Library - Resources for futher reading

Philosophy of Information and Function

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

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

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
(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

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.


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

 Christoph Adami, Introduction to Artificial Life, Telos (Springer-Verlag), 1998.

Evolutionary Biology

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

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

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.

Please report broken links to Dr Keith Farnsworth at QUB