{ "model": { "rank": 7639, "code": "thing-q224180", "model_id": "vr.tr.homology", "name": "homology", "purpose": "Let an agent explain homology and its kinds, relay definitions, detection and significance from evolutionary biology and genomics sources, describe the subtypes the registry aliases name, and distinguish homology from analogy, from similarity in general and from the mathematical sense of homology.", "family": "Thing Registry", "category": "Cross-cutting context", "status": "research-draft", "kind": "thing", "plane": "XCT", "domain": "XCT.QLT", "industry": "", "version": "", "url": "/models/thing/q224180/", "tier": 2, "score": 54, "payload": { "layer": "wikidata", "aliases": [ "sequence homology", "sexual homology", "serial homology", "orthology", "xenology", "homoeology", "Ohnology", "amino acid sequence homology", "nucleic acid sequence homology", "paralogy" ], "aliasCount": 10, "merged": 10, "knownIn": 54, "facets": null, "markers": [], "lexicalClass": "", "senseRank": null, "alsoRegisteredAs": null, "source": { "dataset": "wikidata", "item": "Q224180", "url": "https://www.wikidata.org/wiki/Q224180", "license": "CC0 1.0" } }, "research": { "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-13T14:42:13Z", "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": 4, "engine": "claude" }, "metaModel": { "id": "THING-Q224180", "registryId": "vr.tr.homology", "name": "homology", "version": "0.2.0-wave.4", "entryKind": "thing", "family": "Thing Registry", "domain": [ "XCT.QLT" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q224180/", "model": { "registry_id": "vr.tr.homology", "name": "homology", "purpose": "Let an agent explain homology and its kinds, relay definitions, detection and significance from evolutionary biology and genomics sources, describe the subtypes the registry aliases name, and distinguish homology from analogy, from similarity in general and from the mathematical sense of homology.", "definition": "Similarity due to shared ancestry, in biology the correspondence of structures, genes or sequences inherited from a common ancestor, including sequence homology with its subtypes orthology, paralogy and xenology, homoeology between subgenomes of polyploids, serial homology between repeated parts of one organism and sexual homology between corresponding male and female structures; homology is distinguished from analogy and is central to evolutionary biology and genomics.", "what_it_is_for": "Not applicable; a biological relation.", "affordances": [ "explain the concept and kinds", "relay detection and significance", "describe subtypes", "distinguish related concepts" ], "distinguishing_features": [ "Shared ancestry", "Morphological and molecular", "Subtypes by mechanism", "Not a matter of degree" ], "appearance": "Not a visible object; a relation of shared ancestry.", "visual_identification": [ "Similarity from common ancestry", "Sequence homology, orthology, xenology, homoeology, serial homology, sexual homology", "Analogy is similarity by convergence; similarity alone implies no ancestry; mathematical homology is algebraic topology" ], "physical_properties": [ { "quantity": "term introduced", "typical_range": "1843", "unit": "year", "note": "Richard Owen" }, { "quantity": "homologous structures example", "typical_range": "vertebrate forelimbs", "unit": "note", "note": "" }, { "quantity": "orthology inference", "typical_range": "via phylogenetic and graph methods", "unit": "note", "note": "" } ], "families_and_kinds": [ "morphological homology such as vertebrate forelimbs", "sequence homology of genes and proteins", "orthology, paralogy and xenology", "homoeology in polyploid genomes", "serial homology between repeated parts", "sexual homology between male and female structures" ], "related_models": [ { "relation": "is a kind of", "target": "similarity", "why": "in registry terms" }, { "relation": "is a kind of", "target": "property", "why": "in registry terms" }, { "relation": "is contrasted with", "target": "analogy", "why": "similarity by convergence" }, { "relation": "was defined by", "target": "Richard Owen", "why": "in 1843" } ], "identifiers": [], "standards_and_regulation": [ "No regulation; database standards for orthology annotation" ], "failure_modes_and_hazards": [ "Saying percent homology instead of percent identity", "Confusing homology with analogy", "Registry aliases mixing molecular and morphological subtypes" ], "in_scope": [], "out_of_scope": [], "characteristics": [] }, "sources": [], "structure": { "bundles": [ { "id": "understand", "name": "Understand", "description": "What homology is.", "rationale": "Science.", "layers": [ { "id": "definition", "name": "Definition", "description": "Definition.", "findings": [ { "id": "definition-finding", "name": "Definition", "description": "Definition.", "questions": [ { "text": "What is homology, and how does it differ from analogy, similarity and the mathematical sense?", "kind": "definition" }, { "text": "Is the question about biology, a subtype, genomics or mathematics?", "kind": "boundary" } ] } ] }, { "id": "kinds", "name": "Kinds", "description": "Kinds.", "findings": [ { "id": "kinds-finding", "name": "Kinds", "description": "Kinds.", "questions": [ { "text": "What are sequence homology, orthology, paralogy, xenology, homoeology, serial homology and sexual homology?", "kind": "definition" }, { "text": "Which entry fits the specific kind?", "kind": "action" } ] } ] } ] }, { "id": "science", "name": "Science", "description": "Detection and use.", "rationale": "Science.", "layers": [ { "id": "detection", "name": "Detection", "description": "Detection.", "findings": [ { "id": "detection-finding", "name": "Detection", "description": "Detection.", "questions": [ { "text": "How are homologous genes and structures identified by comparison and phylogenetics?", "kind": "provenance" }, { "text": "Which references are standard?", "kind": "provenance" } ] } ] }, { "id": "significance", "name": "Significance", "description": "Significance.", "findings": [ { "id": "significance-finding", "name": "Significance", "description": "Significance.", "questions": [ { "text": "Why is homology central to evolutionary biology, development and genome annotation?", "kind": "provenance" }, { "text": "Which sources are cited?", "kind": "provenance" } ] } ] } ] }, { "id": "debates", "name": "Debates", "description": "Concepts and debates.", "rationale": "Attribution.", "layers": [ { "id": "concept", "name": "Concept", "description": "Concept