Peer review is the fundamental method of quality control in research. The term “peer” means “an equal.” Peer review is the system whereby researchers are evaluated by each other in the same general field.

Peer review plays a vital role in deciding on acceptance or rejection of papers and oral presentations, approval or rejection of funding applications, appointment and promotion of researchers, and the evaluation of research institutes and academic departments.

Peer review is a system by which the research community can collectively govern itself. Many ethical issues arise in peer review, but the basic principles are that reviewers (sometimes also called referees) must treat all information obtained in the peer review process as confidential, and that they must behave with integrity as responsible, professional scientists. The use of information obtained from these sources for one’s own research or grant application is one form of research misconduct, plagiarism. When in doubt about any ethical issues that might arise during the review process, reviewers should promptly contact the requestor (editor or funding agency) and request guidance.

• Be able to explain the basics of peer review of scientific papers and funding applications
• Be able to explain the types of ethical issues that might arise in the review process
• Be able to explain how reviewers should cope with such issues
• Be able to explain the issues facing the peer review system at present

Peer review is the primary method for research communities to ensure quality control for published journal articles and make decisions on funding applications. At present, one of the important roles of peer review is assuring the credibility of research.

In order for the system to work, all researchers must be willing to do careful reviews, in a timely fashion, when requested to do so. Of course, in cases where they’re temporarily too busy to do the review within the stated deadline, it’s better for researchers to decline the request rather than accept the assignment but then fail to perform the review by the deadline.

Of course, peer review isn’t perfect. Some argue that peer review has only limited impact on the quality of publications and might block highly innovative (but unorthodox) work from being funded or published. But there is no practical alternative to some form of peer review (although various alternatives to the traditional system have been proposed and in some cases are being implemented). Without peer review scientific journals would be filled by poor-quality papers that would obscure good research. And without peer review (imperfect though it may be) there would be no way to fund good research proposals while rejecting lower quality projects.

There are three main types of peer review of scientific papers.

1. Open review refers to the case where reviewers and authors know each other’s identity
2. Single-blind review refers to the case where the reviewer knows the identity of the author, but the reviewer’s identity is not revealed to the author. This type of review is widely used in many fields. If permitted by the journal’s rules (in some cases the editor’s permission may be required) reviewers may choose to reveal their identity to the author.
3. Double-blind review refers to the case where neither the author nor the reviewer knows the other’s identity

A relatively new form of what is, in a broad sense, peer review, namely uploading submitted manuscripts onto a preprint server when they are submitted for publication in a journal, has become widespread. This allows all researchers to read and comment on submitted manuscripts at the same time as the journal’s reviewers. bioRχiv is the main preprint server for biomedical science.

In the peer review process conducted by journals, reviewers are expected to submit their professional, objective, and independent comments. Therefore, it is not acceptable for reviewers to refer to comments posted on these preprint servers.

Reviews of papers submitted to journals and of grant applications use differing review criteria. Journals usually request reviews from experts on the paper’s subject matter. The main criteria considered by the reviewers are the following:

• Whether the article falls within the scope of the journal
• Whether the research is original and significant
• Validity of the methodology
• Whether or not strong evidence supports the conclusions
• Whether the article is well organized and well written
• Whether or not there are any research-ethics issues

Reviewers are asked to advise the editor on the decision regarding the article. The choices usually include: 1) acceptance, 2) minor revision, 3) major revision, and 4) rejection.

Editors make their decisions on the basis of the reviewer’s recommendations. In the event of disagreement, editors may request additional reviews or consult with other members of the editorial board.

The possible decisions on a submitted paper vary somewhat. Some journals also have a category, “moderate revision,” halfway between 2) and 3), above. Some also divide rejection into “rejection with encouragement to resubmit” and “outright rejection.”

Reviewers are expected to honor the confidentiality of manuscripts. They must disclose conflicts of interest to the journal before the review begins and behave professionally and with integrity throughout the peer review process. It is appropriate to decline peer review if there is a concern that you lack the necessary knowledge or that there may be bias in your evaluation.

Peer review of grant applications is widely used by government and private organizations to make funding decisions. The aim is to remove bias and favoritism, and to strive to allocate funding to the most meritorious proposals. Funding applications are typically judged on the following criteria:

• Importance of the research
• Soundness and originality of the methods
• The research to date of the principal investigator(s) and co-investigator(s) and their appropriateness to conduct the proposed research
• Likelihood that the research plan can be successfully carried out
• The percentage of effort to be devoted to the proposed work by the principal investigator(s) and co-investigator(s)
• Appropriateness of the data presented in support of the proposal
• Whether the amount of funding requested is reasonable
• The potential benefits to society of the proposed work

Individuals who review manuscripts submitted for publication and decisions on funding applications must strictly adhere to ethical standards. One example typifying current international standards is “Ethical Guidelines to Publication of Chemical Research,” (first published 2015, revised October 2021) of the American Chemical Society (ACS) [1]. These ethics guidelines, which include the content discussed in the following section, share basic concepts that are usually also applied when reviewing research grant applications.

Integrity is necessary and indispensable in peer review. Strict adherence to ethical guidelines is required in reviews of papers and proposals.

Peer reviewers must treat manuscripts as confidential; they should not share a submitted manuscript or grant proposal with any other person without the permission of the entity that requested the review. Also, Information from papers under review may not be used by reviewers before the papers are published, unless permission is received. For example, if a professor wants to have someone assist with a manuscript review, the professor must receive permission from the editor before sharing the manuscript with them. In this case, “someone” include not only students and researchers in the same laboratory, but also researchers who are considered more qualified than you. After the review is complete, appropriate document destruction procedure should be followed.

