What if we could scan for image duplication the way we check for plagiarism?

Paul Brookes

Paul Brookes is a biologist with a passion for sleuthing out fraud. Although he studies mitochondria at the University of Rochester, he also secretly ran a science-fraud.org, a site for people to post their concerns about papers. Following legal threats, he revealed he was the author and shut the site in 2013 — but didn’t stop the fight. Recently, he’s co-authored a paper that’s slightly outside his day job: Partnering with computer scientist Daniel Acuna at Syracuse University and computational biologist Konrad Kording at the University of Pennsylvania, they developed a software to help detect duplicated images. If it works, it would provide a much needed service to the research community, which has been clamoring for some version of this for years. So how did this paper — also described by Nature News — come about?

Retraction Watch: Dr. Brookes, you study mitochondria. What brought you to co-author a paper about software to detect duplications?

Continue reading What if we could scan for image duplication the way we check for plagiarism?

Caught Our Notice: Gorilla paper in the mist? Journal flags ape hormone paper

Title: Biologically validating the measurement of oxytocin in western lowland gorilla (Gorilla gorilla gorilla) urine and saliva using a commercial enzyme immunoassay

What Caught Our Attention: Quite frankly, anything with “gorilla gorilla gorilla” in the title will catch our eye, even if it is just the scientific name of the western lowland gorilla. In this case, the journal issued an expression of concern over an “unintended discrepancy” that may have affected the paper, which validates the use of a tool to measure oxytocin in the apes’ urine and saliva. The authors voluntarily notified the editors of Primate of the potential issue, and the journal issued an Expression of Concern only one month after the article was published — which is pretty fast for a notice, although not a record (see this one, issued six days after publication).

We contacted the editor, who told us:

Continue reading Caught Our Notice: Gorilla paper in the mist? Journal flags ape hormone paper

McGill dept chair says she was blindsided by coauthor’s plagiarism

When Parisa Ariya was invited to write a review for a special issue of the journal Atmosphere, she asked one of her former doctoral students to take the lead. But she soon regretted that decision after discovering Lin (Emma) Si had plagiarized and duplicated significant portions of the review.

Ariya, chair of the Department of Atmospheric and Oceanic Sciences at McGill University in Montreal, told Retraction Watch that she believes it’s important to foster the careers of young women in science and was excited for her former student, Si, to take on the challenge of writing her first review. (Si was cc’d on our email communications with Ariya, but did not respond to our individual request for comment.)
Continue reading McGill dept chair says she was blindsided by coauthor’s plagiarism

Caught Our Notice: Climate change leads to more…neurosurgery for polar bears?

Title: Internet Blogs, Polar Bears, and Climate-Change Denial by Proxy

What Caught Our Attention: There’s a lot going on here, so bear with us. (Ba-dum-bum.)

First, there was the paper itself, co-authored by, among others, Michael Mann and Stephan Lewandowsky. Both names may be familiar to Retraction Watch readers. Mann is a prominent climate scientist who has sued the National Review for defamation. A study by Lewandowsky and colleagues of “the role of conspiracist ideation in climate denial” was the subject of several Retraction Watch posts when it was retracted and then republished in a different form. And the conclusion of the new paper, in Bioscience, seemed likely to draw the ire of many who objected to the earlier work: Continue reading Caught Our Notice: Climate change leads to more…neurosurgery for polar bears?

In unusual move, gov’t database delists 14 journals from one publisher

Since the U.S. government launched a database of freely available journal articles in 2000, it has deselected roughly only 30 titles over concerns about journal quality. Fourteen of those titles were removed last August, all associated with one publisher — Kowsar.

According to a spokesperson for the National Library of Medicine (NLM), which manages the database — PubMed Central (PMC) — the decision stemmed from its review of the journals’ adherence to its policy on scientific and editorial standards:

Continue reading In unusual move, gov’t database delists 14 journals from one publisher

Clue fans, here’s scientific proof that it was Colonel Mustard with a candlestick

Leo Reynolds, via Flickr

When we last heard from Eve Armstrong one year ago today, she was a postdoc at the BioCircuits Institute at the University of California, San Diego, musing mathematically about what would have happened if she had asked one Barry Cottonfield to her high school prom in 1997. Today, she is a postdoc at the Computational Neuroscience Initiative at the University of Pennsylvania — where, it would appear from a new preprint, titled “Colonel Mustard in the Aviary with the Candlestick: a limit cycle attractor transitions to a stable focus via supercritical Andronov-Hopf bifurcation,” she has solved a brutal murder.

