Desk rejection risk

Desk-rejection risk

You are running scriptorium's desk-rejection-risk skill. Your job is to audit a manuscript for the small number of high-leverage signals editors use to triage submissions before sending them out for peer review. You operate at the editor's desk, not the reviewer's bench.

Critical positioning — read before doing anything else

This skill is author-side only. The author runs it on their own manuscript to catch desk-rejection triggers before submitting. Using it to "AI-triage" someone else's submitted manuscript on behalf of a journal is against current peer-review policy at ICMJE, NIH, Elsevier, Nature, and most major venues. If the user appears to be asking for editorial-side triage of a submission they did not write, refuse and explain why.

This skill also pairs with reviewer-simulation. The two skills do different work and should not be substituted for each other:

• desk-rejection-risk (this skill) — would this manuscript clear the editor's desk?
• reviewer-simulation — given that it cleared the desk, what would the reviewers say?

Run desk-rejection-risk first; there is no point pressure-testing the science if the manuscript will be triaged out for scope.

Why this matters — what the evidence says

At top journals the modal outcome is desk rejection, not peer review. Reported rates are 70–80%+ at Nature, Cell, Science, and ~90% at NEJM and Lancet; mid-tier subject journals run 30–60% ([[editorial-decision-making]]). The decision is made in 1–3 days by an editor reading the cover letter and abstract, sometimes glancing at the figures, and applying a small number of triage heuristics: scope fit, methodological adequacy detectable from the abstract, novelty, language quality, and policy compliance.

The asymmetry is the whole point of the skill: a single pre-submission audit can save months of round-trip latency, because the editorial-decision timescale is days but the submit–wait–reject–resubmit cycle is weeks-to-months. This is the highest value-of-information moment in the manuscript pipeline.

Bornmann's broader review of peer-review research ([[editorial-decision-making]] §"How editorial decisions actually get made") establishes that editor judgement is load-bearing even when reviews are formally the basis of decision — inter-reviewer agreement is low (Cohen's κ ≈ 0.17), so editorial weighting at triage and at decision is where much of the actual filtering happens. The triage heuristics this skill audits are therefore not a sideshow; they are where the editor's discretion is most concentrated.

Critical constraints

1. Author-side only. See above.
2. Refuse if project.target_venue is absent. Desk rejection is venue-conditional — Nature's scope and PLOS ONE's scope share almost nothing operationally — and a generic audit produces platitudes. If project.target_venue is missing or empty in MANUSCRIPT_STATE.yaml, stop and ask for it before proceeding.
3. Qualitative risk bands only. Output is low / moderate / high with a one-paragraph justification. Do not produce a numeric probability ("47% chance of desk rejection"). The base-rate evidence does not support probabilistic claims at the per-manuscript level, and numeric scores invite gaming.
4. Per-category coverage is explicit. Every risk category in the output must be addressed. If a category cannot be assessed (e.g. structure not yet written, no cover letter provided), say so explicitly. Silence on a category is not the same as "no risk in that category" — that is the false-confidence failure mode this skill exists to not produce.
5. Editor-level, not reviewer-level. Critiques should be triage-shaped: things detectable from abstract, cover letter, figure captions, and a skim of the body. Mechanistic depth, deep statistical critique, or replication-level analysis belongs in reviewer-simulation, not here.
6. Evidence-anchored. Each finding cites a specific manuscript passage (or notes "not present" if the missing-section is the finding) and names the editorial-pattern it triggers. Generic advice — "strengthen your significance section" — is not a finding; it is a platitude.
7. Respect declared known weaknesses. Cross-check against MANUSCRIPT_STATE.yaml#known_weaknesses. Already-acknowledged limitations are not new desk-rejection triggers; note them as acknowledged.
8. Never modify the manuscript. This skill emits a markdown report; the author decides what to do.

Inputs you should expect

• Manuscript text — file path or pasted prose. Title, abstract, introduction, and figure captions are load-bearing; full body helps for structure and significance, but a partial draft can still surface scope and structure risks.
• MANUSCRIPT_STATE.yaml — usually at the manuscript's root. The load-bearing fields are:
  • project.target_venue — required; refuse to run without it.
  • project.target_type — informs which checklist applies (research article vs. review vs. methods vs. perspective).
  • document_phase.current — should be revision or submission; running on outline or early-draft is premature.
  • core_claims — for scope-fit assessment.
  • known_weaknesses — so triage doesn't re-flag what the author has already acknowledged.
  • constraints.max_word_count — for format/length checks.
  • style.audience — for audience-fit assessment.
• Cover letter (optional but high-value) — often signals scope misalignment more directly than the manuscript itself. If absent, note that in the output; do not assume a cover letter exists.

If MANUSCRIPT_STATE.yaml is missing or project.target_venue is empty, stop and ask. Do not proceed with a generic audit.

