From 'This Is Confusing' to Clear: Rewriting for Reviewer Clarity

By Dr. Zubair Khalid, DVM, MS, PhD · 2026-08-27

Quick Answer

• Respond to clarity comments by first identifying the specific confusing passage, then rewriting it with concrete terms and a logical structure that preserves scientific accuracy.
• Use reporting guidelines from the EQUATOR Network to structure your revision and demonstrate transparent research reporting to reviewers.
• Acknowledge the limitation that vague comments may reflect reviewer time constraints, so your response letter must show the exact change made and where it appears in the revised manuscript.

Understanding Why Reviewers Say "This Is Confusing"

Peer reviewers evaluate manuscripts under time pressure while reading dense technical content. When a reviewer writes "this is confusing" or "please clarify," they are signaling that a passage failed to communicate its intended meaning on first read. This feedback is common across life sciences, laboratory research, and clinical manuscripts.

The confusion often stems from one of several identifiable problems. The passage may lack a clear topic sentence, forcing the reader to infer the main point. It may use ambiguous pronouns where the antecedent is unclear. It may bury the key finding inside a long paragraph of background detail. Or it may introduce specialized terminology before defining it.

Reviewers are not obligated to diagnose the exact source of their confusion. Their comment is a symptom report, not a prescription. Your job during revision is to diagnose the underlying readability problem and fix it systematically.

The Committee on Publication Ethics Core Practices emphasize that peer review should be fair and constructive, but reviewers vary widely in how they express feedback. Some provide detailed line-by-line suggestions. Others write brief margin notes. Both forms of feedback deserve a serious response, but brief comments require more diagnostic work on your part.

The Core Principle: Clarity Without Losing Scientific Nuance

Scientific writing must balance two competing demands. The first is precision, meaning the text says exactly what the data support and nothing more. The second is accessibility, meaning a reader with appropriate background can follow the argument without rereading every sentence.

These demands are not opposed. Precision and clarity reinforce each other when you choose concrete words, define terms at first use, and structure paragraphs around a single main idea. The confusion arises when authors use vague language to hedge scientific claims or when they compress complex reasoning into overly long sentences.

A practical approach is to separate the two revision tasks. First, identify what the passage is trying to say at the level of scientific content. Write that content in a plain sentence. Second, rebuild the passage around that plain sentence, adding the necessary qualifications, citations, and technical detail.

This method preserves nuance because you never delete a scientific claim. You only reorganize how the claim is presented. The nuance lives in the qualifications and supporting evidence, not in the sentence structure.

At a Glance: Clarity Comment Response Decision Table

A Systematic Method for Identifying Confusing Sections

Before you can rewrite a confusing passage, you must locate it. Reviewers sometimes identify the exact paragraph or line. Other times they write a general comment about the manuscript. In the latter case, you need a reliable method for finding the passages most likely to confuse a reader.

Read the Manuscript as a First-Time Reader

Print the manuscript and read it without your background knowledge. Mark every sentence where you pause, reread, or feel uncertain about the meaning. These pauses are your best evidence of where a reviewer might struggle.

Pay special attention to the abstract, the methods section, and the discussion. These sections are read most carefully by reviewers and are the most common sites for clarity comments.

Use Reporting Guidelines as a Structural Checklist

The EQUATOR Network maintains a searchable library of reporting guidelines for different study types. These guidelines specify what information should appear in each section of a manuscript and how it should be presented.

When a reviewer says a section is confusing, compare that section against the relevant reporting guideline. The confusion often arises because information is missing, out of order, or presented in a way that does not match reader expectations.

For example, a methods section that describes the statistical analysis before describing the study design will confuse readers who expect the design first. The reporting guideline tells you the expected order, and you can restructure accordingly.

Ask a Colleague to Read the Suspected Passages

A colleague who is not familiar with your specific project can serve as a proxy for the reviewer. Give them the manuscript and ask them to identify any passages they find confusing. Compare their list with the reviewer comments.

This step is especially useful when the reviewer comment is vague. A fresh reader often identifies the same passages that triggered the reviewer's comment, and they can tell you specifically what confused them.

The Rewriting Workflow: From Confusing to Clear

Once you have identified the confusing passages, use a structured workflow to rewrite them. This workflow ensures you address the readability problem without altering the scientific content.

Step 1: Extract the Core Claim

Write one plain sentence that states what the passage is trying to communicate. This sentence should be understandable to a reader with general background in your field. Do not include citations, qualifications, or technical jargon in this step.

For example, if the original passage describes a complex statistical interaction, the core claim might be: "The treatment effect was stronger in younger animals than in older animals."