The ACS forbids reviewers to communicate directly with authors; reviewers may reveal their identity to the author only with the editor’s permission, but rules of many other publishers could vary regarding this point. Reviewers should respect the rules of the journal that requested the review.

Before accepting a review request, researchers should decide whether or not they have sufficient knowledge of the subject matter. If they are unsure, they should discuss the matter with the journal editor or grant officer before accepting the review request.

Sometimes it is important for the requestor to receive a review from a critical point of view, but reviewers should never make personal criticisms of authors or grant applicants.

Fairness in the review process means treating one individual’s grant proposal or manuscript submission in the same way as work from any other person. Adhering to a consistent process for reviewing journal articles or grant proposals is essential in fostering the confidence that transparent and appropriate criteria are being used. Being overly critical of work close to the reviewer’s must be avoided, and timeliness in completing reviews is essential.

Some fields may be so small that (even if reviews are theoretically double-blind) the reviewers can identify the author or funding applicant. In such cases reviewers might be motivated to give unduly positive reviews; this, too, must be avoided. Maintaining objectivity in the review process is helped by reviewers refraining from divulging their identities to authors or grant applicants, at least until an appropriate time interval has passed.

Journals commonly ask authors to specify a list of a few (say 5) candidate referees and their e-mail addresses at the time they submit their paper for publication (as well as, sometimes, a list of potential reviewers they would prefer to avoid). However, the final decision on the reviewers is made solely by the editor.

Appropriate selection of peer reviewers by a journal’s editor or by grant officers at funding agencies is essential to maintaining the fairness of the review system. Depending on who is selected, the review results can vary greatly. Therefore, the integrity through review process is important. Also, knowledge and understanding of the research field is also essential when selecting reviewers.

The peer review process is based on the premise that reviewers should have no conflicts of interest (COI). However, in the event that there is some relationship between the reviewers and the author (or funding applicant), taking steps to minimize or eliminate the effects of conflicts of interest is essential, recognizing that it may be very difficult to completely eliminate conflicts of interest.

Reviewers should fully inform journals and funding agencies regarding possible or actual financial or other conflicts of interest when they receive a review request. The editor or program officer can then decide whether they should still do the review or whether they will withdraw the review request.

The American Chemical Society (ACS) recommends that possible conflicts of interest be dealt with as follows:

• “A reviewer should be sensitive to the appearance of a conflict of interest when the manuscript under review is closely related to the reviewer’s work in progress or published.
• “If in doubt, the reviewer should return the manuscript promptly without review, advising the editor of the conflict of interest or bias.
• “Alternatively, the reviewer may wish to furnish a signed review stating the reviewer’s interest in the work, with the understanding that it may, at the editor’s discretion, be transmitted to the author.
• “A reviewer should not evaluate a manuscript authored or co-authored by a person with whom the reviewer has a personal or professional connection if the relationship would bias judgment of the manuscript.”[1]

Imagine a following hypothetical case. Dr. X, a member of the Board of Directors of the Japan Kidney Society, is an expert on collagen diseases of the kidney. Dr. X received a manuscript for review from the International Journal of Kidney Studies. The manuscript describes a series of new findings in patients with lupus nephritis, a special form of collagen disease of the kidney. The findings argue against a theory that Dr. X became famous for. Dr. X believes that there is no one better qualified to review the paper and that they can make a fair judgement, and therefore accepted the invitation to review the paper.

　What do you think about the way Dr. X handled this matter?

1. Because Dr. X has a conflict of interest, Dr. X should have declined the review request.
2. Dr. X should have declined the review request and recommended another expert in this field to the editor as a candidate reviewer.
3. Review it, while making sure not to make negative comments about the author.
4. Review it as sincerely as possible and tell the editor about their conflict of interest.

Authors may sometimes think that there have been clearly unfair or inappropriate reviews of their manuscripts or funding applications. In such cases, they can contact the journal editor or program officer to request reconsideration of the decision. Such appeals should only be made in very serious cases after checking with trusted colleagues to confirm one’s judgment. In some cases, possibly after further review, if the manuscript and the appeal are considered to be meritorious, reconsideration of the unfavorable decision may be possible.

In the event readers have substantive criticisms of a published article, most scholarly journals allow these criticisms to be published as letters to the editor or commentaries. Such critical comments are subject to peer review; if accepted they are published in the journal as papers. The authors of the criticized paper can publish a reply, provided it passes peer review.

In recent years a new way to make public criticisms of published papers has been developed: critics can make their comment public on third-party websites, such as PubPeer. Such criticism is sometimes called “post-publication peer review,” as in a broad sense this is a new form of peer review. Researchers making criticisms of published work in either traditional forums or on websites such as PubPeer should act responsibly regarding both the contents and wording of their remarks.

Many journals ask authors to submit names and email addresses of up to five potential referees when they submit an article for publication. These are only suggestions, and the editor is free to use them or not. In a few recent cases, dishonest authors created fake email accounts under the author’s own control. For example, rather than the potential reviewer’s (say, Prof. Taro Yamada) actual email address (for example, Taro.yamada@xxuniversity.ac.jp), the author created a fake email account (for example, Taro.yamada@xxmail.com) and submitted this to the editor as the email address of the potential referee. When the editor asks Professor Yamada for a review, this request goes to the fake email account controlled by the author who then submits a review of their own article. When such malicious conduct is discovered, the articles will be retracted and the author will be subject to disciplinary action.

Authors, funding applicants, reviewers, editors, and program officers must all behave responsibly for the peer review process to work effectively. Maintaining the confidence of research communities and the public in the integrity and reliability of peer review is essential to our present system for conducting research.