https://w3id.org/np/RASy5lY19_JNPIoAO2F4uf18jTNimzBoNiXxsgy7RabyI/Head https://w3id.org/np/RASy5lY19_JNPIoAO2F4uf18jTNimzBoNiXxsgy7RabyI http://www.nanopub.org/nschema#hasAssertion https://w3id.org/np/RASy5lY19_JNPIoAO2F4uf18jTNimzBoNiXxsgy7RabyI/assertion https://w3id.org/np/RASy5lY19_JNPIoAO2F4uf18jTNimzBoNiXxsgy7RabyI http://www.nanopub.org/nschema#hasProvenance https://w3id.org/np/RASy5lY19_JNPIoAO2F4uf18jTNimzBoNiXxsgy7RabyI/provenance https://w3id.org/np/RASy5lY19_JNPIoAO2F4uf18jTNimzBoNiXxsgy7RabyI http://www.nanopub.org/nschema#hasPublicationInfo https://w3id.org/np/RASy5lY19_JNPIoAO2F4uf18jTNimzBoNiXxsgy7RabyI/pubinfo https://w3id.org/np/RASy5lY19_JNPIoAO2F4uf18jTNimzBoNiXxsgy7RabyI http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://www.nanopub.org/nschema#Nanopublication https://w3id.org/np/RASy5lY19_JNPIoAO2F4uf18jTNimzBoNiXxsgy7RabyI/assertion https://w3id.org/delphi/resource/assessment/darwin1859-ch14-02--claim-test http://purl.org/dc/terms/description The 25 pre-registered lineage names were resolved with the Open Tree TNRS (exact matches, context All life) and an induced subtree of the synthetic tree was requested. Radiolaria and Charophyta are pruned from the synthesis and Proteobacteria and Firmicutes are non-monophyletic and map to internal nodes, so 21 of 25 lineages (0.84) could be placed as tips, below the pre-registered 0.9 threshold. The Dollo progenitor count (maximal clades whose tips all belong to the kingdom; tips of the other kingdom or of neither break a clade) was nevertheless computed for both readings and is reported as exploratory. https://w3id.org/delphi/resource/assessment/darwin1859-ch14-02--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-ch14-02--claim-test http://www.w3.org/2000/01/rdf-schema#comment Measured: 6 independent clades (Dollo progenitors) required for the animals of 1859 (Metazoa + Protozoa) on the Open Tree synthetic tree (n = 21, modern reading: animals 1, plants 3; 1859 reading: animals 6, plants 6). Interpretation: A 'progenitor' is read as an independent root of descent, i.e. a clade on the tree of life containing only members of the kingdom in question; the number of such clades needed to cover the kingdom is the number of progenitors the kingdom requires. Because the 1859 kingdoms differ from modern ones (Darwin's contemporaries placed ciliates, amoebae, foraminifera and gregarines among animals, and fungi, diatoms and blue-green 'algae' among plants), the count is made both for the modern kingdoms and for the kingdoms as understood in 1859; the pre-registered assignment follows the standard mid-19th-century arrangement (von Siebold 1845 for Protozoa; the botanical placement of fungi and algae). Diatoms were disputed (Ehrenberg: animals; most botanists: plants) and are assigned to plants; Euglenozoa were 'Infusoria' and are assigned to animals. The test uses the Open Tree synthetic tree as the independent genealogy; it does not test whether Darwin's own lower guess ('probably all organic beings from one primordial form') is right. https://w3id.org/delphi/resource/assessment/darwin1859-ch14-02--claim-test http://www.w3.org/2000/01/rdf-schema#label Claim test of darwin1859-ch14-02: inconclusive, confidence 0.5 https://w3id.org/delphi/resource/assessment/darwin1859-ch14-02--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-ch14-02/result.json https://w3id.org/delphi/resource/assessment/darwin1859-ch14-02--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-ch14-02--claim-test https://w3id.org/delphi/ontology/admissibleDatasets Planned datasets: opentree-synthetic-tree-api https://w3id.org/delphi/resource/assessment/darwin1859-ch14-02--claim-test https://w3id.org/delphi/ontology/assessmentType claim-test/0.1.0 https://w3id.org/delphi/resource/assessment/darwin1859-ch14-02--claim-test https://w3id.org/delphi/ontology/dataKind biological https://w3id.org/delphi/resource/assessment/darwin1859-ch14-02--claim-test https://w3id.org/delphi/ontology/disconfirmingObservation Pre-registered: REFUTES if under the modern reading animal progenitors > 5 or plant progenitors > animal progenitors. MIXED if the modern reading satisfies both conditions but the 1859 reading violates either. If the Open Tree API is unreachable or fewer than 90% of the listed lineages map to the tree, the result is inconclusive (data-unavailable). https://w3id.org/delphi/resource/assessment/darwin1859-ch14-02--claim-test https://w3id.org/delphi/ontology/evidenceAgainst Exploratory result under the pre-registered counting rule: modern reading animals = 1 (Metazoa), plants = 3; 1859 reading animals = 6 (Metazoa + choanoflagellates, Amoebozoa, Ciliophora, Apicomplexa, Euglenozoa + Heterolobosea, Foraminifera), plants = 6. Both readings would have violated 'plants no more than animals' or 'animals <= 5'. https://w3id.org/delphi/resource/assessment/darwin1859-ch14-02--claim-test https://w3id.org/delphi/ontology/evidenceAgainst The 1859 kingdom assignment of the protists is a reconstruction of mid-19th-century usage and is itself debatable (diatoms and dinoflagellates were disputed then); the 1859 animal count of 5 or 6 sits