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  1. Mark A. Bedau, Optimal Formulation of Complex Chemical Systems with a Genetic Algorithm.
    We demonstrate a method for optimizing desired functionality in real complex chemical systems, using a genetic algorithm. The chemical systems studied here are mixtures of amphiphiles, which spontaneously exhibit a complex variety of self-assembled molecular aggregations, and the property optimized is turbidity. We also experimentally resolve the fitness landscape in some hyper-planes through the space of possible amphiphile formulations, in order to assess the practicality of our optimization method. Our method shows clear and significant progress after testing only 1 % (...)
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  2. Mark A. Bedau, Quantifying the Extent and Intensity of Adaptive Evolution.
    Evolvability is the capacity to create new adaptations, and especially new kinds of adaptations, through the evolutionary process. Evolvability is important both as a theoretical issue in biology and as a practical issue in evolutionary computation. But it is difficult to study evolvability, in part because it is difficult to..
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  3. Mark A. Bedau, The Extent to Which Organisms Construct Their Environments.
    Those interested in the relationship betw een environment structure and behavior — the topic of this special issue of Adaptive Behavior — w ill find much of value in Peter Godfrey-Smith's new book, Complexity and the Function of Mind in Nature (hereafter CFMN; all page citations are to CFMN unless otherw ise indicated). The w riting is clear and concise, aptly balancing precision and breadth, and a host of relevant issues are raised and advanced. Although my comments here w ill (...)
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  4. Mark A. Bedau, Three Illustrations of Artificial Life's Working Hypothesis.
    Artificial life uses computer models to study the essential nature of the characteristic processes of complex adaptive systems proceses such as self-organization, adaptation, and evolution. Work in the field is guided by the working hypothesis that simple computer models can capture the essential nature of these processes. This hypothesis is illustrated by recent results with a simple population of computational agents whose sensorimotor functionality undergo open-ended adaptive evolution. These might illuminate three aspects of complex adaptive systems in general: punctuated equilibrium (...)
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  5. Mark A. Bedau & Andrew Buchanan, Evolutionary Design of a DDPD Model of Ligation.
    Ligation is a form of chemical self-assembly that involves dynamic formation of strong covalent bonds in the presence of weak associative forces. We study an extremely simple form of ligation by means of a dissipative particle dynamics (DPD) model extended to include the dynamic making and breaking of strong bonds, which we term dynamically bonding dissipative particle dynamics (DDPD). Then we use a chemical genetic algorithm (CGA) to optimize the model’s parameters to achieve a limited form of ligation of trimers—a (...)
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  6. Andrew Buchanan & Mark A. Bedau, The Flexible Balance of Evolutionary Novelty and Memory in the Face of Environmental Catastrophes.
    We study the effects of environmental catastrophes on the evolution of a population of sensory-motor agents with individually evolving mutation rates, and compare these effects in a variety of control systems. A catastrophe makes the balance shift toward the need for evolutionary novelty, and we observe the mutation rate evolve upwards. As the population adapts the sensory-motor strategies to the new environment and the balance shifts toward a need for evolutionary memory, the mutation rate falls. These observations support the hypothesis (...)
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  7. Seth Bullock & Mark A. Bedau, Exploring the Dynamics of Adaptation with Evolutionary Activity Plots.
    Evolutionary activity statistics and their visualization are introduced, and their motivation is explained. Examples of their use are described, and their strengths and limitations are discussed. References to more extensive or general accounts of these techniques are provided.
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  8. Jeffrey A. Fletcher, Mark A. Bedau & Martin Zwick, Effect of Environmental Structure on Evolutionary Adaptation.
    Systems Science Ph.D. Program, Portland State University, Portland, Oregon 97207-0751, jeff@sysc.pdx.edu Department of Philosophy, Reed College, 3203 SE Woodstock Boulevard, Portland, Oregon 97202, mab@reed.edu Systems Science Ph.D. Program, Portland State University, Portland, Oregon 97207-0751, zwick@sysc.pdx.edu..
