Stuart Kauffman
Encyclopedia
Stuart Alan Kauffman is an American theoretical biologist
and complex system
s researcher concerning the origin of life on Earth. 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 network
s to simplified genetic circuits.
in 1960, was awarded the BA (Hons) by Oxford University 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 set
s in origin of life research, gene regulatory network
s in developmental biology
, and fitness landscape
s 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 employed complex systems
methodology to attempt to solve 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.
In January 2010 Kauffman joined the University of Vermont
faculty where he will continue his work with UVM's Complex Systems Center. He is also an adviser to the Microbes Mind Forum.
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".
Selected articles
About Stuart Kauffman
Biologist
A biologist is a scientist devoted to and producing results in biology through the study of life. Typically biologists study organisms and their relationship to their environment. Biologists involved in basic research attempt to discover underlying mechanisms that govern how organisms work...
and complex system
Complex system
A complex system is a system composed of interconnected parts that as a whole exhibit one or more properties not obvious from the properties of the individual parts....
s researcher concerning the origin of life on Earth. He is best known for arguing that the complexity of biological systems and organisms might result as much from self-organization
Self-organization
Self-organization is the process where a structure or pattern appears in a system without a central authority or external element imposing it through planning...
and far-from-equilibrium dynamics as from Darwinian natural selection
Natural selection
Natural selection is the nonrandom process by which biologic traits become either more or less common in a population as a function of differential reproduction of their bearers. It is a key mechanism of evolution....
, as well as for applying models of Boolean network
Boolean network
A Boolean network consists of a set of Boolean variables whose state is determined by other variables in the network. They are a particular case of discrete dynamical networks, where time and states are discrete, i.e. they have a bijection onto an integer series...
s to simplified genetic circuits.
Biography
Kauffman graduated from DartmouthDartmouth College
Dartmouth College is a private, Ivy League university in Hanover, New Hampshire, United States. The institution comprises a liberal arts college, Dartmouth Medical School, Thayer School of Engineering, and the Tuck School of Business, as well as 19 graduate programs in the arts and sciences...
in 1960, was awarded the BA (Hons) by Oxford University in 1963, and completed a medical degree (M.D.) at the University of California, San Francisco
University of California, San Francisco
The University of California, San Francisco is one of the world's leading centers of health sciences research, patient care, and education. UCSF's medical, pharmacy, dentistry, nursing, and graduate schools are among the top health science professional schools in the world...
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
University of Chicago
The University of Chicago is a private research university in Chicago, Illinois, USA. It was founded by the American Baptist Education Society with a donation from oil magnate and philanthropist John D. Rockefeller and incorporated in 1890...
, then at the University of Pennsylvania
University of Pennsylvania
The University of Pennsylvania is a private, Ivy League university located in Philadelphia, Pennsylvania, United States. Penn is the fourth-oldest institution of higher education in the United States,Penn is the fourth-oldest using the founding dates claimed by each institution...
from 1975 to 1995, where he rose to Professor of Biochemistry
Biochemistry
Biochemistry, sometimes called biological chemistry, is the study of chemical processes in living organisms, including, but not limited to, living matter. Biochemistry governs all living organisms and living processes...
and Biophysics
Biophysics
Biophysics is an interdisciplinary science that uses the methods of physical science to study biological systems. Studies included under the branches of biophysics span all levels of biological organization, from the molecular scale to whole organisms and ecosystems...
. Kauffman held a MacArthur Fellowship, 1987–1992.
Kauffman rose to prominence through his association with the Santa Fe Institute
Santa Fe Institute
The Santa Fe Institute is an independent, nonprofit theoretical research institute located in Santa Fe and dedicated to the multidisciplinary study of the fundamental principles of complex adaptive systems, including physical, computational, biological, and social systems.The Institute houses a...
(a non-profit research institute dedicated to the study of complex systems
Complex systems
Complex systems present problems in mathematical modelling.The equations from which complex system models are developed generally derive from statistical physics, information theory and non-linear dynamics, and represent organized but unpredictable behaviors of systems of nature that are considered...
), where he was faculty in residence from 1986 to 1997, and through his work on models in various areas of biology
Biology
Biology is a natural science concerned with the study of life and living organisms, including their structure, function, growth, origin, evolution, distribution, and taxonomy. Biology is a vast subject containing many subdivisions, topics, and disciplines...
. These included autocatalytic set
Autocatalytic set
An autocatalytic set is a collection of entities, each of which can be created catalytically by other entities within the set, such that as a whole, the set is able to catalyze its own production. In this way the set as a whole is said to be autocatalytic...
s in origin of life research, gene regulatory network
Gene regulatory network
A gene regulatory network or genetic regulatory network is a collection of DNA segments in a cell whichinteract with each other indirectly and with other substances in the cell, thereby governing the rates at which genes in the network are transcribed into mRNA.In general, each mRNA molecule goes...
s in developmental biology
Developmental biology
Developmental biology is the study of the process by which organisms grow and develop. Modern developmental biology studies the genetic control of cell growth, differentiation and "morphogenesis", which is the process that gives rise to tissues, organs and anatomy.- Related fields of study...
