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Stuart Kauffman in April 2010
|Born||September 28, 1939|
In 1967 and 1969 Kauffman proposed applying models of Random Boolean networks to simplified genetic circuits. These were very early models of large genetic regulatory networks, proposing that cell types are dynamical attractors of such networks and that cell differentiation steps are transitions between attractors. Recent evidence strongly suggests that cell types in humans and other organisms are indeed attractors. In 1971 he suggested that the zygote may not access all the cell type attractors in the repertoire of the genetic network's dynamics, hence some of the unused cell types might be cancers. This suggested the possibility of "cancer differentiation therapy", for which some evidence may now be accumulating.
In 1971, Kauffman proposed the self-organized emergence of collectively autocatalytic sets of polymers, specifically peptides, for the origin of molecular reproduction. Reproducing peptide, DNA, and RNA collectively autocatalytic sets have now been made experimentally. He is best known for arguing that the complexity of biological systems and organisms might result as much from self-organization and far-from-equilibrium dynamics as from Darwinian natural selection. His hypotheses stating that cell types are attractors of such networks, and that genetic regulatory networks are "critical", have found experimental support. It now appears that the brain is also dynamically critical.
Kauffman graduated from Dartmouth in 1960, was awarded the BA (Hons) by Oxford University (where he was a Marshall Scholar) in 1963, and completed a medical degree (M.D.) at the University of California, San Francisco in 1968. After completing his internship, he moved into developmental genetics of the fruitfly, holding appointments first at the University of Chicago, then at the University of Pennsylvania from 1975 to 1995, where he rose to Professor of Biochemistry and Biophysics. Kauffman held a MacArthur Fellowship between 1987–1992. He also holds an Honorary Degree in Science from the University of Louvain; and was awarded a Gold Medal of the Accademia Lincea in Rome.
Kauffman rose to prominence through his association with the Santa Fe Institute (a non-profit research institute dedicated to the study of complex systems), where he was faculty in residence from 1986 to 1997, and through his work on models in various areas of biology. These included autocatalytic sets in origin of life research, gene regulatory networks in developmental biology, and fitness landscapes in evolutionary biology. With Marc Ballivet, Kauffman holds the founding broad biotechnology patents in combinatorial chemistry and applied molecular evolution, first issued in France in 1987, in England in 1989, and later in the US.
In 1996, Kauffman started BiosGroup, a Santa Fe, New Mexico-based for-profit company that applied complex systems methodology to business problems. BiosGroup was acquired by NuTech Solutions in early 2003. NuTech was bought by Netezza in 2008, and later by IBM.
From 2004 to 2009 Kauffman held a joint appointment at the University of Calgary in Biological Sciences and Physics and Astronomy. He was also an Adjunct Professor in the Department of Philosophy at the University of Calgary. He is an iCORE (Informatics Research Circle of Excellence) chair and the director of the Institute for Biocomplexity and Informatics. Kauffman was also invited to help launch the Science and Religion initiative at Harvard Divinity School; serving as Visiting Professor in 2009.
In January 2009 Kauffman became a Finland Distinguished Professor (FiDiPro) at Tampere University of Technology, Department of Signal Processing. The appointment ended in December, 2012. The subject of the FiDiPro research project is the development of delayed stochastic models of genetic regulatory networks based on gene expression data at the single molecule level.
In January 2010 Kauffman joined the University of Vermont faculty where he continued his work for two years with UVM's Complex Systems Center. From early 2011 to April 2013, Kauffman was a regular contributor to the NPR Blog 13.7, Cosmos and Culture * , with topics ranging from the life sciences, systems biology, and medicine, to spirituality, economics, and the law. Kauffman is also a regular contributor to Edge.org. 
In May 2013 Kauffman joined the Institute for Systems Biology, in Seattle Washington. Following the death of his wife, with others, Kauffman cofounded The Elizabeth Kauffman Institute for Transforming Medicine, (the Manifesto * ).
In 2014, Kauffman with Samuli Niiranen and Gabor Vattay was issued a founding patent on the poised realm (see below), an apparently new "state of matter" hovering reversibly between quantum and classical realms.
Kauffman is best known for arguing that the complexity of biological systems and organisms might result as much from self-organization and far-from-equilibrium dynamics as from Darwinian natural selection.
Some biologists and physicists working in Kauffman's area reserve judgment on Kauffman's claims about self-organization and evolution. A case in point is the introduction to the 2002 book Self Organization in Biological Systems. Roger Sansom's Ingenious Genes: How Gene Regulation Networks Evolve to Control Development (MIT Press, 2011) is an extended criticism of Kauffman's models.
Borrowing from spin glass models in physics, Kauffman invented "N-K" fitness landscapes, which have found applications in biology  and economics. In related work, Kauffman and colleagues have examined subcritical, critical, and supracritical behavior in economic systems.
