[ { "@id": "https://w3id.org/np/RATofTrC9VvYtdd1NynYc1FSWYT7Gug6W5y_Z0aYu1dD8/pubinfo", "@graph": [ { "@id": "https://w3id.org/np/RATofTrC9VvYtdd1NynYc1FSWYT7Gug6W5y_Z0aYu1dD8", "http://purl.org/dc/terms/created": [ { "@value": "2026-11-08T16:24:31.821Z", "@type": "http://www.w3.org/2001/XMLSchema#dateTime" } ], "http://purl.org/dc/terms/creator": [ { "@id": "https://orcid.org/0009-0007-4948-9192" } ], "http://purl.org/dc/terms/license": [ { "@id": "https://creativecommons.org/licenses/by/4.0/" } ], "http://purl.org/nanopub/x/hasNanopubType": [ { "@id": "https://w3id.org/delphi/ontology/Assessment" } ], "http://purl.org/nanopub/x/introduces": [ { "@id": "https://w3id.org/delphi/resource/assessment/darwin1859-ch10-08--claim-test" } ], "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "Claim test of darwin1859-ch10-08: supports, confidence 0.6" } ], "https://w3id.org/delphi/ontology/domain": [ { "@id": "https://w3id.org/delphi/resource/domain/darwin-origin-1859" } ] }, { "@id": "https://w3id.org/np/RATofTrC9VvYtdd1NynYc1FSWYT7Gug6W5y_Z0aYu1dD8/sig", "http://purl.org/nanopub/x/hasAlgorithm": [ { "@value": "RSA" } ], "http://purl.org/nanopub/x/hasPublicKey": [ { "@value": "MIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEAyFHtPB6p0mCjDozxlOY9CmO3nBm7Te3jFbXyLmM+G1tGe47Da0jYIbhkl9Oo1ZjxmCa3LCwlEqK8gj6hEIcL4ahW30JXh9HycfKVk1bugkzMEV15tJdTzAU3sGMFnbNsn43xY2LFLy45tApkRm5byEiM7oRRrooIdwoQKnP4Wzq/bfAoJ9qvW+MGkelyOTd1jbSt+KfmT7xKmDfWzAHddUlWwMX2QJOLxDaffOteTop6ZRgPiNmPJKA/S62Gac9XtSYT3oDkZ6/nr5cxxNLpOyxTf5FPISiCe11xYO/unYjY+mwnOfA8yhJIyx1l0O9I0vpOpn+E5TvyHJV+oSTrvwIDAQAB" } ], "http://purl.org/nanopub/x/hasSignature": [ { "@value": "TdOWiFNAxnUPom00PImhcS985GaJ/ijMOwKTL3zShikJWv/CdpmwbqOufaO/n+cNF58KtNiXKDO8d165IPH4BZkYvRLMW0G+1PN4/18gRVI/fcZ+lMlVZb1+jiXfzp3wAYh5zsIf6MV+nxgOJLcCfylkQimTbAKaU/qTFlA7WD2fpFg0ndDjcSjsq+nrk74qBJPNYcDUdmevinV+0jdEduti1hnRgpdoF4lPz3rI5n295cSC+9KLQ4V7rumW+dZX2AXgJ2iHmrCed2FaaOD0B5MdXx76muw++FIYPmmnUxdbS7PifFwA5/6y3CFivhDTp/S+4w9YYOElV0j3Ni8Mog==" } ], "http://purl.org/nanopub/x/hasSignatureTarget": [ { "@id": "https://w3id.org/np/RATofTrC9VvYtdd1NynYc1FSWYT7Gug6W5y_Z0aYu1dD8" } ], "http://purl.org/nanopub/x/signedBy": [ { "@id": "https://orcid.org/0009-0007-4948-9192" } ] } ] }, { "@id": "https://w3id.org/np/RATofTrC9VvYtdd1NynYc1FSWYT7Gug6W5y_Z0aYu1dD8/assertion", "@graph": [ { "@id": "https://w3id.org/delphi/resource/assessment/darwin1859-ch10-08--claim-test", "http://purl.org/dc/terms/description": [ { "@value": "All 79,166 accepted Metazoa genera were fetched from the PBDB taxa API; genera without ages or family were dropped. A family was taken as extinct when none of its genera is flagged extant and none has a last appearance at 0 Ma. Each genus ranges through from firstapp_max_ma to lastapp_min_ma; genus diversity D(t) was counted on a 0.1 Myr grid between the family's first origin and final extinction, and the centre of gravity CG of D over relative time (0 = origin, 1 = extinction) was computed for the 1,866 extinct families with >= 5 genera and >= 10 Myr duration. The median CG, the share below 0.5 and a one-sided Wilcoxon signed-rank test of CG - 0.5 were compared with the pre-registered thresholds; families ending within 2 Myr of the five big mass extinctions and families by era of origin are reported separately." } ], "@type": [ "https://w3id.org/delphi/ontology/Assessment" ], "http://www.w3.org/2000/01/rdf-schema#comment": [ { "@value": "Measured: 0.477 median centre of gravity of