Paper 2 full draft

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 problem, prior hybrid/soft-sensor benchmarks and the exact contribution with verified references.
• Public/profile priority: Prepare Medium deep dive 4 and an accessible answer to when mechanistic knowledge helps.
• Career/relationship/commercial priority: Digest two extremophile founder papers, verify author-company affiliation and prepare three potential partner profiles.

Read v6 · Week 18 · Write Paper 2 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 IV · Threads: B, M, BL, R · Next gate: 20

Where this week sits. - ← From: week 17 experiments and figures; week 14-15 writing process. - → Feeds: week 19 (review), week 20 (submission), week 21 (the extremophile papers become partner-call preparation), week 36 (journal version). - ⟳ Returns in: Medium deep dive M4 and the week 38 talk.

Goals. - 🎯 This week: Paper 2 full draft (Intro, Related work, Methods, Results, Limitations, Reproducibility statement); M4 deep dive; two founder-paper digests with outreach lines. - 🏁 Next milestone: Gate 20. - 🌟 Final: your second preprint, and the start of the partner conversations that make Paper 3 possible.

Mentor check. "My Paper 2 draft makes one strong, bounded claim and lists its limitations before a reviewer does."

• Week 17: 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 18 · Write Paper 2, 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.

Biology/domain unit

Source unit: B18 · Extremophiles

Material: Two founder papers (Puna Bio, Antarka, APEXzymes authors) via Prompt P11

Produce: Outreach lines drafted

Understanding check: You can name the organisms and enzymes they work with

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: M18 · Research craft

Material: Simon Peyton Jones, "How to write a great research paper" (YouTube, 1 h); NeurIPS paper checklist (neurips.cc)

Produce: Paper 2 rewritten with the checklist

Understanding check: Reviewer-2 prompt finds no unsupported claim

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.

Branding: Prepare Medium deep dive 4 and an accessible answer to when mechanistic knowledge helps.

Opportunity action: Digest two extremophile founder papers, verify author-company affiliation and prepare three potential partner profiles.

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.

Do not generalize one simulated process to production performance or industrial savings. Main narrative follows measured learning curves.

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: 20. Complete the acceptance checklist below; do not promote reputation from a draft.

• Monday artifact satisfies: The scope is one simulated bioprocess benchmark.
• Wednesday artifact satisfies: Plots, tables and numerical claims match machine-readable results.
• Friday artifact satisfies: Missing experiments or assumptions are disclosed and review questions are concrete.
• 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: Results section.

Operational first step if stalled: open paper-2-introduction.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 18 of this LABLOOP execution plan.
Read execution-plan/specs.md, execution-plan/DECISIONS.md,
execution-plan/GATES.md and
execution-plan/weeks/week-18-paper-2-full-draft/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 18 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 18 · Write Paper 2. The following is source planning text, not a claim of completion. Apply the explicit evidence corrections in this specification and DECISIONS.md.

Week 18 · Write Paper 2

• Goal: full draft.
• Tue (B18): two extremophile founder papers; outreach lines.
• Thu (M18): Peyton Jones talk + NeurIPS checklist; rewrite.
• Build: Mon: Intro + Related work (hybrid modeling, soft sensors, IndPenSim benchmarks; all verified). Wed: Methods + Results. Fri: Limitations (simulated data, one process, no real plant), Reproducibility statement.
• Sun: M4 deep dive: "When does biology help the model? A data-scarcity study on 100 open batches". L-Sun.
• Only one thing: Results section.