{ "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-12T09:11:46Z", "providers": [ "Codex" ], "breadth": "recalled by Codex without web access - no source was read", "missingProviders": [], "pass": 2, "cost": { "grok": { "seconds": 21.3, "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: 01a094e1-e898-7f53-afcf-b8458a7421c9\n--------\nuser\nDescribe what is already known about one registered thing. Answer as JSON only, no prose around it.\n\nThing: dikaryon\nSense to describe: (none recorded)\nDomain code: PHY.OBJ\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": 79.3, "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: 01a094e1-e89c-7d61-8e9b-f5ed48e85a48\n--------\nuser\nYou are drafting a Vercy meta-model for one registered thing. Answer as JSON only, no prose around it.\n\nThing: dikaryon\nRegistry id: vr.tr.dikaryon\nPlane / domain: PHY / PHY.OBJ\nRegistry definition: (none recorded)\nNames folded into this entry: (none)\n\n\nContex" } }, "enrichment": { "pass": 3, "engine": "claude", "producedAt": "2026-10-06T12:00:00Z", "ingestedAt": "2026-10-06T08:54:52+00:00", "fields": [ "agent_conduct", "ethics", "failure_modes_and_hazards", "owners", "visual_identification" ] }, "gate": { "passed": true, "version": "1.0", "at": "2026-10-07T10:10:27+00:00", "evidence": [ "completeness 1.00", "sense: Wikidata description", "2 live sources", "review by codex: pass" ] } }, "metaModel": { "id": "THING-Q1923203", "registryId": "vr.tr.dikaryon", "name": "dikaryon", "version": "0.1.0-research.1", "entryKind": "thing", "family": "Thing Registry", "domain": [ "PHY.OBJ" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q1923203/", "model": { "registry_id": "vr.tr.dikaryon", "name": "dikaryon", "purpose": "Enable an agent to recognize a fungal dikaryon, assess whether its paired nuclear organization persists, and select appropriate observation, propagation or developmental investigation.", "definition": "A dikaryon is a fungal cell or mycelium in which two genetically distinct haploid nuclei coexist without fusing in each typically dikaryotic compartment, following plasmogamy and preceding karyogamy.", "scope_statement": "This model owns the dikaryon represented by vr.tr.dikaryon: a fungal cellular organization in which two genetically distinct haploid nuclei coexist without fusion, including its realization in cells, hyphal compartments and dikaryotic mycelia.", "in_scope": [ "Evidence for two separate haploid nuclear partners sharing a cytoplasm", "Nuclear partner identity, compatibility and origin", "Maintenance of nuclear pairing during hyphal growth and division", "Spatial extent and persistence of dikaryotic organization", "Formation, loss and developmental termination of the dikaryotic state" ], "out_of_scope": [ "Complete taxonomy, ecology and physiology of the fungal species", "Diploid cells after nuclear fusion", "Heterokaryotic organization without the specific paired nuclear arrangement", "Complete fruiting body, ascus, basidium and spore models", "Laboratory instruments, culture media and general cultivation protocols" ], "distinguishing_features": [ "Resolve two separate nuclei within a shared cellular compartment; total DNA content alone cannot distinguish n+n organization from one diploid nucleus.", "Establish distinct nuclear partners rather than treating any binucleate cell, including a transient postmitotic cell, as a dikaryon.", "Distinguish organized nuclear pairing from a heterokaryon containing an unspecified number or distribution of nuclear types.", "Assess the relevant tissue and developmental stage before extending a local dikaryon observation to an entire mycelium.", "Treat clamp connections as supporting evidence where appropriate, not a universal requirement or sufficient standalone diagnosis." ], "characteristics": [ { "name": "Observation unit", "kind": "category", "unit_or_values": "cell | hyphal compartment | delimited hyphal region | sampled mycelium", "why_it_matters": "Determines the physical extent to which a dikaryon assessment applies." }, { "name": "Nuclear count distribution", "kind": "measurement", "unit_or_values": "nuclei per compartment, with compartment counts and division stage", "why_it_matters": "Reveals paired organization, transient division states and spatial departures from it." }, { "name": "Ploidy of each nuclear partner", "kind": "category", "unit_or_values": "haploid | diploid | other | unresolved, recorded separately for each partner", "why_it_matters": "Separates the n+n arrangement from diploidy and other nuclear configurations." }, { "name": "Nuclear partner identities", "kind": "relation", "unit_or_values": "links to two nuclear genotypes or parental lineages, with identification evidence", "why_it_matters": "Supports distinction between a dikaryon and binucleate material containing equivalent nuclei." }, { "name": "Mating compatibility", "kind": "state", "unit_or_values": "demonstrated | predicted | incompatible under tested conditions | unresolved", "why_it_matters": "Connects partner association to the species-specific mating system without assuming that different isolates are compatible." }, { "name": "Dikaryotic compartment fraction", "kind": "measurement", "unit_or_values": "% of assessed compartments meeting stated criteria, with sample