{"compile":"2026-10-10","canonical":"https://aaronspradlin.grok.me/wiki/protein-audit","json":"https://aaronspradlin.grok.me/page.json?slug=protein-audit","license":"Source-available for noncommercial research and evaluation only. No commercial, product, platform, or service use without written permission.","scientific_breakthrough":false,"slug":"protein-audit","title":"WetLabEngine protein audit","dek":"White-box science contract at the GitHub root. Engine is a Supported tool. Custom protein-mechanism program CLOSED 19 Sep 2026 on current evidence. Folding results stay Restricted/Corrected.","updated":"2026-09-19","status":"applied","claim":"restricted","tags":["protein","audit","biophysics","Villin","WetLabEngine"],"related":["protein-closeout","p53-campaign","mecp2-rett","protein-bridge-v9","applied-stack","tsp-backbone","critical-path","c3-governor","open-science","program","recoverability","for-researchers","x-notebook"],"packages":[{"id":"wetlab-root","name":"WetLabEngine (root)","path":"/","status":"supported"},{"id":"labs-p53","name":"Labs/p53","path":"Labs/p53","status":"restricted"},{"id":"labs-mecp2","name":"Labs/MECP2","path":"Labs/MECP2","status":"restricted"},{"id":"uqcf-bridge-v9-update-bundle","name":"uqcf_bridge_v9_update_bundle","path":"Tmp/TOE/uqcf_bridge_v9_update_bundle","status":"restricted"}],"notes":[{"id":"protein-closeout-2026-09-19","title":"Protein-mechanism program CLOSED on current evidence","date":"2026-09-19","xUrl":"https://x.com/aaronspradlin/status/2101337128169034035"},{"id":"bridge-v9-2026-04-12","title":"Frozen v9 protein bridge on 1UAO / 1L2Y","date":"2026-04-12","xUrl":"https://x.com/aaronspradlin/status/2043198645147967753"},{"id":"villin-2026-04-14","title":"Villin HP35: identical snapshot, different fate","date":"2026-04-14","xUrl":"https://x.com/aaronspradlin/status/2044155484039705016"},{"id":"critical-path-2026-05-01","title":"Retained coherence in live critical path","date":"2026-05-01","xUrl":"https://x.com/aaronspradlin/status/2050029681517433047"},{"id":"c3-2026-03-25","title":"C3++ Stability Governor on Qwen3-4B","date":"2026-03-25","xUrl":"https://x.com/aaronspradlin/status/2036659106350792814"},{"id":"unify-domains-2026-05-10","title":"What unifies proteins, RCLC, critical path, TSP","date":"2026-05-10","xUrl":"https://x.com/aaronspradlin/status/2053553647712338040"}],"claims":[{"status":"supported","text":"As a tool: claims written into findings.json can be numerically confirmed or refuted against the bound raw artifacts. That is the engine’s job. It is not a folding oracle and not a TOE."},{"status":"supported","text":"This compile independently scored Labs/MECP2/findings.json against the bound diagnostics CSVs: 15 CONFIRMED, 1 DEVIATION (Run 5, 3.06 Å vs ≥ 20 Å), 3 INDETERMINATE. Thesis count_runs_meeting passed (16 ≥ 3). That is a tooling reproduction. It is not a Gemini rerun, not a Rett therapy, and not native folding."},{"status":"restricted","text":"On the posted Villin HP35 controlled cases, adding retained state R_t lifts AUC and opens a matched-pair divergence gap versus G_t-only. This is not a claim that AlphaFold is refuted, and it is not a folding oracle.","noteId":"villin-2026-04-14"}],"text":"Author correction: computational signals were real; a distinct transferable new folding mechanism was not established. Final held-out transfer +~2.6% (p≈0.46) / −5.6% (p≈0.49). 16 Sep README: Labs/p53 and Labs/MECP2 withdrawn — do not rely on them as validation. Reopen only for new independent evidence. Full note: /wiki/protein-closeout.