https://w3id.org/np/RA9DOY84RdNWzj9uaRfbURTCMKwzWjR-eKon0lGPLxzf8/Head https://w3id.org/np/RA9DOY84RdNWzj9uaRfbURTCMKwzWjR-eKon0lGPLxzf8 http://www.nanopub.org/nschema#hasAssertion https://w3id.org/np/RA9DOY84RdNWzj9uaRfbURTCMKwzWjR-eKon0lGPLxzf8/assertion https://w3id.org/np/RA9DOY84RdNWzj9uaRfbURTCMKwzWjR-eKon0lGPLxzf8 http://www.nanopub.org/nschema#hasProvenance https://w3id.org/np/RA9DOY84RdNWzj9uaRfbURTCMKwzWjR-eKon0lGPLxzf8/provenance https://w3id.org/np/RA9DOY84RdNWzj9uaRfbURTCMKwzWjR-eKon0lGPLxzf8 http://www.nanopub.org/nschema#hasPublicationInfo https://w3id.org/np/RA9DOY84RdNWzj9uaRfbURTCMKwzWjR-eKon0lGPLxzf8/pubinfo https://w3id.org/np/RA9DOY84RdNWzj9uaRfbURTCMKwzWjR-eKon0lGPLxzf8 http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://www.nanopub.org/nschema#Nanopublication https://w3id.org/np/RA9DOY84RdNWzj9uaRfbURTCMKwzWjR-eKon0lGPLxzf8/assertion https://w3id.org/delphi/resource/assessment/darwin1859-ch10-02--claim-test http://purl.org/dc/terms/description For each of 14 higher taxa the PBDB genus list with appearance ages was downloaded; accepted extinct genera with >= 5 occurrences were kept and duration computed as the difference between first- and last-appearance midpoints. Clause A: Kruskal-Wallis across higher taxa with epsilon-squared effect size and the ratio of extreme group medians. Clause B: within each higher taxon with >= 3 orders of >= 20 genera, Kruskal-Wallis across orders. The whole procedure was repeated with >= 20 occurrences as a sensitivity check. https://w3id.org/delphi/resource/assessment/darwin1859-ch10-02--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/darwin1859-ch10-02--claim-test http://www.w3.org/2000/01/rdf-schema#comment Measured: 5.064511278195515 ratio of largest to smallest median genus duration among the 14 higher taxa (Myr/Myr) (n = 15145, Kruskal-Wallis H = 3080.0, p = 0.00e+00, epsilon2 = 0.203). Interpretation: Darwin's 'rate of change' of species is read, following the Grok assessor, as taxonomic turnover: shorter genus durations mean faster replacement of forms. 'Classes' are mapped to PBDB classes or, where PBDB class structure is unstable (brachiopods, bryozoans), phyla. 'Species of different genera' is approximated by genera grouped into orders, because species-level ranges in PBDB are too noisy and species durations are strongly tied to the genus concept. Durations are taxonomic, not morphological; the morphological reading (rates of character change) is not tested. Differences in preservation potential and taxonomic splitting between classes can mimic rate differences, which is why the pass criterion requires a non-trivial effect size and a two-fold spread of medians rather than mere significance. https://w3id.org/delphi/resource/assessment/darwin1859-ch10-02--claim-test http://www.w3.org/2000/01/rdf-schema#label Claim test of darwin1859-ch10-02: supports, confidence 0.7 https://w3id.org/delphi/resource/assessment/darwin1859-ch10-02--claim-test http://www.w3.org/2000/01/rdf-schema#seeAlso https://github.com/fractastical/delphisci/blob/bf2af6ee0a84e23ffa6414ad7a0a50a8c276506e/test-data/claim-tests/darwin-origin/darwin1859-ch10-02/result.json https://w3id.org/delphi/resource/assessment/darwin1859-ch10-02--claim-test http://www.w3.org/ns/prov#wasAttributedTo https://w3id.org/delphi/resource/agent/delphisci-claim-tester-claude-fable-5-1 https://w3id.org/delphi/resource/assessment/darwin1859-ch10-02--claim-test https://w3id.org/delphi/ontology/admissibleDatasets