Jaime Silva

Many academics might be enthusiastic about the current wave of generative artificial intelligence (GAI), using large language models like ChatGPT or DeepSeek. We show that the reputation of letters to the editor (LTEs), which play important communicative functions in biomedicine recognized by several authors as well as the ICMJE recommendations, is being damaged by the abuse of GAI. There has been a recent surge in LTEs generated by the undeclared use of AI and passed off as human-written. We consider that LTEs should be a forum for human engagement that retain at least two different functions in the age of GAI: to question published conclusions and to generate new ideas. Both of these are essential skills for researchers and clinicians, particularly in their early career. We encourage academics to protect the writing and reading of human LTEs as a forum for human engagement with published research, the empirical facts and the values of medicine. We consider that GAI should only be used for secondary purposes such as editing and translation rather than text generation.

In 2022, a group of 10 international researchers spanning nine countries published an article on the assessment of a Persian version of an interpersonal mindfulness scale (IMS). That article, published in Frontiers in Psychiatry, was retracted on 4 September 2023. The retraction notice cites, as its main factor, abusive authorship practices that have the hallmarks of paper mill engagement. This study aimed to appreciate the literature that has cited that retracted paper. Two years after its retraction, by 1 September 2025, that article has already accumulated 37 citations, according to Google Scholar, Scopus and Web of Science, clustered around two education journals, Hindawi’s (Wiley) Education Research International and Springer Nature’s Language Testing in Asia. These journals cited the retracted article 13 and 5 times, respectively. This paper, while recording the literature that has cited that retracted article, notes that IMS researchers need to be mindful of the literature they cite and rely upon.

It is becoming increasingly common to find papers that are retracted in batches, a phenomenon referred to as mass retractions. These might take place in response to a common event – such as poor editorial handling by a guest editor in a special issue – that compromises the quality of all papers associated with that event. In this paper, a mass retraction is defined as a batch of 15 or more retracted papers, linked temporally or by a specific event. Mass retractions represent a communal mass failure of the system and of stakeholders. Responsible agents should be indicated in retraction notices, which risk become sources of misinformation if essential details are missing. It is also not uncommon to observe disagreement of authors in retraction notices who may feel disenfranchised, especially with journals that claimed peer review as their quality control mechanism. Cases of mass retractions are highlighted, as identified at Retraction Watch. This commentary also questions who are the responsible agents in mass retractions. In addition, a potential risk to journals or publishers that issue mass retractions is noted, namely the possibility that a group of authors – who are essentially clients, and who have all suffered the same fate (i.e., the mass retraction) – might band together and issue a class action lawsuit to seek redress. Frank, open and fair communication by all parties is preferred to collective legal action.

In order for an academic social networking site, like ResearchGate (RG), to be a safe experience for its users, it needs to ensure that it protects them from the presence of fake entities, which present a direct risk to valid users’ safe and enjoyable academic experience. Evidence is provided for the existence of a few accounts of obviously fake and “ghost researchers”, but that must have been created by human entities. Fake “researchers” and accounts with no linkable profile, such as those of “ghost researchers”, should be banned from RG, as they may threaten valid researchers’ positive experience, making it an unsafe platform and an unpleasant social networking experience. Importantly, those accounts are in violation of several of RG’s terms of service.

A retraction notice (RN), at least according to COPE guidance, is meant to be a document that represents transparency. With transparency comes accountability of the agents that are named in the RN. Despite this, while it is not uncommon to see authors’ names listed in RNs, names of editors who are responsible for the editorial decision of retraction may be absent. Their identification is important because editors supposedly oversee the RN’s wording and explicitly approve the issuance and publication of RNs. To gain an initial measure of the presence or absence of editors’ names in RNs, 18 RNs issued by COPE member journals were identified in PubPeer in July and August 2024. The RNs were obtained from the source (i.e., journals’ websites) and examined, noting whether the names of editors are named in RNs, or not. The agreement or disagreement of authors with the retractions and/or the RNs was also noted. Of the 18 RNs examined, all of those from Wiley journals indicated the editors’ name, whereas most other COPE member journals’ RNs did not. Authors’ agreement or disagreement was not indicated in one third of the RNs. The editor responsible for a RN might be the same or different to that when the paper was originally published, so both (where applicable) should be named in the RN. This article posits that the absence of an editor’s name in the RN is problematic from the stand-point of transparency and accountability. A larger and more systematic analysis of a larger body of RNs is warranted.

