Stuart Kauffman

Institute for Systems Biology, Seattle, Washington, United States

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Publications (113)271.35 Total impact

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    Stuart Kauffman
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    ABSTRACT: There is surely some truth to the notion that culture evolves, but the Darwinian view of culture is trivial. Gabora does two things in this paper. First, she levels a reasoned and devastating attack on the adequacy of a Darwinian theory of cultural evolution, showing that cultural evolution violates virtually all prerequisites to be encompassed by Darwin's standard theory. Second, she advances the central concept that it is whole world views that evolve. A world view emerges when the capacity of memories to evoke one another surpasses a phase transition yielding a richly interconnected conceptual web, a world view. She proposes that cultural evolves not through a Darwinian process such as meme theory, but through communal exchange of facets of world views. Each section of her argument is completely convincing.
    10/2014;
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    ABSTRACT: Advances in molecular biology, remote sensing, systems biology, bioinformatics, non-linear science, the physics of complex systems and other fields have rendered a great amount of data that remain to be integrated into models and theories that are capable of accounting for the complexity of ecological systems and the evolutionary dynamics of life. It is thus necessary to provide a solid basis to discuss and reflect on these and other challenges both at the local and global scales. This volume aims to delineate an integrative and interdisciplinary view that suggests new avenues in research and teaching, critically discusses the scope of the diverse methods in the study of complex systems, and points at key open questions. Finally, this book will provide students and specialists with a collection of high quality open access essays that will contribute to integrate Ecology, Evolution and Complexity in the context of basic research and in the field of Sustainability Sciences. - See more at: http://scifunam.fisica.unam.mx/mir/copit/TS0012EN/TS0012EN.html
    Edited by Mariana Benítez, Octavio MIramontes, Alfonso Valiente-Banuet, 07/2014; Copit-arXives., ISBN: 978-1-938128-05-9
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    ABSTRACT: The nature of economic opportunity has recently received significant attention in entrepreneurship, organization science and strategy. The notion of boundedly rational search on an (NK) opportunity landscape has been particularly relevant to these conversations and debates. We argue that the focus on bounded rationality and search is highly problematic for the fields of entrepreneurship and strategy and does not allow us to explain the origins of economic novelty. We contrast the NP problem with the frame problem to illustrate our point, and highlight the role of adjacent possibilities and novel affordances. We discuss the entrepreneurial and economic implications of these arguments by building on unique insights from biology, the natural and computational sciences. Copyright © 2014 Strategic Management Society.
    Strategic Entrepreneurship Journal 06/2014; · 2.05 Impact Factor
  • Stuart A Kauffman
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    ABSTRACT: Despite Darwin, we remain children of Newton, and dream of a grand theory that is epistemologically complete and would allow prediction of the evolution of the biosphere. The main purpose of this article is to show that this dream is false, and bears on studying patterns of evolution. To do so, I must justify the use of the word "function" in biology, when physics has only happenings. The concept of "function" lifts biology irreducibly above physics, for as we shall see, we cannot prestate the ever new biological functions that arise and constitute the very phase space of evolution. Hence, we cannot mathematize the detailed becoming of the biosphere, nor write differential equations for functional variables we do not know ahead of time, nor integrate those equations, so no laws "entail" evolution. The dream of a grand theory fails. In place of entailing laws, I propose a post-entailing law explanatory framework in which Actuals arise in evolution that constitute new boundary conditions that are enabling constraints that create new, typically unprestatable, Adjacent Possible opportunities for further evolution, in which new Actuals arise, in a persistent becoming. Evolution flows into a typically unprestatable succession of Adjacent Possibles. Given the concept of function, the concept of functional closure of an organism making a living in its world becomes central. Implications for patterns in evolution include historical reconstruction, and statistical laws such as the distribution of extinction events, or species per genus, and the use of formal cause, not efficient cause, laws.
    Bio Systems 04/2014; · 1.27 Impact Factor
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    ABSTRACT: Drawing on current biology, we argue that the phase space of economic evolution is not stable. Thus, there are no entailing laws of economic dynamics. In this sense, economic dynamics are creative and the economy is not a causal system. Because economic dynamics are creative, the implicit frame of analysis for the econosphere changes in unprestatable and non-algorithmic ways. New-venture, social, and political entrepreneurs solve the frame problem of the econosphere. Economic evolution is unpredictable, not entailed, and the number of things traded (‘cambiodiversity’) increases over time. Our metatheoretic framework points out how institutions, entrepreneurs, and disparate actors enable what we call ‘novelty intermediation’. We provide examples of novelty intermediation from Rennaissance Italy to Silicon Valley. Our framework does not automatically provide clear policy prescriptions in part because our main result is negative. It may nevertheless provide a useful prolegomenon to a future economics fit for a creative world.
