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Marilyn J. Roossinck - One of the best experts on this subject based on the ideXlab platform.
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Changes in Population Dynamics in Mutualistic versus Pathogenic Viruses
Viruses, 2011Co-Authors: Marilyn J. RoossinckAbstract:Although generally regarded as pathogens, viruses can also be mutualists. A number of examples of extreme mutualism (i.e., Symbiogenesis) have been well studied. Other examples of mutualism are less common, but this is likely because viruses have rarely been thought of as having any beneficial effects on their hosts. The effect of mutualism on the population dynamics of viruses is a topic that has not been addressed experimentally. However, the potential for understanding mutualism and how a virus might become a mutualist may be elucidated by understanding these dynamics.
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Plant Virus Evolution - Plant virus evolution
2008Co-Authors: Marilyn J. RoossinckAbstract:Questions and Concepts in Plant Virus Evolution: a Historical Perspective.- Community Ecology of Plant Viruses.- Emerging Plant Viruses: a Diversity of Mechanisms and Opportunities.- Evolution of Integrated Plant Viruses.- Viroids.- Virus Populations, Mutation Rates and Frequencies.- Genetic Bottlenecks.- Recombination in Plant RNA Viruses.- Symbiosis, Mutualism and Symbiogenesis.- Methods for Analyzing Viral Evolution.- Virus Evolution and Taxonomy.
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Symbiosis versus competition in plant virus evolution
Nature Reviews Microbiology, 2005Co-Authors: Marilyn J. RoossinckAbstract:Darwin's theory of evolution by natural selection has been supported by molecular evidence and by experimental evolution of viruses. However, it might not account for the evolution of all life, and an alternative model of evolution through symbiotic relationships also has gained support. In this review, the evolution of plant viruses has been reinterpreted in light of these two seemingly opposing theories by using evidence from the earliest days of plant virology to the present. Both models of evolution probably apply in different circumstances, but evolution by symbiotic association (Symbiogenesis) is the most likely model for many evolutionary events that have resulted in rapid changes or the formation of new species. In viruses, Symbiogenesis results in genomic reassortment or recombination events among disparate species. These are most noticeable by phylogenetic comparisons of extant viruses from different taxonomic groups. Darwinian natural selection is a gradual process of change produced by random mutations followed by competitive selection. However, extant species indicate that some evolutionary changes have been more rapid than could occur by Darwinian evolution, and the theory of Symbiogenesis, or evolution by the merging of dissimilar symbiotic entities, has gained support in recent years. Plant RNA viruses were shown to compete in early studies on cross-protection, in which mild strains of a virus could protect plants from subsequent infection by more virulent strains. The requirement of this type of competition is that the strains are similar. Symbiosis involves a different paradigm from competition. In mixed infections of plant viruses, there is a potential for symbiotic associations. The definition of symbiosis requires that the entities are dissimilar. Some well described examples of plant viruses that are symbiotic include potyviruses, which are often synergistic with other viruses; luteoviruses, which often require other viruses for dissemination; and satellites, which establish parasitic symbiosis with their helper viruses. The effect of symbiosis on plant virus evolution can be seen in the modular nature of plant virus genes, which show evidence of recombination and reassortment in their evolutionary history when phylogenetic trees for different genes or genome components are analysed. Symbiogenesis is probably a major component of plant virus evolution, allowing evolutionary leaps that could accommodate changing environments and host ranges. However, the gradual process of natural selection undoubtedly fine-tunes the resulting new species through random mutation and selection.
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Symbiosis versus competition in plant virus evolution
Nature reviews. Microbiology, 2005Co-Authors: Marilyn J. RoossinckAbstract:Darwin's theory of evolution by natural selection has been supported by molecular evidence and by experimental evolution of viruses. However, it might not account for the evolution of all life, and an alternative model of evolution through symbiotic relationships also has gained support. In this review, the evolution of plant viruses has been reinterpreted in light of these two seemingly opposing theories by using evidence from the earliest days of plant virology to the present. Both models of evolution probably apply in different circumstances, but evolution by symbiotic association (Symbiogenesis) is the most likely model for many evolutionary events that have resulted in rapid changes or the formation of new species. In viruses, Symbiogenesis results in genomic reassortment or recombination events among disparate species. These are most noticeable by phylogenetic comparisons of extant viruses from different taxonomic groups.
