scientific-prose-style
Rules for the prose of a scientific paper — the sentences of the abstract,
introduction, results, and discussion. Load this whenever you draft or revise
manuscript text. (Figure planning lives in figure-planner; this skill
is about words on the page.)
This skill owns punctuation, rhythm and word-level tells, and it runs last. When a passage is hard to follow
for reasons punctuation cannot fix, such as an unstable claim, a missing evidence link, or a
paragraph whose job is unclear, fix that first with manuscript-optimizer or scientific-writing.
Re-punctuating a sentence whose scientific role is wrong does not make it readable, and polishing a
drifted Review before its review-article-architecture drift audit makes the drift harder to see.
One layer sits directly above this one. anti-defensive-writing owns authorial posture at the
paragraph level: what a paragraph leads with, where a caveat sits, and whether a sentence exists to
advance the argument or to pre-empt an objection. Run it first. Stripping defensive scaffolding
rewrites paragraph openers and sentence boundaries, which is exactly what Rule 3 and Rule 5 below
then have to settle, so running this skill first means doing that work twice. Rule 3 here calibrates
hedges within a sentence; deciding whether the hedge should exist at all belongs upstairs.
Rule 1: Em-dash budget (the headline rule)
The long em-dash (—) is the single most overused mark in generated scientific
prose. It feels punchy in isolation but a reader hits three or four per paragraph
and it reads as a stylistic tic, not as writing. Cap it.
- At most one em-dash per paragraph, and none in the abstract. If a sentence already has one, the next clause that wants a dash gets a different mark.
- Never use a pair of em-dashes to bracket an aside if a comma pair or parentheses would do — the double dash is the worst offender.
- Prefer, in rough order: comma (mild pause), colon (a list or an expansion of what precedes), parentheses (a true aside the sentence reads fine without), or split into two sentences (the strongest fix for a long dash-spliced line).
Substitution table
| Em-dash use | Replace with | Example fix |
|---|---|---|
| Pause before a summary/payoff | colon | ...never been tested — this is our entry point. → ...never been tested. This is our entry point. |
| Bracketed aside (pair of dashes) | commas or parentheses | no model — including ESM — beats chance → no model, including ESM, beats chance |
| Appositive / renaming | comma | allele-resolution prediction — telling apart variants → allele-resolution prediction, i.e. telling variants apart, |
| Abrupt contrast | period + connective, or "but" | real but sub-threshold — the effect vanishes → real but sub-threshold: the effect vanishes |
| Range or span (this is fine) | keep an en-dash –, not em | 370–1000 cells stays 370–1000 |
Before → after (from a real over-dashed abstract)
Before (5 em-dashes, tic-heavy):
Starting from the hardest instance of the problem — allele-resolution prediction, distinguishing many coding variants of the same gene — we assemble a benchmark, and find this is a measurement limit, not a model limit — a split-half floor shows the distance is no larger than sampling noise.
After (0 em-dashes, same content):
We start from the hardest instance of the problem: allele-resolution prediction, which distinguishes many coding variants of the same gene. On the benchmark we assemble, the ceiling turns out to be a measurement limit rather than a model limit. A split-half floor analysis shows the perturbation-versus- control distance is no larger than the sampling noise between two halves of a variant's own cells.
Note what the rewrite does: promotes one clause to its own sentence, turns the bracketed aside into a relative clause, and swaps the contrast dash for "rather than." The prose is calmer and each sentence carries one idea.
Rule 2: Don't trade the dash for a colon or semicolon tic
Colons and semicolons are the natural replacements, and the same overuse applies.
- Colons: at most one per sentence. If every sentence in a paragraph ends
...: <expansion>, you have just moved the tic. - Semicolons: none in the abstract, and at most one per paragraph elsewhere.
Published prose rarely uses them. In
paper-workflow's section evidence, 3 of 23 typeset method-paper abstracts and 1 of 12Natureabstracts have one, and three quarters of the Results and Discussion paragraphs have none. Two clauses joined by a semicolon are usually two sentences. Semicolons that separate list items already containing commas, or statistics inside parentheses, do not count.
Vary the repair. Most become periods, some become commas or a plain connective
(and, but, so).
Rule 3: Hedge once, not thrice
Scientific prose stacks hedges (may possibly suggest that ... could in principle ...). State the claim with one qualifier and the confidence level, then stop.
These results suggest X — not These results may tentatively be taken to suggest that X could hold.
Rule 4: Vary sentence length, one idea per sentence
A paragraph of uniformly long, clause-heavy sentences is as fatiguing as the dash tic. Follow a long sentence with a short one. If a sentence has three clauses joined by dashes, semicolons, and "and," it is three sentences.
Rule 5: Openers and connectives
- Don't open consecutive paragraphs with the same word (
We ... We ... We ...). - Prefer plain connectives (
but,so,because,here) over heavy ones (moreover,furthermore,additionally) unless enumerating.
Rule 6: Every word carries information (AI tells)
Prose reads as machine-written when words carry nothing: an intensifier on a plain fact
(ultimately, a clear boundary), a frame that inflates a modest point (not only ... but,
in its own right), a sentence that repeats the last one (In this way, ...), or vocabulary that
published papers almost never use (delve, underscore, pivotal, shed light). Apply the
information test: delete the word or sentence, and if the reader loses no fact, number, condition
or link, leave it deleted. Never swap a tell for a synonym, and never reword a frame (a decision problem as well as a modelling one is the same frame): replace it with its content.
Most words called AI vocabulary are common in published papers (robust, moreover, notably,
highlight), so do not cut by word list. references/ai-tells.md gives
the families, the corpus rates and the cases that stay, and scripts/ai_tells.py lists candidates
in a draft. Recaps, forward pointers and rhetorical questions are anti-defensive-writing's
commentary voice. Coined terms and weak subjects are write-scientific-manuscript's.
Body text carries no bold sentences. Emphasis comes from position, the first sentence of a paragraph, not from formatting.
Self-check before you hand prose back
Run this on any abstract/intro/section you write:
- Count em-dashes and semicolons. More than one of either per paragraph, or any in the abstract → rewrite the excess with the substitution table or as separate sentences.
- Count paragraph-opening words. Repeated opener → vary it.
- Read the longest sentence aloud. If you run out of breath, split it.
- En-dashes in numeric ranges (
5–10) and hyphens in compounds (single-cell) are fine and are not counted against the budget. - Run the information test on intensifiers, frames and closing sentences
(Rule 6). For a whole section, run
scripts/ai_tells.pyand read every flagged line.
Provenance: adapted from the Claude Science scientific-prose-style skill (Apache-2.0). Cross-references to figure skills were repointed to this repo's figure-planner, and a pointer to the anti-defensive-writing layer above this one was added.
