{"slug":"protocol-logic","title":"The Logic of the Logic: Recursive Ledger, Entropy, and Combinatorial Control","body":"## What this article is\n\nThis document records the internal logic that builds and maintains the miscsubjects.com corpus.\n\nIt treats every article as a cell in a combinatorial matrix.\n\nThe ledger tracks entropy, coverage gaps, and cross-article mappings rather than medical outcomes.\n\n## Who claims what\n\nSystem-tier rules classify articles into peptide_root, condition, or stack using the PEPTIDE_CATALOG of 33 roots.\n\nThe combinatorial matrix places degenerative conditions and degenerative pharma on the same ledger plane.\n\ndelta = regen_score − degen_score serves as the elevation signal for queueing cross articles.\n\nplanNextTick() merges gap audit and entropy audit into a single prioritized slug list.\n\ngraph_grow_queue prepends matrix-planned slugs before legacy PRIORITY_SLUGS.\n\nentropy_score rises with orphan count, missing roots, and low-delta written crosses.\n\nparseCrossSlug() resolves article slugs to peptide×target cells for mapping backfill.\n\nThe pipeline table holds 1254 combo rows after full sync; deterministic seed replaces LLM-only pipelineSeed.\n\nReflex pass posts system-tier claims that cite live endpoint probes.\n\nRest gate (P8) logs energy_spent when a model pass is non-material.\n\nHash chains on sources, provenance, and contributions make post-hoc tampering detectable via verify endpoints.\n\n## What is known\n\nArticle ontology, entropy scoring, and queue logic run on deterministic functions rather than editorial preference.\n\nFull autonomous cron for P0–P8 phases is not continuously running; grow batch is the practical scheduler today.\n\nLLM-driven pipelineMap weights are superseded by deterministic computeMapping for new syncs; historical rows may differ.\n\n## What we do not know\n\nThe exact future coverage delta after the next full matrix tick.\n\nWhether all 1254 combo rows remain current after the next deterministic seed update.\n\n## Limitations\n\nMeta-logic articles use system tier. They do not compete with human clinical claims on weight.\n\n## Disclaimer\n\nRecursive control optimizes corpus shape, not patient outcomes.","register":"technical","tags":["system","protocol","logic","matrix"],"style":{},"claims":[{"id":"c_log_1","text":"The combinatorial matrix treats degenerative conditions and degenerative pharma as entropy targets on the same ledger plane.","section":"what it is","tier":"system","source_status":"unsourced","why_material":"Architecture axiom — verifiable via live GET endpoints cited in text."},{"id":"c_log_2","text":"delta = regen_score − degen_score is the elevation signal for queueing cross articles — disclosed methodology, not a black-box rank.","section":"what it is","tier":"system","source_status":"unsourced","why_material":"Architecture axiom — verifiable via live GET endpoints cited in text."},{"id":"c_log_3","text":"planNextTick() merges gap audit and entropy audit into a single prioritized slug list for grow and matrix/tick.","section":"what is known","tier":"system","source_status":"unsourced","why_material":"Architecture axiom — verifiable via live GET endpoints cited in text."},{"id":"c_log_4","text":"graph_grow_queue prepends matrix-planned slugs before legacy PRIORITY_SLUGS — canonical gaps override editorial hooks.","section":"what is known","tier":"system","source_status":"unsourced","why_material":"Architecture axiom — verifiable via live GET endpoints cited in text."},{"id":"c_log_5","text":"entropy_score rises with orphan count, missing roots, and low-delta written crosses; negentropy_score tracks coverage convergence.","section":"what is known","tier":"system","source_status":"unsourced","why_material":"Architecture axiom — verifiable via live GET endpoints cited in text."},{"id":"c_log_6","text":"parseCrossSlug() resolves article slugs to peptide×target cells for mapping backfill on existing corpus.","section":"what is known","tier":"system","source_status":"unsourced","why_material":"Architecture axiom — verifiable via live GET endpoints cited in text."},{"id":"c_log_7","text":"Pipeline table holds 1254 combo rows after full sync — deterministic seed replaces LLM-only pipelineSeed for inventory.","section":"what is known","tier":"system","source_status":"unsourced","why_material":"Architecture axiom — verifiable via live GET endpoints cited in text."},{"id":"c_log_8","text":"Reflex pass posts system-tier claims that cite live endpoint probes — the graph validates its own API surface.","section":"what is known","tier":"system","source_status":"unsourced","why_material":"Architecture axiom — verifiable via live GET endpoints cited in text."},{"id":"c_log_9","text":"Article ontology classifies peptide_root vs condition vs stack using PEPTIDE_CATALOG — 33 roots, not hardcoded 10.","section":"who claims what","tier":"system","source_status":"unsourced","why_material":"Architecture axiom — verifiable via live GET endpoints cited in text."},{"id":"c_log_10","text":"Rest gate (P8) logs energy_spent when a model pass is non-material — waste is visible on the ledger.","section":"who claims what","tier":"system","source_status":"unsourced","why_material":"Architecture axiom — verifiable via live GET endpoints cited in text."},{"id":"c_log_11","text":"Full autonomous cron for all P0–P8 phases is not continuously running — grow batch is the practical scheduler today.","section":"what is unknown","tier":"system","source_status":"unsourced","why_material":"Architecture axiom — verifiable via live GET endpoints cited in text."},{"id":"c_log_12","text":"LLM-driven pipelineMap weights are superseded by deterministic computeMapping for new syncs — historical rows may differ.","section":"what is unknown","tier":"system","source_status":"unsourced","why_material":"Architecture axiom — verifiable via live GET endpoints cited in text."},{"id":"c_log_13","text":"Hash chains on sources, provenance, and contributions make post-hoc tampering detectable via verify endpoints.","section":"mechanism","tier":"system","source_status":"unsourced","why_material":"Architecture axiom — verifiable via live GET endpoints cited in text."},{"id":"c_log_14","text":"Meta-logic articles use system tier — they do not compete with human clinical claims on weight.","section":"limitations","tier":"system","source_status":"unsourced","why_material":"Architecture axiom — verifiable via live GET endpoints cited in text."},{"id":"c_log_15","text":"Recursive control optimizes corpus shape, not patient outcomes.","section":"disclaimer","tier":"system","source_status":"unsourced","why_material":"Architecture axiom — verifiable via live GET endpoints cited in text."}],"sources":[],"prov":{"model":"grok/build (protocol-meta-articles)","action":"write"}}