Stuart Kauffman in April 2010
|Born||September 28, 1939|
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, as well as for applying models of Boolean networks to simplified genetic circuits. His hypotheses stating that cell types are attractors of such networks, and that genetic regulatory networks are "critical", have found experimental support.
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 residency in Emergency Medicine, 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, 1987–1992.
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. Kauffman holds the founding broad biotechnology patents in combinatorial chemistry and applied molecular evolution.
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.
From 2004 to 2009 Kauffman held a joint appointment at the University of Calgary in Biological Sciences and Physics and Astronomy. He is 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.
In January 2009 Kauffman became a Finland Distinguished Professor (FiDiPro) at Tampere University of Technology, Department of Signal Processing. The appointment is until the end of 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.
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. 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. This topic is also discussed in Stuart Kauffman's recent contribution "Statable and non–prestatable fitness landscapes", which is published as the foreword to the book "Recent Advances in the Theory and Application of Fitness Landscapes".
- 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
- 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.
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.
- 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. 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
- 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.
- Kauffman, S. (2012). "Answering Descartes: Beyond Turing" in The Once and Future Turing Eds. 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 ...,
- Kauffman, S. (2014) "Foreword: Statable and non–prestatable fitness landscapes" in Recent Advances in the Theory and Application of Fitness Landscapes Eds. Hendrik Richter and Andries P. Engelbrecht, Springer-Verlag.
- 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
- "From physics to semiotics" (Kauffman's seminar in the Dept. of Semiotics of the University of Tartu on April 27, 2012)