[ { "@id": "https://w3id.org/np/RAPg-NKn3D_FPXOZ4hGMTcAStdqeS75fULzMyStf72nB8/assertion", "@graph": [ { "@id": "https://w3id.org/delphi/resource/assessment/darwin1859-ch09-07--claim-test", "http://purl.org/dc/terms/description": [ { "@value": "International Phanerozoic stages were taken from Macrostrat (int_type age, timescale 'international ages'). Each unit's max_thick was divided equally across the stages it overlaps, and the median of that thickness was computed before the fossil table was joined. PBDB occs/diversity then supplied marine animal genera by stage. The two youngest stages were dropped. Foote per-capita origination and extinction were residualized on log10 occurrences. One-sided Mann-Whitney tests compared the groups in the pre-registered directions. No subsample was taken." } ], "@type": [ "https://w3id.org/delphi/ontology/Assessment" ], "http://www.w3.org/2000/01/rdf-schema#comment": [ { "@value": "Measured: 0.560721 one-sided p that residual extinction is higher in deposit-rich stages (n = 95, median residual extinction deposit-rich -0.0190 vs deposit-poor -0.0202; group sizes 50 and 45). Interpretation: Darwin's elevation is read as stages that preserved little sedimentary rock, and his subsidence as stages that preserved a lot. That is a proxy from rock thickness, not a measured uplift or subsidence field: no such label was found, and sea level is not used. 'New varieties and species' is read as the Foote per-capita origination rate of marine animal genera. 'Much extinction' is the Foote per-capita extinction rate. 'Fossil-rich deposits' is the PBDB occurrence count in the stage. The claim's scope is coastal and shallow-marine faunas; the table is all marine animal genera, which is wider than the shore. The statement that transitional forms are seldom recorded is not tested. Preserved thickness and fossil counts share a sampling process, so clause (1) is the preservation association and clauses (2) and (3) are the biological rates after residualizing on occurrence count. A pass would still be a global stage-level association, not a demonstration that uplift causes speciation." } ], "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "Claim test of darwin1859-ch09-07: mixed, confidence 0.55" } ], "http://www.w3.org/2000/01/rdf-schema#seeAlso": [ { "@id": "https://github.com/fractastical/delphisci/blob/bf2af6ee0a84e23ffa6414ad7a0a50a8c276506e/test-data/claim-tests/darwin-origin/darwin1859-ch09-07/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": "A public stage-level marine fossil diversity table with boundary-crosser counts and occurrence counts, joined to a public sedimentary-thickness series on the same stage names. The thickness series must not be derived from the fossil rates. A dataset that already labels uplift versus subsidence would be admissible but none was located. Single regions and single clades are narrower than this test and are not substituted after the fact." } ], "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": "Residual origination is higher where rock is thick and residual extinction is higher where rock is thin, both at one-sided p < 0.05." } ], "https://w3id.org/delphi/ontology/evidenceAgainst": [ { "@value": "Deposit-rich and deposit-poor are a median split of preserved Macrostrat thickness, not a measured uplift or subsidence field." }, { "@value": "Fossil occurrence counts and preserved thickness share a sampling process. The occurrence comparison is that preservation association. The rate tests use residuals after log10 occurrence count." }, { "@value": "Macrostrat columns are not a balanced global sample. Project ids and names are reported with the rock series." }, { "@value": "Marine animal genera are