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Stuart Kauffman


Professor Stuart A. Kauffman
FIDIPro at Tampere University of Technology, Finland

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, Finland. 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 are connected.

Current Project at TUT
FidiPro "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

Books
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
Investigations
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 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.

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, 1897-1900.