Lynn Margulis - One of the best experts on this subject based on the ideXlab platform.
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Symbiogenesis: the holobiont as a unit of evolution.
International microbiology : the official journal of the Spanish Society for Microbiology, 2013Co-Authors: Ricardo Guerrero, Lynn Margulis, Mercedes BerlangaAbstract:Symbiogenesis is the result of the permanent coexistence of various bionts to form the holobiont (namely, the host and its microbiota). The holobiome is the sum total of the component genomes in a eukaryotic organism; it comprises the genome of an individual member of a given taxon (the host genome) and the microbiome (the genomes of the symbiotic microbiota). The latter is made up of the genes of a variety of microbial communities that persist over time and are not eliminated by natural selection. Therefore, the holobiome can also be considered as the genomic reflection of the complex network of symbiotic interactions that link an individual member of a given taxon with its associated microbiome. Eukaryotic individuals can be analyzed as coevolved, tightly integrated, prokaryotic communities; in this view, natural selection acts on the holobiont as if it were an integrated unit. The best studied holobionts are those that emerged from symbioses involving insects. The presence of symbiotic associations throughout most of the evolutionary history of insects suggests that they were a driving force in the diversification of this group. Support for the evolutionary importance of Symbiogenesis comes from the observation that the gradual passage from an ancestral to a descendant species by the accumulation of random mutations has not been demonstrated in the field, nor in the laboratory, nor in the fossil record. Instead, Symbiogenesis expands the view of the point-mutationonly as the unique mechanisms of evolution and offers an explanation for the discontinuities in the fossil record (“punctuated equilibrium”). As such, it challenges conventional paradigms in biology. This review describes the relationships between xylophagous insects and their microbiota in an attempt to understand the characteristics that have determined bacterial fidelity over generations and throughout evolutionary history. [ Int Microbiol 2013; 16(3):133-143] Keywords: Symbiogenesis · symbiosis · holobiont · holobiome · microbiota · microbiome · coevolution
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Symbiogenesis. A new principle of evolution rediscovery of Boris Mikhaylovich Kozo-Polyansky (1890–1957)
Paleontological Journal, 2010Co-Authors: Lynn MargulisAbstract:The following is a heavily edited transcript of my illustrated lecture, that included our 14 minute video (with a 2 minute animation model) that shows each step in live organisms hypothesized in the origin of nucleated cells from bacteria (“eukaryosis”). New observations presented with modern examples of live phenomena make us virtually certain that B.M. Kozo-Polyansky’s “new principle” (1924) of the importance of Symbiogenesis in the evolutionary process of at least 2000 million years of life on Earth is correct. The widely touted but undocumented explanation of the origin of evolutionary novelty by “gradual accumulation of random mutations” will be considered an erroneous early 20th century hunch proffered primarily by Englishmen, North Americans and other anglophones. They (Neodarwinist “explanations”) will be replaced by the details of Symbiogenesis: genetic mergers especially speciation by genome acquisition, karyotypic fissions (neocentromere formation, related chromosome change) and D.I. Williamson’s larval transfer concept for animals. Although ignored and dismissed in his life time, Kozo-Polyansky’s brilliant work will be lauded for Symbiogenesis in the same style that Gregor Mendel’s studies of inheritance of “factors” in peas was for recognition of his establishment of diploid organism genetic principles by the beginning of the 20th century. My talk, photographs and moving pictures were presented at the Darwin conference, St. Petersburg, on September 23, 2009 introduced by E. Kolchinsky.