Kazakhstan, a post-Soviet country that began transitioning its research system from the Soviet model to a Western one, instituted an EU-like, meritocracy-based rewards system for publishing between 2009 and 2012. This resulted in a sharp rise in the number of publications between 2012 and 2020. To complement existing studies, Scopus and Web of Science were sourced (16 February – 1 March 2024) to assess the scientific productivity of affiliations in Kazakhstan, noting that growth rate slowed to 6.1% in 2021, 4% in 2022, and 6.8% in 2023 (relative to an average annual growth rate of 35.3% in 2013–2020). In 2023, 20.4% of those publications were in MDPI journals. Separately, the Scopus-indexed retractions associated with Kazakhstani affiliations were assessed for 2013–2023. The vast majority (26/36) of retractions were related to fake peer review, with 14 in Elsevier’s Thinking Skills and Creativity, and the highest volume was in the 2016–2019 period. Of note, none of the 36 Scopus-indexed retracted papers had an associated institutional email. The emphasis on bibliometric indicators has led to an increase in manipulations and unethical actions by individual authors. These actions were driven by the desire to achieve personal and institutional goals, as well as imperfections in regulatory documents and delayed or hesitant actions of authorizing bodies. The findings of this study offer a unique contemporary perspective of scientific productivity in Kazakhstan while shedding light—through the prism of retractions, paper mills, and “predatory” publishing—on the ethics of the publication process.

Letters to the editor (LTEs) are a versatile short-format forum with unique characteristics to allow for cross-pollination of different kinds of philosophical reflection about medicine. Philosophical LTEs have both benefits and possible drawbacks. We draw on a case study to warn against misuse through “CV inflation,” where low-quality ideas may favor a scholar’s publishing metrics more than scholarly debate. Factual inaccuracies in LTEs have implications for authors, publishing, and indexing, and we argue for prudence by editors and restraint by scholars, inviting them to focus on quality, rather than the quantity of LTEs published. When writing LTEs, rigor, readability, and relevance are needed.

The Directory of Open Access Journals is a leading whitelist of open access journals, that is, OAJs that are presumably safe to publish in, or scholarly, because they follow best practices established by COPE/DOAJ/OASPA/WAME. Academics rely on the DOAJ to select OAJs of choice, and filter for particular needs, for example, English-only or no article processing charges. A search of DOAJ-indexed OAJs publishing work on ornamental research identified five OAJs, but 60% of them had incorrect and thus misleading information. The ‘last update’ of all five OAJs were outdated. The DOAJ must ensure that indexed OAJs have updated information. The Editors of OAJs also bear responsibility.

The International Committee of Medical Journal Editors (ICMJE) guidelines are widely employed as an set of ethical standards for biomedical journals, and thus for biomedical researchers. In this paper, we revisit the topic of acknowledgements in academic papers, noting that the former serve as a lesser form of recognition relative to authorship. We note the possible existence of bias, such as a power imbalance due to a status imbalance, as well as the risk of “ghost” acknowledgements. To further ground our ideas, we turned to ChatGPT-4 for input, noting some curious and informative supplementary findings. Curiously, ChatGPT-4 offered a set of recommendations and guidance, comparable to those of the ICMJE.

Keywords: accountability—corrigendum—erratum—ethics—retraction The past three to four years has seen—as far as can be perceived—what appears to be an increase in retractions, possibly due to an increase in awareness. This awareness relates to the issues underlying science publishing, whether these involve authorship issues, publisher-related ethics, or what appears to be an explosion in open access journals, which is making more science more visible to a wider audience. This aspect in itself is an extremely positive development, and we have only to thank the freedom of the Internet and the existence of increasingly global databases, some of which are publisher-controlled, for creating this wider perspective on science and science publishing. However, like anything in life, or society, with such openness comes a darker side. The issue of revelations and anonymous whistle-blowing are all aspects of science publishing that may have been poorly discussed even as little as 5 or 10 years ago. Now, with tools such as Retraction Watch and other blogs that allow for greater awareness and interaction about publishing, and sites like PubPeer or PubMed Commons, which allow for a more frank and open discussion of the issues surrounding individual papers or topics, science publishing has, without a doubt, entered a new era of debate, and scrutiny. Those who do not observe this change, who find it insipid, or who wish to ignore it, ultimately risk becoming its victims. This increase in awareness has also drawn the attention and focus to research misconduct, including duplications, plagiarism, and even the issue of fake peer reviews, and pseudo-scientific journals or paid-for authorship. These are issues that affect all scientists and that have now become the centerpiece of science publishing. Thus, greater awareness, and acceptance, of these issues is required.

