Draft Papers
Drafts on ontological structure, gap detection, and machine-checkable scientific knowledge representation. Every numerical claim in every paper is paired with a cargo test command that re-derives it from the live codebase — see the “Code & Verification” section at the end of each paper.
| # | Paper | Focus |
|---|---|---|
| 1 | Categorical Bioelectricity | First category-theoretic formalization of Levin’s bioelectric framework — 14 biomedical domains as formal ontologies, 21 cross-domain functors, 3 adjunctions |
| 2 | Adjunction Information Loss | A general methodology for using categorical adjunctions to automatically detect missing distinctions in scientific ontologies; applied to the biomedical stack with measured loss percentages |
| 3 | Ontology Diagnostics | A formal meta-ontology — an ontology about ontology engineering — that captures the gap-detection methodology as 29 entities, 14 pipeline steps, and 13 axioms |
Reproducibility
Every paper’s numerical claims can be verified from the codebase by running:
git clone https://github.com/i-am-logger/pr4xis
cd pr4xis
cargo test --workspace
cargo test -p pr4xis-domains test_full_chain_collapse_measurement -- --nocapture
The first command runs the full test suite (4,855 tests as of the document date; re-counted on every run). The second prints the live per-adjunction collapse percentages cited in all three papers — including the 85.2% molecular-bioelectric round-trip loss and the Kv channel discovery.
For the per-claim test index, see the “Code & Verification” section at the bottom of each paper.
Status
- Paper 1 — draft. Awaits a literature-review pass and one scan for stale subset counts.
- Paper 2 — draft. Awaits the methodology generalization section to be fleshed out with at least one non-biomedical adjunction example.
- Paper 3 — draft. Awaits the threshold-validation section to be expanded once more adjunctions are measured (currently 3).
A fourth draft on the syntrometric logic lineage (the structural alignment with Heim’s syntrometry, formalized as a pr4xis ontology with a verified functor) is tracked in #62 — not yet drafted, will land in this directory once #62 lands.
Related
- Novelty argument — the careful prose about what is new vs prior art, with the same intellectual honesty applied to the lineage claims
- Gap detection — the same biomedical result, written for the README audience instead of the journal audience
- Foundations — academic lineage that grounds the broader project
- Concepts — the categorical machinery the papers build on, in plain English