    Journal of Institutional Economics 03/2014; 11(01):1-31. · 0.46 Impact Factor
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    ABSTRACT: In response to Pelikan, Witt, Foster, and Colander, we reiterate our main contributions: (1) our more careful demonstration of why ‘mechanistic’ models have limited application, (2) our account of novelty as a system-level phenomenon, and (3) our identification of ‘novelty intermediation’ as important to creative economic dynamics. We also address some of the criticisms raised by the commenters. Pavel Pelikan's idea of stochastic causality does not somehow eliminate unprestateable change. We do challenge certain strong notions of universal causation, as Ulrich Witt notes, but such notions are probably best abandoned. Although, we do not repudiate mathematical modeling as our paper suggested to John Foster, we may give less scope than Foster to such methods. Finally, we point out the extreme difficulty of implementing the sort of engineering vision Colander articulates.
    Journal of Institutional Economics 03/2014; 11(01):61-68. · 0.46 Impact Factor
  • Stuart A. Kauffman
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    ABSTRACT: Despite Darwin, we remain children of Newton, and dream of a grand theory that is epistemologically complete and would allow prediction of the evolution of the biosphere. The main purpose of this article is to show that this dream is false, and bears on studying patterns of evolution. To do so, I must justify the use of the word “function” in biology, when physics has only happenings. The concept of “function” lifts biology irreducibly above physics, for as we shall see, we cannot prestate the ever new biological functions that arise and constitute the very phase space of evolution. Hence, we cannot mathematize the detailed becoming of the biosphere, nor write differential equations for functional variables we do not know ahead of time, nor integrate those equations, so no laws “entail” evolution. The dream of a grand theory fails. In place of entailing laws, I propose a post-entailing law explanatory framework in which Actuals arise in evolution that constitute new boundary conditions that are enabling constraints that create new, typically unprestatable, Adjacent Possible opportunities for further evolution, in which new Actuals arise, in a persistent becoming. Evolution flows into a typically unprestatable succession of Adjacent Possibles. Given the concept of function, the concept of functional closure of an organism making a living in its world becomes central. Implications for patterns in evolution include historical reconstruction, and statistical laws such as the distribution of extinction events, or species per genus, and the use of formal cause, not efficient cause, laws.
    Biosystems. 01/2014;
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    Sui Huang, Stuart Kauffman
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    ABSTRACT: The increasingly evident limitations of target-selective cancer therapy has stimulated a flurry of ideas for overcoming the development of resistance and recurrence-the near universal reason for therapy failure from which target-selective drugs are not exempt. A widely proposed approach to conquer therapy resistance is to depart from the myopic focus on individual causal pathways and instead target multiple nodes in the cancer cell's gene regulatory network. However, most ideas rely on a simplistic conceptualization of networks: utilizing solely their topology and treating it as a display of causal interactions, while ignoring the integrated dynamics in state space. Here we review the more encompassing formal framework of global network dynamics in which cancer cells, like normal cell types, are high-dimensional attractor states. Then therapy is represented by the network perturbation that will promote the exit from such cancer attractors and reentering a normal attractor. We show in this qualitative and accessible discussion how the idea of a quasi-potential landscape and the theory of least-action-path offer a new formal understanding for computing the set of network nodes (molecular targets) that need to be targeted in concert in order to exit the cancer attractor. But targeting cancer cells based on the network configuration of an "average" cancer cell, however precise, may not suffice to eradicate all tumor cells because of the dynamic non-genetic heterogeneity of cancer cell populations that makes them moving targets and drives the replenishment of the cancer attractor with surviving, non-responsive cells from neighboring abnormal attractors.
