Semi-automated fact-checking for scientific papers? Here’s one method.

Jennifer Byrne

Wouldn’t it be terrific if manuscripts and published papers could be checked automatically for errors? That was the premise behind an algorithmic approach we wrote about last week, and today we bring you a Q&A with Jennifer Byrne, the last author of a new paper in PLOS ONE that describes another approach, this one designed to find incorrect nucleotide sequence reagents. Byrne, a scientist at the University of Sydney, has worked with the first author of the paper, Cyril Labbé, and has become a literature watchdog. Their efforts have already led to retractions. She answered several questions about the new paper.

Retraction Watch (RW): Seek & Blastn allows for “semi-automated fact-checking of nucleotide sequence reagents.” Can you explain what these reagents are used for, and what Seek & Blastn does? Continue reading Semi-automated fact-checking for scientific papers? Here’s one method.

A university thought its misconduct investigation was complete. Then a PubPeer comment appeared.

When Venkata Sudheer Kumar Ramadugu, then a postdoc at the University of Michigan, admitted to the university on June 28 of last year that he had committed research misconduct in a paper that appeared in Chemical Communications in 2017, he also “attested that he did not manipulate any data in his other four co-authored publications published while at the University of Michigan.”

And so, a few days later, Michael J. Imperiale, the university’s research integrity officer, wrote a letter to the U.S. Office of Research Integrity (ORI) informing them of the findings. On August 2, Ramadagu was terminated from Michigan. And on August 3, Ayyalusamy Ramamoorthy, the head of the lab where Ramadagu had worked, wrote a letter to Chemical Communications requesting retraction of the paper.

While the retraction would not appear until the end of November, and ORI sanctions not announced until the end of December, Michigan’s responsibilities seemed to have been discharged as of early August. But documents obtained by Retraction Watch through a public records request detail how that was not the end of the story. Continue reading A university thought its misconduct investigation was complete. Then a PubPeer comment appeared.

Journal retracts creationist paper “because it was published in error”

Charles Darwin

It’s become a sort of Retraction Watch Mad Libs: Author writes a paper that is so far, far, out of the mainstream. Maybe it argues that HIV doesn’t cause AIDS. Or that vaccines cause autism. Truth squads swarm over the paper, taking to blogs and Twitter to wonder, in the exasperated tone of those who have been here before, how on earth it was published in a peer reviewed journal.

Then, in something that approaches — but does not quite qualify as — contrition, the journal in question retracts the paper, mumbling something in a retraction notice about a compromised peer review process, or that ghosts in the machine allowed the paper to be published instead of being rejected.

This week’s parade float entry is a paper in the International Journal of Anthropology and Ethnology, a Springer Nature title that is apparently sponsored by The Institute of Ethnology and Anthropology at the Chinese Academy of Social Sciences, where many of its editorial board members work.

Here’s how Jerry Coyne, a researcher at the University of Chicago who keeps an eye on creationists, described the paper, “A brief history of human evolution: challenging Darwin’s claim,” written by Sarah Umer, in a December 18, 2018 post: Continue reading Journal retracts creationist paper “because it was published in error”

Plagiarism prompts retraction of 25-year-old article by prominent priest

Fr. Thomas Rosica

Retraction Watch readers may have heard about Fr. Thomas Rosica, a priest who recently apologized for plagiarism and resigned from the board of a college. The case, which involved Rosica’s speeches and popular columns, prompted at least two observers to take a look at his scholarly work.

One of those observers was Michael Dougherty, who has a well-earned reputation as the plagiarism police squad in certain fields and recently published Correcting the Scholarly Record for Research Integrity: In the Aftermath of Plagiarism. Dougherty wrote a letter to the journal in question, Worship, on February 20th.

In the letter, which we have posted here, Dougherty writes: Continue reading Plagiarism prompts retraction of 25-year-old article by prominent priest

Weekend reads: The fake sex doctor and his bizarre research; prof alleged to have stolen student’s work; worst scientific scandal of all time?

Before we present this week’s Weekend Reads, a question: Do you enjoy our weekly roundup? If so, we could really use your help. Would you consider a tax-deductible donation to support Weekend Reads, and our daily work? Thanks in advance.

