{"id":"W2145163654","doi":"10.1101/sqb.2009.74.002","title":"Eradicating Typological Thinking in Prokaryotic Systematics and Evolution","year":2009,"lang":"en","type":"review","venue":"Cold Spring Harbor Symposia on Quantitative Biology","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":31,"is_retracted":false,"has_abstract":true,"ca_institutions":"Dalhousie University","funders":"Canadian Institutes of Health Research","keywords":"Tree of life (biology); Prokaryote; Population; Evolutionary biology; Biology; Metagenomics; Value (mathematics); Systematics; Antithesis; Epistemology; Ecology; Phylogenetics; Philosophy; Sociology; Genetics; Computer science; Taxonomy (biology); Demography; Gene","routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":["metaepi_narrow"],"consensus_categories":[],"category_scores_codex":[0.0005211232,0.0004377717,0.001135426,0.0001848769,0.0001450029,0.00002909574,0.0002928505,0.0005119783,7.366973e-7],"category_scores_gemma":[0.0002943199,0.0003584728,0.0001671439,0.0001493303,0.0001756084,0.000001059024,0.0001786914,0.0002896035,0.00001015206],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00009382899,"about_ca_system_score_gemma":0.0001219537,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00001287677,"about_ca_topic_score_gemma":0.00001074689,"domain_scores_codex":[0.9977248,0.0004520252,0.0006378658,0.000728174,0.00008031467,0.0003768122],"domain_scores_gemma":[0.9989082,0.0002081827,0.0004117578,0.0003496573,0.00005530208,0.000066903],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"theoretical_or_conceptual","study_design_gemma":"not_applicable","study_design_scores_codex":[0.0000179023,0.00006272121,0.0009104133,0.00215749,0.0001537196,0.000006154431,0.00003299029,0.000006164965,0.003534087,0.9903607,0.00000540786,0.0027522],"study_design_scores_gemma":[0.000901979,0.004051405,0.009454362,0.01425832,0.0005640282,0.00002189642,0.00008837719,0.000141375,0.0001361016,0.001004733,0.96765,0.00172741],"study_design_candidate":"theoretical_or_conceptual","study_design_consensus":null,"genre_codex":"review","genre_gemma":"review","genre_scores_codex":[0.009725187,0.9886937,0.000233365,0.00003083777,0.0001967987,0.0009173478,0.0000215048,0.0000100721,0.0001711652],"genre_scores_gemma":[0.06304359,0.9340008,0.002569467,0.00005816898,0.0001266593,0.0001389786,0.00001089666,0.00003771728,0.00001364265],"genre_candidate":"review","genre_consensus":"review","teacher_disagreement_score":0.989356,"threshold_uncertainty_score":0.9998868,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03996976961431797,"score_gpt":0.3193897078134357,"score_spread":0.2794199381991177,"validation_status":"score_only:v0-immature-baseline","note":"Baseline scores from an immature model (maturity gate not passed). Scores rank; they never assert a category."}}