Transfer of information between senders and receivers, of one kind or another, is essential to all life. David Lewis introduced a game theoretic model of the simplest case, where one sender and one receiver have pure common interest. How hard or easy is it for evolution to achieve information transfer in Lewis signaling?. The answers involve surprising subtleties. We discuss some if these in terms of evolutionary dynamics in both finite and infinite populations, with and without mutation.

In a small handful of papers in theoretical population genetics, John Gillespie (2000a, 2000b, 2001) argues that a new stochastic process he calls "genetic draft" is evolutionarily more significant than genetic drift. This case study of chance in evolution explores Gillespie's proposed stochastic evolutionary force and sketches the implications of Gillespie's argument for philosophers' explorations of genetic drift.

Mathematical models can be profitably used to establish whether our perception of the external world is accurate. Donald Hoffman and his collaborators have developed a promising mathematical framework within which this question can be addressed and which is based on an exhaustive taxonomy of the different possible relations between perceptual representations and the external world. After reformulating their framework by means of an improved formal system, we discuss their application of evolutionary game theory, which appears to show that an (...) essentially anti-realistic perceptual strategy would in the long run biologically outcompete its rivals. We argue that their model does not take the crucial biological significance of environmental changes into due consideration and propose alternative models which do. We conclude that a partially realistic representation would be favoured in our models. (shrink)

The iterated prisoner’s dilemma (IPD) has been widely used in the biological and social sciences to model dyadic cooperation. While most of this work has focused on the discrete prisoner’s dilemma, in which actors choose between cooperation and defection, there has been some analysis of the continuous IPD, in which actors can choose any level of cooperation from zero to one. Here, we analyse a model of the continuous IPD with a limited strategy set, and show that a generous strategy (...) achieves the maximum possible payoff against its own type. While this strategy is stable in a neighborhood of the equilibrium point, the equilibrium point itself is always vulnerable to invasion by uncooperative strategies, and hence subject to eventual destabilization. The presence of noise or errors has no effect on this result. Instead, generosity is favored because of its role in increasing contributions to the most efficient level, rather than in counteracting the corrosiveness of noise. Computer simulation using a single-locus infinite alleles Gaussian mutation model suggest that outcomes ranging from a stable cooperative polymorphism to complete collapse of cooperation are possible depending on the magnitude of the mutational variance. Also, making the cost of helping a convex function of the amount of help provided makes it more difficult for cooperative strategies to invade a non-cooperative equilibrium, and for the cooperative equilibrium to resist destabilization by noncooperative strategies. (shrink)

Gebserian consciousness structures as expressed in human culture are readily understood as analogous to developmental dynamics in holistic biology, and eastern praxis and philosophy. Probably the most integral and fruitful western paradigm of whole-organism biology is that carefully developed in the Goethean tradition to incorporate an understanding of consciousness. This tradition profoundly understands our early childhood through adult development as a dynamic organic process in time, thus integrating the study of heterochrony and chronobiology with morphology, physiology and consciousness. In (...) addition to revealing compelling convergences with the classic work of Gebser on consciousness structures, this Goethian tradition reveals significant parallels with contemporary studies in the realm of biophysics, the science of complexity and eastern spiritual traditions which regard the body as a coherent field, manifesting dynamic, directed currents of development that can be traced and mapped out. These paradigms recognize the importance of recursive organizing principles that structure the biosphere's spatial dimensions and, in the temporal realm, structure long- and short-term evolutionary cycles. The marriage of Gebserian cultural philosophies with Goethean biology, the science of complexity and eastern praxis traditions leads to a simple, elegant and remarkably broad appreciation of the fundamental role of consciousness as an essential property of dynamic living systems. This synthesis helps address many of the difficult questions faced by students of consciousness in a relatively simple and straightforward manner, beginning with a focus on our own species and close mammalian relatives. Two main conclusions arise from this synthesis. First, although enjoying increased attention recently, the Gebserian and Goethean paradigms were far ahead of their time and so have been overlooked. Second, consciousness must be regarded as a primary biologically-embedded datum of life/existence and not merely an epiphenomenon associated with the function of localized or specific organs. (shrink)

A systematic, rigorous, comprehensive, and unified overview of evolutionary game theory.