range-through genus diversity of extinct animal families (0 = origin, 1 = extinction; < 0.5 = slow decline) (n = 1866, Wilcoxon one-sided p (CG < 0.5) = 1.06e-18; IQR 0.409-0.547). Interpretation: Darwin's 'complete extinction of the species of a group is generally a slower process than their production' is read through clade shape (Gould et al. 1977): if production is fast and extermination slow, the diversity trajectory rises steeply and tapers, giving a centre of gravity in the first half of the clade's duration. Groups are extinct animal families as classified in PBDB (Darwin's 'groups' of genera and families); diversity is counted in genera, because Darwin's species are rarely resolved in the fossil record. Range-through ranges from database first and last appearances are used without sampling correction; the Signor-Lipps effect pulls last appearances earlier and can shorten or lengthen the tail, so the test measures the record as compiled." } ], "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "Claim test of darwin1859-ch10-08: supports, confidence 0.6" } ], "http://www.w3.org/2000/01/rdf-schema#seeAlso": [ { "@id": "https://github.com/fractastical/delphisci/blob/bf2af6ee0a84e23ffa6414ad7a0a50a8c276506e/test-data/claim-tests/darwin-origin/darwin1859-ch10-08/result.json" } ], "http://www.w3.org/ns/prov#wasAttributedTo": [ { "@id": "https://w3id.org/delphi/resource/agent/delphisci-claim-tester-claude-opus-5-5" } ], "https://w3id.org/delphi/ontology/admissibleDatasets": [ { "@value": "A community fossil occurrence database giving first and last appearance ages for genera with family classification, compiled independently of Darwin; open access; at least 100 extinct families with five or more genera." } ], "https://w3id.org/delphi/ontology/assessmentType": [ { "@value": "claim-test/0.1.0" } ], "https://w3id.org/delphi/ontology/dataKind": [ { "@value": "biological" } ], "https://w3id.org/delphi/ontology/disconfirmingObservation": [ { "@value": "Extinct families are symmetric or top-heavy (median centre of gravity at or above 0.5)." } ], "https://w3id.org/delphi/ontology/evidenceAgainst": [ { "@value": "As Darwin himself noted for ammonites, families ending at the big five mass extinctions are the exception: their median CG is 0.523 and only 41% are below 0.5 (n = 359), against 0.468 and 64% for families ending at other times (n = 1,507)." }, { "@value": "Families are PBDB's classification, which includes paraphyletic families; Darwin's 'group' could also be read at the order or class level, which was not tested." }, { "@value": "Genus first and last appearance ages are taken at the outer bounds of the first and last intervals (firstapp_max_ma, lastapp_min_ma), which lengthens every genus range by up to one interval at each end symmetrically." }, { "@value": "No sampling correction was applied. Range-through ranges from database first and last appearances are affected by the Signor-Lipps effect (last appearances drawn earlier); the 'pull of the Recent' does not apply because only extinct families are used. The grok assessor warned that sampling bias can manufacture slow-looking declines; the opposite bias (late-Lazarus truncation) also exists, so the direction of net bias is not known." }, { "@value": "PBDB is a live database; re-running reproduces the method but counts drift as records are added." }, { "@value": "The asymmetry is real but small: median CG 0.477 (IQR 0.41-0.55), 59% of families below 0.5. It holds in every large