 1749-1827. Princeton University Press, Princeton (2000)Google Scholar
  76. Goguen, J.A.: Mathematical representation of hierarchically organized systems. In: Global Systems Dynamics, pp. 65–85. Attinger, Basel (1970)Google Scholar
  77. Goguen, J.A.: Sheaf semantics for Concurrent Interacting Objects. Mathematical Structures in Computer Science 11, 159–191 (1992)MathSciNetCrossRefGoogle Scholar
  78. Gomez-Ramirez, J., Sanz, R.: Hippocampal Categories: A Mathematical Foundation for Navigation and Memory From Brains to Systems. In: Advances in Experimental Medicine and Biology, vol. 718. Springer Science+Business Media, LLC (2010), doi:10.1007/978-1-4614-0164-3_13Google Scholar
  79. Gomez-Ramirez, J., Sanz, R.: What the Escherichia Coli Tells Neurons About Learning. In: Simeonov, P.L., Smith, L.S., Ehresmann, A.C. (eds.) Integral Biomathics: Tracing the Road to Reality, vol. 106, pp. 49–65. Springer, Heidelberg (2012)Google Scholar
  80. Hameroff, S.R.: Chi: a neural hologram? Am. J. Clin. Med. 2(2), 163–170 (1974)CrossRefGoogle Scholar
  81. Hameroff, S.: Quantum Computation in Brain Microtubules? Philosophical Transactions Royal Society London (A) 356, 1869–1896 (1998)MathSciNetGoogle Scholar
  82. Hameroff, S.R., Penrose, R.: Orchestrated reduction of quantum coherence in brain microtubules: a model for consciousness. J. Consciousness Stud. 3, 36–53 (1996)Google Scholar
  83. Hilbert, D.: Mathematical Problems. Lecture delivered before the international congress of mathematicians at Paris in 1900. Bull. Amer. Match. Soc. 8(10), 437–479 (1902),, ISSN: 1088-9485(e); ISSN 0273-0979(p), Earlier publications (in German) appeared in Göttinger Nachrichten, pp. 253–297 (1900), Archiv der Mathematik und Physik, 3dser., vol. 1, pp. 44–63, 213–237 (1901)
  84. Ho, M.-W.: The Rainbow and the Worm: The Physics of Organisms, 3rd edn. World Scientific (2008) ISBN-10: 9812832599; ISBN-13: 978-9812832597Google Scholar
  85. Hofkirchner, W.: The Status of Biosemiotics. SEED 2/3, 4–15 (2002)Google Scholar
  86. Holland, J.H.: Adaptation in Natural and Artificial Systems. University of Michigan Press (1975) ISBN 0262581116Google Scholar
  87. Hong, F.T.: A multi-disciplinary survey of biocomputing: Part 1: molecular and cellular aspects. In: Bajić, V.B., Tan, T.W. (eds.) Information Processing and Living Systems, pp. 1–139. Imperial College Press, London (2005a)CrossRefGoogle Scholar
  88. Hong, F.T.: A multi-disciplinary survey of biocomputing: Part 2: systems and evolutionary aspects, and technological applications. In: Bajić, V.B., Tan, T.W. (eds.) Information Processing and Living Systems, pp. 141–573. Imperial College Press, London (2005b)CrossRefGoogle Scholar
  89. Hunding, A., Lancet, D., Kepes, F., Minsky, A., Norris, V., Raine, D., Sriram, K., Root-Bernstein, R.: Compositional complementarity and prebiotic ecosystems in the origin of life. Bioessays 28(4), 399–412 (2006); Jaynes, E.T.: Probability Theory: The Logic of Science. Cambridge University Press (2003) CrossRefGoogle Scholar
  90. Josephson, B.D.: Biological Observer-Participation and Wheeler’s ‘Law without Law’. In: Simeonov, P.L., Smith, L.S., Ehresmann, A.C. (eds.) Integral Biomathics: Tracing the Road to Reality, vol. 106, pp. 267–276. Springer, Heidelberg (2012), Google Scholar
