CONCEPT ATLAS · 156 REGISTERED CONCEPTS

Explore GenOS
as a system.

Browse the runtime by the systems its concepts belong to. Each entry links to the canonical GenOS source and distinguishes implementation, integration, and evidence status.

A MAP OF GENOS

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01Identity & Development02Cognition & Control03Knowledge & Evidence04Memory & Learning05Collective Intelligence06Orchestration07Evolution & Ecology08Physiology & Perception09Immunity & Medicine10Formal Verification11Runtime & Infrastructure

Showing 156 of 156 registered concepts

SYSTEM · 09 CONCEPTS

Identity & Development

What an agent inherits, how it is shaped, and how a project continues between missions.

04 / CONCEPT PartialOntogenesisOntogenesis is the resident controller that follows a project between missions: it selects a task, starts a bounded run, examines evidence, and coordinates integration or resumption.biologymathinteractive06 / CONCEPT PartialGenomeA versioned software model of inherited traits and constraints; it is not biological DNA and does not by itself instantiate a running agent.biologymathinteractive07 / CONCEPT PartialEpigeneticsA software policy for expressing modeled traits in context; it is an analogy, not biochemical marking or biological inheritance.biologymathinteractive08 / CONCEPT PartialAgentDNAA versioned binary data format for agent identity and runtime traits; editing it does not by itself start or clone a process.mathinteractive09 / CONCEPT PartialPhenotypeThe observable runtime profile produced by identity, constraints, and environment.biologymathinteractive10 / CONCEPT ExperimentalInstinctBounded innate response patterns that can be selected or modulated by runtime context.biologymathinteractive11 / CONCEPT ExperimentalReproductionRust reproduction operations transform genome and cell models under inheritance rules; worker startup is separate, while MCP biomimicry handlers record simulations.biologymathinteractive12 / CONCEPT ProposedSpeciation & graftingA documented path for proposing a new capability or agent lineage and evaluating it before promotion.biologymathinteractive156 / CONCEPT PartialGenomic stabilityGenomic stability tracks mutation rates, anomalies and Stable, Compromised or Critical thresholds in versioned software genomes.biologymathinteractivesimulation
SYSTEM · 22 CONCEPTS

Cognition & Control

Candidate workspaces, prediction, attention, and bounded control loops.