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Symbiogenesis a new principle of evolution rediscovery of boris mikhaylovich kozo polyansky 1890 1957
Paleontological Journal, 2010Co-Authors: Lynn MargulisAbstract:The following is a heavily edited transcript of my illustrated lecture, that included our 14 minute video (with a 2 minute animation model) that shows each step in live organisms hypothesized in the origin of nucleated cells from bacteria (“eukaryosis”). New observations presented with modern examples of live phenomena make us virtually certain that B.M. Kozo-Polyansky’s “new principle” (1924) of the importance of Symbiogenesis in the evolutionary process of at least 2000 million years of life on Earth is correct. The widely touted but undocumented explanation of the origin of evolutionary novelty by “gradual accumulation of random mutations” will be considered an erroneous early 20th century hunch proffered primarily by Englishmen, North Americans and other anglophones. They (Neodarwinist “explanations”) will be replaced by the details of Symbiogenesis: genetic mergers especially speciation by genome acquisition, karyotypic fissions (neocentromere formation, related chromosome change) and D.I. Williamson’s larval transfer concept for animals. Although ignored and dismissed in his life time, Kozo-Polyansky’s brilliant work will be lauded for Symbiogenesis in the same style that Gregor Mendel’s studies of inheritance of “factors” in peas was for recognition of his establishment of diploid organism genetic principles by the beginning of the 20th century. My talk, photographs and moving pictures were presented at the Darwin conference, St. Petersburg, on September 23, 2009 introduced by E. Kolchinsky.
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Symbiogenesis a new principle of evolution
2010Co-Authors: борис михайлович козополянский, Victor Fet, Lynn MargulisAbstract:More than eighty years ago, before we knew much about the structure of cells, Russian botanist Boris Kozo-Polyansky brilliantly outlined the concept of Symbiogenesis, the symbiotic origin of cells with nuclei. It was a half-century later, only when experimental approaches that Kozo-Polyansky lacked were applied to his hypotheses, that scientists began to accept his view that Symbiogenesis could be united with Darwin's concept of natural selection to explain the evolution of life. After decades of neglect, ridicule, and intellectual abuse, Kozo-Polyansky's ideas are now endorsed by virtually all biologists. Kozo-Polyansky's seminal work is presented here for the first time in an outstanding annotated translation, updated with commentaries, references, and modern micrographs of symbiotic phenomena.
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Genome acquisition in horizontal gene transfer: Symbiogenesis and macromolecular sequence analysis.
Methods in molecular biology (Clifton N.J.), 2009Co-Authors: Lynn MargulisAbstract:Phylogenetic diagrams ("trees of life") based on computer-generated analyses of nucleic acid (DNA, RNA) or protein (amino acid residues) sequences are purported to reconstruct evolutionary history of the living organisms from which the macromolecules were isolated (1). "Horizontal gene transfer", an expression that refers to the ad hoc explanation of anomalous distribution of these macromolecular sequences, is an inferred past event to explain evolution that, even in principle, is not documentable. Although the diagrams ("phylogenies") help establish the details of relationships among important and widely distributed essential components of living systems (e.g., DNA of large and small replicons such as plasmids, viruses, genophores), chromatin, or protein enzymes that have conserved their function throughout the history of the evolutionary lineage (e.g., DNA that codes for polymerases or 16/18S ribosomal RNA), the HGT concept is an Alfred North Whiteheadian fallacy of misplaced concreteness (2). It is deeply flawed because of sets of unstated, unwarranted assumptions accepted as fact by practitioners: genomics and proteomic experts. They tend to be zoocentric and in particular anthropocentric computer scientists. Their relative lack of familiarity with the fossil record, hard-won life histories and transmission-genetics, taxonomy, physiology, metabolism, and ecology of the communities in which the organisms invariably reside, and many other aspects of life have led to codification of systematic errors in analysis of their, often superb, molecular data. Here we point to a prodigious but little-known Symbiogenesis literature that contrasts the transfer of sets of genes with HGT taken to mean one or a-very-few-genes at a time.
Thomas Cavalier-smith - One of the best experts on this subject based on the ideXlab platform.
