{"id":"https://openalex.org/W7221463166","doi":"https://doi.org/10.68366/yx30r330","title":"The Origins Transition: From the Encoded Chrysene Cluster to the Originating Genetic Code Mappings \u2014 Structural Consistency, Codon Placement, and a Forced Exchange","display_name":"The Origins Transition: From the Encoded Chrysene Cluster to the Originating Genetic Code Mappings \u2014 Structural Consistency, Codon Placement, and a Forced Exchange","publication_year":2026,"publication_date":"2026-10-11","ids":{"openalex":"https://openalex.org/W7221463166","doi":"https://doi.org/10.68366/yx30r330"},"language":"en","primary_location":{"id":"doi:10.68366/yx30r330","doi":"https://doi.org/10.68366/yx30r330","is_oa":true,"landing_page_url":"https://doi.org/10.68366/yx30r330","pdf_url":"https://chrysene.com/index.php/acf/article/download/57/114","source":{"id":"https://openalex.org/S7407068434","display_name":"Annals of the Chrysene Formalism","issn_l":"3144-2021","issn":["3144-2021"],"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Annals of the Chrysene Formalism","raw_type":"journal-article"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://chrysene.com/index.php/acf/article/download/57/114","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5153838624","display_name":"Charles Schaper","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Charles Schaper","raw_affiliation_strings":["Annals of the Chrysene Formalism San Francisco , California , USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Annals of the Chrysene Formalism San Francisco , California , USA","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":["https://openalex.org/A5153838624"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":14.773,"has_fulltext":true,"cited_by_count":10,"citation_normalized_percentile":{"value":0.99373804,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":99},"biblio":{"volume":"1","issue":"2","first_page":"1076","last_page":"1106"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.8687000274658203,"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"}},"topics":[{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.8687000274658203,"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"}},{"id":"https://openalex.org/T11445","display_name":"Origins and Evolution of Life","score":0.1177000030875206,"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/T12029","display_name":"DNA and Biological Computing","score":0.0010999999940395355,"subfield":{"id":"https://openalex.org/subfields/2614","display_name":"Theoretical Computer Science"},"field":{"id":"https://openalex.org/fields/26","display_name":"Mathematics"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/origin-of-the-genetic-code","display_name":"origin of the genetic code","score":0.8920000195503235},{"id":"https://openalex.org/keywords/chrysene","display_name":"chrysene","score":0.7820000052452087},{"id":"https://openalex.org/keywords/structural-consistency","display_name":"structural consistency","score":0.6489999890327454},{"id":"https://openalex.org/keywords/rna-secondary-structure","display_name":"RNA secondary structure","score":0.4650000035762787},{"id":"https://openalex.org/keywords/codon-degeneracy","display_name":"codon degeneracy","score":0.6460000276565552},{"id":"https://openalex.org/keywords/parity","display_name":"parity","score":0.5260000228881836},{"id":"https://openalex.org/keywords/codon-mapping","display_name":"codon mapping","score":0.3799999952316284}],"concepts":[{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.5964999794960022},{"id":"https://openalex.org/C2777727622","wikidata":"https://www.wikidata.org/wiki/Q5251772","display_name":"Degeneracy (biology)","level":2,"score":0.5134000182151794},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.49540001153945923},{"id":"https://openalex.org/C80899671","wikidata":"https://www.wikidata.org/wiki/Q1304193","display_name":"Vertex (graph theory)","level":3,"score":0.486299991607666},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.33009999990463257},{"id":"https://openalex.org/C118615104","wikidata":"https://www.wikidata.org/wiki/Q121416","display_name":"Discrete mathematics","level":1,"score":0.3246000111103058},{"id":"https://openalex.org/C10853874","wikidata":"https://www.wikidata.org/wiki/Q180618","display_name":"Genetic