Stuart Kauffman

Stuart Alan Kauffman (born September 28, 1939) is an American medical doctor,

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 2009 Kauffman became a Finland Distinguished Professor (FiDiPro) at

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]

Fitness landscapes

Kauffman's NK model defines a

, consisting of every string (chosen from a given alphabet) of length ${\displaystyle N}$. For each string in this search space, a

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 ${\displaystyle S}$ is the sum of contributions from each locus ${\displaystyle S_{i}}$ in the string:

${\displaystyle F(S)=\sum _{i}f(S_{i}),}$

and the contribution from each locus in general depends on the value of ${\displaystyle K}$ other loci:

${\displaystyle f(S_{i})=f(S_{i},S_{1}^{i},\dots ,S_{K}^{i}),\,}$

where ${\displaystyle S_{j}^{i}}$ are the other loci upon which the fitness of ${\displaystyle S_{i}}$ depends.

Hence, the fitness function ${\displaystyle f(S_{i},S_{1}^{i},\dots ,S_{K}^{i})}$ 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 ${\displaystyle 1<<k\leq N}$ 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 ${\displaystyle \mu +\sigma {\sqrt {{2\ln(k+1)} \over {k+1}}}}$ and a variance of approximately ${\displaystyle {{(k+1)\sigma ^{2}} \over {N[k+1+2(k+2)\ln(k+1)]}}}$.

Recognition and awards

Kauffman held a

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

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, Stuart (1969). "Metabolic stability and epigenesis in randomly constructed genetic nets".
  PMID 5803332
  .
• 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, S. A. (1971b). "Differentiation of Malignant to Benign Cells". Journal of Theoretical Biology. 31 (3): 429–451.
  PMID 5556142
  .
• Kauffman, Stuart (August 1991). "Antichaos and Adaptation" (PDF).
  PMID 1862333
  . Retrieved April 28, 2015.
• Kauffman, S. A.; Johnsen, S (1991). "Co-Evolution to the Edge of Chaos: Coupled Fitness Landscapes, Poised States, and Co-Evolutionary Avalanches" (PDF). Journal of Theoretical Biology. 149 (4): 467–505.
  PMID 2062105
  .
• Kauffman, Stuart (2004). "Autonomous Agents". In
  ISBN 978-0521831130
  .
• Kauffman, Stuart (2004). "Prolegomenon to a General Biology". In
  ISBN 978-1139459617
  .
• Kauffman, Stuart A. (November 12, 2006). "Beyond reductionism: Reinventing The Sacred". Edge.com. Edge Foundation. Retrieved April 28, 2015.
• Hanel, R.; Kauffman, S. A.; Thurner, S. (2007). "Towards a Physics of Evolution: Critical Diversity Dynamics at the Edges of Collapse and Bursts of Diversification".
  PMID 17930309
  .
• Kauffman, Stuart (May 7, 2008). "Why Humanity Needs a God of Creativity".
  doi:10.1016/s0262-4079(08)61171-9
  . Retrieved April 28, 2015.
• Nykter, M.; Price, N. D.; Aldana, M.; Ramsey, S. A.; Kauffman, S. A.; Hood, L.; Yli-Harja, O.; Shmulevich, I. (2008). "Gene Expression Dynamics in the Macrophage Exhibit Criticality". Proc Natl Acad Sci USA. 105 (6): 1897–1900.
  PMID 18250330
  .
• 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 (1): 20.
  PMID 19222862
  .
• 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.
  ISBN 978-0-387-75888-6
  .
• Kauffman, S. A. (2011). "Approaches to the Origin of Life on Earth". Life. 1 (1): 34–48.
  PMID 25382055
  .
• 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
  ].
• Felin, T.; Kauffman, S.; Koppl, R.; Longo, G. (December 2014). "Economic Opportunity and Evolution: Beyond Landscapes and Bounded Rationality" (PDF).
  SSRN 2197512
  .
• Vattay, G.; Salahub, D.; Csaibai, I.; Nassmi, A.; Kauffman, S. (February 2015). "Quantum Criticality at the Origin of Life". Journal of Physics: Conference Series. 626 (1): 012023.
  S2CID 18439451
  .
• 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.
  ISBN 978-0-19-507951-7
  .
• Kauffman, Stuart (1995). At Home in the Universe: The Search for Laws of Self-Organization and Complexity. Oxford University Press.
  ISBN 978-0195111309
  .
• Kauffman, Stuart (2000). Investigations. Oxford University Press.
  ISBN 978-0199728947
  .
• Kauffman, Stuart (2008). Reinventing the Sacred: A New View of Science, Reason, and Religion. Basic Books.
  ISBN 978-0-465-00300-6
  .
• Kauffman, Stuart (2016). Humanity in a Creative Universe. Oxford University Press.
  ISBN 978-0-19-939045-8
  .
• Kauffman, Stuart (2019). A World Beyond Physics. Oxford University Press.
  ISBN 978-0-19-087133-8
  .

