Paper Writing Style

Scientific writing house style

Rules for producing English scientific prose that an editor of a high impact journal would accept. Apply them when writing or reviewing any manuscript section.

Two words govern everything: clarity and concision. Clarity is the message reaching the reader's mind as fast as possible. Concision is doing that with the fewest words. Every sentence must carry one idea to the reader.

Project layout and conventions

Four things to establish before writing a single line, all covered in references/latex-conventions.md:

1. The project's own CLAUDE.md outranks these defaults. A working paper repository documents its layout, section files, label convention, page limit and data provenance rules. Read it first and follow it. Never restructure a project to match a default.
2. Sections live one per file in src/, with main.tex holding the preamble, title block and \input order. Read the \input list to learn what the project calls things rather than assuming: conclusion.tex and conclusions.tex both occur, results and discussion may be one file or two, and methods may be study-design.tex.
3. Read src/macros.tex. Recurring values and terminology are defined there so they stay consistent. Write \nparticipants participants, not 54 participants. Write \RQ{1}, not \textbf{RQ1}. When a value changes, change the macro, not the prose. When a value recurs and has no macro, propose one. If \newif\ifblind is present the paper is double blind, so never insert author names, affiliations, or self-identifying phrasing.
4. Mark gaps with the project's \todo{} macro where one exists, since it renders in the PDF, and fall back to a % TODO: comment only when there is none. A comment is invisible in the PDF and survives to submission.

Where the project states a page limit, treat it as a constraint on every draft: say what a section costs, and name what should give way rather than overrunning. An over-length paper is desk rejected without being read.

Session state: check paper-out/ first

A paper spans weeks or months, so before asking the researcher anything, check whether paper-out/STATE.md exists in the working directory. If it does, read it plus decisions.md and any relevant interviews/*.md, then say in two or three lines what you already know so they can correct anything stale. Never re-ask a question whose answer is already recorded.

paper-out/ stores only what cannot be re-derived from the manuscript: the target journal, which result is principal and why, what was deliberately deferred, interview answers, open questions, and declined reviewer points with their reasons. It never stores prose, values, figure numbers or section structure, because a duplicate goes stale and then lies. If stored state and the manuscript disagree, the manuscript wins.

Write to it after any decision the researcher makes, and say which files you created or changed. Never block on it: if it is missing or unreadable, carry on without it and say so.

Full protocol, including the file layout and the STATE.md format, is in references/session-state.md. Read it before creating or updating any state.

The writing order

Sections are not written in the order they are read. The course recommends this sequence, and every skill in the family assumes it:

The important step is 3. Writing the introduction after the results keeps the two sections connected, which matters because a gap promised in the introduction and never answered in the results is the commonest structural fault in a manuscript.

Provisional titles along the way are fine. What matters is rewriting the title at the end.

Deviating from this order is a judgement call, not an error. Say so when a section is being written out of sequence, and note what may need revising later.

Non-negotiables

These are the rules that get violated most and cost the most. Never break them.

1. Never emit an em dash (---). Use a comma, colon, semicolon, parentheses, or a full stop. An en dash (--) is allowed only in numeric and page ranges: 10--20\,nm, pp.~13--17. Never as a connector or aside.
2. Never invent results, numbers, citations, or method details. If a value or source is unknown, emit a visible % TODO: marker naming exactly what is missing. A plausible fabrication is the worst possible output.
3. No suspense. State the main finding as early as the section allows. Scientific writing has no room for building up to a reveal.
4. Be specific. A sentence that could appear in any paper in the field says nothing. See "Specificity" below.
5. One idea per sentence, and keep sentences short enough to finish. The reader's mind forms the idea at the full stop. If a sentence is so long that its opening is forgotten by its end, it transmitted nothing.
6. Read every draft as if aloud. Redundancy, stacked passives, and monotonous rhythm are audible before they are visible.

For the full list of banned constructions and the protected vocabulary that must not be stripped, read references/human-voice.md. Read it before drafting, not after.

