A Case Study of the De Novo Evolution of a Complex Odometric Behavior in Digital Organisms
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{"title"=>"A Case Study of the De Novo Evolution of a Complex Odometric Behavior in Digital Organisms", "type"=>"journal", "authors"=>[{"first_name"=>"Laura M.", "last_name"=>"Grabowski", "scopus_author_id"=>"36726609700"}, {"first_name"=>"David M.", "last_name"=>"Bryson", "scopus_author_id"=>"55617532300"}, {"first_name"=>"Fred C.", "last_name"=>"Dyer", "scopus_author_id"=>"7006288598"}, {"first_name"=>"Robert T.", "last_name"=>"Pennock", "scopus_author_id"=>"6604022755"}, {"first_name"=>"Charles", "last_name"=>"Ofria", "scopus_author_id"=>"8110205600"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"23577113", "pui"=>"368695876", "scopus"=>"2-s2.0-84875988551", "sgr"=>"84875988551", "doi"=>"10.1371/journal.pone.0060466", "issn"=>"19326203"}, "id"=>"4f4e3b71-750d-3a71-ab65-e224a72c0fc0", "abstract"=>"Investigating the evolution of animal behavior is difficult. The fossil record leaves few clues that would allow us to recapitulate the path that evolution took to build a complex behavior, and the large population sizes and long time scales required prevent us from re-evolving such behaviors in a laboratory setting. We present results of a study in which digital organisms-self-replicating computer programs that are subject to mutations and selection-evolved in different environments that required information about past experience for fitness-enhancing behavioral decisions. One population evolved a mechanism for step-counting, a surprisingly complex odometric behavior that was only indirectly related to enhancing fitness. We examine in detail the operation of the evolved mechanism and the evolutionary transitions that produced this striking example of a complex behavior.", "link"=>"http://www.mendeley.com/research/case-study-novo-evolution-complex-odometric-behavior-digital-organisms", "reader_count"=>10, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>2, "Student > Doctoral Student"=>1, "Researcher"=>2, "Student > Ph. D. Student"=>2, "Student > Master"=>1, "Student > Bachelor"=>2}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>2, "Student > Doctoral Student"=>1, "Researcher"=>2, "Student > Ph. D. Student"=>2, "Student > Master"=>1, "Student > Bachelor"=>2}, "reader_count_by_subject_area"=>{"Engineering"=>1, "Agricultural and Biological Sciences"=>3, "Physics and Astronomy"=>1, "Psychology"=>1, "Computer Science"=>3, "Immunology and Microbiology"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Physics and Astronomy"=>{"Physics and Astronomy"=>1}, "Psychology"=>{"Psychology"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>3}, "Computer Science"=>{"Computer Science"=>3}}, "reader_count_by_country"=>{"United States"=>1, "Germany"=>1, "Spain"=>2}, "group_count"=>2}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1018537"], "description"=>"<p>Use of instructions in the step-counting module for traversing right- and left-turn paths. Cells containing “XXXXX” indicate that the instruction is necessary to complete the path following task on paths containing the indicated direction; empty cells indicate that the instruction is not used for following paths in the indicated direction.</p>", "links"=>[], "tags"=>["step-counting", "module", "right-", "left-turn"], "article_id"=>677805, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Laura M. Grabowski", "David M. Bryson", "Fred C. Dyer", "Robert T. Pennock", "Charles Ofria"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0060466.t003", "stats"=>{"downloads"=>1, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Instructions_in_the_step_counting_module_used_for_right_and_left_turn_paths_/677805", "title"=>"Instructions in the step-counting module used for right- and left-turn paths.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-04-08 02:10:05"}
  • {"files"=>["https://ndownloader.figshare.com/files/1018536"], "description"=>"<p>Example excerpt of the execution flow in the counting module of the evolved counting organism's genome. The execution depicted occurs on the map in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0060466#pone-0060466-g001\" target=\"_blank\">Figure 1(b)</a>, starting from the star and facing north. It covers the organism taking a step forward, turning right based on the cue found there, and then taking another step forward. <b>Exec</b> is the number of instructions that have been executed, <b>Site</b> refers to the position in the genome of the instruction, <b>Instruction</b> is the Avida instruction being executed, <b>Facing</b> indicates the compass direction the organism is pointed on the grid, <b>Flow</b> is the genomic position pointed to by the flow-control head, <b>BX</b> and <b>CX</b> are the values stored in the respective registers and <b>Remarks</b> describes how the instruction operates in its current context. Values that are affected by the current instruction are in bold.</p>", "links"=>[], "tags"=>["genetics and genomics", "Computational biology", "computer science", "Evolutionary biology"], "article_id"=>677804, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Laura M. Grabowski", "David M. Bryson", "Fred C. Dyer", "Robert T. Pennock", "Charles Ofria"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0060466.t002", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Example_execution_segment_/677804", "title"=>"Example execution segment.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-04-08 02:10:04"}