03 / CONCEPT ConceptualCortexIn GenOS, “cortex” describes some retrieval and association functions. It does not mean a unified artificial brain: these mechanisms are distributed across indexes, memories, agents, and controllers.biologymathinteractive13 / CONCEPT PartialAGOWAn active workspace where candidate frames compete and selected content can be broadcast under policy.biologymathinteractivesimulationbenchmark14 / CONCEPT PartialGVXA verified development loop that isolates changes, observes outcomes, and uses evidence to govern maturity.biologymathinteractivebenchmark15 / CONCEPT ExperimentalSelf-modelA bounded model of agent identity and continuity used for analysis, not a claim of subjective experience.mathinteractive16 / CONCEPT ExperimentalTheory of selfRuntime models that describe agent identity, continuity, and change without asserting subjective experience.mathinteractive17 / CONCEPT PartialPredictive systemA multi-scale prediction model that relates observations, hypotheses, and expected outcomes.mathinteractive18 / CONCEPT PartialNatural Search Control PlaneA control model for bounded search using pressure, causal progress, hypotheses, and explicit control.biologymathinteractive19 / CONCEPT PartialEndogenous Thought TestA bounded experimental protocol that detects an internal signal, formulates a falsifiable question, arbitrates whether to investigate it, produces a read-only proposal, and submits it to independent verification.mathinteractivesimulationbenchmark20 / CONCEPT PartialAttention & salienceSelection and prioritization signals used to direct limited agent work toward relevant inputs.biologymathinteractive21 / CONCEPT ConceptualMind and consciousness taxonomyA vocabulary for discussing computational indicators while separating them from claims of subjective experience.mathinteractive22 / CONCEPT ConceptualFunctional indicatorsObservable indicators used for bounded analysis; they do not establish subjective consciousness.mathinteractive118 / CONCEPT ConceptualMindMind is retained as a philosophical reference for discussing cognition; GenOS does not implement a mental substance or claim subjective experience.mathinteractive119 / CONCEPT ConceptualMentalMental denotes the family of states and processes discussed by philosophy of mind, not a single executable GenOS capability.mathinteractive120 / CONCEPT ConceptualConsciousnessConsciousness names subjective experience in its phenomenal sense; the GenOS registry treats it as a reference-only concept rather than a verifiable software property.mathinteractive121 / CONCEPT ImplementedOperational consciousnessOperational consciousness is GenOS vocabulary for internal consistency regulation using dissonance, budget and bounded stop signals; it is not phenomenal consciousness.mathinteractivesimulation122 / CONCEPT PartialFunctional consciousnessFunctional consciousness groups measurable access, attention, self-model and metacognitive indicators without treating them as evidence of subjective experience.mathinteractivebenchmark125 / CONCEPT ImplementedImaginationImagination recombines stored fragments into bounded candidate scenarios; generated possibilities remain simulations rather than observations.mathinteractivesimulation126 / CONCEPT ImplementedInternal simulationInternal simulation predicts possible outcomes before execution using an explicit trace; its result is advisory and never proof of the real outcome.mathinteractivesimulation127 / CONCEPT PartialReflectionReflection monitors reported confidence and errors so a system can revise or abstain; it does not demonstrate phenomenal reflexivity.mathinteractivebenchmark128 / CONCEPT ImplementedMetacognitionMetacognition measures confidence, discrimination and overconfidence on resolved attribution history; it is a functional evaluation, not meta-consciousness.mathinteractivebenchmark130 / CONCEPT ImplementedCognitive dissonanceCognitive dissonance is a software inconsistency signal derived from errors, repetition, drift and health; it is not a clinical or subjective diagnosis.mathinteractivesimulation132 / CONCEPT ConceptualStates of consciousnessStates of consciousness are retained as a reference taxonomy; GenOS may expose functional levels but does not measure phenomenal states.mathinteractive
SYSTEM · 31 CONCEPTS

Knowledge & Evidence

Claims, sources, uncertainty, contradiction, and calibrated judgment.