code","level":3,"score":0.31929999589920044},{"id":"https://openalex.org/C52146309","wikidata":"https://www.wikidata.org/wiki/Q7431116","display_name":"Schema (genetic algorithms)","level":2,"score":0.3070000112056732},{"id":"https://openalex.org/C176990463","wikidata":"https://www.wikidata.org/wiki/Q1854186","display_name":"Start codon","level":4,"score":0.30309998989105225},{"id":"https://openalex.org/C20580545","wikidata":"https://www.wikidata.org/wiki/Q28354","display_name":"Stop codon","level":3,"score":0.30230000615119934},{"id":"https://openalex.org/C57493831","wikidata":"https://www.wikidata.org/wiki/Q3134666","display_name":"Projection (relational algebra)","level":2,"score":0.30059999227523804},{"id":"https://openalex.org/C165879259","wikidata":"https://www.wikidata.org/wiki/Q5136690","display_name":"Cluster algebra","level":3,"score":0.2948000133037567},{"id":"https://openalex.org/C2776436953","wikidata":"https://www.wikidata.org/wiki/Q5163215","display_name":"Consistency (knowledge bases)","level":2,"score":0.29010000824928284},{"id":"https://openalex.org/C143392562","wikidata":"https://www.wikidata.org/wiki/Q449111","display_name":"Subdivision","level":2,"score":0.28209999203681946},{"id":"https://openalex.org/C2781204021","wikidata":"https://www.wikidata.org/wiki/Q6497091","display_name":"Lattice (music)","level":2,"score":0.2808000147342682},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.27410000562667847},{"id":"https://openalex.org/C161677786","wikidata":"https://www.wikidata.org/wiki/Q2478475","display_name":"Neighbourhood (mathematics)","level":2,"score":0.27309998869895935},{"id":"https://openalex.org/C2780378348","wikidata":"https://www.wikidata.org/wiki/Q25351438","display_name":"Ring (chemistry)","level":2,"score":0.27300000190734863},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.27250000834465027},{"id":"https://openalex.org/C112876837","wikidata":"https://www.wikidata.org/wiki/Q837518","display_name":"Alphabet","level":2,"score":0.2700999975204468},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.26460000872612},{"id":"https://openalex.org/C168310172","wikidata":"https://www.wikidata.org/wiki/Q493980","display_name":"Quiver","level":2,"score":0.25519999861717224},{"id":"https://openalex.org/C140479938","wikidata":"https://www.wikidata.org/wiki/Q5254619","display_name":"Iterated function","level":2,"score":0.25049999356269836}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.68366/yx30r330","doi":"https://doi.org/10.68366/yx30r330","is_oa":true,"landing_page_url":"https://doi.org/10.68366/yx30r330","pdf_url":"https://chrysene.com/index.php/acf/article/download/57/114","source":{"id":"https://openalex.org/S7407068434","display_name":"Annals of the Chrysene Formalism","issn_l":"3144-2021","issn":["3144-2021"],"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Annals of the Chrysene Formalism","raw_type":"journal-article"}],"best_oa_location":{"id":"doi:10.68366/yx30r330","doi":"https://doi.org/10.68366/yx30r330","is_oa":true,"landing_page_url":"https://doi.org/10.68366/yx30r330","pdf_url":"https://chrysene.com/index.php/acf/article/download/57/114","source":{"id":"https://openalex.org/S7407068434","display_name":"Annals of the Chrysene Formalism","issn_l":"3144-2021","issn":["3144-2021"],"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Annals of the Chrysene Formalism","raw_type":"journal-article"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7221463166.pdf","grobid_xml":"https://content.openalex.org/works/W7221463166.grobid-xml"},"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W7222349859","https://openalex.org/W7223050791","https://openalex.org/W2782973775","https://openalex.org/W7140047971","https://openalex.org/W7140031277","https://openalex.org/W7221135946","https://openalex.org/W7140039048","https://openalex.org/W7171508236","https://openalex.org/W6920999598","https://openalex.org/W2025445740"],"abstract_inverted_index":{"A":[0],"stack":[1,56],"of":[2,11,59,121,133,163,175,182,216,247,289,294,317,348,373,417,433],"six":[3],"substituted":[4],"chrysene":[5,123],"units,":[6],"each":[7],"set":[8,132,432],"in":[9,88,142,233],"one":[10,168,224,267,288,412],"two":[12,255,272,328,