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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." } g_iri { prefix_id: 2 name_id: 4 } } } rows { prefix { value: "https://w3id.org/delphi/ontology/" } } rows { name { value: "Assessment" } } rows { quad { p_iri { prefix_id: 4 name_id: 10 } o_iri { prefix_id: 10 name_id: 14 } } } rows { prefix { value: "http://www.w3.org/2000/01/rdf-schema#" } } rows { name { value: "comment" } } rows { quad { p_iri { prefix_id: 11 } o_literal { lex: "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." } } } rows { name { value: "label" } } rows { quad { p_iri { } o_literal { lex: "Claim test of levin-2023-competency-05: supports, confidence 0.9" } } } rows { name { value: "seeAlso" } } rows { prefix { value: "https://github.com/fractastical/delphisci/blob/bf2af6ee0a84e23ffa6414ad7a0a50a8c276506e/test-data/claim-tests/levin-papers/levin-2023-competency-05/" } } rows { name { value: "result.json" } } rows { quad { p_iri { } o_iri { prefix_id: 12 } } } rows { name { value: "wasAttributedTo" } } rows { prefix { value: "https://w3id.org/delphi/resource/agent/" } } rows { name { value: "delphisci-claim-tester-claude-opus-5-5" } } rows { quad { p_iri { prefix_id: 5 } o_iri { prefix_id: 13 } } } rows { name { value: "admissibleDatasets" } } rows { quad { p_iri { prefix_id: 10 } o_literal { lex: "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." } } } rows { name { value: "assessmentType" } } rows { quad { p_iri { } o_literal { lex: "claim-test/0.1.0" } } } rows { name { value: "dataKind" } } rows { quad { p_iri { } o_literal { lex: "computational" } } } rows { name { value: "disconfirmingObservation" } } rows { quad { p_iri { } o_literal { lex: "Competent genotypic fitness reaching or exceeding hardwired, continuing to climb, or showing less spread at higher competency." } } } rows { name { value: "evidenceAgainst" } } rows { quad { p_iri { } o_literal { lex: "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." } } } rows { quad { o_literal { lex: "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." } } } rows { quad { o_literal { lex: "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." } } } rows { quad { o_literal { lex: "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." } } } rows { quad { o_literal { lex: "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." } } } rows { name { value: "expectedObservation" } } rows { quad { p_iri { } o_literal { lex: "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." } } } rows { name { value: "failCriterion" } } rows { quad { p_iri { } o_literal { lex: "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." } } } rows { name { value: "hasConfidence" } } rows { datatype { value: "http://www.w3.org/2001/XMLSchema#double" } } rows { quad { p_iri { } o_literal { lex: "0.9" datatype: 1 } } } rows { name { value: "hasEvidence" } } rows { prefix { value: "https://w3id.org/delphi/resource/evidence/" } } rows { name { value: "levin-2023-competency-05--claim-test--dataset-1" } } rows { quad { p_iri { } o_iri { prefix_id: 14 } } } rows { name { value: "levin-2023-competency-05--claim-test--dataset-2" } } rows { quad { o_iri { } } } rows { name { value: "levin-2023-competency-05--claim-test--dataset-3" } } rows { quad { o_iri { } } } rows { name { value: "hasVerdict" } } rows { quad { p_iri { prefix_id: 10 } o_literal { lex: "supports" } } } rows { name { value: "hypothesis" } } rows { quad { p_iri { } o_literal { lex: "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." } } } rows { name { value: "inferenceMethod" } } rows { quad { p_iri { } o_literal { lex: "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." } } } rows { name { value: "passCriterion" } } rows { quad { p_iri { } o_literal { lex: "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. 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