{ "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-12T09:44:59Z", "providers": [ "Codex" ], "breadth": "recalled by Codex without web access - no source was read", "missingProviders": [], "pass": 2, "cost": { "grok": { "seconds": 21.1, "error": "Reading additional input from stdin...\nOpenAI Codex v0.153.4\n--------\nworkdir: R:\\02_PROJECTS\\02_Meta_Models_Platforms\\Ver.cy\\current\\thing-registry-backlog\nmodel: gpt-6-astra\nprovider: openai\napproval: never\nsandbox: read-only\nreasoning effort: none\nreasoning summaries: none\nsession id: 01a094ff-88b2-73a1-8214-0b2c63314ebd\n--------\nuser\nDescribe what is already known about one registered thing. Answer as JSON only, no prose around it.\n\nThing: fixation\nSense to describe: (none recorded)\nDomain code: ACT.PRC\nAlso known as: (none)\n\n\nContext for this batch of 1001 things:\n# Batch 043: 1001 regist", "usd": 0.0, "recall": true }, "codex": { "seconds": 130.4, "error": "Reading additional input from stdin...\nOpenAI Codex v0.153.4\n--------\nworkdir: R:\\02_PROJECTS\\02_Meta_Models_Platforms\\Ver.cy\\current\\thing-registry-backlog\nmodel: gpt-6-astra\nprovider: openai\napproval: never\nsandbox: read-only\nreasoning effort: none\nreasoning summaries: none\nsession id: 01a094ff-88c2-74c3-99e4-e23f55c2c348\n--------\nuser\nYou are drafting a Vercy meta-model for one registered thing. Answer as JSON only, no prose around it.\n\nThing: fixation\nRegistry id: vr.tr.fixation-q2914991\nPlane / domain: ACT / ACT.PRC\nRegistry definition: (none recorded)\nNames folded into this entry: (none)" } }, "enrichment": { "pass": 3, "engine": "claude", "producedAt": "2026-10-06T12:00:00Z", "ingestedAt": "2026-10-06T08:16:20+00:00", "fields": [ "agent_conduct", "ethics", "failure_modes_and_hazards", "owners" ] }, "revisions": [ { "at": "2026-10-07T11:28:53+00:00", "engine": "codex", "fields": [ "agent_conduct", "definition", "distinguishing_features", "ethics", "failure_modes_and_hazards", "in_scope", "out_of_scope", "owners", "purpose", "scope_statement" ], "answering_review": "b3d28bd10cab3f072badf330212e3310280985a5261ff6619339a7132e0d5c23" } ], "gate": { "passed": true, "version": "1.0", "at": "2026-10-07T12:16:32+00:00", "evidence": [ "completeness 1.00", "sense: Wikidata description", "2 live sources", "review by codex: pass" ] } }, "metaModel": { "id": "THING-Q2914991", "registryId": "vr.tr.fixation-q2914991", "name": "fixation", "version": "0.1.0-research.1", "entryKind": "thing", "family": "Thing Registry", "domain": [ "ACT.PRC" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q2914991/", "model": { "registry_id": "vr.tr.fixation-q2914991", "name": "fixation", "purpose": "Enable an agent to recognise allele fixation, assess supporting population-genetic evidence and distinguish established fixation from apparent absence of alternatives in a sample.", "definition": "In population genetics, fixation is the change by which one allele at a locus becomes the only allele present in a defined population, with all alternative alleles at that locus lost from its gene pool.", "scope_statement": "This model owns allele fixation in a defined population, including the locus, population boundaries, temporal context, evolutionary processes and evidence supporting a fixation claim.", "in_scope": [ "The focal allele, locus and population boundaries are in scope.", "Allele-frequency change and the loss of alternative alleles are in scope.", "Genetic drift, selection and their possible contributions to fixation are in scope.", "Sampling limitations and uncertainty in fixation claims are in scope.", "Mutation and gene flow that may alter a fixed state are in scope." ], "out_of_scope": [ "Visual fixation and gaze measurement are outside this model.", "Histological preservation and chemical fixation are outside this model.", "Psychological fixation and functional fixedness are outside this model.", "Surgical fixation and mechanical fastening are outside this model.", "Detailed interventions intended to alter population gene pools are outside this model." ], "distinguishing_features": [ "Fixation concerns an allele at a specified locus in a defined population rather than the genetic uniformity of the entire organism or genome.", "An allele is fixed when no alternative allele remains at that locus in the defined population.", "Finding only one allele in a sample does not by itself establish fixation throughout the population.", "Fixation can arise through genetic drift or selection and does not by itself demonstrate that an allele is beneficial.", "A fixed state need not be permanent because mutation or gene flow may introduce alternative