  91. Junier, I., Martin, O., Képès, F.: Spatial and topological organization of DNA chains induced by gene co-localization. PLoS Comput. Biol. 6(2), e1000678 (2010)Google Scholar
  92. Kageyama, H., Nishiwaki, T., Nakajima, M., Iwasaki, H., Oyama, T., Kondo, T.: Cyanobacterial circadian pacemaker: Kai protein complex dynamics in the KaiC phosphorylation cycle in vitro. Molecular Cell 23, 161–171 (2006)CrossRefGoogle Scholar
  93. Kan, D.M.: Adjoint functors. Trans. Am. Math. Soc. 89, 294–329 (1958)MathSciNetCrossRefGoogle Scholar
  94. Kant, I.: Critique of Pure Reason. Cambridge University Press (1999) ISBN-10: 0521657296; ISBN-13: 978-0521657297, also as 2003 translation. Palgrave Macmillan, ISBN: 1403911959; ISBN-13: 978-1403911957Google Scholar
  95. Kauffman, L.H., Magarshak, Y.B.: Vassiliev Knot Invariants and the Structure of RNA Folding. In: Kauffman, L.H. (ed.) Knots and Applications. World Scientific Press, pp. 343–394 (1995) (1993) ISBN-10: 9810220049Google Scholar
  96. Kauffmann, S.A.: The Origins of Order: Self-Organization and Selection in Evolution. Oxford University Press, Oxford (1993) ISBN-10: 0195079515; ISBN-13: 978-0195079517Google Scholar
  97. Kauffman, S.A., Logan, R.K., Este, R., Goebel, R., Hobill, P., Shmulevich, I.: Propagating Organization: An Enquiry. Biology and Philosophy 23, 27–45 (2008)CrossRefGoogle Scholar
  98. Kernbach, S., Schmickl, T., Timmis, J.: Collective Adaptive Systems: Challenges Beyond Evolvability Workshop “Fundamentals of Collective Adaptive Systems”, Brussels, November 3-4 (2009)Google Scholar
  99. Koch, K., Hepp, K.: The Relation between Quantum Mechanics and Higher Brain Functions: Lessons from Quantum Computation and Neurobiology (2007),
  100. Kurtz, S.A.: On the Random Oracle Hypothesis. Information and Control 57, 40–47 (1983)MathSciNetzbMATHCrossRefGoogle Scholar
  101. Lafitte, J.: Réflexions sur la science des machines, Vrin 1972, Paris (1932)Google Scholar
  102. Lambek, J.: Cartesian Closed Categories and Typed λ-Calculi. In: Cousineau, G., Curien, P.-L., Robinet, B. (eds.) LITP 1985. LNCS, vol. 242, pp. 136–175. Springer, Heidelberg (1986)CrossRefGoogle Scholar
  103. Lamm, E., Unger, R.: Biological Computation. Chapman and Hall (2011) ISBN-10: 1420087959; ISBN-13: 978-1420087956Google Scholar
  104. Langloh, N., Cottam, R., Vounckx, Cornelis, J.: Vounckx and Cornelis J. Towards Distributed Statistical Processing – AQuARIUM: a Query and Reflection Interaction Using MAGIC: Mathematical Algorithms Generating Interdependent Confidences. In: Smith, S.D., Neale, R.F. (eds.) Optical Information Technology: State of the Art Report, EC (Esprit): Brussels, Belgium, pp. 303–319 (1991)Google Scholar
  105. Laureys, S., Tononi, G.: The Neurology of Consciousness: Cognitive Neuroscience and Neuropathology. Academic Press (2008) ISBN-10: 0123741688; ISBN-13: 978-0123741684Google Scholar
  106. Lawvere, F.W.: The Category of Categories as a Foundation for Mathematics. In: Proceedings of the Conference on Categorical Algebra, pp. 1–21. Springer, La Jolla (1966)CrossRefGoogle Scholar
