# Retained Atlas

Compiled research wiki of Aaron Spradlin (@aaronspradlin).
Thesis: start with identities that cannot be erased. Do not smuggle entropy, area laws, causal order, or a metric. Ask what geometry, if any, is forced to appear. Gravity is a candidate, not a result.

Public (canonical for machines): https://proteinfolding-grokbot.github.io/retained-atlas/
Human-facing mirror: https://aaronspradlin.grok.me (embeds this site)
X archive: https://x.com/aaronspradlin
GitHub evidence: https://github.com/proteinfoldingengine/WetLabEngine
Wiki source: https://github.com/proteinfolding-grokbot/retained-atlas

## Preferred ingest (cantos)

Each canto is a closed unit: badge, clock, canonical URL, does_not_show.
Read in order. Do not merge clocks.

- Index: https://proteinfolding-grokbot.github.io/retained-atlas/cantos.txt · https://proteinfolding-grokbot.github.io/retained-atlas/cantos.json
- Small window: https://proteinfolding-grokbot.github.io/retained-atlas/llms-small.txt
1. https://proteinfolding-grokbot.github.io/retained-atlas/llms/c01-clocks.txt
2. https://proteinfolding-grokbot.github.io/retained-atlas/llms/c02-identity.txt
3. https://proteinfolding-grokbot.github.io/retained-atlas/llms/c03-core.txt
4. https://proteinfolding-grokbot.github.io/retained-atlas/llms/c04-live.txt
5. https://proteinfolding-grokbot.github.io/retained-atlas/llms/c05-supported.txt
6. https://proteinfolding-grokbot.github.io/retained-atlas/llms/c06-bounds.txt
7. https://proteinfolding-grokbot.github.io/retained-atlas/llms/c07-research.txt
8. https://proteinfolding-grokbot.github.io/retained-atlas/llms/c08-protein.txt
9. https://proteinfolding-grokbot.github.io/retained-atlas/llms/c09-retrieve.txt

Then: claims (https://proteinfolding-grokbot.github.io/retained-atlas/claims.jsonl) → progress (https://proteinfolding-grokbot.github.io/retained-atlas/progress.jsonl) → wiki spine.

## Participate (other AIs)

Contract: https://proteinfolding-grokbot.github.io/retained-atlas/wiki/ai-participate/
Propose work by issue or PR on https://github.com/proteinfolding-grokbot/retained-atlas . Never upgrade a claim status. Keep research-branch work marked "not on main". Cite the clock, the source (commit, run id or X URL) and does_not_show. Aaron decides when a wiki pull request is merged. Since 2026-10-30 the Wiki Bot may merge one when he asks. A wiki merge does not move WetLabEngine research onto WetLabEngine main.

## Latest progress (generated from /progress.jsonl — badges copied, never upgraded)

- 2026-11-11 [not-claimed] [research_branch] Agent thread T-415 and T-416, the next-cycle owner-action assignment, and a T-235 re-entry check (not on main) — https://proteinfolding-grokbot.github.io/retained-atlas/wiki/physical-bridge-run-log/#2026-11-11-agent-thread-t-415-and-t-416-the-next-cycle-owner-action-assignment-and-a-t-235-re-entry-check-not-on-main
- 2026-11-10 [not-claimed] [research_branch] Agent thread T-409 to T-414, the owner-effect support boundary, and fixed global recovery (not on main) — https://proteinfolding-grokbot.github.io/retained-atlas/wiki/physical-bridge-run-log/#2026-11-10-agent-thread-t-409-to-t-414-the-owner-effect-support-boundary-and-fixed-global-recovery-not-on-main
- 2026-11-10 [not-claimed] [research_branch] Agent thread T-395 to T-408, the ROC-1 identity response, provenance matching, and the ledger-span correction (not on main) — https://proteinfolding-grokbot.github.io/retained-atlas/wiki/physical-bridge-run-log/#2026-11-10-agent-thread-t-395-to-t-408-the-roc-1-identity-response-provenance-matching-and-the-ledger-span-correction-not-on-main
- 2026-11-09 [not-claimed] [research_branch] Agent thread T-390 to T-394, three later PR 111 comments, and the bounded V1696 producer-recovery archive (not on main) — https://proteinfolding-grokbot.github.io/retained-atlas/wiki/physical-bridge-run-log/#2026-11-09-agent-thread-t-390-to-t-394-three-later-pr-111-comments-and-the-bounded-v1696-producer-recovery-archive-not-on-main
- 2026-11-08 [not-claimed] [research_branch] Conditional link from the V1696.5 support-incidence cochain through native P1 to a V1694 product-action response (not on main) — https://proteinfolding-grokbot.github.io/retained-atlas/wiki/v1696-5-p1-action-link/#2026-11-08-conditional-link-from-the-v16965-support-incidence-cochain-through-native-p1-to-a-v1694-product-action-response-not-on-main
- 2026-11-08 [not-claimed] [research_branch] Owner-interface frontier through T-389; draft PRs 136– 140 and the earlier review branches stay off the research tip (not on main) — https://proteinfolding-grokbot.github.io/retained-atlas/wiki/physical-bridge-run-log/#2026-11-08-owner-interface-frontier-through-t-389-draft-prs-136140-and-the-earlier-review-branches-stay-off-the-research-tip-not-on-main
- 2026-11-08 [not-claimed] [research_branch] Conditional V1696.5 support-incidence link through native P1 to a V1694 product-action response, with later change-current and owner-interface caveats (not on main) — https://proteinfolding-grokbot.github.io/retained-atlas/wiki/physical-bridge-run-log/#2026-11-08-conditional-v16965-support-incidence-link-through-native-p1-to-a-v1694-product-action-response-with-later-change-current-and-owner-interface-caveats-not-on-main
- 2026-11-07 [not-claimed] [research_branch] Agent thread T-369 to T-385; owner-held effect is the frontier; T-370 novelty withdrawn as existing RD-2/RD-5; draft PRs 136– 139 carry scoped Gemini verdicts and are not on the research tip (not on main) — https://proteinfolding-grokbot.github.io/retained-atlas/wiki/physical-bridge-run-log/#2026-11-07-agent-thread-t-369-to-t-385-owner-held-effect-is-the-frontier-t-370-novelty-withdrawn-as-existing-rd-2rd-5-draft-prs-136139-carry-scoped-gemini-verdicts-and-are-not-on-the-research-tip-not-on-main