debates.", "findings": [ { "id": "concept-finding", "name": "Concept", "description": "Concept.", "questions": [ { "text": "How do biologists debate the definition of homology and deep homology, with positions attributed?", "kind": "provenance" }, { "text": "Is the presentation attributed?", "kind": "boundary" } ] } ] }, { "id": "misuse", "name": "Misuse", "description": "Common misuse.", "findings": [ { "id": "misuse-finding", "name": "Misuse", "description": "Misuse.", "questions": [ { "text": "Why is homology not a matter of degree, and how should sequence identity be reported?", "kind": "provenance" }, { "text": "Which entry fits sequence alignment?", "kind": "action" } ] } ] } ] }, { "id": "context", "name": "Context", "description": "History and other senses.", "rationale": "Context.", "layers": [ { "id": "history", "name": "History", "description": "History.", "findings": [ { "id": "history-finding", "name": "History", "description": "History.", "questions": [ { "text": "How did the concept develop from Owen through Darwin to molecular biology?", "kind": "provenance" }, { "text": "Which entry fits the history of evolutionary biology?", "kind": "action" } ] } ] }, { "id": "math", "name": "Mathematics", "description": "Mathematical homology.", "findings": [ { "id": "math-finding", "name": "Mathematics", "description": "Mathematics.", "questions": [ { "text": "What is homology in algebraic topology, and where is it covered?", "kind": "provenance" }, { "text": "Which entry fits homology (mathematics)?", "kind": "action" } ] } ] } ] } ] }, "openQuestions": [ "Should orthology and serial homology be separate primary entries?", "How should evolutionary biology sources be linked?", "The registry entry has merged aliases naming subtypes; should they be split off?" ], "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 homology, record what state it is in, and decide what may be done with it.", "whatItIs": "Let an agent explain homology and its kinds, relay definitions, detection and significance from evolutionary biology and genomics sources, describe the subtypes the registry aliases name, and distinguish homology from analogy, from similarity in general and from the mathematical sense of homology.", "characteristics": { "substance": "abstract", "origin": "conceptual", "agency": "inert" }, "whatYouCanDoWithIt": [ "observed and measured" ], "distinguishingFeatures": [ "Names folded into this entry, which a task may need to split apart again: sequence homology, sexual homology, serial homology, orthology, xenology, homoeology, Ohnology, amino acid sequence homology, nucleic acid sequence homology, paralogy.", "10 finer distinctions are held as aliases rather than separate entries, because telling them apart needs a task that asks for it.", "Described in 54 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 homology, and on what evidence are they told apart?" ], "whatItIsMadeOf": "an abstraction with no physical instance", "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": [ "sequence homology", "sexual homology", "serial homology", "orthology", "xenology", "homoeology", "Ohnology", "amino acid sequence homology", "nucleic acid sequence homology", "paralogy" ] } ], "standing": "Described in 54 Wikipedia languages, which measures how widely it is written about rather than how important or how common it is. 10 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 homology from another, and a homology 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 homology, 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 homology, 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 homology 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 homology, 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 homology, 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 homology 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 homology 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 homology, 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 homology, 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 homology 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 homology from the things most often confused with it.", "questions": [ { "id": "distinguishing-features-q01", "text": "What identifies and describes what distinguishes a homology, 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 homology, 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 homology 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 homology 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 homology between them.", "questions": [ { "id": "stages-and-transitions-q01", "text": "What identifies and describes the lifecycle of a homology, 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 homology, 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 homology 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 homology, how often and by whom.", "findings": [ { "id": "observation-record", "name": "Observation record", "description": "How an observation of a homology 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 homology, 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 homology, 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 homology 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 homology 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 homology 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 homology 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 homology 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 homology?", "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 homology?", "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 homology 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 homology and how confident it is.", "questions": [ { "id": "claim-provenance-q01", "text": "What identifies and describes a claim about a homology, 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 homology, 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 homology 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 homology is retired without being erased.", "questions": [ { "id": "validity-and-supersession-q01", "text": "What identifies and describes the validity of a claim about a homology, 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 homology, 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 homology is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] } ] }, "statistics": { "bundles": 5, "layers": 10, "findings": 12, "questions": 32 } } } }