    Seminars in Cancer Biology 06/2013; · 9.14 Impact Factor
  • Stuart Kauffman
    Physics of Life Reviews 05/2013; · 9.48 Impact Factor
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    Liane Gabora, Eric O Scott, Stuart Kauffman
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    ABSTRACT: The phenomenon of preadaptation, or exaptation (wherein a trait that originally evolved to solve one problem is co-opted to solve a new problem) presents a formidable challenge to efforts to describe biological phenomena using a classical (Kolmogorovian) mathematical framework. We develop a quantum framework for exaptation with examples from both biological and cultural evolution. The state of a trait is written as a linear superposition of a set of basis states, or possible forms the trait could evolve into, in a complex Hilbert space. These basis states are represented by mutually orthogonal unit vectors, each weighted by an amplitude term. The choice of possible forms (basis states) depends on the adaptive function of interest (e.g., ability to metabolize lactose or thermoregulate), which plays the role of the observable. Observables are represented by self-adjoint operators on the Hilbert space. The possible forms (basis states) corresponding to this adaptive function (observable) are called eigenstates. The framework incorporates key features of exaptation: potentiality, contextuality, nonseparability, and emergence of new features. However, since it requires that one enumerate all possible contexts, its predictive value is limited, consistent with the assertion that there exists no biological equivalent to "laws of motion" by which we can predict the evolution of the biosphere.
    Progress in Biophysics and Molecular Biology 04/2013; · 3.38 Impact Factor
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    ABSTRACT: Technological evolution has been compared to biological evolution by many authors over the last two centuries. As a parallel experiment of innovation involving economic, historical, and social components, artifacts define a universe of evolving properties that displays episodes of diversification and extinction. Here, we critically review previous work comparing the two types of evolution. Like biological evolution, technological evolution is driven by descent with variation and selection, and includes tinkering, convergence, and contingency. At the same time, there are essential differences that make the two types of evolution quite distinct. Major distinctions are illustrated by current specific examples, including the evolution of cornets and the historical dynamics of information technologies. Due to their fast and rich development, the later provide a unique opportunity to study technological evolution at all scales with unprecedented resolution. Despite the presence of patterns suggesting convergent trends between man‐made systems end biological ones, they provide examples of planned design that have no equivalent with natural evolution.
    Complexity 03/2013; 18(4). · 1.03 Impact Factor
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    ABSTRACT: The origins of novelty and nature of economic opportunity have recently received significant attention in organization science, strategy and entrepreneurship. The notion and metaphor of search on an (NK) opportunity landscape — or “phase space” — has been particularly relevant to these conversations and debates. While the landscape and phase space notion has certainly been helpful for explaining some important aspects of economic activity, we argue that it also features some critical deficiencies — particularly in explaining the origins of novelty. Existing notions of landscapes do not fully account for the “empty” spaces of possible action, and the unprestatable adjacent possibilities associated with strategy and economic activity. Furthermore, any activity on this space introduces yet more, unstatable possibilities. Thus, simply focusing on the computational limitations, or bounded rationality, of economic actors is not sufficient for explaining novelty. We argue that the central problem of explaining novel economic activity is not so much one of computational insufficiency (the problem of NP-completeness), but a problem of how to account for the readily manifest, emergent novelty we see in the economic sphere (the “frame” problem). While some have recently highlighted problems with the notion of landscapes and focused on factors such as entrepreneurial enactment or effectuation in generating novelty, we provide alternative foundations. We discuss the implications of these arguments by building on unique insights from biology, the natural and computational sciences. Our approach is not meant to replace existing evolutionary explanations of economic activity. Instead we seek to augment these approaches in an effort to clarify the nature of opportunities and the respective contributions of organisms and environments in the emergence of opportunities.
    SSRN Electronic Journal 01/2013;
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    Liane Gabora, Eric O. Scott, Stuart Kauffman
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    ABSTRACT: The phenomenon of preadaptation, or exaptation (wherein a trait that originally evolved to solve one problem is co-opted to solve a new problem) presents a formidable challenge to efforts to describe biological phenomena using a classical (Kolmogorovian) mathematical framework. We develop a quantum framework for exaptation with examples from both biological and cultural evolution. The state of a trait is written as a linear superposition of a set of basis states, or possible forms the trait could evolve into, in a complex Hilbert space. These basis states are represented by mutually orthogonal unit vectors, each weighted by an amplitude term. The choice of possible forms (basis states) depends on the adaptive function of interest (e.g., ability to metabolize lactose or thermoregulate), which plays the role of the observable. Observables are represented by self-adjoint operators on the Hilbert space. The possible forms (basis states) corresponding to this adaptive function (observable) are called eigenstates. The framework incorporates key features of exaptation: potentiality, contextuality, nonseparability, and emergence of new features. However, since it requires that one enumerate all possible contexts, its predictive value is limited, consistent with the assertion that there exists no biological equivalent to “laws of motion” by which we can predict the evolution of the biosphere.