size", "why_it_matters": "Prevents a mixed or sectoring culture from being represented as uniformly dikaryotic." }, { "name": "Nuclear partitioning structures", "kind": "category", "unit_or_values": "clamp connections | croziers | other observed mechanism | none observed | unresolved", "why_it_matters": "Records lineage-specific structural evidence relevant to maintaining nuclear partners." }, { "name": "Observed state trajectory", "kind": "state", "unit_or_values": "forming | maintained | sectoring or losing a partner | undergoing karyogamy | unresolved", "why_it_matters": "Guides whether to verify establishment, monitor stability or investigate a developmental transition." } ], "affordances": [ "Classify sampled fungal material as confirmed, provisional or unsupported dikaryon using explicit evidence criteria.", "Map nuclear partner distribution across hyphae, compartments and culture sectors.", "Trace a dikaryon to its contributing isolates and recorded mating event.", "Select observations that distinguish nuclear count, nuclear identity and per-nucleus ploidy.", "Assess whether propagation preserves both nuclear partners.", "Identify tissue in which nuclear fusion or partner loss ends the dikaryotic state." ], "agent_conduct": { "may": [ "Describe a dikaryon and its place in the fungal life cycle, citing sources.", "Report microscopy evidence, such as paired nuclei or clamp connections, that supports a dikaryotic state." ], "must_not": [ "Claim a culture is dikaryotic without microscopic or genetic evidence.", "Use dikaryon features alone to declare a wild mushroom safe to eat.", "Release cultures of plant pathogenic fungi outside containment.", "Confuse a dikaryon with a diploid or a heterokaryon in reports." ], "requires_human": [ "Releasing fungal strains into fields or the environment.", "Approving a strain for food production." ] }, "ethics": { "considerations": [ "Many crop diseases are caused by dikaryotic fungi, so handling cultures affects farmers.", "Fungal identification errors can poison people who forage." ], "affected_parties": [ "Farmers and crops", "Foragers", "Researchers" ] }, "owners": { "steward": "The laboratory or culture collection that holds the strain.", "master_systems": [ "Culture collection catalogues" ] }, "visual_identification": [ "Seen only under a microscope, as compartments with two nuclei each.", "In many basidiomycetes, clamp connections at the septa of hyphae." ], "failure_modes_and_hazards": [ "Misreading microscopy leads to wrong strain records.", "Escape of pathogenic cultures." ], "what_it_is_for": [ "Dikaryons occur during the life cycles of many fungi, especially basidiomycetes and some developmental stages of ascomycetes.", "They are studied in fungal genetics, mating biology and development to understand how distinct haploid nuclei coexist before nuclear fusion." ], "facets_not_applicable": { "interfaces": "No generally applicable standard, law or official classification specifically governs the dikaryotic cell state independently of the organism and its use." } }, "sources": [ { "id": "wikidata", "title": "Wikidata item Q1923203: dikaryon", "url": "https://www.wikidata.org/wiki/Q1923203", "url_status": "live", "what_it_supports": "identity and sense of the item", "checked_by": "wikidata-api" }, { "id": "wikipedia-en", "title": "Wikipedia: Dikaryon", "url": "https://en.wikipedia.org/wiki/Dikaryon", "url_status": "live", "what_it_supports": "general description of the item", "checked_by": "wikidata-api sitelink" } ], "structure": { "bundles": [ { "id": "dikaryon-identity", "name": "Dikaryon identity", "description": "Establishes which physical fungal unit carries the paired nuclear organization.", "rationale": "The term can describe a cellular condition or material carrying that condition; an agent must keep these usages connected without assuming uniformity.", "layers": [ { "id": "physical-referent", "name": "Physical referent", "description": "Locates the assessed dikaryon within a specimen or culture.", "findings": [ { "id": "assessment-boundary", "name": "Assessment boundary", "description": "Record whether the assertion concerns one compartment, a hyphal region or a sampled mycelium.", "questions": [ { "text": "What physically delimited cell, hyphal region or culture sample is being called a dikaryon?", "kind": "boundary", "id": "assessment-boundary-q01" }, { "text": "Which observations justify extending that assessment beyond the directly examined compartments?", "kind": "measurement", "id": "assessment-boundary-q02" } ] } ] }, { "id": "nuclear-configuration", "name": "Nuclear configuration", "description": "Separates nuclear number, genetic identity and ploidy.", "findings": [ { "id": "paired-unfused-genomes", "name": "Paired unfused genomes", "description": "Separate nuclei distinguish dikaryotic organization from diploidy; coordinated pairing was studied directly in Schizophyllum commune. [Experimental study](https://pubmed.ncbi.nlm.nih.gov/15342506/)", "questions": [ { "text": "What evidence establishes two separate haploid nuclear partners rather than one diploid nucleus?", "kind": "measurement", "id": "paired-unfused-genomes-q01" }, { "text": "How are distinct nuclear partners distinguished from two equivalent nuclei produced by