{ "model": { "rank": 11742, "code": "thing-q83185", "model_id": "vr.tr.horizontal-gene-transfer", "name": "horizontal gene transfer", "purpose": "Let an agent explain horizontal gene transfer and its mechanisms and evidence, describe its significance for evolution, antibiotic resistance and biotechnology, and support learning in genetics and microbiology.", "family": "Thing Registry", "category": "Activities and processes", "status": "research-draft", "kind": "thing", "plane": "ACT", "domain": "ACT.PRC", "industry": "", "version": "", "url": "/models/thing/q83185/", "tier": 2, "score": 41, "payload": { "layer": "wikidata", "aliases": [ "genome invasion", "introgression", "unidirectional conjugation", "DNA mediated transformation" ], "aliasCount": 4, "merged": 4, "knownIn": 41, "facets": null, "markers": [], "lexicalClass": "", "senseRank": null, "alsoRegisteredAs": null, "source": { "dataset": "wikidata", "item": "Q83185", "url": "https://www.wikidata.org/wiki/Q83185", "license": "CC0 1.0" } }, "research": { "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-12T05:08:45Z", "providers": [ "Claude" ], "breadth": "written by Claude from model knowledge without web access - no source was read, every claim is a lead to verify", "pass": 2, "wave": 2, "engine": "claude" }, "metaModel": { "id": "THING-Q83185", "registryId": "vr.tr.horizontal-gene-transfer", "name": "horizontal gene transfer", "version": "0.2.0-wave.2", "entryKind": "thing", "family": "Thing Registry", "domain": [ "ACT.PRC" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q83185/", "model": { "registry_id": "vr.tr.horizontal-gene-transfer", "name": "horizontal gene transfer", "purpose": "Let an agent explain horizontal gene transfer and its mechanisms and evidence, describe its significance for evolution, antibiotic resistance and biotechnology, and support learning in genetics and microbiology.", "definition": "The movement of genetic material between organisms other than by descent from parent to offspring, occurring in bacteria and archaea through transformation by uptake of DNA, conjugation through cell contact and transduction by viruses, and in eukaryotes through introgression, viral integration and other routes; horizontal gene transfer spreads antibiotic resistance and other traits, complicates the tree of life, and is used in genetic engineering.", "what_it_is_for": "Gene movement between organisms other than by descent.", "affordances": [ "explain mechanisms", "describe significance", "describe biotechnology use", "support learning" ], "distinguishing_features": [ "Non-vertical", "Multiple mechanisms", "Common in prokaryotes", "Evolutionary impact" ], "appearance": "Not physical; a genetic process.", "visual_identification": [ "Genes moving between organisms not parent to offspring", "Transformation, conjugation, transduction, introgression", "Vertical transfer is inheritance; mutation changes existing genes" ], "physical_properties": [], "families_and_kinds": [ "transformation", "conjugation", "transduction", "introgression and hybridisation in eukaryotes", "engineered gene transfer" ], "related_models": [ { "relation": "is a kind of", "target": "genetic transfer", "why": "category" }, { "relation": "is a kind of", "target": "cellular process or phenomenon", "why": "category" }, { "relation": "is related to", "target": "pathogen", "why": "spread of resistance in pathogens" }, { "relation": "is related to", "target": "cloning", "why": "gene transfer in biotechnology" } ], "identifiers": [], "standards_and_regulation": [ "Biosafety rules for genetic engineering", "Antimicrobial resistance surveillance", "Regulation of genetically modified organisms" ], "failure_modes_and_hazards": [ "Spread of antibiotic resistance", "Overstating transfer in eukaryotes", "Confusing mechanisms" ], "in_scope": [], "out_of_scope": [], "characteristics": [] }, "sources": [], "structure": { "bundles": [ { "id": "understand", "name": "Understand", "description": "What horizontal gene transfer is.", "rationale": "Genetics.", "layers": [ { "id": "concept", "name": "Concept", "description": "Concept and mechanisms.", "findings": [ { "id": "concept-finding", "name": "Concept", "description": "Concept.", "questions": [ { "text": "What is horizontal gene transfer, and how do transformation, conjugation and transduction work?", "kind": "definition" }, { "text": "Which mechanism or organism group is meant?", "kind": "boundary" } ] } ] }, { "id": "eukaryotes", "name": "Eukaryotes", "description": "In eukaryotes.", "findings": [ { "id": "eukaryotes-finding", "name": "Eukaryotes", "description": "Eukaryotes.", "questions": [ { "text": "How does gene transfer occur in eukaryotes through introgression and other