    Progress in Biophysics and Molecular Biology 01/2013; · 3.38 Impact Factor
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    ABSTRACT: Widespread unexplained variations in clinical practices and patient outcomes suggest major opportunities for improving the quality and safety of medical care. However, there is little consensus regarding how to best identify and disseminate healthcare improvements and a dearth of theory to guide the debate. Many consider multicenter randomized controlled trials to be the gold standard of evidence-based medicine, although results are often inconclusive or may not be generally applicable due to differences in the contexts within which care is provided. Increasingly, others advocate the use "quality improvement collaboratives", in which multi-institutional teams share information to identify potentially better practices that are subsequently evaluated in the local contexts of specific institutions, but there is concern that such collaborative learning approaches lack the statistical rigor of randomized trials. Using an agent-based model, we show how and why a collaborative learning approach almost invariably leads to greater improvements in expected patient outcomes than more traditional approaches in searching simulated clinical fitness landscapes. This is due to a combination of greater statistical power and more context-dependent evaluation of treatments, especially in complex terrains where some combinations of practices may interact in affecting outcomes. The results of our simulations are consistent with observed limitations of randomized controlled trials and provide important insights into probable reasons for effectiveness of quality improvement collaboratives in the complex socio-technical environments of healthcare institutions. Our approach illustrates how modeling the evolution of medical practice as search on a clinical fitness landscape can aid in identifying and understanding strategies for improving the quality and safety of medical care.
    PLoS ONE 11/2012; 7(11):e49901. · 3.53 Impact Factor
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    Wim Hordijk, Mike Steel, Stuart Kauffman
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    ABSTRACT: This paper presents new results from a detailed study of the structure of autocatalytic sets. We show how autocatalytic sets can be decomposed into smaller autocatalytic subsets, and how these subsets can be identified and classified. We then argue how this has important consequences for the evolvability, enablement, and emergence of autocatalytic sets. We end with some speculation on how all this might lead to a generalized theory of autocatalytic sets, which could possibly be applied to entire ecologies or even economies.
    Acta Biotheoretica 09/2012; · 1.23 Impact Factor
  • M.andrecut, S. A.kauffman
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    ABSTRACT: In this paper we discuss a noisy mean field model for the genetic toggle switch. We show that this model approximates very well the characteristics of the system, observed using the exact Gillespie stochastic simulation algorithm. Also, we show that the system can be made exponentially stable depending on reaction parameters.
    International Journal of Modern Physics B 01/2012; 20(29). · 0.46 Impact Factor
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    Giuseppe Longo, Maël Montévil, Stuart Kauffman
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    ABSTRACT: Biological evolution is a complex blend of ever changing structural stability, variability and emergence of new phenotypes, niches, ecosystems. We wish to argue that the evolution of life marks the end of a physics world view of law entailed dynamics. Our considerations depend upon discussing the variability of the very "contexts of life": the interactions between organisms, biological niches and ecosystems. These are ever changing, intrinsically indeterminate and even unprestatable: we do not know ahead of time the "niches" which constitute the boundary conditions on selection. More generally, by the mathematical unprestatability of the "phase space" (space of possibilities), no laws of motion can be formulated for evolution. We call this radical emergence, from life to life. The purpose of this paper is the integration of variation and diversity in a sound conceptual frame and situate unpredictability at a novel theoretical level, that of the very phase space. Our argument will be carried on in close comparisons with physics and the mathematical constructions of phase spaces in that discipline. The role of (theoretical) symmetries as invariant preserving transformations will allow us to understand the nature of physical phase spaces and to stress the differences required for a sound biological theoretizing. In this frame, we discuss the novel notion of "enablement". This will restrict causal analyses to differential cases (a difference that causes a difference). Mutations or other causal differences will allow us to stress that "non conservation principles" are at the core of evolution, in contrast to physical dynamics, largely based on conservation principles as symmetries. Critical transitions, the main locus of symmetry changes in physics, will be discussed, and lead to "extended criticality" as a conceptual frame for a better understanding of the living state of matter.