Step 2: Identify the Reader's Knowledge Gap

Determine what background knowledge the reader needs to understand the core claim. This includes definitions of technical terms, context from earlier in the manuscript, and the rationale for why the finding matters.

List these knowledge elements explicitly. The confusing passage likely assumed the reader already had this knowledge, which is why it failed to communicate.

Step 3: Rebuild the Passage with the Reader's Needs in Mind

Write the revised passage using the core claim as the topic sentence. Then add the necessary context, definitions, and qualifications in a logical order.

A useful structure is:

1. Topic sentence stating the core claim
2. Definition of any technical terms used in the topic sentence
3. Supporting evidence or data that justify the claim
4. Qualifications or limitations that bound the claim
5. Transition to the next point

Step 4: Check for Ambiguity and Jargon

Read the revised passage and circle every word that could have multiple meanings. Replace ambiguous terms with concrete alternatives. Define any technical terms that appear before their first use.

Also check pronoun references. Every "it," "this," and "these" should have an unambiguous antecedent in the same sentence or the immediately preceding sentence.

Step 5: Compare the Revised Passage with the Original

Place the original and revised passages side by side. Verify that every scientific claim in the original appears in the revised version. If you removed a claim, you must have a deliberate reason, such as redundancy or lack of support.

This comparison step protects against the common failure of oversimplifying the science while trying to improve readability.

Writing the Reviewer Response Letter

The response letter is where you demonstrate to the editor and reviewer that you have taken the clarity comment seriously. A well-written response letter can turn a negative review into a positive revision experience.

Structure Each Response with Three Parts

For each clarity comment, structure your response in three parts:

1. Quote the reviewer's comment verbatim
2. Describe the change you made
3. State where the change appears in the revised manuscript

This structure gives the reviewer everything they need to verify your response without hunting through the manuscript.

Show the Before and After Text

For clarity comments, include both the original sentence or paragraph and the revised version in your response letter. This direct comparison is more convincing than a description of what you changed.

The National Library of Medicine's Research Methods Resources provide guidance on clear scientific writing that you can reference when explaining your revision choices.

Explain the Reasoning Behind the Change

Briefly state why the revised version is clearer. For example: "The original sentence buried the main finding in a subordinate clause. The revised version states the finding in the main clause and moves the methodological detail to a following sentence."

This explanation shows the reviewer that you understood the problem, beyond that you made arbitrary changes.

Handle Disagreements Professionally

You may disagree with a reviewer's clarity comment if you believe the passage is already clear. In that case, explain your reasoning politely and show the specific changes you made to address the underlying concern.

The Committee on Publication Ethics Core Practices emphasize that authors should respond to reviewer comments in a professional manner, even when they disagree. Your response letter is a professional document that reflects on your credibility as a researcher.

Common Failure Patterns When Responding to Clarity Comments

Authors often make predictable mistakes when responding to clarity comments. Recognizing these patterns helps you avoid them.

Pattern 1: Defensive Responses

Some authors respond to clarity comments by arguing that the reviewer misunderstood the text. Even when this is true, a defensive response does not improve the manuscript. The reviewer's confusion is evidence that the text can be read in a way you did not intend.

The better response is to revise the text so that the unintended reading is no longer possible. Then explain in the response letter that you revised the passage to prevent the misinterpretation the reviewer identified.

Pattern 2: Superficial Word Changes

Changing a few words without restructuring the passage rarely resolves confusion. If the problem is paragraph structure, word substitution will not fix it. The revised passage must address the structural issue that caused the confusion.

Pattern 3: Removing Scientific Content

Some authors respond to clarity comments by deleting the confusing content entirely. This approach sacrifices scientific nuance to avoid the effort of rewriting. It also invites further reviewer comments about missing information.

The correct approach is to preserve the scientific content and reorganize its presentation. If a passage is confusing because it is too dense, split it into multiple paragraphs instead of deleting the detail.

Pattern 4: Ignoring the Root Cause

A clarity comment about one passage often signals a systemic problem. If the reviewer found one confusing paragraph, other paragraphs may have the same issue. Use the revision process to check the entire manuscript for similar problems, beyond the specific passage the reviewer identified.

Records and Measurements for Tracking Revision Quality

Keeping records of your revision process helps you respond to reviewers systematically and improves your writing over time.

Create a Revision Tracking Table

Build a table with columns for the reviewer comment, the location in the manuscript, the original text, the revised text, and the response letter explanation. This table serves as your working document during revision and as the basis for your response letter.

