Skip to content

kb/literature/README.md still described G10, and now has a real case instead #3

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
kyu-softmatter merged 1 commit into from
Sep 16, 2026
Merged

kb/literature/README.md still described G10, and now has a real case instead #3

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
52 changes: 39 additions & 13 deletions kb/literature/README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -19,8 +19,10 @@ One file per quantity per subject. `bleach-photons-alexafluor488.md`, not
it came out of. One paper supplying three quantities becomes three files, each
citing it. Files beginning with `_` are not entries.

**No entries yet.** The schema and the rules are here first, so the first entry
does not have to invent them.
**One entry**, [`lifetime-ns-tritc.md`](lifetime-ns-tritc.md) — TRITC's
fluorescence lifetime, which `G20` was refusing for want of. The schema and the
rules were written first so that it did not have to invent them, and they held:
nothing in the template needed changing to file it.

---

Expand All @@ -35,20 +37,37 @@ This repository has two evidence tiers, `measured` and `assumed`, and
worth having: a gate that was returning `BLOCKED` for want of an input can
instead *compute*, and report a margin, a bottleneck, and a difficulty grade.

The photo-perturbation lens is the live case. `bleach_photons` is empty for every
dye in `data/fluorophores.yaml`, so G10 has nothing to count against and the lens
refuses. Supply the number and it computes — and still says no:
The photo-perturbation lens is still the live case, and it is now a real one
rather than an illustration. `lifetime_ns` was `null` for TRITC, so `G20` could
not tell whether emission was linear in power and the lens refused:

```
488 (AlexaFluor488) @ 470 nm 6.2 W/cm^2 -> PASS_WITH_CHANGES
feasibility: MARGINAL evidence: assumed confidence: low advances: NO
TRITC @ 555 nm 153.0 W/cm^2 -> BLOCKED
feasibility: UNKNOWN evidence: assumed confidence: none advances: NO
[FAIL] missing.lifetime
```

Supply the number — 2.2 ns, free dye in PBS — and it computes:

0.20 perturbation.photobleaching ##
```
TRITC @ 555 nm 153.0 W/cm^2 -> PASS
feasibility: ROUTINE evidence: assumed confidence: low advances: NO

10.00 perturbation.saturation ##############################
```

**`advances: NO` beside a margin of 10.00 is the point**, and it is sharper than
the version that used to sit here. That one showed a literature value producing
a margin that said *no*, which is easy to accept. This one produces a margin
that says *yes, comfortably* — and still cannot advance a verdict. A passing
verdict is exactly where a reader is tempted to treat an assumed value as a
measured one.

That 0.20 margin is the point. It says ~100% of the label bleaches over 7200
frames, which is actionable now, and it says so without claiming anyone measured
this dye in this buffer under this illumination.
> **This paragraph illustrated `G10` and `bleach_photons` until 2026-09-16.**
> G10 was removed on 2026-09-09 ([kb/decisions/2026-09-09-g10-photobleaching-removed.md](../decisions/2026-09-09-g10-photobleaching-removed.md))
> and the output above it was hypothetical. The photobleaching arithmetic it
> described is kept in [04 §6](../../docs/04-decision-engine.md), which also
> says why the gate went.

If an entry here ever appears to make a verdict advance, that is a bug in the
gate, not a licence.
Expand All @@ -57,8 +76,15 @@ gate, not a licence.

**Belongs.** A number a gate consumes, which has no local measurement, whose
published value is specific enough to transfer with stated caveats.
`bleach_photons` per dye is the top example — [07 Phase 0](../../docs/07-roadmap.md)
lists it as literature-or-decay-curve, and it is empty across the whole registry.
`lifetime_ns` per dye is the worked example: `G20` reads it, five of seventeen
dyes are still missing it, and no instrument here can measure it directly —
that needs time-resolved detection this setup does not have.

> This said `bleach_photons` was the top example, *"empty across the whole
> registry"* and listed by 07 Phase 0 as literature-or-decay-curve. **No gate
> consumes it now** — it went with G10 — and `docs/07-roadmap.md` no longer
> names it. Still empty, and no longer a number anything is waiting on, which
> is the difference between a gap and a hole.

**Does not belong.**

Expand Down
Loading