{"schema":"https://ver.cy/schemas/card/1.0.0","id":"vr.tr.biological-mechanism","code":"thing-q6804646","url":"https://ver.cy/models/thing/q6804646/","name":"biological mechanism","alternateNames":["biological regulation","cell-intrinsic mechanism","pathophysiological mechanism","physiological mechanism","trauma mechanism","epispore","antigenic modulation"],"kind":"thing","status":"published","version":"0.2.0-wave.3","language":"en","classifiers":{"family":"Thing Registry","category":"Activities and processes","entryKind":"thing","plane":"ACT","domain":["ACT.PRC"],"industry":[],"navPath":"","tags":[],"facets":{}},"whatItIs":"A system of causally interacting biological parts and processes that produces one or more effects, involving entities, activities and interactions at levels from molecules and cells to organisms and populations, including physiological mechanisms that maintain function, pathophysiological mechanisms that produce disease, cell-intrinsic mechanisms operating within a cell, mechanisms of biological regulation, and, in medicine, the mechanism of injury in trauma; mechanistic explanations describe these systems and are a central mode of reasoning in the life sciences, analysed in the philosophy of biology.","purpose":"Let an agent explain what biological mechanisms are and how they are described and discovered, relay the philosophy and practice of mechanistic explanation from biological and philosophical sources, describe kinds of mechanisms, and distinguish mechanism from process, function, pathway and mechanism in the physical or engineering sense.","scope":{"in":[],"out":[],"boundaries":[]},"distinguishingFeatures":["A biological mechanism is a system that produces effects through causal interactions.","It involves entities and their activities.","It can operate across multiple biological levels.","It is discovered experimentally."],"structure":{"bundles":[{"id":"understand","name":"Understand","description":"What a biological mechanism is.","layers":[{"id":"definition","name":"Definition","description":"Definition.","findings":[{"id":"definition-finding","name":"Definition","description":"Definition.","questions":[{"text":"What is a biological mechanism, and how does it differ from a process, a function, a pathway and an engineering mechanism?","kind":"definition"},{"text":"Is the question about the concept, a specific mechanism or a misfiled alias?","kind":"boundary"}]}]},{"id":"kinds","name":"Kinds","description":"Kinds.","findings":[{"id":"kinds-finding","name":"Kinds","description":"Kinds.","questions":[{"text":"What are physiological, pathophysiological, cell-intrinsic, regulatory and trauma mechanisms?","kind":"definition"},{"text":"Which entry fits the specific kind?","kind":"action"}]}]}]},{"id":"explain","name":"Explain","description":"Mechanistic explanation.","layers":[{"id":"philosophy","name":"Philosophy","description":"Philosophy.","findings":[{"id":"philosophy-finding","name":"Philosophy","description":"Philosophy.","questions":[{"text":"How do philosophers such as Machamer, Darden, Craver and Bechtel characterise mechanisms, with positions attributed?","kind":"provenance"},{"text":"Which references are standard?","kind":"provenance"}]}]},{"id":"discovery","name":"Discovery","description":"Discovery.","findings":[{"id":"discovery-finding","name":"Discovery","description":"Discovery.","questions":[{"text":"How do biologists discover mechanisms through intervention, decomposition and modelling?","kind":"provenance"},{"text":"Which sources are cited?","kind":"provenance"}]}]}]},{"id":"apply","name":"Apply","description":"Applications.","layers":[{"id":"medicine","name":"Medicine","description":"Medicine.","findings":[{"id":"medicine-finding","name":"Medicine","description":"Medicine.","questions":[{"text":"How do disease mechanisms and mechanisms of injury guide diagnosis and treatment, in general terms?","kind":"provenance"},{"text":"Which entry fits pathophysiology?","kind":"action"}]}]},{"id":"research","name":"Research","description":"Research.","findings":[{"id":"research-finding","name":"Research","description":"Research.","questions":[{"text":"How do mechanisms organise research programmes and databases?","kind":"provenance"},{"text":"Which entry fits systems biology?","kind":"action"}]}]}]},{"id":"context","name":"Context","description":"History and debate.","layers":[{"id":"history","name":"History","description":"History.","findings":[{"id":"history-finding","name":"History","description":"History.","questions":[{"text":"How did mechanistic thinking develop from Descartes through physiology to molecular biology?","kind":"provenance"},{"text":"Which entry fits the history of