{ "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-12T09:36:53Z", "providers": [ "Codex" ], "breadth": "recalled by Codex without web access - no source was read", "missingProviders": [], "pass": 2, "cost": { "grok": { "seconds": 21.4, "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: 01a094f9-079d-79e2-a5ec-048c6705c992\n--------\nuser\nDescribe what is already known about one registered thing. Answer as JSON only, no prose around it.\n\nThing: eyespot apparatus\nSense to describe: (none recorded)\nDomain code: PHY.LIV\nAlso known as: (none)\n\n\nContext for this batch of 1001 things:\n# Batch 043: 10", "usd": 0.0, "recall": true }, "codex": { "seconds": 71.0, "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: 01a094f9-07aa-76b2-bc69-a9af7cca2a5e\n--------\nuser\nYou are drafting a Vercy meta-model for one registered thing. Answer as JSON only, no prose around it.\n\nThing: eyespot apparatus\nRegistry id: vr.tr.eyespot-apparatus\nPlane / domain: PHY / PHY.LIV\nRegistry definition: (none recorded)\nNames folded into this entr" } }, "enrichment": { "pass": 3, "engine": "claude", "producedAt": "2026-10-06T12:00:00Z", "ingestedAt": "2026-10-06T08:49:49+00:00", "fields": [ "agent_conduct", "ethics", "failure_modes_and_hazards", "owners", "visual_identification" ] }, "gate": { "passed": true, "version": "1.0", "at": "2026-10-07T10:10:28+00:00", "evidence": [ "completeness 1.00", "sense: Wikidata description", "2 live sources", "review by codex: pass" ] } }, "metaModel": { "id": "THING-Q22329156", "registryId": "vr.tr.eyespot-apparatus", "name": "eyespot apparatus", "version": "0.1.0-research.1", "entryKind": "thing", "family": "Thing Registry", "domain": [ "PHY.LIV" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q22329156/", "model": { "registry_id": "vr.tr.eyespot-apparatus", "name": "eyespot apparatus", "purpose": "Enable an agent to recognise an eyespot apparatus, assess its structural and light-sensing state, and select observations or interventions appropriate to its host cell.", "definition": "An eyespot apparatus is a subcellular light-sensing system in certain motile algae and other protists that combines photoreceptors with an associated pigmented optical structure to detect light direction and guide swimming.", "scope_statement": "This model owns the subcellular apparatus that combines an eyespot pigment structure with associated photoreceptive components for directional light sensing, including lineage-specific arrangements and interfaces with cellular movement, under registry entry vr.tr.eyespot-apparatus.", "in_scope": [ "Pigment globules, their organisation, and associated photoreceptive components", "Position within the host cell and alignment between optical and receptor components", "Directional light modulation and stimulus-dependent receptor activity", "Assembly, maintenance, and disruption of the apparatus", "Evidence connecting apparatus condition to host-cell photobehaviour" ], "out_of_scope": [ "Host-organism taxonomy, geographic range, and conservation assessment", "Animal eyes, ocelli, and decorative eyespot markings", "Whole-chloroplast photosynthesis and general pigment metabolism", "Flagellar construction and the complete locomotor system", "Photoreceptor proteins considered independently of their association with the apparatus" ], "distinguishing_features": [ "It is a subcellular apparatus within a host cell, not a species, population, or individual organism.", "A visible pigmented spot alone is insufficient: identification must establish or explicitly leave unresolved its association with photoreceptive components.", "Its identification requires evidence of an organised light-sensing arrangement rather than carotenoid pigmentation alone.", "Architecture is lineage-dependent: Chlamydomonas reinhardtii has chloroplast pigment arrays associated with plasma-membrane receptors, whereas Euglena gracilis has cytosolic eyespot globules associated with a paraflagellar photoreceptive body.", "Directional light sensing must be distinguished from image formation and from a general response to changes in illumination." ], "characteristics": [ { "name": "Host and observation context", "kind": "relation", "unit_or_values": "Host taxon, strain, individual cell, life stage, and culture condition", "why_it_matters": "Prevents a configuration observed in one lineage or condition from becoming a universal requirement." }, { "name": "Apparatus architecture", "kind": "category", "unit_or_values": "Chloroplast-associated arrays with adjacent receptors; cytosolic globules with paraflagellar photoreception; other documented