References

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[ALIFE 2012] 12th International Conference on the Synthesis and Simulation of Living Systems; http://www.alife12.org/

; 2012.

[Ardejani and Orner 2013] Ardejani, Maziar S. and Brendan P. Orner; Obey the Peptide Assembly Rules; Science 340, May 3, 2013; p. 561; 2013.

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[Austumian and Hanggi 2002] Austumian, R. Dean and Peter Hanggi; Brownian Motors; Physics Today, November 2002. Copyright 2002 American Institute of Physics S-0031-9228-0211-010-6. Also at http://users.df.uba.ar/gsolovey/fisica2/bib/ratchets/309.pdf; 2002.

[Ayodeji and Laster 2007] Ayodeji, O. and S. Laster; “Autonomic Computing: Towards a Self-Healing System; Proceedings of the Spring 2007 American Society for Engineering Education Illinois-Indiana Section Conference; American Society for Engineering Education.

[Bolch, et. al. 2006] Bolch, Gunter, Stephan Greiner, Hermann de Meer, Kishor S. Trivedi; Queueing Networks and Markov Chains: Modeling and Performance Evaluation with Computer Science Applications; Second Edition; John Wiley and Sons; Hoboken, NJ; 2006.

[Bulsara and Gammaitoni 1996] Bulsara, Adi and Luca Gammaitoni; Tuning in to Noise; Physics Today, March 1996. Copyright 1996 American Institute of Physics S-0031-9228-9603-030-X. Also at http://www.nipslab.org/files/vol49no3p39-45.pdf; 1996.

[Capra 1996]. Capra, Fritjof; The Web of Life: A New Scientific Understanding of Living Systems; Anchor Books, published by Doubleday, a division of Bantam-Doubleday Dell Publishing Group, Inc.; New York, New York; 1996.

[Chalmers 2003] Chalmers, Matthew; Amino Acid Detected in Space; physicsworld.com; at http://physicsworld.com/cws/article/news/2003/aug/11/amino-acid-detected-in-space.

[Cover and Thomas 1991] Cover, Thomas M. and Joy A. Thomas; Elements of Information Theory; John Wiley & Sons, Inc.; New York; 1991.

[ECAL 2012] 2012 European Conference on Artificial Life; http://eacl2012.org/home/; 2012.

[Darwin 1859] Darwin, Charles; The Origin of Species: By Means of Natural Selection or the Preservation of Favoured Races in the Struggle for Life; John Murray, Albemarle Street; 1859. Bantam Classic, 2008.

[Fletcher, et. al. 2013] Jordan M. Fletcher, Robert L. Harniman, Frederick R. H. Barnes, Aimee L. Boyle, Andrew Collins, Judith Mantell, Thomas H. Sharp, Massimo Antognozzi, Paula J. Booth, Noah Linden, Mervyn J. Miles, Richard B. Sessions, Paul Verkade, Derek N. Woolfson; Self-Assembling Cages from Coiled-Coil Peptide Modules; Science 340, May 3, 2013; p. 561; 2013.

[Forrester 1989], Forrester Jay W.; The Beginning of System Dynamics; Banquet Talk at the international meeting of the System Dynamics Society Stuttgart, Germany; At http://leml.asu.edu/jingle/Web_Pages/EcoMod_Website/Readings/SD+STELLA/Forrester-Begin%27g-SD_1989.pdf; 1989.

[Gulukota and Wolynes 1994] Gulukota, Kamalakar and Peter G. Wolynes; Statistical mechanics of kinetic proofreading of protein folding in vivo; Protein Science (1994), 3:650-668. PNAS USA, Vol. 91, pp 9292-9296, September 1994, biophysics; At http://www.pnas.org/content/91/20/9292.full.pdf;1994.

[Haws 2007] Haws, Mark; Middle World: The restless heart of matter and life; Macmillan; London, New York; 2007.

[Hazen 2005] Hazen, Robert M.; Genesis: The Scientific Quests for Life’s Origin; Joseph Henry Press, Washington, DC; 2005.

[HollandJG 2013] Holland, Grant; Organic Complex Systems web site. At http://organiccomplexsystems.org/ ; 2013.

[HollandJG-I 2011] Holland, Grant; Organic Complex Systems Part I - Principles of Organization; Unpublished manuscript. At http://organiccomplexsystems.org/docs/OCSWorkingDoc/OCSvol1/; 2011.

