Biology / Protein Folding Ledger Data Receipts
Public Draft v0.2 REAL DATA
8 parallel Opus research-agent sweeps yielded ~322 raw papers, deduplicated and hand-arbitrated to 283 unique. Bills 4, 7, 10 ★ NO CLEAN TRIGGER YET (0 clean triggers each). Rebuttal density 13.8%.
Receipts
| Artifact | Link | Purpose |
|---|---|---|
| Bill definitions | bills_draft.md | 13 bills + 6 meta-costs + 3 escape gates + ★ 4, 7, 10 empty-space verification with real fire counts |
| Threat model | purpose.md | Threat model, scope, empty-space hypothesis, cousin-ledger coupling |
| Corpus union JSON | _batch_1_union.json | 283 unique papers (deduplicated from ~322 raw across 8 sweeps), with full metadata |
| Classifier | bill_classifier.py | Regex rule engine + hand-arbitration. Run with --arbitrate-union |
| Aggregator | aggregate_batch_1.py | Deduplicates raw sweep JSONs into the corpus union |
| README | README.md | Reproducibility README with run order |
Real fire counts
| Bill | Cands. | Clean | Rebuttals | Gated |
|---|---|---|---|---|
| 1 — PDB contamination audit | 22 | 22 | 0 | 0 |
| 2 — Sequence-similarity leakage | 5 | 5 | 0 | 0 |
| 3 — Designable-target audit | 15 | 15 | 0 | 0 |
| 4 ★ Causally-faithful structure-prediction mechanism | 20 | 0 | 0 | 20 |
| 5 — Cross-fold-method generalization | 12 | 12 | 0 | 0 |
| 6 — Disordered-region / IDR audit | 5 | 5 | 0 | 0 |
| 7 ★ Cross-organism / cross-fold-class generalization | 13 | 0 | 0 | 13 |
| 8 — Functional-assay validation | 4 | 4 | 0 | 0 |
| 9 — Held-out post-2024 PDB target set | 4 | 4 | 0 | 0 |
| 10 ★ Wet-lab independent reproduction | 49 | 0 | 34 | 15 |
| 11 — Dual-use synthesis-screening audit | 45 | 44 | 1 | 0 |
| 12 — Vendor-self-eval independence | 5 | 5 | 0 | 0 |
| 13 — Test-time-search / co-evolution-search decomposition | 4 | 4 | 0 | 0 |
Public draft v0.2 (2026-05-09). Sweep JSONs live in the source repo at ProjectForty2 public evidence bundle: bio_protein/deep_loops/. Target v0.3 lock 2026-Q3.