{"id":"https://openalex.org/W2554913749","doi":"https://doi.org/10.1162/artl_a_00215","title":"The Structure of Ontogenies in a Model Protocell","display_name":"The Structure of Ontogenies in a Model Protocell","publication_year":2016,"publication_date":"2016-11-01","ids":{"openalex":"https://openalex.org/W2554913749","doi":"https://doi.org/10.1162/artl_a_00215","mag":"2554913749","pmid":"https://pubmed.ncbi.nlm.nih.gov/27824498"},"language":"en","primary_location":{"id":"doi:10.1162/artl_a_00215","is_oa":false,"landing_page_url":"https://doi.org/10.1162/artl_a_00215","pdf_url":null,"source":{"id":"https://openalex.org/S2181302","display_name":"Artificial Life","issn_l":"1064-5462","issn":["1064-5462","1530-9185"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310315718","host_organization_name":"The MIT Press","host_organization_lineage":["https://openalex.org/P4310315718"],"host_organization_lineage_names":["The MIT Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Artificial Life","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5036760070","display_name":"Eran Agmon","orcid":"https://orcid.org/0000-0003-1279-2474"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Eran Agmon","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047198701","display_name":"Alexander J. Gates","orcid":"https://orcid.org/0000-0003-0099-7480"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Alexander J. Gates","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5014235111","display_name":"Randall D. Beer","orcid":"https://orcid.org/0000-0001-7279-3028"},"institutions":[{"id":"https://openalex.org/I592451","display_name":"Indiana University","ror":"https://ror.org/01kg8sb98","country_code":"US","type":"education","lineage":["https://openalex.org/I592451"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Randall D. Beer","raw_affiliation_strings":["Indiana University"],"affiliations":[{"raw_affiliation_string":"Indiana University","institution_ids":["https://openalex.org/I592451"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5036760070"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.9875,"has_fulltext":false,"cited_by_count":13,"citation_normalized_percentile":{"value":0.80563477,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"22","issue":"4","first_page":"499","last_page":"517"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11445","display_name":"Origins and Evolution of Life","score":0.9984999895095825,"subfield":{"id":"https://openalex.org/subfields/3103","display_name":"Astronomy and Astrophysics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11445","display_name":"Origins and Evolution of Life","score":0.9984999895095825,"subfield":{"id":"https://openalex.org/subfields/3103","display_name":"Astronomy and Astrophysics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11252","display_name":"Evolutionary Game Theory and Cooperation","score":0.9937000274658203,"subfield":{"id":"https://openalex.org/subfields/3312","display_name":"Sociology and Political Science"},"field":{"id":"https://openalex.org/fields/33","display_name":"Social Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9860000014305115,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/protocell","display_name":"Protocell","score":0.985586404800415},{"id":"https://openalex.org/keywords/life-span","display_name":"Life span","score":0.5495383739471436},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5244084596633911},{"id":"https://openalex.org/keywords/mechanism","display_name":"Mechanism (biology)","score":0.46470800042152405},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4606286585330963},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.3901517689228058},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.17298126220703125}],"concepts":[{"id":"https://openalex.org/C114032466","wikidata":"https://www.wikidata.org/wiki/Q1389465","display_name":"Protocell","level":3,"score":0.985586404800415},{"id":"https://openalex.org/C2988516024","wikidata":"https://www.wikidata.org/wiki/Q441195","display_name":"Life span","level":2,"score":0.5495383739471436},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5244084596633911},{"id":"https://openalex.org/C89611455","wikidata":"https://www.wikidata.org/wiki/Q6804646","display_name":"Mechanism (biology)","level":2,"score":0.46470800042152405},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4606286585330963},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.3901517689228058},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.17298126220703125},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0},{"id":"https://openalex.org/C41625074","wikidata":"https://www.wikidata.org/wiki/Q176088","display_name":"Membrane","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005075","descriptor_name":"Biological Evolution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005075","descriptor_name":"Biological Evolution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005075","descriptor_name":"Biological