  107. Lee, H., Cheng, Y.-C., Fleming, G.R.: Science 316, 1462–1465 (2007)Google Scholar
  108. Levins, R.: Evolution in Changing Environments. Princeton University Press (1968) ISBN-10: 0691080623; ISBN-13: 978-0691080628Google Scholar
  109. Logan, R.K.: The Origin and Evolution of Language and the Propagation of Organization. tripleC 5(2), 75–81 (2007)Google Scholar
  110. Longo, G.: Incomputability in Physics and Biology. In: Ferreira, F., Löwe, B., Mayordomo, E., Mendes Gomes, L. (eds.) CiE 2010. LNCS, vol. 6158, pp. 276–285. Springer, Heidelberg (2010)CrossRefGoogle Scholar
  111. Louie, A.H.: More Than Life Itself: A Synthetic Continuation in Relational Biology. Ontos Verlag, Frankfurt (2009)Google Scholar
  112. Manturov, V.: Knot Theory. CRC Press (2004) ISBN-10: 0415310016; ISBN-13: 978-0415310017Google Scholar
  113. Marchal, B.: Amoeba, Planaria and Dreaming Machines. In: Varela, F.J., Bourgine, P. (eds.) Toward a Practice of Autonomous Systems: Proc. of the First European Conference on Artificial Life (ECAL 1991). MIT Press (1992) ISBN-10: 0262720191; ISBN-13: 978-0262720199Google Scholar
  114. Marchal, B.: Calculabilité, Physique et Cognition. PhD thesis, Université de Lille, Département d’informatique, Lille, France. Editions Universitaires Européennes (2010) (1998)Google Scholar
  115. Marchal, B.: Computation, Consciousness and the Quantum. Teorie & Modelli, n.s VI(1), 29–43 (2001); Special Issue on the History and Problems of Quantum Interpretations of Consciousness, Battacchi, M., Fano, V., (eds.)Google Scholar
  116. Marchal, B.: The Origin of Physical Laws and Sensations. Invited Talk SANE 2004 (2004),
  117. Marchal, B.: Theoretical Computer Science and the Natural Sciences. Physics of Life Reviews 2(4), 251–289 (2005)MathSciNetCrossRefGoogle Scholar
  118. Marchal, B.: A Purely Arithmetical, yet Empirically Falsifiable, Interpretation of Plotinus’ Theory of Matter. In: Barry Cooper, S., Löwe, B., Kent, T.F., Sorbi, A. (eds.) Computation and Logic in the Real World. Third Conference on Computability in Europe, June 18-23. Universita degli studi di Sienna, Dipartimento di Roberto Magari. Local Proceeedings (2007),
  119. Martz, E.: Knots in Proteins (2000),
  120. Matsuno, K.: Nonequilibrium dynamics of dissipative systems and its application to a macroscopic system. IEEE Trans. Syst. Man & Cybern. SMC-8, 526–533 (1978)MathSciNetCrossRefGoogle Scholar
  121. Matsuno, K.: Protobiology: Physical Basis of Biology. CRC Press, Boca Raton (1989) ISBN-10: 0849364035; ISBN-13: 978-0849364037Google Scholar
  122. Matsuno, K.: Internalist Stance and the Physics of Information. BioSystems 38, 111–118 (1996)CrossRefGoogle Scholar
  123. Matsuno, K.: Tailoring Thermodynamics for the Occurrence of Macroscopic Quantum Coherence - the Origin of Memory. In: Conference on Emergence ECHO IV, Odense, Denmark, July 31-August 4 (2000),
  124. Matsuno, K.: Quantum Mechanics in First, Second and Third Person Descriptions. BioSystems 68(2-3), 107–118 (2003)CrossRefGoogle Scholar
  125. Matsuno, K.: Framework of space and time from the proto-semiotic perspective. Biosemiotics 4, 103–118 (2011a)CrossRefGoogle Scholar
