Publishing a research paper is usually cause for celebration, after what is typically years of effort. Our recent paper in which we found that unexpectedly high proportions of papers in two journals described at least one wrongly identified reagent should have been no exception.

But alas. Any of our celebrations have been tempered by Springer Nature’s bizarre introduction of an unrelated figure into the paper. Here’s what has happened so far.

We initially posted the manuscript on bioRxiv in February 2023, and then submitted it to a journal. Unusually, we withdrew the manuscript after 4 rounds of revisions, as the editors required changes to our discussion of research paper mills that we did not accept. We then submitted the revised version to Naunyn-Schmiedeberg’s Archives of Pharmacology. The manuscript was accepted after further revisions and published online on January 9, 2024. 

However, on checking the published version, I was dismayed to find that Figure 1 had been replaced by an unrelated figure that we neither produced nor submitted for publication. The error was easy to spot: The correct Figure 1 compared the journal impact factors of Molecular Cancer and Oncogene from 2014-2021, while the substituted figure shows an unrelated Kaplan Meier plot. The proof returned to Springer Nature included the correct versions of all of the figures, so neither the authors nor the journal were responsible for the error.

I immediately wrote to Springer Nature about the error and copied the NSAP Editor in Chief, Roland Seifert. As I found the error on the day that the article was published, we hoped that the figure could be simply and quickly replaced. However, following email exchanges with Springer Nature representatives, it appears that: 

The problem here is that at the moment of online publication the paper becomes part of the scientific literature and the metadata of the publication are distributed to all relevant Abstracting+Indexing services. Though technically it would not be a problem to remove the paper from the website, we cannot do this since it is already officially published.” 

To date, while the publisher has now fixed the PDF, the incorrect figure remains visible in the freely available HTML version to users who have not cleared their caches. The publication has been accessed more than 300 times. Springer Nature has yet to provide an explanation of how the figure substitution occurred.

Clearly, a nonsensical figure in a paper about incorrect reagents is particularly unfortunate. It is similarly unfortunate that a publisher error that probably required minutes to achieve has no similarly quick path to correction. In the meantime, the authors’, the journal’s and the editor’s reputations risk being compromised, and time is wasted on communications that could have been devoted to celebrating this paper, or writing the next one.

While we are probably not the only group to have experienced a figure substitution by a publisher, some such errors may have gone unnoticed, as many authors might not expect or check for publisher errors. 

The possibility of figure replacements by publishers highlights another advantage of preprints- the correct version of Figure 1 remains online at bioRxiv.

Jennifer Byrne is conjoint Professor of Molecular Oncology and leads the PRIMeR group at the University of Sydney, Australia.

Like Retraction Watch? You can make a tax-deductible contribution to support our work, subscribe to our free daily digest or paid weekly update, follow us on Twitter, like us on Facebook, or add us to your RSS reader. If you find a retraction that’s not in The Retraction Watch Database, you can let us know here. For comments or feedback, email us at team@retractionwatch.com.

A journal says a content management mishap led to the publication, and subsequent retraction, of a gag essay not intended for wide distribution. 

Why the retraction happened three and a half years after the paper’s publication remains murky.

This story belongs to the early days of the COVID-19 pandemic, back when Proteins: Structure, Function, and Bioinformatics, a Wiley title, used to gather spoof papers for its annual April Fools edition.  

As Kristofer Barr, an assistant research integrity auditor at Wiley, told us: 

The “April Fools” series was a longstanding tradition promoted on Proteins’ homepage, which included humorous editorials written by members of the research community. The intention of these editorials was to present a humorous take on an important topic in the field. Each article went through a process by which they were made into PDFs and these PDFs were promoted on a separate page on the journal’s website apart from other content published in Early View or in-issue. The editorials were never intended to be published alongside research content nor indexed in PubMed.

But one such manuscript, “Citius, Altius, Fortius,” managed somehow to jump from house organ to the real journal, spoiling the fun for everyone. The title of the cheeky paper refers to the motto for the Olympic games – “Faster, Higher, Stronger.” 

The piece was written by Joanna Lange and Gert Vriend, of Radboud University Medical Centre in The Netherlands (Vriend also appears to be affiliated with the Baco Institute of Protein Science , in the Philippines.) 

The episode reminds us a bit of one of our earliest posts, back in 2010, about the retraction of a paper from a virology journal which speculated – with tongue in cheek –  that Jesus had healed a febrile woman of her bout of flu. 

