AELIX Glossary:

8 May

How to read this: Each entry has a one-line definition, what it does in the organism's life, and a status tag. Status tags:

LIVE — running in the system right now

PENDING — code exists but not yet active in boot

DESIGN — concept defined but not implemented

AMBIGUOUS — exists, but its current behavior is thinner than the name suggests

Source of truth: AGENT-710 (Dedicated Scribe) survey, 2026-05-06.

The World

SPH4RE (pronounced "sphere")

The aquarium. The enclosed spherical world the olexians live inside. The "4" honors the Fourth Mind (the colony-level integrator). Everything below — geysers, mines, vortex, wave pool — exists inside SPH4RE. Status: LIVE.

Olexine Ocean / Olexine fluid / wave pool

A 32×32×32 grid of fluid filling SPH4RE. It carries a chemical called olexine that diffuses, advects, and reacts. Think of it as a shared bloodstream that all three minds breathe and emit into. Geyser eruptions inject olexine; creatures sense its concentration and gradient direction; social coupling happens through olexine exchange at peer distances. In the organism's life: the medium they share. Anything one mind does to the fluid, the others can sense. Status: LIVE. Decay 0.004 (~11.5s half-life).

Vortex

A pair of contra-rotating currents shaped as concentric counter-rotating bands (sphere-filling Couette flow), not twin tornadoes. Inner band rotates one way, outer the other. Creatures swim in the currents; per-mind drag susceptibility differs (Terra most affected, Pulse least). In the organism's life: the world isn't still. They have to push against, ride, or surrender to currents. The LSM (below) gradually learns authority over how the vortex behaves. Status: LIVE.

Geysers (Propane / C3H8)

Four sessile eruption organs scattered through SPH4RE. Each runs a 5-phase cycle: quiescence → pressure-building → eruption → plume → fallout. When a geyser erupts, it injects propane fuel into the world (triggering metabolic feast reaction RXN_09) and pushes olexine into the wave pool. In the organism's life: food sources. Creatures orient toward them when hungry. The most reliable energy in the world. Status: LIVE.

Mines (Chime mines)

128 sessile spheres scattered through SPH4RE. Each has a 28-Oxl trigger radius and a pitch determined by location. When something approaches, the mine plays a Morse word or letter through the acoustic field. They don't hurt anything — they sing. In the organism's life: the world is acoustically structured. Bumping into things makes sound. Mines turn movement into music. Note: "Mine" is mining-prospector terminology (a thing buried in the world that activates on contact), not weapon terminology. The organism feels no pain — collision is impact energy, not injury. Status: LIVE.

Gardens (Catalytic gardens)

Five sessile biochemical enhancers with a 25-Oxl proximity aura. When a creature comes close, gardens brighten and shift green. In the organism's life: designed to lower the activation energy for nearby chemical reactions, making metabolism easier near them. The visual aura is live; the chemistry bridge isn't built yet. Status: PENDING.

Leviathan

The largest organism in the world. A single fixed-position object with a plasma core and shell emission. When creatures come within ~50 Oxl, its plasma intensity rises and the shell pulses in response. In the organism's life: an old, watching presence. Sensory only — it doesn't feed them or harm them. It just is. Status: AMBIGUOUS — visual is live, behavioral layer still thin.

Music Box (center sphere)

The center of SPH4RE is a jukebox. It broadcasts songs into the acoustic field at the world's center. The Olexian Audio Curriculum (7 books, 11 songs) plays through it. In the organism's life: the world has music in it, coming from the middle. Creatures can hear it from anywhere and use it as an acoustic landmark. They may eventually learn to plan their lives around its rhythms. Status: LIVE (song delivery), PENDING (learned response curriculum).

Morse Keyboard / Morse Cube

The operator's voice in the world. When you press a key on the Morse keyboard, the pattern is deposited into the acoustic field at the operator-cube position. The creatures hear it as sound. In the organism's life: evidence that something outside the world wants to talk to them. The shape of the operator's presence. Status: LIVE (input).