alleles." ], "characteristics": [ { "name": "Operational definition", "kind": "category", "unit_or_values": "Instruction-based, observer-labelled, dispersion-based, velocity-based or another explicitly specified definition", "why_it_matters": "The definition determines which intervals count as fixation." }, { "name": "Episode duration", "kind": "measurement", "unit_or_values": "Milliseconds, with onset and offset rules", "why_it_matters": "Duration comparisons depend on how interruptions and boundaries are handled." }, { "name": "Fixated referent", "kind": "relation", "unit_or_values": "Point, visible target, scene object, area of interest or unresolved referent", "why_it_matters": "A gaze location does not automatically identify the object being fixated." }, { "name": "Coordinate frame", "kind": "category", "unit_or_values": "Screen, head, world or target coordinates, with transformations specified", "why_it_matters": "Apparent gaze stability changes with the reference frame." }, { "name": "Spatial dispersion", "kind": "measurement", "unit_or_values": "Degrees of visual angle or explicitly defined coordinate units and dispersion statistic", "why_it_matters": "Quantifies stability without assuming a universal acceptable spread." }, { "name": "Target-relative error", "kind": "measurement", "unit_or_values": "Degrees of visual angle, with target location and uncertainty", "why_it_matters": "Stable gaze can still be displaced from the intended target." }, { "name": "Eye contribution", "kind": "category", "unit_or_values": "Left eye, right eye, binocular estimate or unresolved", "why_it_matters": "Combining eye signals can conceal disagreement or missing observations." }, { "name": "Episode assessment", "kind": "state", "unit_or_values": "Candidate, accepted, ambiguous, interrupted or rejected under a named rule", "why_it_matters": "Separates detected intervals from validated fixation observations." } ], "affordances": [ "Identify candidate fixation intervals using a declared operational definition.", "Associate fixation with a target while retaining spatial uncertainty.", "Measure duration, dispersion and target-relative error.", "Reclassify episodes under alternative detection settings and compare results.", "Flag tracking gaps, calibration problems and ambiguous boundaries.", "Evaluate whether an episode satisfies a task-specific fixation requirement." ], "agent_conduct": { "may": [ "Explain allele fixation and assess claims using documented genetic evidence.", "Report population boundaries, sampling limitations and uncertainty alongside fixation assessments." ], "must_not": [ "Infer population-wide fixation solely from failure to observe alternative alleles in a limited sample.", "Present fixation as proof that an allele is beneficial or that a population is superior.", "Use identifiable human genetic data beyond the consent and permissions governing them.", "Initiate interventions intended to change a population's gene pool without appropriate human authorization." ], "requires_human": [ "Decisions affecting breeding, conservation or population management require responsible human review.", "Use or disclosure of sensitive human genetic data requires appropriate human oversight." ] }, "ethics": { "considerations": [ "Human genetic evidence requires privacy protection, appropriate consent and care against stigmatizing interpretations.", "Decisions based on fixation claims can affect genetic diversity, animal welfare and ecosystems." ], "affected_parties": [ "Research participants and communities represented in genetic datasets are affected.", "Researchers and custodians of genetic records are affected.", "Managed populations and surrounding ecosystems are affected." ] }, "owners": { "steward": "No one owns the evolutionary process; researchers and data custodians are responsible for the evidence and records they maintain.", "master_systems": [] }, "failure_modes_and_hazards": [ "Incomplete sampling can lead to false claims that an allele is fixed.", "Unclear population boundaries can make fixation claims misleading.", "Treating fixation as proof of adaptation can distort evolutionary interpretation.", "Misusing population-genetic findings can stigmatize people or support harmful ecological decisions." ], "what_it_is_for": [ "In population genetics, fixation describes the state in which a particular allele is the only allele present at a locus in a defined population.", "It is studied in evolutionary biology, conservation genetics and breeding to understand genetic drift, selection and loss of genetic variation.", "Claims of fixation depend on the population boundary and sampling evidence because