https://w3id.org/np/RAxCJRXQcfMJC2n5EDQJAGnHsXYs_pPFY8_7ZU9fmpIU0/Head https://w3id.org/np/RAxCJRXQcfMJC2n5EDQJAGnHsXYs_pPFY8_7ZU9fmpIU0 http://www.nanopub.org/nschema#hasAssertion https://w3id.org/np/RAxCJRXQcfMJC2n5EDQJAGnHsXYs_pPFY8_7ZU9fmpIU0/assertion https://w3id.org/np/RAxCJRXQcfMJC2n5EDQJAGnHsXYs_pPFY8_7ZU9fmpIU0 http://www.nanopub.org/nschema#hasProvenance https://w3id.org/np/RAxCJRXQcfMJC2n5EDQJAGnHsXYs_pPFY8_7ZU9fmpIU0/provenance https://w3id.org/np/RAxCJRXQcfMJC2n5EDQJAGnHsXYs_pPFY8_7ZU9fmpIU0 http://www.nanopub.org/nschema#hasPublicationInfo https://w3id.org/np/RAxCJRXQcfMJC2n5EDQJAGnHsXYs_pPFY8_7ZU9fmpIU0/pubinfo https://w3id.org/np/RAxCJRXQcfMJC2n5EDQJAGnHsXYs_pPFY8_7ZU9fmpIU0 http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://www.nanopub.org/nschema#Nanopublication https://w3id.org/np/RAxCJRXQcfMJC2n5EDQJAGnHsXYs_pPFY8_7ZU9fmpIU0/assertion https://w3id.org/delphi/resource/assessment/darwin1859-ch06-17--claim-test--pr-107 http://purl.org/dc/terms/description For each frozen species, selected one NCBI protein whose Gene Name is RAG1 and whose length is between 600 and 1400 (RefSeq NP_ preferred, then XP_, then the longest; 29 kept, 0 dropped). Computed cosine distance of amino-acid 3-mer counts. D_class is the mean distance over same-class different-habit pairs (n=63); D_habit is the mean over same-habit different-class pairs (n=88). C_cross and H_cross are the nearest-neighbor fractions defined in the pass criterion. The same statistics were computed on edge counts of the Open Tree induced subtree (context Vertebrates) for the species that mapped to a unique tip. The verdict follows the pre-registered combination of the sequence outcome (pass) and the tree outcome (pass). https://w3id.org/delphi/resource/assessment/darwin1859-ch06-17--claim-test--pr-107 http://www.w3.org/1999/02/22-rdf-syntax-ns#type https://w3id.org/delphi/ontology/Assessment https://w3id.org/delphi/resource/assessment/darwin1859-ch06-17--claim-test--pr-107 http://www.w3.org/2000/01/rdf-schema#comment Measured: 0.862069 C_cross, fraction of sequenced species whose nearest different-habit neighbor is the same class (RAG1 3-mer cosine distance) (n = 29, D_habit/D_class = 1.64114; H_cross = 0.37931 (11/29); C_cross = 25/29). Interpretation: Darwin defines unity of type as the fundamental agreement in structure among organisms of the same class, quite independent of their habits of life, and says that agreement is explained by unity of descent. The classes in this test are those structural classes. The sequences are not the structures: RAG1 is used because a tree built from it does not use the skeletal characters that define the classes, which is the non-circular comparison the assessments ask for. Habits are assigned from natural history and crossed with class so that 'explained by descent' and 'explained by habits of life' predict different nearest neighbors. The test does not score a morphological character matrix. It asks whether the groups that morphology already carved — the classes — match an independent genealogy better than habits do. Gliding is coded with flight. A semi-aquatic alligator is coded aquatic. Terrestrial is a residual land-living bin, not one locomotor gait. No aerial amphibian and no aerial fish entered the frozen list, because the NCBI protein records for the gliding frogs and flying fishes that were checked are fragments shorter than 600 amino acids, and mixing those fragments with full-length RAG1 would change the 3-mer distance for a reason that is not biology. Python bivittatus replaces Crotalus horridus, which had no full-length RAG1, as the second terrestrial reptile. https://w3id.org/delphi/resource/assessment/darwin1859-ch06-17--claim-test--pr-107 http://www.w3.org/2000/01/rdf-schema#label Claim test of darwin1859-ch06-17 (pr-107): supports, confidence 0.55 https://w3id.org/delphi/resource/assessment/darwin1859-ch06-17--claim-test--pr-107 http://www.w3.org/2000/01/rdf-schema#seeAlso https://github.com/fractastical/delphisci/blob/bf2af6ee0a84e23ffa6414ad7a0a50a8c276506e/test-data/claim-tests/darwin-origin/darwin1859-ch06-17/pr-107/result.json https://w3id.org/delphi/resource/assessment/darwin1859-ch06-17--claim-test--pr-107 http://www.w3.org/ns/prov#wasAttributedTo https://w3id.org/delphi/resource/agent/delphisci-claim-tester-grok-4-7 https://w3id.org/delphi/resource/assessment/darwin1859-ch06-17--claim-test--pr-107 https://w3id.org/delphi/ontology/admissibleDatasets A homologous protein sequenced independently of the skeletal characters that define the classes, for living vertebrates whose class and habit were assigned before the sequences were read, plus an independently estimated phylogeny of the same species. Habit labels are the study design, not a measurement taken from the sequence. The sample has to cross class with habit so that unity of type and unity of habit make different