[HollandJG-II 2011] Holland, Grant; Organic Complex Systems Part II- Organodynamics; Unpublished manuscript. At http://organiccomplexsystems.org/docs/OCSWorkingDoc/OCSvol2/; 2011.

[HollandJG-III 2011] Holland, Grant; Organic Complex Systems Part III - Considerations and Implications; Unpublished manuscript. At http://organiccomplexsystems.org/docs/OCSWorkingDoc/OCSvol3/; 2011.

[HollandJGa 2012] Holland, Grant; Overview document. Organic Complex Systems: Chance, Order and Evolutionary Transformation in Living and Lifelike Organisms; Unpublished manuscript. At http://organiccomplexsystems.org/docs/OCSOverviewArticle/; 2012.

[IBM Autonomic 2001] IBM Corporation, “Autonomic computing - a manifesto”, www.research.ibm.com/autonomic, 2001.

[IEEE ALIFE 2012] 2012 Seventeenth International Symposium on Artificial Life and Robotics (AROB 17th 2012); http://www.ieee.org/conferences_events/conferences/conferencedetails/; 2012.

[Jaynes 1957] Jaynes, E. T.; Information Theory and Statistical Mechanics; The Physical Review, Vol. 106, No 4, 620-630, May 15, 1957. Also at http://www.weizmann.ac.il/complex/tlusty/courses/InfoInBio/Papers/JaynesInformationTheory.pdf, 1957.

[Karplus and Weaver 1957] Karplus, Martin and David L. Weaver; Protein folding dynamics: the diffusion-collision model and experimental data; Protein Science (1994), 3:650-668. Cambridge University Press. Copyright 1994 The Protein Society. At http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2142854/pdf/8003983.pdf; 1994. [Khinchin 1957] Khinchin, A. I; The Mathematical Foundations of Information Theory; Dover Publications, Inc.; 1957; New York.

[Kleeman 2009] Kleeman, Richard; course syllabus: Information Theory and Predictability; Syllabus at: http://www.math.nyu.edu/faculty/kleeman/syllabusinfo.html; 2009.

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[Leff 2012] Leff, Harvey S.; Removing the Mystery of Entropy and Thermodynamics – Part I; The Physics Teacher, Vol. 50, p. 28; January 2012.

[Meadows 2008] Meadows, Donella H.; Thinking in Systems: A Primer; The Sustainability Institute; Chelsea Green Publishing Company. 2008.

[Monod 1972] Monod, Jacques; Chance and Necessity: An Essay on the Natural Philosophy of Modern Biology; 1972; vintage Books; NY, NY.

[Nowak 2006] Nowak, Martin A.; Evolutionary Dynamics: Exploring the Equations of Life; Harvard University Press. 2006.

[Prigogine 1996] Prigogine, Ilya; The End of Certainty: Time, Chaos, and the New Laws of Nature; 1996; The Free Press, New York.

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[Shannon 1963] Shannon, Claude E.; The Mathematical Theory of Communication; First Paperback Edition; University of Illinois Press; 1963.

[Strogatz1994] Strogatz, Steven H.; Nonlinear Dynamics and Chaos: With Applications to Physics, Biology, Chemistry and Engineering; Westview Press, 1994.

[syntheticbiology.org 2012] Web site of OpenWetWare, an open organization started by a group from MIT and Harvard; http://syntheticbiology.org/; 2012.

[Tolman 1938] Tolman, Richard C.; The Principles of Statistical Mechanics; Oxford University Press; 1938; unabridged Dover Edition; Dover Publications, Inc. New York; 1979.

[Vedral 2010] Vedral, Vlatko; Decoding Reality: The Universe as Quantum Information; Oxford University Press; Oxford, New York; 2010.

[Watson 1970] Watson, James D.; Molecular Biology of the Gene: Second Edition; W. A. Benjamin, Inc., Cambridge, New York; 1970.

[Wilkinson 2006] Wilkinson, Darren J.; Stochastic Modelling for Systems Biology; published by Chapman & Hall/CRC; April 2006.

[Zierenburg, et. all 2000] Zierenburg, Robert A., Michael W. W. Adams, Alissa J. Sharp; Life in extreme environments: Hydrothermal vents; Proceedings of the National Academy of Science; vol. 97, no. 24; http://www.pnas.org/content/97/24/12961.full, November 1, 2000.