    01/2012;
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    ABSTRACT: Our current understanding of evolution is so tightly linked to template-dependent replication of DNA and RNA molecules that the old idea from Oparin of a self-reproducing 'garbage bag' ('coacervate') of chemicals that predated fully-fledged cell-like entities seems to be farfetched to most scientists today. However, this is exactly the kind of scheme we propose for how Darwinian evolution could have occurred prior to template replication. We cannot confirm previous claims that autocatalytic sets of organic polymer molecules could undergo evolution in any interesting sense by themselves. While we and others have previously imagined inhibition would result in selectability, we found that it produced multiple attractors in an autocatalytic set that cannot be selected for. Instead, we discovered that if general conditions are satisfied, the accumulation of adaptations in chemical reaction networks can occur. These conditions are the existence of rare reactions producing viable cores (analogous to a genotype), that sustains a molecular periphery (analogous to a phenotype). We conclude that only when a chemical reaction network consists of many such viable cores, can it be evolvable. When many cores are enclosed in a compartment there is competition between cores within the same compartment, and when there are many compartments, there is between-compartment competition due to the phenotypic effects of cores and their periphery at the compartment level. Acquisition of cores by rare chemical events, and loss of cores at division, allows macromutation, limited heredity and selectability, thus explaining how a poor man's natural selection could have operated prior to genetic templates. This is the only demonstration to date of a mechanism by which pre-template accumulation of adaptation could occur.
    Biology Direct 01/2012; 7:1; discussion 1. · 4.04 Impact Factor
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    ABSTRACT: Biological proteins are known to fold into specific 3D conformations. However, the fundamental question has remained: Do they fold because they are biological, and evolution has selected sequences which fold? Or is folding a common trait, widespread throughout sequence space? To address this question arbitrary, unevolved, random-sequence proteins were examined for structural features found in folded, biological proteins. Libraries of long (71 residue), random-sequence polypeptides, with ensemble amino acid composition near the mean for natural globular proteins, were expressed as cleavable fusions with ubiquitin. The structural properties of both the purified pools and individual isolates were then probed using circular dichroism, fluorescence emission, and fluorescence quenching techniques. Despite this necessarily sparse "sampling" of sequence space, structural properties that define globular biological proteins, namely collapsed conformations, secondary structure, and cooperative unfolding, were found to be prevalent among unevolved sequences. Thus, for polypeptides the size of small proteins, natural selection is not necessary to account for the compact and cooperative folded states observed in nature.
    Genes. 12/2011; 2(3):608-26.

Publication Stats

6k Citations
271.35 Total Impact Points

Institutions

  • 2014
    • Institute for Systems Biology
      Seattle, Washington, United States
  • 2013
    • Tampere University of Technology
      Tammerfors, Province of Western Finland, Finland
    • University of British Columbia - Okanagan
      • Department of Psychology
      Kelowna, British Columbia, Canada
  • 2010–2013
    • University of Vermont
      • • Department of Mathematics and Statistics
      • • Department of Complex Systems
      Burlington, Vermont, United States
  • 1987–2013
    • Santa Fe Institute
      Santa Fe, New Mexico, United States
    • Hospital of the University of Pennsylvania
      • Department of Biochemistry and Biophysics
      Philadelphia, Pennsylvania, United States
  • 1970–2013
    • The University of Calgary
      • Institute for Biocomplexity and Informatics
      Calgary, Alberta, Canada
  • 2011
    • Università Ca' Foscari Venezia
      Venetia, Veneto, Italy
  • 2007
    • University of Toronto
      Toronto, Ontario, Canada
    • Università degli Studi di Modena e Reggio Emilia
      • Department of Communication and Economics
      Modène, Emilia-Romagna, Italy
  • 2006
    • George Mason University
      Fairfax, Virginia, United States
  • 2004–2005
    • University of New Mexico
      • Department of Cell Biology and Physiology
      Albuquerque, New Mexico, United States
  • 1986–1993
    • University of Pennsylvania
      • • Department of Biochemistry and Biophysics
      • • Department of Medicine
      Philadelphia, PA, United States
    • Clarkson University
      • Department of Biology
      Potsdam, NY, United States
  • 1989
    • Los Alamos National Laboratory
      • Center for Nonlinear Studies
      Los Alamos, California, United States
  • 1972–1975
    • University of Chicago
      Chicago, Illinois, United States
  • 1974
    • National Cancer Institute (USA)
      Maryland, United States
  • 1973
    • University of Rochester
      • Department of Physics and Astronomy
      Rochester, New York, United States
  • 1969
    • University of California, San Francisco
      • Department of Anatomy
      San Francisco, California, United States