The 'We Respectfully Disagree' Phrasebook

By Dr. Zubair Khalid, DVM, MS, PhD · 2026-08-28

Quick Answer

• Use structured, professional phrases that acknowledge the reviewer's point before presenting your counterargument, which preserves credibility and reduces defensiveness.
• Select phrases by intent, such as acknowledging partial validity, offering alternative evidence, or requesting clarification, and pair each with a specific example.
• A key limitation is that no phrase replaces sound scientific reasoning, and your disagreement must be supported by data or methodological justification.

Understanding the Purpose of Diplomatic Disagreement

Peer review is a cornerstone of scholarly communication. The process depends on reviewers who volunteer their time to assess manuscripts, identify weaknesses, and suggest improvements. When you receive comments that you believe are incorrect, incomplete, or based on a misunderstanding, you must respond. The response letter is your opportunity to clarify your work and defend your conclusions. The way you phrase that defense matters.

The Committee on Publication Ethics Core Practices describe peer review as a process that should be fair and rigorous. Journals expect authors to engage with reviewer comments in a professional manner. A response that is dismissive or confrontational can damage your credibility and may lead to unnecessary revisions or rejection. A response that is respectful and evidence-based can strengthen your manuscript and demonstrate your expertise.

The goal is not to win an argument. The goal is to produce the best possible version of your research. This means you must be willing to consider the reviewer's perspective, even when you disagree. You must also be prepared to explain why your approach is valid, using the evidence you have collected. The phrasebook that follows provides language to help you do this effectively.

At a Glance

This table summarizes the main categories of disagreement phrases and when to use them.

Core Principles of Professional Disagreement

Separate the Person from the Problem

Reviewers are not adversaries. They are professionals who have agreed to evaluate your work. Their comments are about the manuscript, not about you. When you respond, you are addressing the comment, not the person. This separation is essential for maintaining a professional tone. You can disagree with a comment while respecting the reviewer's effort and expertise.

Acknowledge Before You Disagree

A simple acknowledgment can change the tone of your response. It shows the reviewer that you have read and considered their comment. This does not mean you agree with the comment. It means you recognize the effort the reviewer has made. For example, you might say, "We thank the reviewer for this thoughtful comment." This opening creates a constructive atmosphere for the disagreement that follows.

Provide Evidence for Your Position

Your disagreement must be grounded in evidence. This evidence can come from your data, your methods, or the existing literature. The National Library of Medicine provides access to a wide range of biomedical books and research-method references that can support your arguments. When you cite evidence, you show the reviewer that your position is based on more than personal preference.

Be Willing to Change Your Mind

Disagreement is not the same as stubbornness. If the reviewer raises a point that is correct, you should accept it and revise your manuscript. This is a sign of good scholarship. It is also a sign of respect for the review process. The Committee on Publication Ethics Core Practices emphasize the importance of integrity in research. Part of that integrity is being honest about the strengths and weaknesses of your work.

Practical Workflow for Responding to Reviewers

The process of responding to reviewers is a structured task. A clear workflow helps you manage the work and produce a response that is complete and professional.

Step 1: Read All Comments Carefully

Read every comment from every reviewer. Do not skim. Take notes on the main points. Identify the comments that require a response. Some comments may be simple requests for clarification. Others may be substantive challenges to your methods or conclusions. You need to understand each comment before you can respond.

Step 2: Categorize the Comments

Use the categories from the phrasebook to sort the comments. This will help you to plan your responses. You may have comments that acknowledge partial validity, comments that require alternative evidence, and comments that require clarification. Categorizing the comments helps you to see the overall shape of the review.

Step 3: Draft Your Responses

For each comment, draft a response. Start with an acknowledgment. Then, state your position. Then, provide your evidence. Use the phrasebook to find the right language. Do not rush this step. A well-drafted response is clear and concise.

Step 4: Revise the Manuscript

Your response letter is not the only deliverable. You must also revise the manuscript to reflect your responses. If you have agreed to a change, make the change. If you have explained why you disagree, make sure the manuscript is clear on the point. The reviewer will check the manuscript to see if you have addressed the comments.

Step 5: Review the Complete Package

Before you submit, review the response letter and the revised manuscript together. Make sure that every comment has a response and that every response is reflected in the manuscript. This is a final quality check. It helps you to catch any errors or omissions.

Options and Tradeoffs in Your Response

There are different ways to respond to a reviewer. The approach you choose depends on the situation.

