Comment on `Avalanche Dynamics in Evolution, Growth and Depinning Models'
This paper is withdrawn.
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Search indexed arXiv papers on artificial intelligence, large language models, computer vision and robotics. Read source abstracts and follow links to arXiv.
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Propagation of Information in Populations of Self-Replicating Code
We observe the propagation of information in a system of self-replicating strings of code (``Artificial Life'') as a function of fitness and mutation rate. Comparison with theoretical predictions based on the reaction-diffusion equation shows that the response of the artificial system to fluctuations (\eg velocity of the information wave as a function of relative fitness) closely follows that of natural systems. We find that the relaxation time of the system depends on the speed of propagation of information and the size of the system. This analysis offers the possibility of determining the minimal system size for observation of non-equilibrium effects at fixed mutation rate.
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Isologous Diversification: A Theory of Cell Differentiation
Isologous diversification theory for cell differentiation is proposed, based on simulations of interacting cells with biochemical networks and cell division process following consumption of some chemicals. According to the simulations of the interaction-based dynamical systems model, the following scenario of the cell differentiation is proposed. (1) Up to some threshold number, divisions bring about almost identical cells with synchronized biochemical oscillations. (2)As the number is increased the oscillations lose the synchrony, leading to groups of cells with different phases of oscillations. (3)Amplitudes of oscillation and averaged chemical compositions start to differ by groups of cells. The differentiated behavior of states is transmitted to daughter cells. (4)Recursivity is formed so that the daughter cells keep the identical chemical character. This ``memory" is made possible through the transfer of initial conditions. (5) Successive differentiation proceeds. Mechanism of tumor cell formation, origin of stem cells, anomalous differentiation by transplantations, apoptosis and other features of cell differentiation process are also discussed, with some novel predictions. (Keywords: differentiation, chemical network, cell division, clustering, open chaos)
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Stability of periodic solutions in series arrays of Josephson junctions with internal Capacitance
A mystery surrounds the stability properties of the splay-phase periodic solutions to a series array of N Josephson junction oscillators. Contrary to what one would expect from dynamical systems theory, the splay state appears to be neutrally stable for a wide range of system parameters. It has been explained why the splay state must be neutrally stable when the Stewart-McCumber parameter beta is zero. In this paper we complete the explanation of the apparent neutral stability; we show that the splay state is typically hyperbolic -- either asymptotically stable or unstable -- when beta > 0. We conclude that there is only a single unit Floquet multiplier, based on accurate and systematic computations of the Floquet multipliers for beta ranging from 0 to 10. However, N-2 multipliers are extremely close to 1 for beta larger than about 1. In addition, two more Floquet multipliers approach 1 as beta becomes large. We visualize the global dynamics responsible for these nearly degenerate multipliers, and then estimate them accurately by a multiple time-scale analysis. For N=4 junctions the analysis also predicts that the system converges toward either the in-phase state, the splay state, or two clusters of two oscillators, depending on the parameters.
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Dynamical Equilibrium of Interacting Ant Societies
The sustainable biodiversity associated with a specific ecological niche as a function of land area is analysed computationally by considering the interaction of ant societies over a collection of islands. A power law relationship between sustainable species and land area is observed. We will further consider the effect a perturbative inflow of ants has upon the model.
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Analysis, Synthesis, and Estimation of Fractal-Rate Stochastic Point Processes
Fractal and fractal-rate stochastic point processes (FSPPs and FRSPPs) provide useful models for describing a broad range of diverse phenomena, including electron transport in amorphous semiconductors, computer-network traffic, and sequences of neuronal action potentials. A particularly useful statistic of these processes is the fractal exponent $α$, which may be estimated for any FSPP or FRSPP by using a variety of statistical methods. Simulated FSPPs and FRSPPs consistently exhibit bias in this fractal exponent, however, rendering the study and analysis of these processes non-trivial. In this paper, we examine the synthesis and estimation of FRSPPs by carrying out a systematic series of simulations for several different types of FRSPP over a range of design values for $α$. The discrepancy between the desired and achieved values of $α$ is shown to arise from finite data size and from the character of the point-process generation mechanism. In the context of point-process simulation, reduction of this discrepancy requires generating data sets with either a large number of points, or with low jitter in the generation of the points. In the context of fractal data analysis, the results presented here suggest caution when interpreting fractal exponents estimated from experimental data sets.
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TRANSIMS traffic flow characteristics
Knowledge of fundamental traffic flow characteristics of traffic simulation models is an essential requirement when using these models for the planning, design, and operation of transportation systems. In this paper we discuss the following: a description of how features relevant to traffic flow are currently under implementation in the TRANSIMS microsimulation, a proposition for standardized traffic flow tests for traffic simulation models, and the results of these tests for two different versions of the TRANSIMS microsimulation.
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A condition for the genotype-phenotype mapping: Causality
The appropriate choice of the genotype-phenotype mapping in combination with the mutation operator is important for a successful evolutionary search process. We suggest a measure to quantify the quality of this combination by addressing the question whether the relation among distances is carried over from one space to the other. Search processes which do not destroy the neighbourhood structure are termed strongly causal. We apply the proposed measure to parameter and structure optimisation problems in order to assess the combination (mapping, mutation operator) and at the same time to be able to propose improved settings.
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Experiences with iterated traffic microsimulations in Dallas
This paper reports experiences with iterated traffic microsimulations in the context of a Dallas study. ``Iterated microsimulations'' here means that the information generated by a microsimulation is fed back into the route planner so that the simulated individuals can adjust their routes to circumvent congestion. This paper gives an overview over what has been done in the Dallas context to better understand the relaxation process, and how to judge the robustness of the results.