routes, and how common is it?", "kind": "provenance" }, { "text": "Which findings are contested?", "kind": "boundary" } ] } ] } ] }, { "id": "significance", "name": "Significance", "description": "Significance.", "rationale": "Science.", "layers": [ { "id": "evolution", "name": "Evolution", "description": "Evolution.", "findings": [ { "id": "evolution-finding", "name": "Evolution", "description": "Evolution.", "questions": [ { "text": "How does horizontal gene transfer affect evolution and the concept of the tree of life?", "kind": "provenance" }, { "text": "Which entry fits phylogenetics?", "kind": "action" } ] } ] }, { "id": "resistance", "name": "Resistance", "description": "Antibiotic resistance.", "findings": [ { "id": "resistance-finding", "name": "Resistance", "description": "Resistance.", "questions": [ { "text": "How does gene transfer spread antibiotic resistance, and how is it monitored?", "kind": "provenance" }, { "text": "Which entry fits antimicrobial resistance?", "kind": "action" } ] } ] } ] }, { "id": "apply", "name": "Apply", "description": "Detection and biotechnology.", "rationale": "Practice.", "layers": [ { "id": "detect", "name": "Detect", "description": "Detecting transfer.", "findings": [ { "id": "detect-finding", "name": "Detect", "description": "Detection.", "questions": [ { "text": "How is horizontal gene transfer detected in genomes?", "kind": "provenance" }, { "text": "Which entry fits genomics?", "kind": "action" } ] } ] }, { "id": "biotech", "name": "Biotech", "description": "Biotechnology.", "findings": [ { "id": "biotech-finding", "name": "Biotech", "description": "Biotechnology.", "questions": [ { "text": "How is gene transfer harnessed in genetic engineering, and how is it regulated?", "kind": "provenance" }, { "text": "Which entry fits genetic engineering?", "kind": "action" } ] } ] } ] }, { "id": "learn", "name": "Learn", "description": "History and teaching.", "rationale": "Education.", "layers": [ { "id": "history", "name": "History", "description": "History.", "findings": [ { "id": "history-finding", "name": "History", "description": "History.", "questions": [ { "text": "How was horizontal gene transfer discovered, from Griffith and Avery to modern genomics?", "kind": "provenance" }, { "text": "Which references are standard?", "kind": "provenance" } ] } ] }, { "id": "teach", "name": "Teach", "description": "Teaching.", "findings": [ { "id": "teach-finding", "name": "Teach", "description": "Teaching.", "questions": [ { "text": "How can horizontal gene transfer be taught?", "kind": "action" }, { "text": "Which misconceptions arise?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "Should each mechanism be a separate entry?", "How should resistance surveillance be linked?", "How should research literature be linked?" ], "statistics": { "bundles": 4, "layers": 8, "findings": 8, "questions": 16 } }, "draft": { "generator": "vr.draft.v3", "status": "draft-generated", "researched": false, "archetype": "abstract concept", "method": "Written from the archetype playbook - what this kind of thing needs beyond identity and provenance - and from the structure that recurred across 6,333 models already researched by two engines. Applied to this entry by rule. No source was read for this thing and no claim here is researched. This entry carries no facets of its own, so they were inferred from its domain - a guess about a whole domain applied to one thing.", "facetsInferred": true, "nextPass": "A researcher replaces this draft with a sourced specification. Treat every sentence below as a proposal to argue with.", "purpose": "Give an agent a durable, checkable way to recognise a horizontal gene transfer, record what state it is in, and decide what may be done with it.", "whatItIs": "Let an agent explain horizontal gene transfer and its mechanisms and evidence, describe its significance for evolution, antibiotic resistance and biotechnology, and support learning in genetics and microbiology.", "characteristics": { "substance": "activity", "origin": "conceptual", "agency": "inert" }, "whatYouCanDoWithIt": [ "observed and measured" ], "distinguishingFeatures": [ "Names folded into this entry, which a task may need to split apart again: genome invasion, introgression, unidirectional conjugation, DNA mediated transformation.", "4 finer distinctions are held as aliases rather than separate entries, because telling them apart needs a task that asks for it.", "Described in 41 Wikipedia languages, which is a measure of how widely the thing is known, not of how important it is." ], "openQuestionsForResearch": [ "Which of the bundles below does a real task actually need, and which are ceremony?", "What does this thing have that the