mitosis?", "kind": "definition", "id": "paired-unfused-genomes-q02" } ] } ] } ] }, { "id": "partner-origin-and-establishment", "name": "Partner origin and establishment", "description": "Records how the two nuclear partners came to coexist.", "rationale": "A dikaryon cannot be adequately characterized by nuclear count without understanding partner identity and the route of establishment.", "layers": [ { "id": "nuclear-lineage", "name": "Nuclear lineage", "description": "Connects each partner to its identified genetic source.", "findings": [ { "id": "partner-provenance", "name": "Partner provenance", "description": "Keep nuclear lineage assignments separate from the identity of the culture containing them.", "questions": [ { "text": "Which parental isolates or nuclear lineages contributed the two partners?", "kind": "provenance", "id": "partner-provenance-q01" }, { "text": "Which markers resolve the partners, and what uncertainty remains in their assignments?", "kind": "measurement", "id": "partner-provenance-q02" } ] } ] }, { "id": "establishment-route", "name": "Establishment route", "description": "Captures compatibility and the observed transition into dikaryotic organization.", "findings": [ { "id": "compatible-association", "name": "Compatible association", "description": "Record the relevant mating system and evidence that a persistent nuclear association was established.", "questions": [ { "text": "What species-specific compatibility evidence supports association of these nuclear partners?", "kind": "definition", "id": "compatible-association-q01" }, { "text": "Was establishment observed after a recorded mating event, inherited in starting material or inferred retrospectively?", "kind": "provenance", "id": "compatible-association-q02" } ] } ] } ] }, { "id": "pair-maintenance", "name": "Pair maintenance", "description": "Examines how growing fungal material retains the two nuclear partners.", "rationale": "A single binucleate observation does not establish persistence through division, septation and branching.", "layers": [ { "id": "division-and-partitioning", "name": "Division and partitioning", "description": "Tracks partner replication and distribution into descendant compartments.", "findings": [ { "id": "daughter-compartment-inheritance", "name": "Daughter compartment inheritance", "description": "Evaluate nuclear inheritance directly; clamp connections are absent in some stable dikaryons. [Coprinopsis cinerea study](https://pmc.ncbi.nlm.nih.gov/articles/PMC3761312/)", "questions": [ { "text": "Do descendant compartments retain representatives of both nuclear partners after division and septation?", "kind": "measurement", "id": "daughter-compartment-inheritance-q01" }, { "text": "What observed role do clamp connections, croziers or another partitioning mechanism play in this material?", "kind": "measurement", "id": "daughter-compartment-inheritance-q02" } ] } ] }, { "id": "spatial-and-temporal-stability", "name": "Spatial and temporal stability", "description": "Distinguishes maintained organization from transient counts and persistent sectors.", "findings": [ { "id": "partner-retention-pattern", "name": "Partner retention pattern", "description": "Record where and when pairing persists, including departures associated with growth or passage.", "questions": [ { "text": "What fraction of assessed compartments retains the paired organization across locations and observation times?", "kind": "measurement", "id": "partner-retention-pattern-q01" }, { "text": "Do departures represent a division stage, partner loss, altered nuclear abundance or a separately growing sector?", "kind": "boundary", "id": "partner-retention-pattern-q02" } ] } ] } ] }, { "id": "developmental-placement", "name": "Developmental placement", "description": "Places the dikaryon within the particular fungus's tissue organization and nuclear cycle.", "rationale": "The extent and duration of dikaryosis cannot be inferred uniformly across fungal lineages.", "layers": [ { "id": "dikaryotic-tissue-and-duration", "name": "Dikaryotic tissue and duration", "description": "Locates the state in vegetative or reproductive development.", "findings": [ { "id": "life-cycle-occupancy", "name": "Life-cycle occupancy", "description": "Separate the duration of observed dikaryosis from assumptions based on fungal group membership.", "questions": [ { "text": "Which vegetative or reproductive tissues are demonstrated to be dikaryotic in this organism?", "kind": "boundary", "id": "life-cycle-occupancy-q01" }, { "text": "For how long and through which developmental stages has the state been observed?", "kind": "measurement", "id": "life-cycle-occupancy-q02" } ] } ] }, { "id": "exit-from-dikaryosis", "name": "Exit from dikaryosis", "description": "Identifies transitions that terminate the paired unfused nuclear condition.", "findings": [ { "id": "fusion-or-partner-loss", "name": "Fusion or partner loss", "description": "Distinguish karyogamy from disappearance or segregation of a nuclear partner.", "questions": [ { "text": "What evidence distinguishes nuclear fusion from loss of one partner in the observed transition?", "kind": "measurement", "id": "fusion-or-partner-loss-q01" }, { "text": "At which cell or tissue boundary should the record hand off to a diploid or other nuclear-state