Stuart A. Kauffman
FIDIPro at Tampere University of Technology
Icore chair and Institute head at
University of Calgary’s Institute for Biocomplexity and Informatics, IBI
Originally a medical doctor, Kauffman is an emeritus professor of biochemistry
at the University of Pennsylvania, and a seminal member and an external
professor of the Santa Fe Institute. Also a MacArthur Fellow and a Trotter Prize
winner, Kauffman has published three major books, among them is At Home in
the Universe: The Search for the Laws of Self-Organization and Complexity
(1995), which the Oxford University Press says “weaves together the excitement
of intellectual discovery and a fertile mix of insights to give the general
reader a fascinating look at this new science − and at the forces for order that
lie at the edge of chaos.”
The FidiPro program brings Kauffman to Tampere University of Technology. The subject
of the program is stochastic modeling of gene regulatory networks. The project will
focus on modeling the gene regulatory networks using gene expression data. The
expertise of the Institute for Biocomplexity and Informatics and the modeling
experience of the CSB-group led by professor Olli Yli-Harja support each other very
well. The results are expected to help in understanding the mechanisms of diseases
so that diseases could be identified in an early phase. They are also to be used in
predicting the individual effects of different medicines therefore helping to select
the best possible treatment for each patient.
Stuart Kauffman is also the director of the Institute for Biocomplexity and Informatics
(IBI). He is the pioneer and the founding father of biocomplexity research.
Kauffman was able to look at gene regulatory networks from a new and different
point of view, and it was this ground-breaking perspective that has ever since
attracted new researchers and scientists worldwide.
Kauffman himself got interested in gene regulatory networks at San Francisco
medical school in 1964 when he wanted to unravel the mysteries of cell
differentiation. Quickly noticing the possibilities of his revolutionary ideas,
he started working on biocomplexity and was eventually able to show that the
behaviour of genetic networks depends critically on the level at which the genes
Current Project at TUT
"Modelling and Reverse Engineering of Delayed Stochastic Models of Genetic
Regulatory Networks". The subject of the FiDiPro research project is the development
of delayed stochastic models of genetic regulatory networks. The project focuses
on modelling the dynamics of genetic regulatory networks based on gene expression
data at the single molecule level. The expertise of Professor Kauffman in the
fields of theoretical biology, complexity and systems biology and the competence
of the research group led by Professor Olli Yli-Harja serve each other very well.
The research results are expected to enhance our understanding of gene networks
dynamics including in the case of diseases, namely cancer. The results can be
utilised to better understand the appearance of cancer, its progression and
predicting the effects of differentiation therapy on patients. The long term goal
is the development of personalized medicine, where doctors can choose the best
treatment for each patient.
Finnish host: Tampere University of Technology, Department of Signal Processing,
Ph.D., Prof. Olli Yli-Harja
The Origins of Order: Self-Organization and Selection in Evolution
At Home in the Universe,
The Search for the Laws of Self-Organization and Complexity
Reinventing the Sacred: A New View of Science, Reason and Religion
A Selection of Publications
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
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.
Andre S. Ribeiro, Rui Zhu, S. A. Kauffman (2006) “A General Modeling
Strategy for Gene Regulatory Networks with Stochastic Dynamics”, Journal
of Computational Biology 13 (9), 1630-1639.
Andre S. Ribeiro, Stuart A. Kauffman, Jason Lloyd-Price, Bjorn Samuelsson,
and Joshua Socolar (2008), “Mutual Information in Random Boolean models of
regulatory networks”, Physical Review E 77(1)
Nykter, M., Price, N. D. , Aldana, M., Ramsey, S. A. , Kauffman, S. A.,
Hood, L., Yli-Harja, O., Shmulevich, I., "Gene Expression Dynamics in
the Macrophage Exhibit Criticality," Proceedings of the National
Academy of Sciences of the USA, February 12, 2008, vol. 105, no. 6,
Wikipedia: Stuart Kauffman
Biocomplexity and Informatics iCORE Chair.
Beyond reductionism: Reinventing The Sacred, paper by Kauffman on
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).
Tampere University of Technology
Computational Systems Biology group
TUT Department of Signal Processing
Multimedia, interactive and downloads
Video presentation "Reinventing The Sacred" Stuart Kauffman on his new
book. Video talk for a Conference in Doha, Qatar, produced, May 17.2008
Video presentation "The adjacent possible" by Kauffman on autonomous agents.
An online chat with Stuart Kauffman on a complexity organization website.
A lecture entitled "Rethinking Natural Law" given by Stuart Kauffman at Tampere University of Technology on June 22th 2009 (for download)
Towards a Post-Reductionist Science: The Open Universe, lecture notes for "Rethinking Natural Law"
Five Problems in the Philosophy of Mind