The week at Retraction Watch featured the retraction of a highly cited paper on the effects of discrimination on gay lives; a look at the possibility of scientific error checkers; and a study of deficiencies in institutional misconduct investigations. Here’s what was happening elsewhere: Continue reading Weekend reads: The fake sex doctor and his bizarre research; prof alleged to have stolen student’s work; worst scientific scandal of all time?

Retraction Watch readers, we need your help to be able to continue our work

Dear Retraction Watch readers:

Maybe you’re a researcher who likes keeping up with developments in scientific integrity. Maybe you’re a reporter who has found a story idea on the blog. Maybe you’re an ethics instructor who uses the site to find case studies. Or a publisher who uses our blog to screen authors who submit manuscripts — we know at least two who do.

Whether you fall into one of those categories or another, we need your help. Continue reading Retraction Watch readers, we need your help to be able to continue our work

Author, author? Dispute over authorship leads to two retraction notices, and confusion

Testosterone

An endocrinology journal has pulled a 2017 paper by a group from Russia and Romania because, well, maybe it’s just better if you read for yourself.

The article, “Testosterone promotes anxiolytic-like behavior in gonadectomized male rats via blockade of the 5-HT1A receptors,” appeared in General and Comparative Endocrinology, an Elsevier publication.

The paper in fact has two retraction notices. One, which is rather less informative than the second, reads: Continue reading Author, author? Dispute over authorship leads to two retraction notices, and confusion

Will scientific error checkers become as ubiquitous as spell-checkers?

Jonathan Wren

How common are calculation errors in the scientific literature? And can they be caught by an algorithm?  James Heathers and Nick Brown came up with two methods — GRIM and SPRITE — to find such mistakes. And a 2017 study of which we just became aware offers another approach.

Jonathan Wren and Constantin Georgescu of the Oklahoma Medical Research Foundation used an algorithmic approach to mine abstracts on MEDLINE for statistical ratios (e.g., hazard or odds ratios), as well as their associated confidence intervals and p-values. They analyzed whether these calculations were compatible with each other. (Wren’s PhD advisor, Skip Garner, is also known for creating such algorithms, to spot duplications.)

After analyzing almost half a million such figures, the authors found  that up to 7.5% were discrepant and likely represented calculation errors. When they examined p-values, they found that 1.44% of the total would have altered the study’s conclusion (i.e., changed significance) if they had been performed correctly.  

We asked Wren — who says he thinks automatic scientific error-checkers will one day be as common as automatic spell-checkers are now — to answer a few questions about his paper’s approach. This Q&A has been slightly edited for clarity.

Retraction Watch (RW): What prompted you to perform your study? Continue reading Will scientific error checkers become as ubiquitous as spell-checkers?

Study claiming hate cuts 12 years off gay lives retracted

Low Library, Columbia University

After years of back and forth, a highly cited paper that appeared to show that gay people who live in areas where people were highly prejudiced against them had a significantly shorter life expectancy has been retracted.

The paper, “Structural stigma and all-cause mortality in sexual minority populations,”  was published in 2014 by Mark Hatzenbuehler of Columbia University and colleagues. As we reported last year, Mark Regnerus, of the University of Texas at Austin, published a paper describing his failed attempts to replicate the study in 2016: Continue reading Study claiming hate cuts 12 years off gay lives retracted

New study finds “important deficiencies” in university reports of misconduct

via NASA

Retraction Watch readers may recall the name Yoshihiro Sato. The late researcher’s retraction total — now at 51 — gives him the number four spot on our leaderboard. He’s there because of the work of four researchers, Andrew Grey, Mark Bolland, and Greg Gamble, all of the University of Auckland, and Alison Avenell, of the University of Aberdeen, who have spent years analyzing Sato’s papers and found a staggering number of issues.
Those issues included fabricated data, falsified data, plagiarism, and implausible productivity, among others. In 2017, Grey and colleagues contacted four institutions where Sato or his co-authors had worked, and all four started investigations. In a new paper in Research Integrity and Peer Review, they describe some of what happened next:

Continue reading New study finds “important deficiencies” in university reports of misconduct