We found the abstract for the spoof, which reads: 

2020 is a leap year. That means that we have one day extra and, if the Olympic games had survived the corona crisis, we would all be watching television and ask the eternal question whether Olympic records will for ever be broken and broken again, or that there are limits to human biology1 . In this article we ask the same question, but rather than discussing aspects of Citius, Altius, and Fortius of athletes we will discuss them for macromolecules. It is remarkable how many parallels can be found between Olympic records in these two seemingly different worlds. People involved in structure validation and re-refinement try to make us believe that most aspects of macromolecular structures can be caught by a number that has some constant value with little variation around it. We will show here that the PDB2 databank proves this idea to be wrong. In the protein structure world, it holds for many that “participating is more important than winning”, but some, fortunately, still go for the record books.

It continues: 

Cheating is a favourite pass-time for many, especially when feeling that we can get away with it  (e.g. https://en.wikipedia.org/wiki/Tax_returns_of_Donald_Trump). But cheating happens  everywhere else too; like in the Olympics (https://www.britannica.com/list/8-olympic-cheating- scandals) and, amazingly, even in crystallography13-16. The Olympic games have been marred by a large number of doping abuse cases, and the number of athletes caught increase from games to games (https://en.wikipedia.org/wiki/Doping_at_the_Olympic_Games). The systematic country-wide doping abuse of East-Germany, though, remained undetected too long to be backed up by physical evidence. Something similar is going on in crystallography. In pre-history, structures were built by hand (see e.g. Figure 1) and cheating was difficult because one could always check the conclusions by travelling to the lab that built the model, and remeasure everything.

Protein models as they were built in the good old days; before computers came around to spoil the fun. These metal models had one big problem, all residues of a certain type always had the same bond lengths and bond angles. (Figure courtesy A Finkelstein)  At some moment, though, computers became available, and from then on crystallographers could cheat much more eloquently by using refinement software with restraints and constraints, and parameter sets like those of Engh and Huber. Fortunately, not all crystallographers do this …

Unless you’re a protein scientist, the humor here is likely to fall a bit flat. The funniest part of the piece, as far as we can tell, is the disclosure statement: 

These authors contributed equally little to this work.

We were surprised to find the paper has been cited (just once), according to Clarivate Analytics’ Web of Science. The reference seems not to indicate the authors knew the article was a lark.

Wiley didn’t catch the rogue publication until this year, during an internal audit. Per Barr: 

In late 2023, a team member noticed the erroneous publication of one of these editorials, which was likely the result of a miscommunication within our production staff. Our integrity group, following COPE guidelines, advised that it was necessary to retract the article.  The Editor-in-Chief of Proteins and both authors agreed that the mistakenly-published editorial would receive a retraction, and we thank them for their quick action to help correct the record.

Nikolay Dokholyan, the editor-in-chief of Proteins, lamented the joke gone wrong: 

The story of this article is just a set of unfortunate events. Wiley published it accidentally. We had a tradition of April’s fool articles, which are not for publication. Wiley made a mistake and published it. Upon revealing the mistake, they fixed it. Having said that, there is nothing wrong with the science. Wiley has a problem mixing humor and science since it may make erroneous perceptions.

In fact, the retraction notice appears to suggest blame for the error lies with the editors:

The above article, published online on 12 June 2020 in Wiley Online Library (wileyonlinelibrary.com), has been retracted by agreement between the authors, the journal’s Editor-in-Chief Dr. Nikolay Dokholyan, and John Wiley & Sons, Inc. The above article is a humorous editorial contribution surrounding a specialized topic, and was not intended for full online publication as part of the journal’s scholarly content. Due to an editorial mistake, the above article was published online in Early View. John Wiley & Sons, Inc. takes full responsibility for the erroneous publication of this article.

Regardless, Dokholyan confirmed April is no longer a month of mirth at his journal – no more jokes about misfolded proteins in its pages:  

we stopped this tradition.

Barr added: 

Upon agreement with the Editor-in-Chief and the lead author of this series, we have taken steps to move previous “April Fools Day” editorials to a separate platform, which will ensure the articles are presented in context and will not be mistaken as genuine scholarly content. Before this incident, the journal had already intended to retire the April Fools series.

Vriend told us he had been submitting the joke pieces for a decade before the one that went awry: 

I will indeed miss it a bit. But, to be honest, I was/am running out of ideas. This year I had still something nice, there is a relation (not correlation, and hopefully nothing causal) between the style of the american president and the length and spread in the length of bond-lengths in amino acid side-chains…   But the world will never learn about this amazing fact…

Larks may be carefree, but science may be deaf to their songs.

Like Retraction Watch? You can make a tax-deductible contribution to support our work, subscribe to our free daily digest or paid weekly update, follow us on Twitter, like us on Facebook, or add us to your RSS reader. If you find a retraction that’s not in The Retraction Watch Database, you can let us know here. For comments or feedback, email us at team@retractionwatch.com.

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