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they were fetched with headless Chrome and checksummed) and writes derived tables (committed). analysis.py computes, per Nautilus specimen, the median of dm[i]/dm[i-8] over the 45-degree stations (one revolution; all stations are post-hatching, first dm 18-27 mm); per ammonoid species, the median of dm[n]/dm[n-1] over half-whorl stations with dm >= 5 mm; per gastropod specimen, the median of r[k+2]/r[k] where r is the perpendicular distance of each digitised aperture's centroid from the coiling axis (apertures 180 deg apart; replicate digitisations pooled), then the median per species. Each r is converted to alpha = arccot(ln r / 2 pi) and the pre-registered band fractions are evaluated." } ], "@type": [ "https://w3id.org/delphi/ontology/Assessment" ], "http://www.w3.org/2000/01/rdf-schema#comment": [ { "@value": "Measured: 80.48 degrees, median constant angle of Nautilus pompilius (r = 2.87 per revolution) (n = 93, Nautilus IQR 80.27-80.68 deg (r 2.81-2.94); population medians 80.4 (Indonesia), 80.4 (Malaysia), 80.7 (Philippines)). Interpretation: Thompson defines the constant angle through the per-whorl ratio of radii or whorl breadths, r = e^(2 pi cot alpha), and reads the angle off that ratio; the test therefore measures r and converts it with his own formula rather than fitting tangent angles to outlines. Modern 'whorl expansion rate' (Korn: WER = (dm1/dm2)^2 across half a whorl; Raup: W per revolution) is the same quantity for a planispiral shell. 'Ordinary ammonitoid shells' is operationalized as the species in a large published cross-section dataset (Devonian-Jurassic), 'typically spiral gastropods' as the 25 fossil and modern helicospiral species measured by Collins et al. 2021; neither sample was chosen by the tester. Deviation from the pre-registration: Collins et al. publish no per-revolution W (their W_e is a fitted rate of aperture-area increase), so r was computed directly from their raw digitised apertures (distance of the aperture centroid from the coiling axis at 180-degree steps, r = r[k+2]/r[k]), which is Thompson's own quantity; Nautilus r was likewise taken directly as dm[i]/dm[i-8] over the 45-degree stations rather than through WER." } ], "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "Claim test of thompson1917-ch11-10: refutes, confidence 0.6" } ], "http://www.w3.org/2000/01/rdf-schema#seeAlso": [ { "@id": "https://github.com/fractastical/delphisci/blob/bf2af6ee0a84e23ffa6414ad7a0a50a8c276506e/test-data/claim-tests/thompson-growth-form/thompson1917-ch11-10/result.json" } ], "http://www.w3.org/ns/prov#wasAttributedTo": [ { "@id": "https://w3id.org/delphi/resource/agent/delphisci-claim-tester-claude-fable-5-1-thinking-high" } ], "https://w3id.org/delphi/ontology/admissibleDatasets": [ { "@value": "Planned datasets: tajika-2018-nautilus-pompilius-dryad-4cb86, walton-korn-2018-ammonoid-ontogeny-dryad-c17p8, collins-2021-helicospiral-gastropods-dryad-p5hqbzknw" } ], "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": "Pre-registered. 'refutes' if the Nautilus median alpha is outside [76, 84] deg, or if in either the ammonoid or the gastropod sample fewer than 40% of species fall in [80, 85] deg, or more than 20% fall below 80 deg. Anything between the pass and fail thresholds is 'mixed'. If the gastropod expansion parameter cannot be mapped to a per-revolution ratio from the dataset's documentation, part (c) is reported as not operationalizable and the verdict rests on (a) and (b) with a caveat." } ], "https://w3id.org/delphi/ontology/evidenceAgainst": [ { "@value": "Per-species r is a median over ontogeny; whorl expansion drifts during growth (see thompson1917-ch11-08), so an adult-only or juvenile-only convention would move alpha by a fraction of a degree." }, { "@value": "Sensitivity (not pre-registered, computed in a side check): the ammonoid in-band fraction is 0.26 with no size threshold, 0.32 at dm >= 5 mm (pre-registered), 0.29 at dm >= 10 mm, 0.26 at dm >= 20 mm, and 0.33 using only each species' last measured revolution; the median alpha stays at 85.5-85.6 deg and the below-80 fraction at 0 throughout, so the verdict does not depend on the threshold." }, { "@value": "The Nautilus part of the claim ('in the neighbourhood of 80 deg', 'about three times') is confirmed closely: median 80.5 deg, r = 2.87, with very low scatter across 93 specimens