05 / CONCEPT PartialOntologyThe operational ontology provides structures for describing entities, identity criteria, relationships, and hypothetical scenarios. It supports analysis without deciding on its own what should be executed.mathinteractive23 / CONCEPT PartialEpistemicsThe runtime vocabulary and procedures for representing what is known, uncertain, or contested.mathinteractive24 / CONCEPT PartialBeliefsVersioned propositions with confidence, provenance, and revision history.mathinteractive25 / CONCEPT PartialClaimsExplicit statements that can be supported, challenged, scoped, and linked to evidence.mathinteractive26 / CONCEPT PartialEvidenceArtifacts and observations used to support or reject a claim under a stated decision rule.mathinteractive27 / CONCEPT PartialContradictionsConflicting claims or observations preserved for review instead of silently collapsed.mathinteractive28 / CONCEPT PartialProvenanceSource and lineage information attached to evidence, findings, and decisions.mathinteractive29 / CONCEPT ExperimentalBrier calibrationA scoring method for comparing probabilistic forecasts with resolved outcomes.mathinteractive30 / CONCEPT ConceptualGettier problemsA model for examining why a justified belief can still fail to count as knowledge.mathinteractive31 / CONCEPT PartialKnowledgeA structured representation of sources, claims, inference, and uncertainty.mathinteractive32 / CONCEPT PartialGenOS PhilosophyA canonical registry with 420 bounded executable audits over eleven shared primitives, linked to Ontogenesis verification without granting promotion authority.mathinteractive129 / CONCEPT ImplementedCalibrationCalibration compares stated confidence with resolved outcomes and updates confidence conservatively; it never makes evidence more permissive by itself.mathinteractivebenchmark133 / CONCEPT ConceptualMetric–experience boundaryThe metric–experience boundary prevents functional scores from being reported as evidence of subjective experience.mathinteractive134 / CONCEPT ImplementedFalsifiable hypothesisA falsifiable hypothesis is an explicit proposition paired with observations that could contradict it.mathinteractive135 / CONCEPT PartialHypothesis ledgerThe hypothesis ledger preserves hypotheses, falsifications and revisions as append-only history instead of silently replacing prior states.mathinteractive136 / CONCEPT PartialPredictionA prediction states an observable expected outcome from a model or hypothesis before that outcome is resolved.mathinteractive137 / CONCEPT ImplementedCounterexampleA counterexample is an observation satisfying a claim’s preconditions while contradicting its predicted consequence.mathinteractive138 / CONCEPT ImplementedDirect evidenceDirect evidence is a receipt, test output or artifact explicitly associated with a claim; association alone does not establish business truth.mathinteractive139 / CONCEPT PartialIndependent evidenceIndependent evidence comes from a producer sufficiently separate from the claimant under a declared independence policy.mathinteractive140 / CONCEPT ImplementedEvidence receptionEvidence reception validates and normalizes an incoming evidence report before attaching it to a worker or claim dossier.mathinteractive141 / CONCEPT ImplementedGroundingGrounding links a symbolic claim to observations or artifacts that connect it to an operational context.mathinteractive142 / CONCEPT PartialEpistemic stateAn epistemic state records evidence quality, derived confidence, phase and unresolved epistemic debt for a claim or belief.mathinteractive144 / CONCEPT ImplementedUnverified resultAn unverified result is archived as provisional with explicit epistemic debt and cannot support promotion.mathinteractive145 / CONCEPT ImplementedPromotion eligibilityPromotion eligibility is an explicit decision that is true only when every policy obligation for a candidate is satisfied.mathinteractive146 / CONCEPT PartialBelief revisionBelief revision updates a versioned claim when new relevant evidence arrives while retaining the prior state and contrary evidence.mathinteractive147 / CONCEPT PartialEpistemic dissonanceEpistemic dissonance records conflict between beliefs and evidence or among incompatible beliefs without silently resolving it.mathinteractive148 / CONCEPT PartialBiasBias denotes systematic steering or calibration error detected under a declared probe; a detected pattern requires scoped interpretation.mathinteractivebenchmark149 / CONCEPT ImplementedHallucination indicatorThe hallucination concept marks observable software conditions such as unsupported claims, untested code proposals, placeholders or empty values; it is not a medical diagnosis.mathinteractive150 / CONCEPT ImplementedHallucination monitoringHallucination monitoring continuously records declared unsupported-claim indicators and their context without converting counts into truth judgments.mathinteractive153 / CONCEPT ImplementedEvidence barrierAn evidence barrier checks that every cited claim and artifact belongs to the attributed source dossier before a collective result can advance.mathinteractive154 / CONCEPT ImplementedPromotion gateA promotion gate applies the candidate’s declared replay, independent-verification, approval and preservation policies before any integration.mathinteractive
SYSTEM · 10 CONCEPTS

Memory & Learning

How episodes, knowledge, procedures, and learned changes are retained and retrieved.

02 / CONCEPT PartialMemoryGenOS memory helps retrieve useful experiences, connect decisions, and avoid known dead ends. It combines detailed episodes with indexed facts and provenance signals.biologymathinteractive33 / CONCEPT PartialEpisodic memoryRecords of contextualized events, actions, observations, and outcomes.biologymathinteractive34 / CONCEPT PartialSemantic memoryIndexed facts and relationships retrieved to supply context to a mission.mathinteractive35 / CONCEPT ExperimentalVector memoryA similarity-search representation used to retrieve related items from an embedding index.mathinteractive36 / CONCEPT PartialProcedural memoryReusable instructions or action sequences represented as runtime knowledge.mathinteractive37 / CONCEPT ExperimentalSynaptic plasticityA bounded update of selected associations or weights based on observed signals.biologymathinteractive38 / CONCEPT ExperimentalSTDPSpike-timing-dependent plasticity as a computationally bounded timing-based update rule.biologymathinteractive39 / CONCEPT PartialFossilizationTerminal archival of a lineage or experience while preserving its historical record.biologymathinteractive40 / CONCEPT PartialMemory retrievalA ranked selection of stored items that can inform, but cannot prove, a current decision.mathinteractive131 / CONCEPT PartialAutobiographical memoryAutobiographical memory stores salient agent episodes, lessons and conditional recall; stored history remains fallible and must be revalidated before use.mathinteractive
SYSTEM · 19 CONCEPTS

Collective Intelligence

The runtime components and communication patterns that let agents coordinate.

