Showing posts with label special issues. Show all posts
Showing posts with label special issues. Show all posts

Monday, 23 December 2024

Finland vs. Germany: the case of MDPI

It's been an odd week for the academic publisher MDPI. On 16th December, Finland's Publication Forum (known as JUFO) announced that from January 2025 it was downgrading its classification of 271 open access journals to the lowest level, zero. By my calculations, this includes 187 journals from MDPI and 82 from Frontiers, plus 2 others. This is likely to deter Finnish researchers from submitting work to these journals, as the rating indicates they are of low quality. As explained in an article in the Times Higher Education, JUFO justified its decision on the grounds that these journals “aim to increase the number of publications with the minimum time spend for editorial work and quality assessment”. 

Then the very next day, 17th December, MDPI announced that it had secured a national publishing agreement with ZB Med, which offered substantial discounts to authors from over 100 German Universities publishing in MDPI journals. On Bluesky, this news was not greeted with the universal joy that ZB Med might have anticipated, with comments such as "an embarrassment", "shocking", and "a catastrophe".

To understand the background, it's worth reading a thread on Bluesky by Mark Hanson, one of the authors of a landmark paper entitled "The Strain on Scientific Publishing". This article showed that MDPI and Frontiers stand out from other publishers in terms of having an exponential growth in number of papers published in recent years, a massive shift to special issues as a vehicle for this increase, and a sharp drop in publication lag from 2016 to 2022.

In their annual report for 2023, MDPI described annualised publication growth of 20.4%. They stated that they have over 295,693 academic editors on editorial boards, and a median lag of 17 days from receipt of a paper to the first editorial decision and 6 weeks from submission to publication. It's not clear whether the 17 day figure includes desk rejections, but even if it does, this is remarkably fast. Of course, you could argue (and I'm sure the publishers will argue) that if you are publishing a lot more and doing it faster, you are just being efficient. However, an alternative view, and one that is apparently held by JUFO, is that this speedy processing goes hand in hand with poor editorial quality control.

The problem here is that anyone who has worked as a journal editor knows that, while a 17 day turnaround might be a good goal to aim for, it is generally not feasible. There is a limited pool of experts who can do a thorough peer review, and often one has to ask as many as 20 people to do a review in order to achieve 2 or 3 reviews. So it can take at least a couple of weeks to secure reviewers, and then it is likely to be another couple of weeks before all reviewers have completed a comprehensive review. Given these constraints, most editors would be happy if they could achieve a median time to first decision of 34 days - i.e. double that reported by MDPI. So the sheer speed of decision making - regarded by MDPI as a selling point for authors - is a red flag.

It seems that speed is achieved by adopting a rather unorthodox process of assigning peer reviewers, where the involvement of an academic editor is optional: "At least two review reports are collected for each submitted article. The academic editor can suggest reviewers during pre-check. Alternatively, MDPI editorial staff will use qualified Editorial Board members, qualified reviewers from our database, or new reviewers identified by web searches for related articles." The impression is that, in order to meet targets, editorial staff will select peer reviewers who can be relied upon to respond immediately to requests to review.

A guest post on this blog by René Aquarius supported these suspicions and further suggested that reviewers who are critical may be sidelined. After writing an initial negative review, René had promptly agreed to review a revision of a paper, but was then told his review was not needed - this is quite remarkable, given that most editors would be delighted if a competent reviewer agreed to do a timely re-review. It's worth looking not just at René's blogpost but also the comments from others, which indicate his experience is not unique.

A further issue concerns the fate of papers receiving negative reviews. René found that the paper he had rejected popped up as a new submission in another MDPI journal, and after negative reviews there, it was published in a third journal. This raises questions about MDPI's reported rejection rate of around 50%. If each of these resubmissions was counted as a new submission, the rejection rate would appear to be 66%, but given that the same paper was recycled from journal to journal before eventual acceptance, the actual rate was 0%. 