Multiple realization occurs when a natural kind is variably realized at more basic levels and the common physical structure of the realizers is not essential for supporting nomological statements. It has been suggested that this phenomenon may be an outcome of natural selection acting over multiple realizers that perform an adaptive function. In this paper, we make the following contributions. First, we present a revision of this model, characterized by stricter equilibrium conditions and superior explanatory power. Second, we present a (...) typology of multiple realization that provides a plausible account of the differences between across- and within-species multiple realization. Third, we perform a formal analysis of the dynamics of multiple realization that sheds light on the differences between multiple realization at different levels of organization. (shrink)

ABSTRACT Multiple realization occurs when a natural kind is variably realized at more basic levels and the common physical structure of the realizers is not essential for supporting nomological statements. It has been suggested that this phenomenon may be an outcome of natural selection acting over multiple realizers that perform an adaptive function. In this paper, we make the following contributions. First, we present a revision of this model, characterized by stricter equilibrium conditions and superior explanatory power. Second, we present (...) a typology of multiple realization that provides a plausible account of the differences between across- and within-species multiple realization. Third, we perform a formal analysis of the dynamics of multiple realization that sheds light on the differences between multiple realization at different levels of organization. (shrink)

The concept of fitness is central to evolutionary biology. Models of evolutionary change typically use some quantity called “fitness” which measures an organism’s reproductive success. But what exactly does it mean that fitness is such a measure? In what follows, we look at the interplay between abstract evolutionary models and quantitative measures of fitness and develop a measurement-theoretic perspective on fitness in order to explore what makes certain measures of fitness significant.

The article discusses evolutionary aspects of mimicry from a semiotic viewpoint. The concept of semiotic scaffolding is used for this approach, and its relations with the concepts of exaptation and semiotic co-option are explained. Different dimensions of scaffolding are brought out as ontogenetic, evolutionary, physiological and cognitive. These dimensions allow for interpreting mimicry as a system that scaffolds itself. With the help of a number of mimicry cases, e.g. butterfly eyespots, brood parasitism, and plant mimesis, the evolutionary (...) dynamics of mimicry in the open bio-semiosphere is investigated. The main argument is that biological mimicry largely develops through sign relations and communicative relations between organisms. It is proposed that mimicry systems should be described as two-layered structures composed of the ecological composition of the species involved and the semiotic structure of their communication. (shrink)

Studies on the conservation of the inferred transcriptional regulatory network of prokaryotes have suggested that specific transcription factors are less‐widely conserved in comparison to their target genes. This observation implied that, at large evolutionary distances, the turnover of specific transcription factors through loss and non‐orthologous displacement might be a major factor in the adaptive radiation of prokaryotes. However, the recent work of Hershberg and Margalit1 suggests that, at shorter phylogenetic scales, the evolutionary dynamics of the bacterial transcriptional (...) regulatory network might exhibit distinct patterns. The authors find previously unnoticed relationships between the regulatory mode (activation or repression), the number of regulatory interactions and their conservation patterns in γ‐proteobacteria. These relationships might be shaped by the differences in the adaptive value and mode of operation of different regulatory interactions. BioEssays 29:625–629, 2007. © 2007 Wiley Periodicals, Inc. (shrink)

We study the coupled dynamics of two populations of random replicators by means of statistical mechanics methods, and focus on the effects of relative population size, strategy correlations and heterogeneities in the respective cooperation pressures. To this end we generalise existing path-integral approaches to replicator systems with random asymmetric couplings. This technique allows one to formulate an effective dynamical theory, which is exact in the thermodynamic limit and which can be solved for persistent order parameters in a fixed-point regime (...) regardless of the symmetry of the interactions. The onset of instability can be determined self-consistently. We calculate quantities such as the diversity of the respective populations and their fitnesses in the stationary state, and compare results with data from a numerical integration of the replicator equations. -/- . (shrink)

