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 discussed in his book Origins of Order (1993). In 1967[1] and 1969[2] he used random
Boolean networks to investigate generic self-organizing properties of gene regulatory networks, proposing that cell types are dynamical attractors in gene regulatory networks and that cell differentiation can be understood as transitions between attractors. Recent evidence suggests that cell types in humans and other organisms are attractors.[3][4] In 1971 he suggested that a zygote may not be able to access all the cell type attractors in its gene regulatory network during development and that some of the developmentally inaccessible cell types might be cancer cell types.[5] This suggested the possibility of "cancer differentiation therapy". He also proposed the self-organized emergence of collectively
autocatalytic sets of
polymers, specifically
peptides, for the origin of molecular reproduction,[6][7] which have found experimental support.[8][9]
From 2005 to 2009 Kauffman held a joint appointment at the
University of Calgary in biological sciences, physics, and astronomy. He was also an adjunct professor in the Department of Philosophy at the
University of Calgary. He was 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 2010 Kauffman joined the
University of Vermont faculty where he continued his work for two years with UVM's Complex Systems Center.[16] From early 2011 to April 2013, Kauffman was a regular contributor to the
NPR Blog 13.7, Cosmos and Culture,[17] with topics ranging from the life sciences, systems biology, and medicine, to spirituality, economics, and the law.[17]
In May 2013 he joined the Institute for Systems Biology, in Seattle, Washington. Following the death of his wife, Kauffman cofounded Transforming Medicine: The Elizabeth Kauffman Institute.[18]
In 2014, Kauffman with Samuli Niiranen and Gabor Vattay was issued a founding patent[19] on the poised realm (see below), an apparently new "state of matter" hovering reversibly between quantum and classical realms.[20]
In 2015, he was invited to help initiate a general a discussion on rethinking economic growth for the
United Nations.[21] Around the same time, he did research with
University of Oxford professor
Teppo Felin.[22]
Kauffman's NK model defines a
combinatorialphase space, consisting of every string (chosen from a given alphabet) of length . For each string in this search space, a
scalar value (called the fitness) is defined. If a distance
metric is defined between strings, the resulting structure is a landscape.
Fitness values are defined according to the specific incarnation of the model, but the key feature of the NK model is that the fitness of a given string is the sum of contributions from each locus in the string:
and the contribution from each locus in general depends on the value of other loci:
where are the other loci upon which the fitness of depends.
Hence, the fitness function is a
mapping between strings of length K + 1 and scalars, which Weinberger's later work calls "fitness contributions". Such fitness contributions are often chosen randomly from some specified probability distribution.
In 1991, Weinberger published a detailed analysis[23] of the case in which and the fitness contributions are chosen randomly. His analytical estimate of the number of local optima was later shown to be flawed.[citation needed] However, numerical experiments included in Weinberger's analysis support his analytical result that the expected fitness of a string is normally distributed with a mean of approximately
and a variance of approximately
.
Recognition and awards
Kauffman held a
MacArthur Fellowship between 1987 and 1992. He also holds an Honorary Degree in Science from the University of Louvain (1997); He was awarded the Norbert Wiener Memorial Gold Medal for
Cybernetics in 1973, the Gold Medal of the
Accademia dei Lincei in Rome in 1990, the Trotter Prize for Information and Complexity in 2001, and the Herbert Simon award for Complex Systems in 2013. He became a Fellow of the
Royal Society of Canada in 2009.
Works
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 in three areas of
evolutionary biology, namely
population dynamics,
molecular evolution, and
morphogenesis. With respect to molecular biology, Kauffman's
structuralist approach has been criticized for ignoring the role of
energy in driving
biochemical reactions in cells, which can fairly be called self-
catalyzing but which do not simply self-organize.[24] Some biologists and physicists working in Kauffman's area have questioned his claims about self-organization and evolution. A case in point is some comments in the 2001 book Self-Organization in Biological Systems.[25] Roger Sansom's 2011 book Ingenious Genes: How Gene Regulation Networks Evolve to Control Development is an extended criticism of Kauffman's model of self-organization in relation to gene regulatory networks.[26]
Borrowing from
spin glass models in physics, Kauffman invented "N-K" fitness landscapes, which have found applications in biology[27] and economics.[28][29] In related work, Kauffman and colleagues have examined subcritical, critical, and
supracritical behavior in economic systems.[30]
Kauffman's 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. He published on this topic in his paper "Answering Descartes: beyond Turing".[31] With Giuseppe Longo and Maël Montévil, he wrote (January 2012) "No Entailing Laws, But Enablement in the Evolution of the Biosphere",[32] which argued that evolution is not "law entailed" like physics.