One good thing about MDPI is that it gives authors the option of making peer review open. However, analysis of published peer reviews further dents confidence in the rigour of the peer review process. A commentary in Science covering the work of Maria Ángeles Oviedo García noted how some MDPI peer reviews contained repetitive phrases that suggested they were generated by a template. They were superficial and did not engage seriously with the content of the article. In some cases the reviewer freely admitted a lack of expertise in the topic of the article, and in others, there was evidence of coercive citation (i.e., authors being told to cite the work of a specific individual, sometimes the editor).

Comments on Reddit cannot, of course, be treated as hard evidence, but they raise further questions about the peer review process at MDPI. Several commenters described having recommended rejection as a peer reviewer only to find that the paper was published without their comments. If negative peer review comments are selectively suppressed in the public record, this would be a serious breach of ethical standards by the publisher.

Lack of competent peer review and/or editorial malpractice is also suggested by the publication of papers in MDPI that fall well below the threshold of acceptable science. Of course, quality judgements are subjective, and it's common for researchers to complain "How did this get past peer review?" But in the case of MDPI journals, one finds articles that are so poor that they suggest the editor was either corrupt or asleep on the job. I have covered some examples in previous blogposts, here, and here.

The Finns are not alone in being concerned about research quality in MDPI journals. The Swiss National Science Foundation did not mention specific publishers by name, but in November 2023 they withdrew funding for articles published in special issues. Since 2023, the Directory of Open Access Journals has withdrawn 19 MDPI journals from its index for "Not adhering to best practice". Details are not provided, but these tend to be journals where guest editors have used special issues to publish a high volume of articles by themselves and close collaborators - another red flag for scientific quality. Yet another issue is citation manipulation, where editors or peer reviewers demand inclusion of specific references in a revision of an article in order to boost their own citation count. In February 2024, China released its latest Early Warning List of journals that are deemed to be "untrustworthy, predatory or not serving the Chinese research community’s interests". This included four MDPI journals listed for citation manipulation.

A final red flag about MDPI is that it seems remarkably averse to retracting articles. Hindawi publishing, which was bought by Wiley in 2021, was heavily criticised for allowing a flood of paper-milled articles to be published, but it did subsequently retract over 13,000 of them (just under 5% of 267K articles), before the closure of the brand. A search on Web of Science for documents classified as "retracted publication" or "retraction" and published by "MDPI or MDPI Ag" turned up a mere 582 retractions since 2010, which amounts to 0.04% of the 1.4 million articles listed on the database.

I've heard various arguments against JUFO's action, such as: many papers published in MDPI journals are fine; you should judge an article by its content, not where it is published; authors should be free to prefer speed over scrutiny if they wish. The reason why I support JUFO, and think ZB Med is rash to sign an agreement, is because if the peer review process is not managed by experienced and respected academic editors with specialist subject knowledge, then we need to consider the impact, not just on individual authors, but on the scientific literature as a whole. If we allow trivia, fatally flawed studies or pseudoscience to be represented as "peer-reviewed" this contaminates the research literature, with adverse consequences for everyone.

Wednesday, 4 September 2024

Now you see it, now you don't: the strange world of disappearing Special Issues at MDPI

 

There is growing awareness that Special Issues have become a menace in the world of academic publishing, because they provide a convenient way for large volumes of low quality work to be published in journals that profit from a healthy article processing charge. There has been a consequent backlash against Special Issues, with various attempts to rein them in. Here I'll describe the backstory and show how such attempts are being subverted. 

Basically, when it became normative for journals to publish open access papers in exchange for an article processing charge, many publishers saw an opportunity to grow their business by expanding the number of articles they published. There was one snag: to maintain quality standards, one requires academic editors to oversee the peer review process and decide what to publish. The solution was to recruit large numbers of temporary "guest editors", each of whom could invite authors to submit to a Special Issue in their area of expertise; this cleverly solved two problems at once: it provided a way to increase the number of submissions to the journal, and it avoided overloading regular academic editors. In addition, if an eminent person could be persuaded to act as guest editor, this would encourage researchers to submit their work to a Special Issue.