Agreeing with the Reviewer

This is the simplest option. If the reviewer is correct, you should agree and make the change. This is not a failure. It is a sign of good scholarship. The Committee on Publication Ethics Core Practices emphasize the importance of honesty and integrity. Agreeing with a correct comment is part of that.

Disagreeing with the Reviewer

This is the more difficult option. You must explain why you disagree. You must provide evidence. You must do this in a respectful way. The phrasebook provides language for this. The key is to focus on the evidence, not on the reviewer.

Compromising with the Reviewer

Sometimes you can find a middle ground. You may not agree with the reviewer's interpretation, but you can add a clarification that addresses their concern. This is a common outcome. It shows that you are willing to work with the reviewer to improve the manuscript.

Observations and Measurements in Your Response

Your response should be based on your observations and measurements. This is the evidence that supports your position. When you disagree with a reviewer, you should point to the specific data that support your interpretation. This is more persuasive than a general statement.

Using Your Data

Your data are the foundation of your response. If the reviewer questions your interpretation, you can point to the data that support your interpretation. You can also explain the methods you used to collect the data. This shows the reviewer that your conclusions are based on a solid foundation.

Using the Literature

The literature is another source of evidence. If the reviewer makes a claim that is contradicted by published studies, you can cite those studies. The National Library of Medicine provides access to a wide range of biomedical books and research-method references. You can use these to support your arguments.

Using Reporting Guidelines

Reporting guidelines can also be useful. The EQUATOR Network provides a comprehensive collection of reporting guidelines for different types of studies. If the reviewer questions your methods, you can point to the relevant reporting guideline to show that your approach is consistent with best practice. This is a strong form of evidence.

Records and Documentation

Your response letter is a record of your interaction with the reviewer. It is important to keep a clear record of your responses. This is useful for your own reference and for the editor.

The Response Letter

The response letter is the main record. It should be organized by comment. Each comment should be followed by your response. This makes it easy for the editor and the reviewer to check your work. The letter should be clear and concise.

The Revised Manuscript

The revised manuscript is the other record. It should show the changes you have made. You can use track changes or a different color to highlight the changes. This makes it easy for the reviewer to see what you have done.

The Data and Methods

Your data and methods are also records. They support your responses. If you have made changes to the methods, you should document those changes. This is important for transparency and reproducibility.

Common Failure Patterns

There are several common mistakes that authors make when responding to reviewers. These mistakes can damage your credibility and reduce the chances of acceptance.

Being Dismissive

A dismissive response rejects the reviewer's comment without consideration. This is a failure. It shows a lack of respect for the review process. It also makes it more likely that the editor will side with the reviewer.

Being Defensive

A defensive response focuses on protecting your own work instead of addressing the comment. This is a failure. It makes it difficult to have a productive conversation. The goal is to improve the work, not to defend it.

Being Vague

A vague response does not provide a clear answer. This is a failure. It leaves the reviewer confused. It also makes it difficult for the editor to evaluate your response. You need to be specific about what you have done and why.

Ignoring the Comment

Ignoring a comment is the worst failure. It shows that you have not read the review carefully. It also makes it impossible for the editor to see that you have addressed the comment. Every comment must be addressed.

Limitations and Boundaries

The phrasebook is a tool, not a solution. It cannot replace the need for sound scientific reasoning. The phrases are only useful if they are backed by evidence. A phrase that is not supported by evidence is empty.

The Limits of Language

Language can help you to communicate, but it cannot substitute for substance. If you disagree with a reviewer, you must have a reason. The phrasebook can help you to express that reason, but it cannot create the reason.

The Limits of the Review Process

The review process is not perfect. Reviewers can make mistakes. They can misunderstand your work. They can be biased. The phrasebook can help you to respond to these issues, but it cannot fix them. You must be prepared to accept that the process is not always fair.

The Limits of Your Own Work

Your work is not perfect. There may be weaknesses that the reviewer has identified. You must be honest about these weaknesses. The phrasebook cannot help you to hide them. It can only help you to communicate about them.

Safety and Regulatory Context

The review process is part of the broader research enterprise. It is governed by ethical principles and, in some cases, by regulations.

Publication Ethics

The Committee on Publication Ethics Core Practices provide a framework for ethical behavior in research and publication. These practices cover authorship, peer review, data, conflicts of interest, and misconduct. Your response to reviewers should be consistent with these practices.

Data Management and Sharing

The National Institutes of Health Data Management and Sharing Policy requires researchers to plan for the management and sharing of data. Your response to reviewers may need to address data-sharing issues. The policy is available at the NIH sharing website.