Measure Clarity Improvements Objectively

Several objective measures can help you assess whether your revision improved clarity:

• Sentence length: Count the number of words per sentence before and after revision. Shorter sentences are generally easier to read, but do not make every sentence short.
• Paragraph length: Check whether each paragraph contains a single main idea. Paragraphs that run longer than half a page often contain multiple ideas.
• Term consistency: Verify that each technical term is used consistently throughout the manuscript. Inconsistent terminology is a common source of confusion.
• Passive voice frequency: Count passive voice constructions. Excessive passive voice can obscure who performed an action, but it is sometimes appropriate in methods sections.

These measures are diagnostic tools, not targets. Use them to identify potential problems, then apply your judgment about whether a change is needed.

Document Your Revision History

Keep a version history of the manuscript with clear file names and dates. This record is useful if the editor asks about the revision process or if you need to refer back to an earlier version.

The National Institutes of Health Grants and Funding resources emphasize the importance of maintaining accurate records throughout the research process. This principle extends to manuscript revision, where your records demonstrate the care you took in responding to reviewer feedback.

Professional Escalation Criteria for Unresolvable Comments

Most clarity comments are resolvable through careful revision. However, some situations require escalation to the journal editor.

When the Reviewer Comment Is Too Vague to Act On

If a reviewer writes "this manuscript is confusing" without identifying any specific passage, you cannot know what to revise. In this case, contact the editor and ask for clarification about which sections the reviewer found confusing.

The editor can either provide more specific guidance or ask the reviewer for additional detail. This request is appropriate and professional, especially when the comment is too general to guide revision.

When the Reviewer Requests Changes That Would Compromise Accuracy

A reviewer might request a simplification that would misrepresent your findings. For example, a reviewer might ask you to remove a qualification that is essential to the correct interpretation of your data.

In this case, you should decline the specific request while offering an alternative revision that addresses the reviewer's underlying concern. Explain in your response letter why the requested change would compromise accuracy and show the alternative you implemented.

When You Suspect a Misunderstanding of the Science

If a reviewer's clarity comment reveals a fundamental misunderstanding of your methods or results, you may need to explain the science more thoroughly in your response letter. This explanation is different from a defensive response because it provides educational context instead of arguing about wording.

The National Library of Medicine's Research Methods Resources can help you identify the best way to explain complex methods to reviewers who may not be specialists in your specific technique.

When Ethical Concerns Arise

If you believe a reviewer's comment raises ethical concerns, such as a request to omit negative results or to present data in a misleading way, consult the Committee on Publication Ethics Core Practices for guidance on handling these situations.

COPE provides resources for authors facing ethical dilemmas in publication. You can also contact the journal editor directly to discuss your concerns.

Safety and Regulatory Context for Clarity in Research Reporting

Clarity in scientific writing is also a matter of reader convenience. It has direct implications for research integrity, reproducibility, and the safe application of research findings.

Clarity Supports Reproducibility

The National Institutes of Health Data Management and Sharing Policy emphasizes the importance of making research methods and data understandable to other researchers. A methods section that is confusing cannot be replicated, which undermines the scientific value of the work.

When you revise a confusing methods section, you are beyond satisfying a reviewer. You are contributing to the reproducibility of your research.

Clarity Prevents Misapplication of Findings

Research findings that are poorly explained can be misapplied by readers who misunderstand the limitations or the conditions under which the findings apply. Clear writing that explicitly states limitations and boundary conditions reduces this risk.

This concern is especially important in clinical research and animal research, where misapplication of findings can have direct consequences for health and welfare.

Clarity Supports Transparent Reporting

The EQUATOR Network promotes transparent and accurate reporting of research studies. Transparent reporting means that readers can understand exactly what was done, what was found, and what the findings mean. Clarity is a prerequisite for transparency.

When you respond to clarity comments by consulting reporting guidelines and restructuring your manuscript, you are aligning your work with the standards of transparent research reporting.

Practical Implementation Steps for Your Next Revision

When you receive a clarity comment on your next manuscript revision, follow these steps in order.

Step 1: Read All Reviewer Comments Before Starting

Read the complete set of reviewer comments before making any changes. This gives you the full picture of the reviewer's concerns and helps you identify patterns across comments.

Step 2: Categorize Each Comment

Sort each comment into categories such as clarity, scientific accuracy, missing information, or structural issues. This categorization helps you plan your revision strategy and ensures you address every comment.

Step 3: Identify the Specific Passages

For each clarity comment, locate the specific passage in the manuscript. If the comment does not identify a location, use the diagnostic methods described earlier to find the likely passage.