In 2015, the Retraction Watch leadership, Adam Marcus and Ivan Oransky, retracted an article that they had written for The Lab Times in 2013. According to Marcus and Oransky, in the 2013 piece, they had offered “bad advice” to academics. In the 2013 piece, Marcus and Oransky suggested that when an error, actual or potential, was detected in a published paper, that they should first contact – by name or anonymously – the editor, then the author, and finally the research institute, following Committee on Publication Ethics guidelines. They also recommended readers to copy Retraction Watch on their communications – most likely so that Retraction Watch could gather a scoop – suggesting even that by mentioning or copying Retraction Watch would twist the arm of the editor, and perhaps speed up – or influence – the journal’s action, or decision. Offering such bad, flawed and unscholarly advice, claiming boldly, without any citations “that cronyism can protect obvious fraud”, the 2013 Lab Times piece was a clear act of antiscience advice. Clearly recognizing their own bad advice, and flawed and misleading logic, but taking considerable time to do so, Adam Marcus and Ivan Oransky retracted their 2013 article in December of 2015, but replaced it with a substitute offering even worse advice, indicating to concerned academics to scrap their 2013 advice of contacting authors, editors and academic institutes, and opting instead for a potentially biased anonymous option, using a whistle-blower website, PubPeer. Marcus and Oransky failed to indicate any financial or other conflicts of interest in their Lab Times piece. This is important, because, as we now know, the marriage between these watchdogs has been in the pipe-line for years now, reaching public prominence in early 2016 during a meeting in UC Berkeley, and culminating in generous financial backing – in the hundreds of thousands of US$ – by the Laura and John Arnold Foundation, to both Retraction Watch and PubPeer. This commentary examines how the retraction of one badly written journalistic piece for lack of professionalism led to the emergence of an even worse article full of biases. Perspectives on how this could be interpreted, and what should happen, are provided.

Many journals and publishers employ online submission systems to process manuscripts. In some cases, one “template” format exists, but it is then molded slightly to suit the specific needs of each journal, a decision made by the editor-in-chief or editors. In the past few years, there has been an increase in the number of cases in which OSSs have been abused, mostly by the authorship, either through the creation of fake identities or the use of false e-mail accounts. Although the abusive or fraudulent authors are at fault in such cases, the fact that such cases remained undetected for so long is of concern. Moreover, the current OSSs are imperfect, have security issues and may not be able to detect false information, except through post-submission verification. Sting operations, which involve the submission of false manuscripts with false identities and false affiliations, are no less unethical, and those who abuse the publishing protocol deserve to be as reprimanded as those who abuse OSSs. Finally, I question the ethics of editors or publishers creating OSS accounts on behalf of reviewers prior to obtaining their explicit permission. doi: 10.5294/pebi.2016.20.2.3.

The natural instinct for members of the Committee on Publication Ethics, which now number almost 12,200, as well as academia, is to assume that this organization works under strict and clearly defined ethical parameters, with a solid vision, and an independent mandate that is not influenced by power, think tanks, or partisan interests. Naturally, whistle-blowing and science shaming are not practices that one would usually associate with an ethics organization like COPE, because they involve ethically and morally questionable practices. Despite this, ethical borders have become blurred between the objectives of Retraction Watch and PubPeer, two self-moderated science watchdogs that rely heavily on these questionable practices, in their efforts to grow and survive, and the values espoused by COPE. A Retraction Watch post, in which the former COPE Chair, Virginia Barbour, made a claim of apparent harassment, is the most striking example of the dangers when collaboration may take place between science-shaming websites, and an ethics organization, COPE. These bonds appear to have been in development for a number of years already, with the inclusion of Elizabeth Wager, the former COPE Chair, as a director of The Center for Science Integrity Inc., Retraction Watch’s parent organization. Retraction Watch was financed by, among other groups, the Laura and John Arnold Foundation, whose leader, John Arnold, an ex-Enron trader, declared a “war on bad science”, which may naturally include the destruction of aspects of science as well. Retraction Watch embraces several infamous pseudonymous personas under the broad umbrella of freedom of speech, liaising thereby with PubPeer. There is no doubt that errors in the literature need correcting, but this apparent connection with COPE raises questions about the basic ethical foundation of this relationship. Are scientists to embrace this bond between COPE and science watchdogs and pseudonymous whistle-blowers as the new normal in the correction of the scientific literature? This opinion piece puts forward arguments why the author believes that the ethical compass of COPE has become skewed.