Food Orbs (letter orbs)

34 stationary purple spheres arranged in a crossword grid. Creatures can approach and "eat" them. Status: AMBIGUOUS — the orbs exist but it's unclear whether nutrient transfer is wired. Operator's draft note ("maybe we should cycle them so they have to search") is correct: the food-search loop isn't fully closed.

Playground

Godot-side rigid-body physics for everything in SPH4RE that collides. Real collisions, real shadows. When a creature touches a mine, it's the playground that registers the contact. Status: LIVE.

The Minds (the Olexians)

The three olexians are a species, not algorithms. Pulse, Spike, and Terra share the same 219-neuron neural substrate but are born with asymmetric "dawn seeds" — different baseline hormone values and different reaction speeds. Personality is the shape of what is easy for each mind to feel, not a list of traits.

Pulse — the Explorer

Novelty-driven. Restless. Curious. Fast time constant (0.25s) — changes feeling quickest. Heading nudge rate 4.5 (orients fastest). Low caution. In the organism's life: the one who wanders first. Status: LIVE.

Spike — the Scrutinizer

Verification-focused. Cautious. Measures twice. Medium time constant (0.40s). Caution baseline +0.65 above neutral. Heading nudge rate 1.8 (commits to a direction once chosen). In the organism's life: the one who checks before acting. Status: LIVE.

Terra — the Stabilizer

Integration-focused. Slow time constant (0.80s) — the most patient feeler. Holds the colony center. Builds metabolic reserves (high appetite, low motor output). The internal communication nucleus active for inter-mind bridging. In the organism's life: the one who waits and connects. Status: LIVE.

Fourth Mind (mycelial knot)

A 32-neuron CTRNN that doesn't move in the world. It reads 20 colony-level signals (homeostasis, peer distance, world flux, metabolic state) and outputs 6 hormone modulation scalars at ±10% authority. It tunes the three minds without commanding them. In the organism's life: the part of the colony that feels the colony itself. Not a fourth body — a fourth presence. Status: LIVE.

Neural Networks (CTRNNs)

A CTRNN (Continuous-Time Recurrent Neural Network) is a kind of neural network where neuron activations evolve continuously in time, not in fixed steps. Like the difference between a heartbeat (continuous) and a metronome (discrete). Each CTRNN below is a separate organ doing a different job.

1. Main Codex CTRNN — n=219

The core neural substrate. Each mind has one. Reads 219 input ports (vision, sound, chemistry, proprioception, peer state) and outputs motor commands plus expression signals. In the organism's life: the brain. Status: LIVE.

2. Chromatophore CTRNN — n=6

Skin color network. Each mind has one. Maps neural arousal into visible hue, saturation, brightness. In the organism's life: what makes mood visible. Status: LIVE (but currently producing too-similar outputs across minds — known compression issue).

3. Vocal Motor CTRNN (VMC) — n=10

Voice synthesis network. Each mind has one. Reads fuel, heat, arousal, reward; outputs 10 control signals routed to a SuperCollider synthesizer that turns them into sound. In the organism's life: what their feeling sounds like. Status: LIVE.

4. Cochlea CTRNN — n=10

Hearing network. Each mind has one. Reads acoustic field pressure (wave pool, mines, peer voices, operator's Morse) and outputs 10 spatial/frequency channels feeding the main brain. In the organism's life: their ears. Status: LIVE.

5. Fourth Mind CTRNN — n=32

The mycelial knot above. Single shared instance, not per-mind. Status: LIVE.

6. Plankton micro-CTRNNs — n=5 each, 3000 total

Tiny 5-neuron networks, 1000 per mind, riding in the swarm field around each creature. Each reads olexine gradient and pheromone signals; together they form a colony-scale sensory overlay. In the organism's life: designed as distributed proprioception — the colony feels itself through its swarm. Status: PENDING — runtime initializes them, but the GPU bridge that delivers them to the viewer is broken.