arrangement; unresolved", "why_it_matters": "Determines which compartments and components must be examined." }, { "name": "Pigment structure dimensions", "kind": "measurement", "unit_or_values": "Length and width in µm; globule diameter in nm; globule and layer counts", "why_it_matters": "Supports comparison of assembly and structural changes using comparable imaging methods." }, { "name": "Pigment composition", "kind": "category", "unit_or_values": "Identified carotenoids with analytical method; unresolved", "why_it_matters": "Visible colour cannot establish molecular composition or functional competence." }, { "name": "Receptor identity and localisation", "kind": "relation", "unit_or_values": "Receptor or receptor complex linked to its cellular compartment and localisation evidence", "why_it_matters": "Separates pigment-based optical modulation from molecular photoreception." }, { "name": "Optical and receptor alignment", "kind": "measurement", "unit_or_values": "Component separation in nm or µm; orientation in degrees relative to defined cellular axes", "why_it_matters": "Relative positioning can affect directional sensitivity even when components are present." }, { "name": "Assembly condition", "kind": "state", "unit_or_values": "Assembling; structurally intact; disorganised; reduced; absent under validated observation; unresolved", "why_it_matters": "Distinguishes developmental or structural changes from failures of detection." }, { "name": "Light-response profile", "kind": "measurement", "unit_or_values": "Response versus wavelength in nm, photon irradiance in µmol photons m−2 s−1, incidence angle in degrees, and time in ms or s", "why_it_matters": "A functional judgement requires a specified stimulus and measured endpoint." } ], "affordances": [ "Identify a candidate apparatus using host context, microscopy, and receptor-localisation evidence.", "Measure pigment organisation and its alignment with photoreceptive components.", "Select illumination conditions for testing directional sensitivity.", "Compare apparatus structure and photobehaviour across developmental states or controlled perturbations.", "Distinguish an apparatus defect from impaired motility or compromised cell condition.", "Record unresolved component identities or causal mechanisms without treating them as established." ], "agent_conduct": { "may": [ "Describe the eyespot apparatus and how algae use it to sense light, from reliable sources.", "Record its presence and position in microscopy observations of protists." ], "must_not": [ "Confuse the eyespot apparatus with an animal eye in descriptions or data.", "Present preliminary research on eyespots as established fact.", "Release genetically modified algae from a laboratory without approval." ], "requires_human": [ "Approving experiments with genetically modified algae outside contained facilities." ] }, "ethics": { "considerations": [ "Research on algal light sensing feeds into biotechnology that needs responsible oversight." ], "affected_parties": [ "Researchers and students", "Aquatic ecosystems" ] }, "owners": { "steward": "Nobody owns the structure; the laboratory or keeper answers for each culture.", "master_systems": [] }, "visual_identification": [ "A small red or orange spot inside a single-celled alga, seen under a light microscope.", "Lies near the base of the flagella in swimming cells such as Chlamydomonas or Euglena." ], "failure_modes_and_hazards": [ "Damage to the eyespot leaves the cell unable to steer towards light." ], "what_it_is_for": [ "An eyespot apparatus occurs in certain motile algae and other protists, where it contributes to sensing the direction of light.", "Its signals help the host cell adjust swimming in relation to illumination and conditions relevant to photosynthesis.", "Researchers study the apparatus through microscopy and measurements of cellular responses to light." ], "facets_not_applicable": { "interfaces": "No dedicated technical standard or regulation applies to the eyespot apparatus itself as a naturally occurring subcellular system." } }, "sources": [ { "id": "wikidata", "title": "Wikidata item Q22329156: eyespot apparatus", "url": "https://www.wikidata.org/wiki/Q22329156", "url_status": "live", "what_it_supports": "identity and sense of the item", "checked_by": "wikidata-api" }, { "id": "wikipedia-en", "title": "Wikipedia: Eyespot apparatus", "url": "https://en.wikipedia.org/wiki/Eyespot_apparatus", "url_status": "live", "what_it_supports": "general description of the item", "checked_by": "wikidata-api sitelink" } ], "structure": { "bundles": [ { "id": "identity-and-lineage", "name": "Identity and lineage", "description": "Establish