exactly at Darwin's 'four or five', so the verdict under that reading is sensitive to those choices. https://w3id.org/delphi/resource/assessment/darwin1859-ch14-02--claim-test https://w3id.org/delphi/ontology/evidenceAgainst The modern-reading plant count of 3 is driven by a single placement: the synthetic tree nests Cryptophyceae (assigned to neither kingdom) inside Archaeplastida, sister to Chloroplastida, so Rhodophyta and Glaucophyta are split off. Whether cryptophytes belong inside Archaeplastida is an open question in the literature; under the alternative counting rule that ignores tips assigned to neither kingdom (not pre-registered), the counts are modern animals 1, plants 1; 1859 animals 5, plants 4, which would have satisfied Darwin's bound under both readings. https://w3id.org/delphi/resource/assessment/darwin1859-ch14-02--claim-test https://w3id.org/delphi/ontology/evidenceAgainst The synthetic tree has no branch support and the eukaryote backbone is a supertree of heterogeneous studies. https://w3id.org/delphi/resource/assessment/darwin1859-ch14-02--claim-test https://w3id.org/delphi/ontology/evidenceAgainst Verdict follows the pre-registered rule: only 21 of 25 lineages (0.84 < 0.9) could be placed as tips. The four unplaceable lineages (Radiolaria, Charophyta, Proteobacteria, Firmicutes) do not by themselves change any count, so the threshold was set too strictly; this is recorded rather than relaxed after the fact. https://w3id.org/delphi/resource/assessment/darwin1859-ch14-02--claim-test https://w3id.org/delphi/ontology/expectedObservation Pre-registered: on the Open Tree of Life synthetic tree induced on a fixed set of major lineages (listed below with their 1859 kingdom assignment), count for each kingdom the Dollo number of progenitors = number of maximal clades whose tips all belong to that kingdom (tips of the other kingdom or of neither break a clade). Two readings are scored. Modern reading: animals = Metazoa, plants = Embryophyta + the other Archaeplastida. 1859 reading: animals = Metazoa plus the 'Protozoa' then placed among animals (Infusoria, Rhizopoda, Gregarinida), plants = land plants, green, red and brown algae, diatoms, fungi and blue-green algae. SUPPORTS if under BOTH readings animal progenitors <= 5 and plant progenitors <= animal progenitors. https://w3id.org/delphi/resource/assessment/darwin1859-ch14-02--claim-test https://w3id.org/delphi/ontology/failCriterion Pre-registered: REFUTES if under the modern reading animal progenitors > 5 or plant progenitors > animal progenitors. MIXED if the modern reading satisfies both conditions but the 1859 reading violates either. If the Open Tree API is unreachable or fewer than 90% of the listed lineages map to the tree, the result is inconclusive (data-unavailable). https://w3id.org/delphi/resource/assessment/darwin1859-ch14-02--claim-test https://w3id.org/delphi/ontology/hasConfidence 0.5 https://w3id.org/delphi/resource/assessment/darwin1859-ch14-02--claim-test https://w3id.org/delphi/ontology/hasEvidence https://w3id.org/delphi/resource/evidence/darwin1859-ch14-02--claim-test--dataset-1 https://w3id.org/delphi/resource/assessment/darwin1859-ch14-02--claim-test https://w3id.org/delphi/ontology/hasVerdict inconclusive https://w3id.org/delphi/resource/assessment/darwin1859-ch14-02--claim-test https://w3id.org/delphi/ontology/hypothesis On an independently estimated tree of life, the organisms Darwin called animals fall into at most four or five separate clades that contain no plants, and the organisms he called plants fall into no more such clades than the animals do. https://w3id.org/delphi/resource/assessment/darwin1859-ch14-02--claim-test https://w3id.org/delphi/ontology/inferenceMethod The 25 pre-registered lineage names were resolved with the Open Tree TNRS (exact matches, context All life) and an induced subtree of the synthetic tree was requested. Radiolaria and Charophyta are pruned from the synthesis and Proteobacteria and Firmicutes are non-monophyletic and map to internal nodes, so 21 of 25 lineages (0.84) could be placed as tips, below the pre-registered 0.9 threshold. The Dollo progenitor count (maximal clades whose tips all belong to the kingdom; tips of the other kingdom or of neither break a clade) was nevertheless computed for both readings and is reported as exploratory. https://w3id.org/delphi/resource/assessment/darwin1859-ch14-02--claim-test https://w3id.org/delphi/ontology/passCriterion Pre-registered: on the Open Tree of Life synthetic tree induced on a fixed set of major lineages (listed below with their 1859 kingdom assignment), count for each kingdom the Dollo number of progenitors = number of maximal clades whose tips all belong to that kingdom (tips of the other kingdom or of neither break a clade). Two readings are scored. Modern reading: animals = Metazoa, plants = Embryophyta + the other Archaeplastida. 1859 reading: animals = Metazoa plus the 'Protozoa' then placed among animals (Infusoria, Rhizopoda, Gregarinida), plants = land plants, green, red and brown algae, diatoms, fungi and blue-green algae. 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