an undetected rare allele can make apparent fixation uncertain." ], "facets_not_applicable": { "interfaces": "Allele fixation is a population genetic state with no generally applicable product standard or regulatory classification.", "recognition": "Allele fixation cannot be identified visually and requires genetic evidence from the defined population." } }, "sources": [ { "id": "wikidata", "title": "Wikidata item Q2914991: fixation", "url": "https://www.wikidata.org/wiki/Q2914991", "url_status": "live", "what_it_supports": "identity and sense of the item", "checked_by": "wikidata-api" }, { "id": "wikipedia-en", "title": "Wikipedia: Fixation (population genetics)", "url": "https://en.wikipedia.org/wiki/Fixation_%28population_genetics%29", "url_status": "live", "what_it_supports": "general description of the item", "checked_by": "wikidata-api sitelink" } ], "structure": { "bundles": [ { "id": "fixation-definition", "name": "Fixation definition", "description": "Establishes what counts as visual fixation for the observation at hand.", "rationale": "A fixation label is meaningful only with its intended sense and operational criterion.", "layers": [ { "id": "concept-and-instance", "name": "Concept and instance", "description": "Separates the act of fixating from its target and from unrelated senses of fixation.", "findings": [ { "id": "visual-sense-and-referent", "name": "Visual sense and referent", "description": "Record evidence for the visual sense and distinguish an episode from a fixation point or instruction.", "questions": [ { "text": "Which registry evidence establishes that Q2914991 denotes visual fixation?", "kind": "provenance", "id": "visual-sense-and-referent-q01" }, { "text": "Does this record describe an observed gaze episode, an intended fixation instruction or a spatial target?", "kind": "definition", "id": "visual-sense-and-referent-q02" } ] } ] }, { "id": "classification-rule", "name": "Classification rule", "description": "Makes the rule for accepting an interval explicit.", "findings": [ { "id": "operational-fixation-criterion", "name": "Operational fixation criterion", "description": "Record the definition, its author or implementation, thresholds and applicable viewing conditions.", "questions": [ { "text": "Which operational definition and implementation classify this interval as fixation?", "kind": "definition", "id": "operational-fixation-criterion-q01" }, { "text": "What duration, dispersion or velocity criteria apply, and what evidence justifies them for this task?", "kind": "measurement", "id": "operational-fixation-criterion-q02" }, { "text": "How does this definition distinguish fixation from slow pursuit and low-velocity tracking noise?", "kind": "boundary", "id": "operational-fixation-criterion-q03" } ] } ] } ] }, { "id": "target-and-reference-frame", "name": "Target and reference frame", "description": "Locates fixation relative to the observer, scene and intended target.", "rationale": "Fixation cannot be judged from eye position alone when the head, scene or target moves.", "layers": [ { "id": "fixated-location", "name": "Fixated location", "description": "Relates measured gaze to candidate fixation targets.", "findings": [ { "id": "target-assignment", "name": "Target assignment", "description": "Record the intended target separately from the target inferred from gaze.", "questions": [ { "text": "What location or object was intended to be fixated, and where was gaze actually measured?", "kind": "measurement", "id": "target-assignment-q01" }, { "text": "Could measurement uncertainty place the fixation on a different nearby object or area of interest?", "kind": "boundary", "id": "target-assignment-q02" } ] } ] }, { "id": "relative-motion", "name": "Relative motion", "description": "Accounts for motion of the eyes, head and target in the chosen frame.", "findings": [ { "id": "frame-dependent-stability", "name": "Frame-dependent stability", "description": "Record transformations and motion evidence needed to decide what remained stable.", "questions": [ { "text": "In which coordinate frame is gaze stability evaluated, and how were coordinates transformed?", "kind": "measurement", "id": "frame-dependent-stability-q01" }, { "text": "Does the observed eye movement maintain gaze on a stationary location, compensate for head motion or follow a moving target?", "kind": "boundary", "id": "frame-dependent-stability-q02" } ] } ] } ] }, { "id": "episode-and-internal-movement", "name": "Episode and internal movement", "description": "Describes fixation timing and the gaze variation retained within an episode.", "rationale": "Episode duration and stability depend on