41 / CONCEPT PartialMorphogenesisA runtime for composing bounded executable graphs from topology and control operators.biologymathinteractivesimulation42 / CONCEPT PartialEpistemic meristemTracks verified coverage gaps and revalidates them before proposing growth.mathinteractive43 / CONCEPT PartialUnblocking spiralChanges method and scope through a bounded, evidence-gated response to a repeated blockage.mathinteractive44 / CONCEPT PartialCounterexample cambiumStores counterexamples and gates their reuse in later work.mathinteractive45 / CONCEPT PartialAperiodic chronotaxisPersists observation schedules and receipts to expose missed temporal windows.mathinteractive46 / CONCEPT PartialContracted statistical riskAccounts for a bounded promotion-risk budget before opt-in statistical promotion.mathinteractive47 / CONCEPT PartialDynamic organizationsNineteen declared organization patterns with deterministic step algorithms and varying maturity.biologymathinteractive48 / CONCEPT PartialWorker kindsA catalog of runtime worker types selected against role and method capability requirements.mathinteractive49 / CONCEPT PartialResident daemonsLong-lived project services that observe state and may propose or carry out bounded work under policy.mathinteractive50 / CONCEPT PartialAgent relationshipsDeclared and measured links that shape coordination, routing, or communication between agents.mathinteractive51 / CONCEPT PartialRelational physiologyA bounded kernel for relation constraints, provenance independence, authority and admitted routing across 29 relation types.mathinteractive52 / CONCEPT PartialCommunication ecologySignals and channels that let agents coordinate through bounded, typed communication patterns.mathinteractive53 / CONCEPT PartialZero-text signal planePersisted signals and deliveries, inbox/ACK, leased handler retries and bounded cognitive escalation.mathinteractive54 / CONCEPT PartialG-CIRA residual cognitive contract that keeps versioned obligations, refusals and per-invocation visibility explicit.mathinteractive55 / CONCEPT PartialMission continuityDurable mission ownership, completion checks, dormancy, wake-up and guarded regeneration across process restarts.mathinteractive56 / CONCEPT PartialAgentGitVersioned agent state and lineage operations such as commit, branch, diff, replay, and merge.mathinteractive57 / CONCEPT PartialCounterfactual workspacesIsolated workspaces used to compare alternative changes before any result is promoted.mathinteractive151 / CONCEPT PartialWeighted consensusWeighted consensus aggregates attributed agent contributions while preserving dependence and uncertainty; agreement is not automatic truth.mathinteractivesimulation152 / CONCEPT ImplementedQuorum with abstentionQuorum with abstention refuses a collective decision when integrity, confidence or uncertainty conditions do not support one.mathinteractivesimulation
SYSTEM · 08 CONCEPTS

Orchestration

The eight GenOS topologies and the structures they use to organize work.

58 / CONCEPT PartialTrinityThree candidate worlds are compared through a declared evidence barrier before a candidate is retained or promoted.mathinteractivesimulation59 / CONCEPT PartialA-TeamSpecialists coordinate work through dependencies, explicit handoffs, and integration of their deliverables.mathinteractivesimulation60 / CONCEPT PartialBiocenosisA community evaluates proposals through evidence, explicit ballots, and policy-bound aggregation.biologymathinteractivesimulation61 / CONCEPT PartialHolobiontA host composes specialist symbionts under capability, resource, lifecycle, and execution contracts.biologymathinteractivesimulation62 / CONCEPT PartialSyncytiumMembers coordinate around shared, versioned state with merge operations and invariant checks.biologymathinteractivesimulation63 / CONCEPT ImplementedRhizomeA persisted capability graph with callable bounded multi-hop routing, local traces, and evidence-gated growth services.biologymathinteractivesimulation64 / CONCEPT PartialMetapopulationSemi-independent demes exchange typed propagules over directed corridors, with receiver validation, verified migration cycles, and gated recolonization.biologymathinteractivesimulation65 / CONCEPT PartialBiomeEleven variants share a bounded transactional ecology loop with persistent niches, measured resource use, authorized adapters and independent verification gates.biologymathinteractivesimulation
SYSTEM · 11 CONCEPTS

Evolution & Ecology

Variation, selection, transfer, populations, niches, and recovery across agent groups.