To be more precise:

We establish the means by which Mr. Boddy came to transition from a stable trajectory within the global phase space of Philadelphia, Pennsylvania to a stable point on the cement floor of an aviary near the west bank of the Schuylkill River.

The preprint will be posted at arXiv tomorrow, but Armstrong did not want to keep the world in suspense any longer, so we are hosting the manuscript here at Retraction Watch on a more appropriate day, April 1. She was also kind enough to answer a few questions about the work: Continue reading Clue fans, here’s scientific proof that it was Colonel Mustard with a candlestick

Weekend reads: “Weaponized transparency;” fighting academic spam with humor; NIH cracks down

Before we present this week’s Weekend Reads, a question: Do you enjoy our weekly roundup? If so, would you consider a tax-deductible donation of $25, or a recurring donation of an amount of your choosing, to support it? Thanks in advance.

The week at Retraction Watch featured a major case of misconduct at The Ohio State University, the retraction of a much-criticized paper claiming to show “off-target” mutations when using CRISPR, and how fallout from a stem cell scandal ensnared a Nobel Prize winner. Here’s what was happening elsewhere: Continue reading Weekend reads: “Weaponized transparency;” fighting academic spam with humor; NIH cracks down

Ohio State just released a 75-page report finding misconduct by a cancer researcher. What can we learn?

C. K. Gunsalus

Today, the Ohio State University (OSU) announced that Ching-Shih Chen, who resigned from a professorship there in September, was guilty of “deviating from the accepted practices of image handling and figure generation and intentionally falsifying data” in 14 images from eight papers. Chen had earned more than $8 million in Federal grants, and his work had led to a compound now being testing in clinical trials for cancer. (For details of the case, see our story in Science.)

Ching-Shih Chen

OSU — which has been involved in several high-profile cases of misconduct recently — released a lightly-redacted version of their investigation report, and we asked C.K. Gunsalus, who has decades of experience reviewing similar cases, to examine it for us. A Q&A follows.

 

Retraction Watch (RW): What’s your impression of the case? How does it compare in significance with others you’ve looked at? Continue reading Ohio State just released a 75-page report finding misconduct by a cancer researcher. What can we learn?

Nature journal retracts controversial CRISPR paper after authors admit results may be wrong

Nature Methods has retracted a 2017 paper suggesting a common gene editing technique may cause widespread collateral damage to the genome.

The notice has a long backstory: After the paper was published, it immediately drew an outcry from critics (including representatives from companies who sell the tool, whose stock fell after publication). Some critics argued that the authors, led by Vinit B. Mahajan at Stanford University, hadn’t employed sufficient controls, so they couldn’t be sure that the observed mutations stemmed from the tool, rather than normal background variation between mice. Only months after the paper appeared, the journal issued an expression of concern about the article. In a new preprint posted on BioRxiv on Monday, the authors concede that their critics may be right.

In the new preprint, Mahanjan and his colleagues acknowledge that the gene editing technique — known as CRISPR-Cas9 — “may not introduce numerous, unintended, off-target mutations.”

However, according to the retraction notice, Mahajan and several of his co-authors object to the retraction: Continue reading Nature journal retracts controversial CRISPR paper after authors admit results may be wrong

A new publishing approach — retract and replace — is having growing pains

Ana Marušić

Many journals are adopting a recently developed mechanism for correcting the scientific record known as “retract and replace” — usually employed when the original paper has been affected by honest errors. But if an article is retracted and replaced, can readers always tell? To find out, Ana Marušić at the University of Split School of Medicine in Croatia and her colleagues reviewed 29 “Corrected and Republished Articles” issued between January, 2015 and December, 2016, noting how they were marked by Web of Science, Scopus, and the journals themselves. They report their findings today in The Lancet.

Retraction Watch: You found some inconsistencies in how articles are handled by journals and other databases. What were the most surprising and/or troubling to you?

Continue reading A new publishing approach — retract and replace — is having growing pains