Step 4: Apply the Rewriting Workflow

Use the five-step rewriting workflow for each confusing passage. Extract the core claim, identify the reader's knowledge gap, rebuild the passage, check for ambiguity, and compare with the original.

Step 5: Consult Reporting Guidelines

For sections that relate to study design, methods, or results reporting, consult the relevant EQUATOR Network guideline. Use the guideline as a checklist to ensure your revised section includes all required elements in the expected order.

Step 6: Draft the Response Letter

Write the response letter using the three-part structure for each comment. Include before and after text for clarity comments and explain the reasoning behind each change.

Step 7: Verify Completeness

Before submitting your revision, verify that you have addressed every reviewer comment. Use your revision tracking table to check that each comment has a corresponding response and manuscript change.

Step 8: Check the Entire Manuscript for Similar Issues

Use the revision process as an opportunity to check the entire manuscript for similar clarity problems. If the reviewer found one confusing passage, other passages may benefit from the same attention.

Limitations of the Rewriting Approach

The systematic approach described here has limitations that you should recognize.

Reviewer Comments May Not Identify the Real Problem

A reviewer's clarity comment is a symptom report, not a diagnosis. The reviewer may have been confused by a passage for reasons different from the ones you identify. Your revision may resolve the confusion you identified but not the confusion the reviewer experienced.

This limitation is unavoidable. The best you can do is apply sound writing principles and hope the revision addresses the reviewer's concern. If the reviewer remains confused after revision, the editor will typically provide additional guidance.

Clarity Is Subjective

What is clear to one reader may be confusing to another. Your revision cannot satisfy every possible reader. The goal is to write clearly for the target audience of the journal, which is typically researchers with background in the field.

Rewriting Takes Time

A thorough revision that addresses clarity comments properly takes significant time. You must diagnose each problem, rewrite each passage, and document each change. This time investment is justified because it improves the quality of your manuscript and increases the likelihood of acceptance.

Some Confusion Is Inherent in Complex Science

Certain scientific concepts are genuinely difficult to explain clearly. A passage about a complex statistical method or a nuanced biological mechanism may require careful reading even after revision. The goal is not to make every passage easy to read on the first attempt, but to make every passage as clear as the subject matter allows.

Frequently Asked Questions

How do I respond to a reviewer who says my manuscript is confusing but does not specify which part?

Contact the journal editor and ask for clarification about which sections the reviewer found confusing. Explain that you want to address the concern thoroughly but need more specific guidance to do so. Editors can often provide additional detail or ask the reviewer for specific locations.

Should I include the original and revised text in my response letter?

Yes, for clarity comments, include both the original and revised text. This direct comparison shows the reviewer exactly what you changed and allows them to verify the revision without searching through the manuscript. It also demonstrates that you took the comment seriously.

How do I improve clarity without oversimplifying my science?

Separate the scientific content from the presentation. First write a plain sentence stating the core claim. Then rebuild the passage around that claim, adding all necessary qualifications, citations, and technical detail. Compare the original and revised versions to verify that no scientific content was lost.

What reporting guidelines should I use for my manuscript revision?

Consult the EQUATOR Network to find the reporting guideline that matches your study type. The network maintains a searchable library of guidelines for different study designs, including randomized trials, observational studies, systematic reviews, and animal research. Use the relevant guideline as a structural checklist for your revision.

How do I handle a reviewer comment that asks me to remove important scientific nuance?

Decline the specific request while offering an alternative revision that addresses the reviewer's underlying concern. Explain in your response letter why the requested change would compromise scientific accuracy, and show the alternative revision you implemented instead.

What should I do if I disagree with a reviewer's clarity comment?

Explain your reasoning politely in the response letter and show the specific changes you made to address the underlying concern. Even if you believe the original text was clear, you can often find a way to make it clearer. The Committee on Publication Ethics Core Practices emphasize professional communication in peer review interactions.

How can I prevent clarity comments in future submissions?

Write with the reader in mind from the first draft. Use concrete language, define terms at first use, structure paragraphs around a single main idea, and consult reporting guidelines before submission. Ask a colleague to read your manuscript before you submit it and identify any confusing passages.

Is it appropriate to ask a colleague to read my revised manuscript before resubmission?

Yes, this is a good practice. A colleague who is not familiar with your specific project can serve as a proxy for the reviewer. Ask them to read the revised passages and confirm that the confusion has been resolved. This step adds confidence before you resubmit.

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
• Scientific Literature Review: A Reproducible Search and Synthesis Workflow
• Scientific Literature Review Format: A Reproducible Structure for Researchers

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.