  • {"files"=>["https://ndownloader.figshare.com/files/1018533"], "description"=>"<p>(<b>A</b>) Modified ancestral left-turn path, with extended path end. The organism successfully travels the entire path, stepping exactly one cell off the end and then stopping. (<b>B</b>) Modified ancestral right-turn path, with extended path end. The organism turns and retraces its steps before reaching the path end. (<b>C</b>) Unfamiliar left-turn path. The organism turns incorrectly at the first turn. The organism neither traverses the path nor replicates in this environment. (<b>D</b>) Unfamiliar long right-turn path. The organism traverses the entire path but fails to self-replicate.</p>", "links"=>[], "tags"=>["trajectories", "step-counting", "traversing", "unfamiliar"], "article_id"=>677801, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Laura M. Grabowski", "David M. Bryson", "Fred C. Dyer", "Robert T. Pennock", "Charles Ofria"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0060466.g002", "stats"=>{"downloads"=>0, "page_views"=>23, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Example_trajectories_of_the_step_counting_organism_traversing_unfamiliar_paths_/677801", "title"=>"Example trajectories of the step-counting organism traversing unfamiliar paths.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-04-08 02:10:01"}
  • {"files"=>["https://ndownloader.figshare.com/files/1018531"], "description"=>"<p>The organism's trajectory is shown with the black line, beginning at the green star and ending at the red octagon (note: in some cases the organism doubles back along its own path). On the left-turn path (<b>A</b>), the organism traverses the path, steps off the end and stops to finish replication. On the right-turn path (<b>B</b>), the organism has retraced its steps from the end of the path to its final location (red octagon).</p>", "links"=>[], "tags"=>["evolved", "case-study", "paths"], "article_id"=>677799, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Laura M. Grabowski", "David M. Bryson", "Fred C. Dyer", "Robert T. Pennock", "Charles Ofria"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0060466.g001", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Trajectories_of_evolved_case_study_organism_on_paths_experienced_during_evolution_/677799", "title"=>"Trajectories of evolved case-study organism on paths experienced during evolution.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-04-08 02:09:59"}
  • {"files"=>["https://ndownloader.figshare.com/files/1018538"], "description"=>"<p>Detail of the instructions in the counting module of the evolved counting organism's genome. <b>Site</b> refers to the position in the genome of the instruction, <b>Instruction</b> is the specific Avida instruction, and <b>Instruction Functionality</b> describes how the instruction operates.</p>", "links"=>[], "tags"=>["evolved", "counting"], "article_id"=>677806, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Laura M. Grabowski", "David M. Bryson", "Fred C. Dyer", "Robert T. Pennock", "Charles Ofria"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0060466.t001", "stats"=>{"downloads"=>1, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Detail_of_evolved_counting_organism_s_genome_/677806", "title"=>"Detail of evolved counting organism's genome.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-04-08 02:10:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/1018535"], "description"=>"<p>The increment instruction in the counting routine was replaced with a neutral instruction (nop-X). (<b>A</b>) Left-turn path. The organism stops at the first turn and fails to replicate. (<b>B</b>) Right-turn path, with extended path end. The organism misses the second turn, wanders for a couple steps, stops, but successfully completes its replication, although with a much reduced metabolic rate from the unmodified genome.</p>", "links"=>[], "tags"=>["trajectories", "modified", "step-counting", "traversing", "ancestral"], "article_id"=>677803, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Laura M. Grabowski", "David M. Bryson", "Fred C. Dyer", "Robert T. Pennock", "Charles Ofria"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0060466.g003", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Example_trajectories_of_the_modified_step_counting_organism_traversing_ancestral_paths_/677803", "title"=>"Example trajectories of the modified step-counting organism traversing ancestral paths.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-04-08 02:10:03"}

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Relative Metric

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