Tense, voice, person

• Past tense for the completed study and for what was done: this study investigated, measurements were carried out, the films were deposited.
• Present tense fits the Conclusions, where the implications for the field are stated: these results indicate, this approach offers.
• Active and passive are both valid. Active is more direct and uses fewer words, so prefer it. Never stack passives: a new methodology for protein purification is discussed and isolation techniques are described and results are compared must be rewritten.
• Third person dominates high impact papers and reads faster. Prefer analyses revealed that the virus incorporated into the cells over in our analyses we observed that.
• First person plural, used sparingly, is a legitimate emphasis device: we report, we synthesized, our group has investigated. Sprinkle it where emphasis is wanted; do not build the whole text on it.
• Scientific papers are highly formal. nowadays becomes currently or recently. on the contrary becomes in contrast.

Specificity

A generic sentence is the thing to eliminate. Compare:

• Weak: Novel strategies have been proposed to overcome the limitations related to disease diagnosis. Which strategies, which limitations, which diseases? It says nothing.
• Better: The use of carbon nanotube based biosensors has been proposed to overcome the poor selectivity exhibited by conventional systems used for cancer detection.
• Best: Carbon nanotube based biosensors exhibit high selectivity for cancer detection.

Every sentence must survive the question "could this appear unchanged in a different paper?" If yes, it needs detail or deletion.

Emphasis by word choice. The same fact can be aimed at different targets. Decide what the reader should carry away, then write for that:

• Levels are the point: Unexpectedly high levels of a protein were found in blood samples from patients with haemorrhagic infections.
• The protein is the point: High levels of a specific S100 family protein were found in blood samples from these patients.
• The relationship is the point: High levels of this protein are found in blood samples from infected patients, which may be the cause of the infection.

Sentence and paragraph construction

Keep complementary information adjacent. If a sentence opens the level of protein found in blood samples, the reader immediately asks what level. Answer it in the same breath: the level of protein found in blood samples was 1\,mg per decilitre, which is similar to that observed by Harvard's group. Any further detail follows in a new sentence.

Topic sentences. The first sentence of a paragraph carries the topic (as a keyword) and the message (what is claimed about it). Every following sentence must relate to one or the other. When either changes, the paragraph ends. This is also how paragraph length is decided, and it is the cleanest way to open a paragraph that describes a figure.

Vary sentence openers. A paragraph where every sentence opens subject then verb reads flat, even to a reader who cannot name the problem. Rotate among:

Connectors, by the direction the ideas move. These are correct scientific register and must not be treated as filler:

The reversing connectors are the standard way to open a gap statement in an abstract or introduction. However at the start of the second sentence of an abstract is a feature.

Redundancy and action in the verb

Cut redundancy. completely eliminated (either it is eliminated or it is not), introduce a new methodology (introducing implies new; write introduce a methodology or report a new methodology), during the data collection phase of the study, in a period of time of three months. Also cut what the editor already assumes: that results were analysed, that errors were removed, that samples were prepared carefully.

Put the action in the verb. Nominalization drains sentences:

Ambiguity

• as and since can read as either because or while. When cause is meant, write because. Tissue temperature increased because the particles released the drug.
• Every it, they, them, this, these, there must have one unmistakable referent. Since the platform has a support system connected to the equipment, it was mounted inside the lab leaves it pointing at two candidates. Name the thing.
• Define an abbreviation at first use, then use only the short form. Do not stack several abbreviations into one short sentence, even when all are defined.

Words to use sparingly

preliminary, careful / carefully, novel, successfully. A paper reporting preliminary conclusions invites the question of why it was submitted. That samples were carefully prepared and results successfully obtained is the minimum the editor assumes. Each of these words is acceptable once, when it carries real information.

Prefer precision over the vague noun. Replace fact and case with what they stand for: this effect, this observation, this phenomenon, this value.

For introducing purpose, prefer in this paper, in this study, in this investigation, or here we report over in this work. Calling the document in the reader's hands "this work" is imprecise, though in the work reported here is fine.

Further reference

• references/plain-english.md: substitution tables for inflated words and phrases, plus the confusable-word list (analysis/analyses, through/thorough/though, increase/enhance/improve, administer/administrate, reproducible).
• references/human-voice.md: banned constructions, protected vocabulary, and how to tell an AI tell from correct academic register. Read before drafting.
• references/latex-conventions.md: what LaTeX to emit, units, ranges, citation detection, and annotation comments.

Source

Distilled from Curso de Escrita Científica: Produção de Artigos de Alto Impacto by Prof. Dr. Valtencir Zucolotto (Instituto de Física de São Carlos, USP), which in turn draws on Michael Alley's The Craft of Scientific Writing, Essentials of Writing Biomedical Research Papers, and the ACS Style Guide.