\n\nproteinfoldingengine/WetLabEngine is Aaron Spradlin’s public working tree. The repository root is a white-box protein-simulation audit engine. Nested under Labs/ are two GitHub-only coarse-grained campaigns (p53, MECP2). Nested under Tmp/TOE are the geometry-from-information packages this wiki already indexes, plus the April 2026 folding-side bridge packet on 1UAO and 1L2Y. Villin HP35 R_t is the X-posted controlled-case result. Those four protein objects are one research area only because they share an author, a science-contract style, and a GitHub tree — not because they share a proven law.\n\nThe engine can confirm or refute a numeric constraint in findings.json. That is a Supported tooling claim. p53, MECP2, Villin HP35, and frozen v9 on 1UAO/1L2Y are Restricted in-silico results. None of them is a folding oracle, a cancer or Rett therapy, AlphaFold refuted, or a TOE confirmation.\n\nRepository map\n\nThe engine\n\nWetLabEngine is an open-source audit engine for protein simulation campaigns. A JSON manifest (findings.json) defines experiments, human-readable claims, and machine-testable constraints (for example best_final_RMSD_A ≤ 20.0). UnifiedAuditEngine.py (v5.7 in the current tree) checks those constraints against CSVs, PDBs, and images, then optionally sends artifacts to Gemini for qualitative review. Output is Biophysics_Final_Report.md plus machine-readable JSON. ManuscriptBuilder.py writes the prose body; the appendix is assembled deterministically from the verification report so the AI cannot rewrite the verdict table.\n\nScience contract: SCHEMA.md, findings.json v2.2 (p53) / v3.3 (MECP2). Every metric in a constraint must be declared in metrics_vocabulary.\nDeterministic verdicts: CONFIRMED, DEVIATION, INDETERMINATE. Tail-median RMSD from diagnostics_timeseries.csv is the preferred single source of truth.\nAI peer review is qualitative and does not override the numeric verdict. Claim-integrity and cross-artifact triage are logged beside it.\nThesis block: count_runs_meeting aggregation across the campaign. The engine can fail a thesis even if individual runs pass.\nLicense on the repo: CC BY-NC-SA 4.0, plus Spradlin’s later commercial-use restriction on the public research stream.\n\n{\n  \"canonical_claim\": {\n    \"type\": \"rescue_protocol\",\n    \"statement\": \"Contact-anneal + PhiKan083 improves Y220C (RMSD ≤ 20 Å).\",\n    \"constraints\": [\n      { \"metric\": \"best_final_RMSD_A\", \"op\": \"<=\", \"value\": 20.0 }\n    ]\n  }\n}\n\nAs a tool: claims written into findings.json can be numerically confirmed or refuted against the bound raw artifacts. That is the engine’s job. It is not a folding oracle and not a TOE.\n\nRun this first\n\nGitHub is the working copy. This page is the cheapest entry. Start with Labs/MECP2, not Villin and not a new disease protein. The posted UnifiedAuditEngine.py is Colab-oriented: it hardcodes PROJECT_NAME = MECP2, clones ProteinFoldingEngine/Results-AI-Audit-Engine, looks for Projects/MECP2/findings.json, and exits if a Gemini key is missing. Do not expect python UnifiedAuditEngine.py to score Labs/MECP2 as a local folder.\n\nFull engine (his README): Colab + API_KEY.txt + Gemini qualitative review. Deterministic half (this atlas): a stdlib script that reads findings.json and tail-median RMSD from diagnostics_timeseries.csv. PNG/PDB Git LFS files are not required. This compile ran the deterministic half on 7 Sep 2026. Gemini peer review was not rerun.\n\nClone only Labs/MECP2. Skip git lfs pull — CSVs and findings.json are ordinary files.\nDownload wetlab_deterministic_audit.py from this page (Open source). It is a pedagogical reconstruction of verdict_from_constraint, not a dump of UnifiedAuditEngine.py.\npython3 wetlab_deterministic_audit.py Labs/MECP2\nGreen: CONFIRMED 15, DEVIATION 1, INDETERMINATE 3, and smoke PASS on Run 5.