Problems soon became apparent though. Dubious individuals, including those running paper mills, seized the opportunity to volunteer as guest editors, and then proceeded to fill Special Issues with papers that were at best low quality and at worse fraudulent. As described in this blogpost, the publisher Wiley, was badly hit by fallout from the Special Issues programme, with its Hindawi brand being 'sunsetted' in 2023 . In addition, the Swiss National Science Foundation declared they would not fund APCs for articles in Special Issues, on the grounds that the increase in the number of special issues was associated with shorter processing times and lower rejection rates, suggestive of rushed and superficial peer review. Other commentators noted the reputational risks of overreliance on Special Issues.

Some publishers that had adopted the same strategy for growth looked on nervously, but basically took the line that the golden goose should be tethered rather than killed, introducing various stringent conditions around how Special Issues operated. The publisher MDPI, one of those that had massive growth in Special Issues in recent years, issued detailed guidelines.

One of these concerned guest editors publishing in their own special issues. These guidelines have undergone subtle changes over time, as evidenced by these comparisons of different versions (accessed via Wayback Machine):
JUNE 2022: The special issue may publish contributions from the Guest Editor(s), but the number of such contributions should be limited to 20%, to ensure the diversity and inclusiveness of authorship representing the research area of the Special Issue.... Any article submitted by a Guest Editor will be handled by a member of the Editorial Board.

 21 JAN 2023: The special issue may publish contributions from the Guest Editor(s), but the number of such contributions should be limited, to ensure the diversity and inclusiveness of authorship representing the research area of the Special Issue. Any article submitted by a Guest Editor will be handled by a member of the Editorial Board.

2 JAN 2024: The special issue may publish contributions from the Guest Editor(s), but the number of such contributions should be limited to 25%, to ensure the diversity and inclusiveness of authorship representing the research area of the Special Issue. Any article submitted by a Guest Editor will be handled by a member of the Editorial Board.

3 MAY 2024: The special issue may publish contributions from the Guest Editor(s), but the number of such contributions should be limited, to ensure the diversity and inclusiveness of authorship representing the research area of the Special Issue. Any article submitted by a Guest Editor will be handled by a member of the Editorial Board.

The May 2024 version of guidelines is nonspecific but problematic, because it is out of alignment with criteria for accreditation by the Directory of Open Access Journals (DOAJ) , who state "Papers submitted to a special issue by the guest editor(s) must be handled under an independent review process and make up no more than 25% of the issue's total". Most of MDPI's journals are listed on DOAJ, which is a signal of trustworthiness.

So, how well is MDPI doing in terms of the DOAJ criteria? I was first prompted to ask this question when writing about an article in a Special Issue of Journal of Personalized Medicine that claimed to "reverse autism symptoms". You can read my critique of that article here; one question it raised was how on earth did it ever get published? I noted that the paper was handled by a guest editor, Richard E. Frye, who had coauthored 7 of the 14 articles in the Special Issue. I subsequently found that between 2021 and 2024 he had published 30 articles in Journal of Personalized Medicine, most in three special issues where he was guest editor. I'm pleased to say that DOAJ have now delisted the journal from their Directory. But this raises the question of how well MDPI is regulating their guest editors to prevent them going rogue and using a Special Issue as a repository for papers by themselves and their cronies.

To check up on this, I took a look at Special Issues published in 2023-2024 in 28 other MDPI journals*, focusing particularly on those with implications for public health. What I found was concerning at four levels. 

