Material (γ) — the scale of the threshold, not the locus of difference
γ barely separates taxa: cross-species CV 0.1–2%, corr(γ,GC)=0.998, warm-blooded genes at the same γ as cold-blooded. A threshold scale, not the locus.
γ (=−mean NN stacking ΔG) is the scale of the R19 switch threshold (spinodal ∝ γ^1.5, barrier γ²/4). Across orthogonal master switches it barely changes — cross-species CV 0.1–2%, corr(γ, GC) = 0.998 — and warm-blooded genes sit at the same γ position as cold-blooded ones. So γ cannot partition taxa: the difference lives not in the readable material but in SET, STATE, and DWELL.
What γ is
γ is the negative mean of nearest-neighbor stacking free energy (−mean NN ΔG, SantaLucia 1998), read mechanically from the sequence. It sets the threshold scale of the R19 double well: barrier = γ²/4, spinodal |h_sp| = (2/3√3)·γ^1.5. The R19 dynamics are ṡ = −(s³ − γs − h). The larger γ, the deeper the switch; the smaller, the shallower. γ is the scale of the threshold, not in itself the sign, quantity, or on/off of a trait.
The γ census
| comparison | genes | species | cross-species γ CV |
|---|---|---|---|
| mammal master loci | POU5F1·SOX2·PAX6·NODAL … | human·mouse·elephant | 0.5% |
| primate growth-plate | FGFR3·IHH·NPR2·PTHLH·SOX9 | 5 | 2.0% |
| cat vs tiger | GHRHR·IGF2/H19·POU1F1 | 2 | 0.1% |
Across all 51 reads, corr(γ, GC) = 0.998 — γ is an affine read of GC. Per-gene cross-species CV is tiny (GHRHR 0.0%, IGF2/H19 0.1%), so what sets γ is the gene, not the organism; within one animal the gene-to-gene γ spread (cat 0.292) exceeds the cross-species gap.
Decisive: nine warm-blooded mammal master genes (γ 1.264–1.295) sit at the same γ position as cold-blooded fish/frog UCP1 (1.221·1.264). The full γ range 1.221–1.619 has no taxonomic gap — one continuous band.
A scale, not a locus
γ is measured and admissible but one axis (≈GC). Nearly invariant across every orthogonal comparison, it is not the locus of taxonomic difference but the scale of the threshold. That γ barely fails to partition taxa is the thesis: the difference among animals, species, and kingdoms is not written in the readable material. Where it is instead is the subject of the next chapters — SET, STATE, and DWELL.
What γ does / does not do
| γ does | γ does not do |
|---|---|
| measure stacking stiffness (SantaLucia) | partition taxa (nearly invariant → not the locus) |
| set the R19 threshold scale (spinodal ∝ γ^1.5, barrier γ²/4) | a switch's on/off (snake ZRS γ identical) |
| carry genome-GC composition signal | copy count, wiring, dosage, sign (brake/accel) |
Failure log
- Genome-GC confound: the plant/animal γ gap (0.22) is GC composition, not switch grammar — not a taxonomic signal.
- Blind to on/off: snake ZRS γ is identical to human (1.290 vs 1.264) yet limb presence differs — γ cannot distinguish on/off, detailed under STATE.