biology?","kind":"action"}]}]},{"id":"debate","name":"Debate","description":"Debates.","findings":[{"id":"debate-finding","name":"Debate","description":"Debate.","questions":[{"text":"What debates exist about mechanism, reductionism and emergence in biology, with positions attributed?","kind":"provenance"},{"text":"Is the presentation neutral?","kind":"boundary"}]}]}]}]},"agentConduct":{"may":["Explain what a biological mechanism is and how mechanistic explanations are built.","Describe a stated mechanism with its evidence and the level at which it operates."],"mustNot":["Present a hypothesized mechanism as established.","Use mechanism claims to promote unproven treatments.","Overgeneralize findings from model organisms to humans."],"requiresHuman":["Using a mechanism claim to support a medical or policy decision."]},"ethics":{"considerations":["Mechanistic stories can lend false authority to weak evidence.","Health claims based on mechanisms alone can mislead patients."],"affectedParties":["Patients","Students and researchers"]},"owners":{"steward":"Nobody owns the concept; it belongs to biology and the philosophy of science.","roles":[],"masterSystems":[]},"relations":[{"target":"Q2996394","type":"parent","note":"registry parent class"},{"target":"biological process","type":"related","note":"in registry terms"},{"target":"philosophy of biology","type":"related","note":"as mechanistic explanation"},{"target":"biological function","type":"related","note":"a role rather than a cause"},{"target":"signal transduction","type":"related","note":"as a cellular mechanism"}],"interaction":{"identity":{"applicability":"required","items":["Vercy registry: vr.tr.biological-mechanism","Wikidata: Q6804646 (https://www.wikidata.org/wiki/Q6804646)"]},"properties":{"applicability":"not-applicable","items":[]},"recognition":{"applicability":"optional","items":["A biological mechanism is a system of interacting parts and processes that produces a biological phenomenon.","Examples include physiological, pathophysiological, cell-intrinsic and regulatory mechanisms, as well as trauma mechanisms.","A process is what happens, a function is a role, a pathway is a sequence, and a machine mechanism is engineering.","Not a visible object; an explanatory account."]},"capabilities":{"applicability":"required","items":["explain the concept","relay mechanistic explanation","describe kinds","distinguish related terms"]},"hazards":{"applicability":"required","items":["Confusing mechanism with function or process","Treating proposed mechanisms as established","Registry alias epispore appears misfiled"]},"interfaces":{"applicability":"required","items":["No regulation; Gene Ontology and ontology conventions for processes and regulation"]},"context":{"applicability":"required","items":["Not applicable; an explanatory concept.","physiological mechanisms","pathophysiological and disease mechanisms","cell-intrinsic and cell-extrinsic mechanisms","mechanisms of biological regulation","developmental and evolutionary mechanisms","mechanisms of injury in trauma medicine","registry alias epispore, a spore structure, which appears misfiled"]}},"sources":[{"title":"Wikidata item Q6804646: biological mechanism","url":"https://www.wikidata.org/wiki/Q6804646","note":"identity and sense of the item"},{"title":"Wikipedia: Mechanism (biology)","url":"https://en.wikipedia.org/wiki/Mechanism_%28biology%29","note":"general description of the item"}],"openQuestions":["Should pathophysiology and biological regulation be separate primary entries?","How should philosophical and biological sources be linked?","The registry alias epispore should be reviewed"],"resources":{"spec":"/models/things/publications/thing-q6804646/spec.json"},"provenance":{"origin":"thing registry research (pass 2)","builtFrom":["models/things/publications/thing-q6804646/spec.json"],"providers":["Claude"],"researchStatus":"unreviewed","generatedAt":"2026-09-13T05:44:29Z","builder":"tools/build_cards.py@1.0.0"},"completeness":{"sections":{"classifiers":"filled","whatItIs":"filled","purpose":"filled","distinguishingFeatures":"filled","structure":"filled","agentConduct":"filled","ethics":"filled","owners":"filled","relations":"filled","interaction.identity":"filled","interaction.properties":"not-applicable","interaction.recognition":"filled","interaction.capabilities":"filled","interaction.hazards":"filled","interaction.interfaces":"filled","interaction.context":"filled","sources":"filled"},"notes":{"_gate":"Published through the thing publication gate 1.0 on 2026-10-07T10:10:32+00:00: completeness 1.00; sense: Wikidata description; 2 live sources; review by codex: pass","interaction.properties":"Plane ACT: no invented physical properties."},"score":1.0}}