[ { "@id": "https://w3id.org/np/RASFvRnJPK8TYlrXMxtXGlXALlXHuL1bhf3xUNfoOY-Wg/assertion", "@graph": [ { "@id": "https://w3id.org/delphi/resource/assessment/levin-2023-competency-12--claim-test", "http://purl.org/dc/terms/description": [ { "@value": "analysis.py ran 100 independent 1000-generation populations of the evolvable-competency genetic algorithm. At each generation the best pre-development genome was the lowest-index maximizer of the authors' exponential fitness on the 51-length vector. A locus counts as changed when that allele differs on the next generation. Counts cover the 999 transitions from generation 1 to generation 1000. The competency mean was compared with each of the 50 structural means, and each pair was given a one-sided sign test. Development uses the vectorized adjacent-inversion sorter from the competency-04 test, which accepts a swap exactly when the authors' fitness check would." } ], "@type": [ "https://w3id.org/delphi/ontology/Assessment" ], "http://www.w3.org/2000/01/rdf-schema#comment": [ { "@value": "Measured: 129.47 mean number of generation-to-generation changes of the competency locus in the best pre-development genome, over 999 transitions (n = 100, SD across runs of the competency-locus count: 48.0932; fixed seed 20261102). Interpretation: Simulation-result claim. The paper's results sentence says the competency-gene frequency was much higher than the average of the fifty structural genes; the discussion, the figure 6 title, and this claim say it changed more often than any structural gene. The verdict uses the claim's wording (any gene), and the average is reported beside it. The released plotGeneChangeFrequency does not trace which mutation moved a cell. It counts allele differences, between consecutive generations, in the best pre-development genome. That is the measurement used here. The best genome is chosen by fitness of the 51-vector, as in their get_max, not by phenotypic fitness. This run shows whether that program behaves as claimed. It does not show that cells do this." } ], "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "Claim test of levin-2023-competency-12: refutes, confidence 0.72" } ], "http://www.w3.org/2000/01/rdf-schema#seeAlso": [ { "@id": "https://github.com/fractastical/delphisci/blob/bf2af6ee0a84e23ffa6414ad7a0a50a8c276506e/test-data/claim-tests/levin-papers/levin-2023-competency-12/result.json" } ], "http://www.w3.org/ns/prov#wasAttributedTo": [ { "@id": "https://w3id.org/delphi/resource/agent/delphisci-claim-tester-grok-4-7" } ], "https://w3id.org/delphi/ontology/admissibleDatasets": [ { "@value": "Runs of the evolvable-competency 1D embryogeny model as specified by the authors' released code at the pinned commit: 50 structural genes with values in [1, 50], competency gene initialised by randint(1, 15) so values in [1, 14], mutated by randint(1, 500) so values in [1, 499], population 100, top 10 percent selected on phenotypic fitness of the developed structural genes, crossover cut in [11, 50), per-individual point-mutation probability 0.6 hitting one of 51 loci. The paper's closed intervals [1, 15] and [1, 500] are not used, because the released randint calls are exclusive at the top. Saved output matrices are not in the repository; a reimplementation that matches these rules is admissible and must be labelled as one. A biological table is not admissible for this simulation-result claim." } ], "https://w3id.org/delphi/ontology/assessmentType": [ { "@value": "claim-test/0.1.0" } ], "https://w3id.org/delphi/ontology/dataKind": [ { "@value": "computational" } ], "https://w3id.org/delphi/ontology/disconfirmingObservation": [ { "@value": "At least one structural locus has a mean change count greater than or equal to the competency locus." } ], "https://w3id.org/delphi/ontology/evidenceAgainst": [ { "@value": "A passing or failing computational result shows how this program behaves. It does not show that cells or evolution do this." }, { "@value": "Released randint calls are exclusive at the top, so competency genes start in [1, 14] and mutate into [1, 499]. The paper states the closed intervals [1, 15] and [1, 500]." }, { "@value": "The competency locus changed 129.47 times on average (SD 48.09). Every structural locus changed more often: the quietest 302.38 times, the average of the fifty 377.30, and locus 24 448.75. In 0 of 100 runs did the competency locus change more often than every structural locus. The one-sided sign test that competency exceeds a structural locus has p = 1 for all 50 loci." }, { "@value": "The measurement follows plotGeneChangeFrequency: allele differences of the best pre-development genome. Replacing the winner by crossover counts as a change at every locus that differs. It does not isolate point mutations, and it does not count developmental cell swaps." }, { "@value": "The results-section sentence, that