Field: Life Sciences

A field overlay: it supplements, not replaces, the general agent_docs. Read it before discipline-specific writing. It encodes the conventions and reviewer expectations of life-science venues so the agent does not write ML-paper prose into a Cell submission, and does not skip the reporting standard a journal will desk-check.

Activate it in CLAUDE.project.md → Field overlay.

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Venues & where content goes

• Main text vs supplement: the figures that carry the thesis and the key controls go in the main text. Replicate panels, full blots/gels, gating strategies, extended dose–response, and exhaustive tables go to supplementary / extended data — but the uncropped originals of every blot must be available.
• A data-availability statement and (for the relevant study type) the reporting-standard checklist are not optional — editors check for them before review.

Structure (IMRaD, with field specifics)

A typical layout: Introduction → Results → Discussion → Methods (often last/online) → References. Differences to honor:

• Results before Methods is common; Methods may be a condensed main-text block plus a fuller "Online/Extended Methods." Write Methods to enable repetition, not to summarize (agent_docs/reproducibility.md).
• Results and Discussion are usually separate. Keep what you observed (Results, past tense) apart from what it means (Discussion, present tense for interpretation) — see agent_docs/academic-style.md tense table.
• Figures carry the argument. Each figure makes one point; the legend defines n, the statistical test, what the error bars are, and the scale bar. A claim in the text points to the panel that supports it.

Reporting standards (match the study type)

Editors expect the right checklist; a missing item is a pre-emptable reviewer comment (agent_docs/reproducibility.md).

These are checklists, not prose generators — they tell you what must be present, not what to claim. Run the relevant one before submission.

Ethics & approvals (state them — reviewers and editors require it)

• Human subjects: an IRB / research-ethics-committee approval (with protocol number) and a statement that informed consent was obtained. Identifiable data requires consent for publication.
• Animal work: IACUC (or national equivalent, e.g. Home Office / AWERB) approval, the approved protocol number, and adherence to ARRIVE. State species, strain, sex, age/weight, housing, and humane endpoints.
• Ethics statement placement: a dedicated Methods subsection ("Ethics statement") naming the approving body and protocol ID. The kit does not invent an approval number — if you do not have it, write [VALUE — verify], never a plausible-looking ID (CLAUDE.md → Source-Grounded Writing).

Wet-lab reproducibility (the field's defining rigor bar)

State enough that a competent stranger could repeat the experiment (agent_docs/reproducibility.md):

data/raw/ is immutable (enforced by protect-sources.sh) — derive processed tables into new files, never edit raw instrument output in place.

Statistics (see agent_docs/statistics.md)

• Appropriate test for the data. Match the test to design and distribution: t-test/ANOVA for approximately normal data, Mann–Whitney / Kruskal–Wallis for non-normal, paired tests for paired designs. Name the test in the legend; do not default to a t-test on skewed counts.
• Multiple comparisons: correct (Tukey, Holm, Benjamini–Hochberg FDR) when running a family of tests. Omics is the extreme case — thousands of genes/features demand FDR control; report adjusted p / q-values, not raw p.
• Define the error bars. SD, SEM, or 95% CI — and which in every legend. SEM is not SD; reporting SEM because it is smaller is misleading. Report effect size + uncertainty, not just "p < 0.05."
• n is the number of independent units, stated per comparison. Pseudoreplication (treating technical replicates or cells-from-one-animal as independent n) inflates significance — a classic reviewer catch.
• Show the data, not just bars. For small n, prefer dot/scatter plots over bar charts that hide the distribution; reviewers increasingly require individual data points overlaid. A bar with an error whisker over n = 3 conceals more than it shows.
• Pre-specify exclusions. Outlier removal and inclusion criteria are stated before unblinding and documented in Methods; undisclosed exclusion is p-hacking (agent_docs/statistics.md).

Figure integrity (a real journal/reviewer concern — do not gloss it)

Journals run automated image-forensics screening; violations trigger correction or retraction.

• No inappropriate image manipulation. Adjustments (brightness/contrast) must be linear and applied to the whole image, disclosed in the legend. Never splice lanes/bands, clone-stamp, erase, or selectively enhance a feature.
• Disclose splicing. If non-adjacent gel lanes are shown together, a dividing line and a note are mandatory; provide the uncropped original.
• Quantify blots from raw, unsaturated images, not from the figure JPEG; state how densitometry was normalized (loading control).
• The kit writes about figures; it does not fabricate a panel, a band, or a representative image that was not produced (CLAUDE.md → Source-Grounded Writing). A "representative" image must be genuinely representative of the quantified n.

Calibration in this field (overclaim → calibrated)

The verb/scope ladder of agent_docs/academic-style.md, applied to biology:

Pattern: bound the claim to the model system, attach the control that licenses it, and drop the verb to what the design supports.

Data availability (deposit + accession)

Most venues require deposition in a community repository before acceptance, with the accession in the paper:

The accession is a real identifier off the deposit — subject to the no-fabrication rule (block-fabrication.sh blocks fake-shaped DOIs). If the deposit does not exist yet, write [VALUE — verify], never an invented GSE/PXD/DOI.

Citations, terminology & nomenclature

• Cite the primary source, not a review, for a specific experimental claim; reserve reviews for background and synthesis. A mechanistic assertion traces to the paper that showed it (CLAUDE.md → Source-Grounded Writing).
• Style: numbered (Vancouver, common in Cell/Nature) or author–year per venue. Cite the published version when one exists, not just the bioRxiv id.
• Lock vocabulary per MANUSCRIPT_MAP.md → Terminology. One term per concept — do not alternate "knockdown" / "silencing" / "depletion" for the same intervention if they imply different mechanisms (RNAi vs CRISPRi vs degron).
• Gene/protein conventions: human genes italic uppercase (TP53), protein roman (TP53/p53); mouse genes italic initial-cap (Trp53). Follow the organism's nomenclature authority (HGNC, MGI). Define non-obvious gene symbols on first use.
• Species names italic, genus capitalized, binomial spelled out at first use then abbreviated (Drosophila melanogaster → D. melanogaster).
• Common knowledge for this audience needs no citation (e.g. "DNA is transcribed to RNA"); calibrate to the venue's readership.
• Units & symbols per agent_docs/statistics.md; brace-protect acronyms/gene symbols in BibTeX titles so casing survives — {DNA}, {CRISPR}, {TP53}.

Typical reviewer concerns (pre-empt them)

MANUSCRIPT_MAP.md additions for life-science papers

Add to your map's Claims that need extra care:

• An in-vitro / cell-line result does not license an in-vivo or clinical claim — state the model and its limits.
• A correlation across samples (expression vs phenotype) does not license a causal/mechanistic claim without a perturbation experiment.
• A "representative" image must reflect the full quantified n, not the best field of view.
• Generalization beyond the tested species/strain/cell line/condition is out of scope unless shown.

Add to Data & reproducibility: the reporting standard in force (ARRIVE / STROBE / PRISMA / MIAME / MINSEQE), ethics-approval IDs (or [VALUE — verify]), replicate definition (biological vs technical) and n, and the deposition target with accession (or [VALUE — verify] until minted).