what counts as this apparatus in the observed host.", "rationale": "The registry entry represents a cellular structure with multiple architectures, not an organism or a single universal organelle configuration.", "layers": [ { "id": "apparatus-boundary", "name": "Apparatus boundary", "description": "Separate the complete functional arrangement from its visible pigment component.", "findings": [ { "id": "pigment-plus-photoreception", "name": "Pigment structure and photoreception", "description": "Record the pigment structure and associated photoreceptive components separately before asserting the complete apparatus. Terminology can distinguish the eyespot from the larger apparatus. Source: [Kato et al.](https://pmc.ncbi.nlm.nih.gov/articles/PMC7155050/).", "questions": [ { "text": "Does 'eyespot' in this observation mean the pigment globules or the complete photoreceptive apparatus?", "kind": "definition", "id": "pigment-plus-photoreception-q01" }, { "text": "What evidence associates the observed pigment structure with photoreceptive components?", "kind": "provenance", "id": "pigment-plus-photoreception-q02" } ] } ] }, { "id": "host-specific-architecture", "name": "Host-specific architecture", "description": "Qualify anatomical expectations by host identity.", "findings": [ { "id": "compartment-pattern", "name": "Compartment pattern", "description": "Chlamydomonas and Euglena demonstrate different pigment and receptor compartment arrangements; record the observed arrangement without assuming evolutionary equivalence. Source: [Kato et al.](https://pmc.ncbi.nlm.nih.gov/articles/PMC7155050/).", "questions": [ { "text": "Which taxon, strain, and cellular stage support the proposed architectural identification?", "kind": "provenance", "id": "compartment-pattern-q01" }, { "text": "Which components lie in the chloroplast, cytosol, plasma membrane, or paraflagellar region?", "kind": "boundary", "id": "compartment-pattern-q02" } ] } ] } ] }, { "id": "pigment-optics-and-geometry", "name": "Pigment optics and geometry", "description": "Describe the pigment structure and its spatial contribution to light sensing.", "rationale": "Pigment presence alone does not establish the geometry or optical effect needed for directional sensing.", "layers": [ { "id": "globule-organisation", "name": "Globule organisation", "description": "Resolve pigment bodies, arrays, and surrounding membranes.", "findings": [ { "id": "array-structure", "name": "Array structure", "description": "Measure globule size, packing, and layer organisation where present. Ordered chloroplast globule layers are documented in Chlamydomonas reinhardtii. Source: [Schmidt et al.](https://pmc.ncbi.nlm.nih.gov/articles/PMC1533972/).", "questions": [ { "text": "What globule dimensions, packing pattern, and layer count are resolved by the imaging method?", "kind": "measurement", "id": "array-structure-q01" }, { "text": "Which observations distinguish eyespot globules from neighbouring lipid bodies or other pigment deposits?", "kind": "boundary", "id": "array-structure-q02" } ] } ] }, { "id": "directional-optics", "name": "Directional optics", "description": "Assess how geometry changes illumination reaching the receptor.", "findings": [ { "id": "optical-effect", "name": "Optical effect", "description": "Distinguish measured shielding or reflection from proposed mechanisms. Euglena eyespots should not automatically inherit the reflective role attributed to ordered algal arrays. Source: [Kato et al.](https://pmc.ncbi.nlm.nih.gov/articles/PMC7155050/).", "questions": [ { "text": "How does illumination at the receptor vary with light direction relative to the pigment structure?", "kind": "measurement", "id": "optical-effect-q01" }, { "text": "Is the assigned shielding or reflective role measured in this host or inferred from another system?", "kind": "provenance", "id": "optical-effect-q02" } ] } ] } ] }, { "id": "photoreception-and-movement-interface", "name": "Photoreception and movement interface", "description": "Connect local light detection to cellular responses while retaining the apparatus boundary.", "rationale": "A cell's movement is an indirect readout that can fail for reasons outside the eyespot apparatus.", "layers": [ { "id": "receptor-response", "name": "Receptor response", "description": "Identify the photoreceptive component and characterise its response.", "findings": [ { "id": "localised-light-detection", "name": "Localised light detection", "description": "Record receptor identity, localisation, and stimulus-response evidence independently. Channelrhodopsins are documented photoreceptors in