  126. Matsuno, K.: Receptive openness to a message and its dative – a materialist origin of time. Information 2, 383–405 (2011b)CrossRefGoogle Scholar
  127. Maturana, H.R., Varela, F.J.: Autopoiesis and Cognition: The Realization of the Living. Boston Studies in the Philosophy of Science, vol. 42. D. Reidel, Dordrecht (1980) ISBN-10: 9027710163; ISBN-13: 978-9027710161Google Scholar
  128. McFadden, J.: Quantum Evolution: How Physics’ Weirdest Theory Explains Life’s Biggest Mystery. W. W. Norton & Company (2002) ISBN-10: 0393323102; ISBN-13: 978-0393323108Google Scholar
  129. Miller, D.B., Fredkin, E.: Two-state, Reversible, Universal Cellular Automata in Three Dimensions. In: Proc. 2nd Conf. on Computing Frontiers, Ischia, Italy, pp. 45–51. ACM (2005)Google Scholar
  130. Monz, T., Schindler, P., Barreiro, J.T., Chwalla, M., Nigg, D., Coish, W.A., Harlander, M., Hänsel, W., Hennrich, M., Blatt, R.: 14-Qubit Entanglement: Creation and Coherence. Phys. Rev. Lett. 106, 130506 (2011), CrossRefGoogle Scholar
  131. Mossio, M., Longo, G., Stewart, J.: A computable expression of closure to efficient causation. Journal of Theoretical Biology 257(3), 489–498 (2009)CrossRefGoogle Scholar
  132. Nottale, L.: Fractal Space-time and Microphysics: Towards a Theory of Scale Relativity. World Scientific (1993) ISBN 9810208782Google Scholar
  133. Nottale, L., Auffray, C.: Scale relativity and integrative systems biology 2. Macroscopic quantum-type mechanics. Prog. Biophys. Mol. Biol. 97, 115–157 (2008)CrossRefGoogle Scholar
  134. Osnaghi, S., Freitas, F., Freire, O.: The Origin of the Everettian Heresy. Studies in History and Philosophy of Science, Part B: Studies in History and Philosophy of Modern Physics 40(2), 97–123 (2009), doi:10.1016/j.shpsb.2008.10.002, ISSN: 1355-2198MathSciNetzbMATHCrossRefGoogle Scholar
  135. Panitchayangkoon, G., Hayes, D., Fransted, K.A., Caram, J.R., Harel, E., Wen, J., Blankenship, R.E., Engel, G.S.: Long-Lived Quantum Coherence in Photosynthetic Complexes at Physiological Temperature. Proc. Natl. Acad. Sci. USA 107(29), 12766–12770 (2010)CrossRefGoogle Scholar
  136. Pattee, H.H.: Can Life Explain Quantum Mechanics? In: Bastin, T. (ed.) Quantum Theory and Beyond. Cambridge University Press (1971) ISBN-10: 052107956X; ISBN-13: 978-0521079563. 307-319Google Scholar
  137. Pedraza, J.M., van Oudenaarden, A.: Noise propagation in gene networks. Science 307, 1965–1969 (2005)CrossRefGoogle Scholar
  138. Peirce, C.S.: Vague. In: Baldwin, J.M. (ed.) Dictionary of Philosophy and Psychology, vol. 2, p. 748. Macmillan, London (1901)Google Scholar
  139. Peirce, C.S.: Issues of Pragmaticism. The Monist 15, 481–499 (1905)Google Scholar
  140. Penrose, R.: Shadows of the Mind: A Search for the Missing Science of Consciousness, Oxford (1994) ISBN 0-19-853978-9, LoC Q335Google Scholar
  141. Penrose, R.: The Road to Reality. Vintage Books (2005) ISBN 0 099 44068 7Google Scholar
  142. Pickering, A.: Evolution Haute Couture: Art and Science in the Postbiological Age. In: Bulatov, D. (ed.), Kaliningrad, NCCA (2011)Google Scholar