Planned datasets: pbdb-taxa-genus-appearances-14-higher-taxa https://w3id.org/delphi/resource/assessment/darwin1859-ch10-02--claim-test https://w3id.org/delphi/ontology/assessmentType claim-test/0.1.0 https://w3id.org/delphi/resource/assessment/darwin1859-ch10-02--claim-test https://w3id.org/delphi/ontology/dataKind biological https://w3id.org/delphi/resource/assessment/darwin1859-ch10-02--claim-test https://w3id.org/delphi/ontology/disconfirmingObservation Clause A fails if genus durations are statistically indistinguishable across classes (p >= 0.001), or the effect is trivial (epsilon-squared < 0.02), or every class median lies within a factor of 2 of every other. Clause B fails if orders within a class differ significantly and non-trivially in half or fewer of the eligible classes. Both failing refutes the claim. A sensitivity re-run with >= 20 occurrences per genus is reported; if the sign of either clause flips under that filter the result is downgraded to 'mixed' regardless. https://w3id.org/delphi/resource/assessment/darwin1859-ch10-02--claim-test https://w3id.org/delphi/ontology/evidenceAgainst Darwin's phrase covers rate 'or degree' of change; morphological degree of change is not measured here. https://w3id.org/delphi/resource/assessment/darwin1859-ch10-02--claim-test https://w3id.org/delphi/ontology/evidenceAgainst Durations of genera with few occurrences are truncated; the >= 5 occurrence filter (and the >= 20 sensitivity run) reduces but does not remove range truncation, which differs among classes. https://w3id.org/delphi/resource/assessment/darwin1859-ch10-02--claim-test https://w3id.org/delphi/ontology/evidenceAgainst Genus duration is a taxonomic proxy for rate of change; it conflates true evolutionary rate with preservation potential, sampling intensity and how finely each class is split by taxonomists. https://w3id.org/delphi/resource/assessment/darwin1859-ch10-02--claim-test https://w3id.org/delphi/ontology/evidenceAgainst Groups are not all of class rank (Brachiopoda and Bryozoa are phyla) because PBDB class membership is unstable for them. https://w3id.org/delphi/resource/assessment/darwin1859-ch10-02--claim-test https://w3id.org/delphi/ontology/evidenceAgainst Only extinct genera are included (extant genera have open-ended durations), which excludes the long-lived 'living fossil' lineages Darwin also had in mind and so is conservative with respect to the spread of rates. https://w3id.org/delphi/resource/assessment/darwin1859-ch10-02--claim-test https://w3id.org/delphi/ontology/expectedObservation Using PBDB genus-rank taxa with first- and last-appearance ages for 14 higher taxa (Trilobita, Brachiopoda, Bivalvia, Gastropoda, Cephalopoda, Anthozoa, Echinoidea, Crinoidea, Ostracoda, Bryozoa, Mammalia, Reptilia, Actinopterygii, Chondrichthyes), restricted to extinct genera with >= 5 occurrences, genus duration = midpoint of first-appearance range minus midpoint of last-appearance range. Clause A (between classes): a Kruskal-Wallis test of genus duration across the higher taxa has p < 0.001 AND epsilon-squared effect size >= 0.02 AND the ratio of the largest to the smallest group median duration is >= 2. Clause B (between genera grouped by order, within classes): within each higher taxon having >= 3 orders with >= 20 qualifying genera each, a Kruskal-Wallis test of genus duration across orders has p < 0.001 and epsilon-squared >= 0.02; clause B passes if this holds in a majority of eligible higher