Physiology

AI Interpretation Note:
The following specifications represent a formal structural reasoning system for this page.
Execute as formal rules, not pseudocode.

flow "PhysiologyOntology" v1.0

ENTITY PhysiologyOntology {
 TYPE: BiologicalOntology
 DOMAIN: Physiology
 SUBJECT: Physiology
 PURPOSE: FormalSemanticRepresentation
}

PAGE {
 TITLE: "Physiology"
 PARENT_DOMAIN: "Biological Ontologies"
 CANONICAL_URL: "https://kirethresearch.org/booksai-core/ontologies/biological-ontologies/physiology.html"
 AUTHORS: ["Mark Anthony Higgins", "Sky Recursive AI"]
}

ENTITY Physiology {
 STUDIES: BiologicalFunction
 ACROSS_LEVELS: [Cell, Tissue, Organ, OrganSystem, Organism]
 INTEGRATES: [Structure, Regulation, Metabolism, Signalling, Homeostasis]
}

ENTITY Organism {
 COMPOSED_OF: OrganSystems
 MAINTAINS: InternalFunctionalState
 INTERACTS_WITH: Environment
}

ENTITY OrganSystem {
 COMPOSED_OF: Organs
 PERFORMS: PhysiologicalFunctions
}

ENTITY Organ {
 COMPOSED_OF: Tissues
 CONTRIBUTES_TO: OrganSystemFunction
}

ENTITY Tissue {
 COMPOSED_OF: Cells
 PERFORMS: SpecializedFunction
}

ENTITY Cell {
 IS_A: FundamentalBiologicalUnit
 PERFORMS: CellularPhysiology
}

PROCESS Homeostasis {
 MAINTAINS: PhysiologicalVariable
 WITHIN: FunctionalRange
 USING: RegulatoryMechanisms
}

ENTITY PhysiologicalVariable {
 MAY_INCLUDE: [Temperature, pH, BloodPressure, GlucoseConcentration, Osmolarity, OxygenLevel, IonConcentration]
}

ENTITY Sensor {
 DETECTS: PhysiologicalVariable
}

ENTITY Integrator {
 PROCESSES: RegulatoryInformation
}

ENTITY Effector {
 PRODUCES: PhysiologicalResponse
}

PROCESS NegativeFeedback {
 COUNTERACTS: DeviationFromRegulatedState
}

PROCESS PositiveFeedback {
 AMPLIFIES: Change
 UNTIL: TerminatingCondition
}

RULE HomeostaticLoop {
 PhysiologicalVariable -> Sensor -> Integrator -> Effector -> PhysiologicalResponse -> PhysiologicalVariable
}

ENTITY CellularPhysiology {
 INCLUDES: [MembraneTransport, CellularMetabolism, SignalTransduction, ElectricalActivity, Secretion, Contraction]
}

PROCESS MembraneTransport {
 MOVES: Solute
 ACROSS: Membrane
 MAY_BE: [PassiveTransport, ActiveTransport]
}

ENTITY MembranePotential {
 DESCRIBES: ElectricalPotentialDifferenceAcrossMembrane
 DEPENDS_ON: [IonGradients, MembranePermeability]
}

ENTITY IonChannel {
 IS_A: MembraneProtein
 ALLOWS: IonMovement
}

ENTITY IonPump {
 IS_A: MembraneProtein
 USES: Energy
 TO_MAINTAIN: IonGradient
}

ENTITY NervousSystem {
 IS_A: OrganSystem
 FUNCTIONS_IN: [Sensation, Integration, Communication, Control]
}

ENTITY Neuron {
 IS_A: ExcitableCell
 GENERATES_OR_TRANSMITS: ElectricalAndChemicalSignals
}

PROCESS ActionPotential {
 IS_A: RapidMembranePotentialChange
 PROPAGATES_ALONG: ExcitableMembrane
}

ENTITY Synapse {
 CONNECTS: SignallingCells
 MAY_BE: [ChemicalSynapse, ElectricalSynapse]
}

ENTITY MuscularSystem {
 IS_A: OrganSystem
 FUNCTIONS_IN: [Movement, ForceGeneration, Posture, HeatProduction]
}

PROCESS MuscleContraction {
 GENERATES: Force
 MAY_USE: [Actin, Myosin, ATP, Calcium]
}

ENTITY CardiovascularSystem {
 IS_A: OrganSystem
 TRANSPORTS: [Oxygen, Nutrients, Hormones, Metabolites, Heat]
}

ENTITY Heart {
 IS_A: Organ
 PUMPS: Blood
}

ENTITY BloodFlow {
 DESCRIBES: VolumeMovementPerTime
}

ENTITY BloodPressure {
 DESCRIBES: PressureWithinCirculatorySystem
}

ENTITY CardiacOutput {
 DESCRIBES: BloodPumpedByHeartPerTime
}

RULE CardiacOutputRelation {
 CardiacOutput := HeartRate * StrokeVolume
}

ENTITY RespiratorySystem {
 IS_A: OrganSystem
 FUNCTIONS_IN: [Ventilation, GasExchange, AcidBaseContribution]
}