Evolution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058045","descriptor_name":"Artificial Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058045","descriptor_name":"Artificial Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058045","descriptor_name":"Artificial Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1162/artl_a_00215","is_oa":false,"landing_page_url":"https://doi.org/10.1162/artl_a_00215","pdf_url":null,"source":{"id":"https://openalex.org/S2181302","display_name":"Artificial Life","issn_l":"1064-5462","issn":["1064-5462","1530-9185"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310315718","host_organization_name":"The MIT Press","host_organization_lineage":["https://openalex.org/P4310315718"],"host_organization_lineage_names":["The MIT Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Artificial Life","raw_type":"journal-article"},{"id":"pmid:27824498","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27824498","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Artificial life","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.5,"display_name":"Life in Land","id":"https://metadata.un.org/sdg/15"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":25,"referenced_works":["https://openalex.org/W126525084","https://openalex.org/W1788939232","https://openalex.org/W1897867550","https://openalex.org/W1916207017","https://openalex.org/W2001141328","https://openalex.org/W2005345311","https://openalex.org/W2011214280","https://openalex.org/W2014805262","https://openalex.org/W2021114157","https://openalex.org/W2064604759","https://openalex.org/W2068670723","https://openalex.org/W2085892590","https://openalex.org/W2093020640","https://openalex.org/W2098884957","https://openalex.org/W2120043163","https://openalex.org/W2146875013","https://openalex.org/W2148606196","https://openalex.org/W2150593711","https://openalex.org/W2151525702","https://openalex.org/W2164998314","https://openalex.org/W2289970606","https://openalex.org/W2333302965","https://openalex.org/W2751555667","https://openalex.org/W2919661847","https://openalex.org/W6605160798"],"related_works":["https://openalex.org/W2998115572","https://openalex.org/W2488224828","https://openalex.org/W2033867172","https://openalex.org/W2499941174","https://openalex.org/W4324018125","https://openalex.org/W3119990432","https://openalex.org/W4390267564","https://openalex.org/W4229081462","https://openalex.org/W2330839048","https://openalex.org/W4390135158"],"abstract_inverted_index":{"Emergent":[0],"individuals":[1,22,39],"are":[2,192],"often":[3],"characterized":[4],"with":[5,24],"respect":[6],"to":[7,12,35,42,78,128],"their":[8,10,36,43,47],"viability:":[9],"ability":[11],"maintain":[13],"themselves":[14],"and":[15,45,81,106,144,170,194,216,229],"persist":[16],"in":[17,94,141,180,231],"variable":[18],"environments.":[19],"As":[20],"such":[21],"interact":[23],"an":[25,55,123,207],"environment,":[26,44],"they":[27],"undergo":[28],"sequences":[29],"of":[30,49,63,68,89,110,131,165,187,213,226],"structural":[31,85],"changes":[32,140],"that":[33,40,136,148,198],"correspond":[34],"ontogenies.":[37],"Ultimately,":[38],"adapt":[41],"increase":[46],"chances":[48],"survival,":[50],"persist.":[51],"This":[52,126],"article":[53],"provides":[54,219],"initial":[56,124],"step":[57],"towards":[58],"a":[59,75,133,145,172,181,188,220],"more":[60,232],"formal":[61],"treatment":[62],"these":[64,199],"concepts.":[65],"A":[66],"network":[67,91,175],"possible":[69],"ontogenies":[70],"is":[71,116,196],"uncovered":[72],"by":[73],"subjecting":[74],"model":[76,215],"protocell":[77,97,179],"sequential":[79],"perturbations":[80],"mapping":[82],"the":[83,96,108,111,177,185,224],"resulting":[84],"configurations.":[86],"The":[87,211],"analysis":[88],"this":[90,214],"reveals":[92],"trends":[93],"how":[95,102,107,138,158],"can":[98],"move":[99],"between":[100],"configurations,":[101],"its":[103],"morphology":[104],"changes,":[105],"role":[109],"environment":[112],"varies":[113],"throughout.":[114],"Viability":[115],"defined":[117],"as":[118],"expected":[119],"life":[120],"span":[121],"given":[122],"configuration.":[125],"leads":[127],"two":[129],"notions":[130],"adaptivity:":[132],"local":[134],"adaptivity":[135,147,230],"addresses":[137],"viability":[139],"plastic":[142],"transitions,":[143],"global":[146],"looks":[149],"at":[150],"longer-term":[151],"tendencies":[152],"for":[153,176,222],"increased":[154],"viability.":[155],"To":[156],"demonstrate":[157],"different":[159,163,182],"protocell-environment":[160],"pairings":[161],"produce":[162],"patterns":[164],"ontogenic":[166,174],"change,":[167],"we":[168],"generate":[169],"analyze":[171],"second":[173],"same":[178],"environment.":[183],"Finally,":[184],"mechanisms":[186],"minimal":[189],"adaptive":[190],"transition":[191],"analyzed,":[193],"it":[195],"shown":[197],"rely":[200],"on":[201],"distributed":[202],"spatial":[203],"processes":[204],"rather":[205],"than":[206],"explicit":[208],"regulatory":[209],"mechanism.":[210],"combination":[212],"analytical":[217],"techniques":[218],"foundation":[221],"studying":[223],"emergence":[225],"viability,":[227],"ontogeny,":[228],"biologically":[233],"realistic":[234],"systems.":[235]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