Overview The evolution of multicellularity raises questions regarding genomic and developmental commonalities and discordances, selective advantages and disadvantages, physical determinants of development, and the origins of morphological novelties. It also represents a change in the definition of individuality, because a new organism emerges from interactions among single cells. This volume considers these and other questions, with contributions that explore the origins and consequences of the evolution of multicellularity, addressing a range of topics, organisms, and experimental protocols. Each section focuses on (...) selected topics or particular lineages that present a significant insight or challenge. The contributors consider the fossil record of the paleontological circumstances in which animal multicellularity evolved; cooptation, recurrent patterns, modularity, and plausible pathways for multicellular evolution in plants; theoretical approaches to the amoebozoa and fungi (cellular slime molds having long provided a robust model system for exploring the evolution of multicellularity), plants, and animals; genomic toolkits of metazoan multicellularity; and philosophical aspects of the meaning of individuality in light of multicellular evolution. Contributors Maja Adamska, Argyris Arnellos, Juan A. Arias, Eugenio Azpeitia, Mariana Benítez, Adriano Bonforti, John Tyler Bonner, Peter L. Conlin, A. Keith Dunker, Salva Duran-Nebreda, Ana E. Escalante, Valeria Hernández-Hernández, Kunihiko Kaneko, Andrew H. Knoll, Stephan G. König, Daniel J. G. Lahr, Ottoline Leyser, Alan C. Love, Raul Montañez, Emilio Mora van Cauwelaert, Alvaro Moreno, Vidyanand Nanjundiah, Aurora M. Nedelcu, Stuart A. Newman, Karl J. Niklas, William C. Ratcliff, Iñaki Ruiz-Trillo, Ricard Solé . (shrink)

Protein structure is dynamic: the intrinsic flexibility of polypeptides facilitates a range of conformational fluctuations, and individual protein chains can assemble into complexes. Proteins are also dynamic in evolution: significant variations in secondary, tertiary and quaternary structure can be observed among divergent members of a protein family. Recent work has highlighted intriguing similarities between these structural and evolutionary dynamics occurring at various levels. Here we review evidence showing how evolutionary changes in protein sequence and structure are often (...) closely related to local protein flexibility and disorder, large‐scale motions and quaternary structure assembly. We suggest that these correspondences can be largely explained by neutral evolution, while deviations between structural and evolutionary dynamics can provide valuable functional insights. Finally, we address future prospects for the field and practical applications that arise from a deeper understanding of the intimate relationship between protein structure, dynamics, function and evolution. (shrink)

. Interpreted dynamical systems are dynamical systems with an additional interpretation mapping by which propositional formulas are assigned to system states. The dynamics of such systems may be described in terms of qualitative laws for which a satisfaction clause is defined. We show that the systems Cand CL of nonmonotonic logic are adequate with respect to the corresponding description of the classes of interpreted ordered and interpreted hierarchical systems, respectively. Inhibition networks, artificial neural networks, logic programs, and evolutionary (...) systems are instances of such interpreted dynamical systems, and thus our results entail that each of them may be described correctly and, in a sense, even completely by qualitative laws that obey the rules of a nonmonotonic logic system. (shrink)

In this paper, we propose a new predator-prey nonlinear dynamic evolutionary model of real estate enterprises considering the large, medium, and small real estate enterprises for three different prey teams. A 5D predator-prey nonlinear dynamic evolutionary system in the real estate market is established, where the large, medium, and small real estate enterprises correspond to three differential equations, provincial and local officials, and the central government correspond to the other two differential equations. Nonlinear dynamic analysis on a 5D (...) predator-prey evolutionary system in the real estate market, containing the analysis of equilibrium points and stabilities, is made. The corresponding discrete system is simulated, and the simulation results about Lyapunov spectrum, bifurcation diagram, sequence diagram, and phase diagram are given. Compared with the work of Yang et al. in which all real estate enterprises corresponded to one differential equation, in our proposed model, the large, medium, and small real estate enterprises correspond to three differential equations which is more accordant with the specific circumstance of real estate companies. (shrink)

Evolutionary genetics is concerned with natural selection and neutral drift, to the virtual exclusion of almost everything else. In its current focus on DNA variation, it reduces phenotypes to symbols. Varying phenotypes, however, are the units of evolution, and, if we want a comprehensive theory of evolution, we need to consider both the internal and external evolutionary forces that shape the development of phenotypes. Genetic systems are redundant, modular and subject to a variety of genomic mechanisms of “turnover” (...) (transposition, gene conversion, unequal crossingover, slippage and so on). As such the construction and spread of novel combinations of modules by turnover, in particular within gene promoters, contributes significantly to the evolution of phenotypes. Furthermore, redundancy, turnover and modularity lead to ever more complex networks of genetic interactions and ever more functions for a given module. The significant interaction between genomic turnover and natural selection leads to a molecular coevolution between interacting modules and hence facilitates the establishment of biological novelties. BioEssays 22:1153–1159, 2000. © 2000 John Wiley & Sons, Inc. (shrink)

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.