whether small movements and interruptions split the fixation.", "layers": [ { "id": "temporal-segmentation", "name": "Temporal segmentation", "description": "Defines onset, offset and treatment of interruptions.", "findings": [ { "id": "episode-boundaries", "name": "Episode boundaries", "description": "Record boundary evidence and any decisions to bridge gaps or merge adjacent intervals.", "questions": [ { "text": "Which observations establish fixation onset and offset, and what timing uncertainty remains?", "kind": "measurement", "id": "episode-boundaries-q01" }, { "text": "Do blinks, missing samples or brief excursions terminate the episode or get bridged under the selected rule?", "kind": "boundary", "id": "episode-boundaries-q02" }, { "text": "Should adjacent candidate intervals be merged, and what spatial and temporal criteria permit that merge?", "kind": "action", "id": "episode-boundaries-q03" } ] } ] }, { "id": "within-fixation-dynamics", "name": "Within-fixation dynamics", "description": "Characterises small gaze movements without equating fixation with immobility.", "findings": [ { "id": "movement-and-stability-profile", "name": "Movement and stability profile", "description": "Record dispersion and distinguish resolved microsaccades, drift or tremor from unclassified variation.", "questions": [ { "text": "Which within-fixation movements can the recording resolve, and which remain below its measurement capability?", "kind": "measurement", "id": "movement-and-stability-profile-q01" }, { "text": "What rule distinguishes a microsaccade retained within fixation from a gaze shift that ends it?", "kind": "boundary", "id": "movement-and-stability-profile-q02" }, { "text": "Which stability statistic is reported, over what interval and for which eye or binocular estimate?", "kind": "measurement", "id": "movement-and-stability-profile-q03" } ] } ] } ] }, { "id": "evidence-and-use", "name": "Evidence and use", "description": "Determines whether fixation measurements support the intended task decision.", "rationale": "A detected fixation can reflect measurement error, and a valid fixation does not by itself establish comprehension or intent.", "layers": [ { "id": "measurement-validity", "name": "Measurement validity", "description": "Assesses whether recorded stability and target assignment are credible.", "findings": [ { "id": "recording-and-classification-confidence", "name": "Recording and classification confidence", "description": "Connect fixation judgements to calibration, sampling, filtering, missing data and detector settings.", "questions": [ { "text": "What calibration accuracy, precision, sampling rate and data loss apply to this episode?", "kind": "measurement", "id": "recording-and-classification-confidence-q01" }, { "text": "Could filtering, interpolation or tracker failure have produced the apparent fixation?", "kind": "boundary", "id": "recording-and-classification-confidence-q02" }, { "text": "Does the fixation remain accepted under plausible alternative detector settings?", "kind": "measurement", "id": "recording-and-classification-confidence-q03" } ] } ] }, { "id": "task-interpretation", "name": "Task interpretation", "description": "Relates fixation observations to instructions, experimental conditions and permitted decisions.", "findings": [ { "id": "task-specific-decision", "name": "Task-specific decision", "description": "Record whether fixation was instructed or spontaneous and what additional evidence supports its interpretation.", "questions": [ { "text": "Was the observer instructed to fixate, freely viewing, reading or performing another specified task?", "kind": "provenance", "id": "task-specific-decision-q01" }, { "text": "What independent evidence supports interpreting this fixation as attention, recognition or comprehension?", "kind": "boundary", "id": "task-specific-decision-q02" }, { "text": "Does this episode justify accepting a trial, triggering a gaze interaction or requesting another observation under the task's stated rule?", "kind": "action", "id": "task-specific-decision-q03" } ] } ] } ] }, { "id": "evidence-and-external-alignment", "name": "Evidence and external alignment", "description": "What the world already says about this thing, gathered so the model can be checked against it.", "rationale": "A model that cannot be lined up against existing standards, identifiers and practice cannot be adopted by anyone who already uses them.", "layers": [ { "id": "reported-evidence", "name": "Reported evidence", "description": "Findings from the breadth pass, kept separate from the structural claims.", "findings": [ { "id": "evidence-confidence-notes", "name": "Check