competency changes were much higher than the average of the fifty structural genes, fails on the same counts." }, { "@value": "This is an independent reimplementation, not an execution of the authors' script. The random stream is NumPy's Generator, not their np.random stream. Their saved Genomes.npy is not in the repository, so their figure was not re-scored." } ], "https://w3id.org/delphi/ontology/expectedObservation": [ { "@value": "The mean change count of the competency locus exceeds the mean change count of each of the 50 structural loci, and each of those 50 paired comparisons is significant by a one-sided sign test at p < 0.05." } ], "https://w3id.org/delphi/ontology/failCriterion": [ { "@value": "Pre-registered: refutes if mean_c is less than or equal to at least one structural locus mean (the claim that the competency gene changes more often than any of the fifty structural genes is false as a point estimate, which includes failing to beat the average of the fifty). Mixed if mean_c exceeds every structural mean but at least one sign test has p >= 0.05. No other outcome is allowed." } ], "https://w3id.org/delphi/ontology/hasConfidence": [ { "@value": "0.72", "@type": "http://www.w3.org/2001/XMLSchema#double" } ], "https://w3id.org/delphi/ontology/hasEvidence": [ { "@id": "https://w3id.org/delphi/resource/evidence/levin-2023-competency-12--claim-test--dataset-1" }, { "@id": "https://w3id.org/delphi/resource/evidence/levin-2023-competency-12--claim-test--dataset-2" }, { "@id": "https://w3id.org/delphi/resource/evidence/levin-2023-competency-12--claim-test--dataset-3" } ], "https://w3id.org/delphi/ontology/hasVerdict": [ { "@value": "refutes" } ], "https://w3id.org/delphi/ontology/hypothesis": [ { "@value": "In the Shreesha and Levin (2023) 1D embryogeny model with an evolvable competency gene, over 1000 generations the competency locus of the best genome changes between consecutive generations more often than every one of the fifty structural loci." } ], "https://w3id.org/delphi/ontology/inferenceMethod": [ { "@value": "Total locus-change counts of the best genome over 999 generation transitions, averaged over 100 runs. Verdict from the pre-registered comparison of the competency mean with each structural mean, plus an exact one-sided sign test per locus at p < 0.05. The authors' time average of the cumulative curve is recorded and does not decide the verdict." } ], "https://w3id.org/delphi/ontology/passCriterion": [ { "@value": "Pre-registered, locked before any run of this test. 100 independent runs of 1000 generations (the figure 6 caption's n, not the repository default of 10). For each run, store the pre-development genome of all 100 embryos at each generation. The best genome is the lowest-index maximizer of the authors' exponential fitness applied to the full 51-length vector (structural genes plus the competency gene), with ncr = C(50,2) = 1225 and a non-inversion defined by <=, matching get_max in Exp3-EvolvableCompetency.py. A locus changes when that best genome's allele differs from the next generation's best genome. Count changes over the 999 transitions from generation 1 to 1000. Let mean_c be the mean over runs of the competency-locus count and mean_j the mean over runs of structural locus j. Pass (supports) only if mean_c is strictly greater than every mean_j and, for every structural locus, a one-sided sign test has p < 0.05: among runs with an untied pair, the count of runs where the competency count exceeds that locus, under Binomial(n_untied, 0.5). Ties are excluded. A locus with no untied runs fails the significance requirement." } ], "https://w3id.org/delphi/ontology/preregistered": [ { "@value": "false", "@type": "http://www.w3.org/2001/XMLSchema#boolean" } ] }, { "@id": "https://w3id.org/delphi/resource/evidence/levin-2023-competency-12--claim-test--dataset-1", "http://purl.org/dc/terms/description": [ { "@value": "pre-registered locus-change counts; summary in derived/measured.json" } ], "http://purl.org/dc/terms/license": [ { "@value": "" } ], "@type": [ "https://w3id.org/delphi/ontology/EvidenceItem" ], "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "Dataset: 100 runs of 1000 generations of the evolvable-competency model, locus-change counts (generated by analysis.py)" } ] }, { "@id": "https://w3id.org/delphi/resource/evidence/levin-2023-competency-12--claim-test--dataset-2", "http://purl.org/dc/terms/description": [ { "@value": "model description and figure 6 caption; not the measurement" } ], "http://purl.org/dc/terms/license": [ { "@value": "CC BY 4.0" } ], "@type": [ "https://w3id.org/delphi/ontology/EvidenceItem" ], "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "Dataset: Shreesha L, Levin M (2023) Cellular Competency during Development Alters Evolutionary Dynamics in an Artificial Embryogeny Model. 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