Philosophy of Information and Function
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Information: A Very Short
Introduction by Luciano Floridi Semantic Concepts of Information (Staford Encyclopedia of Philosopy) - Floridi The teleological notion of 'function' - Karen Neander Floridi, L. (2005). Is semantic information meaningful data? Philosophy and Phenomenological Research, 70(2):351–370. Informational realism - L. Floridi Biological Function, in Routledge Encyclopedia of Philosophy (December, 2011). K. Neander. Information and the Nature of Reality: From Physics to Metaphysics Paul Davies (2010) ISBN-10: 0521762251 A Defence of Informational Structural Realism, Synthese, 2008, 161.2, 219-253. L. Floridi Information, invited contribution to the Encyclopedia of Science, Technology, and Ethics, (ESTE) edited by Carl Mitcham (Macmillan, 2005). - L. Floridi Data, article for the International Encyclopedia of the Social Sciences, 2nd edition, editor in chief William A. Darity (Detroit: Macmillan, 2008). L. Floridi. |
Mathematical Information Theory & Thermodynamics
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Information Theory Primer for Molecular Biologists. Tom Schneider The Use of Information Theory in Evolutionary Biology. Christoph Adami Second Law of Thermodynamics - not a bad tutorial Entropy and Information - Kubat & Zeman (1975): old but still useful, with excellent first chapter by Paul Davies. Entropy: The devil on the pillion - J. Zernike (1972) Hard to get, but worth it. ISBN 90 2010 580 9 Gell-Mann, M. and Lloyd, S. (1996). Information measures, effective complexity, and total information. Complexity, 2(1):44–52. McAllister, J. (2003). Effective complexity as a measure of information content. Philosophy of Science, 70(2):302–307. |
Complexity and Network Theory
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Information measures of
complexity, emergence, self-organization, homeostasis, and autopoiesis.
(Gershenson et al.) The world as evolving information, by Carlos Gershenson S.I. Walker, B. Callahan, G. Arya, J.D. Barry, T. Bhattacharya, S. Grigoryev, M. Pellegrini, K. Rippe, S.M. Rosenberg (2013) Evolutionary Dynamics and Information Hierarchies in Biological Systems. Annals. N.Y. Acad. Sci. USA. |
Information Theory for Molecular Biology |
A brief review of molecular information theory -
T. D. Schneider Shannon Information Theory and Molecular Biology (2008) - F. Fabris Schneider, T. D.(1991). Theory of molecular machines. 1. Channel capacity of molecular machines. Journal of Theoretical Biology, 148(1):83–123. Schneider, T. D. (2006). Claude Shannon: Biologist. IEEE Engineering In Medicine and Biology Magazine, 25(1):30–33. Schneider, T. D. (2000). Evolution of biological information. Nucleic Acids Res., 28:2794–2799. Rhee, Cheong and Levchenko (2013) The application of information theory to biochemical signaling systems. Lehn, J.M. Toward Self-Organization and Complex Matter. Science 29 March 2002: 295 no. 5564 pp. 2400-2403 DOI: 10.1126/science.1071063 we also recommend: Lehn, J.M. Supramolecular Chemistry: Concepts and Perspectives. (available here) |
Thermodynamics of
Life
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Kaila, V. R. I. and Annila, A.
(2008). Natural selection for least action. Proceed- ings of the Royal
Society A-Mathematical Physical and Engineering Sciences,
464(2099):3055–3070 Prigogine, I. (1977). Self-Organization in Non-Equilibrium Systems. Wiley, New York. |
Biocomplexity
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C. Adami. Biological Complexity and Biochemical Information.
In: Encyclopedia of Complexity and Systems Science, R. Meyers, ed.,
Springer Verlag (2009), pp 489-511. Modular Evolution: How Natural Selection Produces Biological Complexity (2010) - Lucio Vinicius. ISBN-10: 0521728770 Gell-Mann, M. and Lloyd, S. (1996). Information measures, effective complexity, and total information. Complexity, 2(1):44–52. Adami, C., Ofria, C., and Collier, T. C. (2000). Evolution of biological complexity. PNAS, 97(9):4463–4468. Kauffman, S. A. (1993). Origins of Order: Self-Organization and Selection in Evolution. Oxford University Press, Oxford, UK. Annila, A. and Kuismanen, E. (2009). Natural hierarchy emerges from energy dispersal. Biosystems, 95(3):227–233. Carroll, S. (2001). Chance and necessity: the evolution of morphological complexity and diversity. Nature, 409(6823):1102–1109. |
Origins of Life and Astrobiology |
Paul Davies, The Fifth Miracle,
Simon and Schuster, 1999. Information Theory, Evolution, and The Origin of Life - H.P. Yockey (2005). ISBN-10: 0521802938 Annila, A. and Annila, E. (2008). Why did life emerge? International Journal of Astrobiology, 7(3-4):293–300. N. Vaiyda, S.I. Walker and N. Lehman (2013) Recycling of Informational Units Leads to Selection of Replicators in a Prebiotic Soup. Chemistry & Biology 20: 241 – 252. S.I. Walker and P.C.W. Davies (2013) The Algorithmic Origins of Life. J. Roy. Soc. Interface 6:20120869. Preprint Bitbol, M. and Luisi, P. (2004). Autopoiesis with or without cognition: defining life at its edge. Journal of the Royal Society Interface, 1(1):99–107. Rosen, R. (1991). Life Itself: A Comprehensive Inquiry into the Nature, Origin, and Fabrication of Life. Columbia University Press., New York. Farnsworth, K.D. An organisational systems-biology view of viruses explains why they are not alive. BioSystems 2020. Preprint |
Artificial Life and Computing
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Christoph Adami,
Introduction to Artificial Life, Telos (Springer-Verlag), 1998. |
Evolutionary Biology
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C. Adami. The Use of Information Theory in Evolutionary Biology,
Annals NY Acad. Sciences 1256 (2012) 49-65. |
Biodiversity and Function |
Dimensionality of Biodiversity:
Structure,Phylogeny & Function (2012) Lyashevska & Farnsworth. Functional Information of Biodiversity: the source of value? (2012) Farnsworth et al. Lyashevska, O. and Farnsworth, K. D. (2012). How many dimensions of biodi- versity do we need? Ecological Indicators, 18:485–492. |
Synthesis Papers
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What is
Life? (1944) Erwin Schrodinger - the inspiration for this website
and project. Living is Information Processing: molecules to ecosystems (2013) - Farnsworth et al. The Natural Philosophy of Entropy by Salthe Information Theory, Evolution, and The Origin of Life - H.P. Yockey (2005). ISBN-10: 0521802938 |
Code Biology
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Barbieri, M. (2018). What is code biology? Biosystems 164:1,10. Barbieri, M. (2003). The Organic Codes: An Introduction to Semantic Biology. Cambridge University Press, Cambridge. Barbieri, M. (2015). Code Biology: A New Science of Life. Springer, Heidelberg. |