wider than Darwin's coastal and shallow-marine faunas. Genera stand in for varieties and species." }, { "@value": "Of 35481 Macrostrat units, 24141 (68%) are project 1 (North America)." }, { "@value": "The short unit records have no environment field, so the thickness sum is all sedimentary units, not marine units only." }, { "@value": "The two stages closest to the present were dropped before the rates were compared, because boundary crossers there meet the Recent." }, { "@value": "Transitional forms were not counted." } ], "https://w3id.org/delphi/ontology/expectedObservation": [ { "@value": "Deposit-rich stages have more occurrences and higher residual extinction rates; deposit-poor stages have higher residual origination rates." } ], "https://w3id.org/delphi/ontology/failCriterion": [ { "@value": "Pre-registered. REFUTES if both rate tests are significant (one-sided p < 0.05) in the opposite direction: residual origination higher in deposit-rich stages and residual extinction higher in deposit-poor stages. Any other completed comparison is mixed. Inconclusive if the marine diversity table or the Macrostrat thickness series cannot be fetched, if thickness or the Foote columns are absent, if fewer than 40 stages match by name, or if either group has fewer than 15 analysed stages (underpowered)." } ], "https://w3id.org/delphi/ontology/hasConfidence": [ { "@value": "0.55", "@type": "http://www.w3.org/2001/XMLSchema#double" } ], "https://w3id.org/delphi/ontology/hasEvidence": [ { "@id": "https://w3id.org/delphi/resource/evidence/darwin1859-ch09-07--claim-test--dataset-1" }, { "@id": "https://w3id.org/delphi/resource/evidence/darwin1859-ch09-07--claim-test--dataset-2" } ], "https://w3id.org/delphi/ontology/hasVerdict": [ { "@value": "mixed" } ], "https://w3id.org/delphi/ontology/hypothesis": [ { "@value": "Stages with more preserved sedimentary rock (the subsidence proxy) have more fossil occurrences and higher per-capita extinction, and stages with less preserved rock (the elevation proxy) have higher per-capita origination, after a sampling control on the rates." } ], "https://w3id.org/delphi/ontology/inferenceMethod": [ { "@value": "Median split of allocated Macrostrat max_thick (a unit's thickness divided equally across the international stages it overlaps). One-sided Mann-Whitney on occurrence counts and on residuals of Foote rates given log10 occurrences. Threshold p < 0.05. All matched stages except the two youngest and stages with X_bt = 0 or non-positive duration." } ], "https://w3id.org/delphi/ontology/passCriterion": [ { "@value": "Pre-registered. The uplift/subsidence label is built only from Macrostrat rock thickness, before any origination or extinction rate is computed. A stage is deposit-rich (subsidence proxy) if its allocated sedimentary thickness is greater than or equal to the median thickness of Phanerozoic international stages, and deposit-poor (elevation proxy) otherwise. Median is computed on the rock series alone. Marine animal genera, PBDB occs/diversity, stage resolution, envtype=marine. Drop the two stages closest to the present. Foote per-capita rates: p = ln((X_bt+X_Ft)/X_bt)/dt and q = ln((X_bt+X_bL)/X_bt)/dt, only where X_bt > 0 and dt > 0. Sampling control: residuals of p and of q from an OLS regression on log10(occurrence count), fit on the analysed stages, group label not in the regression. SUPPORTS if all three one-sided Mann-Whitney tests have p < 0.05 in the predicted direction: (1) occurrence count higher in deposit-rich stages; (2) residual extinction rate higher in deposit-rich stages; (3) residual origination rate higher in deposit-poor stages. No subsample." } ], "https://w3id.org/delphi/ontology/preregistered": [ { "@value": "false", "@type": "http://www.w3.org/2001/XMLSchema#boolean" } ] }, { "@id": "https://w3id.org/delphi/resource/evidence/darwin1859-ch09-07--claim-test--dataset-1", "http://purl.org/dc/terms/description": [ { "@value": "preserved sedimentary thickness used as the elevation/subsidence proxy" } ], "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: Macrostrat API v2 intervals and units" } ], "http://www.w3.org/ns/prov#atLocation": [ { "@id": "https://macrostrat.org/api/v2/defs/intervals?format=json" }, { "@id": "https://macrostrat.org/api/v2/defs/projects?format=json" }, { "@id": "https://macrostrat.org/api/v2/units?response=short&format=json" } ], "http://www.w3.org/ns/prov#wasDerivedFrom": [ { "@id": "https://macrostrat.org/" } ], "https://w3id.org/delphi/ontology/hasChecksum": [ { "@value": "sha256:53d4962b0231a023ce5d81ef3641ff76b583f40dfed302fd80c239ec2e8b6033" }, { "@value": "sha256:8faeaf91a0f053520343d3fb86a50858ccd8780fc00146dda3b9a041184742a1" }, { "@value": "sha256:d7a0d9113e39dc27097e089aa028f6e2ac8ac8e187f613054fc83ea3f796c4ca" } ] }, { "@id": "https://w3id.org/delphi/resource/evidence/darwin1859-ch09-07--claim-test--dataset-2", "http://purl.org/dc/terms/description": [ { "@value": "stage-level boundary-crosser counts and occurrence counts" } ], "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: Paleobiology Database occs/diversity, marine Animalia genera by stage" } ], "http://www.w3.org/ns/prov#atLocation": [ { "@id": "https://paleobiodb.org/data1.2/occs/diversity.json?base_name=Animalia&interval=Phanerozoic&envtype=marine&count=genera&time_reso=stage&vocab=pbdb" } ], "http://www.w3.org/ns/prov#wasDerivedFrom": [ { "@id": "https://paleobiodb.org/" } ], "https://w3id.org/delphi/ontology/hasChecksum": [ { "@value": "sha256:ee5c0eb527fd0a8687987e292abef8f6a2038806eadbd7ca2dbed40838f81a1a" } ] }, { "@id": "https://w3id.org/delphi/resource/claim/darwin1859-ch09-07", "https://w3id.org/delphi/ontology/hasAssessment": [ { "@id": "https://w3id.org/delphi/resource/assessment/darwin1859-ch09-07--claim-test" } ] } ] }, { "@id": "https://w3id.org/np/RAPg-NKn3D_FPXOZ4hGMTcAStdqeS75fULzMyStf72nB8/pubinfo", "@graph": [ { "@id": "https://w3id.org/np/RAPg-NKn3D_FPXOZ4hGMTcAStdqeS75fULzMyStf72nB8", "http://purl.org/dc/terms/created": [ { "@value": "2026-11-08T16:24:31.817Z", "@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-ch09-07--claim-test" } ], "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "Claim test of darwin1859-ch09-07: mixed, confidence 0.55" } ], "https://w3id.org/delphi/ontology/domain": [ { "@id": "https://w3id.org/delphi/resource/domain/darwin-origin-1859" } ] }, { "@id": "https://w3id.org/np/RAPg-NKn3D_FPXOZ4hGMTcAStdqeS75fULzMyStf72nB8/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": "Jix6Sl2a9BrYfCSdZYguxgtDeqovgh5jXZ1UqNUMrlX78qQkgOBy4v07Ij9RuH2lmge4cNl0fms7nJcCwdDF/0657kzpX4IJZhSY14TSOtIHHvnp8kQB2JYUnGg560GbRAkdcir8ubUcqw85nheICjTQauHyI1c/zaZSIsT4Wu7WuzFQ7UZRvezh7S6mec7pyd2Z0BxNJvv8zRxckeYJk59d68ZDiRa7L5n1O/EyPMiEM5JFh8jKEyP/e7ugnIbiUm/LebXHzvuntYL86qAI+ISUjGi5W8yAJ81uE0iM3seckHNOS9AZ6Z1Cx+u1VhVgrYb8j48BXQPf/XUapJkUgg==" } ], "http://purl.org/nanopub/x/hasSignatureTarget": [ { "@id": "https://w3id.org/np/RAPg-NKn3D_FPXOZ4hGMTcAStdqeS75fULzMyStf72nB8" } ], "http://purl.org/nanopub/x/signedBy": [ { "@id": "https://orcid.org/0009-0007-4948-9192" } ] } ] }, { "@id": "https://w3id.org/np/RAPg-NKn3D_FPXOZ4hGMTcAStdqeS75fULzMyStf72nB8/provenance", "@graph": [ { "@id": "https://w3id.org/delphi/resource/agent/delphisci-claim-tester-grok-4-7", "@type": [ "http://www.w3.org/ns/prov#SoftwareAgent" ], "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "delphisci claim tester (grok-4.7; 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