https://w3id.org/np/RAEOakX6ZWGSOQc14jSPmF-O-P8CGFZkMbbfBsc97u0tY/Head https://w3id.org/np/RAEOakX6ZWGSOQc14jSPmF-O-P8CGFZkMbbfBsc97u0tY http://www.nanopub.org/nschema#hasAssertion https://w3id.org/np/RAEOakX6ZWGSOQc14jSPmF-O-P8CGFZkMbbfBsc97u0tY/assertion https://w3id.org/np/RAEOakX6ZWGSOQc14jSPmF-O-P8CGFZkMbbfBsc97u0tY http://www.nanopub.org/nschema#hasProvenance https://w3id.org/np/RAEOakX6ZWGSOQc14jSPmF-O-P8CGFZkMbbfBsc97u0tY/provenance https://w3id.org/np/RAEOakX6ZWGSOQc14jSPmF-O-P8CGFZkMbbfBsc97u0tY http://www.nanopub.org/nschema#hasPublicationInfo https://w3id.org/np/RAEOakX6ZWGSOQc14jSPmF-O-P8CGFZkMbbfBsc97u0tY/pubinfo https://w3id.org/np/RAEOakX6ZWGSOQc14jSPmF-O-P8CGFZkMbbfBsc97u0tY http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://www.nanopub.org/nschema#Nanopublication https://w3id.org/np/RAEOakX6ZWGSOQc14jSPmF-O-P8CGFZkMbbfBsc97u0tY/assertion https://w3id.org/delphi/resource/assessment/darwin1859-ch14-12--claim-test http://purl.org/dc/terms/description For each of 96 Phanerozoic stages (two youngest dropped) the fraction of marine animal genera present that are also recorded after the stage (X_bt + X_Ft over all present) was computed from the PBDB diversity table. The stage with the lowest crossing fraction (Stage 4) was identified and the same table was retrieved for nine major lineages to count survivors across that boundary. https://w3id.org/delphi/resource/assessment/darwin1859-ch14-12--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-ch14-12--claim-test http://www.w3.org/2000/01/rdf-schema#comment Measured: 0.29391304347826086 minimum stage-boundary crossing fraction of marine animal genera (Phanerozoic) (n = 96). Interpretation: Darwin's 'cataclysm desolating the whole world' is read as an event after which (nearly) no lineages persist, detectable as a stage boundary crossed by very few genera in very few lineages. 'The ordinary succession by generation has never once been broken' is tested only for the Phanerozoic marine record, where stage-level genus ranges exist; the Precambrian ancestry 'long before the Silurian' is outside what occurrence data can show. Boundary-crossing fractions are biased downward by incomplete sampling (Signor-Lipps and Lazarus effects), which makes the test conservative with respect to the claim. Thresholds of 10% and 7/9 lineages are deliberately lenient about mass extinctions, which Darwin did not deny in degree, and strict about total desolation, which he denied. https://w3id.org/delphi/resource/assessment/darwin1859-ch14-12--claim-test http://www.w3.org/2000/01/rdf-schema#label Claim test of darwin1859-ch14-12: supports, confidence 0.85 https://w3id.org/delphi/resource/assessment/darwin1859-ch14-12--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-ch14-12/result.json https://w3id.org/delphi/resource/assessment/darwin1859-ch14-12--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-ch14-12--claim-test https://w3id.org/delphi/ontology/admissibleDatasets Planned datasets: pbdb-occs-diversity-marine-genera-by-stage, pbdb-occs-diversity-marine-genera-by-stage-per-phylum https://w3id.org/delphi/resource/assessment/darwin1859-ch14-12--claim-test https://w3id.org/delphi/ontology/assessmentType claim-test/0.1.0 https://w3id.org/delphi/resource/assessment/darwin1859-ch14-12--claim-test https://w3id.org/delphi/ontology/dataKind biological https://w3id.org/delphi/resource/assessment/darwin1859-ch14-12--claim-test https://w3id.org/delphi/ontology/disconfirmingObservation Refuted if the fossil record contains a stage boundary across which fewer than 5% of marine animal genera persist, or at which survivors are absent from three or more of the nine major lineages, which would indicate a near-total biotic reset incompatible with unbroken descent. The Precambrian part of the claim ('long before the Silurian') cannot be tested with this data and is excluded from the verdict. https://w3id.org/delphi/resource/assessment/darwin1859-ch14-12--claim-test https://w3id.org/delphi/ontology/evidenceAgainst Boundary-crossing fractions are depressed by incomplete sampling (Signor-Lipps, Lazarus taxa) and by stage boundaries having been drawn at faunal breaks; both biases work against the claim, so a pass is conservative. https://w3id.org/delphi/resource/assessment/darwin1859-ch14-12--claim-test https://w3id.org/delphi/ontology/evidenceAgainst