Scope — the circadian clock as a self-sustained oscillator network

The ~24 hour circadian clock is a self-sustained coupled limit-cycle oscillator network (SCN master + peripheral clocks) on the shared R19 substrate, not a light-driven timer: it free-runs and is only entrained by light. The one node with a named master gene carries a measured BMAL1 well (γ = 1.33348); the ~24 h period is a cited anchor while the mechanism is derived. Disease is clock–environment misalignment.

This package fills the research body of the circadian volume. It emerges the clock's nodes from a measured gene, runs the oscillator dynamics — free-running, entrainment, master-vs-network, setpoint gating, misalignment — on the vendored FitzHugh–Nagumo substrate, and exports a single timing signal to the homeostatic setpoints of the sibling packages and to the mind volume's affect layer. Every number is produced by shipped deterministic code; the absolute period is the only [L] anchor; the felt quality of mood stays in mind (consciousness_claim = 0).

The clock is an oscillator, not a stopwatch driven by light

The circadian system keeps ~24 hour time. The naive picture — an external light cycle pushing a passive timer — is wrong, and the correction is the whole programme: the clock is a self-sustained limit-cycle oscillator that free-runs with no input and is merely entrained by light. On this framework's shared FitzHugh–Nagumo (R19) substrate that is the same bistable cell the rest of the atlas uses, now run in its oscillatory window. The package adds the dynamics the clock needs — coupling, entrainment, setpoint gating — on top of that vendored substrate; it re-derives no constant and re-emerges no organ owned elsewhere.

Four nodes, one measured gene

The clock is four nodes: an SCN master oscillator, the molecular core clock loop (BMAL1/CLOCK ↔ PER/CRY transcription–translation feedback), a peripheral clock network (liver / muscle / adipose), and the light-entrainment input (retina → SCN). Node identity and developmental order are owned by DNA and never fitted; the one node with a named master gene, the core loop, carries a measured BMAL1 well of γ = 1.33348 (gene 406, NC_000011.10), fetched through the same nearest-neighbour DNA pipeline the framework uses everywhere — a measured input, graded [V], never chosen to hit a target. The SCN and peripheral nodes are circuits with no single master gene (diffuse).

Period is a cited anchor; mechanism is what is derived

One honesty line governs every chapter. The absolute ~24 hour period is a cited [L] anchor, not an emergent number: the substrate runs in fast arbitrary-time cycles for cheap probes, and absolute phase has no zero in it ([O]). What is derived is the mechanism — self-sustension, the phase-response curve, the synchronisation transition, setpoint gating, the misalignment sign — and every such number in these pages is produced by the shipped deterministic engine (seed = 19, result sha256 417823934d6e…, 2× identical).

Disease axis and the two seams out

Disease here is clock–environment misalignment: the clock runs, but at the wrong phase relative to the demand schedule (shift work, jet lag), and the defended setpoints it gates lose their daily organisation. The package is SSOT for circadian phase / timing and exports a gating signal to the thermometabolic, hemodynamic, ionic and immune setpoints of the sibling packages. Its sharpest seam is into the mind volume: misalignment flattens the gated HPA cortisol rhythm, and that flattening is the circadian depression contributor the mind paper explicitly left locked. No felt-state claim crosses that seam.