\nOptional: python3 wetlab_deterministic_audit.py Labs/p53 --no-smoke. Expect Run 9 INDETERMINATE if the ContactAnneal folder is missing.\nTo run his full engine, follow the repo README in Colab with a Gemini key. That path clones a different data repo.\n\ngit clone --depth 1 --filter=blob:none --sparse https://github.com/proteinfoldingengine/WetLabEngine.git\ncd WetLabEngine\ngit sparse-checkout set Labs/MECP2\n# put wetlab_deterministic_audit.py in this directory (download from this page), then:\npython3 wetlab_deterministic_audit.py Labs/MECP2\n\nCONFIRMED 15   DEVIATION 1   INDETERMINATE 3\nthesis count_runs_meeting (best_final_RMSD_A <= 4.5): 16 >= 3  PASS\nsmoke PASS: Run 5 is DEVIATION (tail-median RMSD 3.06 Å vs contracted ≥ 20 Å).\n\nRun 5 is the smoke test that the engine can fail a claim. If it comes back CONFIRMED, stop and inspect — do not drop the DEVIATION.\nThesis count_runs_meeting can pass while a run-level claim fails: Run 5’s 3.06 Å still counts toward RMSD ≤ 4.5.\ndataset_root in findings.json is a Colab path (/content/Results-AI-Audit-Engine/Projects/MECP2). The smoke script ignores it and resolves source_folder under the campaign directory you cloned.\nLive /labs is a recoverability toy. It is not this auditor.\n\nThis compile independently scored Labs/MECP2/findings.json against the bound diagnostics CSVs: 15 CONFIRMED, 1 DEVIATION (Run 5, 3.06 Å vs ≥ 20 Å), 3 INDETERMINATE. Thesis count_runs_meeting passed (16 ≥ 3). That is a tooling reproduction. It is not a Gemini rerun, not a Rett therapy, and not native folding.\n\nVillin HP35 — the X result\n\nOn 14 Apr 2026 Aaron asked Grok to peer-review a Villin HP35 claim from the WetLabEngine pipeline. The posted numbers: two chains with identical visible conformation can still have different folding fates because of hidden retained history R_t. G_t-only models miss it. Grok’s in-thread review treated the pipeline as working on controlled/sample cases. A 26 Apr follow-up used stronger AlphaFold language; this atlas keeps the 14 Apr speculative tag as the governing voice.\n\n\\mathrm{AUC}(G_t+R_t)\\approx 0.9569 \\quad\\text{vs}\\quad G_t\\ \\text{alone}\n\nThe ROC lift (AUC G_t + R_t ≈ 0.9569 vs G_t alone) shows real predictive signal from R_t. The matched-state divergence (50.2 % far-R_t vs 1.3 % close-R_t, +48.9 % spread) directly falsifies pure visible-state completeness.\n\nThis is all speculative and they have better things to do for now then react to another one of the wild claims.\n\nOn the posted Villin HP35 controlled cases, adding retained state R_t lifts AUC and opens a matched-pair divergence gap versus G_t-only. This is not a claim that AlphaFold is refuted, and it is not a folding oracle.\n\nX ledger versus GitHub-only labs\n\nSame pattern, other domains\n\nThe 1 May 2026 critical-path post treats protein folding, fractal TSP, SPARC holdouts, and live project plans as rhyming recoverability problems: preserve what remained coherent, deform what is stressed, reset only what went stale. Recurrence is not a unification proof. The 10 May question — what unifies proteins, RCLC, critical path, and TSP — is still open. The C3++ governor is the LLM-side instrument of the same idea. The applied recoverability stack is the hub for those three Python labs.\n\np53 campaign (Labs/p53)\nMECP2 Rett campaign (Labs/MECP2)\nFrozen v9 on 1UAO / 1L2Y\nLive protein lab\nApplied recoverability stack\nDeterministic auditor (this atlas)\nUnifiedAuditEngine.py v5.7\nSCHEMA.md\nWetLabEngine on GitHub\nLabs/p53\nLabs/MECP2","howToCite":"Spradlin, A. (2026-10-10). WetLabEngine protein audit. Retained Atlas. https://aaronspradlin.grok.me/wiki/protein-audit. Keep claim badge: restricted."}