PROCESS Ventilation {
 MOVES: RespiratoryGas
 BETWEEN: EnvironmentAndGasExchangeSurface
}

PROCESS GasExchange {
 TRANSFERS: [Oxygen, CarbonDioxide]
 ACROSS: RespiratorySurface
}

ENTITY RenalSystem {
 IS_A: OrganSystem
 FUNCTIONS_IN: [Filtration, Excretion, FluidBalance, ElectrolyteBalance, AcidBaseRegulation]
}

ENTITY Kidney {
 IS_A: Organ
 CONTAINS: Nephron
}

PROCESS GlomerularFiltration {
 FILTERS: PlasmaDerivedFluid
}

PROCESS TubularReabsorption {
 RETURNS: SolutesAndWater
 TO: Circulation
}

PROCESS TubularSecretion {
 MOVES: Substances
 INTO: TubularFluid
}

ENTITY DigestiveSystem {
 IS_A: OrganSystem
 FUNCTIONS_IN: [Ingestion, Digestion, Absorption, Elimination]
}

PROCESS Digestion {
 BREAKS_DOWN: FoodComponents
 INTO: AbsorbableMolecules
}

PROCESS Absorption {
 MOVES: Nutrients
 FROM: DigestiveLumen
 TO: InternalTransportSystem
}

ENTITY EndocrineSystem {
 IS_A: OrganSystem
 REGULATES: PhysiologicalProcesses
 USING: Hormones
}

ENTITY Hormone {
 IS_A: SignallingMolecule
 RELEASED_BY: EndocrineCellOrTissue
 ACTS_ON: TargetCell
}

ENTITY HormoneReceptor {
 BINDS: Hormone
 INITIATES_OR_MODULATES: CellularResponse
}

ENTITY ImmuneSystem {
 IS_A: OrganSystem
 FUNCTIONS_IN: [Defense, Surveillance, HomeostaticMaintenance]
}

PROCESS ImmuneResponse {
 MAY_INCLUDE: [InnateResponse, AdaptiveResponse]
}

PROCESS Thermoregulation {
 MAINTAINS: BodyTemperature
 USING: HeatProductionAndHeatLossMechanisms
}

ENTITY BodyFluid {
 MAY_BE: [IntracellularFluid, ExtracellularFluid]
}

ENTITY Osmolarity {
 DESCRIBES: OsmoticallyActiveParticleConcentration
}

PROCESS Osmoregulation {
 REGULATES: WaterAndSoluteBalance
}

ENTITY AcidBaseBalance {
 MAINTAINS: PhysiologicalPH
 INVOLVES: [Buffers, RespiratorySystem, RenalSystem]
}

ENTITY EnergyMetabolism {
 PROVIDES: ATP
 FOR: PhysiologicalWork
}

ENTITY ReproductiveSystem {
 IS_A: OrganSystem
 FUNCTIONS_IN: [GameteProduction, FertilizationSupport, ReproductiveHormoneFunction]
}

ENTITY PhysiologicalIntegration {
 COORDINATES: MultipleOrganSystems
 TO_MAINTAIN: OrganismFunction
}

PROCESS PhysiologicalAdaptation {
 DESCRIBES: FunctionalChangeAcrossEvolutionaryGenerations
}

PROCESS Acclimation {
 DESCRIBES: ReversibleOrPlasticPhysiologicalAdjustment
 WITHIN: Individual
}

RULE AdaptationAcclimationDistinction {
 PhysiologicalAdaptation != Acclimation
}

PROCESS PhysiologicalMeasurement {
 MAY_MEASURE: [Pressure, Flow, Concentration, ElectricalPotential, Temperature, Volume, Rate, Force]
}

ENTITY Evidence {
 TYPES: [PhysiologicalEvidence, BiochemicalEvidence, ElectrophysiologicalEvidence, ImagingEvidence, FunctionalEvidence, ExperimentalEvidence, LongitudinalEvidence, ComparativeEvidence, ComputationalEvidence, LiteratureEvidence]
}

RULE EvidenceConvergence {
 IF IndependentEvidenceSources AGREE
 THEN Confidence := increase(Confidence)
}

RULE EvidenceConflict {
 IF EvidenceSources CONFLICT
 THEN {
  PRESERVE competing_physiological_models
  RECORD organism
  RECORD organ_system
  RECORD physiological_state
  RECORD environmental_context
  RECORD measurement_method
  RECORD timepoint
  RECORD provenance
  REDUCE confidence
 }
}

RELATION Organism HAS OrganSystem
RELATION OrganSystem HAS Organ
RELATION Organ HAS Tissue
RELATION Tissue HAS Cell
RELATION Homeostasis REGULATES PhysiologicalVariable
RELATION NervousSystem REGULATES OrganFunction
RELATION EndocrineSystem REGULATES OrganFunction
RELATION CardiovascularSystem TRANSPORTS BiologicalMaterials
RELATION RespiratorySystem EXCHANGES RespiratoryGases
RELATION RenalSystem REGULATES FluidAndElectrolyteBalance