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Sentient Networks
In this paper we consider the question whether a distributed network of sensors and data processors can form "perceptions" based on the sensory data. Because sensory data can have exponentially many explanations, the use of a central data processor to analyze the outputs from a large ensemble of sensors will in general introduce unacceptable latencies for responding to dangerous situations. A better idea is to use a distributed "Helmholtz machine" architecture in which the collective state of the network as a whole provides an explanation for the sensory data.
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Effects of neutral selection on the evolution of molecular species
We introduce a new model of evolution on a fitness landscape possessing a tunable degree of neutrality. The model allows us to study the general properties of molecular species undergoing neutral evolution. We find that a number of phenomena seen in RNA sequence-structure maps are present also in our general model. Examples are the occurrence of "common" structures which occupy a fraction of the genotype space which tends to unity as the length of the genotype increases, and the formation of percolating neutral networks which cover the genotype space in such a way that a member of such a network can be found within a small radius of any point in the space. We also describe a number of new phenomena which appear to be general properties of neutrally evolving systems. In particular, we show that the maximum fitness attained during the adaptive walk of a population evolving on such a fitness landscape increases with increasing degree of neutrality, and is directly related to the fitness of the most fit percolating network.
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Adaptive Competition, Market Efficiency, Phase Transitions and Spin-Glasses
We analyze a simple model of adaptive competition which captures essential features of a variety of adaptive competitive systems in the social and biological sciences. Each of N agents, at each time step of a game, joins one of two groups. The agents in the minority group are awarded a point, while the agents in the majority group get nothing. Each agent has a fixed set of strategies drawn at the beginning of the game from a common pool, and chooses his current best-performing strategy to determine which group to join. For a fixed N, the system exhibits a phase change as a function of the size of the common strategy pool from which the agents initially draw their strategies. For small pool sizes, the system is in an efficient market phase. All information that can be used by the agents' strategies is traded away, no agent can accumulate more points than would an agent making random guesses, and thus the commons suffer,since relatively few points are awarded to the agents in total. For large initial strategy pool sizes, the system is in an inefficient market phase, in which there is predictive information available to the agents' strategies, and some agents can do better than random at accumulating points. In this phase, the total number of points awarded to the agents is greater than in a game in which all agents guess randomly, and so the commons do relatively well. At a critical size of the strategy pool marking the cross-over from the efficient market to the inefficient market phases, the commons do best. This critical size of the pool grows monotonically with N. The behavior of this system has some features reminiscent of a spin-glass.
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Geometric statistical inference
Finite sample size corrections to the reparametrization-invariant solution of the inverse problem of probability are computed, and shown to converge uniformly to the correct distribution.
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Modelling coevolution in multispecies communities
We introduce the Webworld model, which links together the ecological modelling of food web structure with the evolutionary modelling of speciation and extinction events. The model describes dynamics of ecological communities on an evolutionary timescale. Species are defined as sets of characteristic features, and these features are used to determine interaction scores between species. A simple rule is used to transfer resources from the external environment through the food web to each of the species, and to determine mean population sizes. A time step in the model represents a speciation event. A new species is added with features similar to those of one of the existing species and a new food web structure is then calculated. The new species may (i) add stably to the web, (ii) become extinct immediately because it is poorly adapted, or (iii) cause one or more other species to become extinct due to competition for resources. We measure various properties of the model webs and compare these with data on real food webs. These properties include the proportions of basal, intermediate and top species, the number of links per species and the number of trophic levels. We also study the evolutionary dynamics of the model ecosystem by following the fluctuations in the total number of species in the web. Extinction avalanches occur when novel organisms arise which are significantly better adapted than existing ones. We discuss these results in relation to the observed extinction events in the fossil record, and to the theory of self-organized criticality.
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Invariant closure for the Fokker-Planck equation
We develop the principle of dynamic invariance to obtain closed moment equations from the Fokker-Planck kinetic equation. The analysis is carried out to explicit formulae for computation of the lowest eigenvalue and of the corresponding eigenfunction for arbitrary potentials.
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Emergence of Rules in Cell Society: Differentiation, Hierarchy, and Stability
A dynamic model for cell differentiation is studied, where cells with internal chemical reaction dynamics interact with each other and replicate. It leads to spontaneous differentiation of cells and determination, as is discussed in the isologous diversification. Following features of the differentiation are obtained: (1)Hierarchical differentiation from a ``stem'' cell to other cell types, with the emergence of the interaction-dependent rules for differentiation; (2)Global stability of an ensemble of cells consisting of several cell types, that is sustained by the emergent, autonomous control on the rate of differentiation; (3)Existence of several cell colonies with different cell-type distributions. The results provide a novel viewpoint on the origin of complex cell society, while relevance to some biological problems, especially to the hemopoietic system, is also discussed.
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Large-scale evolution and extinction in a hierarchically structured environment
A class of models for large-scale evolution and mass extinctions is presented. These models incorporate environmental changes on all scales, from influences on a single species to global effects. This is a step towards a unified picture of mass extinctions, which enables one to study coevolutionary effects and external abiotic influences with the same means. The generic features of such models are studied in a simple version, in which all environmental changes are generated at random and without feedback from other parts of the system.
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Critical Exponent of Species-Size Distribution in Evolution
We analyze the geometry of the species- and genotype-size distribution in evolving and adapting populations of single-stranded self-replicating genomes: here programs in the Avida world. We find that a scale-free distribution (power law) emerges in complex landscapes that achieve a separation of two fundamental time scales: the relaxation time (time for population to return to equilibrium after a perturbation) and the time between mutations that produce fitter genotypes. The latter can be dialed by changing the mutation rate. In the scaling regime, we determine the critical exponent of the distribution of sizes and strengths of avalanches in a system without coevolution, described by first-order phase transitions in single finite niches.
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