Kauffman's recent work translates his biological findings to the mind body problem and issues in neuroscience, proposing attributes of a new "poised realm" that hovers indefinitely between quantum coherence and classicality. Kauffman published on this topic in Answering Descartes: Beyond Turing. With colleagues Giuseppe Longo and Maël Montévil, Stuart Kauffman wrote (January 2012) "No entailing laws, but enablement in the evolution of the biosphere," which aims to show that evolution is not law entailed, as is physics, and that, without selection, evolution enables its own future possibilities.
Kauffman's recent work is posted on Physics ArXiv, including "Beyond the Stalemate: Mind/Body, Quantum Mechanics, Free Will, Possible Panpsychism, Possible Solution to the Quantum Enigma" (October 2014) and "Quantum Criticality at the Origin of Life" (February 2015).
He has published over 300 articles and 4 books: Origins of Order; At Home in the Universe; Investigations (Oxford University Press, 1993, 1995, 2000); and Reinventing the Sacred (Basic Books, 2008). A fifth book, Humanity in a Creative Universe is under contract for 2015, with Oxford University Press.
- 1993, Origins of Order: Self-Organization and Selection in Evolution, Oxford University Press, Technical monograph. ISBN 0-19-507951-5
- 1995, At Home in the Universe: The Search for Laws of Self-Organization and Complexity. Oxford University Press.
- 2000, Investigations. Oxford University Press.
- 2008, Reinventing the Sacred: A New View of Science, Reason, and Religion. [Basic Books] - ISBN 0-465-00300-1
- 2015, Humanity in a Creative Universe (in press) Oxford University Press, N.Y.
- 1969, "Metabolic stability and epigenesis in randomly constructed genetic nets," in: Journal of Theoretical Biology, 22:437–467, 1969.
- 1991, "Antichaos and Adaptation," in: Scientific American, August 1991.
- 2004, "Prolegomenon to a General Biology", in William A. Dembski, Michael Ruse, eds., Debating Design: From Darwin to DNA, Cambridge University Press.
- 2004, "Autonomous Agents", in John D. Barrow, P.C.W. Davies, and C.L. Harper Jr., eds., Science and Ultimate Reality: Quantum Theory, Cosmology, and Complexity, Cambridge University Press.
- 2008 "Why Humanity Needs a God of Creativity", New Scientist .
- 2014, "Transforming Medicine: A Manifesto", Scientific American, Worldview .
- 2014, "Beyond the Stalemate: Conscious Mind-Body - Quantum Mechanics - Free Will - Possible Panpsychism - Possible Interpretation of Quantum Enigma". 
- 2015, "Seeker Stuart Kauffman on Free Will, God, ESP and Other Mysteries"; Scientific American 
About Stuart Kauffman
- MacKenzie, Dana (2002). "The Science of Surprise", Discover Magazine, Vol. 23, No. 2, 59–63, February 2002.
- Kauffman about Kauffman: (Video)
- Goldstein, Jeffrey A. (2008). Book Review of "Reinventing the Sacred: A New View of Science, Reason, and Religion", by Stuart Kauffman. In Emergence: Complexity & Organization, 10(3), 117–130.
- Di Bernardo, M., I sentieri evolutivi della complessità biologica nell'opera di S. A. Kauffman, Mimesis, Milano 2011.
- A Richard Kroeling Film: Thinker of Untold Dreams: A Portrait of Stuart Kauffman
- Kauffman, S. A. and McCulloch, W. S. (1967). Random Nets of Formal Genes. Quarterly Progress Report 34, Research Laboratory of Electronics, Massachusetts Institute of Technology.
- Kauffman, S. A. (1969). Metabolic Stability and Epigenesis in Randomly Constructed Genetic Nets. J Theor Biol 22, 437-467.
- Huang, S. and Kauffman, S. A. (2009). Complex Gene Regulatory Networks - from Structure to Biological Observables: Cell Fate Determination. Encyclopedia of Complexity and Systems Science, Editor : R. A. Meyers, Book Title: Encyclopedia of Complexity and Systems Science, Publisher: Springer, ISBN 978-0-387-75888-6
- Kauffman, S. A. (1971). Differentiation of Malignant to Benign Cells. J Theor Biol 311, 429-451.
- Sui Huang, S., Hu, L. Kauffman, S., Zhang, W., Shmulevich, I. (2009).Using cell fate attractors to uncover transcriptional regulation of HL60 neutrophil differentiation. BMC Systems Biology 3: 20.
