Stuart Kauffman | |
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![]() Stuart Kauffman in April 2010 | |
Born | September 28, 1939 |
Alma mater | Dartmouth College Oxford University University of California, San Francisco |
Known for | NK model, origin of life, gene regulatory networks, adjacent possible, poised realm |
Awards | Wiener Medal (1969) Marshall Scholar MacArthur Fellow |
Scientific career | |
Institutions | University of Chicago University of Pennsylvania University of Calgary |
Stuart Alan Kauffman (born September 28, 1939) is an American medical doctor, theoretical biologist, and complex systems researcher who studies the origin of life on Earth. He was a professor at the University of Chicago, University of Pennsylvania, and University of Calgary. He is currently emeritus professor of biochemistry at the University of Pennsylvania and affiliate faculty at the Institute for Systems Biology. He has a number of awards including a MacArthur Fellowship and a Wiener Medal.
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]
Kauffman graduated from Dartmouth in 1960, was awarded the BA (Hons) by Oxford University (where he was a Marshall Scholar) in 1963, and completed a medical degree (M.D.) at the University of California, San Francisco in 1968. After completing his internship, he moved into developmental genetics of the fruit fly, holding appointments first at the University of Chicago from 1969 to 1973, the National Cancer Institute from 1973 to 1975, and then at the University of Pennsylvania from 1975 to 1994, where he rose to professor of biochemistry and biophysics.
Kauffman became known 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 sets in origin of life research, gene regulatory networks in developmental biology, and fitness landscapes in evolutionary biology. With Marc Ballivet, Kauffman holds the founding broad biotechnology patents in combinatorial chemistry and applied molecular evolution, first issued in France in 1987, [10] in England in 1989, and later in North America. [11] [12]
In 1996, with Ernst and Young, Kauffman started BiosGroup, a Santa Fe, New Mexico-based for-profit company that applied complex systems methodology to business problems. BiosGroup was acquired by NuTech Solutions in early 2003. NuTech was bought by Netezza in 2008, and later by IBM. [13] [14] [15]
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 Tampere University of Technology, Department of Signal Processing. The appointment ended in December, 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 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 combinatorial phase 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 .
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.
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]
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.
Natural selection is the differential survival and reproduction of individuals due to differences in phenotype. It is a key mechanism of evolution, the change in the heritable traits characteristic of a population over generations. Charles Darwin popularised the term "natural selection", contrasting it with artificial selection, which is intentional, whereas natural selection is not.
The neutral theory of molecular evolution holds that most evolutionary changes occur at the molecular level, and most of the variation within and between species are due to random genetic drift of mutant alleles that are selectively neutral. The theory applies only for evolution at the molecular level, and is compatible with phenotypic evolution being shaped by natural selection as postulated by Charles Darwin.
The term autopoiesis refers to a system capable of producing and maintaining itself by creating its own parts. The term was introduced in the 1972 publication Autopoiesis and Cognition: The Realization of the Living by Chilean biologists Humberto Maturana and Francisco Varela to define the self-maintaining chemistry of living cells.
Robert Rosen was an American theoretical biologist and Professor of Biophysics at Dalhousie University.
Self-organization, also called spontaneous order in the social sciences, is a process where some form of overall order arises from local interactions between parts of an initially disordered system. The process can be spontaneous when sufficient energy is available, not needing control by any external agent. It is often triggered by seemingly random fluctuations, amplified by positive feedback. The resulting organization is wholly decentralized, distributed over all the components of the system. As such, the organization is typically robust and able to survive or self-repair substantial perturbation. Chaos theory discusses self-organization in terms of islands of predictability in a sea of chaotic unpredictability.
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. Genotypes which are similar are said to be "close" to each other, while those that are very different are "far" from each other. The set of all possible genotypes, their degree of similarity, and their related fitness values is then called a fitness landscape. The idea of a fitness landscape is a metaphor to help explain flawed forms in evolution by natural selection, including exploits and glitches in animals like their reactions to supernormal stimuli.
A generegulatory network (GRN) is a collection of molecular regulators that interact with each other and with other substances in the cell to govern the gene expression levels of mRNA and proteins which, in turn, determine the function of the cell. GRN also play a central role in morphogenesis, the creation of body structures, which in turn is central to evolutionary developmental biology (evo-devo).
The edge of chaos is a transition space between order and disorder that is hypothesized to exist within a wide variety of systems. This transition zone is a region of bounded instability that engenders a constant dynamic interplay between order and disorder.
