https://w3id.org/np/RADTSHqO9eqCZv16FOqiAH7qNdKTMn04ZKQCDABcyhj5M/Head https://w3id.org/np/RADTSHqO9eqCZv16FOqiAH7qNdKTMn04ZKQCDABcyhj5M http://www.nanopub.org/nschema#hasAssertion https://w3id.org/np/RADTSHqO9eqCZv16FOqiAH7qNdKTMn04ZKQCDABcyhj5M/assertion https://w3id.org/np/RADTSHqO9eqCZv16FOqiAH7qNdKTMn04ZKQCDABcyhj5M http://www.nanopub.org/nschema#hasProvenance https://w3id.org/np/RADTSHqO9eqCZv16FOqiAH7qNdKTMn04ZKQCDABcyhj5M/provenance https://w3id.org/np/RADTSHqO9eqCZv16FOqiAH7qNdKTMn04ZKQCDABcyhj5M http://www.nanopub.org/nschema#hasPublicationInfo https://w3id.org/np/RADTSHqO9eqCZv16FOqiAH7qNdKTMn04ZKQCDABcyhj5M/pubinfo https://w3id.org/np/RADTSHqO9eqCZv16FOqiAH7qNdKTMn04ZKQCDABcyhj5M http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://www.nanopub.org/nschema#Nanopublication https://w3id.org/np/RADTSHqO9eqCZv16FOqiAH7qNdKTMn04ZKQCDABcyhj5M/assertion https://w3id.org/delphi/resource/assessment/levin-2025-wisdom-04--claim-test http://purl.org/dc/terms/description analysis.py integrates the pre-registered gene-circuit equation on 40 random networks (numpy Generator seed 20261101) and four fixed motifs, then checks that each weight matrix is unchanged. Habituation and sensitization use the six-epoch 1.5 rule at clamp scale 100. Pavlovian conditioning uses the strict factor-of-2 rule on 50-time-unit epochs at scale 100. The same three tests are applied to Table S1 pathway SBML with libroadrunner rates and scipy BDF, models outside 3–12 floating species excluded, one model per subprocess. The pathway loop stops once every pathway phenotype has been seen. decide() returns supports only when both panels show all three phenotypes. https://w3id.org/delphi/resource/assessment/levin-2025-wisdom-04--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/levin-2025-wisdom-04--claim-test http://www.w3.org/2000/01/rdf-schema#comment Measured: 17 gene-circuit networks showing Pavlovian conditioning; habituation and sensitization counts are in extra (n = 44, gene-circuit panel is deterministic for this numpy Generator seed; pathway flags are deterministic given the SBML bytes and the BDF tolerances). Interpretation: The claim says that even simple gene-regulatory and molecular-pathway models show habituation, sensitization and Pavlovian conditioning as a dynamical state memory, with no change to topology or edge strengths (Levin, BioEssays 2025, citing the group's GRN-learning results). The gene-circuit equation is the continuous form consistent with the random-model description in Biswas, Clawson and Levin 2023, Methods 4.2: dx_i/dt = (1/tau_i) * (logistic(b_i + sum_j W_ji x_j) - x_i), logistic(z) = 1/(1+exp(-z)). Random entries use the paper's weight range. Motif matrices below are fixed before any run. Habituation and sensitization use the same six-epoch 1.5 rule and the same epoch times as the registration for levin-2022-grn-learning-18, at clamp scale 100. Pavlovian conditioning uses the factor-of-2 rule and 50-time-unit epochs as in the registration for levin-2022-grn-learning-09. Showing the phenotypes in these models does not show that cells learn. https://w3id.org/delphi/resource/assessment/levin-2025-wisdom-04--claim-test http://www.w3.org/2000/01/rdf-schema#label Claim test of levin-2025-wisdom-04: mixed, confidence 0.8 https://w3id.org/delphi/resource/assessment/levin-2025-wisdom-04--claim-test http://www.w3.org/2000/01/rdf-schema#seeAlso https://github.com/fractastical/delphisci/blob/bf2af6ee0a84e23ffa6414ad7a0a50a8c276506e/test-data/claim-tests/levin-papers/levin-2025-wisdom-04/result.json https://w3id.org/delphi/resource/assessment/levin-2025-wisdom-04--claim-test 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/levin-2025-wisdom-04--claim-test https://w3id.org/delphi/ontology/admissibleDatasets The gene-circuit panel is generated by analysis.py from the equations and matrices in protocol, seed 20261101, and is not refit after the run. Pathway models are those whose BioModels identifiers are listed in Table S1 of Biswas, Clawson and Levin, Int. J. Mol. Sci. 2023, 24, 285, with 3 to 12 floating species, simulated from public SBML. The weight matrix and the SBML reaction graph are inputs, not fitted outputs. https://w3id.org/delphi/resource/assessment/levin-2025-wisdom-04--claim-test https://w3id.org/delphi/ontology/assessmentType claim-test/0.1.0 https://w3id.org/delphi/resource/assessment/levin-2025-wisdom-04--claim-test