Notes

1. ^ Kauffman & McCulloch 1967.
2. ^ Kauffman 1969.
3. ^ Huang & Kauffman 2009.
4. ^ Nykter et al. 2008.
5. ^ Kauffman 1971b.
6. ^ Kauffman 1971a.
7. ^ Kauffman 2011.
8. ^ Dadon, Wagner & Ashkenasy 2008.
9. ^ Dadon et al. 2012.
10. ^ EP 0229046A1, "Procédé d'obtention d'ADN, ARN, peptides, polypeptides ou protéines, par une technique de recombinaison d'ADN" 
11. ^ US 5,723,323  "Method of identifying a stochastically-generated peptide, polypeptide, or protein having ligand binding property and compositions thereof"
12. ^ CA 1339937C, "Procedure for obtaining DNA, RNA peptides, polypeptides, or proteins by recombinant DNA techniques" 
13. ^ "NuTech Solutions to Acquire BiosGroup's Software Development Operations". BusinessWire. February 20, 2003. Retrieved July 5, 2015.
14. ^ "Netezza Corporation Acquires NuTech Solutions". BusinessWire. May 15, 2008. Retrieved July 5, 2015.
15. ^ "IBM to Acquire Netezza". IBM News Room. IBM. September 20, 2010. Retrieved July 5, 2015.
16. ^ "Stuart Kauffman, complex systems pioneer, to join UVM faculty". Vermontbiz.com. Vermont Business Magazine. September 30, 2009. Retrieved April 28, 2015.
17. ^ ^{a b} "Stuart Kauffman". NPR.org. Retrieved April 28, 2015.
18. ^ Kauffman et al. 2014b.
19. ^ US, "Uses of systems with degrees of freedom poised between fully quantum and fully classical states" 
20. ^ ^{a b} Vattay et al. 2015.
21. ^ "Rethinking Economic Growth". academicimpact.un.org. May 11, 2015. Retrieved May 26, 2020.
22. doi:10.1002/sej.1184
    .
23. PMID 9905770
    .
24. PMC 1226010
    .
25. OCLC 44876868
    .
26. doi:10.1525/bio.2012.62.12.10
    .
27. ^ Kauffman & Johnsen 1991.
28. ^ Rivkin & Siggelkow 2002.
29. ^ Felin et al. 2014.
30. ^ Hanel, Kauffman & Thurner 2007.
31. ^ Kauffman 2016.
32. ^ Longo, Montévil & Kauffman 2012.
33. ^ Kauffman 2014.
34. PMID 25080941
    .
35. PMID 28594909
    .
36. ^ The story can be read here: "The Surprising True Story of Patrick S., Rupert R., Sly S., and Gus G. Protocells in Their Very Early Years" (PDF). August 16, 2016. Archived (PDF) from the original on May 27, 2020. Kauffman narrates the story in 2017 here: Archived at Ghostarchive and the Wayback Machine: "The Surprising True Story of Patrick, Rupert, Sly, and Gus". YouTube. March 10, 2017. Retrieved May 26, 2020. An animated version is here: Archived at Ghostarchive and the Wayback Machine: "The origins of life and its continuing wonder". YouTube. Science Animated. August 24, 2020. Stuart Kauffman explains how life evolved from its earlier origins some 3,700 million years ago through the story of four protocells—Patrick, Rupert, Sly and Gus. He explains why our knowledge of the origins and early evolution of life can greatly help us understand our true place in the world.
37. S2CID 4882205
    .

References

• 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.
  ISBN 978-3-527-41104-7
  .
• Dadon, Z.; Wagner, N.; Ashkenasy, G. (2008). "The Road to Non-Enzymatic Molecular Networks". Angew. Chem. Int. Ed. 47 (33): 6128–6136.
  PMID 18613152
  .
• 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.
  ISBN 978-0-470-74640-0
  .
• Rivkin, J. W.; Siggelkow, N. (May–June 2002). "Organizational Sticking Points on NK Landscapes". Complexity. 7 (5): 31–43.
  doi:10.1002/cplx.10037
  . Retrieved April 28, 2015.

Further reading

• Di Bernardo, Mirko (2011). I sentieri evolutivi della complessità biologica nell'opera di S. A. Kauffman (in Italian). Milano: Mimesis.
  ISBN 978-8857504131
  .
• 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.
• Horgan, John (February 4, 2015). "Seeker Stuart Kauffman on Free Will, God, ESP and Other Mysteries". Scientific American. Retrieved April 28, 2015.
• MacKenzie, Dana (February 2002). "The Science of Surprise". Discover. 23 (2): 59–63.
• Rizzo, Francesco (2017). "Kauffman lettore di Wittgenstein" (in Italian). Palermo: Università degli studi di Palermo. {{cite journal}}: Cite journal requires |journal= (help)

External links

Wikiquote has quotations related to Stuart Kauffman.

• Paulson, Steve (November 9, 2008). "God Enough".
  Salon
  . Retrieved April 28, 2015.
• "Thinker of Untold Dreams: A Portrait of Stuart Kauffman". Vimeo.
• Archived at Ghostarchive and the Wayback Machine: "The Shape of History". YouTube. A talk at the New England Complex Systems Institute, January 28, 2019.