phylum (Chordata 0.485, Arthropoda 0.473, Mollusca 0.462, Brachiopoda 0.489, Echinodermata 0.456, Cnidaria 0.473) and in Paleozoic-, Mesozoic- and Cenozoic-originating families (0.477, 0.482, 0.475). The test passes the pre-registered thresholds, but 'generally a slower process' is supported only as a modest tendency, not a strong rule." } ], "https://w3id.org/delphi/ontology/expectedObservation": [ { "@value": "Most extinct families have a diversity centre of gravity below 0.5 of their duration (early peak, longer decline)." } ], "https://w3id.org/delphi/ontology/failCriterion": [ { "@value": "Pre-registered: REFUTES if the median CG >= 0.5. Any other outcome is MIXED. Fewer than 100 qualifying families: inconclusive (underpowered); PBDB API unreachable: inconclusive (data-unavailable). Descriptive secondary statistics: median CG and share below 0.5 for families ending at the five big mass extinctions (end-Ordovician 443.8, Late Devonian 372.2, end-Permian 251.9, end-Triassic 201.4, end-Cretaceous 66.0 Ma, within 2 Myr) versus all others, and for Paleozoic-, Mesozoic- and Cenozoic-originating families." } ], "https://w3id.org/delphi/ontology/hasConfidence": [ { "@value": "0.6", "@type": "http://www.w3.org/2001/XMLSchema#double" } ], "https://w3id.org/delphi/ontology/hasEvidence": [ { "@id": "https://w3id.org/delphi/resource/evidence/darwin1859-ch10-08--claim-test--dataset-1" } ], "https://w3id.org/delphi/ontology/hasVerdict": [ { "@value": "supports" } ], "https://w3id.org/delphi/ontology/hypothesis": [ { "@value": "Extinct animal families in the fossil record are bottom-heavy: their genus diversity peaks early in their history and tapers over a longer decline, so the centre of gravity of the diversity trajectory lies in the first half of the family's duration." } ], "https://w3id.org/delphi/ontology/inferenceMethod": [ { "@value": "Range-through genus diversity per family on a 0.1 Myr grid; centre of gravity relative to family duration; one-sided Wilcoxon signed-rank test against 0.5 with p < 0.01, median < 0.5 and share below 0.5 >= 55% for support; median >= 0.5 refutes." } ], "https://w3id.org/delphi/ontology/passCriterion": [ { "@value": "Pre-registered: from the Paleobiology Database taxa API, all accepted animal (Metazoa) genera with first and last appearance ages and family assignment. A family is extinct if none of its genera is flagged extant and every genus has lastapp_min_ma > 0. Each genus ranges from firstapp_max_ma to lastapp_min_ma; the family's range is the union. Diversity D(t) = number of genera ranging through t on a 0.1 Myr grid. Centre of gravity CG = sum(D(t) * tau(t)) / sum(D(t)), tau = (family origin - t) / (family origin - family end), so CG < 0.5 means diversity is concentrated early and decline is slower than rise. Families qualify with >= 5 genera and duration >= 10 Myr. SUPPORTS if the median CG < 0.5, the one-sided Wilcoxon signed-rank test of CG - 0.5 < 0 has p < 0.01, and at least 55% of families have CG < 0.5." } ], "https://w3id.org/delphi/ontology/preregistered": [ { "@value": "false", "@type": "http://www.w3.org/2001/XMLSchema#boolean" } ] }, { "@id": "https://w3id.org/delphi/resource/evidence/darwin1859-ch10-08--claim-test--dataset-1", "http://purl.org/dc/terms/description": [ { "@value": "first and last appearance ages, extant flag and family of 79,166 accepted animal genera" } ], "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: Paleobiology Database data service 1.2, taxa/list: accepted Metazoa genera with first and last appearance ages (show=app) and classification (show=class)" } ], "http://www.w3.org/ns/prov#atLocation": [ { "@id": "https://paleobiodb.org/data1.2/taxa/list.json?base_name=Metazoa&rank=genus&taxon_status=accepted&show=app,class" } ], "http://www.w3.org/ns/prov#wasDerivedFrom": [ { "@id": "https://paleobiodb.org/data1.2/taxa/list_doc.html" } ], "https://w3id.org/delphi/ontology/hasChecksum": [ { "@value": "sha256:3eccaf17a012bf19b9726439c5dd5005402291d7d30f32ccfa1a3955d706a70c" } ] }, { "@id": "https://w3id.org/delphi/resource/claim/darwin1859-ch10-08", "https://w3id.org/delphi/ontology/hasAssessment": [ { "@id": "https://w3id.org/delphi/resource/assessment/darwin1859-ch10-08--claim-test" } ] } ] }, { "@id": "https://w3id.org/np/RATofTrC9VvYtdd1NynYc1FSWYT7Gug6W5y_Z0aYu1dD8/Head", "@graph": [ { "@id": "https://w3id.org/np/RATofTrC9VvYtdd1NynYc1FSWYT7Gug6W5y_Z0aYu1dD8", "http://www.nanopub.org/nschema#hasAssertion": [ { "@id": "https://w3id.org/np/RATofTrC9VvYtdd1NynYc1FSWYT7Gug6W5y_Z0aYu1dD8/assertion" } ], "http://www.nanopub.org/nschema#hasProvenance": [ { "@id": "https://w3id.org/np/RATofTrC9VvYtdd1NynYc1FSWYT7Gug6W5y_Z0aYu1dD8/provenance" } ], "http://www.nanopub.org/nschema#hasPublicationInfo": [ { "@id": "https://w3id.org/np/RATofTrC9VvYtdd1NynYc1FSWYT7Gug6W5y_Z0aYu1dD8/pubinfo" } ], "@type": [ "http://www.nanopub.org/nschema#Nanopublication" ] } ] }, { "@id": "https://w3id.org/np/RATofTrC9VvYtdd1NynYc1FSWYT7Gug6W5y_Z0aYu1dD8/provenance", "@graph": [ { "@id": "https://w3id.org/delphi/resource/agent/delphisci-claim-tester-claude-opus-5-5", "@type": [ "http://www.w3.org/ns/prov#SoftwareAgent" ], "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "delphisci claim tester (claude-opus-5.5; cursor local subagent)" } ], "http://www.w3.org/ns/prov#actedOnBehalfOf": [ { "@id": "https://orcid.org/0009-0007-4948-9192" } ], "https://w3id.org/delphi/ontology/usesModel": [ { "@id": "https://w3id.org/delphi/resource/model/claude-opus-5-5" } ] }, { "@id": "https://w3id.org/delphi/resource/model/claude-opus-5-5", "http://purl.org/dc/terms/identifier": [ { "@value": "claude-opus-5.5" } ], "@type": [ "https://w3id.org/delphi/ontology/LanguageModel" ] }, { "@id": "https://w3id.org/np/RATofTrC9VvYtdd1NynYc1FSWYT7Gug6W5y_Z0aYu1dD8/assertion", "http://www.w3.org/ns/prov#wasAttributedTo": [ { "@id": "https://w3id.org/delphi/resource/agent/delphisci-claim-tester-claude-opus-5-5" } ], "http://www.w3.org/ns/prov#wasDerivedFrom": [ { "@id": "https://github.com/fractastical/delphisci/blob/bf2af6ee0a84e23ffa6414ad7a0a50a8c276506e/test-data/claim-tests/darwin-origin/darwin1859-ch10-08/result.json" } ], "http://www.w3.org/ns/prov#wasGeneratedBy": [ { "@id": "https://w3id.org/np/RATofTrC9VvYtdd1NynYc1FSWYT7Gug6W5y_Z0aYu1dD8/test" } ] }, { "@id": "https://w3id.org/np/RATofTrC9VvYtdd1NynYc1FSWYT7Gug6W5y_Z0aYu1dD8/test", "@type": [ "http://www.w3.org/ns/prov#Activity" ], "http://www.w3.org/ns/prov#qualifiedAssociation": [ { "@id": "https://w3id.org/np/RATofTrC9VvYtdd1NynYc1FSWYT7Gug6W5y_Z0aYu1dD8/plan" } ], "http://www.w3.org/ns/prov#wasAssociatedWith": [ { "@id": "https://w3id.org/delphi/resource/agent/delphisci-claim-tester-claude-opus-5-5" } ] }, { "@id": "https://w3id.org/np/RATofTrC9VvYtdd1NynYc1FSWYT7Gug6W5y_Z0aYu1dD8/plan", "http://www.w3.org/ns/prov#hadPlan": [ { "@id": "https://github.com/fractastical/delphisci/blob/bf2af6ee0a84e23ffa6414ad7a0a50a8c276506e/test-data/claim-tests/README.md" } ] } ] } ]