https://w3id.org/np/RAK0AOLorOrLMS_ra2At5u6C1jAthOrBlcIHVPrdADTr4/Head https://w3id.org/np/RAK0AOLorOrLMS_ra2At5u6C1jAthOrBlcIHVPrdADTr4 http://www.nanopub.org/nschema#hasAssertion https://w3id.org/np/RAK0AOLorOrLMS_ra2At5u6C1jAthOrBlcIHVPrdADTr4/assertion https://w3id.org/np/RAK0AOLorOrLMS_ra2At5u6C1jAthOrBlcIHVPrdADTr4 http://www.nanopub.org/nschema#hasProvenance https://w3id.org/np/RAK0AOLorOrLMS_ra2At5u6C1jAthOrBlcIHVPrdADTr4/provenance https://w3id.org/np/RAK0AOLorOrLMS_ra2At5u6C1jAthOrBlcIHVPrdADTr4 http://www.nanopub.org/nschema#hasPublicationInfo https://w3id.org/np/RAK0AOLorOrLMS_ra2At5u6C1jAthOrBlcIHVPrdADTr4/pubinfo https://w3id.org/np/RAK0AOLorOrLMS_ra2At5u6C1jAthOrBlcIHVPrdADTr4 http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://www.nanopub.org/nschema#Nanopublication https://w3id.org/np/RAK0AOLorOrLMS_ra2At5u6C1jAthOrBlcIHVPrdADTr4/assertion https://w3id.org/delphi/resource/assessment/levin-2023-competency-05--claim-test http://purl.org/dc/terms/description analysis.py imports run() from the levin-2023-competency-04 re-implementation and re-runs hardwired and competency 20, 100 and 400 populations, 100 repeats of 250 generations each, from a new master seed. It compares best genotypic fitness at generation 250 with hardwired by one-sided Welch t-tests, measures the change in the mean genotypic curve between generations 126-150 and 226-250, the across-repeat SD of best genotypic fitness over generations 51-250 per level, and best phenotypic fitness at generation 250. https://w3id.org/delphi/resource/assessment/levin-2023-competency-05--claim-test http://www.w3.org/1999/02/22-rdf-syntax-ns#type https://w3id.org/delphi/ontology/Assessment https://w3id.org/delphi/resource/assessment/levin-2023-competency-05--claim-test http://www.w3.org/2000/01/rdf-schema#comment Measured: 0.583921 mean best genotypic fitness at generation 250, competency 400 (hardwired: see extra) (n = 100, Monte Carlo; fixed seed, deterministic for a given numpy version). Interpretation: Simulation-result claim, tested by replication. 'Genotypic fitness of the best individual' is taken, as in the authors' Exp1 code, as the maximum pre-development fitness in the population each generation. 'Plateaued' is operationalised as < 0.03 change in the repeat-mean curve between generations 126-150 and 226-250; 'wider variance' as the across-repeat SD of best genotypic fitness averaged over generations 51-250; 'high phenotypic fitness' as mean best phenotypic fitness >= 0.95 at generation 250. 'Reduced selective pressure on structural genes' is the authors' interpretation of the lower plateau and is not measured separately. https://w3id.org/delphi/resource/assessment/levin-2023-competency-05--claim-test http://www.w3.org/2000/01/rdf-schema#label Claim test of levin-2023-competency-05: supports, confidence 0.9 https://w3id.org/delphi/resource/assessment/levin-2023-competency-05--claim-test http://www.w3.org/2000/01/rdf-schema#seeAlso https://github.com/fractastical/delphisci/blob/bf2af6ee0a84e23ffa6414ad7a0a50a8c276506e/test-data/claim-tests/levin-papers/levin-2023-competency-05/result.json https://w3id.org/delphi/resource/assessment/levin-2023-competency-05--claim-test http://www.w3.org/ns/prov#wasAttributedTo https://w3id.org/delphi/resource/agent/delphisci-claim-tester-claude-opus-5-5 https://w3id.org/delphi/resource/assessment/levin-2023-competency-05--claim-test https://w3id.org/delphi/ontology/admissibleDatasets Runs of the model exactly as specified in the paper and its supplement (50-cell arrays, 100 embryos, top-10% phenotypic selection, crossover, mutation probability 0.6, competency 20/100/400); unspecified details from the authors' public code; fresh random seeds independent of the companion test levin-2023-competency-04. https://w3id.org/delphi/resource/assessment/levin-2023-competency-05--claim-test