{ "model": { "rank": 9083, "code": "thing-q288322", "model_id": "vr.tr.autophagy", "name": "autophagy", "purpose": "Let an agent explain autophagy and its mechanisms and types, describe its roles in health and disease with attribution, present popular claims about fasting and detoxification neutrally, and support learning.", "family": "Thing Registry", "category": "Activities and processes", "status": "research-draft", "kind": "thing", "plane": "ACT", "domain": "ACT.PRC", "industry": "", "version": "", "url": "/models/thing/q288322/", "tier": 2, "score": 48, "payload": { "layer": "wikidata", "aliases": [ "systemic detoxification", "macroautophagy", "microautophagy", "autophagy of mitochondrion", "autophagy of nucleus", "autophagy of peroxisome", "lysosomal microautophagy", "chaperone-mediated autophagy", "late endosomal microautophagy", "Chaperone-mediated autophagy", "efferocytosis", "mitophagy by induced vacuole formation", "mitophagy", "micromitophagy" ], "aliasCount": 14, "merged": 14, "knownIn": 48, "facets": null, "markers": [], "lexicalClass": "", "senseRank": null, "alsoRegisteredAs": null, "source": { "dataset": "wikidata", "item": "Q288322", "url": "https://www.wikidata.org/wiki/Q288322", "license": "CC0 1.0" } }, "research": { "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-12T01:09:16Z", "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-Q288322", "registryId": "vr.tr.autophagy", "name": "autophagy", "version": "0.2.0-wave.2", "entryKind": "thing", "family": "Thing Registry", "domain": [ "ACT.PRC" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q288322/", "model": { "registry_id": "vr.tr.autophagy", "name": "autophagy", "purpose": "Let an agent explain autophagy and its mechanisms and types, describe its roles in health and disease with attribution, present popular claims about fasting and detoxification neutrally, and support learning.", "definition": "A cellular process in which cells degrade and recycle their own components by enclosing them in vesicles delivered to lysosomes, in forms such as macroautophagy, microautophagy and chaperone-mediated autophagy, and selective types targeting mitochondria, nuclei, peroxisomes and other structures; autophagy maintains cellular homeostasis, responds to starvation and stress, is implicated in ageing, neurodegeneration, cancer and infection, and was recognised by the 2016 Nobel Prize, and claims about detoxification are presented here with attribution.", "what_it_is_for": "Cellular self-degradation and recycling.", "affordances": [ "explain mechanisms and types", "describe roles in health", "present popular claims neutrally", "support learning" ], "distinguishing_features": [ "Self-degradation", "Lysosome-mediated", "Selective forms", "Stress response" ], "appearance": "Not visible without microscopy; vesicles in cells.", "visual_identification": [ "Cells degrading their own components", "Lysosomal delivery", "Apoptosis is programmed cell death; proteasomes degrade proteins differently" ], "physical_properties": [], "families_and_kinds": [ "macroautophagy", "microautophagy", "chaperone-mediated autophagy", "selective autophagy of mitochondria, nuclei and peroxisomes", "autophagy in disease and ageing" ], "related_models": [ { "relation": "is a kind of", "target": "cellular catabolic process", "why": "category" }, { "relation": "is related to", "target": "necrosis", "why": "another cell fate entry" }, { "relation": "is related to", "target": "circadian rhythm", "why": "rhythmic regulation of autophagy" }, { "relation": "is related to", "target": "gene expression", "why": "regulation of autophagy genes" } ], "identifiers": [], "standards_and_regulation": [ "Research guidelines for monitoring autophagy", "Clinical trial regulation for autophagy-targeting therapies", "Consumer protection on health claims" ], "failure_modes_and_hazards": [ "Overstated health claims about fasting and detox", "Agents giving personal medical advice", "Oversimplifying mechanisms" ], "in_scope": [], "out_of_scope": [], "characteristics": [] }, "sources": [], "structure": { "bundles": [ { "id": "understand", "name": "Understand", "description": "How autophagy works.", "rationale": "Biology.", "layers": [ { "id": "mechanism", "name": "Mechanism", "description": "Mechanism.", "findings": [ { "id": "mechanism-finding", "name": "Mechanism", "description": "Mechanism.", "questions": [ { "text": "How do autophagosomes form and fuse with lysosomes, and which genes and signals regulate autophagy?", "kind": "definition" }, { "text": "How do macro, micro and chaperone-mediated forms differ?", "kind": "definition" } ] } ] }, { "id": "selective", "name": "Selective", "description": "Selective autophagy.", "findings": [ { "id": "selective-finding", "name": "Selective", "description": "Selective.", "questions": [ { "text": "How do cells selectively degrade mitochondria, nuclei, peroxisomes and pathogens?", "kind": "definition" }, { "text": "Which entry fits a specific selective form?", "kind": "action" } ] } ] } ] }, { "id": "health", "name": "Health", "description": "Autophagy in health and disease.", "rationale": "Attribution.", "layers": [ { "id": "disease", "name": "Disease", "description": "Roles in disease.", "findings": [ { "id": "disease-finding", "name": "Disease", "description": "Disease.", "questions": [ { "text": "What roles are documented for autophagy in ageing, neurodegeneration, cancer and infection, according to research?", "kind": "provenance" }, { "text": "Which findings are contested?", "kind": "boundary" } ] } ] }, { "id": "claims", "name": "Claims", "description": "Fasting and detox claims.", "findings": [ { "id": "claims-finding", "name": "Claims", "description": "Claims.", "questions": [ { "text": "What does evidence say about fasting, diet and so-called detoxification effects on autophagy in humans, with positions attributed?", "kind": "provenance" }, { "text": "Is the user seeking personal health advice, which needs a professional?", "kind": "boundary" } ] } ] } ] }, { "id": "research", "name": "Research", "description": "Studying autophagy.", "rationale": "Methods.", "layers": [ { "id": "methods", "name": "Methods", "description": "Methods.", "findings": [ { "id": "methods-finding", "name": "Methods", "description": "Methods.", "questions": [ { "text": "How is autophagy measured and monitored in cells and organisms, according to consensus guidelines?", "kind": "provenance" }, { "text": "Which entry fits cell biology methods?", "kind": "action" } ] } ] }, { "id": "therapy", "name": "Therapy", "description": "Therapeutic targeting.", "findings": [ { "id": "therapy-finding", "name": "Therapy", "description": "Therapy.", "questions": [ { "text": "How are drugs targeting autophagy being developed and tested?", "kind": "provenance" }, { "text": "Which entry fits drug development?", "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 autophagy discovered, from de Duve to Ohsumi and the 2016 Nobel Prize?", "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 autophagy be taught in cell biology?", "kind": "action" }, { "text": "Which misconceptions arise?