As a continued theme in citation abuses and the need to reform the culture of citation in academic publishing, as well as an extension of the exploration of authors’ rights, this letter highlights a case in which an author’s name was abused in a fabricated citation in a preprints.org preprint that was ultimately retracted. As a punitive measure, the preprints’ authors were blacklisted. The first author then republished (minus the previous co-authors) a modified preprint at another preprint server, Research Square, where it was also retracted for the presence of fictitious citations. In such cases, it is argued that authors whose names are abused in fictitious citations, created by ChatGPT or otherwise, as identified by real authors or the paper’s readers, should have the right to not want to be cited in this manner, because it may carry with it negative reputational consequences. There are also negative reputational consequences for journals which appear in fictional citations.

The ‘publish or perish’ culture has induced an unhealthy aspect of academic publishing in the biomedical sciences, namely of illegitimate authorship. Such a position can be obtained when an authorship slot is offered as a gift (e.g., to a sponsor, or researcher in a senior position), without their intellectual or scientific participation, or it can be hidden (ghost authorship), in which the paper (or parts thereof) is written by a third party (individual, or company). In a more industrialized setting, ghost authorship takes place via the sale of papers using “paper mills”, including of specific author slots (i.e., positions in a line of authors). While author-based persistent identifiers like ORCID, or authorship attribution schemes like CRediT, sound noble and offer some form of validation, those systems still operate on a culture of blind trust (in submitting authors). This paper debates a few of the authorship-related issues currently plaguing biomedical journals.

Medical practitioners and healthcare workers rely on information accuracy in academic journals. Some Covid-19 papers contain “tortured phrases”, nonstandard English expressions, or imprecise or erroneous terms, that give the impression of jargon but are not. Most post-publication attention paid to Covid-19 literature has focused on the accuracy of biomedical aspects, the validity of claims, or the robustness of data, but little has been published on linguistic specificity. This paper highlights the existence of “tortured phrases” in select Covid-19 literature, arguing that they could serve as a class of epistemic marker when evaluating the integrity of the scientific and biomedical literature.

Academic publishing is undergoing a highly transformative process, and many established rules and value systems that are in place, such as traditional peer review (TPR) and preprints, are facing unprecedented challenges, including as a result of post-publication peer review. The integrity and validity of the academic literature continue to rely naively on blind trust, while TPR and preprints continue to fail to effectively screen out errors, fraud, and misconduct. Imperfect TPR invariably results in imperfect papers that have passed through varying levels of rigor of screening and validation. If errors or misconduct were not detected during TPR’s editorial screening, but are detected at the post-publication stage, an opportunity is created to correct the academic record. Currently, the most common forms of correcting the academic literature are errata, corrigenda, expressions of concern, and retractions or withdrawals. Some additional measures to correct the literature have emerged, including manuscript versioning, amendments, partial retractions and retract and replace. Preprints can also be corrected if their version is updated. This paper discusses the risks, benefits and limitations of these forms of correcting the academic literature.

Purpose Whistle-blowing, which has become an integral part of the post-publication peer-review movement, is being fortified by social media. Anonymous commenting on blogs as well as Tweets about suspicions of academic misconduct can spread quickly on social media sites like Twitter. The purpose of this paper is to examine two cases to expand the discussion about how complex post-publication peer review is and to contextualize the use of social media within this movement. Design/methodology/approach This paper examines a Twitter-based exchange between an established pseudonymous blogger and science critic, Neuroskeptic, and Elizabeth Wager, the former COPE Chair, within a wider discussion of the use of social media in post-publication peer review. The paper also discusses false claims made on Twitter by another science watchdog, Leonid Schneider. The policies of 15 publishers related to anonymous or pseudonymous whistle-blowing are examined. Findings Four issues in the Neuroskeptic–Wager case were debated: the solicitation by Wager to publish in RIPR; the use of commercial software by Neuroskeptic to make anonymous reports to journals; the links between “publication ethics” leaders and whistle-blowers or pseudonymous identities; the issues of transparency and possible hidden conflicts of interest. Only one publisher (Wiley) out of 15 scientific publishers examined claimed in its official ethical guidelines that anonymous reports should be investigated in the same way as named reports, while three publishers (Inderscience, PLOS and Springer Nature) referred to the COPE guidelines. Originality/value No such Twitter-based case has yet been examined in detail in the publishing ethics literature.

As part of a continuous process to explore the factors that might weaken or corrupt traditional peer review, in this paper, we query the ethics, fairness and validity of the request, by editors, of authors to suggest peer reviewers during the submission process. One of the reasons for the current crisis in science pertains to a loss in trust as a result of a flawed peer review which is by nature biased unless it is open peer review. As we indicate, the fact that some editors and journals rely on authors’ suggestions in terms of who should peer review their paper already instills a potential way to abuse the trust of the submission and publishing system. An author-suggested peer reviewer choice might also tempt authors to seek reviewers who might be more receptive or sympathetic to the authors’ message or results, and thus favor the outcome of that paper. Authors should thus not be placed in such a potentially ethically compromising situation, especially as a mandatory condition for submission. However, the fact that they do not have an opt-out choice during the submission process—especially when using an online submission system that makes such a suggestion compulsory—may constitute a violation of authors’ rights.