In evolutionary biology, inclusive fitness is one of two metrics of evolutionary success as defined by W. D. Hamilton in 1964:
Orchestrated objective reduction is a highly controversial theory postulating that consciousness originates at the quantum level inside neurons. The mechanism is held to be a quantum process called objective reduction that is orchestrated by cellular structures called microtubules. It is proposed that the theory may answer the hard problem of consciousness and provide a mechanism for free will. The hypothesis was first put forward in the early 1990s by Nobel laureate for physics Roger Penrose, and anaesthesiologist Stuart Hameroff. The hypothesis combines approaches from molecular biology, neuroscience, pharmacology, philosophy, quantum information theory, and quantum gravity.
Biological or process structuralism is a school of biological thought that objects to an exclusively Darwinian or adaptationist explanation of natural selection such as is described in the 20th century's modern synthesis. It proposes instead that evolution is guided differently, by physical forces which shape the development of an animal's body, and sometimes implies that these forces supersede selection altogether.
A Boolean network consists of a discrete set of boolean variables each of which has a Boolean function assigned to it which takes inputs from a subset of those variables and output that determines the state of the variable it is assigned to. This set of functions in effect determines a topology (connectivity) on the set of variables, which then become nodes in a network. Usually, the dynamics of the system is taken as a discrete time series where the state of the entire network at time t+1 is determined by evaluating each variable's function on the state of the network at time t. This may be done synchronously or asynchronously.
Adiabatic quantum computation (AQC) is a form of quantum computing which relies on the adiabatic theorem to perform calculations and is closely related to quantum annealing.
Natural computing, also called natural computation, is a terminology introduced to encompass three classes of methods: 1) those that take inspiration from nature for the development of novel problem-solving techniques; 2) those that are based on the use of computers to synthesize natural phenomena; and 3) those that employ natural materials to compute. The main fields of research that compose these three branches are artificial neural networks, evolutionary algorithms, swarm intelligence, artificial immune systems, fractal geometry, artificial life, DNA computing, and quantum computing, among others.
Within biological systems, degeneracy occurs when structurally dissimilar components/pathways can perform similar functions under certain conditions, but perform distinct functions in other conditions. Degeneracy is thus a relational property that requires comparing the behavior of two or more components. In particular, if degeneracy is present in a pair of components, then there will exist conditions where the pair will appear functionally redundant but other conditions where they will appear functionally distinct.
The NK model is a mathematical model described by its primary inventor Stuart Kauffman as a "tunably rugged" fitness landscape. "Tunable ruggedness" captures the intuition that both the overall size of the landscape and the number of its local "hills and valleys" can be adjusted via changes to its two parameters, and , with being the length of a string of evolution and determining the level of landscape ruggedness.
In evolutionary biology, robustness of a biological system is the persistence of a certain characteristic or trait in a system under perturbations or conditions of uncertainty. Robustness in development is known as canalization. According to the kind of perturbation involved, robustness can be classified as mutational, environmental, recombinational, or behavioral robustness etc. Robustness is achieved through the combination of many genetic and molecular mechanisms and can evolve by either direct or indirect selection. Several model systems have been developed to experimentally study robustness and its evolutionary consequences.
The Bianconi–Barabási model is a model in network science that explains the growth of complex evolving networks. This model can explain that nodes with different characteristics acquire links at different rates. It predicts that a node's growth depends on its fitness and can calculate the degree distribution. The Bianconi–Barabási model is named after its inventors Ginestra Bianconi and Albert-László Barabási. This model is a variant of the Barabási–Albert model. The model can be mapped to a Bose gas and this mapping can predict a topological phase transition between a "rich-get-richer" phase and a "winner-takes-all" phase.
Epistasis is a phenomenon in genetics in which the effect of a gene mutation is dependent on the presence or absence of mutations in one or more other genes, respectively termed modifier genes. In other words, the effect of the mutation is dependent on the genetic background in which it appears. Epistatic mutations therefore have different effects on their own than when they occur together. Originally, the term epistasis specifically meant that the effect of a gene variant is masked by that of different gene.
Constructive neutral evolution(CNE) is a theory that seeks to explain how complex systems can evolve through neutral transitions and spread through a population by chance fixation (genetic drift). Constructive neutral evolution is a competitor for both adaptationist explanations for the emergence of complex traits and hypotheses positing that a complex trait emerged as a response to a deleterious development in an organism. Constructive neutral evolution often leads to irreversible or "irremediable" complexity and produces systems which, instead of being finely adapted for performing a task, represent an excess complexity that has been described with terms such as "runaway bureaucracy" or even a "Rube Goldberg machine".