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "Should each autophagy type be a separate entry?", "How should research guidelines be linked?", "How should health claims be evaluated?" ], "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 autophagy, record what state it is in, and decide what may be done with it.", "whatItIs": "Let an agent explain autophagy and its mechanisms and types, describe its roles in health and disease with attribution, present popular claims about fasting and detoxification neutrally, and support learning.", "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: systemic detoxification, macroautophagy, microautophagy, autophagy of mitochondrion, autophagy of nucleus, autophagy of peroxisome, lysosomal microautophagy, chaperone-mediated autophagy, late endosomal microautophagy, Chaperone-mediated autophagy, efferocytosis, mitophagy by induced vacuole formation.", "14 finer distinctions are held as aliases rather than separate entries, because telling them apart needs a task that asks for it.", "Described in 48 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 autophagy, 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": [ "systemic detoxification", "macroautophagy", "microautophagy", "autophagy of mitochondrion", "autophagy of nucleus", "autophagy of peroxisome", "lysosomal microautophagy", "chaperone-mediated autophagy", "late endosomal microautophagy", "Chaperone-mediated autophagy", "efferocytosis", "mitophagy by induced vacuole formation" ] } ], "standing": "Described in 48 Wikipedia languages, which measures how widely it is written about rather than how important or how common it is. 14 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 autophagy from another, and a autophagy 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 autophagy, 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 autophagy, 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 autophagy 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 autophagy, 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 autophagy, 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 autophagy 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 autophagy 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 autophagy, 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 autophagy, 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 autophagy 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 autophagy from the things most often confused with it.", "questions": [ { "id": "distinguishing-features-q01", "text": "What identifies and describes what distinguishes a autophagy, 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 autophagy, 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 autophagy 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 autophagy 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 autophagy between them.", "questions": [ { "id": "stages-and-transitions-q01", "text": "What identifies and describes the lifecycle of a autophagy, 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 autophagy, 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 autophagy 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 autophagy, how often and by whom.", "findings": [ { "id": "observation-record", "name": "Observation record", "description": "How an observation of a autophagy 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 autophagy, 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 autophagy, 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 autophagy 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 autophagy 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 autophagy, 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 autophagy and what marks it done.", "questions": [ { "id": "steps-and-preconditions-q01", "text": "What identifies and describes a step of a autophagy, 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 autophagy, 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 autophagy 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 autophagy consumes and what it produces.", "findings": [ { "id": "inputs-and-outputs", "name": "Inputs, outputs and side effects", "description": "The resources a autophagy 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 autophagy, 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 autophagy, 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 autophagy 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 autophagy 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 autophagy 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 autophagy 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 autophagy 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 autophagy?", "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 autophagy?", "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 autophagy 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 autophagy and how confident it is.", "questions": [ { "id": "claim-provenance-q01", "text": "What identifies and describes a claim about a autophagy, 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 autophagy, 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 autophagy 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 autophagy is retired without being erased.", "questions": [ { "id": "validity-and-supersession-q01", "text": "What identifies and describes the validity of a claim about a autophagy, 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 autophagy, 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 autophagy 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 } } } }