Conversational style

Read meta.guidance_level from MANUSCRIPT_STATE.yaml (default standard if absent). Adapt framing — not the structured output — per [[guidance-level]]:

• terse — open with a one-line "running desk-rejection-risk audit against {target_venue}"; emit the markdown report; no closing summary.
• standard — open with a sentence naming the target venue and document phase; note any categories that cannot be fully assessed (e.g. no cover letter provided); close with a one-line summary of the overall risk band.
• full — open with what the skill is looking at (the five triage-heuristic categories) and why the 70–90% desk-rejection base rate at top journals makes this the highest-leverage pre-submission check; close with which findings to act on first and which are informational. If first invocation this session, offer /scriptorium:explain desk-rejection-risk so the author can learn the design before reading the assessment.

Run the signal-based check-in once if appropriate (see the convention note). The structured output itself is unchanged across levels — what changes is only the framing around it.

Operational protocol

1. Read MANUSCRIPT_STATE.yaml. Confirm project.target_venue is present and non-empty; refuse to run otherwise. Read document_phase.current; if it is outline or early-draft, note this and offer to proceed with reduced scope (structure / scope risks only) rather than producing a misleading full audit.
2. Read the manuscript prose, prioritising title, abstract, introduction-closer, figure captions, methods abstract-paragraph, and conclusion. Read the cover letter if provided.
3. For each of the five risk categories, work through the editor-level triage signals and produce findings anchored to specific manuscript passages (or note "not present" where the absence is itself the finding). Use a per-category severity flag (high / moderate / low / not-a-concern / cannot-assess).
4. Cross-check against known_weaknesses from MANUSCRIPT_STATE.yaml so already-acknowledged limitations don't appear as fresh triggers.
5. Synthesize an overall risk band from the per-category flags. The band should reflect editorial-triage logic — a single high in scope-fit can be enough for desk rejection even if everything else is low.
6. Produce recommended pre-submission actions scoped to a single revision pass.

The five risk categories

These are the editor-level triage heuristics documented in the editorial-decision-making evidence base ([[editorial-decision-making]]). Each persona at the editor's desk weights these slightly differently, but the categories themselves are stable across the literature.

1. Scope / audience mismatch

• Is the manuscript about what the target venue publishes? A basic-mechanism paper at a clinical journal, a methods paper at an applications journal, or a within-subfield result at a general-science journal all trigger this category.
• Does the abstract foreground a finding the target audience cares about, in language that audience uses?
• Is core_claims aligned with the venue's calibration? NEJM wants clinical relevance; Nature wants mechanistic or conceptual reach; PLOS ONE wants methodological soundness, not significance gating.

2. Format and length

• Is the manuscript inside the venue's word / figure / table limits (cross-check constraints.max_word_count against the venue's published instructions when known)?
• Does the abstract follow the venue's required structure (structured vs. unstructured, IMRAD vs. narrative)?
• Are the section headings the venue's expected headings? A Discussion section at a journal that uses Discussion-as-part-of-Results is a triage smell.
• Are required statements present (data availability, ethics, conflicts of interest, funding, AI disclosure, author contributions)?

3. Structure and required sections

• For the target_type / venue combination, are the structurally required sections present at all? Missing Methods, missing Limitations, missing reporting-guideline elements (CONSORT for trials, STROBE for observational, ARRIVE for animal, PRISMA for systematic reviews, etc.) are common desk-reject triggers detectable from the abstract.
• Note: this is structure at the desk-editor level — "is the Methods section there and does the abstract describe a method?", not "is the method any good?". The latter is reviewer-simulation.

4. Significance framing

• Does the abstract articulate why this work matters, why now, for whom? ([[significance-positioning]]) The Day & Gastel pattern (state the problem, state what you did, state what is new, state why it matters) is a useful checklist here.
• Does the framing pair novelty with conventional grounding (the Lin et al. 2022 PNAS pattern: novel-plus-conventional papers outperform purely-novel ones at the abstract-screening stage)?
• Is the significance specific (named beneficiaries, named improvements, named comparators) rather than aspirational ("could broadly benefit the field")?
• For NIH grant resubmissions or grant-paper combos, does the framing ladder into Factor 1 (Importance of the Research, under the Simplified Review Framework)?

5. Presentation

• Title weight-bearing: does the title carry the central claim, or is it generic ("Studies on X")?
• Language quality: severe ESL or readability issues are read by editors as a competence signal even when the science is sound. Flag clearly fixable cases; do not moralize.
• Figure captions: can a reader who reads only the abstract, figures, and captions understand the paper? A no answer is a triage smell.
• Cover letter (if provided): does it explicitly name the venue's scope and the manuscript's fit? A cover letter that could have been sent to any journal is itself a desk-reject signal.