and three populations." }, { "@value": "The ammonoid sample (Walton & Korn 2018) was assembled to study pachyconic and globular conchs and is 82% Palaeozoic; globular Palaeozoic goniatites have low expansion rates, so it is probably biased towards high alpha relative to the Mesozoic ammonites Thompson likely had in mind (the 3 Jurassic and 6 of 11 Permian species are in band)." }, { "@value": "The gastropod sample is 26 species dominated by four struthiolariid/turritellid species from New Zealand and Australia; species were weighted equally, but it is not a random sample of 'typically spiral' gastropods. r for gastropods was measured on digitised apertures in a single sectioned plane (centroid distance from the axis), which is noisier than CT-based cephalopod diameters." }, { "@value": "The verdict follows the pre-registered rule, which fails because only 32% of ammonoid species (threshold 40%) and 46% of gastropod species fall inside 80-85 deg. The failure is one-sided: no ammonoid and no gastropod species, and only 5% of Nautilus, fall below 80 deg, so 'very seldom less than 80 deg' is strongly supported; the typical ammonoid and gastropod sits at 85-86 deg (r 1.5-1.7), just above Thompson's upper bound rather than inside it." } ], "https://w3id.org/delphi/ontology/expectedObservation": [ { "@value": "Pre-registered. (a) Nautilus pompilius: per specimen, the median whorl expansion rate WER (Korn's definition, (dm1/dm2)^2 over half a whorl, which equals the per-revolution diameter ratio r) over all measured post-embryonic stages; the median across specimens, converted to alpha, must lie in [78, 82] deg (r in 2.6-3.5). (b) Ammonoids: per species, the median WER over measured stages with conch diameter >= 5 mm (excluding the embryonic ammonitella), converted to alpha; at least 50% of species must have alpha in [80, 85] deg and at most 10% alpha < 80 deg. (c) Gastropods: per specimen (then averaged per species), the fitted per-revolution whorl expansion rate W from the Collins et al. 2021 helicospiral fits, converted to alpha the same way; at least 50% of species in [80, 85] deg and at most 10% below 80 deg. All three of (a), (b), (c) must hold for 'supports'." } ], "https://w3id.org/delphi/ontology/failCriterion": [ { "@value": "Pre-registered. 'refutes' if the Nautilus median alpha is outside [76, 84] deg, or if in either the ammonoid or the gastropod sample fewer than 40% of species fall in [80, 85] deg, or more than 20% fall below 80 deg. Anything between the pass and fail thresholds is 'mixed'. If the gastropod expansion parameter cannot be mapped to a per-revolution ratio from the dataset's documentation, part (c) is reported as not operationalizable and the verdict rests on (a) and (b) with a caveat." } ], "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/thompson1917-ch11-10--claim-test--dataset-1" }, { "@id": "https://w3id.org/delphi/resource/evidence/thompson1917-ch11-10--claim-test--dataset-2" }, { "@id": "https://w3id.org/delphi/resource/evidence/thompson1917-ch11-10--claim-test--dataset-3" } ], "https://w3id.org/delphi/ontology/hasVerdict": [ { "@value": "refutes" } ], "https://w3id.org/delphi/ontology/hypothesis": [ { "@value": "If whorl breadths (equivalently conch diameters one revolution apart) expand by a factor r per whorl, the constant angle is alpha = arccot(ln r / 2 pi) (Thompson's own table: r = 1.5 -> 86.3 deg, 2.0 -> 83.7 deg, 2.5 -> 81.7 deg, 3.0 -> 80.1 deg, 3.5 -> 78.7 deg). The claim then predicts: Nautilus r about 3, alpha about 80 deg; for ordinary ammonoids and typically spiral gastropods alpha is usually between 80 and 85 deg (r between 1.72 and 3.00) and very seldom below 80 deg (r > 3.00)." } ], "https://w3id.org/delphi/ontology/inferenceMethod": [ { "@value": "fetch.py obtains the files (Dryad downloads sit behind a browser proof-of-work challenge; they were fetched with headless Chrome and checksummed) and writes derived tables (committed). analysis.py computes, per Nautilus specimen, the median of dm[i]/dm[i-8] over the 45-degree stations (one revolution; all stations are post-hatching, first dm 18-27 mm); per ammonoid species, the median of dm[n]/dm[n-1] over half-whorl stations with dm >= 5 mm; per gastropod specimen, the median of r[k+2]/r[k] where r is the perpendicular distance of each digitised aperture's centroid from the coiling axis (apertures 180 deg apart; replicate digitisations