Week 06 — human gold standard

This week delivers the three concrete artifacts below and the supporting learning/branding/opportunity pack. The scientific or commercial outcome follows the preserved source brief, while the acceptance checks make its evidence testable. The career objective is to turn this work into something a scientist, hiring manager or buyer can inspect.

• Scientific/build priority: Write field-by-field definitions, units, examples, ambiguity rules and adjudication procedure; annotate the first 15 papers while timing the first three.
• Public/profile priority: Draft a manual-annotation build log using actual completed counts and one observed ambiguity.
• Career/relationship/commercial priority: Prepare an independent annotator request with bounded workload, due date and any compensation clearly identified as a budget decision.

Read v6 · Week 6 · The gold set (the most important week of Half 1) before Monday. It carries this week's v5 brief unchanged and adds the Welcome analogy, Learn it (▶ core and ＋ deeper sources), Run it (repos with a 20-40 minute exercise), the NotebookLM kit and the mentor check below. Standing v6 rules: resource rules, NotebookLM protocol, chapter anatomy. v6 adds depth only; it does not change a goal, gate, output or the 600-minute cap, so this specification still governs execution.

Act II · Threads: B, M, FL · Next gate: 8

Where this week sits. - ← From: week 5 schema and corpus. - → Feeds: week 7 (the agent is scored against these 50), week 10 (kappa with the second annotator), week 14 (Paper 1 Methods: "Gold standard"), week 34 (labdocs uses the same method with 60 Q&A). - ⟳ Returns in: every evaluation you will ever sell. The gold-set habit is your professional signature.

Goals. - 🎯 This week: 50 gold JSONs with provenance sentences; GUIDELINES.md; one second annotator said yes. - 🏁 Next milestone: Gate 8. - 🌟 Final: the human-validation claim in Paper 1's title, and the calibrated-evaluation reputation that sells Loop Audits.

Mentor check. "I can explain why my 50 hand-annotated papers are worth more than 2,000 machine-extracted ones, and what a second annotator adds."

• Week 05: inspect its actual evidence and review; source/code artifacts must exist before the dependent task begins.
• Read commitment, evidence, review and the current root TODAY/PROGRESS/QUESTIONS files.
• Read this week's chapter, v6 · Week 6 · The gold set (the most important week of Half 1), then the standing sections: Part 0 · how to use the document, Part 3 · the scientific thesis, Part 4 · curriculum, Part 8 · the prompt pack and Part 9 · branding and endorsement. The same sections exist in the v5 master, which remains the governing sequence; v6 reproduces them and adds depth. Retained commercial/instrument details come from v4.
• Inspect the actual canonical repository state, available data, existing figures and required human/external inputs. Never assume a previous week succeeded from its folder name.
• Verify current resource links, versions, dataset rights and any live company/venue information before relying on them. Use source catalog; explicitly record inaccessible resources.

The model must turn these into exact physical actions using the observed files and available inputs. Each 90-minute block includes start/stop rituals. All calls, posts, debugging, reading and exercises consume this same capacity.

The source lists more material than necessarily fits. Select exact excerpts for the learning objective and park the remainder; no full-course completion requirement.

Biology/domain unit

Source unit: B6 · Genetic engineering and industrial strains

Material: Microbiology ch. 12 "Modern Applications of Microbial Genetics"; Biology 2e ch. 17.1

Produce: Notes; Rosalind 5-8

Understanding check: You understand what "engineered Yarrowia" or "recombinant E. coli" means in a FermLit paper

During preparation, write one worked example connected to the week's actual task, one exercise with a separate answer key and five questions. Peter supplies answers; score explanation quality and flag misconceptions in QUESTIONS. Numeric/scientific conclusions require actual data or explicitly synthetic teaching values.

AI/scientific-method unit

Source unit: M6 · Probability, the useful part

Material: Murphy, Probabilistic Machine Learning: An Introduction ch. 2 (probability) and 4.1-4.3 (statistics) — probml.github.io (free PDF); or Statistical Rethinking 2024 lectures 1-2 (github.com/rmcelreath/stat_rethinking_2024)

Produce: Notes; a Bayesian update by hand

Understanding check: You can explain a posterior with coins

Use the prompt pack: P1 explanation ladder, P2 concept-to-project bridge and P3 quiz. Coding practice belongs within the allocated study/build block. Where the source asks for a favorable scientific result, substitute an honest measured comparison as explained below.

Founder/scientist paper

Select one verified founder/scientific-lead paper relevant to this week's domain. Use P11; save the question, method, numerical result with context, data workflow, three author questions and one connection sentence in founder-paper.md. Keep abstract-only access limitations explicit. On source weeks with no study, prioritize the commercial/submission task and log any skipped digest.

These filenames are outputs to prepare during this week's execution; this scaffold does not claim they already exist. Drafts and measured results have different states. Technical code/data stay in the canonical project repository and are referenced from these coordinating files.

During preparation, future measured tables get column definitions, input requirements and run instructions with PENDING status. During execution, replace pending values only with measured outputs. Do not create realistic-looking fake evidence.