  1. Every single journal I looked at had Special Issues that broke the DOAJ rule of no more than 25% papers co-authored by guest editors (something DOAJ refer to as "endogeny").  Some of these can be found on PubPeer, flagged with the term "stuffedSI". 
  2. A minority of Special Issues conformed to the description of a "successful Special Issue" envisaged by the MDPI guidelines: "Normally, a successful Special Issue consists of 10 or more papers, in addition to an editorial (optional) written by the Guest Editor(s)." For the journals I looked at around 60% of Special Issues had fewer than 10 articles. 
  3. Quite often, the listed guest editors did not actually do any editing. One can check this by comparing the Action Editor listed for each article. Here's one example, where a different editor was needed for three of the nine papers to avoid conflict of interest, because they were co-authored by the guest editors;  but the guest editors are not listed as action editors for any of the other six papers in the special issue. 
  4. As I did this analysis, I became aware that some articles changed status. For instance, Richard E. Frye, mentioned above, had additional articles in the Journal of Personalized Medicine that were originally part of a Special Issue that are now listed as just belonging to a Section. see https://pubpeer.com/publications/BA21B22CA3FED62B6D3F679978F591#1.This change was not transparent, but was evident when earlier versions of the website were accessed using the Wayback Machine. Some of these are flagged with the term "stealth correction" on PubPeer.

This final observation was particularly worrying, because it indicated that the publisher could change the Special Issue status of articles post-publication. The concern is that lack of oversight of guest editors has created a mechanism whereby authors can propose a Special Issue, get taken on as a guest editor, and then have papers accepted there (either their own, or from friends, which could include papermillers), after which the Special Issue status is removed. In fact, given the growing nervousness around Special Issues, removal of Special Issue status could be an advantage.

When I have discussed with colleagues these and other issues around MDPI practices, I find that credible researchers tell me that there are some excellent journals published by MDPI. It seems unfortunate that, in seeking rapid growth via the mechanism of Special Issues, the publisher has risked its reputation by giving editorial responsibility to numerous guest editors without adequate oversight, and encouraged quantity over quality. Furthermore, the lack of transparency demonstrated by the publisher covertly removing Special Issue status from articles by guest editors does not appear consistent with their stated commitment to ethical policies. 

 *The code for this analysis and a summary chart for the 28 journals can be found on Github.

Tuesday, 23 July 2024

Collapse of scientific standards at MDPI journals: a case study

 

"Here's one for you", said my husband, as he browsed the online Daily Telegraph*: "Severe autism can be reversed, groundbreaking study suggests".  My heart did not lift up at this news, which was also covered in the Daily Mail; it is a near certainty that any study making such claims is flawed. But I found it hard to believe just how flawed it turned out to be.  

 

The article, by D'Adamo et al.,  was published in a special issue of an MDPI journal, the Journal of Personalized Medicine.  The special issue "A Personalized Medicine Approach to the Diagnosis and Management of Autism Spectrum Disorder: Beyond Genetic Syndromes" appears largely to be a vehicle for papers by the guest editor Richard E. Frye, who co-authored 3/4 editorials, 3/9 articles and 1/1 review in this collection.  He was editor but not an author on the paper by D'Adamo et al, which is categorised as a "case report".

 

Essentially, this is a description of development of a pair of non-identical twin girls who were diagnosed with autism at 20 months of age, along with various gastric and motor conditions, and were subsequently subjected to a remarkable list of interventions, viz:

·      Parents worked with an autism parent coach who informed them about the link between "total allostatic load" and developmental disorders, a concept promoted by the Documenting Hope Project that one of the authors is affiliated with

·      Parents accessed resources, including free webinars, through Epidemic Answers

·      Parents took part in a parent forum called "Healing Together"

·      Applied Behavior Analysis (ABA) from 22 mo to 33 mo

·      Speech Therapy starting at 24 mo

·      Rigorous diet and nutrition intervention eliminating sources of glutamate, following Reduced Excitatory Inflammatory Diet

·      A strict gluten-free, casein-free diet that was low in sugar and additives

·      Dietary supplements, including omega-3 fatty acids, multivitamins, vitamin D, carnitine, 5-methyltetrahydrofolate and "bio-individualized homeopathic remedies"

·      Family consulted a naturopathic doctor who used IntellxxDNA genomics tool to recommend diet rich in tryptophan, vitamins B12, B6 and folate, betaine and choline, lion's mane mushroom and resolvins, as well as some dietary variants specific to each twin.