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  9. Mark A. Bedau (2013). Minimal Memetics and the Evolution of Patented Technology. Foundations of Science 18 (4):791-807.
    The nature and status of cultural evolution and its connection with biological evolution are controversial in part because of Richard Dawkin’s suggestion that the scientific study of culture should include “memetics,” an analog of genetics in which genes are replaced by “memes”—the hypothetical units of cultural evolution. Memetics takes different forms; I focus on its minimal form, which claims merely that natural selection shapes to some extent the evolution of some aspects of culture. Advocates and critics of memetics disagree about (...)
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  10. Mark A. Bedau (2013). Weak Emergence Drives the Science, Epistemology, and Metaphysics of Synthetic Biology. Biological Theory 8 (4):334-345.
    Top-down synthetic biology makes partly synthetic cells by redesigning simple natural forms of life, and bottom-up synthetic biology aims to make fully synthetic cells using only entirely nonliving components. Within synthetic biology the notions of complexity and emergence are quite controversial, but the imprecision of key notions makes the discussion inconclusive. I employ a precise notion of weak emergent property, which is a robust characteristic of the behavior of complex bottom-up causal webs, where a complex causal web is one that (...)
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  11. Ulrich Krohs & Mark A. Bedau (2013). Interdisciplinary Interconnections in Synthetic Biology. Biological Theory 8 (4):313-317.
  12. Mark A. Bedau (2012). A Functional Account of Degrees of Minimal Chemical Life. Synthese 185 (1):73-88.
    This paper describes and defends the view that minimal chemical life essentially involves the chemical integration of three chemical functionalities: containment, metabolism, and program (Rasmussen et al. in Protocells: bridging nonliving and living matter, 2009a ). This view is illustrated and explained with the help of CMP and Rasmussen diagrams (Rasmussen et al. In: Rasmussen et al. (eds.) in Protocells: bridging nonliving and living matter, 71–100, 2009b ), both of which represent the key chemical functional dependencies among containment, metabolism, and (...)
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  13. Mark A. Bedau (2012). Introduction to Philosophical Problems About Life. Synthese 185 (1):1-3.
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  14. Hugues Bersini, Pasquale Stano, Pier Luigi Luisi & Mark A. Bedau (2012). Philosophical and Scientific Perspectives on Emergence. Synthese 185 (2):165-169.
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  15. Anita L. Allen, Stephen Bates, Mark A. Bedau, Jessica Berg, Nicole Deming, Ryan Blum, Benjamin Boltin, Nancy Berlinger, Harold Braswell & Daniel Callahan (2011). Following is the Comprehensive Index for Volume 41 of the Hastings Center Report, Covering All Feature Material From 2011. Letters Have Not Been Included. Ffl Complete Issues Are Available for Volume 41 (2011) and May Be Purchased From Wiley-Blackwell; E-Mail: Cs-Journals@ Wiley. Com. [REVIEW] Hastings Center Report 41.
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  16. Mark A. Bedau (2011). The Intrinsic Scientific Value of Reprogramming Life. Hastings Center Report 41 (4):29-31.
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  17. Mark A. Bedau (2010). 3 Weak Emergence and Context-Sensitive Reduction. In Antonella Corradini & Timothy O'Connor (eds.), Emergence in Science and Philosophy. Routledge. 6--46.
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  18. Mark A. Bedau (2009). Living Technology Today and Tomorrow. Technoetic Arts: A Journal of Speculative Research 7 (2):199-206.
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  19. Mark A. Bedau, Richard Crandall & Michael J. Raven, Cryptographic Hash Functions Based on ALife. PSIpress.
    There is a long history of cryptographic hash functions, i.e. functions mapping variable-length strings to fixed-length strings, and such functions are also expected to enjoy certain security properties. Hash functions can be effected via modular arithmetic, permutation-based schemes, chaotic mixing, and so on. Herein we introduce the notion of an artificial-life (ALife) hash function (ALHF), whereby the requisite mixing action of a good hash function is accomplished via ALife rules that give rise to complex evolution of a given system. Various (...)