Kauffman's 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)[33] and "Quantum Criticality at the Origin of Life" (February 2015).[20]
Kauffman has contributed to the emerging field of cumulative technological evolution by introducing a mathematics of the adjacent possible.[34][35]
He has published over 350 articles and 6 books: The Origins of Order (1993), At Home in the Universe (1995), Investigations (2000), Reinventing the Sacred (2008), Humanity in a Creative Universe (2016), and A World Beyond Physics (2019).
In 2016, Kauffman wrote a children's story, "Patrick, Rupert, Sly & Gus Protocells", a narrative about unprestatable niche creation in the biosphere, which was later produced as a short animated video.[36]
In 2017, exploring the concept that reality consists of both ontologically real "possibles" (res potentia) and ontologically real "actuals" (res extensa), Kauffman co-authored, with Ruth Kastner and Michael Epperson, "Taking Heisenberg's Potentia Seriously".[37]
Publications
Selected articles
Kauffman, S. A.; McCulloch, W. S. (1967). Random Nets of Formal Genes (Technical report). Quarterly Progress Report 34. Cambridge, MA: Research Laboratory of Electronics, Massachusetts Institute of Technology.
Kauffman, S. A. (1971a). "Cellular Homeostasis, Epigenesis, and Replication in Randomly Aggregated Macromolecular Systems". Journal of Cybernetics. 1 (1): 71–96.
doi:
10.1080/01969727108545830.
Kauffman, Stuart (2004). "Autonomous Agents". In
Barrow, John D.;
Davies, Paul C. W.; Harper, Charles L. Jr. (eds.). Science and Ultimate Reality: Quantum Theory, Cosmology, and Complexity. Cambridge University Press.
ISBN978-0521831130.
Huang, S.; Kauffman, S. A. (2009). "Complex Gene Regulatory Networks - from Structure to Biological Observables: Cell Fate Determination". In Meyers, R. A. (ed.). Encyclopedia of Complexity and Systems Science. Springer.
ISBN978-0-387-75888-6.
Longo, G.; Montévil, M.; Kauffman, S. (January 2012). "No entailing laws, but enablement in the evolution of the biosphere".
arXiv:1201.2069 [
q-bio.OT].
Kauffman, Stuart; Hill, Colin; Hood, Leroy; Huang, Sui (2014b).
"Transforming Medicine: A Manifesto". Scientific American Worldview. Archived from
the original on July 13, 2014. Retrieved April 28, 2015.
Kauffman, Stuart (October 2014). "Beyond the Stalemate: Conscious Mind-Body - Quantum Mechanics - Free Will - Possible Panpsychism - Possible Interpretation of Quantum Enigma".
arXiv:1410.2127 [
physics.hist-ph].
Kauffman, S. (2016). "Answering Descartes: Beyond Turing". In
Cooper, S. Barry;
Hodges, Andrew (eds.). The Once and Future Turing. Cambridge University Press.
Books
Kauffman, Stuart (1993). The Origins of Order: Self Organization and Selection in Evolution. Oxford University Press.
ISBN978-0-19-507951-7.
Kauffman, Stuart (1995). At Home in the Universe: The Search for Laws of Self-Organization and Complexity. Oxford University Press.
ISBN978-0195111309.
^EP 0229046A1, "Procédé d'obtention d'ADN, ARN, peptides, polypeptides ou protéines, par une technique de recombinaison d'ADN"
^US 5,723,323 "Method of identifying a stochastically-generated peptide, polypeptide, or protein having ligand binding property and compositions thereof"
^CA 1339937C, "Procedure for obtaining DNA, RNA peptides, polypeptides, or proteins by recombinant DNA techniques"
Chialvo, D. R. (2013). "Critical Brain Dynamics at Large Scale". In Plenz D.; Niebur, E.; Schuster H. G. (eds.). Criticality in Neural Systems. Vol. 1. Wiley.
ISBN978-3-527-41104-7.
Dadon, Z.; Wagner, N.; Ashkenasy, G. (2008). "The Road to Non-Enzymatic Molecular Networks". Angew. Chem. Int. Ed. 47 (33): 6128–6136.
doi:
10.1002/anie.200702552.
PMID18613152.
Dadon, Z.; Wagner, N.; Cohen-Luria, R.; 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 Gale, P. A.; Steed J. W. (eds.). Supramolecular Chemistry: From Molecules to Nanomaterials. John Wiley and Sons, Ltd.
ISBN978-0-470-74640-0.
Di Bernardo, Mirko (2011). I sentieri evolutivi della complessità biologica nell'opera di S. A. Kauffman (in Italian). Milano: Mimesis.
ISBN978-8857504131.
Goldstein, Jeffrey A. (2008). "Book Review of Reinventing the Sacred: A New View of Science, Reason, and Religion, by Stuart Kauffman". Emergence: Complexity & Organization. 10 (3): 117–130.