- Kauffman, S. A. (1971) Cellular Homeostasis, Epigenesis, and Replication in Randomly Aggregated Macromolecular Systems. Journal of Cybernetics 1, 71- 96
- Kauffman, SA (2011) Approaches to the Origin of Life on Earth. Life. 1(1), 34-48; doi:10.3390/life1010034
- Dadon Z, Wagner N, Ashkenasy G (2008) "The Road to Non-Enzymatic Molecular Networks" Angew. Chem. Int. 47, 6128.
- Dadon Z, Wagner N, Cohen-Luria R, and Ashkenasy G. (2012) Reaction Networks. Wagner and Askkenazy's (2008) results demonstrate that molecular replication need not be based on DNA or RNA template replication, still the dominate view for the origin of life. In: Ed. Gale PA and Steed JW. Supramolecular Chemistry: From Molecules to Nanomaterials. John Wiley and Sons, Ltd. ISBN 978-0-470-74640-0.
- Huang, S. and Kauffman, S. A. (2009) Complex Gene Regulatory Networks - from Structure to Biological Observables: Cell Fate Determination. Encyclopedia of Complexity and Systems Science, Editor : R. A. Meyers, Book Title: Encyclopedia of Complexity and Systems Science,Publisher: Springer,ISBN: ISBN 978-0-387-75888-6
- Nykter, M., Price, N. D., Aldana, M., Ramsey, S. A., Kauffman, S. A., Hood, L., Yli-Harja, O. and Shmulevich, I. (2008) Gene Expression Dynamics in the Macrophage Exhibit Criticality. Proc Natl Acad Sci USA 105(6): 1897-1900
- Chialvo, D. R, Critical Brain Dynamics at Large Scale, in Criticality in Neural Systems. 1 By Niebur E, Plenz D, Schuster HG. (eds.) 2013. ISBN 978-3-527-41104-7
- US 5,723,323," Method of identifying a stochastically-generated peptide, polypeptide, or protein having ligand binding property and compositions thereof"
- iCORE Home
- "Projects and professors selected by Tekes to the Finland Distinguished Professor Programme (FiDiPro)". March 20, 2009. Retrieved November 27, 2009.
- "Stuart Kauffman, complex systems pioneer, to join UVM faculty". Retrieved November 27, 2009.
- (US 20120071333A1 (12)PatentApplicationPublication (10)Pub.No.:US2012/0071333A1 (19)United States).
- Vattay, G, Salahub, D, Csaibai, I,Nassmi, A, and Kauffman, S. (2015). Quantum Criticality at the Origin of Life. ArXiv Feb 2015.
- Kauffman, S. A. and Johnsen, S. (1991). Co-Evolution to the Edge of Chaos: Coupled Fitness Landscapes, Poised States, and Co-Evolutionary Avalanches. J Theor Biol 149, 467-505.
- Rivkin, J. W., Siggelkow, N. (2003). Organizational Sticking Points on NK Landscapes. Harvard Business School, Cambridge, MA.
- Felin, T., Kauffman, S., Koppl, R., Longo, G. (December 2014). "Economic Opportunity and Evolution: Beyond Landscapes and Bounded Rationality". Strategic Entrepreneurship Journal 8 (4): 269–282. doi:10.1002/sej.1184.
- Hanel, R., Kauffman, S. A. and Thurner, S. (2007). Towards a Physics of Evolution: Critical Diversity Dynamics at the Edges of Collapse and Bursts of Diversification. Phys Rev E 76, 036110.
- Kauffman, S. (2014). "Answering Descartes: Beyond Turing" in The Once and Future Turing Eds. S. Barry Cooper and Andrew Hodges, Cambridge University Press.
- Longo G, Montévil M, and Kauffman S (2012) No entailing laws, but enablement in the evolution of ...,
- An online chat with Stuart Kauffman on a complexity organization website.
- Video presentation "The adjacent possible" by Kauffman on autonomous agents.
- Biocomplexity and Informatics iCORE Chair.
- Beyond reductionism: Reinventing The Sacred, paper by Kauffman on reductionism.
- Video presentation "Reinventing The Sacred" Stuart Kauffman on his new book. Video talk for a Conference in Doha, Katar, produced, May 17, 2008[dead link]
- SYNCD.org Stuart Kauffman about the need of a "transnational mythic structure"
- Tech Nation discussion with Dr. Moira Gunn on his book "Reinventing the Sacred" (recorded June 6, 2008).[dead link]
- "God Enough" by Steve Paulson Interview with Stuart Kauffman (2008).
- Stuart Kauffman homepage at Tampere University of Technology
- Kauffman's lecture videos at Tampere in April 2010
- Interviews, University of Vermont
- "From physics to semiotics" (Kauffman's seminar in the Dept. of Semiotics of the University of Tartu on April 27, 2012)
- Stuart Kauffman on "The End of a Physics Worldview: Heraclitus and the Watershed of Life"