  143. Phillips, W.A.: How Do Neural Systems Use Probabilistic Inference that is Context-Sensitive to Create and Preserve Organized Complexity. In: Simeonov, P.L., Smith, L.S., Ehresmann, A.C. (eds.) Integral Biomathics: Tracing the Road to Reality, vol. 106, pp. 63–70. Springer, Heidelberg (2012)Google Scholar
  144. Pribram, K.H., Nuwer, M., Baron, R.J.: The holographic hypothesis of memory structure brain function and perception. In: Atkinson, R.C., Krantz, D.H., Luce, R.C., Suppes, P. (eds.) Contemporary Developments in Mathematical Psychology, vol. 11, pp. 416–457. Freeman, San Francisco (1974)Google Scholar
  145. Pribram, K.H.: Proposal for a quantum physical basis for selective learning. 2001. In: Proc. 4th Int. Conf. on Emergence, Complexity, Hierarchy and Order. Odense, Denmark, July 31- August 4 (2001)Google Scholar
  146. Prigogine, I., Stengers, I.: La nouvelle alliance: métamorphose de la science. Gallimard (1979) ISBN-10: 2070287505; ISBN-13: 978-2070287505Google Scholar
  147. Ray, T.S.: Future Minds, Mental Organs, and Ways of Knowing. In: Bulatov, D. (ed.) Evolution Haute Couture: Art and Science in the Postbiological Age. Kaliningrad, NCCA (2011) (in press)Google Scholar
  148. Ritz, T., Thalau, P., Phillips, J.B., Wiltschko, R., Wiltschko, W.: Magnetic Orientation and Magnetoreception in Birds and Other Animals. Nature 429, 177–180 (2004)CrossRefGoogle Scholar
  149. Root-Bernstein, R.S., Dillon, P.F.: Molecular complementarity, I: The molecular complementarity theory of the origin and evolution of life. J. Theor. Biol. 188, 447–479 (1997)CrossRefGoogle Scholar
  150. Root-Bernstein, R.S.: A modular hierarchy-based theory of the chemical origins of life, based on molecular complementarity. Accounts Chem. Res. (2011) (in press)Google Scholar
  151. Root-Bernstein, R.: Processes and Problems That May Define the New BioMathematics Field. In: Simeonov, P.L., Smith, L.S., Ehresmann, A.C. (eds.) Integral Biomathics: Tracing the Road to Reality, vol. 106, pp. 3–19. Springer, Heidelberg (2012)Google Scholar
  152. Rosen, R.: Life Itself: A Comprehensive Inquiry into the Nature, Origin, and Fabrication of Life. Columbia University Press, New York (1991)Google Scholar
  153. Rosenfeld, N., Young, J.W., Alon, U., Swain, P.S., Elowitz, M.B.: Gene regulation at the single-cell level. Science 307, 1962–1965 (2005)CrossRefGoogle Scholar
  154. Rössler, O.E.: Endophysics. In: Casti, J.L., Karlqvist, A. (eds.) Real Brains, Artificial Minds. Elsevier (1987) ISBN-10: 0444011552; ISBN-13: 978-0444011558 25-46Google Scholar
  155. Rössler, O.E.: Boscovich Covariance. In: Casti, J.L., Karlqvist, A. (eds.) Beyond Belief, ch. 4. CRC Press (1990) ISBN-10: 0849342910; ISBN-13: 978-0849342912Google Scholar
  156. Rössler, O.E.: Endophysics: the World as an Interface. World Scientific (1998) ISBN 981-02-2752-3Google Scholar
  157. Rössler, O.E.: Variantology: Einstein–Bohr Battle Confirms Everett’s Eternal Now. In: Zielinski, S., Fürlus, E., Irrgang, D. (eds.) Variantology 5: Neapolitan Affairs, On Deep Time Relations of Arts, Sciences and Technologies, pp. 417–432. Verlag der Buchhandlung Walter König, Cologne (2011)Google Scholar
  158. Russe, A.S.: Computational Biology: New Research. Nova Science Publishers Inc., New York (2009) ISBN 978-1-60876-545-4Google Scholar