predictions. https://w3id.org/delphi/resource/assessment/darwin1859-ch06-17--claim-test--pr-107 https://w3id.org/delphi/ontology/assessmentType claim-test/0.1.0 https://w3id.org/delphi/resource/assessment/darwin1859-ch06-17--claim-test--pr-107 https://w3id.org/delphi/ontology/dataKind biological https://w3id.org/delphi/resource/assessment/darwin1859-ch06-17--claim-test--pr-107 https://w3id.org/delphi/ontology/disconfirmingObservation Ecological analogues are closer in RAG1 sequence than different-habit classmates, or habit matches the nearest other-class neighbor more often than class matches the nearest other-habit neighbor. https://w3id.org/delphi/resource/assessment/darwin1859-ch06-17--claim-test--pr-107 https://w3id.org/delphi/ontology/evidenceAgainst After the distances were computed: the misses sit on Darwin's Reptilia as coded here (crocodilians in, birds out). On the Open Tree the alligator's nearest different-habit neighbors are the ostrich and the kiwi, and both flightless birds' nearest different-habit neighbor is the alligator, so that class cut is not a descent group. On RAG1 the turtle and the alligator also fall nearer the ostrich than a terrestrial reptile, and both caecilians fall nearer the ostrich than another amphibian; the tree does not put the caecilians with birds, so that part belongs to the 3-mer distance. H_cross on RAG1 is 0.379, just under the pre-registered ceiling of 0.40, because several aquatic species have an aquatic neighbor in another class. The thresholds were not changed. https://w3id.org/delphi/resource/assessment/darwin1859-ch06-17--claim-test--pr-107 https://w3id.org/delphi/ontology/evidenceAgainst Before this registration, RAG1 protein record counts and sequence lengths (slen) were read from NCBI esummary for the candidate species, and species with no protein in the 600–1400 window were dropped. No FASTA sequence was downloaded, no 3-mer distance was computed, and the Open Tree induced subtree was not requested. The Open Tree 'about' record and the TNRS context list were requested only to confirm the service and the context name Vertebrates. https://w3id.org/delphi/resource/assessment/darwin1859-ch06-17--claim-test--pr-107 https://w3id.org/delphi/ontology/evidenceAgainst Open Tree's synthetic tree is informed by taxonomy as well as by published trees, so a pass on the tree alone would be weaker than a pass on RAG1. The tree is a replicate and cannot by itself support the claim. https://w3id.org/delphi/resource/assessment/darwin1859-ch06-17--claim-test--pr-107 https://w3id.org/delphi/ontology/evidenceAgainst The author expects the classes to be recovered, because published molecular phylogenies already place mammals, birds, reptiles, amphibians and ray-finned fishes as separate clades. The habit contrast is the part that could still fail this particular distance. The thresholds were not adjusted after seeing any distance. https://w3id.org/delphi/resource/assessment/darwin1859-ch06-17--claim-test--pr-107 https://w3id.org/delphi/ontology/evidenceAgainst Three-mer cosine distance tracks amino-acid composition as well as shared peptides. It is not an aligned evolutionary distance. That is a property of the pre-registered method, not a reason to switch methods after the fact. https://w3id.org/delphi/resource/assessment/darwin1859-ch06-17--claim-test--pr-107 https://w3id.org/delphi/ontology/evidenceAgainst Two species in the same class and the same habit (the two swifts, the two penguins, the two Xenopus) are excluded from both mean-distance pair sets. Nearest neighbors are taken across the other factor so that those pairs do not force C_cross and H_cross to be equal. https://w3id.org/delphi/resource/assessment/darwin1859-ch06-17--claim-test--pr-107 https://w3id.org/delphi/ontology/expectedObservation Within this crossed set of classes and habits, RAG1 similarity groups species by class rather than by habit: classmates with different habits are closer than ecological analogues, the nearest different-habit neighbor is usually a classmate, and the nearest different-class neighbor usually does not share the habit. https://w3id.org/delphi/resource/assessment/darwin1859-ch06-17--claim-test--pr-107 https://w3id.org/delphi/ontology/failCriterion Pre-registered. The sequence test refutes the claim if the sample-size conditions in the pass criterion hold and either the mean same-habit different-class distance is strictly less than the mean same-class different-habit distance, or C_cross is strictly less than H_cross. If the sample-size conditions fail, the verdict is inconclusive (underpowered if some proteins were retrieved, data-unavailable if fewer than 4 proteins or the NCBI protein service cannot be queried). If the sample is large enough and the result is neither the pass nor the fail, the sequence result is mixed. A tree result alone does not refute and does not upgrade a mixed or failed sequence