·      Neuro-sensory motor reflex integration given by an occupational therapist

·      Environmental evaluation of the home for air quality, mould and moisture, culminating in a visit by a Building Biology Environmental Consultant who identified possible water damage.

·      Cranial osteopathy, as recommended by a developmental optometrist.

 

When first diagnosed, the girls were given an assessment called the Autism Treatment Evaluation Checklist, which was repeated after 18 months. Scores declined (i.e. improved) for both girls, with one twin improving substantially, and the other less so.

 

I haven't been able to find any norms for the ATEC, but there's a bit of data on trajectories in a study by Mahapatra et al (2018) and this shows that scores normally improve between the age of 2 and 3 years.  We may also note that the ATEC is completed by a parent, and so may be influenced by parental expectations of improvement.

 

The authors conclude the study demonstrates "the clear environmental and lifestyle influences on ASD" and that there is "comparatively greater impact of these types of factors than genetics".  Neither conclusion is warranted. We can't know whether these changes would have occurred in the absence of the numerous interventions that the children were given.  If the interventions did have an effect, it would be impossible to tell which were the key ingredients, because all were given together.

 

The authors grudgingly state "...while effective at reversing ASD diagnoses, the comprehensive approach that was employed in this case may not yet be widely generalizable".  But they didn't show their approach was effective - at least not by any conventional standards of evidence-based intervention. 

 

Another limitation they noted was that this was an expensive regimen that might be out of reach for parents with limited resources.

 

Should the journalists who gave this study coverage be criticised? I think the answer is yes: science journalists can't be expected to be experts in all areas of science, but they should be aware of some basic principles, such as the need for adequate sample sizes and control groups in intervention studies, and the need to be careful in assuming causality. They can, if uncertain, ask the Science Media Centre to put them in touch with knowledgeable experts who could advise. This is particularly important for a sensitive subject matter such as autism, where publicity for unfounded interventions that portray autism as a "disease" requiring "healing" has potential to do harm.  At minimum, they might have noted the ethics statement that with only two children involved, "this is not considered a systematic investigation designed to contribute to generalizable knowledge."  So how on earth did this come to be emblazoned across national newspapers as a "groundbreaking study"?

 

Having said that, though, my strongest criticism is for the MDPI publishers, who have encouraged an explosion in "special Issues" of their journals, with scant scrutiny of the quality of published articles - each of which brings in an Article Processing Charge of CHF 2600 (around £2,200, or US $2,900). The proliferation of anecdotal reports in the literature gives ammunition to those who wish to promote all kinds of unevidenced treatments: they can point to these "peer reviewed" papers as evidence of scientific respectability.

 

In the longer term, the lax editorial standards that admit pseudoscience into the research literature will further damage the already tarnished MDPI brand, and we can only hope that papers published in the Journal of Personalized Medicine will be discounted by serious journalists. But meanwhile, every practitioner with a dubious product to sell will see this journal as a perfect outlet for their promotional material. 

 

*The headline has been modified and now reads "Autism can be reversed, scientists discover", but it still describes the study as a 'trial', which is isn't.

 

 

References

D’Adamo, C. R., Nelson, J. L., Miller, S. N., Rickert Hong, M., Lambert, E., & Tallman Ruhm, H. (2024). Reversal of autism symptoms among dizygotic twins through a personalized lifestyle and environmental modification approach: A case report and review of the literature. Journal of Personalized Medicine, 14(6), Article 6. https://doi.org/10.3390/jpm14060641

 

Mahapatra, S., Vyshedsky, D., Martinez, S., Kannel, B., Braverman, J., Edelson, S. M., & Vyshedskiy, A. (2018). Autism Treatment Evaluation Checklist (ATEC) Norms: A “Growth Chart” for ATEC score changes as a function of age. Children, 5(2), Article 2. https://doi.org/10.3390/children5020025