Scientific Writing

Scientific Writing

Purpose

Produce clear scientific prose without inventing evidence or concealing uncertainty. Keep drafting, evidence verification, and submission approval as separate stages.

The accountable human authors control scientific decisions and final approval. AI is not an author, and generated fluency is never evidence [SW-S01, SW-S03].

Non-negotiable safety rules

Confidentiality

Do not send unpublished manuscripts, peer-review or editorial material, sensitive or restricted data, PHI or other personal data, proprietary content, or source documents to an external service without:

1. explicit authorization from a person or body empowered to grant it; and
2. a documented review of journal, institutional, funder, consent, ethics, contractual, legal, and data-use policy.

When authorization or policy is unclear, keep processing local and use only the minimum metadata needed. De-identification requires expert review; removing obvious names is not sufficient. See references/authorship_ai_confidentiality.md.

No fabrication

Never invent or complete:

• citations, references, DOI, PMID, PMCID, ISBN, URLs, or quotations;
• results, data values, denominators, sample sizes, units, effect estimates, uncertainty, statistical tests, or significance claims;
• methods, materials, protocol details, software versions, analysis choices, or deviations;
• registrations, approvals, consent, ethics statements, participant details, or dates;
• authors, author order, CRediT roles, acknowledgments, or permissions;
• funding, sponsor roles, conflicts, data or code availability, or AI disclosures.

Use an explicit missing, unverified, or not-applicable state. Do not substitute plausible boilerplate.

Evidence binding

Every factual or numeric manuscript claim must map to verified evidence IDs. A human verifier must open the source, confirm the proposition and locator, verify bibliographic metadata, and record who verified it and when.

Search snippets, generated summaries, memory, and another work's bibliography may aid discovery but do not verify a claim. See references/evidence_workflow.md.

Scientific fidelity

• Preserve uncertainty and alternative explanations.
• Distinguish confirmatory, exploratory, descriptive, and post hoc work.
• Keep methods and results consistent.
• Reconcile units, denominators, sample sizes, populations, time points, and labels.
• Report negative, null, adverse, unexpected, failed, and inconclusive findings when they belong to the study record.
• State concrete limitations and bound generalizability.
• Do not convert association into causation or non-significance into equivalence.

Route by the requested work

Apply the relevant workflow to the requested document or section. Mark missing evidence and policy inputs unresolved while completing authorized local drafting and audits; preserve the human verification and approval requirements below.

Use only the relevant references; an editorial change does not require creating an unrelated manuscript workspace. Preserve evidence IDs during drafting and reconcile affected registries before prose when facts change. Re-run affected audits.

Completion and approval

Local scripts are deterministic, bounded, dependency-free, and network-free. They check structure and consistency; they do not verify source support, certify guideline adherence, or authorize submission. Use CLI reference for exact commands and the workflow inventory for scaffold assets and supporting resources.

Only accountable humans may:

• resolve scientific ambiguities;
• approve author order and declarations;
• approve external disclosure or transfer;
• set submission_ready to true;
• remove the draft banner;
• authorize submission.

Formatting cannot convert an incomplete evidence record into a submission-ready paper. Keep unresolved claims, policies, and approvals explicit in the deliverable. Do not ask for restricted source material if metadata or a local user-run audit is sufficient.

Policy evidence labels such as SW-S01 resolve in the source ledger.

When this skill materially contributes to a manuscript, report, presentation, or code release, follow the current-version citation procedure.