result. https://w3id.org/delphi/resource/assessment/darwin1859-ch06-17--claim-test--pr-107 https://w3id.org/delphi/ontology/hasConfidence 0.55 https://w3id.org/delphi/resource/assessment/darwin1859-ch06-17--claim-test--pr-107 https://w3id.org/delphi/ontology/hasEvidence https://w3id.org/delphi/resource/evidence/darwin1859-ch06-17--claim-test--pr-107--dataset-1 https://w3id.org/delphi/resource/assessment/darwin1859-ch06-17--claim-test--pr-107 https://w3id.org/delphi/ontology/hasEvidence https://w3id.org/delphi/resource/evidence/darwin1859-ch06-17--claim-test--pr-107--dataset-2 https://w3id.org/delphi/resource/assessment/darwin1859-ch06-17--claim-test--pr-107 https://w3id.org/delphi/ontology/hasEvidence https://w3id.org/delphi/resource/evidence/darwin1859-ch06-17--claim-test--pr-107--dataset-3 https://w3id.org/delphi/resource/assessment/darwin1859-ch06-17--claim-test--pr-107 https://w3id.org/delphi/ontology/hasVerdict supports https://w3id.org/delphi/resource/assessment/darwin1859-ch06-17--claim-test--pr-107 https://w3id.org/delphi/ontology/hypothesis If the structural agreement that defines a class is explained by common descent and is independent of habits of life, then species of the same class are closer in an independently estimated molecular sequence than species that only share a habit, and a species' nearest neighbor among different habits is a classmate far more often than its nearest neighbor among different classes shares its habit. https://w3id.org/delphi/resource/assessment/darwin1859-ch06-17--claim-test--pr-107 https://w3id.org/delphi/ontology/inferenceMethod Cosine distance of amino-acid 3-mer counts. Compare mean distances of the two crossed pair types, and compare nearest-neighbor match rates C_cross and H_cross, against the thresholds in pass_criterion and fail_criterion. The Open Tree synthetic tree supplies topological distance as a replicate with the same thresholds. https://w3id.org/delphi/resource/assessment/darwin1859-ch06-17--claim-test--pr-107 https://w3id.org/delphi/ontology/passCriterion Pre-registered, on RAG1 protein 3-mer cosine distance. All of the following: at least 12 species yield a protein of length 600 to 1400; at least 4 class labels and at least 3 habits are each represented by 2 or more of those species; there are at least 10 same-class different-habit pairs and 10 same-habit different-class pairs; the mean distance of same-habit different-class pairs is at least 1.25 times the mean distance of same-class different-habit pairs; C_cross is at least 0.75; H_cross is at most 0.40. C_cross is the fraction of species whose nearest neighbor among species of a different habit has the same class. H_cross is the fraction whose nearest neighbor among species of a different class has the same habit. Ties count as a match only if every tied neighbor matches. The same inequalities on Open Tree topological distance (edges between tips), for at least 75% of the sequenced species, are a required replicate: if the sequence test passes and the tree replicate fails or is mixed, the verdict is mixed; if the tree cannot be built, the sequence verdict stands. https://w3id.org/delphi/resource/assessment/darwin1859-ch06-17--claim-test--pr-107 https://w3id.org/delphi/ontology/preregistered false https://w3id.org/delphi/resource/claim/darwin1859-ch06-17 https://w3id.org/delphi/ontology/hasAssessment https://w3id.org/delphi/resource/assessment/darwin1859-ch06-17--claim-test--pr-107 https://w3id.org/delphi/resource/evidence/darwin1859-ch06-17--claim-test--pr-107--dataset-1 http://purl.org/dc/terms/description homologous RAG1 protein sequences used for the 3-mer distances https://w3id.org/delphi/resource/evidence/darwin1859-ch06-17--claim-test--pr-107--dataset-1 http://purl.org/dc/terms/license NCBI sequence records are freely accessible. Information created by or for the US government on the NCBI site is in the public domain (https://www.ncbi.nlm.nih.gov/home/about/policies/). Individual GenBank records may be submissions from outside the US government. https://w3id.org/delphi/resource/evidence/darwin1859-ch06-17--claim-test--pr-107--dataset-1 http://www.w3.org/1999/02/22-rdf-syntax-ns#type https://w3id.org/delphi/ontology/EvidenceItem https://w3id.org/delphi/resource/evidence/darwin1859-ch06-17--claim-test--pr-107--dataset-1 http://www.w3.org/2000/01/rdf-schema#label Dataset: NCBI Protein RAG1 records for the frozen species list https://w3id.org/delphi/resource/evidence/darwin1859-ch06-17--claim-test--pr-107--dataset-1 http://www.w3.org/ns/prov#atLocation https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=protein&id=1318010517&rettype=fasta&retmode=text https://w3id.org/delphi/resource/evidence/darwin1859-ch06-17--claim-test--pr-107--dataset-1 http://www.w3.org/ns/prov#atLocation https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=protein&id=1335171188&rettype=fasta&retmode=text 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