pooled), then the median per species. Each r is converted to alpha = arccot(ln r / 2 pi) and the pre-registered band fractions are evaluated." } ], "https://w3id.org/delphi/ontology/passCriterion": [ { "@value": "Pre-registered. (a) Nautilus pompilius: per specimen, the median whorl expansion rate WER (Korn's definition, (dm1/dm2)^2 over half a whorl, which equals the per-revolution diameter ratio r) over all measured post-embryonic stages; the median across specimens, converted to alpha, must lie in [78, 82] deg (r in 2.6-3.5). (b) Ammonoids: per species, the median WER over measured stages with conch diameter >= 5 mm (excluding the embryonic ammonitella), converted to alpha; at least 50% of species must have alpha in [80, 85] deg and at most 10% alpha < 80 deg. (c) Gastropods: per specimen (then averaged per species), the fitted per-revolution whorl expansion rate W from the Collins et al. 2021 helicospiral fits, converted to alpha the same way; at least 50% of species in [80, 85] deg and at most 10% below 80 deg. All three of (a), (b), (c) must hold for 'supports'." } ], "https://w3id.org/delphi/ontology/preregistered": [ { "@value": "false", "@type": "http://www.w3.org/2001/XMLSchema#boolean" } ] }, { "@id": "https://w3id.org/delphi/resource/evidence/thompson1917-ch11-10--claim-test--dataset-1", "http://purl.org/dc/terms/description": [ { "@value": "Nautilus per-revolution expansion ratio" } ], "http://purl.org/dc/terms/license": [ { "@value": "CC0 1.0" } ], "@type": [ "https://w3id.org/delphi/ontology/EvidenceItem" ], "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "Dataset: Data from: Intraspecific variation in cephalopod conchs changes during ontogeny: perspectives from three-dimensional morphometry of Nautilus pompilius" } ], "http://www.w3.org/ns/prov#atLocation": [ { "@id": "https://datadryad.org/downloads/file_stream/75500" } ], "http://www.w3.org/ns/prov#wasDerivedFrom": [ { "@id": "https://datadryad.org/dataset/doi:10.5061/dryad.4cb86" } ], "https://w3id.org/delphi/ontology/hasChecksum": [ { "@value": "sha256:db9ee691bc10f3c03ce78340f61c5b6f2fd98f9c3b1a1f3e194b8353aee4bb9f" } ] }, { "@id": "https://w3id.org/delphi/resource/evidence/thompson1917-ch11-10--claim-test--dataset-2", "http://purl.org/dc/terms/description": [ { "@value": "ammonoid per-revolution expansion ratio per species" } ], "http://purl.org/dc/terms/license": [ { "@value": "CC0 1.0" } ], "@type": [ "https://w3id.org/delphi/ontology/EvidenceItem" ], "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "Dataset: Data from: Iterative ontogenetic development of ammonoid conch shapes from the Devonian through to the Jurassic (Walton & Korn)" } ], "http://www.w3.org/ns/prov#atLocation": [ { "@id": "https://zenodo.org/api/records/4937032/files/Ontogenetic_Conch_Parameter_Data.xlsx/content" } ], "http://www.w3.org/ns/prov#wasDerivedFrom": [ { "@id": "https://datadryad.org/dataset/doi:10.5061/dryad.c17p8" } ], "https://w3id.org/delphi/ontology/hasChecksum": [ { "@value": "sha256:fbe2012f1d420ef7b292141ae0ed0ea8d046c4c15303663565dc72e0727ebe40" } ] }, { "@id": "https://w3id.org/delphi/resource/evidence/thompson1917-ch11-10--claim-test--dataset-3", "http://purl.org/dc/terms/description": [ { "@value": "gastropod per-revolution expansion ratio of the aperture centroid's distance from the coiling axis, per species" } ], "http://purl.org/dc/terms/license": [ { "@value": "CC0 1.0" } ], "@type": [ "https://w3id.org/delphi/ontology/EvidenceItem" ], "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "Dataset: Data associated with: Going round the twist - An empirical analysis of shell coiling in helicospiral gastropods" } ], "http://www.w3.org/ns/prov#atLocation": [ { "@id": "https://datadryad.org/downloads/file_stream/547236" }, { "@id": "https://datadryad.org/downloads/file_stream/547239" } ], "http://www.w3.org/ns/prov#wasDerivedFrom": [ { "@id": "https://datadryad.org/dataset/doi:10.5061/dryad.p5hqbzknw" } ], "https://w3id.org/delphi/ontology/hasChecksum": [ { "@value": "sha256:a034e43eb95a22dffe10b1f8d0e83ab43b0e592e8e1d646513da7ab8dfbc7a39" }, { "@value": "sha256:edab9e356820a43984bcf8130359ec29f7e6c00ca3995292fcd922ba2cb3a2a9" } ] }, { "@id": "https://w3id.org/delphi/resource/claim/thompson1917-ch11-10", "https://w3id.org/delphi/ontology/hasAssessment": [ { "@id": "https://w3id.org/delphi/resource/assessment/thompson1917-ch11-10--claim-test" } ] } ] } ]