epi-sigillin

Epigenetic runtime parameter mutation for the GenesisAeon UTAC/CREP framework.

Analogous to how environmental signals alter gene expression without changing the underlying DNA sequence, epi-sigillin lets a system's entropy level "methylate" (suppress) or "de-methylate" (activate) CREP tensor components — and rewrite CREP-YAML parameter files — at runtime. This turns the otherwise static Sigillin narrative→CREP interface into a dynamic, self-adapting one.

Installation

pip install epi-sigillin

Usage

from epi_sigillin import EpiSigillin

system = EpiSigillin(seed=42)

# Run 100 epigenetic mutation cycles driven by a synthetic entropy trajectory
summary = system.run_cycle(duration_cycles=100)

print(summary["final_crep_state"])     # {"C", "R", "E", "P", "Gamma"} (effective)
print(system.methylation_state())      # {"C", "R", "E", "P"} methylation levels
print(system.get_phase_events())       # histone-mark transition events

# Rewrite a CREP-YAML file based on the current entropy level
system.mutate_yaml("crep_params.yaml", entropy_level=0.9)

# Inherit 50% of a parent cycle's methylation state into a new cycle
system.inherit_from(summary["methylation_state"])

Diamond Interface

EpiSigillin implements the GenesisAeon Diamond-Template contract used across the ecosystem:

Plus package-specific extensions: methylation_state(), mutate_yaml(), inherit_from().

Epigenetic UTAC mapping

Methylation rule (suppression, H(t) > H*): P_effective = P · exp(-α · (H - H*) / K)

De-methylation rule (activation, H(t) < H*): E_effective = E · (1 + β · (H* - H) / K)

Histone modification analogy: H3K4me3 (activation) ↔ high E activation during low entropy; H3K27me3 (repression) ↔ P suppression during high entropy; H3K9me3 (heterochromatin) ↔ complete CREP freezing ("crisis mode").

epi-sigillin has no fixed Γ of its own — it is the Γ-modulator for every other GenesisAeon package: Γ_epi = f(S_total), dynamic by design.

Role in the GenesisAeon Ecosystem

epi-sigillin is Package 28 (P28) in the GenesisAeon ecosystem, domain epigenetics, scale systemic. It sits above the other domain packages, modulating their CREP tensors rather than producing one of its own — the epigenetic-computational bridge between the static Sigillin narrative interface and the live genesis-os runtime.

Development

git clone https://github.com/GenesisAeon/epi-sigillin.git
cd epi-sigillin
pip install -e ".[dev]"
pytest --cov=src
ruff check src tests
mypy src

Citation

DOI will be assigned automatically on first GitHub Release once Zenodo–GitHub integration is enabled for this repo.

Reference: Greenberg, M.V.C. & Bourc'his, D. (2019). The diverse roles of DNA methylation in mammalian development. Nature Reviews Molecular Cell Biology 20, 590–607. DOI: 10.1038/s41580-019-0160-9