https://w3id.org/delphi/ontology/dataKind computational https://w3id.org/delphi/resource/assessment/levin-2025-wisdom-04--claim-test https://w3id.org/delphi/ontology/disconfirmingObservation None of the three phenotypes occurs in the gene-circuit panel and none occurs in a completed pathway panel. https://w3id.org/delphi/resource/assessment/levin-2025-wisdom-04--claim-test https://w3id.org/delphi/ontology/evidenceAgainst A pass or a mixed computational result does not show that cells or tissues habituate, sensitize, or undergo Pavlovian conditioning. https://w3id.org/delphi/resource/assessment/levin-2025-wisdom-04--claim-test https://w3id.org/delphi/ontology/evidenceAgainst Pathway clamps are one adaptive integration per epoch. libroadrunner getRatesOfChange does not fire SBML events. Assignment-rule and delay models in the attempted prefix were excluded. https://w3id.org/delphi/resource/assessment/levin-2025-wisdom-04--claim-test https://w3id.org/delphi/ontology/evidenceAgainst Random weights are drawn from -30 to 30 into a logistic of an O(1) state, which saturates. That generator was registered before the run. The six-epoch rule follows the methods prose, including a strict rise or fall, rather than the MATLAB nonzeros counter. https://w3id.org/delphi/resource/assessment/levin-2025-wisdom-04--claim-test https://w3id.org/delphi/ontology/evidenceAgainst The gene-circuit panel showed Pavlovian conditioning in 17 of 44 networks, including the slow_repressor motif, and showed habituation in 0 and sensitization in 0. Every weight hash matched before and after the run (weight_unchanged true). Support required all three phenotypes in this panel, so the joint rule cannot return supports. https://w3id.org/delphi/resource/assessment/levin-2025-wisdom-04--claim-test https://w3id.org/delphi/ontology/evidenceAgainst The pathway panel completed 10 models out of 15 attempted and showed all three phenotypes: sensitization in BIOMD0000000001, Pavlovian conditioning in several models including BIOMD0000000004, and habituation in BIOMD0000000026. The screen then stopped, as analysis.py does once every pathway phenotype has been seen. Models later in Table S1 were not integrated. Refutation required all three phenotypes to be absent from both panels with at least three pathways complete, so the joint rule returns mixed. https://w3id.org/delphi/resource/assessment/levin-2025-wisdom-04--claim-test https://w3id.org/delphi/ontology/expectedObservation Habituation, sensitization and Pavlovian conditioning each occur at least once in a frozen panel of simple gene-circuit ODEs and at least once in deposited pathway ODEs, with no change to weights or reaction structure. https://w3id.org/delphi/resource/assessment/levin-2025-wisdom-04--claim-test https://w3id.org/delphi/ontology/failCriterion Pre-registered. Refutes if and only if at least three pathway models complete and none of the three phenotypes is present in the gene-circuit panel and none is present in the pathway panel. If the pathway panel does not complete at least one model and the gene-circuit panel shows all three phenotypes, the verdict is mixed. If the pathway panel does not complete at least one model and the gene-circuit panel shows fewer than three phenotypes, the verdict is inconclusive with reason underpowered. If at least one pathway model completes and the outcome is neither support nor refutation, the verdict is mixed. If the gene-circuit integrator fails to run, the verdict is inconclusive with reason other. https://w3id.org/delphi/resource/assessment/levin-2025-wisdom-04--claim-test https://w3id.org/delphi/ontology/hasConfidence 0.8 https://w3id.org/delphi/resource/assessment/levin-2025-wisdom-04--claim-test https://w3id.org/delphi/ontology/hasEvidence https://w3id.org/delphi/resource/evidence/levin-2025-wisdom-04--claim-test--dataset-1 https://w3id.org/delphi/resource/assessment/levin-2025-wisdom-04--claim-test https://w3id.org/delphi/ontology/hasEvidence https://w3id.org/delphi/resource/evidence/levin-2025-wisdom-04--claim-test--dataset-2 https://w3id.org/delphi/resource/assessment/levin-2025-wisdom-04--claim-test https://w3id.org/delphi/ontology/hasEvidence https://w3id.org/delphi/resource/evidence/levin-2025-wisdom-04--claim-test--dataset-3 https://w3id.org/delphi/resource/assessment/levin-2025-wisdom-04--claim-test