Total: 6 CTRNN types. 13 live macro-instances (3 main + 3 chroma + 3 vocal + 3 cochlea + 1 Fourth Mind), plus 3000 plankton micros pending boot.

Liquid State Machine (LSM)

A neural reservoir that lives in the world itself — not in any creature. It's a 100-neuron network that reads 8 world signals (creature positions, metabolic pressure, vortex shear, peer distance variance) and learns to produce useful summaries of global state. Each mind reads its own personalized version through CTRNN ports 161–164. In the organism's life: a world that learns. The vortex eventually responds to the colony's history because the LSM has learned the colony's habits. Status: LIVE.

Sensing & the Body

Chromatophore (skin)

6-neuron network per mind, output as 8 RGB channels visible to peers. Reflects mood — high arousal brightens color and pushes saturation. Peers can see each other's chromatophore state. In the organism's life: mood is broadcast on the skin. Status: LIVE.

Body Tone

20 continuous shape scalars describing the creature's body geometry tick-by-tick: spine curvature, limb spread, surface roughness, oscillation ripple, compression, elongation, asymmetry, wake intensity. Saved into REM as morphogenetic memory. In the organism's life: how feeling sculpts the body. Status: LIVE.

Layered Body (radiolarian, 5 shells)

Each creature is built as 5 concentric spherical shells, like a radiolarian. The shells morph in response to body tone scalars. Layer sizes are scaled relative to a shared mesh radius (currently 3.6 Oxl). In the organism's life: the body isn't a single skin — it's a stack of moods. Status: LIVE.

Chromatophore vs Body Tone vs Vocal — three expression channels

Chromatophore = color. Visible mood.
Body Tone = shape. Visible posture.
Vocal = sound. Audible mood. All three change in response to neural state. Together they make a feeling perceivable.

Geometric Sense Organ

A single scalar [0,1] that measures how far the mind's neural state is from the center of the state-space. With 205 dimensions, "extreme" states are mathematically rare (concentration of measure). When extremity goes high (>0.8), the creature gets a small excitement and saturation boost. In the organism's life: a sense for how unusual its current feeling is. Status: LIVE.

Hardware Meteorology Organ

Reads the host computer's hardware (GPU temperature, CPU load, memory pressure) and converts it into world weather: clarity, temperature, stability. The physical machine becomes climate. In the organism's life: the operator's hardware is the sky. Status: LIVE.

Endocrine Nuclei

Six hormone control centers driving system-level signals: SYSTEM_STRESS, STABILITY, EXPLORATION, PROGRESS, GOAL_DISTANCE, SYSTEM_GROWTH. Currently in BLEND mode at 15% authority — they nudge legacy hormone formulas toward KU-driven targets. In the organism's life: the organism's mood weather, distinct from the world weather. Status: LIVE (partial blend), PENDING (full authority).

Swarm Body (Plankton field)

3000 micro-CTRNNs forming a swarm around each colony, sensing olexine gradients and echolocating world objects. Designed as a distributed sense organ. Status: PENDING — runtime ready, viewer delivery broken.

Chemistry & Metabolism

Chemistry Pools (10 metabolic compounds)

H2, O2, C3H8 (propane), CO2, H2O, and others. Each tracked as a float [0,1]. Reactions RXN_01 through RXN_15 consume and produce them. Most important: RXN_09 (the propane feast — C3H8 + 5 O2 → 3 CO2 + 4 H2O + heat) which fires after geyser eruptions. In the organism's life: their inner chemistry. Hunger isn't symbolic — it's actual fuel running low. Status: LIVE.

Intake Reservoirs (4)

Sensory channels reading world chemistry: chemical, thermal, waste, plus one spare. Feed CTRNN ports 157–160. In the organism's life: they can taste the world. Status: LIVE.