The current debate over extending inheritance and its evolutionary impact has focused on adding new categories of non-genetic factors to the classical transmission of DNA, and on trying to redefine inheritance. Transmitted factors have been mainly characterized by their directions of transmission and the way they store variations. In this paper, we leave aside the issue of defining inheritance. We rather try to build an evolutionary conceptual framework that allows for tracing most, if not all forms of transmission (...) and makes sense of their different tempos and modes. We discuss three key distinctions that should in particular be the targets of theoretical and empirical investigation, and try to assess the interplay among them and evolutionary dynamics. We distinguish two channels of transmission, two measurements of the temporal dynamics of transmission, respectively across and within generations, and two types of transmitted factors according to their evolutionary relevance. By implementing these three distinctions we can then map different forms of transmission over a continuous space describing the combination of their varying dynamical features. While our aim is not to provide yet another model of inheritance, putting together these distinctions and crossing them, we manage to offer an inclusive conceptual framework of transmission, grounded in empirical observation, and coherent with evolutionary theory. This interestingly opens possibilities for qualitative and quantitative analyses, and is a necessary step, we argue, in order to question the interplay between the dynamics of evolution and the dynamics of multiple forms of transmission. (shrink)

David Hull's analysis of conceptual change in science, as presentedin his book, Science as a Process (1988), provides a useful framework for understanding one of the scientific controversies in which he actively and constructively intervened, the units of selectiondebates in evolutionary biology. What follows is a brief overview ofthose debates and some reflections on them.

This paper discusses the explanatory significance of the equilibrium concept in the context of an example of extremely complicated dynamical behavior. In particular, numerical evidence is presented for the existence of chaotic dynamics on a "strange attractor" in the evolutionary game dynamics introduced by Taylor and Jonker [also known as the "replicator dynamics"]. This phenomenon is present already in four strategy evolutionary games where the dynamics takes place in a simplex in three dimensional space-the (...) lowest number of dimensions in which such a strange attractor is possible. From a dynamical point of view, it is the attractor-rather than the equilibrium-that is of prime interest. (shrink)

Four principal papers and a total of 43 peer commentaries on the evolutionary origins of morality. To what extent is human morality the outcome of a continuous development from motives, emotions and social behaviour found in nonhuman animals? Jerome Kagan, Hans Kummer, Peter Railton and others discuss the first principal paper by primatologists Jessica Flack and Frans de Waal. The second paper, by cultural anthropologist Christopher Boehm, synthesizes social science and biological evidence to support his theory of how our (...) hominid ancestors became moral. In the third paper philosopher Elliott Sober and evolutionary biologist David Sloan Wilson argue that an evolutionary understanding of human nature allows sacrifice for others and ultimate desires for another's good. Finally Brian Skyrms argues that game theory based on adaptive dynamics must join the social scientist's use of rational choice and classical game theory to explain cooperation. (shrink)

Skyrms' investigations of dynamic deliberation are traced through his book of 1990 and his subsequent investigation of dynamic deliberation based on inductive rules to his recent results about chaos generated by evolutionary game dynamics. It is argued that the dynamics studied in the book, and the inductive dynamics as well, need to be supplemented to yield the correct recommendation in an example game. Some features about information feedback are pointed out. Finally, it is suggested that more (...) work is needed to assess whether Skyrms' results about chaos have any interesting implications for plausible game theoretic representations of interactions among human agents. (shrink)

Evolutionary systems biology (ESB) aims to integrate methods from systems biology and evolutionary biology to go beyond the current limitations in both fields. This article clarifies some conceptual difficulties of this integration project, and shows how they can be overcome. The main challenge we consider involves the integration of evolutionary biology with developmental dynamics, illustrated with two examples. First, we examine historical tensions between efforts to define general evolutionary principles and articulation of detailed mechanistic explanations (...) of specific traits. Next, these tensions are further clarified by considering a recent case from another field focused on developmental dynamics: stem cell biology. In the stem cell case, incompatible explanatory aims block integration. Experimental approaches aim at mechanistic explanation while dynamical system models offer explanation in terms of general principles. We then discuss an ESB case in which integration succeeds: search for general attractors using a dynamical systems framework synergizes with the experimental search for detailed mechanisms. Contrasts between the positive and negative cases suggest general lessons for achieving an integrated understanding of developmental and evolutionary dynamics. The key integrative move is to acknowledge two complementary aims, both relevant to explanation: identifying the space of possible dynamic states and trajectories, and mechanistic understanding of causal interactions underlying a specific phenomenon of interest. These two aims can support one another in a joint project characterizing dynamic aspects of evolving lineages. This more inclusive project can lead to insights that cannot be reached by either approach in isolation. (shrink)

