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28
SelfEvolution in a Constructive Binary String System
 Artificial Life
, 1998
"... This paper focuses on the phenomena of evolution whose appearance is notable because no explicit mutation, recombination or artificial selection operators are introduced. We call the system selfevolving because every variation is performed by the objects themselves in their machine form. Keywords: ..."
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Cited by 35 (17 self)
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This paper focuses on the phenomena of evolution whose appearance is notable because no explicit mutation, recombination or artificial selection operators are introduced. We call the system selfevolving because every variation is performed by the objects themselves in their machine form. Keywords: artificial chemistry, autocatalytic reaction system, molecular computing, prebiotic evolution, selforganization, selfprogramming 1
Artificial Chemistries  A Review
, 2000
"... This article reviews the growing body of scientific work in Artificial Chemistry. First, common motivations and fundamental concepts are introduced. Second, current research activities are discussed along three application dimensions: modelling, information processing and optimization. Finally, comm ..."
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Cited by 34 (4 self)
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This article reviews the growing body of scientific work in Artificial Chemistry. First, common motivations and fundamental concepts are introduced. Second, current research activities are discussed along three application dimensions: modelling, information processing and optimization. Finally, common phenomena among the different systems are summarized. It is argued here that Artificial Chemistries are "the right stuff" for the study of prebiotic and biochemical evolution, and they provide a productive framework for questions regarding the origin and evolution of organizations in general. Furthermore, Artificial Chemistries have a broad application range to practical problems as shown in this review.
The Influence of Mutation on Autocatalytic Reaction Networks
, 1994
"... A particular class of ordinary differential equations (ODE) describing catalyzed, templateinduced, and erroneous replication is investigated. The ODEs can be split into a replicator part accounting for the correct replication and a mutation term accounting for all miscopying processes. The set of a ..."
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Cited by 15 (5 self)
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A particular class of ordinary differential equations (ODE) describing catalyzed, templateinduced, and erroneous replication is investigated. The ODEs can be split into a replicator part accounting for the correct replication and a mutation term accounting for all miscopying processes. The set of all species is divided into the catalytically active "viable" species and an errortail subsuming all other species. Neglecting both the intermutation among the viable species and the reflux from the errortail allows for an extensive analysis of the autocatalytic network. If mutation rates are small enough a perturbation approach is feasible showing that mutation in general simplifies the qualitative behavior of the dynamical system. Special cases, such as Schlogl's model, the uniform model, and the hypercycle show that the viable species become unstable beyond a critical mutation rate: there is an analogue to the errorthreshold of the quasispecies model also in nonlinear autocatalytic r...
Uniform persistence and flows near a closed positively invariant set
 J. Dynam. Differential Equations
, 1994
"... In this paper, the behavior of a continuous flow in the vicinity of a closed positively.invariant subset in a metric space is investigated. The main theorem in this part in some sense generalizes previous results concerning classification of the flow near a compact invariant set in a locally compact ..."
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Cited by 13 (5 self)
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In this paper, the behavior of a continuous flow in the vicinity of a closed positively.invariant subset in a metric space is investigated. The main theorem in this part in some sense generalizes previous results concerning classification of the flow near a compact invariant set in a locally compact metric space which was described by UraKimura (1960) and Bhatia (1969). By applying the obtained main theorem, we are able to prove two persistence theorems. In the first one, several equivalent statements are established, which unify and generalize earlier results based on Liapunovlike functions and those about the equiyalence of weak uniform persistence and uniform persistence. The second theorem generalizes the classical uniform persistence theorems based on analysis of the flow on the boundary by relaxing point dissipativity and invariance of the boundary. Several examples are given which show that our theorems will apply to a wider rarity of ecological models.
Selection Dynamics in Autocatalytic Systems: Templates Replicating Through Binary Ligation
, 1997
"... The theory of autocatalytic binary ligation is reviewed within the context of a consistently applied MichaelisMenten quasisteadystate approximation to obtain explicit analytical results describing timecourse data from experiments. A detailed protocol for the stepwise elucidation of a minimal se ..."