Research Integrity

Research integrity is the foundation of the scientific enterprise. It is the responsibility of every researcher to maintain the highest standards of integrity. Your response to reviewers should reflect this commitment.

Professional Escalation Criteria

There are situations where you may need to escalate a concern beyond the normal review process.

When to Contact the Editor

You should contact the editor if you believe that a reviewer has been unprofessional or biased. You should also contact the editor if you believe that the review process has been unfair. The editor is responsible for managing the review process.

When to Contact the Institution

You should contact your institution if you believe that there has been a breach of research integrity. This could include data fabrication, plagiarism, or other misconduct. The Committee on Publication Ethics Core Practices provide guidance on how to handle these situations.

When to Contact a Funding Agency

You should contact a funding agency if you believe that a reviewer has a conflict of interest that has affected the review. The National Institutes of Health Grants and Funding provides guidance on conflicts of interest in the review process. You can find this information on the NIH Grants and Funding website.

The Phrasebook: 30 Phrases by Intent

The following is a curated list of 30 phrases, organized by intent. Each phrase is accompanied by an example of usage in context.

Acknowledging Partial Validity

1. "We agree that this is an important point, and we have added a discussion of this issue to the revised manuscript."
2. "We appreciate the reviewer's suggestion. We have incorporated this point into our discussion."
3. "We agree that the reviewer has identified a limitation of our study. We have acknowledged this limitation in the revised manuscript."
4. "We thank the reviewer for this comment. We have clarified our rationale in the revised manuscript."
5. "We agree that the interpretation is possible. We have added a sentence to the discussion to acknowledge this alternative interpretation."
6. "We appreciate the reviewer's perspective. We have revised the text to be more precise."
7. "We agree that the methods could be described more clearly. We have revised the methods section to provide more detail."
8. "We thank the reviewer for this suggestion. We have added a reference to support this point."
9. "We agree that the data could be interpreted in different ways. We have added a discussion of this issue."
10. "We appreciate the reviewer's comment. We have revised the conclusion to be more cautious."

Offering Alternative Evidence

1. "We appreciate the reviewer's comment. However, our data indicate a different interpretation. We have explained this in the revised manuscript."
2. "We thank the reviewer for this suggestion. We have considered this alternative, but we believe our approach is more appropriate for the following reasons."
3. "We appreciate the reviewer's concern. However, we believe that our approach is consistent with the reporting guidelines for this type of study."
4. "We thank the reviewer for this comment. We have considered this point, but we believe that our interpretation is supported by the evidence."
5. "We appreciate the reviewer's suggestion. However, we believe that the alternative approach would introduce a bias."
6. "We thank the reviewer for this comment. We have considered this point, but we believe that our methods are appropriate for the research question."
7. "We appreciate the reviewer's concern. However, we believe that the data do not support this interpretation."
8. "We thank the reviewer for this suggestion. We have considered this alternative, but we believe that our approach is more robust."
9. "We appreciate the reviewer's comment. However, we believe that the reviewer has misunderstood the methods."
10. "We thank the reviewer for this comment. We have considered this point, but we believe that the conclusions are supported by the data."

Requesting Clarification

1. "We thank the reviewer for this comment. We are unsure we understand the reviewer's request. Could you please clarify?"
2. "We appreciate the reviewer's comment. We would like to clarify the reviewer's intent. Could you please provide more detail?"
3. "We thank the reviewer for this suggestion. We are not sure we understand the point. Could you please explain?"
4. "We appreciate the reviewer's comment. We would like to understand the reviewer's concern. Could you please provide an example?"
5. "We thank the reviewer for this comment. We are unsure what the reviewer is asking us to do. Could you please clarify?"
6. "We appreciate the reviewer's suggestion. We would like to understand the reviewer's rationale. Could you please explain?"
7. "We thank the reviewer for this comment. We are not sure we understand the reviewer's point. Could you please provide more context?"
8. "We appreciate the reviewer's comment. We would like to clarify the reviewer's request. Could you please specify the section of the manuscript?"
9. "We thank the reviewer for this suggestion. We are not sure we understand the reviewer's concern. Could you please provide a reference?"
10. "We appreciate the reviewer's comment. We would like to understand the reviewer's perspective. Could you please elaborate?"

Using the Phrasebook in Context

The phrases are not meant to be used verbatim. They are meant to be adapted to your specific situation. You should use the phrase as a starting point and then add your own specific details.

