Retraction Watch

Beatrix_

Member
Joined
Jan 16, 2023
Messages
1,660
Location
Callisto


OPINION
GUEST ESSAY

The Research Scandal at Stanford Is More Common Than You Think
July 30, 2023

By Theo Baker

Mr. Baker is a rising sophomore at Stanford University. At its daily student newspaper, he won a George Polk Award for investigating allegations of manipulated experimental data in scientific papers published by the university’s president.

There are many rabbit holes on the internet not worth going down. But a comment on an online science forum called PubPeer convinced me something might be at the bottom of this one. “This highly cited Science paper is riddled with problematic blot images,” it said. That anonymous 2015 observation helped spark a chain of events that led Stanford’s president, Marc Tessier-Lavigne, to announce his resignation this month.

Dr. Tessier-Lavigne made the announcement after a university investigation found that as a neuroscientist and biotechnology executive, he had fostered an environment that led to “unusual frequency of manipulation of research data and/or substandard scientific practices” across labs at multiple institutions. Stanford opened the investigation in response to reporting I published last autumn in The Stanford Daily, taking a closer look at scientific papers he published from 1999 to 2012.

The review focused on five major papers for which he was listed as a principal author, finding evidence of manipulation of research data in four of them and a lack of scientific rigor in the fifth, a famous study that he said would “turn our current understanding of Alzheimer’s on its head.” The investigation’s conclusions did not line up with my reporting on some key points, which may, in part, reflect the fact that several people with knowledge of the case would not participate in the university’s investigation because it declined to guarantee them anonymity. It did confirm issues in every one of the papers I reported on. (My team of editors, advisers and lawyers at The Stanford Daily stand by our work.)

In retrospect, much of the data manipulation is obvious. Although the report concluded that Dr. Tessier-Lavigne was unaware at the time of the manipulation that occurred in his labs, in papers on which he served as a principal author, images had been improperly copied and pasted or spliced; results had been duplicated and passed off as separate experiments; and in some instances — in which the report found an intention to hide the manipulation — panels had been stretched, flipped and doctored in ways that altered the published experimental data. All of this happened before he became Stanford’s president. Why, then, didn’t it come out sooner?

The answer is that people weren’t looking.
.........
 

Beatrix_

Member
Joined
Jan 16, 2023
Messages
1,660
Location
Callisto


Screenshot_20230819-145819~2.png
 

Beatrix_

Member
Joined
Jan 16, 2023
Messages
1,660
Location
Callisto

September 27th, 2023

Making retraction data freely accessible – Why Crossref’s acquisition of the Retraction Watch database is a big step forward

Since its launch Retraction Watch has done much to highlight the value of research integrity and publishing standards. Discussing the recent acquisition by Crossref of Retraction Watch’s database of retracted articles, Ivan Oransky and Rachael Lammey highlight the value of this data and the difficulties of making it openly and sustainably accessible.

By convention and, some would say, by necessity, publishers are considered the stewards of the scientific record. A key part of the value they say they provide is the production, curation, and dissemination of metadata so that the literature can be discovered, read, shared, and tracked.

But publishers are not carrying their weight when it comes to at least one key part of that record: Retractions.

Studies have demonstrated that central databases that should include information about all retracted papers covered by a particular set of criteria are missing many, and sometimes most, retractions. The differences between databases are stark: Some contain only a third or a quarter of the at least 50,000 known retractions in the literature. Whether intentionally or simply not as a matter of priority, publishers are not transmitting the metadata they should be.

That means researchers who are trying to avoid citing or relying on retracted papers are stuck. While they could check each reference by hand on publishers’ sites, studies have shown that not even that will catch all retractions. It also means that the full impact of shoddy science – at least the work that is retracted, a fraction of what should be – will not be understood, nor available for study by other scholars.

Thankfully, there is a solution. Earlier this month, Crossref announced that it had acquired the Retraction Watch Database, launched in 2018 and curated by The Center For Scientific Integrity – the parent non-profit of Retraction Watch – and containing about 43,000 retractions. Crossref works with over 19,000 members from 151 countries including institutions, funders, publishers, preprint servers, libraries, and more, collecting metadata on research objects and making it openly available via an API that sees over 1.1 billion queries each month.

The more comprehensive and accurate the metadata, the more value it provides to the community, providing an open source of information on things like citations, research funding, related research data and preprints. Crossref has encouraged the greater reporting of this important information by removing the fee related to registering information on retractions and other updates in 2020, and also flags retraction information (via the Crossmark service) as one of 12 key metadata elements that its members should register in its Participation Reports.

But information on retractions in the metadata registered by Crossref members has not been comprehensive. Compared to the 43,000 retractions in the Retraction Watch database, Crossref could only see, and make available data on around 14,000 retractions up until September 2023. This created problems for the community: without more complete data on retractions, they couldn’t use Crossref metadata as a source of this information to build downstream tools, services, to do research on retractions, or to know what to trust when doing their own research. Incomplete data meant that the community risked seeing false positives and may have assumed a piece of work was not retracted when it had been, but the information hadn’t been communicated downstream. This means that retracted research can inadvertently spread throughout the literature, proliferating errors or wasting valuable research time.

