Four reproductive organs emerge from measured master-gene γ
Four reproductive organs emerge on the substrate from measured master-gene γ: germline (DAZL 1.3803), testis (SOX9 1.4598), ovary (FOXL2 1.4829) and reproductive tract (WT1 1.5182). Developmental order is argsort(γ) — germline → testis → ovary → tract — a sim-verified readout over measured, never-fitted constants.
Each γ is minus the mean nearest-neighbour stacking free energy (SantaLucia 1998) over the proximal promoter (TSS−2000..+500, GRCh38) — the identical pipeline the DNA atlas uses. The values reproduce offline bit-for-bit from cached promoters and are validated by recovering the vendored SOX9 anchor (γ=1.4598, GC=0.545). Developmental order is a γ-readout over measured organs [V]; germline-first matches PGC specification preceding gonadal differentiation.
γ is measured from the promoter, never fitted
The identity constant of each organ is read directly from its master gene’s promoter sequence. The method is the same nearest-neighbour stacking calculation the DNA morphogenesis atlas uses, so the reproductive masters are received, not invented.
The three formerly to-measure masters (FOXL2, DAZL, WT1) were measured through this pipeline and cached, so the values reproduce offline bit-for-bit without the network. The pipeline is accepted only because it recovers the vendored SOX9 anchor to four decimals (γ=1.4598, GC=0.545).
The four organs and their forced quantities
Each measured γ fixes a functional spinodal (presence threshold) and a relative dwell size; only the relative ordering of size is forced, the absolute scale is open.
| master gene | organ | γ (measured) | functional spinodal | rel. size (dwell) | dynamical class |
|---|---|---|---|---|---|
| DAZL | germline | 1.3803 | 0.6242 | 1.4742 | germline |
| SOX9 | gonad testis | 1.4598 | 0.6789 | 1.6034 | germline-support |
| FOXL2 | gonad ovary | 1.4829 | 0.6950 | 1.6416 | oscillator |
| WT1 | reproductive tract | 1.5182 | 0.7200 | 1.7006 | structural |
Developmental order is a γ-readout
Sorting the four organs by ascending γ gives the emergence order germline → testis → ovary → tract. This is a derived ordering over measured constants, not a fitted timeline; germline-first is consistent with primordial-germ-cell specification preceding gonadal differentiation (a sign sanity-check).
The shared FHN oscillator runs at γ=1 because rhythm depends on the recovery timescale τs, not on the identity γ; the measured γ values drive emergence and ordering, while the dynamics chapters (§3–§7) vary only τs.