Genus-level survival understates species-level loss; Darwin's claim concerns continuity of descent, for which any surviving lineage suffices, so genus level is appropriate. https://w3id.org/delphi/resource/assessment/darwin1859-ch14-12--claim-test https://w3id.org/delphi/ontology/evidenceAgainst Only the Phanerozoic marine record is tested; the claim's Precambrian ancestry statement and terrestrial life are untested. https://w3id.org/delphi/resource/assessment/darwin1859-ch14-12--claim-test https://w3id.org/delphi/ontology/evidenceAgainst Stage-level resolution cannot distinguish a single instantaneous event from a protracted crisis within one stage. https://w3id.org/delphi/resource/assessment/darwin1859-ch14-12--claim-test https://w3id.org/delphi/ontology/expectedObservation Using PBDB occs/diversity stage-level tables for marine Animalia genera (Phanerozoic) and the same table for each of nine marine animal phyla/classes (Mollusca, Brachiopoda, Arthropoda, Echinodermata, Cnidaria, Bryozoa, Porifera, Annelida, Chordata), define for each stage i the boundary-crossing fraction C_i = (X_bt + X_Ft) / (X_bt + X_Ft + X_bL + X_FL), the share of genera present in stage i that are also recorded after it (range-through or first-appearing and continuing). Exclude the two youngest stages (Recent edge). Pass if (1) the minimum C_i over all retained Phanerozoic stage boundaries is >= 0.10 (at no point did fewer than one in ten marine genera survive), AND (2) at the stage with the minimum C_i, at least 7 of the 9 phyla/classes have C_i > 0 (survivors in at least seven major lineages), AND (3) the median C_i over all stages is >= 0.5. Verdict 'supports' if all three hold; 'mixed' if (1) and (2) hold but (3) fails, or if (1) fails only marginally (0.05 <= min C_i < 0.10) while (2) holds; 'refutes' if any boundary has min C_i < 0.05 or fewer than 7 of 9 lineages have survivors at the worst boundary. https://w3id.org/delphi/resource/assessment/darwin1859-ch14-12--claim-test https://w3id.org/delphi/ontology/failCriterion Refuted if the fossil record contains a stage boundary across which fewer than 5% of marine animal genera persist, or at which survivors are absent from three or more of the nine major lineages, which would indicate a near-total biotic reset incompatible with unbroken descent. The Precambrian part of the claim ('long before the Silurian') cannot be tested with this data and is excluded from the verdict. https://w3id.org/delphi/resource/assessment/darwin1859-ch14-12--claim-test https://w3id.org/delphi/ontology/hasConfidence 0.85 https://w3id.org/delphi/resource/assessment/darwin1859-ch14-12--claim-test https://w3id.org/delphi/ontology/hasEvidence https://w3id.org/delphi/resource/evidence/darwin1859-ch14-12--claim-test--dataset-1 https://w3id.org/delphi/resource/assessment/darwin1859-ch14-12--claim-test https://w3id.org/delphi/ontology/hasEvidence https://w3id.org/delphi/resource/evidence/darwin1859-ch14-12--claim-test--dataset-2 https://w3id.org/delphi/resource/assessment/darwin1859-ch14-12--claim-test https://w3id.org/delphi/ontology/hasVerdict supports https://w3id.org/delphi/resource/assessment/darwin1859-ch14-12--claim-test https://w3id.org/delphi/ontology/hypothesis If no cataclysm ever desolated the whole world and the succession by generation was never broken, then at every stage boundary of the Phanerozoic a substantial share of the marine animal genera present must cross into the next stage, and survivors must be found in every major animal phylum even at the worst boundary. https://w3id.org/delphi/resource/assessment/darwin1859-ch14-12--claim-test https://w3id.org/delphi/ontology/inferenceMethod For each of 96 Phanerozoic stages (two youngest dropped) the fraction of marine animal genera present that are also recorded after the stage (X_bt + X_Ft over all present) was computed from the PBDB diversity table. The stage with the lowest crossing fraction (Stage 4) was identified and the same table was retrieved for nine major lineages to count survivors across that boundary. https://w3id.org/delphi/resource/assessment/darwin1859-ch14-12--claim-test https://w3id.org/delphi/ontology/passCriterion Using PBDB occs/diversity stage-level tables for marine Animalia genera (Phanerozoic) and the same table for each of nine marine animal phyla/classes (Mollusca, Brachiopoda, Arthropoda, Echinodermata, Cnidaria, Bryozoa, Porifera, Annelida, Chordata), define for each stage i the boundary-crossing fraction C_i = (X_bt + X_Ft) / (X_bt + X_Ft + X_bL + X_FL), the share of genera present in stage i that are also recorded after it (range-through or first-appearing and continuing). Exclude the two youngest stages (Recent edge). Pass if (1) the minimum C_i over all retained Phanerozoic stage boundaries is >= 0.10 (at no point did fewer than one in ten marine genera survive), AND (2) at the stage with the minimum C_i, at least 7 of the 9 phyla/classes have C_i > 0 (survivors in at least seven major lineages), AND (3) the median C_i over all stages is >= 0.5. Verdict 'supports' if all three hold; 'mixed' if (1) and (2) hold but (3) fails, or if (1) fails only marginally (0.05 <= min C_i < 0.10) while (2) holds; 'refutes' if any boundary has min C_i < 0.05 or fewer than 7 of 9 lineages have survivors at the worst boundary. https://w3id.org/delphi/resource/assessment/darwin1859-ch14-12--claim-test https://w3id.org/delphi/ontology/preregistered false https://w3id.org/delphi/resource/claim/darwin1859-ch14-12 https://w3id.org/delphi/ontology/hasAssessment https://w3id.org/delphi/resource/assessment/darwin1859-ch14-12--claim-test https://w3id.org/delphi/resource/evidence/darwin1859-ch14-12--claim-test--dataset-1 http://purl.org/dc/terms/description overall boundary-crossing fractions https://w3id.org/delphi/resource/evidence/darwin1859-ch14-12--claim-test--dataset-1 http://purl.org/dc/terms/license CC BY 4.0 https://w3id.org/delphi/resource/evidence/darwin1859-ch14-12--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-ch14-12--claim-test--dataset-1 http://www.w3.org/2000/01/rdf-schema#label Dataset: Paleobiology Database occs/diversity: marine Animalia genus range categories per stage, Phanerozoic https://w3id.org/delphi/resource/evidence/darwin1859-ch14-12--claim-test--dataset-1 http://www.w3.org/ns/prov#atLocation https://paleobiodb.org/data1.2/occs/diversity.json?base_name=Animalia&interval=Phanerozoic&envtype=marine&count=genera&time_reso=stage&vocab=pbdb https://w3id.org/delphi/resource/evidence/darwin1859-ch14-12--claim-test--dataset-1 http://www.w3.org/ns/prov#wasDerivedFrom https://paleobiodb.org/data1.2/occs/diversity_doc.html https://w3id.org/delphi/resource/evidence/darwin1859-ch14-12--claim-test--dataset-1 https://w3id.org/delphi/ontology/hasChecksum sha256:e69eb14ca490331dc5e44aee5a83c599c3c46ec1db01ed0d47076bc5993f75f1 https://w3id.org/delphi/resource/evidence/darwin1859-ch14-12--claim-test--dataset-2 http://purl.org/dc/terms/description survivors per lineage at the worst boundary https://w3id.org/delphi/resource/evidence/darwin1859-ch14-12--claim-test--dataset-2 http://purl.org/dc/terms/license CC BY 4.0 https://w3id.org/delphi/resource/evidence/darwin1859-ch14-12--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/darwin1859-ch14-12--claim-test--dataset-2 http://www.w3.org/2000/01/rdf-schema#label Dataset: Paleobiology Database occs/diversity for nine marine animal lineages (Mollusca, Brachiopoda, Arthropoda, Echinodermata, Cnidaria, Bryozoa, Porifera, Annelida, Chordata) https://w3id.org/delphi/resource/evidence/darwin1859-ch14-12--claim-test--dataset-2 http://www.w3.org/ns/prov#atLocation 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https://w3id.org/delphi/resource/evidence/darwin1859-ch14-12--claim-test--dataset-2 http://www.w3.org/ns/prov#atLocation https://paleobiodb.org/data1.2/occs/diversity.json?base_name=Chordata&interval=Phanerozoic&envtype=marine&count=genera&time_reso=stage&vocab=pbdb https://w3id.org/delphi/resource/evidence/darwin1859-ch14-12--claim-test--dataset-2 http://www.w3.org/ns/prov#atLocation https://paleobiodb.org/data1.2/occs/diversity.json?base_name=Cnidaria&interval=Phanerozoic&envtype=marine&count=genera&time_reso=stage&vocab=pbdb https://w3id.org/delphi/resource/evidence/darwin1859-ch14-12--claim-test--dataset-2 http://www.w3.org/ns/prov#atLocation https://paleobiodb.org/data1.2/occs/diversity.json?base_name=Echinodermata&interval=Phanerozoic&envtype=marine&count=genera&time_reso=stage&vocab=pbdb https://w3id.org/delphi/resource/evidence/darwin1859-ch14-12--claim-test--dataset-2 http://www.w3.org/ns/prov#atLocation 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