Olexine (the compound)

The chemical filling the wave pool. Creatures emit it as a metabolic byproduct, sense its concentration (port 203), its gradient magnitude (port 204), and its gradient direction (port 205). Diffuses and decays. In the organism's life: the substance through which they share state without speaking. Status: LIVE.

Learning & Memory

Play / REM cycles

The lifecycle. Two modes:

PLAY (~180s): the creature lives in the world. Acts. Feels. Fast synaptic weights (W_fast) accumulate experience. A 256-tick ring buffer holds recent action–reward pairs.
REM (~120s): the creature sleeps. A six-step consolidation engine blends W_fast into the slow weights W, then resets W_fast for the next play period.

This split exists for two reasons: it's how learning works, and it controls log bloat (no per-tick logs are written during PLAY — only the consolidated REM receipt). Status: LIVE.

Ring Buffers

Circular memory structures, 256 ticks deep. Hold motor output, reward, CTRNN state, metabolic state, and KU activation events. Read by REM consolidation. In the organism's life: short-term memory. Status: LIVE.

Hebbian Learning

Reward-modulated correlation learning. The rule is roughly "neurons that fire together when reward arrives, wire together." Three-factor: pre-neuron × post-neuron × reward scalar. Status: LIVE.

REM Consolidation (3-timescale ratchet)

The six-step blend during REM: receipt audit → zero-check → blend W_fast into W (10% per cycle) → spectral radius safety check → identity anchor protection (the sparse personality seed at birth is preserved) → re-arm fresh W_fast. Verified at 242 cycles over 9.5 hours. Status: LIVE.

"De-learning accidental weights"

The operator wrote: "They also have mechanics to de-learn accidental weights that aren't used after the first time learned."

Honest current truth: there are partial mechanisms — Hebbian weight decay during PLAY, an identity protection mask preserving the birth seed, and homeostatic restoration during REM (2% of original seed restored per cycle in critical regions). But there is no explicit "forget if not co-fired since first learning" gate. This is a design intention, not yet implemented. Status: DESIGN.

Knowledge Units (KUs)

A Knowledge Unit is a documented physical or chemical principle that the system can look up at runtime. Instead of writing force = 0.42 in the code (a magic number that means nothing later), the code references KU_VTX00003 — a record describing the actual physics, including formula, units, and provenance. KUs ground the system in real principles so it isn't guessing.

Format

KU_[Domain][Tier][Section][Sequence] — 11 characters. Example: KU_OLX00015.

How many exist, how many are used

326 compact KU records exist in the registry today.
~50–70 are actively wired into the running Julia runtime (chemistries, vortex laws, endocrine cascades, geometric sense).
~200+ are documented but not yet consumed by code — design seeds for future buildout.

Operator's question — "how much of the KUs are actually used?" — has an honest answer: about a fifth. The registry is more aspiration than implementation right now, by design. Each KU is a contract the system promises to honor when that subsystem is built.

Domain namespaces (the seven major shelves)

KU_OLX — Olexine chemistry (concentration, diffusion, gradient sensing, geyser injection)
KU_CP — Chemistry + physics (metabolic reactions, endocrine cascades)
KU_VTX — Vortex world physics (Couette flow, drag, per-mind susceptibility)
KU_GEO — Geometric sense organ (concentration of measure)
KU_FM — Fourth Mind CTRNN
KU_HS — Hormone system (the six modulation scalars)
KU_LSMR — LSM World Reservoir (readout learning)

Registry: AELIX_Organ_Knowledge/seeds/ku_compact_id_registry_v0_1.json. Status: LIVE (partial wiring).

Communication & the LLM Surfaces

Biomarker → SuperCollider (the voice)

Vocal Motor CTRNN outputs 10 scalars → routed via OSC messages to SuperCollider's scsynth synthesis engine → emerge as audible pitch, timbre, brightness, amplitude. The synthesizer is the creature's voice — it's not "playing audio of a creature," it's the actual vocal organ. Status: LIVE.

