Write Scientific Manuscript

Write Scientific Manuscripts

Make the science easy to follow before making the prose elegant. Optimize in this order: scientific logic, reader comprehension, evidential precision, then style.

Where this sits

This skill owns clarity and logic diagnosis. It carries no house style and no punctuation budget.

• manuscript-optimizer when the problem is above the prose: the claim hierarchy, evidence chain, or figure logic is unstable. Fix that first. Polishing a paragraph whose scientific role is wrong wastes the edit.
• scientific-writing when a section needs drafting or rewriting into full paragraphs, or when the task names a citation style or a reporting guideline.
• scientific-prose-style last, for punctuation and rhythm. This file deliberately carries no em-dash rule; that skill owns it, and its cap is at most one em dash per paragraph and none in the abstract.
• results-section-revision when only Results subsection flow and paragraph openings need repair.
• review-article-architecture when the piece is a Review, survey, or Perspective.
• rebuttal-response when the prose is a reply to reviewers rather than manuscript text. The claim-calibration ladder there is the same one used below.

Establish the intended meaning

Before rewriting, determine:

1. What single point must the reader understand?
2. What information must the reader already know for that point to make sense?
3. What evidence supports it?
4. What inference is justified, and what remains uncertain?
5. Why does the point matter at this location in the manuscript?

Do not polish a sentence whose scientific role is unclear. If necessary, briefly diagnose the logic before drafting.

For file-based revision, identify the authoritative version and preserve citations, figure references, terminology, numbers, and formatting. Read the file before editing it, and rebuild the document when the edit could disturb layout, floats, or cross-references.

Write for a broad scientific reader

• Assume intelligence but not local project knowledge.
• Introduce the biological or methodological problem before project-specific machinery.
• Define an uncommon term when first needed, not several paragraphs earlier.
• Make referents explicit. Replace ambiguous this, these, and it when the reader could plausibly choose the wrong antecedent.
• State the logical connection instead of asking the reader to infer it.
• Prefer a concrete subject and verb over abstract noun chains.
• Preserve necessary technical detail, but move secondary detail away from the sentence carrying the main claim.

Broad accessibility does not mean removing precision. Keep exact distinctions when they change the scientific meaning.

Put logic first

Give each paragraph one main job. Use this default progression when applicable:

1. Topic sentence: state the paragraph's point or function.
2. Necessary setup: provide only the context needed to understand the evidence.
3. Evidence or reasoning: report the relevant result, comparison, or limitation.
4. Interpretation: explain what the evidence means at the supported strength.
5. Connection: show why the next paragraph or section follows.

Do not force all five elements into every paragraph. Do require the first sentence to orient the reader. Avoid paragraphs that begin with implementation detail and reveal their purpose only at the end.

Build explicit bridges between adjacent claims. A valid sentence can still be misplaced if it does not answer the question raised immediately before it.

Read section-logic.md when restructuring a section, an abstract, or a full manuscript.

Prefer the simplest accurate language

• Use familiar scientific words when they express the same meaning.
• Prefer short, direct constructions, but vary sentence length naturally.
• Keep one principal claim per sentence unless two claims are inseparable.
• Use active voice when it makes the actor or logic clearer; use passive voice when the procedure or result is the natural focus.
• Remove throat-clearing, duplicated meaning, ornamental transitions, and empty intensifiers.
• Avoid compressed strings of nouns and stacked modifiers.
• Do not replace a clear ordinary word merely to sound more sophisticated.
• Do not use a fragmentary series of very short sentences when the causal or contrastive relation is clearer in one well-formed sentence.

Aim for the mature, restrained vocabulary common in strong general-science journals. Treat Nature style as clarity, economy, reader guidance, and calibrated claims, not as a list of fashionable words.

Read language-guide.md when performing sentence-level revision or terminology cleanup.

Do not invent terminology casually

Use a new label only when all of the following are true:

• the concept is genuinely distinct from established terms;
• the distinction is important more than once;
• existing terminology would be misleading or unwieldy;
• the label can be defined in one direct sentence;
• the same label will be used consistently afterward.

Otherwise, describe the phenomenon directly. Do not capitalize, hyphenate, abbreviate, or name an ordinary analytical step to manufacture novelty. Search the manuscript and, when needed, the relevant literature before asserting that a term is standard or introducing a replacement.

Preserve established field terminology even when it is less elegant than a newly invented alternative. If the source uses an unclear coined term, explain the issue and propose a conventional replacement rather than silently creating another term.