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Cited by 11 (7 self)
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The theory of autocatalytic binary ligation is reviewed within the context of a consistently applied MichaelisMenten quasisteadystate approximation to obtain explicit analytical results describing timecourse data from experiments. A detailed protocol for the stepwise elucidation of a minimal set of experimental parameters is outlined. The kinetic equations are then generalized to cases of self and crosscatalysis among an arbitrary number of different templates and applied to experiments involving just two templates. Depending on the values of various kinetic parameters such systems can display exclusionary Darwinian selection corresponding to an exponential growth law, selective coexistence or coexistence of all species characteristic of a parabolic growth law; the intermediate behaviour arises as a property of the full mechanism analysed here. Our results are applicable to the classical case of selfreplicating nucleic acids and their analogues as well as to newly discovered sel...
Landscapes and Effective Fitness
, 2003
"... The concept of a fitness landscape arose in theoretical biology, while that of effective fitness has its origin in evolutionary computation. Both have emerged as useful conceptual tools with which to understand the dynamics of evolutionary processes, especially in the presence of complex genotypeph ..."
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Cited by 11 (2 self)
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The concept of a fitness landscape arose in theoretical biology, while that of effective fitness has its origin in evolutionary computation. Both have emerged as useful conceptual tools with which to understand the dynamics of evolutionary processes, especially in the presence of complex genotypephenotype relations. In this contribution we attempt to provide a unified discussion of these two approaches, discussing both their advantages and disadvantages in the context of some simple models. We also discuss how fitness and effective fitness change under various transformations of the configuration space of the underlying genetic model, concentrating on coarse graining transformations and on a particular coordinate transformation that provides an appropriate basis for illuminating the structure and consequences of recombination.
RNA in Silico  The Computational Biology of RNA Secondary Structures
 Adv. Complex Syst
, 1999
"... . RNA secondary structures provide a unique computer model for investigating the most important aspects of structural and evolutionary biology. The existence of efficient algorithms for solving the folding problem, i.e., for predicting the secondary structure given only the sequence, allows the ..."
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Cited by 10 (4 self)
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. RNA secondary structures provide a unique computer model for investigating the most important aspects of structural and evolutionary biology. The existence of efficient algorithms for solving the folding problem, i.e., for predicting the secondary structure given only the sequence, allows the construction of realistic computer simulations. The notion of a "landscape" 2 C. Flamm, I.L. Hofacker, P.F. Stadler underlies both the structure formation (folding) and the (in vitro) evolution of RNA. Evolutionary adaptation may be seen as hill climbing process on a fitness landscape which is determined by the phenotype of the RNA molecule (within the model this is its secondary structure) and the selection constraints acting on the molecules. We find that a substantial fraction of point mutations do not change an RNA secondary structure. On the other hand, a comparable fraction of mutations leads to very different structures. This interplay of smoothness and ruggedness (or robust...
The Evolution of Diversity in Replicator Networks
, 1998
"... Novel species are introduced into a network of interacting replicators either (i) as mutants of members of the network or (ii) as unrelated immigrants. We consider the metapopulation dynamics of such a system. In the first case the appearance of mutants leads to a slow growth of the replicator netw ..."
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Cited by 8 (5 self)
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Novel species are introduced into a network of interacting replicators either (i) as mutants of members of the network or (ii) as unrelated immigrants. We consider the metapopulation dynamics of such a system. In the first case the appearance of mutants leads to a slow growth of the replicator network, proportional to the logarithm of the number of mutation events. Surprisingly, replicator evolved by mutant incorporation are always permanent, despite the fact that permanence is in general a very rare phenomenon. In the second case, on the other hands, immigrants lead to frequent breakdowns of the entire network and hence to complete extinction. In both cases individual species are shortlived, the distribution of survival times is exponential. Keywords Replicator Equation  Metapopulation Dynamics  Mutation  Immigration  Permanence 1. Introduction Selfreplication on molecular level is the crucial "invention" for the origin and maintainance of life. One of the central qu...
Evolvability of Complex Characters: Population Dependent Fourier Decomposition of Fitness Landscapes over Recombination Spaces
, 1999
"... this paper is the following, rather surprising ..."
Autocatalytic Replication in a CSTR and Constant Organization
, 1995
"... The dynamics of a network of autocatalytically replicating species in a continuously stirred tank reactor can be described by a replicator equation in the limit of small flux rates. ..."
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Cited by 7 (7 self)
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The dynamics of a network of autocatalytically replicating species in a continuously stirred tank reactor can be described by a replicator equation in the limit of small flux rates.