taxa. Verdict 'supports' if A and B pass; 'mixed' if exactly one passes; 'refutes' if neither. https://w3id.org/delphi/resource/assessment/darwin1859-ch10-02--claim-test https://w3id.org/delphi/ontology/failCriterion Clause A fails if genus durations are statistically indistinguishable across classes (p >= 0.001), or the effect is trivial (epsilon-squared < 0.02), or every class median lies within a factor of 2 of every other. Clause B fails if orders within a class differ significantly and non-trivially in half or fewer of the eligible classes. Both failing refutes the claim. A sensitivity re-run with >= 20 occurrences per genus is reported; if the sign of either clause flips under that filter the result is downgraded to 'mixed' regardless. https://w3id.org/delphi/resource/assessment/darwin1859-ch10-02--claim-test https://w3id.org/delphi/ontology/hasConfidence 0.7 https://w3id.org/delphi/resource/assessment/darwin1859-ch10-02--claim-test https://w3id.org/delphi/ontology/hasEvidence https://w3id.org/delphi/resource/evidence/darwin1859-ch10-02--claim-test--dataset-1 https://w3id.org/delphi/resource/assessment/darwin1859-ch10-02--claim-test https://w3id.org/delphi/ontology/hasVerdict supports https://w3id.org/delphi/resource/assessment/darwin1859-ch10-02--claim-test https://w3id.org/delphi/ontology/hypothesis If different classes and genera change at different rates, then taxonomic turnover measured as the stratigraphic duration of extinct genera in the Paleobiology Database should differ substantially among major animal classes, and, within classes, among orders. https://w3id.org/delphi/resource/assessment/darwin1859-ch10-02--claim-test https://w3id.org/delphi/ontology/inferenceMethod For each of 14 higher taxa the PBDB genus list with appearance ages was downloaded; accepted extinct genera with >= 5 occurrences were kept and duration computed as the difference between first- and last-appearance midpoints. Clause A: Kruskal-Wallis across higher taxa with epsilon-squared effect size and the ratio of extreme group medians. Clause B: within each higher taxon with >= 3 orders of >= 20 genera, Kruskal-Wallis across orders. The whole procedure was repeated with >= 20 occurrences as a sensitivity check. https://w3id.org/delphi/resource/assessment/darwin1859-ch10-02--claim-test https://w3id.org/delphi/ontology/passCriterion Using PBDB genus-rank taxa with first- and last-appearance ages for 14 higher taxa (Trilobita, Brachiopoda, Bivalvia, Gastropoda, Cephalopoda, Anthozoa, Echinoidea, Crinoidea, Ostracoda, Bryozoa, Mammalia, Reptilia, Actinopterygii, Chondrichthyes), restricted to extinct genera with >= 5 occurrences, genus duration = midpoint of first-appearance range minus midpoint of last-appearance range. Clause A (between classes): a Kruskal-Wallis test of genus duration across the higher taxa has p < 0.001 AND epsilon-squared effect size >= 0.02 AND the ratio of the largest to the smallest group median duration is >= 2. Clause B (between genera grouped by order, within classes): within each higher taxon having >= 3 orders with >= 20 qualifying genera each, a Kruskal-Wallis test of genus duration across orders has p < 0.001 and epsilon-squared >= 0.02; clause B passes if this holds in a majority of eligible higher taxa. Verdict 'supports' if A and B pass; 'mixed' if exactly one passes; 'refutes' if neither. https://w3id.org/delphi/resource/assessment/darwin1859-ch10-02--claim-test https://w3id.org/delphi/ontology/preregistered