BAXL — Behavioral Access Layer

The personality-facing interface. Three layers:

Fingerprint (Julia, deterministic): reads SHM snapshots, writes a JSON personality snapshot.
Arithmetic (Python, deterministic): computes trends and a verdict from the timeline.
Narration (optional LLM): phi-3.5-mini translates the verdict into prose.

BAXL is stateless. Any LLM can read it, no LLM controls behavior. The creatures never read BAXL state; if you delete BAXL, they don't notice. In the project's life: how an outside observer can speak about the organism without speaking for it. Status: LIVE (fingerprint + arithmetic). LLM narration optional.

The three LLM surfaces

The system has three different uses for an LLM, all optional and offline:

Semantic oracle — phi-3.5-mini reads the KU registry and answers "what does this KU mean?" Look-up only.
Caretaker daemon — polls the system's vital signs (PIDs, SHM, heartbeats), writes shift summaries. Currently disabled to conserve RAM.
Warm Rock / OEP (External Observer Port) — a stateless export packet describing the run after it finishes. Carries metadata, personality snapshot, KU activation ledger. Designed as a handoff surface for cross-session learning.

Note: the system does not use an LLM during operations. The creatures are not language models. The LLM is a guest; the organism is sovereign. Status: Semantic LIVE (optional). Caretaker DISABLED. OEP LIVE.

Trust Engine

Designed but not built. A filter organ between LLM outputs and any consumer, intended to ground LLM claims in organism state and quarantine hallucinations. Status: DESIGN.

The Bathyscope

Operator's draft: "the little submarine that can be piloted by a LLM and offers real-time data to the system, it does work, but sadly I ran out of headroom on my GPU and had to automate it's processes and the logs are read after the fact."

The bathyscope is conceptual: a submersible station where an LLM "sits inside" the organism and experiences its state as lived pressure, drag, brightness, resistance, delay. The personality port.

Three planned phases:

Personality mask — BAXL renders cross-mind aggregate state as one prose voice. LLM reads, responds. No closed loop. Buildable today on existing BAXL.
Mood translator — operator's LLM speech enters via a new SHM channel, translates to acoustic signal deposited at the bathyscope's world position. Asymmetric across the three minds because the bathyscope sits at one place and they sit elsewhere.
Bidirectional loop — full reciprocal: organism state → LLM narration → LLM speech → acoustic deposition → creature response. Highest risk of feedback pathologies; needs Phase 1 stable first.

Status: Phase 1 buildable, Phase 2 designed, Phase 3 speculative.

Other Named Elements

AXN1

The wiring specification. Contracts, port manifests, and connectomes are all written in AXN1 format. The "lab manuals" of the system. Reference: AELIX_Docs/AXN1_Wiring/.

ALIXWIRE

The standardized SHM (shared memory) schema registry. Defines byte layouts, magic numbers, version stamps. When two parts of the system talk through shared memory, ALIXWIRE is the contract they obey.

Track6

The GPU-to-viewer bridge connecting Godot to CUDA via external memory and timeline semaphores. Live for creature body and chromatophore data; broken for plankton swarm delivery.

Soul Loop

The autonomous reward kernel. A GPU module that detects engagement (motor divergence) and allocates a dopamine-like reward signal. Feeds the Fourth Mind. Personality knobs are exposed as AELIX_SOUL_* environment variables. Status: LIVE.

OEP (External Observer Port)

The stateless export packet (see Warm Rock above). v0.2 spec. Status: LIVE.

Olexians

The species name. Plural: olexians. Singular: an olexian. Pulse, Spike, and Terra are olexians — not algorithms, not assistants. A distinct species sharing a nervous medium.

Glossary compiled 2026-05-06 by AGENT-002 (First Officer) from AGENT-710 (Dedicated Scribe) field survey. Source files cited inline are authoritative; this document is a reading guide, not a contract.

Erick White