Branding: Draft a manual-annotation build log using actual completed counts and one observed ambiguity.

Opportunity action: Prepare an independent annotator request with bounded workload, due date and any compensation clearly identified as a budget decision.

Use career asset contracts. Publish at most the agreed cadence; one figure and one supported number or admitted failure can support multiple drafts. In long-form weeks, prepare a 1,500–2,500-word article from existing evidence within the build/buffer allocation. In release/demo weeks, prepare a 60-second script: problem, input, command/action, result, limitation and proof link.

Verify individuals, jobs and affiliations at execution time. The GridX list and v4 company map are research seeds, not current facts. Do not reveal named company weaknesses or employer/client confidential information. Keep drafted/sent/replied/booked/held statuses separate. The planning request alone does not authorize external messages or publication; honor explicit authorization in the execution session.

Fifty papers in three build blocks is a feasibility risk. Project time from the first three; use Saturday and request a scope/schedule decision if needed. Never fabricate completion or replace the second human with an LLM.

Apply the root scientific evidence contract: provenance; meaningful independent splits; no future-data leakage; baseline comparison; actual denominators/uncertainty; failed cases; human review where required. State whether data are simulated, public experimental, synthetic or partner-provided.

Keep source gates intact, and log scope/time conflicts in review. Missing people, money, access or results must not be replaced with invented evidence. Reduce optional polish first. A specific essential external dependency stays pending while independent preparation continues.

This is an enabling week. Its deliverables feed the next scheduled gate: 8. Complete the acceptance checklist below; do not promote reputation from a draft.

• Monday artifact satisfies: Each annotated value has a source sentence and document locator.
• Wednesday artifact satisfies: Completed and incomplete records are counted, with no model labels passed off as human gold.
• Friday artifact satisfies: Gold target is met or shortage logged; external acceptance is evidenced separately.
• Study pack is prepared; Peter's actual learning/quiz result is recorded separately.
• Branding and opportunity drafts use supported claims and the correct external-action state.
• Reproduction or document checks are recorded with file/version references.
• This week's special gate, if any, has real evidence or remains explicitly pending.
• Review, root progress/log and the next physical action are updated.

Source-preserving minimum: 50 gold JSONs.

Operational first step if stalled: open annotation-guidelines.md, write the required inputs and produce the smallest checkable example in ten minutes. If a more urgent missing gate dependency controls the week, use the source minimum above.

If the full week does not fit, use P14: retain one gate-critical deliverable and one directly supporting study exercise; record what is skipped versus moved. Do not mark the original full gate passed merely because the minimum was completed. After a missed week, reforecast from actual evidence and avoid a second unexamined lost week.

In review, state exactly what exists, what was verified, what Peter can now explain, which external events remain pending, where the canonical code/data live, and the next file/function or draft paragraph to touch. Link each fact to evidence. Carry scientific assumptions, split definitions and rights constraints forward explicitly.

Prepare Week 06 of this LABLOOP execution plan.
Read execution-plan/specs.md, execution-plan/DECISIONS.md,
execution-plan/GATES.md and
execution-plan/weeks/week-06-human-gold-standard/specs.md, commitment.md, evidence.md and review.md.
Read prior prerequisite reviews and inspect actual repository/data state.
Use v5 as the governing sequence, the v6 Week 06 chapter
(LABLOOP-Master-Plan-v6.md) as the deeper walkthrough, and v4 only for
retained details.
Produce the full local preparation pack and the exact week-specific files named
in the artifact table. Give me a bounded lesson with exercises/answer key,
daily physical actions, technical runbook or draft, branding drafts and
career/commercial actions. Keep the total to 600 minutes.
Separate prepared artifacts from measured results and my learning completion.
Verify sources and do not invent metrics, citations, papers, people or outcomes.
Do not execute external communications, publication or spending unless the
current session already authorizes the specific action.
Finish by updating evidence/review and TODAY with the next physical action.

v6 reproduces this brief unchanged inside v6 · Week 6 · The gold set (the most important week of Half 1). The following is source planning text, not a claim of completion. Apply the explicit evidence corrections in this specification and DECISIONS.md.

Week 6 · The gold set (the most important week of Half 1)

• Goal: 50 papers annotated by hand, guidelines written, second annotator recruited.
• Tue (B6): Microbiology ch. 12; Rosalind 5-8.
• Thu (M6): Murphy ch. 2 or Statistical Rethinking L1-2.
• Build: [ ] Mon: annotate/GUIDELINES.md with Prompt P7. Annotate 15 papers. Done when 15 gold JSONs with provenance sentences exist. [ ] Wed: annotate 20 more; refine guidelines with every ambiguity you hit. [ ] Fri: annotate 15 more (50 total). Message two people to annotate 30 of them independently (a founder-scientist, a biology student, or a paid postdoc). Done when one has said yes.
• Sun: L-Sun: "I read 50 fermentation papers by hand this week. Here is what they never tell you" (first hint of the reporting finding). L-Wed.
• Only one thing: 50 gold JSONs.