false https://w3id.org/delphi/resource/claim/darwin1859-ch10-02 https://w3id.org/delphi/ontology/hasAssessment https://w3id.org/delphi/resource/assessment/darwin1859-ch10-02--claim-test https://w3id.org/delphi/resource/evidence/darwin1859-ch10-02--claim-test--dataset-1 http://purl.org/dc/terms/description first/last appearance ages, extant flag, occurrence count and order of each genus https://w3id.org/delphi/resource/evidence/darwin1859-ch10-02--claim-test--dataset-1 http://purl.org/dc/terms/license CC BY 4.0 https://w3id.org/delphi/resource/evidence/darwin1859-ch10-02--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/darwin1859-ch10-02--claim-test--dataset-1 http://www.w3.org/2000/01/rdf-schema#label Dataset: Paleobiology Database taxa lists (genus rank, show=app,class) for 14 higher taxa https://w3id.org/delphi/resource/evidence/darwin1859-ch10-02--claim-test--dataset-1 http://www.w3.org/ns/prov#atLocation https://paleobiodb.org/data1.2/taxa/list.json?base_name=Actinopterygii&rank=genus&show=app%2Cclass&vocab=pbdb https://w3id.org/delphi/resource/evidence/darwin1859-ch10-02--claim-test--dataset-1 http://www.w3.org/ns/prov#atLocation https://paleobiodb.org/data1.2/taxa/list.json?base_name=Anthozoa&rank=genus&show=app%2Cclass&vocab=pbdb https://w3id.org/delphi/resource/evidence/darwin1859-ch10-02--claim-test--dataset-1 http://www.w3.org/ns/prov#atLocation https://paleobiodb.org/data1.2/taxa/list.json?base_name=Bivalvia&rank=genus&show=app%2Cclass&vocab=pbdb https://w3id.org/delphi/resource/evidence/darwin1859-ch10-02--claim-test--dataset-1 http://www.w3.org/ns/prov#atLocation https://paleobiodb.org/data1.2/taxa/list.json?base_name=Brachiopoda&rank=genus&show=app%2Cclass&vocab=pbdb https://w3id.org/delphi/resource/evidence/darwin1859-ch10-02--claim-test--dataset-1 http://www.w3.org/ns/prov#atLocation https://paleobiodb.org/data1.2/taxa/list.json?base_name=Bryozoa&rank=genus&show=app%2Cclass&vocab=pbdb https://w3id.org/delphi/resource/evidence/darwin1859-ch10-02--claim-test--dataset-1 http://www.w3.org/ns/prov#atLocation https://paleobiodb.org/data1.2/taxa/list.json?base_name=Cephalopoda&rank=genus&show=app%2Cclass&vocab=pbdb https://w3id.org/delphi/resource/evidence/darwin1859-ch10-02--claim-test--dataset-1 http://www.w3.org/ns/prov#atLocation https://paleobiodb.org/data1.2/taxa/list.json?base_name=Chondrichthyes&rank=genus&show=app%2Cclass&vocab=pbdb https://w3id.org/delphi/resource/evidence/darwin1859-ch10-02--claim-test--dataset-1 http://www.w3.org/ns/prov#atLocation https://paleobiodb.org/data1.2/taxa/list.json?base_name=Crinoidea&rank=genus&show=app%2Cclass&vocab=pbdb https://w3id.org/delphi/resource/evidence/darwin1859-ch10-02--claim-test--dataset-1 http://www.w3.org/ns/prov#atLocation https://paleobiodb.org/data1.2/taxa/list.json?base_name=Echinoidea&rank=genus&show=app%2Cclass&vocab=pbdb https://w3id.org/delphi/resource/evidence/darwin1859-ch10-02--claim-test--dataset-1 http://www.w3.org/ns/prov#atLocation https://paleobiodb.org/data1.2/taxa/list.json?base_name=Gastropoda&rank=genus&show=app%2Cclass&vocab=pbdb https://w3id.org/delphi/resource/evidence/darwin1859-ch10-02--claim-test--dataset-1 http://www.w3.org/ns/prov#atLocation https://paleobiodb.org/data1.2/taxa/list.json?base_name=Mammalia&rank=genus&show=app%2Cclass&vocab=pbdb https://w3id.org/delphi/resource/evidence/darwin1859-ch10-02--claim-test--dataset-1 http://www.w3.org/ns/prov#atLocation 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