Example 1: Acknowledging Partial Validity

Reviewer: "The authors should discuss the limitations of their study."

Your response: "We agree that this is an important point. We have added a discussion of the limitations of our study to the revised manuscript. Specifically, we have noted that our sample size was relatively small and that our findings may not be generalizable to other populations."

Example 2: Offering Alternative Evidence

Reviewer: "The authors should use a different statistical test."

Your response: "We appreciate the reviewer's suggestion. However, we believe that our analysis is appropriate for the research question. We have used a t-test to compare the means of two groups. We have explained our rationale in the revised manuscript."

Example 3: Requesting Clarification

Reviewer: "The authors should discuss the implications of their findings."

Your response: "We thank the reviewer for this comment. We are not sure we understand the reviewer's request. Could you please clarify whether you are asking us to discuss the implications for clinical practice or the implications for future research?"

The Role of the Editor

The editor is the intermediary between the authors and the reviewers. The editor is responsible for making the final decision on the manuscript. The editor will read your response letter and the revised manuscript. The editor will also consider the reviewer's comments.

The Editor's Perspective

The editor wants to make a decision. The editor wants to be fair to the authors and to the reviewers. The editor wants to ensure that the manuscript is of high quality. Your response letter should help the editor to make a decision.

The Editor's Decision

The editor can accept the manuscript, reject the manuscript, or request further revisions. The editor's decision is based on the quality of the manuscript and the response to the reviewers. A good response letter can help to persuade the editor to accept the manuscript.

Frequently Asked Questions

How should I begin a response to a reviewer comment I disagree with?

Start with a brief acknowledgment of the reviewer's effort, such as "We thank the reviewer for this comment." Then state your position and provide your evidence. This opening shows respect for the review process and creates a constructive tone for the disagreement that follows.

What is the best way to offer alternative evidence to a reviewer?

Present your data or methodological reasoning directly and connect it to the specific comment. For example, you might say, "We appreciate the reviewer's suggestion. However, our data indicate a different interpretation, which we have now explained in the text." This approach shows that you have considered the comment and have a substantive basis for your position.

When should I request clarification from a reviewer?

Request clarification when a comment is ambiguous or unclear. It is better to ask for clarification than to guess and respond to the wrong point. A request for clarification shows that you are taking the comment seriously and want to address it accurately.

How do I respond to a reviewer who has misunderstood my methods?

Politely explain the methods in more detail and point to the relevant sections of the manuscript. You can also reference reporting guidelines from the EQUATOR Network to show that your approach is consistent with best practice. This provides a strong basis for your position.

What should I do if a reviewer asks for a change that would compromise the integrity of the study?

You should decline the change and explain why it would compromise the study. Provide evidence from your data or the literature to support your position. If the reviewer persists, you can contact the editor to explain the situation. The Committee on Publication Ethics Core Practices provide guidance on handling such conflicts.

How can I use reporting guidelines to support my response?

Reporting guidelines can help you to show that your methods are consistent with best practice. If a reviewer questions your methods, you can point to the relevant reporting guideline from the EQUATOR Network to demonstrate that your approach is appropriate for the study type.

What is the role of the editor in the review process?

The editor is responsible for making the final decision on the manuscript. The editor will read your response letter and the revised manuscript and consider the reviewer's comments. Your response letter should help the editor to make a fair and informed decision.

How should I handle a reviewer comment that is clearly biased or unprofessional?

You should respond professionally and focus on the evidence. If you believe the reviewer has been biased or unprofessional, you can contact the editor to express your concern. The editor is responsible for managing the review process and ensuring that it is fair.

Using the Evidence

Related Articles

• Meta-Analysis vs Peer Review: Understanding the Differences
• Peer Review Metrics: What They Are and How to Use Them
• Responding to Peer Review: A Structured Revision and Response Process
• Meta-Analysis vs Systematic Review: What's the Difference?
• Single Cell Rna Seq Review

References and Further Reading

• Research Methods Resources. National Library of Medicine.
• EQUATOR Network. EQUATOR Network.
• Core Practices. Committee on Publication Ethics.
• NIH Grants and Funding. National Institutes of Health.
• ORCID for Researchers. ORCID.
• Data Management and Sharing Policy. National Institutes of Health.
• NCBI Literature Resources. National Center for Biotechnology Information.
• PubMed. National Library of Medicine.

This article is educational and does not replace institutional policy, professional advice, or applicable safety and regulatory requirements.