, and fitness landscape
Fitness landscape
In evolutionary biology, fitness landscapes or adaptive landscapes are used to visualize the relationship between genotypes and reproductive success. It is assumed that every genotype has a well-defined replication rate . This fitness is the "height" of the landscape...
s in evolutionary biology. Kauffman holds the founding broad biotechnology patents in combinatorial chemistry
Combinatorial chemistry
Combinatorial chemistry involves the rapid synthesis or the computer simulation of a large number of different but structurally related molecules or materials...
and applied molecular evolution
Molecular evolution
Molecular evolution is in part a process of evolution at the scale of DNA, RNA, and proteins. Molecular evolution emerged as a scientific field in the 1960s as researchers from molecular biology, evolutionary biology and population genetics sought to understand recent discoveries on the structure...
.
In 1996, Kauffman started BiosGroup
BiosGroup
BiosGroup, founded in 1997 by Stuart Kauffman and Ernst & Young , was a spin off from the Santa Fe Institute. The company aimed to commercialize complexity science software in applications that helped companies manage projects and supply chains...
, a Santa Fe
Santa Fe, New Mexico
Santa Fe is the capital of the U.S. state of New Mexico. It is the fourth-largest city in the state and is the seat of . Santa Fe had a population of 67,947 in the 2010 census...
, New Mexico
New Mexico
New Mexico is a state located in the southwest and western regions of the United States. New Mexico is also usually considered one of the Mountain States. With a population density of 16 per square mile, New Mexico is the sixth-most sparsely inhabited U.S...
-based for-profit company that employed complex systems
Complex systems
Complex systems present problems in mathematical modelling.The equations from which complex system models are developed generally derive from statistical physics, information theory and non-linear dynamics, and represent organized but unpredictable behaviors of systems of nature that are considered...
methodology to attempt to solve business problems. BiosGroup was acquired by NuTech Solutions in early 2003. NuTech was bought by Netezza
Netezza
Netezza designs and markets high-performance data warehouse appliances and advanced analytics applications for uses including enterprise data warehousing, business intelligence, predictive analytics and business continuity planning....
in 2008.
From 2004 to 2009 Kauffman held a joint appointment at the University of Calgary
University of Calgary
The University of Calgary is a public research university located in Calgary, Alberta, Canada. Founded in 1966 the U of C is composed of 14 faculties and more than 85 research institutes and centres.More than 25,000 undergraduate and 5,500 graduate students are currently...
in Biological Sciences and Physics and Astronomy. He is also an Adjunct Professor in the Department of Philosophy at the University of Calgary
University of Calgary
The University of Calgary is a public research university located in Calgary, Alberta, Canada. Founded in 1966 the U of C is composed of 14 faculties and more than 85 research institutes and centres.More than 25,000 undergraduate and 5,500 graduate students are currently...
. 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
Stochastic calculus
Stochastic calculus is a branch of mathematics that operates on stochastic processes. It allows a consistent theory of integration to be defined for integrals of stochastic processes with respect to stochastic processes...
of genetic regulatory networks based on gene expression
Gene expression
Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product. These products are often proteins, but in non-protein coding genes such as ribosomal RNA , transfer RNA or small nuclear RNA genes, the product is a functional RNA...
data at the single molecule level.
In January 2010 Kauffman joined the University of Vermont
University of Vermont
The University of Vermont comprises seven undergraduate schools, an honors college, a graduate college, and a college of medicine. The Honors College does not offer its own degrees; students in the Honors College concurrently enroll in one of the university's seven undergraduate colleges or...
faculty where he will continue his work with UVM's Complex Systems Center. He is also an adviser to the Microbes Mind Forum.
Work
Kauffman is best known for arguing that the complexity of biological systems and organisms might result as much from self-organizationSelf-organization
Self-organization is the process where a structure or pattern appears in a system without a central authority or external element imposing it through planning...
and far-from-equilibrium dynamics as from Darwinian natural selection
Natural selection
Natural selection is the nonrandom process by which biologic traits become either more or less common in a population as a function of differential reproduction of their bearers. It is a key mechanism of evolution....
.
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".
Publications
Select bibliography- 1993, Origins of Order: Self-Organization and Selection in Evolution, Oxford University Press, Technical monograph. ISBN 0195079515
- 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 0465003001
Selected articles
- 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.
External links
- 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 reductionismReductionismReductionism can mean either an approach to understanding the nature of complex things by reducing them to the interactions of their parts, or to simpler or more fundamental things or a philosophical position that a complex system is nothing but the sum of its parts, and that an account of it can...
. - Video presentation "Reinventing The Sacred" Stuart Kauffman on his new book. Video talk for a Conference in Doha, Katar, produced, May 17.2008
- 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).
- "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