335,383],"orientations,":[13],"admits":[14],"exactly":[15,287,386],"twenty":[16,45,213],"classes":[17],"under":[18,84],"the":[19,27,29,35,55,66,74,89,94,122,164,184,188,191,202,205,212,260,276,295,299,302,315,322,331,367,379,382,387,390,398,411,415,418,422,430],"symmetries":[20],"available":[21],"to":[22,73,195,204,228],"it.":[23],"That":[24],"count":[25],"bounds":[26],"products":[28],"assembly":[30],"can":[31],"make":[32],"and":[33,54,113,130,144,153,171,190,220,286,312,344,355,375],"fixes":[34],"reading":[36],"length":[37],"at":[38,48,180,245,327,385],"three.":[39],"It":[40],"does":[41],"not":[42,71,352],"say":[43,357],"which":[44,49,91,421],"products,":[46],"nor":[47],"codons":[50,112],"they":[51,76],"sit":[52],"\u2014":[53,179,311,420],"it":[57,313,428],"speaks":[58],"contains":[60],"no":[61,145],"nucleobase.":[62],"This":[63],"paper":[64],"takes":[65,208],"second":[67],"question.":[68],"Bases":[69],"are":[70,77,151,284,363],"added":[72],"stack:":[75],"what":[78,358],"its":[79,217],"orientation":[80],"pattern":[81],"is":[82,147,158,198,252,304,309,314,325,346,376,410,429],"called,":[83],"an":[85,258,338],"assignment":[86,129,339,416],"specified":[87,413],"filing,":[90],"also":[92],"exhibits":[93],"resulting":[95],"object,":[96],"namely":[97],"RNA":[98],"intercalated":[99],"with":[100,126,187],"tethered":[101],"chrysene.":[102],"On":[103],"that":[104,265,301,340,345],"object":[105],"we":[106,356],"state":[107],"a":[108,115,118,127,131,172,176,235,243,279,371],"consistency":[109,323,342],"relation":[110,324],"between":[111],"structures,":[114,214],"structure":[116,156,161,408],"being":[117],"connected":[119],"subgraph":[120,207],"skeleton":[124],"together":[125,139,306],"terminal":[128,236],"heteroatom":[134],"insertions.":[135],"The":[136,155],"stages":[137],"persist":[138],"rather":[140],"than":[141,200],"sequence,":[143],"chronology":[146],"claimed.":[148],"Three":[149],"results":[150,362],"finite":[152],"checkable.":[154],"space":[157],"three-parameter:":[159],"every":[160],"consists":[162],"reaction":[165],"site,":[166],"optionally":[167],"further":[169,361],"vertex,":[170],"contiguous":[173],"arc":[174],"single":[177],"ring":[178],"nineteen":[181],"twenty,":[183],"exception":[185],"stated":[186],"theorem":[189],"obvious":[192],"repair":[193],"shown":[194],"fail.":[196],"Excision":[197],"coarser":[199],"structure:":[201],"map":[203],"underlying":[206],"eleven":[209],"values":[210],"on":[211,378],"five":[215],"fibres":[218],"non-trivial":[219],"covering":[221],"fourteen,":[222],"so":[223,264],"excision":[225],"carries":[226],"up":[227],"three":[229,282],"structures":[230,256],"differing":[231,384],"only":[232],"how":[234],"vertex":[237],"ends.":[238],"And":[239,397],"block":[240,402,407],"degeneracy":[241],"follows":[242],"rule":[244],"sixteen":[246,248],"blocks.":[249],"One":[250],"placement":[251,308,316],"forced.":[253],"Exactly":[254],"require":[257],"element":[259],"carrier":[261],"cannot":[262],"supply,":[263],"either":[266],"delivery":[268],"serves":[269],"both":[270,292],"or":[271,330],"must":[273],"coincide.":[274],"Of":[275],"eighteen":[277],"positions":[278,293],"code":[280,369,392],"assigns,":[281],"pairs":[283],"complementary":[285],"those":[290],"has":[291],"size":[296],"required.":[297],"Under":[298],"hypothesis":[300],"pair":[303],"delivered":[305],"their":[307],"unique":[310],"neither":[318,347],"observed":[319,332],"code.":[320],"Either":[321],"wrong":[326],"exchanges,":[329],"codes":[333],"stand":[334],"exchanges":[336],"from":[337,370,394,406],"structural":[341],"selects":[343],"them.":[349],"We":[350],"do":[351],"decide":[353],"this,":[354],"would.":[359],"Two":[360],"recorded.":[364],"Parity":[365],"excludes":[366],"standard":[368,391],"class":[372],"assignments":[374],"silent":[377],"mitochondrial":[380],"one,":[381],"blocks":[388],"where":[389],"departs":[393],"normal":[395],"form.":[396],"base":[399],"partition":[400],"governing":[401],"degeneracy,":[403],"recovered":[404],"here":[405],"alone,":[409],"by":[414],"filing":[419],"argument":[423],"nowhere":[424],"uses.":[425],"What":[426],"invariant":[427],"level":[431],"remains":[434],"open.":[435]},"counts_by_year":[{"year":2026,"cited_by_count":10}],"updated_date":"2026-11-07T11:25:07.637180","created_date":"2026-10-12T00:00:00"}