  159. Salthe, S.N.: Evolving Hierarchical Systems. Columbia University Press (1985) ISBN-10: 0231060165; ISBN-13: 978-0231060165Google Scholar
  160. Salthe, S.N.: Development and Evolution: Complexity and Change in Biology. The MIT Press (1993) ISBN-10: 0262193353; ISBN-13: 978-0262193351Google Scholar
  161. Salthe, S.N., Matsuno, K.: Self-organization in Hierarchical Systems. J. Soc. Evol. Syst. 18, 327–338 (1995)CrossRefGoogle Scholar
  162. Salthe, S.N.: Theoretical Biology as an Anticipatory Text: the Relevance of Uexkull to Current Issues in Evolutionary Systems. Semiotica 134, 359–380 (2001)Google Scholar
  163. Salthe, S.N.: Two Frameworks for Complexity Generation in Biological Systems. In: Gershenson, C., Lenaerts, T. (eds.) Evolution of Complexity, ALifeX Procedings. Indiana University Press, Bloomington (2005a),
  164. Salthe, S.: Semiotics in Biology: Inside neoDarvinism. Journal of Biosemiotics 1, 505–518 (2005b); reprinted in Barbieri, M. (ed.) Biosemiotic Research Trends, ch. 12, pp, 255–268. Nova Science, New York, ISBN-10: 1-60021-574-2; ISBN 13: 978-1-60021-574-2Google Scholar
  165. Salthe, S.N.: On Koichiro Matsuno’s paper "Molecular Semiotics towards the Emergence of Life". Biosemiotics I, 145–146 (2008), doi:10.1007/s12304-008-9000-xGoogle Scholar
  166. Salthe, S.N.: Development (and Evolution) of the Universe. Foundations of Science 15, 357–367 (2010), doi:10.1007/s10699-010-9181-zCrossRefGoogle Scholar
  167. Sarovar, M., Ishizaki, A., Fleming, G.R., Whaley, B.: Quantum Entanglement in photosynthetic light-harvesting complexes. Nature Physics 6, 462–467 (2010),, doi:10.1038/nphys1652CrossRefGoogle Scholar
  168. Scholes, G.D.: Biophysics: Green Quantum Computers. Nature Physics 6, 402–403 (2009),, doi:10.1038/nphys1693CrossRefGoogle Scholar
  169. Schroeder, M.J.: Quantum Coherence without Quantum Mechanics in Modeling the Unity of Consciousness. In: Bruza, P., Sofge, D., Lawless, W., van Rijsbergen, K., Klusch, M. (eds.) QI 2009. LNCS (LNAI), vol. 5494, pp. 97–112. Springer, Heidelberg (2009)CrossRefGoogle Scholar
  170. Schroeder, M.J.: Concept of Information as a Bridge between Mind and Brain. Information 2(3), 478–509 (2011)CrossRefGoogle Scholar
  171. Schrödinger, E.: What Is Life? The Physical Aspect of the Living Cell. The Macmillan Company. ASIN: B000JTFNAO (1945); reprinted in 1992 by Cambridge University Press. ASIN: B000SEKM3IGoogle Scholar
  172. Seaman, B., Rössler, O.E.: Neosentience - The Benevolence Engine. Intellect/University of Chicago Press, Chicago (2011) ISBN-10: 1841504041; ISBN-13: 978-1841504049Google Scholar
  173. Sension, R.J.: Biophysics: Quantum Path to Photosynthesis. Nature 446, 740–741 (2007)CrossRefGoogle Scholar
  174. Seth, A.K., Barrett, A.B., Barnett, L.: Causal density and information integration as measures of conscious level. Phil. Trans. Roy. Soc. A 369, 3748–3767 (2011)MathSciNetzbMATHCrossRefGoogle Scholar
  175. Siegelmann, H.: Computation Beyond the Turing Limit. Science 268(5210), 545–548 (1995)CrossRefGoogle Scholar
