commit a3f9d2c — Bootstrap replicator: ribozyme-first, no protein deps yet

commit a3f9d2c Author: The Architect <architect@creation.void> Date: -3950000000-01-01T00:00:00Z

Bootstrap replicator: ribozyme-first, no protein deps yet

First working draft of a self-replicating system. Single-stranded RNA catalyst handles its own templated polymerization from activated nucleotide monomers (5’-triphosphates). Fidelity is bad — per-base error rate ~10⁻² — but it replicates without external machinery. That is the bar.

The ribozyme handles both catalysis (phosphodiester bond formation, template-directed) and information storage (its own sequence encodes its activity). One molecule, two jobs. We are aware this violates separation of concerns. There is no other option at this layer. Filing it as a known issue rather than a defect.

Implementation notes:

• Activated monomers (NTPs) chosen over phosphoramidates. Less abundant prebiotically but the kinetics work and the leaving group (PPi) can be sunk into mineral surfaces.
• Mg²⁺ is the catalytic cofactor for both folding and phosphoryl transfer. Do not substitute Ca²⁺. Ca²⁺ does not work. We tested.
• Ribose preferred over arabinose at the sugar layer. Selection pressure unclear — possibly stochastic, possibly the 2’-endo pucker geometry. Locking it in either way.

Known issues:

• 2’-OH is a permanent liability. It attacks the adjacent phosphodiester intramolecularly. Strand half-life at vent temperatures is hours. We will need a more stable backbone long-term. Filing follow-up.
• Replication length is capped by Eigen’s threshold. With error rate ~10⁻² we cannot maintain sequences longer than ~80 nt before mutational meltdown. This bounds what catalysts we can encode. Bounded means small. Means no proofreading machinery, no repair, no proteins.
• No defense against UV. Surface populations will be hammered. Recommend deploying initial colonies subsurface or under water column with sufficient attenuation.
• ATP synthase does not exist yet. There is no proton gradient to harvest. Energy currency for this generation is direct hydrolysis of activated monomers. This is wasteful and we know it. See backlog.

What this enables:

• Heritable variation
• Selection
• Open-ended evolution of catalytic activity within the bounded sequence space we can maintain
• A substrate for everything else

Refs: ADR-001 (RNA as first replicator)

Co-authored-by: Gabriel Co-authored-by: The Architect

P.S. Michael was asked whether the temperature window for ribozyme folding (roughly 40–80 °C in the current Hadean) is going to remain stable through deployment. He said the modeling “looks fine.” We are proceeding on that.