Recently there has been some interest in studying the explanation of meaning by using signaling games. I shall argue that the meaning of signals in signaling games remains sufficiently unclear to motivate further investigation. In particular, the possibility of distinguishing imperatives and indicatives at a fundamental level will be explored. Thereby I am trying to preserve the generality of the signaling games framework while bringing it closer to human languages. A number of convergence results for the evolutionary dynamics (...) of our models will be proved. (shrink)

Dynamo: Diagrams for Evolutionary Game Dynamics is free, open-source software used to create phase diagrams and other images related to dynamical systems from evolutionary game theory. We describe how to use the software’s default settings to generate phase diagrams quickly and easily. We then explain how to take advantage of the software’s intermediate and advanced features to create diagrams that highlight the key properties of the dynamical system under study. Sample code and output are provided to help (...) demonstrate the software’s capabilities. (shrink)

Millions of scientific articles are published each year, making it difficult to stay abreast of advances within even the smallest subdisciplines. Traditional approaches to the study of science, such as the history and philosophy of science, involve closely reading a relatively small set of journal articles. And yet many questions benefit from casting a wider net: Is most scientific change gradual or revolutionary? What are the key sources of scientific novelty? Over the past several decades, a massive effort to digitize (...) the academic literature and equip computers with algorithms that can distantly read and analyze a digital database has taken us one step closer to answering these questions. The Dynamics of Science brings together a diverse array of contributors to examine the largely unexplored computational frontiers of history and philosophy of science. Together, they reveal how tools and data from automated textual analysis, or machine "reading," combined with methods and models from game theory and cultural evolutionary theory, can begin to answer fundamental questions about the nature and history of science. (shrink)

When social scientists began employing evolutionary game theory (EGT) in their disciplines, the question arose what the appropriate interpretation of the formal EGT framework would be. Social scientists have given different answer, of which I distinguish three basic kinds. I then proceed to uncover the conceptual tension between the formal framework of EGT, its application in the social sciences, and these three interpretations. First, I argue that EGT under the biological interpretation has a limited application in the social sciences, (...) chiefly because strategy replication often cannot be sensibly interpreted as strategy bearer reproduction in this domain. Second, I show that alternative replication mechanisms imply interpersonal comparability of strategy payoffs. Giving a meaningful interpretation to such comparisons is not an easy task for many social situations, and thus limits the applicability of EGT in this domain. Third, I argue that giving a new interpretation both to strategy replication and selection solves the issue of interpersonal comparability, but at the costs of making the new interpretation incompatible with natural selection interpretations of EGT. To the extent that social scientists seek such a natural selection interpretation, they face a dilemma: either face the challenge that interpersonal comparisons pose, or give up on the natural selection interpretation. By identifying these tensions, my analysis pleas for greater awareness of the specific purposes of EGT modelling in the social sciences, and for greater sensitivity to the underlying microstructure on which the evolutionary dynamics and other EGT solution concepts supervene. (shrink)

"The evolutionary vision" is a term coined by economist Kenneth E. Boulding to describe a unified view of evolution that encompasses all levels of reality, from the cosmic or physical through the biological, ecological, and sociobiological to the sociocultural. It focuses less on systems or any particular entity than on the processes through which they evolve. In this volume various approaches to the self-organization of matter and information are outlined by authors who are among the chief developers of this (...) new paradigm. They focus on the general laws governing evolutionary dynamics across all levels of evolution, including the evolution of humans and human systems. (shrink)

Evolutionary game theoretic accounts of justice attempt to explain our willingness to follow certain principles of justice by appealing to robustness properties possessed by those principles. Skyrms (1996) offers one sketch of how such an account might go for divide-the-dollar, the simplest version of the Nash bargaining game, using the replicator dynamics of Taylor and Jonker (1978). In a recent article, D'Arms et al. (1998) criticize his account and describe a model which, they allege, undermines his theory. I (...) sketch a theory of evolutionary explanations of justice which avoids their methodological criticisms, and develop a spatial model of divide-the-dollar with more robust convergence properties than the models of Skyrms (1996) and D'Arms et al. (1998). (shrink)