https://w3id.org/np/RATofTrC9VvYtdd1NynYc1FSWYT7Gug6W5y_Z0aYu1dD8
.trig | .trig.txt | .jelly | .jelly.txt | .jsonld | .jsonld.txt | .nq | .nq.txt | .xml | .xml.txt
@prefix this: <https://w3id.org/np/RATofTrC9VvYtdd1NynYc1FSWYT7Gug6W5y_Z0aYu1dD8> .
@prefix sub: <https://w3id.org/np/RATofTrC9VvYtdd1NynYc1FSWYT7Gug6W5y_Z0aYu1dD8/> .
@prefix np: <http://www.nanopub.org/nschema#> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix prov: <http://www.w3.org/ns/prov#> .
@prefix npx: <http://purl.org/nanopub/x/> .
@prefix dc: <http://purl.org/dc/terms/> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
sub:Head {
this: a np:Nanopublication;
np:hasAssertion sub:assertion;
np:hasProvenance sub:provenance;
np:hasPublicationInfo sub:pubinfo .
}
sub:assertion {
<https://w3id.org/delphi/resource/assessment/darwin1859-ch10-08--claim-test> a <https://w3id.org/delphi/ontology/Assessment>;
dc:description "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.";
<http://www.w3.org/2000/01/rdf-schema#comment> "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> "Claim test of darwin1859-ch10-08: supports, confidence 0.6";
<http://www.w3.org/2000/01/rdf-schema#seeAlso> <https://github.com/fractastical/delphisci/blob/bf2af6ee0a84e23ffa6414ad7a0a50a8c276506e/test-data/claim-tests/darwin-origin/darwin1859-ch10-08/result.json>;
prov:wasAttributedTo <https://w3id.org/delphi/resource/agent/delphisci-claim-tester-claude-opus-5-5>;
<https://w3id.org/delphi/ontology/admissibleDatasets> "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> "claim-test/0.1.0";
<https://w3id.org/delphi/ontology/dataKind> "biological";
<https://w3id.org/delphi/ontology/disconfirmingObservation> "Extinct families are symmetric or top-heavy (median centre of gravity at or above 0.5).";
<https://w3id.org/delphi/ontology/evidenceAgainst> "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).",
"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.",
"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.",
"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.",
"PBDB is a live database; re-running reproduces the method but counts drift as records are added.",
"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> "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> "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> "0.6"^^xsd:double;
<https://w3id.org/delphi/ontology/hasEvidence> <https://w3id.org/delphi/resource/evidence/darwin1859-ch10-08--claim-test--dataset-1>;
<https://w3id.org/delphi/ontology/hasVerdict> "supports";
<https://w3id.org/delphi/ontology/hypothesis> "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> "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> "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> "false"^^xsd:boolean .
<https://w3id.org/delphi/resource/claim/darwin1859-ch10-08> <https://w3id.org/delphi/ontology/hasAssessment>
<https://w3id.org/delphi/resource/assessment/darwin1859-ch10-08--claim-test> .
<https://w3id.org/delphi/resource/evidence/darwin1859-ch10-08--claim-test--dataset-1>
a <https://w3id.org/delphi/ontology/EvidenceItem>;
dc:description "first and last appearance ages, extant flag and family of 79,166 accepted animal genera";
dc:license "CC BY 4.0";
<http://www.w3.org/2000/01/rdf-schema#label> "Dataset: Paleobiology Database data service 1.2, taxa/list: accepted Metazoa genera with first and last appearance ages (show=app) and classification (show=class)";
prov:atLocation <https://paleobiodb.org/data1.2/taxa/list.json?base_name=Metazoa&rank=genus&taxon_status=accepted&show=app,class>;
prov:wasDerivedFrom <https://paleobiodb.org/data1.2/taxa/list_doc.html>;
<https://w3id.org/delphi/ontology/hasChecksum> "sha256:3eccaf17a012bf19b9726439c5dd5005402291d7d30f32ccfa1a3955d706a70c" .