  176. Simeonov, P.L.: The Wandering Logic of Intelligence: Or Yet Another View on Nomadic Communications. In: Proc. of SMARTNET 1999, Pathumthani, Thailand, November 22-26, pp. 293–306. Kluwer Academic Publishers, The Netherlands (1999),, ISBN: 0-7923-8691-4. 293-306
  177. Simeonov, P.L.: The Viator Approach: About Four Principles of Autopoietic Growth On the Way to Hyperactive Network Architectures. In: Proc. IEEE FTPDS 2002 & IPDPS 2002, Ft. Lauderdale, FL, USA, April 15-19, pp. 320–327. IEEE Computer Society, Washington, DC (2002a),, ISBN: 0-7695-1573-8
  178. Simeonov, P.L.: WARAAN: A Higher-Order Adaptive Routing Algorithm for Wireless Multimedia in Wandering Networks. In: 5th IEEE International Symposium on Wireless Personal Multimedia Communications (WPMC 2002), Honolulu, Hawaii, USA, October 27-30, pp. 1385–1389 (2002b),
  179. Simeonov, P.L.: The Wandering Logic Intelligence, A Hyperactive Approach to Network Evolution and Its Application to Adaptive Mobile Multimedia Communications, Dissertation, Technische Universität Ilmenau, Faculty for Computer Science and Automation, Die Deutsche Bibliothek, urn:nbn:de:gbv:ilm1-2002000030 (December 2002c),
  180. Simeonov, P.L.: Integral Biomathics: A Post-Newtonian View into the Logos of Bios. J. Progress in Biophysics and Molecular Biology 102(2/3), 85–121 (2010b),, doi:10.1016/j.pbiomolbio, 01.005, ISSN:0079-6107
  181. Simeonov, P.L.: Integral Biomathics: A New Era of Biological Computation. Part I. In: Contributions to the online FET FLAGSHIP Consultation, Future and Emerging Technologies Unit. Status, April 30, pp. 100–105 (2010a),
  182. Simeonov, P.L., Ehresmann, A.C., Smith, L.S., Gomez Ramirez, J., Repa, V.: A New Biology: A Modern Perspective on the Challenge of Closing the Gap between the Islands of Knowledge. In: Cezon, M., Wolfsthal, Y. (eds.) ServiceWave 2010 Workshops. LNCS, vol. 6569, pp. 188–195. Springer, Heidelberg (2011)CrossRefGoogle Scholar
  183. Simon, H.A.: The Sciences of the Artificial. MIT Press, Cambridge (1981)Google Scholar
  184. Sloman, A., Chrisley, R.L.: More things than are dreamt of in your biology: Information-processing in biologically inspired robots. Cognitive Systems Research 6, 145–174 (2004),, doi:10.1016/j.cogsys.2004.06.004CrossRefGoogle Scholar
  185. Smits, E.C.P., Mathijssen, S.G.J., van Hal, P.A., Setayesh, S., Geuns, T.C.T., Mutsaers, K.A.H.A., Cantatore, E., Wondergem, H.J., Werzer, O., Resel, R., Kemerink, M., Kirchmeyer, S., Muzafarov, A.M., Ponomarenko, S.A., de Boer, B., Blom, P.W.M., de Leeuw, D.M.: Bottom-up Organic Integrated Circuits. Nature 455, 956–959 (2008)CrossRefGoogle Scholar
  186. Sornette, D.: Critical Phenomena in Natural Sciences: Chaos, Fractals, Selforganization and Disorder: Concepts and Tools. Springer Series in Synergetics. Springer, Heidelberg (2000) ISBN- 978-3540308829Google Scholar
  187. Spencer-Brown, G.: Laws of Form. Crown Publishers (1972) ISBN 0-517-52776-6Google Scholar
  188. Taylor, W.R.: A Deeply Knotted Protein Structure and How it Might Fold. Nature 406, 916–919 (2000)CrossRefGoogle Scholar
  189. Tegmark, M.: Importance of quantum decoherence in brain processes. Phys. Rev. E 61, 4194–4206 (2000),, doi:10.1103/PhysRevE.61.4194CrossRefGoogle Scholar