Chlamydomonas reinhardtii; this identity is not a universal eyespot requirement. Source: [Kato et al.](https://pmc.ncbi.nlm.nih.gov/articles/PMC7155050/).", "questions": [ { "text": "Which receptor is supported by molecular and localisation evidence in this host?", "kind": "provenance", "id": "localised-light-detection-q01" }, { "text": "What wavelength, irradiance, and response latency characterise the measured receptor activity?", "kind": "measurement", "id": "localised-light-detection-q02" } ] } ] }, { "id": "behavioural-coupling", "name": "Behavioural coupling", "description": "Separate directional navigation from other light-induced movements.", "findings": [ { "id": "photobehaviour-readout", "name": "Photobehaviour readout", "description": "Record movement toward or away from a light direction separately from transient avoidance responses, and qualify attribution to the apparatus with motility controls.", "questions": [ { "text": "Does the assay measure directional phototaxis, a transient light response, or a change in swimming speed?", "kind": "definition", "id": "photobehaviour-readout-q01" }, { "text": "Which control shows that an altered response is not explained by loss of flagellar motility?", "kind": "action", "id": "photobehaviour-readout-q02" } ] } ] } ] }, { "id": "assembly-and-structural-state", "name": "Assembly and structural state", "description": "Track apparatus formation, placement, and structural disruption.", "rationale": "Component presence, correct placement, and functional assembly are distinct states.", "layers": [ { "id": "formation-and-placement", "name": "Formation and placement", "description": "Relate assembly to the host cell cycle and positioning machinery.", "findings": [ { "id": "assembly-context", "name": "Assembly context", "description": "Chlamydomonas reinhardtii eyespots assemble after division and associate with a defined microtubule rootlet; apply this pattern only where supported. Source: [Boyd et al.](https://pubmed.ncbi.nlm.nih.gov/21372178/).", "questions": [ { "text": "At what cell-cycle stage was apparatus formation or reorganisation observed?", "kind": "measurement", "id": "assembly-context-q01" }, { "text": "What evidence links apparatus position to a cellular landmark or assembly factor in this host?", "kind": "provenance", "id": "assembly-context-q02" } ] } ] }, { "id": "component-integrity", "name": "Component integrity", "description": "Distinguish loss of pigment, receptor organisation, and alignment.", "findings": [ { "id": "structural-defect-classification", "name": "Structural defect classification", "description": "Classify observed defects by affected component rather than assigning a single functional state from spot visibility.", "questions": [ { "text": "Are pigment globules, receptor localisation, component alignment, or several of these altered?", "kind": "measurement", "id": "structural-defect-classification-q01" }, { "text": "What additional observation is needed before a visually undetected apparatus can be classified as absent?", "kind": "action", "id": "structural-defect-classification-q02" } ] } ] } ] }, { "id": "observation-and-perturbation", "name": "Observation and perturbation", "description": "Support interpretable examinations and experiments on the apparatus.", "rationale": "Imaging, illumination, and pigment interventions can change the structure or behaviour being assessed.", "layers": [ { "id": "measurement-context", "name": "Measurement context", "description": "Retain conditions needed to interpret structural and functional observations.", "findings": [ { "id": "assay-interpretability", "name": "Assay interpretability", "description": "Associate each result with cell preparation, illumination history, spatial resolution, and whether the specimen was alive or fixed.", "questions": [ { "text": "Was the apparatus observed in a live, fixed, sectioned, or isolated preparation?", "kind": "provenance", "id": "assay-interpretability-q01" }, { "text": "What resolution and illumination history limit conclusions about component alignment or light sensitivity?", "kind": "measurement", "id": "assay-interpretability-q02" } ] } ] }, { "id": "causal-interventions", "name": "Causal interventions", "description": "Evaluate whether a manipulation specifically explains an apparatus-associated change.", "findings": [ { "id": "perturbation-attribution", "name": "Perturbation attribution", "description": "Record the targeted pigment, receptor, or assembly process alongside possible host-cell effects and evidence of recovery or rescue.", "questions": [ { "text": "Which apparatus component is targeted, and which