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Symbiogenesis: Mechanisms, Evolutionary Consequences, and Systematic Implications
Annual Review of Ecology Evolution and Systematics, 2013Co-Authors: Thomas Cavalier-smithAbstract:Symbiogenesis is the extremely rare, but permanent merger of two organisms from phylogenetically distant lineages into one radically more complex organism. Three examples are exceptionally important: intracellular enslavement by an early eukaryote of an α-proteobacterium by host protein insertion to make mitochondria; later conversion of a cyanobacterium into the first chloroplast, thereby forming kingdom Plantae; and secondary enslavement of a red alga to yield more complex membrane topology in the phagophototrophic kingdom Chromista. Two other cases involved independent acquisition of green-algal chloroplasts by ancestrally phagotrophic lineages, yielding chlorarachnean algae (phylum Cercozoa, within the chromist infrakingdom Rhizaria) and euglenophyte algae (phylum Euglenozoa, within the protozoan subkingdom Eozoa). Less radically, chloroplast replacement occurred within dinoflagellate Chromista by two symbiogeneses: Green-algal or haptophyte chloroplasts replaced ancestral peridinin-containing chlorop...
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Chloroplast Evolution: Secondary Symbiogenesis and Multiple Losses
Current biology : CB, 2002Co-Authors: Thomas Cavalier-smithAbstract:Chloroplasts originated from cyanobacteria only once, but have been laterally transferred to other lineages by symbiogenetic cell mergers. Such secondary Symbiogenesis is rarer and chloroplast losses commoner than often assumed.
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Membrane heredity and early chloroplast evolution
Trends in plant science, 2000Co-Authors: Thomas Cavalier-smithAbstract:Membrane heredity was central to the unique symbiogenetic origin from cyanobacteria of chloroplasts in the ancestor of Plantae (green plants, red algae, glaucophytes) and to subsequent lateral transfers of plastids to form even more complex photosynthetic chimeras. Each Symbiogenesis integrated disparate genomes and several radically different genetic membranes into a more complex cell. The common ancestor of Plantae evolved transit machinery for plastid protein import. In later secondary symbiogeneses, signal sequences were added to target proteins across host perialgal membranes: independently into green algal plastids (euglenoids, chlorarachneans) and red algal plastids (alveolates, chromists). Conservatism and innovation during early plastid diversification are discussed.
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Propaganda of Symbiogenesis
Nature, 1993Co-Authors: Thomas Cavalier-smithAbstract:Concepts of Symbiogenesis: A Historical and Critical Study of the Research of Russian Botanists. By L. N. Khakhina. Edited by L. Margulis and M. McMenamin. Translated by S. Merkel and R. Coalson. Yale University Press: 1992. Pp. 177. $37, £22.50.
Nathalie Gontier - One of the best experts on this subject based on the ideXlab platform.
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Symbiogenesis, History of
Encyclopedia of Evolutionary Biology, 2016Co-Authors: Nathalie GontierAbstract:Symbiogenesis is an evolutionary mechanism caused by hereditary symbiosis. Symbiogenesis theories were introduced in early twentieth-century Russia, when Merezhkowsky, Faminstyn, and Kozo-Polyansky recognized that organellar structures present in the eukaryotic cell evolved through Symbiogenesis. Symbiogenesis research subsequently spread to Europe and the Americas through the works of von Faber, Portier, Buchner, Schneider, Wallin, and Lederberg. Nonetheless, Symbiogenesis theories were excluded from the Modern Synthesis that advanced a selectionist account of evolution, and were only reintroduced by Margulis, from the 1960s onward. Her Serial Endosymbiotic Theory gives a synthetic account of how Symbiogenesis underlies the origin of the four eukaryotic kingdoms. Today, Symbiogenesis research associates with research on lateral gene transfer, mobile genetic elements, viriome and microbiome studies, and the Gaia Hypothesis, making Symbiogenesis one of the candidates for an Extended Synthesis.