facets do not capture at all?", "Which neighbouring kind is most often confused with a horizontal gene transfer, and on what evidence are they told apart?" ], "whatItIsMadeOf": "something that happens over time", "physicalCharacter": [ "Does nothing on its own; everything it does, something else did to it.", "These come from the domain this entry sits in rather than from the entry itself, so treat them as a first guess about the whole domain applied to one thing." ], "whatCanBeDoneWithIt": [ "observe it, measure it, record its state" ], "howItIsRecognised": [ "Nothing to see. What is recognised is an instance of it, and which instances count is exactly what is argued about." ], "relatedModels": [ { "relation": "covers", "note": "Finer kinds folded into this entry because telling them apart needs a task that asks for it. Each is a model waiting to be split out when one does.", "targets": [ "genome invasion", "introgression", "unidirectional conjugation", "DNA mediated transformation" ] } ], "standing": "Described in 41 Wikipedia languages, which measures how widely it is written about rather than how important or how common it is. 4 finer distinctions are held inside this entry as names rather than as separate models.", "structure": { "bundles": [ { "id": "identity-and-classification", "name": "Identity, naming and classification", "description": "How an agent tells one horizontal gene transfer from another, and a horizontal gene transfer from things that resemble it.", "rationale": "Recognition comes before every other claim. Without stable identity nothing else in the model can be trusted to be about the same thing twice.", "layers": [ { "id": "naming-and-identifiers", "name": "Names and identifiers", "description": "The names this thing goes by and the identifiers that survive translation and time.", "findings": [ { "id": "preferred-name-and-aliases", "name": "Preferred name, aliases and local names", "description": "Which name to use, which names mean the same thing, and which merely sound similar.", "questions": [ { "id": "preferred-name-and-aliases-q01", "text": "What identifies and describes the name of a horizontal gene transfer, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "preferred-name-and-aliases-q02", "text": "Who or what asserted this about the name of a horizontal gene transfer, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "preferred-name-and-aliases-q03", "text": "What may an agent decide or do once the name of a horizontal gene transfer is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] }, { "id": "stable-identifiers", "name": "Stable identifiers and external keys", "description": "Identifiers that keep pointing at this kind of thing across systems and languages.", "questions": [ { "id": "stable-identifiers-q01", "text": "What identifies and describes an identifier for a horizontal gene transfer, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "stable-identifiers-q02", "text": "Who or what asserted this about an identifier for a horizontal gene transfer, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "stable-identifiers-q03", "text": "What may an agent decide or do once an identifier for a horizontal gene transfer is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] }, { "id": "classification-and-granularity", "name": "Classification and granularity", "description": "Where a horizontal gene transfer sits among kinds, and how finely a task needs to cut it.", "findings": [ { "id": "kind-and-parents", "name": "Kind, parents and neighbouring kinds", "description": "The classes this thing belongs to and the ones it is next to.", "questions": [ { "id": "kind-and-parents-q01", "text": "What identifies and describes the kind of a horizontal gene transfer, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "kind-and-parents-q02", "text": "Who or what asserted this about the kind of a horizontal gene transfer, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "kind-and-parents-q03", "text": "What may an agent decide or do once the kind of a horizontal gene transfer is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] }, { "id": "distinguishing-features", "name": "Distinguishing features", "description": "What separates a horizontal gene transfer from the things most often confused with it.", "questions": [ { "id": "distinguishing-features-q01", "text": "What identifies and describes what distinguishes a horizontal gene transfer, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "distinguishing-features-q02", "text": "Who or what asserted this about what distinguishes a horizontal gene transfer, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "distinguishing-features-q03", "text": "What may an agent