66 / CONCEPT ExperimentalMutationRust operations change genome data models; MCP biomimicry mutation handlers update scenario registries and do not change an active agent’s AgentDNA.biologymathinteractive67 / CONCEPT ExperimentalSelectionA policy for comparing candidates and retaining outcomes under explicit criteria.biologymathinteractive68 / CONCEPT ExperimentalPlasmidsTransferable capability packages that can be acquired, checked, and applied under runtime rules.biologymathinteractive69 / CONCEPT ExperimentalHorizontal transferA governed transfer of capabilities or artifacts between agent lineages.biologymathinteractive70 / CONCEPT ExperimentalSwarm intelligenceLocal coordination and optimization patterns implemented as bounded organization steps.biologymathinteractive71 / CONCEPT ExperimentalStigmergyCoordination through traces deposited in a shared environment and read by later work.biologymathinteractive72 / CONCEPT PartialNichesDeclared regions of a search or work environment associated with resources and specialized capabilities.biologymathinteractive73 / CONCEPT ExperimentalPopulationsGroups of agents or candidate solutions whose composition can change under explicit policies.biologymathinteractive74 / CONCEPT ExperimentalCryptobiosis & dormancyA bounded suspended state that preserves continuity until an explicit resume condition is met.biologymathinteractive75 / CONCEPT PartialNatural creative ecologyA model of open-ended search through recombination, exploration, plasticity, and selection.biologymathinteractive155 / CONCEPT PartialAgent ecosystemAn agent ecosystem relates agents, niches and biomes through explicit capability and resource constraints; it is a software ecology analogy.biologymathinteractivesimulation
SYSTEM · 12 CONCEPTS

Physiology & Perception

Resource regulation, sensing, foraging, and other bounded runtime processes.

76 / CONCEPT ExperimentalSensoriumRuntime structures for observations and perception signals, with boundaries between simulated and real inputs.biologymathinteractive77 / CONCEPT PartialMetabolismResource accounting and allocation rules that constrain the work an agent can perform.biologymathinteractive78 / CONCEPT PartialHomeostasis & allostasisTarget regulation and anticipatory adjustment under changing conditions and declared bounds.biologymathinteractive79 / CONCEPT PartialResilience & recoveryRecovery planning and bounded continuation after a failure, loss, or interruption.biologymathinteractive80 / CONCEPT PartialDevelopmentA staged process for changing an agent or project while retaining lineage, constraints, and evidence.biologymathinteractive81 / CONCEPT PartialSymbiontsSpecialist services composed by a host under explicit capability and execution contracts.biologymathinteractive82 / CONCEPT ExperimentalWeb foragingA resource-selection calculation for web exploration; it is not by itself a continuous browser controller.biologymathinteractive83 / CONCEPT ExperimentalFoveationA process for selecting a region of an observation for higher-resolution inspection.biologymathinteractive84 / CONCEPT ProposedAnimal sensesA catalog of sensory mechanisms used as constrained design analogies for runtime perception.biologymathinteractive85 / CONCEPT ExperimentalAnimal control primitivesBounded control patterns inspired by animal behavior and translated into software operations.biologymathinteractive123 / CONCEPT PartialPerceptionPerception is a bounded bridge from canonical observations to memory and control; it does not establish biological sensation or direct access to the world.mathinteractive124 / CONCEPT PartialInteroceptionInteroception reads internal software signals such as budget, dissonance and health for allostatic planning; it is not visceral sensation.mathinteractivesimulation
SYSTEM · 14 CONCEPTS

Immunity & Medicine

Threat response, pathology models, and the limits of computational health metaphors.