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  20. Mark A. Bedau (2008). Is Weak Emergence Just in the Mind? Minds and Machines 18 (4):443-459.
    Weak emergence is the view that a system’s macro properties can be explained by its micro properties but only in an especially complicated way. This paper explains a version of weak emergence based on the notion of explanatory incompressibility and “crawling the causal web.” Then it examines three reasons why weak emergence might be thought to be just in the mind. The first reason is based on contrasting mere epistemological emergence with a form of ontological emergence that involves irreducible downward (...)
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  21. Mark A. Bedau (2004). A Case Study in Objectifying Values in Science. In Peter K. Machamer & Gereon Wolters (eds.), Science, Values, and Objectivity. University of Pittsburgh Press. 190.
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  22. Mark A. Bedau (2003). Artificial Life: Organization, Adaptation and Complexity From the Bottom Up. Trends in Cognitive Sciences 7 (11):505-512.
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  23. Norman H. Packard & Mark A. Bedau (2003). Artificial Life. In L. Nadel (ed.), Encyclopedia of Cognitive Science. Nature Publishing Group. 505-512.
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  24. Steen Rasmussen, Michael J. Raven, Gordon N. Keating & Mark A. Bedau (2003). Collective Intelligence of the Artificial Life Community on Its Own Successes, Failures, and Future. Artificial Life 9:207-235.
    We describe a novel Internet-based method for building consensus and clarifying con icts in large stakeholder groups facing complex issues, and we use the method to survey and map the scienti c and organizational perspectives of the arti cial life community during the Seventh International Conference on Arti cial Life (summer 2000). The issues addressed in this survey included arti cial life’s main successes, main failures, main open scienti c questions, and main strategies for the future, as well as the (...)
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  25. Mark A. Bedau (2002). Downward Causation and the Autonomy of Weak Emergence. Principia 6 (1):5-50.
    Weak emergence has been offered as an explication of the ubiquitous notion of emergence used in complexity science (Bedau 1997). After outlining the problem of emergence and comparing weak emergence with the two other main objectivist approaches to emergence, this paper explains a version of weak emergence and illustrates it with cellular automata. Then it explains the sort of downward causation and explanatory autonomy involved in weak emergence.
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  26. Mark A. Bedau (1998). Philosophical Content and Method of Artificial Life. In T. W. Bynum & J. Moor (eds.), The Digital Phoenix. Cambridge: Blackwell. 135--152.
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  27. Mark A. Bedau (1997). Emergent Models of Supple Dynamics in Life and Mind. Brain and Cognition 34:5-27.
    The dynamical patterns in mental phenomena have a characteristic suppleness&emdash;a looseness or softness that persistently resists precise formulation&emdash;which apparently underlies the frame problem of artificial intelligence. This suppleness also undermines contemporary philosophical functionalist attempts to define mental capacities. Living systems display an analogous form of supple dynamics. However, the supple dynamics of living systems have been captured in recent artificial life models, due to the emergent architecture of those models. This suggests that analogous emergent models might be able to explain (...)
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  28. Mark A. Bedau (1997). Weak Emergence. Philosophical Perspectives 11 (s11):375-399.
    An innocent form of emergence—what I call "weak emergence"—is now a commonplace in a thriving interdisciplinary nexus of scientific activity—sometimes called the "sciences of complexity"—that include connectionist modelling, non-linear dynamics (popularly known as "chaos" theory), and artificial life.1 After defining it, illustrating it in two contexts, and reviewing the available evidence, I conclude that the scientific and philosophical prospects for weak emergence are bright.
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  29. Mark A. Bedau (1996). The Nature of Life. In Margaret A. Boden (ed.), The Philosophy of Artificial Life. Oxford University Press. 332--357.
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