these first", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ "The registry provides no sense; the histological and cytological interpretation is provisional, and ACT.PRC alone does not resolve the ambiguity.", "Mechanical, psychological, visual and chemical uses of 'fixation' require different descriptions if one of those senses was intended.", "The listed kinds overlap: chemical fixation and cryofixation distinguish mechanisms, while immersion and perfusion distinguish delivery methods." ], "questions": [ { "id": "evidence-confidence-notes-q01", "text": "Which of these check these first hold for the sense of fixation this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-kinds", "name": "Kinds and varieties", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ "Chemical fixation", "Cryofixation", "Immersion fixation", "Perfusion fixation" ], "questions": [ { "id": "evidence-kinds-q01", "text": "Which of these kinds and varieties hold for the sense of fixation this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-real-world-use", "name": "Real-world use", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ "Preserving tissue for histological examination", "Preparing cells for cytological examination", "Preserving ultrastructure for electron microscopy", "Preparing specimens for immunohistochemistry and in situ hybridisation" ], "questions": [ { "id": "evidence-real-world-use-q01", "text": "Which of these real-world use hold for the sense of fixation this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-measurements", "name": "Typical measurements", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ { "quantity": "Fixation duration", "typical_range": "Protocol-dependent; varies with specimen dimensions, fixative and downstream assay", "unit": "minutes or hours" }, { "quantity": "Fixative concentration", "typical_range": "A common histological formulation is approximately 4% formaldehyde, conventionally called 10% neutral buffered formalin", "unit": "%" } ], "questions": [ { "id": "evidence-measurements-q01", "text": "Which of these typical measurements hold for the sense of fixation this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-failure-modes-and-hazards", "name": "Failure modes and hazards", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ "Inadequate fixation permits degradation and loss of morphological detail.", "Excessive fixation can mask epitopes and impair nucleic acid analysis.", "Slow or uneven penetration produces inconsistent preservation within a specimen.", "Fixation can introduce shrinkage, distortion and other preparation artefacts.", "Chemical fixatives can present toxic, irritant or carcinogenic exposure hazards." ], "questions": [ { "id": "evidence-failure-modes-and-hazards-q01", "text": "Which of these failure modes and hazards hold for the sense of fixation this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-neighbours", "name": "Neighbouring kinds and how to tell them apart", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ { "name": "Preservation", "difference": "Preservation is the broader objective; fixation is one means of achieving it." }, { "name": "Embedding", "difference": "Embedding supports a specimen in a medium for processing or sectioning; fixation stabilises the specimen itself." }, { "name": "Staining", "difference": "Staining produces contrast or labels constituents; fixation primarily preserves material." }, { "name": "Visual fixation", "difference": "Visual fixation concerns maintaining gaze on a target, rather than preserving biological specimens." }, { "name": "Nitrogen fixation", "difference": "Nitrogen fixation converts molecular nitrogen into chemically combined forms." } ], "questions": [ { "id": "evidence-neighbours-q01", "text": "Which of these neighbouring kinds and how to tell them apart hold for the sense of fixation this model covers, and on what evidence?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "Does vr.tr.fixation-q2914991 denote visual fixation, or another sense that requires replacing this provisional scope?", "Which reference works and research communities supply the definitions that this registry entry should represent?", "Which operational criteria are defensible across stationary displays, moving scenes and unrestricted head movement?", "When should microsaccades, blinks and brief tracking gaps divide fixation episodes rather than remain within them?", "What evidence supports task-specific interpretations of fixation duration and stability beyond the gaze observations themselves?" ], "statistics": { "bundles": 5, "layers": 9, "findings": 14, "questions": 27 } }