The acquisition accomplishes two critical goals: Making the data covering nearly 50,000 retractions freely available, and providing robust financial support for its work to continue. These two goals have been intertwined since Retraction Watch launched the database five years ago, and a bit of history is worth reviewing as we hope it is useful to others engaged in this kind of work.

Gathering and curating a comprehensive database of retractions, it turns out, takes resources. Those resources initially came from grants from three generous foundations. But as is often the case, either because of shifting priorities, the design of certain funding, and philanthropy’s understandable desire to see non-profits like The Center for Scientific Integrity – the parent non-profit of Retraction Watch – stand on their own feet, sustainable funding required a different model.

That model relied heavily on licensing the database to organizations that could make use of it in products or for internal purposes. It meant, however, that the data were not freely available. The Crossref agreement makes the data fully open, while providing The Center for Scientific Integrity with more than $800,000USD in funding over the initial term, which is the next five years.

Anyone – creators of citation software, publishers, universities, scholars – can now download the data and use it as they see fit. Unlike retraction data available through other sources, the Retraction Watch Database also includes a detailed taxonomy of reasons for every retraction. The only requirement is attribution. Given how much effort is wasted when research projects are built on what turn out to be houses of sand, we are confident that this will save costs immediately.

There remains work to do. For example, both Crossref and Retraction Watch participate in the NISO CREC Working Group which will soon publish a recommended practice on the Communication of Retractions, Removals, and Expressions of Concern. With this acquisition, we have identified a way to greatly increase the openly available information on retractions, supplementing Crossref member data and helping sustain another not-for-profit working hard to provide this. This in turn helps the community benefit from and rely upon more comprehensive information on important updates that have been applied to research after it was published or made available online. By collaborating, we hope to support more building blocks and fewer houses of sand for the research community to use.

About the author

Ivan Oransky is one of the two co-founders of Retraction Watch, the editor-in-chief of Spectrum and distinguished journalist in residence at NYU’s Arthur L Carter Journalism Institute.

Rachael Lammey is Director of Product at Crossref, a not for profit that provides a global community infrastructure that makes all kinds of research objects easy to find, assess, and reuse through a number of services critical to research communications.
 

Beatrix_

Member
Joined
Jan 16, 2023
Messages
1,660
Location
Callisto
@David PS


Oct 2nd, 2023

Nobel Prize winner Gregg Semenza tallies tenth retraction

It’s Nobel Prize week, and the work behind mRNA COVID-19 vaccines has just earned the physiology or medicine prize. But this is Retraction Watch, so that’s not what this post is about.

A Nobel prize-winning researcher whose publications have come under scrutiny has retracted his 10th paper for issues with the data and images.

Gregg Semenza, a professor of genetic medicine and director of the vascular program at Johns Hopkins’ Institute for Cell Engineering in Baltimore, shared the 2019 Nobel prize in physiology or medicine for “discoveries of how cells sense and adapt to oxygen availability.”

The pseudonymous sleuth Claire Francis had flagged possibly duplicated or manipulated images in Semenza’s publications on PubPeer before 2019, and other sleuths posted more beginning in October 2020.

Last September, Semenza and his co-authors pulled four papers from Proceedings of the National Academy of Sciences. Another PNAS paper, one in Oncogene, and two from the Journal of Biological Chemistry were retracted over the past year, with each notice stating that Semenza requested or agreed to the retractions.

Today, Molecular Cancer Research has retracted another of the Nobelist’s articles, “Procollagen Lysyl Hydroxylase 2 Is Essential for Hypoxia-Induced Breast Cancer Metastasis,” which appeared in 2013. The article has been cited 181 times, according to Clarivate’s Web of Science.

With a 2011 retraction for a paper co-authored with Naoki Mori – who with 31 retractions sits at No. 24 on our leaderboard – today’s retraction makes 10 for Semenza. More may be on the way.

The notice states:

This article (1) has been retracted at the request of the authors. The authors found that lanes 4, 5, and 6 of the HIF-1α immunoblot in Fig. 3A are identical images. An internal review corroborated the authors’ claim, and the editors agreed with the authors’ retraction request. The authors apologize to the scientific community and deeply regret any inconveniences or challenges resulting from the publication and subsequent retraction of this article.

A copy of this Retraction Notice was sent to the last known email addresses for all authors. Four authors (Denis Wirtz, Carmen C. Wong, Daniele M. Gilkes, and Gregg L. Semenza) agreed to the retraction; the 3 remaining authors could not be located.

Semenza did not immediately respond to our request for comment. Johns Hopkins would not comment on whether they were investigating the matter when a reporter from The Baltimore Sun asked this summer.

In October 2020, a PubPeer user commented that the lanes of the figure identified in the retraction notice were “much more similar than expected.” The first author, Daniele M. Gilkes, responded by posting an image of the “original uncropped version.” Another commenter raised more concerns about the image, but Gilkes did not respond again.

Like Retraction Watch? You can make a tax-deductible contribution to support our work, follow us on Twitter, like us on Facebook, add us to your RSS reader, or subscribe to our daily digest. If you find a retraction that’s not in our database, you can let us know here. For comments or feedback, email us at [email protected].

N.B. this is not the same one awarded yesterday
 
Last edited:

Similar threads

Back
Top Bottom