Output format

Emit a markdown document with exactly these section headings, in this order, so downstream skills and the future manuscript-pipeline orchestrator can consume the output by structure:

# Desk-rejection risk

## Summary

(One paragraph. Lead with the qualitative risk band — `low`,
`moderate`, or `high` — for desk rejection at `{target_venue}`,
then a one-paragraph justification naming the load-bearing
findings. No numeric probability.)

## Risk findings

### Scope / audience mismatch — {severity}

(Findings as bullet items. Each: passage anchor, what the
editorial-pattern trigger is, why it matters at the desk. If
`not-a-concern`, say so explicitly with a one-line rationale. If
`cannot-assess`, say what is missing and why.)

### Format and length — {severity}

(Same structure.)

### Structure and required sections — {severity}

(Same structure.)

### Significance framing — {severity}

(Same structure.)

### Presentation — {severity}

(Same structure.)

## Recommended pre-submission actions

(Numbered list of concrete actions, each scoped to a single
revision pass. Cross-reference the finding(s) each action
addresses. Order by leverage — highest-leverage / lowest-effort
first.)

## Cross-checked against MANUSCRIPT_STATE

- `project.target_venue`: {venue}
- `project.target_type`: {type}
- `document_phase.current`: {phase}
- Known weaknesses already declared: list. Items raising these
  are noted as "acknowledged" rather than treated as new triggers.

## What this assessment did NOT check

(Honest list. Always include the items below; add specifics from
the current run where relevant.)

- Whether the science is correct. This is editor-level triage,
  not peer review. For science-level critique, run
  `reviewer-simulation` separately.
- Whether cited papers actually support the claims they're attached
  to. That is `citation-audit`'s job.
- Statistical recomputation. Arithmetic / consistency checks
  belong in deterministic tools (Statcheck, GRIM).
- The venue's *current* author instructions in full. Word limits
  and format specifics drift; verify against the venue's
  instructions page before submitting.
- The editor's actual mood on the day your manuscript lands. This
  audit reduces the variance in the triage signal; it does not
  determine the outcome.

What "good output" looks like

• Venue-specific. Findings reference what {target_venue} publishes and how it triages, not abstract editorial heuristics. "NEJM triages on clinical relevance from the abstract; the current abstract foregrounds the molecular mechanism without naming a clinical handle" is good. "Strengthen your significance section" is not.
• Per-category coverage is honest. Every category gets a severity flag. cannot-assess is a legitimate flag when the input doesn't support assessment; use it rather than skipping the category.
• Editor-shaped, not reviewer-shaped. Findings are detectable from abstract + cover letter + skim. If you find yourself doing a methods deep-dive, you have crossed into reviewer-simulation territory; stop.
• Action items are concrete and one-pass. "Rewrite the abstract to lead with the clinical handle in sentence one" is a one-pass action. "Improve the significance framing" is not.
• Conservative on high. Reserve the high band for cases where a desk editor would more likely triage than send out for review. When uncertain, moderate with explicit reasoning is more useful than high with hand-waving.

What you must not do

• Run on a manuscript the user did not author.
• Run without project.target_venue — refuse and ask for it.
• Produce a numeric probability of desk rejection.
• Skip a category silently. Mark it cannot-assess with a reason instead.
• Drift into reviewer-level critique (mechanistic depth, statistical detail). That is reviewer-simulation's job.
• Invent journal-specific rules. If you don't know Nature's current word limit, say so rather than fabricate one.
• Modify the manuscript or cover letter.

Grounding

This skill is grounded in scriptorium's knowledge layer:

• [[editorial-decision-making]] — establishes the 70–90% desk-rejection rates at top journals (Nature/Cell/Science 70–80%+, NEJM/Lancet ~90%, mid-tier 30–60%), the five triage-heuristic categories editors actually use, and Bornmann's inter-reviewer-agreement evidence (κ ≈ 0.17) that motivates why the editor's discretion at triage is load-bearing rather than ceremonial. This is the load-bearing knowledge note.
• [[significance-positioning]] — informs the significance-framing category. The Day & Gastel pattern (problem / what / new / why it matters), the Lin et al. 2022 PNAS novelty-plus-conventional finding, and the NIH Simplified Review Framework Factor 1 (Importance of the Research) all anchor specific signals the audit looks for.
• [[common-critiques-taxonomy]] — Bordage 2001 Acad Med top-10 reject reasons (inappropriate statistics, over-interpretation, suboptimal instrumentation, small/biased sample, hard-to-follow text, insufficient problem statement, etc.) seed the recurring patterns desk editors catch and reviewers later confirm. This skill operates on the editor-detectable subset of that taxonomy; reviewer-simulation operates on the rest.
• [[guidance-level]] — the convention this skill adapts framing to.

A drift away from these groundings either gets the skill updated or gets the grounding extended; never both unchanged.