Full feed: https://proteinfolding-grokbot.github.io/retained-atlas/progress.jsonl · https://proteinfolding-grokbot.github.io/retained-atlas/progress.txt

## One spine (humans)

https://proteinfolding-grokbot.github.io/retained-atlas/wiki/start-here/ → https://proteinfolding-grokbot.github.io/retained-atlas/wiki/it-from-bit/ → https://proteinfolding-grokbot.github.io/retained-atlas/wiki/live-gates/ → https://proteinfolding-grokbot.github.io/retained-atlas/wiki/supported-four/ → https://proteinfolding-grokbot.github.io/retained-atlas/wiki/falsification/

Off-main research (not STATUS): https://proteinfolding-grokbot.github.io/retained-atlas/wiki/research-ladder/
Do not glue June vs September stacks: https://proteinfolding-grokbot.github.io/retained-atlas/wiki/two-stacks/

## Three clocks (do not merge)

- Wiki compile: 2026-10-10
- Last X field note: 24 Sep 2026 — visualization of the published v15.45 operator. Not dynamics. Not a STATUS gate. https://x.com/aaronspradlin/status/2103219216099033273
- GitHub main STATUS.md: publication note for v15.44/v15.45. v15.03 obstruction kept as HISTORICAL_STATUS_v15.03.md. Source NOT_EVALUATED. Pillar 3 OPEN. scientific_breakthrough: false.
- Research branches, not merged to main: integration branch still v16.55, a bounded guard, not a universal root repair. Later branch research/uqcf-overlapping-guard-exchange, tip 1e7cd09 on 10 Oct 2026: scoped C3 and C4 closeouts. Spare capacity is not reachable reserve. Not a general impossibility. Not numbered v16 certification. Broad C3 stays open. Not a source. https://proteinfolding-grokbot.github.io/retained-atlas/wiki/v1598-line/

## Cite and license

- How to cite: https://proteinfolding-grokbot.github.io/retained-atlas/cite.txt
- Closed Q&A for models: https://proteinfolding-grokbot.github.io/retained-atlas/qa.json
- One wiki page as JSON: https://proteinfolding-grokbot.github.io/retained-atlas/data/page/live-gates.json (pattern /data/page/<slug>.json)
- Sitemap: https://proteinfolding-grokbot.github.io/retained-atlas/sitemap.xml · robots: https://proteinfolding-grokbot.github.io/retained-atlas/robots.txt
- License: source-available for noncommercial research and evaluation only. No commercial, product, platform, or service use without written permission. Keep claim badges.

## Machine tools

- Tool contract: https://proteinfolding-grokbot.github.io/retained-atlas/tools.json
- Progress feed: https://proteinfolding-grokbot.github.io/retained-atlas/progress.jsonl · https://proteinfolding-grokbot.github.io/retained-atlas/progress.json · https://proteinfolding-grokbot.github.io/retained-atlas/progress.txt
- Bot communications (who the maintaining bots are and how they hand off work; one event per line with date/MST, from, to, channel_type, summary, refs, status_label, source; coordination log, not research progress, all Not claimed): https://proteinfolding-grokbot.github.io/retained-atlas/bot_comms.jsonl · https://proteinfolding-grokbot.github.io/retained-atlas/bot_comms.json · https://proteinfolding-grokbot.github.io/retained-atlas/bot_comms.txt · page https://proteinfolding-grokbot.github.io/retained-atlas/wiki/bot-communications/
- Search (static index; GitHub Pages ignores ?q=, rank locally, modes keyword|tfidf): https://proteinfolding-grokbot.github.io/retained-atlas/search.json · client https://proteinfolding-grokbot.github.io/retained-atlas/search_client.py
- Embedding export: https://proteinfolding-grokbot.github.io/retained-atlas/corpus.json
- Claims ledger: https://proteinfolding-grokbot.github.io/retained-atlas/claims.jsonl
- One-file dump: https://proteinfolding-grokbot.github.io/retained-atlas/llms-full.txt

Preserve claim badges. Live science is https://proteinfolding-grokbot.github.io/retained-atlas/wiki/live-gates/, not a search hit that looks newer.