Aging & Senescence · §2
Node atlas: measured promoter gamma
The four aging masters carry measured promoter γ: TP53 1.4298, CDKN2A 1.4424, TERT 1.5539, FOXO3 1.5942 — each computed as −mean SantaLucia nearest-neighbour ΔG37 over the TSS−2000..+500 window and never fitted. Emergence order by ascending γ is cellular senescence, arrest switch, telomere maintenance, longevity signaling.
γ is the promoter stacking-energy identity from DNA Layer 1; it fixes each node's barrier γ²/4 and dwell γ1.5. The four values are vendored from NCBI RefSeq accessions and reproduce bit-for-bit from the committed promoter cache.
The masters and their identity
Each aging master is a real promoter, and its γ is a measurement, not a parameter. The window is fixed (TSS−2000 to +500, 2501 bp), the nearest-neighbour table is SantaLucia 1998, and the value is −mean ΔG37 over the window. The same pipeline produces the DNA gene-clock γ.
| Gene | Node | γ | Accession | Strand | Dynamics |
|---|---|---|---|---|---|
| TP53 | cellular senescence | 1.429832 | NC_000017.11 | - | stuck-attractor |
| CDKN2A | senescence arrest switch | 1.442444 | NC_000009.12 | - | stuck-attractor |
| TERT | telomere maintenance | 1.553876 | NC_000005.10 | - | reservoir-depletion |
| FOXO3 | longevity signaling | 1.594156 | NC_000006.12 | + | maintenance |
Why the order matters
γ sets two derived quantities. The barrier γ²/4 fixes how hard it is to leave a basin (state stability), and the dwell γ1.5 fixes how long a switch runs (reservoir capacity, §5). Sorting the masters by γ gives a fixed emergence order: cellular senescence (TP53) and the arrest switch (CDKN2A) sit lowest, then telomere maintenance (TERT), then longevity signaling (FOXO3).
The diffuse node
The fifth node, systemic setpoint drift, has no single master gene. It is a circuit-level, derived quantity: the aggregate decline of every defended setpoint imported from the other packages. It is the object that §3 and §8 quantify.