Hypotheses Index¶

This directory holds committed scientific hypotheses in Falsification Card form. Each file is a self-contained artifact: the claim, the assumptions it rests on, the killshot menu ranked by information weight per dollar, pre-committed thresholds for Alive / Killed / Pending / Retracted, kill switches, execution log, and survival score.

The schema and the rationale live in linter-design.md. This page is the entry point and the index.

What "Committed" Means¶

A hypothesis is committed when it is written to a file in this directory with a first git commit. That commit is the pre-registration: the claim, the initial assumption stack, and the killshot menu are frozen as of that SHA. Any subsequent edit creates a new commit with a visible diff. This is the git-native equivalent of the brief's call for {claim, killshots, thresholds} hashing — see linter-design.md §6.

Convention: the hypothesis file's first commit is the load-bearing one. Subsequent commits carry rationale in the commit message (e.g., H01: tighten lactoferrin threshold from 100 to 500 mg/L — Ward 1995 submerged baseline is 2 g/L, 500 mg/L is the Phase B acceptance floor). The git log is the audit trail.

Committing to a hypothesis is a commitment to attempt to falsify it, not a commitment to defend it. A hypothesis that survives zero killshots after a year isn't defended; it's pruned or retracted.

File Naming¶

Pattern: H0N-slug.md where N is zero-padded two-digit (H01, H02, …, H99). Three digits (H001, H002) when the collection exceeds 99.
slug is short, hyphenated, mnemonic. Prefer 2–4 words. Example: H01-ward-dual-cassette.md.
No dates, no authors, no status in the filename. Those live in frontmatter (committed:, status:) and mutate over time. Filenames are stable identifiers.

Current Hypotheses¶

ID	Title	Status	Committed	Link
H01	Can a Ward-derived dual-cassette retain active UOX and lactoferrin in solid-state A. oryzae?	Pending	2026-04-24	H01-ward-dual-cassette.md
H02	Engineered Faecalibacterium prausnitzii is a testable WT-ABCG2-induction chassis; direct butyrate rescue of Q141K remains unvalidated	Stub	2026-05-05	H02-engineered-lbp-thesis.md
H03	Selective kidney delivery could make URAT1 siRNA a long-horizon gout modality	Stub	2026-05-05	H03-sirna-urat1-thesis.md
H04	Modern scientific rigor (chokepoint-mapping + ChEMBL cross-check + bioavailability honesty + falsification card discipline) applied to TCM materia medica produces actionable, gout-relevant findings beyond what reductionist single-compound analysis or holistic "alternative medicine" framings produce in isolation	Stub	2026-05-05	H04-tcm-rigor-intersection.md
H05	An engineered soluble DAF/CD55 SCR1-4 construct is a candidate CP0 modulator	Stub	2026-05-05	H05-daf-scr14-cp0-thesis.md
H07	Clomiphene-associated urate elevation is mediated primarily by intestinal estrogen-receptor antagonism	Retracted	2026-05-07	H07-clomid-intestinal-er-antagonism.md
H08	Can a gut-lumen uricase sink produce clinically meaningful serum-urate reduction under physiological substrate, oxygen, transit, access, survival, and peroxide constraints?	Open	2026-07-13	H08-gut-lumen-sink-platform-thesis.md
H09	A qualified engineered-A. oryzae configuration may be reproducible across controlled production sites if identity, propagation, contamination, activity, preservation, assay, and release controls hold; this is an optional koji-track production model, not a project-level assumption	Active stub	2026-05-15	H09-community-fermentation-reliability.md
H10	Clomiphene exposure and serum urate are positively coupled in a susceptible high-androgen phenotype	Pending	2026-07-17	H10-clomiphene-dose-urate-coupling.md

(Add new rows as hypotheses are committed. Sort by ID.)

Lifecycle¶

Commit. Write the Falsification Card (claim, assumption stack, killshot menu, thresholds, kill switches, empty log) to H0N-slug.md. Git commit. Status: Pending.
Lint. Run Falsification Lint (manual / agent invocation) against the committed file. The linter reads the hypothesis + cross-referenced wiki pages, may propose additional killshots or assumptions, and may suggest the cheapest-upstream redirect per the brief's hero interaction. The author decides what to adopt; adoption creates a new commit with the diff visible.
Test. Execute killshots in the order the menu dictates — cheapest, highest-info first. Record results inline in the Log table. Each executed killshot updates status and survival_count.
Log outcome. For each killshot: date, killshot identifier, outcome (killed / survived / ambiguous), notes, and any deviations from the pre-committed protocol. Survival-count and survival-score are updated per linter-design.md §6.
Update status. Pending → Alive on first survived killshot. Pending or Alive → Killed on first threshold-crossing kill. Status can move Alive → Killed if a later killshot crosses a threshold; it can move Killed → Alive only via Retraction (§ below).
Retract if needed. If a founding premise or provenance claim proves invalid, withdraw the card and state why. If a counted killshot is later invalidated (bad control, assay artifact, substrate batch problem), document the retraction and recompute status from the remaining valid tests. A materially different replacement claim receives a new hypothesis ID.

The lifecycle is sequential per hypothesis but not per directory. Multiple hypotheses can be at different lifecycle stages simultaneously.

Status Meanings¶

Pending. Committed, no killshot yet executed. The default initial state.
Alive. At least one killshot has been run; the claim has not been falsified per its pre-committed thresholds. Survival count > 0.
Killed. At least one killshot has crossed its Killed threshold. The claim is falsified. Documented in the Log with the killshot result.
Retracted. The card was withdrawn because a founding premise or provenance claim failed, or a previously counted result was invalidated. The file states whether a recount is pending or a replacement hypothesis supersedes the claim.

A hypothesis with status Killed is not deleted. The file stays; the killed claim is part of the wiki's epistemic history. A Killed hypothesis can motivate a new committed hypothesis (a revised claim at a new file, H0M-*), but the Killed file itself is preserved.

Relationship to `synthesis/` (architecture: synthesis/README.md) and `wiki/open-questions.md`¶

A Research Conjecture on its mechanism-owning wiki page is the durable current-state home for a grounded but untested connection. It separates sourced premises from the novel leap and names a discriminating observation.
synthesis/queue/ is temporary action state. A reviewed synthesis finding may call for a conjecture, evidence correction, experiment, or hypothesis, but the queue file is deleted when that action lands.
open-questions.md is a concise cross-wiki index. It links to selected conjectures and unresolved questions without copying their reasoning.
hypotheses/ is where a specific, falsifiable claim gets a Falsification Card and a commit. Not everything in synthesis or open-questions becomes a hypothesis — only the ones the user is ready to commit resources against.

Flow (typical): synthesis finding → Research Conjecture on the owning page → optional open-questions link → (when ready to commit) hypotheses/H0N → Falsification Lint → execute killshots → update status.

An unconfirmed conjecture is not a failed hypothesis. Delete it when duplicated, no longer useful, or when a required premise fails; Git preserves the prior text. A COMP or experiment kills only the exact claim and regime it tested. Surviving adjacent leads remain unless their own premises collapse.

Conventions Summary¶

One file per hypothesis. Filename is the stable identifier.
First commit is the pre-registration. Subsequent edits are visible diffs with rationale in commit message.
Status is frontmatter (status:). Survival count is frontmatter (survival_count:).
Killshot menu is a table, sorted by score descending.
Thresholds are pre-committed — declared before the first killshot runs.
Failure modes are tagged from linter-design.md §5.
Retraction history is in-line, not in a separate directory. Visibility is the point.