model?", "kind": "boundary", "id": "fusion-or-partner-loss-q02" } ] } ] } ] }, { "id": "verification-and-propagation", "name": "Verification and propagation", "description": "Connects diagnostic evidence to decisions about sampling and maintaining dikaryotic material.", "rationale": "An agent needs to know which assessments are justified and whether handling preserves the defining nuclear association.", "layers": [ { "id": "diagnostic-evidence", "name": "Diagnostic evidence", "description": "Combines microscopy and genetic evidence without treating either as universally decisive.", "findings": [ { "id": "evidence-sufficiency", "name": "Evidence sufficiency", "description": "Assess whether methods establish co-residence of the partners rather than merely detecting two genotypes in pooled material.", "questions": [ { "text": "Which observations demonstrate that both nuclear partners occupy the same compartments rather than separate mixed hyphae?", "kind": "measurement", "id": "evidence-sufficiency-q01" }, { "text": "What additional observation would resolve the current uncertainty in a provisional dikaryon assessment?", "kind": "action", "id": "evidence-sufficiency-q02" } ] } ] }, { "id": "propagation-fidelity", "name": "Propagation fidelity", "description": "Evaluates retention of the paired state after transfer, storage or experimental manipulation.", "findings": [ { "id": "post-handling-verification", "name": "Post-handling verification", "description": "Treat continued growth and continued dikaryosis as separate outcomes requiring appropriate evidence.", "questions": [ { "text": "Which propagation or storage method has been shown to retain both partners in this material?", "kind": "action", "id": "post-handling-verification-q01" }, { "text": "What post-handling checks establish partner identity and dikaryotic organization before further use?", "kind": "action", "id": "post-handling-verification-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": [ "The entry denotes a nuclear organization or a fungal structure exhibiting it, rather than a taxonomic kind of organism.", "Duration, distribution and maintenance of the dikaryotic condition vary among fungal groups; clamp connections are not universal.", "Nuclear counts can vary during division and between compartments; the characteristic n+n organization is the defining reference state." ], "questions": [ { "id": "evidence-confidence-notes-q01", "text": "Which of these check these first hold for the sense of dikaryon 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": [ "Basidiomycete dikaryons, often maintained through extensive mycelial growth", "Ascomycete dikaryons, usually restricted to ascogenous hyphae and developing asci" ], "questions": [ { "id": "evidence-kinds-q01", "text": "Which of these kinds and varieties hold for the sense of dikaryon 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": [ "Study of fungal mating compatibility, nuclear coordination and sexual reproduction", "Breeding and cultivation of mushroom-forming fungi with dikaryotic mycelia" ], "questions": [ { "id": "evidence-real-world-use-q01", "text": "Which of these real-world use hold for the sense of dikaryon 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": "Nuclei per dikaryotic cell or hyphal compartment", "typical_range": "2 in the characteristic state", "unit": "nuclei" }, { "quantity": "Ploidy of each paired nucleus", "typical_range": "Haploid (n); the pair is conventionally written n+n", "unit": "chromosome sets per nucleus" } ], "questions": [ { "id": "evidence-measurements-q01", "text": "Which of these typical measurements hold for the sense of dikaryon 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": "Heterokaryon", "difference": "A heterokaryon contains genetically different nuclei in shared cytoplasm; a dikaryon is the specifically paired, two-haploid-nucleus condition." }, { "name": "Diploid cell", "difference": "A diploid cell has two chromosome sets within one nucleus; a dikaryon retains the haploid sets in separate nuclei." }, { "name": "Monokaryon", "difference": "A monokaryon has one nucleus per characteristic compartment rather than the paired nuclei of a dikaryon." }, { "name": "Dikarya", "difference": "Dikarya is the fungal clade containing Ascomycota and Basidiomycota; a dikaryon is a cellular or mycelial condition." } ], "questions": [ { "id": "evidence-neighbours-q01", "text": "Which of these neighbouring kinds and how to tell them apart hold for the sense of dikaryon this model covers, and on what evidence?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "Which authoritative definition should govern atypical material with two persistent nuclear lineages but variable numbers of nuclei per compartment?", "What lineage-specific evidence is sufficient to confirm dikaryosis when clamp connections or croziers are absent?", "How should the model represent genetic divergence arising within either nuclear lineage during prolonged growth?", "What sampling coverage justifies describing an entire mycelium as dikaryotic when different sectors have different nuclear states?", "Which propagation and storage conditions preserve the paired state for each relevant species or strain?" ], "statistics": { "bundles": 6, "layers": 11, "findings": 15, "questions": 25 } }