}
sub:provenance {
<https://w3id.org/delphi/resource/agent/delphisci-claim-tester-claude-opus-5-5> a
prov:SoftwareAgent;
<http://www.w3.org/2000/01/rdf-schema#label> "delphisci claim tester (claude-opus-5.5; cursor local subagent)";
prov:actedOnBehalfOf <https://orcid.org/0009-0007-4948-9192>;
<https://w3id.org/delphi/ontology/usesModel> <https://w3id.org/delphi/resource/model/claude-opus-5-5> .
<https://w3id.org/delphi/resource/model/claude-opus-5-5> a <https://w3id.org/delphi/ontology/LanguageModel>;
dc:identifier "claude-opus-5.5" .
sub:assertion prov:wasAttributedTo <https://w3id.org/delphi/resource/agent/delphisci-claim-tester-claude-opus-5-5>;
prov:wasDerivedFrom <https://github.com/fractastical/delphisci/blob/bf2af6ee0a84e23ffa6414ad7a0a50a8c276506e/test-data/claim-tests/darwin-origin/darwin1859-ch10-08/result.json>;
prov:wasGeneratedBy sub:test .
sub:plan prov:hadPlan <https://github.com/fractastical/delphisci/blob/bf2af6ee0a84e23ffa6414ad7a0a50a8c276506e/test-data/claim-tests/README.md> .
sub:test a prov:Activity;
prov:qualifiedAssociation sub:plan;
prov:wasAssociatedWith <https://w3id.org/delphi/resource/agent/delphisci-claim-tester-claude-opus-5-5> .
}
sub:pubinfo {
this: dc:created "2026-11-08T16:24:31.821Z"^^xsd:dateTime;
dc:creator <https://orcid.org/0009-0007-4948-9192>;
dc:license <https://creativecommons.org/licenses/by/4.0/>;
npx:hasNanopubType <https://w3id.org/delphi/ontology/Assessment>;
npx:introduces <https://w3id.org/delphi/resource/assessment/darwin1859-ch10-08--claim-test>;
<http://www.w3.org/2000/01/rdf-schema#label> "Claim test of darwin1859-ch10-08: supports, confidence 0.6";
<https://w3id.org/delphi/ontology/domain> <https://w3id.org/delphi/resource/domain/darwin-origin-1859> .
sub:sig npx:hasAlgorithm "RSA";
npx:hasPublicKey "MIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEAyFHtPB6p0mCjDozxlOY9CmO3nBm7Te3jFbXyLmM+G1tGe47Da0jYIbhkl9Oo1ZjxmCa3LCwlEqK8gj6hEIcL4ahW30JXh9HycfKVk1bugkzMEV15tJdTzAU3sGMFnbNsn43xY2LFLy45tApkRm5byEiM7oRRrooIdwoQKnP4Wzq/bfAoJ9qvW+MGkelyOTd1jbSt+KfmT7xKmDfWzAHddUlWwMX2QJOLxDaffOteTop6ZRgPiNmPJKA/S62Gac9XtSYT3oDkZ6/nr5cxxNLpOyxTf5FPISiCe11xYO/unYjY+mwnOfA8yhJIyx1l0O9I0vpOpn+E5TvyHJV+oSTrvwIDAQAB";
npx:hasSignature "TdOWiFNAxnUPom00PImhcS985GaJ/ijMOwKTL3zShikJWv/CdpmwbqOufaO/n+cNF58KtNiXKDO8d165IPH4BZkYvRLMW0G+1PN4/18gRVI/fcZ+lMlVZb1+jiXfzp3wAYh5zsIf6MV+nxgOJLcCfylkQimTbAKaU/qTFlA7WD2fpFg0ndDjcSjsq+nrk74qBJPNYcDUdmevinV+0jdEduti1hnRgpdoF4lPz3rI5n295cSC+9KLQ4V7rumW+dZX2AXgJ2iHmrCed2FaaOD0B5MdXx76muw++FIYPmmnUxdbS7PifFwA5/6y3CFivhDTp/S+4w9YYOElV0j3Ni8Mog==";
npx:hasSignatureTarget this:;
npx:signedBy <https://orcid.org/0009-0007-4948-9192> .
}