https://w3id.org/delphi/ontology/assessmentType claim-test/0.1.0 https://w3id.org/delphi/resource/assessment/levin-2023-competency-05--claim-test https://w3id.org/delphi/ontology/dataKind computational https://w3id.org/delphi/resource/assessment/levin-2023-competency-05--claim-test https://w3id.org/delphi/ontology/disconfirmingObservation Competent genotypic fitness reaching or exceeding hardwired, continuing to climb, or showing less spread at higher competency. https://w3id.org/delphi/resource/assessment/levin-2023-competency-05--claim-test https://w3id.org/delphi/ontology/evidenceAgainst All pre-registered criteria hold: genotypic fitness at generation 250 is 0.973, 0.872 and 0.584 at competency 20, 100 and 400 vs 1.000 hardwired (all p < 1e-80); the curves change by < 0.003 between the two windows; across-repeat SD rises 0.0040 < 0.0094 < 0.0211; phenotypic fitness is 1.0 at every level. https://w3id.org/delphi/resource/assessment/levin-2023-competency-05--claim-test https://w3id.org/delphi/ontology/evidenceAgainst How long genotypic fitness tracks hardwired before plateauing depends strongly on competency: the competent mean first falls 0.02 below hardwired at generation 85, 33 and 6 for competency 20, 100 and 400. 'Rose briefly' fits competency 400 best; at competency 20 the genotypic curve follows hardwired for most of the climb. https://w3id.org/delphi/resource/assessment/levin-2023-competency-05--claim-test https://w3id.org/delphi/ontology/evidenceAgainst The companion test levin-2023-competency-04 had already reported generation-250 genotypic means (0.97, 0.87, 0.59) before this test was pre-registered, so the direction of criterion A was known; this run uses independent seeds. https://w3id.org/delphi/resource/assessment/levin-2023-competency-05--claim-test https://w3id.org/delphi/ontology/evidenceAgainst The repository was restructured while this test ran (claim-tests/ moved to test-data/claim-tests/, books/ to claim-sources/); the pre-registered planned_datasets keep the old paths. https://w3id.org/delphi/resource/assessment/levin-2023-competency-05--claim-test https://w3id.org/delphi/ontology/evidenceAgainst This is a replication of a simulation, not an empirical test: it shows what follows from the stated model, not what real cellular competency does. https://w3id.org/delphi/resource/assessment/levin-2023-competency-05--claim-test https://w3id.org/delphi/ontology/expectedObservation Competent populations' best genotypic fitness rises for a few generations, then flattens below the hardwired curve, with across-repeat spread increasing with competency level and phenotypic fitness near maximal. https://w3id.org/delphi/resource/assessment/levin-2023-competency-05--claim-test https://w3id.org/delphi/ontology/failCriterion Pre-registered: refutes if any competent level's mean best genotypic fitness at generation 250 is >= hardwired, or the generation-51-250 SD at competency 400 is below that at competency 20, or any competent level's genotypic mean curve still rises by more than 0.1 between the 126-150 and 226-250 windows. Any other failure of (A)-(D) -> mixed. https://w3id.org/delphi/resource/assessment/levin-2023-competency-05--claim-test https://w3id.org/delphi/ontology/hasConfidence 0.9 https://w3id.org/delphi/resource/assessment/levin-2023-competency-05--claim-test https://w3id.org/delphi/ontology/hasEvidence https://w3id.org/delphi/resource/evidence/levin-2023-competency-05--claim-test--dataset-1 https://w3id.org/delphi/resource/assessment/levin-2023-competency-05--claim-test https://w3id.org/delphi/ontology/hasEvidence https://w3id.org/delphi/resource/evidence/levin-2023-competency-05--claim-test--dataset-2 https://w3id.org/delphi/resource/assessment/levin-2023-competency-05--claim-test https://w3id.org/delphi/ontology/hasEvidence