decide or do once what distinguishes a horizontal gene transfer is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] }, { "id": "state-and-lifecycle", "name": "State and lifecycle", "description": "The states a horizontal gene transfer passes through and the events that move it between them.", "rationale": "Most decisions about a thing depend on what state it is in now, which is a claim with a time on it, not a property.", "layers": [ { "id": "lifecycle-stages", "name": "Lifecycle stages", "description": "From coming into existence to ceasing to be one of these.", "findings": [ { "id": "stages-and-transitions", "name": "Stages and transitions", "description": "The stages worth naming and what moves a horizontal gene transfer between them.", "questions": [ { "id": "stages-and-transitions-q01", "text": "What identifies and describes the lifecycle of a horizontal gene transfer, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "stages-and-transitions-q02", "text": "Who or what asserted this about the lifecycle of a horizontal gene transfer, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "stages-and-transitions-q03", "text": "What may an agent decide or do once the lifecycle of a horizontal gene transfer is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] }, { "id": "observations-and-status", "name": "Observations and current status", "description": "What is observed about a horizontal gene transfer, how often and by whom.", "findings": [ { "id": "observation-record", "name": "Observation record", "description": "How an observation of a horizontal gene transfer is recorded so that it can be superseded rather than overwritten.", "questions": [ { "id": "observation-record-q01", "text": "What identifies and describes an observation of a horizontal gene transfer, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "observation-record-q02", "text": "Who or what asserted this about an observation of a horizontal gene transfer, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "observation-record-q03", "text": "What may an agent decide or do once an observation of a horizontal gene transfer is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] }, { "id": "process-and-outcome", "name": "Process, inputs and outcome", "description": "How a horizontal gene transfer proceeds, what it needs and what it leaves behind.", "rationale": "An activity is known by its steps and its results, and both have to be recordable while it is still running.", "layers": [ { "id": "steps-and-sequence", "name": "Steps and sequence", "description": "The steps of a horizontal gene transfer, their order and what may run in parallel.", "findings": [ { "id": "steps-and-preconditions", "name": "Steps, preconditions and completion", "description": "What has to be true before each step of a horizontal gene transfer and what marks it done.", "questions": [ { "id": "steps-and-preconditions-q01", "text": "What identifies and describes a step of a horizontal gene transfer, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "steps-and-preconditions-q02", "text": "Who or what asserted this about a step of a horizontal gene transfer, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "steps-and-preconditions-q03", "text": "What may an agent decide or do once a step of a horizontal gene transfer is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] }, { "id": "inputs-and-results", "name": "Inputs, resources and results", "description": "What a horizontal gene transfer consumes and what it produces.", "findings": [ { "id": "inputs-and-outputs", "name": "Inputs, outputs and side effects", "description": "The resources a horizontal gene transfer takes and the results it leaves, wanted or not.", "questions": [ { "id": "inputs-and-outputs-q01", "text": "What identifies and describes the inputs and results of a horizontal gene transfer, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "inputs-and-outputs-q02", "text": "Who or what asserted this about the inputs and results of a horizontal gene transfer, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "inputs-and-outputs-q03", "text": "What may an agent decide or do once the inputs and results of a horizontal gene transfer is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] }, { "id": "definitions-in-contest", "name": "Definitions and who holds them", "description": "What horizontal gene transfer is taken to mean, and by whom.", "rationale": "When a field disagrees about a concept, the disagreement is the content. A model that picks one definition silently destroys the information.", "layers": [ { "id": "competing-definitions", "name": "Competing definitions", "description": "The main readings and the traditions behind