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Reticulate Evolution: Symbiogenesis, Lateral Gene Transfer, Hybridization and Infectious heredity
Interdisciplinary Evolution Research, 2015Co-Authors: Nathalie GontierAbstract:Reticulate Evolution Everywhere.- Can We Understand Evolution Without Symbiogenesis?.- Symbiosis: Evolution's Co-Author.- Novel Endosymbioses as a Catalyst of Fast Speciation.- Historical and Epistemological Perspectives on What Lateral Gene Transfer Mechanisms Contribute to Our Understanding of Evolution.- Plasmids: Histories of a Concept.- Symbiosis Between Non-Transferable Plasmids and Prokaryote Cells.- Host-Symbiont-Pathogen-Host Interactions: Wolbachia, Vector-Transmitted Human Pathogens and the Importance of Quantitative Models of Multipartite Coevolution.- Evolution of The Human Microbiome and Impacts on Human Health, Infectious Disease and Hominid Evolution.- Divergence-With-Gene-Flow: What Humans and Other Mammals Got Up To.- A Multiset Model of Multi-Species Evolution to Solve Big Deceptive Problems.
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introducing universal Symbiogenesis
Finds and Results from the Swedish Cyprus Expedition: A Gender Perspective at the Medelhavsmuseet, 2012Co-Authors: Nathalie GontierAbstract:One of Neurath’s ambitions was to increase the uniformity of scientific languages. A modern day attempt to obtain this goal of a uniform scientific language can be found in the field of evolutionary epistemology. Evolutionary epistemologists are characterized by their quest for universal formulas of evolution that can explain evolutionary change in a variety of phenomena. The most known are universal selectionist accounts. The latter are introduced and implemented within philosophy of science and extra-philosophical fields alike. But what about other evolutionary theories such as Symbiogenesis? The process of Symbiogenesis need not be confined to either the microcosm or the origin of eukaryotic beings. On the contrary, just as natural selection today is being universalized by evolutionary biologists and evolutionary epistemologists, so Symbiogenesis can be universalized as well. It will be argued that in its universalized form, Symbiogenesis can provide: (1) a general tool to examine various forms of interaction between different biological organisms, and (2) new metaphors for extra-biological fields such as cosmology, the cultural sciences, and language. Furthermore universal Symbiogenesis can complement, if not provide an alternative, for universal selectionist accounts of evolution. As such, universal Symbiogenesis can provide a scientific language that enables more uniformity between different disciplines.
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Special Sciences and the Unity of Science - Introducing Universal Symbiogenesis
Special Sciences and the Unity of Science, 2011Co-Authors: Nathalie GontierAbstract:One of Neurath’s ambitions was to increase the uniformity of scientific languages. A modern day attempt to obtain this goal of a uniform scientific language can be found in the field of evolutionary epistemology. Evolutionary epistemologists are characterized by their quest for universal formulas of evolution that can explain evolutionary change in a variety of phenomena. The most known are universal selectionist accounts. The latter are introduced and implemented within philosophy of science and extra-philosophical fields alike. But what about other evolutionary theories such as Symbiogenesis? The process of Symbiogenesis need not be confined to either the microcosm or the origin of eukaryotic beings. On the contrary, just as natural selection today is being universalized by evolutionary biologists and evolutionary epistemologists, so Symbiogenesis can be universalized as well. It will be argued that in its universalized form, Symbiogenesis can provide: (1) a general tool to examine various forms of interaction between different biological organisms, and (2) new metaphors for extra-biological fields such as cosmology, the cultural sciences, and language. Furthermore universal Symbiogenesis can complement, if not provide an alternative, for universal selectionist accounts of evolution. As such, universal Symbiogenesis can provide a scientific language that enables more uniformity between different disciplines.
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Universal Symbiogenesis : An alternative to universal selectionist accounts of evolution
Symbiosis, 2007Co-Authors: Nathalie GontierAbstract:The process of Symbiogenesis need not be confined to either the microcosm or the origin of eukaryotic beings. On the contrary, just as natural selection today is being universalized by evolutionary biologists and evolutionary epistemologists, Symbiogenesis can be universalized as well. It will be argued that in its universalized form, Symbiogenesis can provide: (1) a general tool to examine various forms of interaction between different biological organisms (regular Symbiogenesis, hybridization, virus-host interactions), and (2) new metaphors for extra-biological fields such as cosmology, the cultural sciences, and language. Universal Symbiogenesis can thus complement universal selectionist accounts of evolution.