https://w3id.org/delphi/resource/evidence/levin-2023-competency-05--claim-test--dataset-3 https://w3id.org/delphi/resource/assessment/levin-2023-competency-05--claim-test https://w3id.org/delphi/ontology/hasVerdict supports https://w3id.org/delphi/resource/assessment/levin-2023-competency-05--claim-test https://w3id.org/delphi/ontology/hypothesis In a re-run of the Shreesha & Levin (2023) Experiment 1 model (fixed competency 20/100/400 vs hardwired, 100 repeats x 250 generations), the best genotypic fitness of each competent population stops rising and stays below the hardwired population's, its spread across repeats grows with competency, while phenotypic fitness stays high. https://w3id.org/delphi/resource/assessment/levin-2023-competency-05--claim-test https://w3id.org/delphi/ontology/inferenceMethod Mean curves over 100 repeats; one-sided Welch t-test at generation 250 (alpha 0.001); plateau as window-mean difference < 0.03; spread as mean across-repeat SD over generations 51-250 compared across levels. https://w3id.org/delphi/resource/assessment/levin-2023-competency-05--claim-test https://w3id.org/delphi/ontology/passCriterion Pre-registered, with 'best genotypic fitness' = the maximum genotypic (pre-development) fitness in the population each generation, as in the authors' code: (A) at generation 250 each competent population's mean best genotypic fitness is below hardwired, one-sided Welch t-test p < 0.001; (B) plateau: for each competency level, |mean of the mean curve over generations 226-250 minus mean over generations 126-150| < 0.03; (C) the across-repeat standard deviation of best genotypic fitness, averaged over generations 51-250, is strictly ordered competency 20 < 100 < 400; (D) mean best phenotypic fitness at generation 250 >= 0.95 for every competency level. All four -> supports. https://w3id.org/delphi/resource/assessment/levin-2023-competency-05--claim-test https://w3id.org/delphi/ontology/preregistered false https://w3id.org/delphi/resource/claim/levin-2023-competency-05 https://w3id.org/delphi/ontology/hasAssessment https://w3id.org/delphi/resource/assessment/levin-2023-competency-05--claim-test https://w3id.org/delphi/resource/evidence/levin-2023-competency-05--claim-test--dataset-1 http://purl.org/dc/terms/description per-generation best genotypic and phenotypic fitness; mean and SD curves in derived/genotypic_curves.json https://w3id.org/delphi/resource/evidence/levin-2023-competency-05--claim-test--dataset-1 http://purl.org/dc/terms/license https://w3id.org/delphi/resource/evidence/levin-2023-competency-05--claim-test--dataset-1 http://www.w3.org/1999/02/22-rdf-syntax-ns#type https://w3id.org/delphi/ontology/EvidenceItem https://w3id.org/delphi/resource/evidence/levin-2023-competency-05--claim-test--dataset-1 http://www.w3.org/2000/01/rdf-schema#label Dataset: Re-run of the Shreesha & Levin (2023) Experiment 1 re-implementation, 100 repeats x 250 generations x 4 populations (generated by analysis.py) https://w3id.org/delphi/resource/evidence/levin-2023-competency-05--claim-test--dataset-2 http://purl.org/dc/terms/description model specification (Sections 2-3, Discussion); full text vendored in claim-sources/levin-papers/inputs/2023-competency.txt https://w3id.org/delphi/resource/evidence/levin-2023-competency-05--claim-test--dataset-2 http://purl.org/dc/terms/license CC BY 4.0 https://w3id.org/delphi/resource/evidence/levin-2023-competency-05--claim-test--dataset-2 http://www.w3.org/1999/02/22-rdf-syntax-ns#type https://w3id.org/delphi/ontology/EvidenceItem https://w3id.org/delphi/resource/evidence/levin-2023-competency-05--claim-test--dataset-2 http://www.w3.org/2000/01/rdf-schema#label Dataset: Shreesha L, Levin M (2023) Cellular Competency during Development Alters Evolutionary Dynamics in an Artificial Embryogeny Model. 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