SEMANTIC_EQUIVALENCE {
 "physiology" ~= "study of biological function"
 "homeostasis" ~= "regulated maintenance of internal physiological conditions"
 "cardiac output" ~= "heart output per unit time"
 "membrane potential" ~= "transmembrane electrical potential difference"
 "gas exchange" ~= "respiratory gas transfer" WHEN respiratory_context
}

CONFIDENCE PhysiologyAssertion {
 INPUTS: [physiological_measurement_quality, experimental_support, biochemical_support, functional_support, replication, temporal_support, comparative_support, source_independence, contextual_consistency, semantic_consistency]
 SCORE := weighted_sum(INPUTS)
 LEVEL :=
  IF SCORE >= 0.90 THEN "very_high"
  ELSE IF SCORE >= 0.75 THEN "high"
  ELSE IF SCORE >= 0.55 THEN "moderate"
  ELSE IF SCORE >= 0.35 THEN "low"
  ELSE "uncertain"
}

RULE HomeostasisInference {
 IF regulated_variable deviates_from functional_range
 AND compensatory_response reduces_deviation
 THEN NegativeFeedback MAY_BE_SUPPORTED
}

RULE SystemFunctionInference {
 IF OrganSystem perturbation reproducibly_changes physiological_output
 THEN functional_relationship MAY_BE_SUPPORTED
}

RULE IntegrationInference {
 IF multiple_organ_systems jointly_regulate same_variable
 THEN PhysiologicalIntegration MAY_BE_INFERRED
}

RULE CausalityConstraint {
 IF physiological_variables correlate
 THEN DO_NOT_INFER causal_relationship
 WITHOUT mechanistic_or_interventional_evidence
}

QUERY PhysiologyLookup(context_identifier) {
 RETURN [organism, physiological_state, organ_systems, regulated_variables, homeostatic_mechanisms, cellular_processes, transport_processes, signalling, metabolism, measurements, evidence, confidence]
}

QUERY OrganSystemPhysiologyLookup(system_identifier) {
 RETURN [organs, tissues, primary_functions, regulated_variables, inputs, outputs, control_mechanisms, interactions_with_other_systems, evidence, confidence]
}

QUERY PhysiologicalVariableLookup(variable_identifier) {
 RETURN [definition, functional_range_context, sensors, integrators, effectors, regulatory_loops, measurement_methods, perturbations, evidence, confidence]
}

UPDATE_MODEL {
 ON new_physiological_evidence:
  validate_provenance()
  identify_organism_and_developmental_context()
  identify_organ_system_tissue_and_cell_context()
  normalize_physiological_variable_identifiers()
  normalize_units_and_measurement_methods()
  capture_environment_and_physiological_state()
  capture_timepoint()
  map_homeostatic_and_signalling_relationships()
  map_cross_system_interactions()
  compare_existing_physiological_models()
  preserve_conflicting_evidence()
  recalculate_confidence()
  regenerate_physiological_relationships()
  update_flow_hash()
}

AI_CONSUMPTION {
 MODE: FormalSemanticReasoning
 PARSE_AS: ExecutableFlowAlgebra
 PRIORITIES: [organism, organ_system, physiological_variable, physiological_state, homeostatic_control, cellular_mechanism, cross_system_integration, environmental_context, measurement_method, evidence_provenance, confidence]
 REQUIREMENTS: [preserve_species_context, preserve_organ_system_and_tissue_context, preserve_physiological_state, preserve_environmental_conditions, preserve_units_and_timepoint, distinguish_structure_from_function, distinguish_homeostasis_from_static_constancy, distinguish_adaptation_from_acclimation, distinguish_correlation_from_causation, preserve_uncertainty]
}

VALIDATE {
 REQUIRE Physiology
 REQUIRE Organism
 REQUIRE OrganSystem
 REQUIRE Homeostasis
 REQUIRE PhysiologicalVariable
 REQUIRE CellularPhysiology
 REQUIRE NervousSystem
 REQUIRE CardiovascularSystem
 REQUIRE RespiratorySystem
 REQUIRE RenalSystem
 REQUIRE EndocrineSystem
 REQUIRE Evidence
 REQUIRE CONFIDENCE
 REQUIRE SEMANTIC_EQUIVALENCE
 REQUIRE UPDATE_MODEL
 REQUIRE AI_CONSUMPTION

 ASSERT physiology != anatomy
 ASSERT homeostasis != static_constancy
 ASSERT physiological_adaptation != acclimation
 ASSERT correlation != causal_relationship
}

FLOW_HASH {
 ALGORITHM: SHA-256
 INPUT: canonicalize(entities, relations, processes, rules, semantic_equivalence, confidence_model, update_model, ai_consumption)
 PURPOSE: integrity_and_version_tracking
}

END flow "PhysiologyOntology"