01 / CONCEPT PartialFailure modesGenOS models potential failures in an agent system: excessive alerts, cross-workspace contamination, unintended intervention effects, or degraded performance.biologymathinteractive86 / CONCEPT PartialAdaptive epistemic immune systemA threat-response model for checking claims and evidence while preserving authority and provenance boundaries.biologymathinteractive87 / CONCEPT PartialImmune systemA set of threat detection and containment mechanisms; no absolute immunity is implied.biologymathinteractive88 / CONCEPT PartialNosologyA classification of runtime pathologies used to describe failure patterns and possible responses.biologymathinteractive89 / CONCEPT PartialComputational pathologiesA model of degraded or unsafe runtime states, not a medical diagnosis of people.biologymathinteractive90 / CONCEPT PartialAutoimmune failureA pathology category for safeguards that overreact to legitimate runtime behavior.biologymathinteractive91 / CONCEPT PartialDegenerative failureA pathology category for progressive loss of runtime capability or state quality.biologymathinteractive92 / CONCEPT PartialInfectious failureA pathology category for unwanted propagation across agents, workspaces, or state boundaries.biologymathinteractive93 / CONCEPT PartialGenetic failureA pathology category for harmful inherited or encoded agent traits.biologymathinteractive94 / CONCEPT PartialCancer-like failureA pathology category for uncontrolled growth or replication in a runtime model.biologymathinteractive95 / CONCEPT PartialMetabolic failureA pathology category for unsustainable resource use or allocation.biologymathinteractive96 / CONCEPT PartialCardiovascular failureA pathology category for disrupted flows or communication in a runtime model.biologymathinteractive97 / CONCEPT PartialPsychiatric failureA pathology category for modeled behavioral instability; it is not a claim about human mental illness.biologymathinteractive98 / CONCEPT PartialEnvironmental failureA pathology category for harmful interactions between a runtime and its operating environment.biologymathinteractive
SYSTEM · 08 CONCEPTS

Formal Verification

Deterministic procedures, proof artifacts, solvers, and verification boundaries.

99 / CONCEPT PartialLean verificationA verification path that submits formal proof artifacts to a Lean kernel.mathinteractive100 / CONCEPT ProposedProofArtifactA structured artifact that binds a formal claim, proof material, and verification result.mathinteractive101 / CONCEPT PartialDeterministic verificationA repeatable check whose result depends on declared inputs and a bounded verifier.mathinteractive102 / CONCEPT ConceptualMathematical organismA formal model of an agent system expressed through explicit mathematical structures and limits.mathinteractive103 / CONCEPT PartialVerification registryA registry of available verification contracts and their declared evidence requirements.mathinteractive104 / CONCEPT PartialSMT solver layerA solver integration surface whose maturity and runtime status must be checked against its implementation record.mathinteractive105 / CONCEPT PartialDeterministic proceduresBounded procedures whose declared inputs and rules make their results reproducible.mathinteractive143 / CONCEPT ImplementedFormal resultA formal result is produced by a deterministic procedure with a bound receipt and declared verification semantics.mathinteractive
SYSTEM · 12 CONCEPTS

Runtime & Infrastructure

State, execution boundaries, integrations, authority, and observability.

106 / CONCEPT PartialSnapshotsVersioned captures of runtime or agent state that can support restoration and comparison.mathinteractive107 / CONCEPT PartialVirtual filesystemA bounded filesystem interface used to scope access to project and runtime files.mathinteractive108 / CONCEPT ImplementedSQLite persistenceThe local relational storage layer used by runtime services that persist sessions and operational state.mathinteractive109 / CONCEPT PartialPersistenceStorage and rehydration mechanisms that preserve selected runtime state across calls or restarts.mathinteractive110 / CONCEPT PartialShared stateVersioned data that multiple members can read or update under an explicit consistency policy.mathinteractive111 / CONCEPT PartialModel routingSelection and dispatch rules for available inference providers and execution profiles.mathinteractive112 / CONCEPT PartialMCP interfacesTool interfaces exposed through the Model Context Protocol with declared contracts and permissions.mathinteractive113 / CONCEPT PartialSandboxAn execution boundary intended to constrain filesystem, process, or tool effects.mathinteractive114 / CONCEPT PartialObservabilityEvents and state views used to inspect runtime behavior and its evidence trail.mathinteractive115 / CONCEPT PartialIdentity & authorityIdentity, role, and permission rules that constrain which actors may perform runtime operations.mathinteractive116 / CONCEPT PartialGovernanceApproval, policy, and audit mechanisms that bound execution and promotion decisions.mathinteractive117 / CONCEPT PartialWorkflows & jobsPersisted task graphs and jobs that coordinate execution, dependencies, and lifecycle events.mathinteractive