Common Pitfalls When Responding to Peer Review

A revision decision is neither an acceptance nor a polite rejection. It is an invitation to show that the manuscript can withstand closer examination. How authors interpret the reports, decide what to change and explain their decisions often determines whether the next editorial assessment is straightforward or frustrating.

The purpose of a response letter is not to demonstrate agreement with every reviewer. Its purpose is to show that each concern has been understood, considered scientifically and addressed either through a revision or a reasoned explanation.

Begin with the editor’s decision

Authors often start by answering the reviewer whose report appears first. This can obscure the priorities of the revision. The editor’s letter should be read before any detailed response is drafted because it indicates which concerns are central to the decision.

Several reviewers may raise different versions of the same problem. One may question the experimental design, another the interpretation and a third the wording of the conclusion. These comments should not necessarily be treated as separate tasks. Together, they may indicate that the manuscript makes a claim more strongly than the design can support.

Grouping related comments by scientific issue helps reveal where a single substantial revision can resolve several points at once. It also reduces the risk of making isolated textual changes that leave the underlying problem untouched.

Do not answer the first reading

Reviewer reports can be blunt, especially after months of work on a study. An immediate response is rarely the best one. Read the reports, set them aside and return when the distinction between an uncomfortable tone and a valid scientific concern is easier to see.

A poorly phrased comment can still identify a real weakness. Conversely, a confident and detailed recommendation may not be appropriate for the study. Tone and scientific value should be assessed separately.

Responses written defensively tend to explain why the original manuscript was already correct. That is usually less useful than asking why the reader reached a different interpretation. If a reviewer misunderstood a result, another reader may do the same. The manuscript may need clarification even when the underlying science does not change.

A reviewer’s request is not an instruction

Reviewers advise; editors decide. Authors should take every comment seriously, but they are not required to perform every requested experiment or accept every proposed interpretation.

The important question is what the requested work is intended to resolve. A new experiment may be necessary when a principal conclusion depends on an untested assumption. It may be unnecessary when it would open a separate research question without changing the central result.

In some cases, narrowing a claim is scientifically preferable to adding a large body of weak or hurried data. If the experiment cannot be completed reliably within the revision period, the authors can explain the limitation, revise the relevant conclusion and identify the question as future work.

A refusal should nevertheless be specific. “This experiment is beyond the scope of the study” is not sufficient on its own. Explain why it lies outside the study’s design, what evidence already addresses the reviewer’s concern and how the manuscript has been revised to avoid overstating the conclusion.

Do not revise the response letter without revising the paper

One of the most common problems is a detailed response explaining an issue that remains unclear in the manuscript. The published paper must stand without the response letter. Any explanation needed to interpret the work should therefore appear in the revised manuscript.

Statements such as “we have clarified this point” are difficult to assess unless the response identifies where the change was made. Provide page and line numbers where the journal format allows them, and quote the revised wording when it is short enough to do so clearly.

The reverse problem also occurs: authors make extensive changes but provide only a brief response. Reviewers then have to search the manuscript to determine what changed. This creates unnecessary work and increases the likelihood that a substantive revision will be overlooked.

Partial corrections can create new inconsistencies

Changing a claim in the discussion may require corresponding changes to the title, abstract, results headings, figure legends and conclusion. Revisions made only at the point identified by the reviewer can leave different parts of the paper making different claims.

The same applies to terminology and numerical values. If an analysis is repeated or a sample is excluded, every affected table, figure, supplementary file and statement of sample size must be checked. An apparently minor statistical revision can propagate through much of the paper.

Maintain one master version of the manuscript and one master response document. Parallel files edited independently by several co-authors are a reliable way to reintroduce deleted text, lose figure changes and submit inconsistent versions.

Address difficult comments explicitly

Avoiding the most difficult point rarely makes it disappear. A reviewer who is invited to assess the revision is likely to return first to the concern they considered most important.

If two reviewers offer conflicting recommendations, do not attempt to satisfy both silently. Explain the conflict to the editor, state which approach was taken and give the scientific reason. Editors are responsible for weighing reviewer advice and can resolve requests that cannot reasonably be reconciled.

Authors should also distinguish between comments that affect validity and those that reflect preference. Questions about controls, statistical analysis, data quality and unsupported conclusions generally require substantive attention. Suggestions about ordering, terminology or an alternative interpretation may allow more editorial judgement.

Keep the response factual and easy to verify

The response letter may be read by the editor, the original reviewers and, in journals with published peer-review histories, future readers. The language should therefore remain professional even when the review was frustrating.

Excessive gratitude, apology or flattery adds length without improving the scientific exchange. A brief acknowledgement is enough. The body of the response should concentrate on what was changed, what evidence supports the decision and where the revision can be found.

This structure allows the reviewer to see the concern, the authors’ reasoning and the resulting change without reconstructing the exchange from several documents.

Coordinate the revision across the author group

The corresponding author should not complete a substantial revision in isolation. Comments concerning experimental design, statistics or interpretation need input from the authors responsible for those parts of the work.

Before resubmission, every author should see the revised manuscript and understand any changes to the main conclusions. New analyses may also require revised contribution statements, data deposits or supplementary information.

A final read by someone who did not draft the responses is particularly valuable. They can check whether the argument is understandable without relying on discussions that occurred within the author group.

A good revision makes the paper easier to judge

Peer review does not always improve a manuscript automatically. Its value depends partly on the quality of the reports and partly on how carefully the authors interpret them.

The strongest revisions do more than comply with a list of requests. They identify where the paper was vulnerable to doubt, correct what can be corrected and state clearly where the evidence ends. This gives the editor a manuscript that is easier to evaluate and leaves the scientific record more precise than it was at first submission.