Retractions of COVID-19 literature in both preprints and the peer-reviewed literature serve as a reminder that there are still challenging issues underlying the integrity of the biomedical literature. The risks to academia become larger when such retractions take place in high-ranking biomedical journals. In some cases, retractions result from unreliable or nonexistent data, an issue that could easily be avoided by having open data policies, but there have also been retractions due to oversight in peer review and editorial verification. As COVID-19 continues to affect academics and societies around the world, failures in peer review might also constitute a public health risk. The effectiveness by which COVID-19 literature is corrected, including through retractions, depends on the stringency of measures in place to detect errors and to correct erroneous literature. It also relies on the stringent implementation of open data policies.

This paper explores that the topic of ethics dumping, its causes and potential remedies. In ED, the weaknesses or gaps in ethics policies and systems of lower income countries are intentionally exploited for intellectual or financial gains through research and publishing by higher income countries with a more stringent or complex ethical infrastructure in which such research and publishing practices would not be permitted. Several examples are provided. Possible ED needs to be evaluated before research takes place, and detected prior to publication as an academic paper, because it might lead to a collaborative effort between a wealthier country with restrictive ethical policies and a less wealthy country with more permissive policies. Consequently, if that collaboration ultimately results in an academic paper, there are ethical ramifications of ED to scholarly communication. Institutional review board approval is central to avoid ED-based collaborations. Blind trust and goodwill alone cannot eliminate the exploitation of indigenous or “vulnerable” populations’ intellect and resources. Combining community-based participatory research using clear codes of research conduct and a simple but robust verification system in academic publishing may reduce the risks of ED-based research from being published.

PurposeThe issue of “predatory” publishing and the scholarly value of journals that claim to operate within an academic framework, namely, by using peer review and editorial quality control, but do not, while attempting to extract open access (OA) or other publication-related fees, is an extremely important topic that affects academics around the globe. Until 2017, global academia relied on two now-defunct Jeffrey Beall “predatory” OA publishing blacklists to select their choice of publishing venue. This paper aims to explore how media has played a role in spinning public impressions about this issue.Design/methodology/approachThe authors focus on a 2017New York Timesarticle by Gina Kolata, on a selected number of peer reviewed published papers on the topic of “predatory” publications and on an editorial by the Editor-in-Chief ofREM, a SciELO- and Scopus-indexed OA journal.FindingsThe Kolata article offers biased, inaccurate and potentially misleading information about the state of “predatory” publishing: it relies heavily on the assumption that the now-defunct Beall blacklists were accurate when in fact they are not; it relies on a paper published in a non-predatory (i.e., non-Beall-listed) non-OA journal that claimed incorrectly the existence of financial rewards by faculty members of a Canadian business school from “predatory” publications; it praised a sting operation that used methods of deception and falsification to achieve its conclusions. The authors show how misleading information by theNew York Timeswas transposed downstream via theREMeditorial.Originality/valueEducation of academics.

In this opinion piece, some of the practices of academic publication in the biomedical field related to the rewarding, or the lack thereof, of peer reviewers are described and discussed. The role and possibly exploitative relationship of mainstream, established publishers of prestigious journals towards their contributors (authors), and peer reviewers is considered. In addition, the role and accountability of publishers and contributors in “predatory” journals is assessed. Professionals who are recruited by the publishing industry, especially the for-profit industry, either as peer reviewers or editors, to complete a professional task, should be rewarded financially as professionals, as for other sectors of the economy, and not simply exploited for free. Points systems or discounts off a publisher’s products do not constitute sufficient, or fair, compensation.

The blogosphere is full of personalities with masks, or pseudonyms. Although not a desired state of public communication, one could excuse the use of pseudonyms in blogs and social media, which are generally unregulated or weakly regulated. However, in science publishing, there are increasingly strict rules regarding the use of false identities for authors, the lack of institutional or contact details, and the lack of conflicts of interest, and such instances are generally considered to be misconduct. This is because these violations of publishing protocol decrease trust and confidence in science and bring disrepute to those scientists who conform to the rules set out by journals and publishers and abide by them. Thus, when cases are encountered where trust and protocol in publishing are breached, these deserve to be highlighted. In this letter, I focus on Neuroskeptic, a highly prominent science critic, primarily on the blogosphere and in social media, highlighting the dangers associated with the use of pseudonyms in academic publishing.