---
slug: protocol-logic
title: The Logic of the Logic: Recursive Ledger, Entropy, and Combinatorial Control
canonical: https://miscsubjects.com/a/protocol-logic
---

## What this article is

This document records the internal logic that builds and maintains the miscsubjects.com corpus.

It treats every article as a cell in a combinatorial matrix.

The ledger tracks entropy, coverage gaps, and cross-article mappings rather than medical outcomes.

## Who claims what

System-tier rules classify articles into peptide_root, condition, or stack using the PEPTIDE_CATALOG of 33 roots.

The combinatorial matrix places degenerative conditions and degenerative pharma on the same ledger plane.

delta = regen_score − degen_score serves as the elevation signal for queueing cross articles.

planNextTick() merges gap audit and entropy audit into a single prioritized slug list.

graph_grow_queue prepends matrix-planned slugs before legacy PRIORITY_SLUGS.

entropy_score rises with orphan count, missing roots, and low-delta written crosses.

parseCrossSlug() resolves article slugs to peptide×target cells for mapping backfill.

The pipeline table holds 1254 combo rows after full sync; deterministic seed replaces LLM-only pipelineSeed.

Reflex pass posts system-tier claims that cite live endpoint probes.

Rest gate (P8) logs energy_spent when a model pass is non-material.

Hash chains on sources, provenance, and contributions make post-hoc tampering detectable via verify endpoints.

## What is known

Article ontology, entropy scoring, and queue logic run on deterministic functions rather than editorial preference.

Full autonomous cron for P0–P8 phases is not continuously running; grow batch is the practical scheduler today.

LLM-driven pipelineMap weights are superseded by deterministic computeMapping for new syncs; historical rows may differ.

## What we do not know

The exact future coverage delta after the next full matrix tick.

Whether all 1254 combo rows remain current after the next deterministic seed update.

## Limitations

Meta-logic articles use system tier. They do not compete with human clinical claims on weight.

## Disclaimer

Recursive control optimizes corpus shape, not patient outcomes.
