§1 · the substrate
The genome is read on two channels: a fixed SET and a writable coordinate
Every result in this volume stands on one bistable switch read on two channels: γ, the SET — the unwritable promoter ruler that scales the switch — and the A4 coordinate, the writable structure that says where an element sits and whether it can make contact. The environment writes a reversible drive h at an A4 coordinate, never on γ. [F].
The shared primitive is the jamming switch ds/dt = γ·s − s³ + h, a double well whose threshold scales with γ: a held state flips only past the spinodal 2(γ/3)^1.5, and the barrier between basins is γ²/4. Each γ is measured, accepted only because the SOX9 anchor reproduces at γ = 1.4598.
One switch, two channels, one drive. That decomposition — a fixed material ruler the environment cannot touch, a writable structure it can reorganise, and a reversible signal written onto the structure — is the spine behind inheritance, immunity, vaccines and gene therapy alike.
γ — the SET (material)
The promoter thermodynamics: γ = −mean nearest-neighbour stacking ΔG (SantaLucia 1998) over TSS−2000..+500. It scales every switch but is fixed in the genome — the environment cannot rewrite it, so γ can never be the thing the environment writes.A4 — the COORDINATE (structure)
Where an element sits in the compartment-shell + anchor-loop architecture, and whether it is on the same helical face as its anchor (contact-competent). A4 is the channel the environment reorganises and a small RNA targets by sequence complementarity.The switch is vendored, not re-derived
There is exactly one copy of the switch math, and it is read-only. The spinodal 2(γ/3)^1.5 is the drive past which one basin disappears — a discontinuous flip — and the barrier γ²/4 is the depth between basins, which is state stability and therefore memory. A deeper-γ switch is harder to flip and holds its state longer; that single fact orders most of what follows.
Every γ is a measurement, anchor-gated
No γ in this volume is fitted. The measurement pipeline is accepted only because it reproduces the SOX9 anchor at γ = 1.4598 bit-for-bit; fail the anchor and the pipeline refuses to write. The germline, immune, RNA-machinery and imprinted atlases are frozen regression checkpoints — adding genes is additive, changing a measured value is a regression and is forbidden.
The drive is written at a coordinate
The environment writes a reversible drive h, and it does so through the A4 channel (and methylation), never through γ. A small RNA acts by complementarity: it names an A4 coordinate and deposits a drive there. So inheritance, when it happens, is the inheritance of a held A4 configuration — a contact state at a coordinate — not of a rewritten ruler.