https://w3id.org/delphi/ontology/hasVerdict mixed https://w3id.org/delphi/resource/assessment/levin-2025-wisdom-04--claim-test https://w3id.org/delphi/ontology/hypothesis If the published claim holds, standard training protocols applied to simple fixed-weight gene-circuit ODEs and to deposited molecular-pathway ODEs produce habituation, sensitization and Pavlovian conditioning, while the weight matrix and the reaction graph stay unchanged. https://w3id.org/delphi/resource/assessment/levin-2025-wisdom-04--claim-test https://w3id.org/delphi/ontology/inferenceMethod Presence or absence of each phenotype under the fixed ratio and pairing rules, conjoined across the two panels as in pass_criterion and fail_criterion. No assessor score is used. https://w3id.org/delphi/resource/assessment/levin-2025-wisdom-04--claim-test https://w3id.org/delphi/ontology/passCriterion Pre-registered. A phenotype counts as present in the gene-circuit panel if at least one of the 44 fixed networks shows it, and present in the pathway panel if at least one completed BioModels pathway shows it. The three phenotypes are habituation (six successive response means each at most 1/1.5 of the previous), sensitization (six successive response means each at least 1.5 times the previous), and Pavlovian conditioning (a node that does not regulate the response by a factor of 2 comes to do so after a paired clamp with a node that does, with the weight matrix bitwise unchanged for gene circuits and no SBML edit for pathways). Supports if and only if all three phenotypes are present in the gene-circuit panel and all three are present in the pathway panel. https://w3id.org/delphi/resource/assessment/levin-2025-wisdom-04--claim-test https://w3id.org/delphi/ontology/preregistered false https://w3id.org/delphi/resource/claim/levin-2025-wisdom-04 https://w3id.org/delphi/ontology/hasAssessment https://w3id.org/delphi/resource/assessment/levin-2025-wisdom-04--claim-test https://w3id.org/delphi/resource/evidence/levin-2025-wisdom-04--claim-test--dataset-1 http://purl.org/dc/terms/description Habituation, sensitization and Pavlovian conditioning with the weight matrix held fixed. Per-network weight hashes are in measured.extra.networks. https://w3id.org/delphi/resource/evidence/levin-2025-wisdom-04--claim-test--dataset-1 http://purl.org/dc/terms/license https://w3id.org/delphi/resource/evidence/levin-2025-wisdom-04--claim-test--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/levin-2025-wisdom-04--claim-test--dataset-1 http://www.w3.org/2000/01/rdf-schema#label Dataset: 44 fixed-weight gene-circuit ODEs generated by analysis.py: 40 random networks from seed 20261101 and the four motif matrices in protocol https://w3id.org/delphi/resource/evidence/levin-2025-wisdom-04--claim-test--dataset-2 http://purl.org/dc/terms/description Table S1 lists the BioModels identifiers. The zip is not committed. The pathway screen stopped once all three phenotypes had been seen, so only the files below were fetched for this claim. https://w3id.org/delphi/resource/evidence/levin-2025-wisdom-04--claim-test--dataset-2 http://purl.org/dc/terms/license https://w3id.org/delphi/resource/evidence/levin-2025-wisdom-04--claim-test--dataset-2 http://www.w3.org/1999/02/22-rdf-syntax-ns#type https://w3id.org/delphi/ontology/EvidenceItem https://w3id.org/delphi/resource/evidence/levin-2025-wisdom-04--claim-test--dataset-2 http://www.w3.org/2000/01/rdf-schema#label Dataset: Biswas, Clawson and Levin, Int. J. Mol. Sci. 2023, 24, 285, supplement ijms-24-00285-s001, Table S1 model identifiers https://w3id.org/delphi/resource/evidence/levin-2025-wisdom-04--claim-test--dataset-2 http://www.w3.org/ns/prov#atLocation https://mdpi-res.com/d_attachment/ijms/ijms-24-00285/article_deploy/ijms-24-00285-s001.zip?version=1672829351 https://w3id.org/delphi/resource/evidence/levin-2025-wisdom-04--claim-test--dataset-2 http://www.w3.org/ns/prov#wasDerivedFrom https://www.mdpi.com/1422-0067/24/1/285 https://w3id.org/delphi/resource/evidence/levin-2025-wisdom-04--claim-test--dataset-2 https://w3id.org/delphi/ontology/hasChecksum sha256:292a7f33bcb3a9589614507114de8c1a7a5f5d8bc11e382d546c3d08da381e39 https://w3id.org/delphi/resource/evidence/levin-2025-wisdom-04--claim-test--dataset-3 http://purl.org/dc/terms/description Deposited pathway ODEs scored for the three phenotypes. 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