them.", "findings": [ { "id": "definition-map", "name": "Definitions and their holders", "description": "Each definition with the school or body that holds it.", "questions": [ { "id": "definition-map-q01", "text": "Which definitions of horizontal gene transfer are in use, and which tradition or body holds each?", "kind": "definition" }, { "id": "definition-map-q02", "text": "What turns on the difference between them in practice?", "kind": "boundary" } ] } ] }, { "id": "operationalisation", "name": "Operationalisation", "description": "How it is measured or applied when it has to be.", "findings": [ { "id": "operational-record", "name": "Measures and proxies", "description": "Instruments and indicators used to stand in for it.", "questions": [ { "id": "operational-record-q01", "text": "How is horizontal gene transfer operationalised or measured in practice, and by what instrument?", "kind": "measurement" }, { "id": "operational-record-q02", "text": "What does that operationalisation leave out, and when does that matter?", "kind": "boundary" } ] } ] } ] }, { "id": "instances-and-use", "name": "Instances, use and consequence", "description": "What counts as an instance of horizontal gene transfer and what follows from calling something that.", "rationale": "Applying a concept is an act with consequences, so a model must say what the label licenses and what it does not.", "layers": [ { "id": "instances", "name": "What counts as an instance", "description": "Clear cases, borderline cases and non-cases.", "findings": [ { "id": "instance-tests", "name": "Tests for an instance", "description": "What would settle whether something falls under it.", "questions": [ { "id": "instance-tests-q01", "text": "What would settle whether something is an instance of horizontal gene transfer?", "kind": "boundary" }, { "id": "instance-tests-q02", "text": "Which borderline cases are argued about, and on what grounds?", "kind": "definition" } ] } ] }, { "id": "consequence", "name": "Consequence of application", "description": "Rights, duties or decisions that follow from the label.", "findings": [ { "id": "consequence-record", "name": "What the label licenses", "description": "What an agent may do once something is classified this way.", "questions": [ { "id": "consequence-record-q01", "text": "What follows practically once something is treated as horizontal gene transfer?", "kind": "action" }, { "id": "consequence-record-q02", "text": "What must an agent not infer from the label alone?", "kind": "action" } ] } ] } ] }, { "id": "provenance-and-evidence", "name": "Provenance, evidence and time", "description": "Where every claim about a horizontal gene transfer came from and when it held.", "rationale": "A claim without a source and a time cannot be superseded, only overwritten, and an agent that overwrites loses the ability to explain itself.", "layers": [ { "id": "source-and-authority", "name": "Source and authority", "description": "Who said it, on what evidence, and how strongly.", "findings": [ { "id": "claim-provenance", "name": "Claim provenance and confidence", "description": "The authority behind each claim about a horizontal gene transfer and how confident it is.", "questions": [ { "id": "claim-provenance-q01", "text": "What identifies and describes a claim about a horizontal gene transfer, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "claim-provenance-q02", "text": "Who or what asserted this about a claim about a horizontal gene transfer, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "claim-provenance-q03", "text": "What may an agent decide or do once a claim about a horizontal gene transfer is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] }, { "id": "time-and-versions", "name": "Time, versions and supersession", "description": "When a claim was true, when it was learnt, and what replaced it.", "findings": [ { "id": "validity-and-supersession", "name": "Validity period and supersession", "description": "How an old claim about a horizontal gene transfer is retired without being erased.", "questions": [ { "id": "validity-and-supersession-q01", "text": "What identifies and describes the validity of a claim about a horizontal gene transfer, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "validity-and-supersession-q02", "text": "Who or what asserted this about the validity of a claim about a horizontal gene transfer, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "validity-and-supersession-q03", "text": "What may an agent decide or do once the validity of a claim about a horizontal gene transfer is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] } ] }, "statistics": { "bundles": 6, "layers": 12, "findings": 14, "questions": 38 } } } }