Larry Bull - One of the best experts on this subject based on the ideXlab platform.
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Artificial Symbiogenesis and Differing Reproduction Rates
Artificial Life, 2010Co-Authors: Larry BullAbstract:Symbiosis is the phenomenon in which organisms of different species live together in close association. Symbiogenesis is the name given to the process by which symbiotic partners combine and unify. This letter reconsiders previous work using the NKCS model of coevolution to explore Symbiogenesis. In particular, the role of different replication rates between the coevolving partners is considered. This is shown to provide a broader scope for the emergence of endosymbioses and subsequent horizontal gene transfers.
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Symbiogenesis in Learning Classifier Systems
Artificial Life, 2001Co-Authors: Andy Tomlinson, Larry BullAbstract:Symbiosis is the phenomenon in which organisms of different species live together in close association, resulting in a raised level of fitness for one or more of the organisms. Symbiogenesis is the name given to the process by which symbiotic partners combine and unify, that is, become genetically linked, giving rise to new morphologies and physiologies evolutionarily more advanced than their constituents. The importance of this process in the evolution of complexity is now well established. Learning classifier systems are a machine learning technique that uses both evolutionary computing techniques and reinforcement learning to develop a population of cooperative rules to solve a given task. In this article we examine the use of Symbiogenesis within the classifier system rule base to improve their performance. Results show that incorporating simple rule linkage does not give any benefits. The concept of (temporal) encapsulation is then added to the symbiotic rules and shown to improve performance in ambiguous/non-Markov environments.
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On Evolving Social Systems: Communication, Speciation and Symbiogenesis
Computational & Mathematical Organization Theory, 1999Co-Authors: Larry BullAbstract:In this paper we introduce three enhancements for evolutionary computing techniques in social environments. We describe the use of the genetic algorithm to evolve communicating rule-based systems, where each rule-based system represents an agent in a social/multi-agent environment. It is shown that the evolution of multiple cooperating agents can give improved performance over the evolution of an equivalent single agent, i.e. non-social, system. We examine the performance of two social system configurations as approaches to the control of gait in a wall climbing quadrupedal robot, where each leg of the quadruped is controlled by a communicating agent. We then introduce two social-level operators—speciation and Symbiogenesis—which aim to reduce the amount of knowledge required a priori by automatically manipulating the system‘s social structure and describe their use in conjunction with the communicating rule-based systems. The reasons for implementing these kinds of operators are discussed and we then examine their performance in developing the controller of the wall-climbing quadruped. We find that the use of such operators can give improved performance over static population/agent configurations.
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evolutionary computing in multi agent environments specification and Symbiogenesis
Parallel Problem Solving from Nature, 1996Co-Authors: Larry Bull, Terence C. FogartyAbstract:In this paper we introduce two macro-level operators to enhance the use of population-based evolutionary computing techniques in multiagent environments: speciation and Symbiogenesis. We describe their use in conjunction with the genetic algorithm to evolve Pittsburgh-style classifier systems, where each classifier system represents an agent in a cooperative multi-agent system. The reasons for implementing these kinds of operators are discussed and we then examine their performance in developing a controller for the gait of a wall-climbing quadrupedal robot, where each leg of the quadruped is controlled by a classifier system. We find that the use of such operators can give improved performance over static population/agent configurations.
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PPSN - Evolutionary Computing in Multi-Agent Environments: Specification and Symbiogenesis
Parallel Problem Solving from Nature — PPSN IV, 1996Co-Authors: Larry Bull, Terence C. FogartyAbstract:In this paper we introduce two macro-level operators to enhance the use of population-based evolutionary computing techniques in multiagent environments: speciation and Symbiogenesis. We describe their use in conjunction with the genetic algorithm to evolve Pittsburgh-style classifier systems, where each classifier system represents an agent in a cooperative multi-agent system. The reasons for implementing these kinds of operators are discussed and we then examine their performance in developing a controller for the gait of a wall-climbing quadrupedal robot, where each leg of the quadruped is controlled by a classifier system. We find that the use of such operators can give improved performance over static population/agent configurations.