other cellular processes could the intervention affect?", "kind": "boundary", "id": "perturbation-attribution-q01" }, { "text": "Which matched control or rescue would support attributing the observed photobehaviour change to the apparatus?", "kind": "action", "id": "perturbation-attribution-q02" } ] } ] } ] }, { "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": [ "This entry describes a cellular apparatus, not an organism or taxon; taxonomic authorities and conservation assessments do not apply to it.", "Eyespot organization and photoreceptor chemistry differ across lineages; the Chlamydomonas arrangement should not be generalized to all protists.", "Terminology varies over whether 'eyespot' includes the photoreceptor apparatus or only its pigmented optical component." ], "questions": [ { "id": "evidence-confidence-notes-q01", "text": "Which of these check these first hold for the sense of eyespot apparatus 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": [ "Chloroplast-associated eyespot apparatus of green algae such as Chlamydomonas", "Extraplastidial eyespot apparatus of euglenoids such as Euglena" ], "questions": [ { "id": "evidence-kinds-q01", "text": "Which of these kinds and varieties hold for the sense of eyespot apparatus 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": [ "Guides phototaxis, helping cells move toward or away from illumination.", "Provides experimental systems for studying photoreception, cellular polarity and flagellar coordination.", "Research on Chlamydomonas photoreceptors contributed to the development of channelrhodopsin-based optogenetics." ], "questions": [ { "id": "evidence-real-world-use-q01", "text": "Which of these real-world use hold for the sense of eyespot apparatus 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": "Phototactic response", "typical_range": "Species- and condition-dependent; measured as swimming direction relative to incident light", "unit": "degrees" }, { "quantity": "Spectral sensitivity", "typical_range": "Species- and photoreceptor-dependent; characterized by an action spectrum", "unit": "nm" } ], "questions": [ { "id": "evidence-measurements-q01", "text": "Which of these typical measurements hold for the sense of eyespot apparatus 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": [ "Disruption of pigment organization or eyespot positioning can impair directional light sensing.", "Defective photoreceptors or downstream signaling can reduce or abolish phototaxis.", "Defective flagellar coordination can prevent an appropriate swimming response despite light detection." ], "questions": [ { "id": "evidence-failure-modes-and-hazards-q01", "text": "Which of these failure modes and hazards hold for the sense of eyespot apparatus 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": "Stigma", "difference": "Often used synonymously with eyespot, but can refer specifically to the pigmented component rather than the entire photoreceptor-associated apparatus." }, { "name": "Photoreceptor protein", "difference": "A molecule that detects light; the eyespot apparatus includes cellular structures that support directional sensing." }, { "name": "Chloroplast", "difference": "A photosynthetic organelle that contains the pigment layers of some eyespots; an eyespot apparatus has a specialized sensory role and may span multiple cellular compartments." }, { "name": "Ocellus", "difference": "A simple animal eye composed of cells or tissues, whereas the protist eyespot apparatus is subcellular." }, { "name": "Eyespot coloration", "difference": "An eye-like marking on an organism, such as a butterfly wing pattern, rather than a light-sensing apparatus." } ], "questions": [ { "id": "evidence-neighbours-q01", "text": "Which of these neighbouring kinds and how to tell them apart hold for the sense of eyespot apparatus this model covers, and on what evidence?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "Does the registry intend to include all protist structures called eyespot apparatuses, including architectures beyond the Chlamydomonas and Euglena examples?", "What minimum anatomical and functional evidence should distinguish a complete apparatus from an isolated stigma or pigment aggregate?", "Which proposed optical mechanisms have been directly demonstrated in each included lineage?", "What host-specific reference ranges distinguish normal assembly variation from structural defects?", "Which assay combinations can reliably separate apparatus dysfunction from altered light adaptation, cell condition, or motility?" ], "statistics": { "bundles": 6, "layers": 11, "findings": 16, "questions": 26 } }