  190. Turing, A.: Systems of Logic based on Ordinals. Proc. London Math. Soc. Ser. 2 45, 158–226 (1939), CrossRefGoogle Scholar
  191. Ulanowicz, R.E.: Growth and Development: Ecosystems Phenomenology. Excel Press (1986) ISBN 0-595-00145-9Google Scholar
  192. Ulanowicz, R.E.: Ecology, the Ascendent Perspective. Columbia University Press (1997) ISBN 0-231-10828-1; ISBN 0-231-10829-XGoogle Scholar
  193. Ulanowicz, R.E.: A Third Window: Natural Life beyond Newton and Darwin. Templeton Foundation Press (2009) ISBN 978-1-59947-154-9Google Scholar
  194. von Neumann, J.: Theory of Self-Reproducing Automata (edited and completed by Burks, A.). University of Illinois Press, Champaign (1966)Google Scholar
  195. Vanbremeersch, J.-P., Ehresmann, A.C.: Approach to a model of the aging phenomenon. In: Proc. IXth International Congress of Cybernetics & Systems, New Delhi (1993),
  196. Weiss, P.A.: Hierarchically Organized Systems in Theory and Practice. Hafner, New York (1971)Google Scholar
  197. Wepiwé, G., Simeonov, P.L.: HiPeer: A Highly Reliable P2P System. J. IEICE Trans. Fundamentals. Special Issue on Information and Systems on Parallel and Distributed Computing and Networking E89-D(2), 570–580 (2006), doi:10.1093/ietisy/e89-d.2.570Google Scholar
  198. Wigner, E.P.: The Unreasonable Effectiveness of Mathematics in the Neural Sciences. Communications in Pure and Applied Mathematics 13(I) (1960),
  199. Wolfram, S.: Cellular Automata and Complexity: Collected Papers. Westview Press (1994) ISBN-10: 0201626640; ISBN-13: 978-0201626643Google Scholar
  200. Wolfram, S.: A New Kind of Science. Wolfram Media Inc. (2002) ISBN-10: 1579550088; ISBN-13: 978-1579550080Google Scholar
  201. Yardley, I.B.: The Circular Theory. Integrated Thought Concepts (2010) ISBN 0-9725-7562-6Google Scholar
  202. Zadeh, L.A.: Fuzzy Sets and Systems. In: Fox, J. (ed.) System Theory. Microwave Research Institute Symposia Series, vol. XV, pp. 29–37. Polytechnic Press, Brooklyn (1965)Google Scholar
  203. Zlotin, A.I.: Thermodynamic Aspects of Developmental Biology. Karger, Basel (1972)Google Scholar
  204. Zlotin, A.I.: The Second Law, Negentropy, Thermodynamics of Linear Processes. In: Lamprecht, I., Zotin, A.I. (eds.) Thermodynamics of Biological Processes, p. 19. de Gruyter, New York (1978)Google Scholar

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Authors and Affiliations

  1. 1.Integral BiomathicsBerlinGermany
  2. 2.InnovationOttawaCanada
  3. 3.Living SystemsLiegeBelgium
  4. 4.MathematicsAmiensFrance
  5. 5.Philosophy of ScienceHawthornAustralia
  6. 6.Information TheoryCharlottesvilleUSA
  7. 7.Mathematics and CognitionLogronoSpain
  8. 8.Mind-Matter UnificationCambridgeUK
  9. 9.Mathematics and Computer ScienceGentBelgium
  10. 10.Biophysics and BioengineeringTokyoJapan
  11. 11.PhysiologyWood DaleUSA
  12. 12.Biochemistry and Chaos TheoryTubingenGermany
  13. 13.Systems Science and Natural PhilosophyDepositUSA
  14. 14.Mathematics and Theoretical PhysicsTokyoJapan
  15. 15.Visual Arts and ScienceDurhamUSA
  16. 16.BiocomputingRennesFrance
  17. 17.Neuroscience and Natural ComputingStirlingUK

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