Structural biology corrections highlight best of the scientific process

Nature_latest-coverIf you need evidence of the value of transparency in science, check out a pair of recent corrections in the structural biology literature.

This past August, researchers led by Qiu-Xing Jiang at the University of Texas Southwestern Medical Center corrected their study, first published in February 2014 in eLife, of prion-like protein aggregates called MAVS filaments, to which they had ascribed the incorrect “helical symmetry.” In March, Richard Blumberg of Harvard Medical School, and colleagues corrected their 2014 Nature study of a protein complex called CEACAM1/TIM-3, whose structure they had attempted to solve using x-ray crystallography.

In both cases, external researchers were able to download and reanalyze the authors’ own data from public data repositories, making it quickly apparent what had gone wrong and how it needed to be fixed — highlighting the very best of a scientific process that is supposed to be self-correcting and collaborative. Continue reading Structural biology corrections highlight best of the scientific process

Software glitch — not intentional manipulation — sunk immunology paper, says author

kuo photo
A black box appears over the control lane on the left

New evidence suggests a retracted paper was felled not by intentional manipulation — as it first appeared — but by a software glitch.

In 2014, we reported that Biochemical Journal had retracted a paper on suspicion it contained “shoddy Photoshopping”  — someone appeared to have blacked out a control lane in one figure. Now there’s evidence that it wasn’t done on purpose: An investigation at Duke into eight papers, including the Biochemical Journal paper, did not find evidence of misconduct; lead author Paul Kuo, currently chair of surgery at Loyola Medicine, told us that a glitch in the software caused the black box. Nevertheless, the journal does not plan to un-retract the paper. Continue reading Software glitch — not intentional manipulation — sunk immunology paper, says author

Retractions aren’t enough: Why science has bigger problems

Andrew Gelman
Andrew Gelman

Scientific fraud isn’t what keeps Andrew Gelman, a professor of statistics at Columbia University in New York, up at night. Rather, it’s the sheer number of unreliable studies — uncorrected, unretracted — that have littered the literature. He tells us more, below.

Whatever the vast majority of retractions are, they’re a tiny fraction of the number of papers that are just wrong — by which I mean they present no good empirical evidence for their claims.

I’ve personally had to correct two of my published articles.   Continue reading Retractions aren’t enough: Why science has bigger problems

Journal pulls parasite paper over potential for patient harm

Parasitology ResearchA journal has retracted a paper about a molecular diagnosis for leishmaniasis out of concern it could lead to incorrect clinical diagnoses. 

According to Parasitology Research, all data behind the figures in the main manuscript and supporting information are correct, but the authors’ misinterpretation of the data could lead doctors to diagnose patients incorrectly. 

Let’s take a look at the retraction notice, which tells us a bit more about the nature of the problem: Continue reading Journal pulls parasite paper over potential for patient harm

Nature fixes highly cited paper suggesting food additives hurt the gut

Nature_latest coverA 2015 study about dietary emulsifiers has been corrected by Nature after another researcher pointed out a few ambiguities.

When it first appeared, the study — which showed emulsifiers cause inflammation in the guts of mice — received a fair amount of media attention, including from Nature’s own news department. But since publication, a researcher noted some imprecision around the ages of mice used in the sample, affecting the paper’s calculations of weight gain over time. Andrew Gewirtz, co-author of the study from Georgia State University, told us the change did not affect the conclusions of the paper.

Here’s the corrigendum for “Dietary emulsifiers impact the mouse gut microbiota promoting colitis and metabolic syndrome”: Continue reading Nature fixes highly cited paper suggesting food additives hurt the gut

What happened after a journal decided to get tough on plagiarism?

Reiss
Carol Shoshkes Reiss

In July 2015, DNA and Cell Biology began routinely scanning manuscript submissions for plagiarism using iThenticate; since then, it’s rejected between four and six manuscripts each month for that reason alone. Additional submissions have been rejected after the journal realized the authors had digitally altered figures. The level of misconduct “shocked” editor-in-chief Carol Shoshkes Reiss, as she wrote in a recent editorial for the journal. She spoke to us about the strict measures the journal has adopted in response to these incidents.

Retraction Watch: Why did you decide to begin scanning submissions for plagiarized text using iThenticate™ software in July, 2015? Did something prompt that decision? Continue reading What happened after a journal decided to get tough on plagiarism?

PLOS ONE pulls maize paper with Photoshopped images

PLOS OnePLOS ONE has retracted a paper after editors learned that some of the images had been manipulated using Photoshop.

First author of the paper, Chuan Li, confirmed that he was responsible, and told Retraction Watch he apologizes for his “low-level mistake.”

Zhongfu Ni, last author of the paper from the China Agricultural University in Beijing, told us that all the co-authors agree with the retraction.

Here’s the retraction notice: Continue reading PLOS ONE pulls maize paper with Photoshopped images

Doing the right thing: Authors share data, retract when colleague finds error

no spine minimum. full size. Editor: Holly JEM: Leslie RTP: Karen Geist ancac3

A pair of chemical engineers has retracted a paper after another researcher was unable to replicate their work, in a case that we consider an example of doing the right thing.

Dennis Prieve, at Carnegie Mellon University, was interested in applying the paper — on how systems of molecules known as “reverse micelles” conduct electrical charge — to his own work, but was having trouble repeating the calculations. So Prieve contacted the authors — John Berg and his PhD student Edward Michor, based at the University of Washington — who supplied him with their original data.

It took several weeks of back and forth to figure out the problem, Michor told us, as the paper was published in 2012, so he had to decipher his old notes. When they found that several incorrect values were used in the paper, the authors issued a retraction notice, published in March:

Continue reading Doing the right thing: Authors share data, retract when colleague finds error

In precedent break, BMJ explains why it rejected controversial “weekend effect” paper

After the reviewer of a rejected paper was publicly outed, the BMJ has taken the unusual step of explaining why it chose not to publish the paper.

The paper — eventually published in another journal — raised hackles for suggesting that there is no “weekend effect,” or a higher mortality rate in hospitals on Saturday and Sunday. This caught the attention of UK policy makers, who have proposed changing policies to compensate for any supposed “weekend effect.”

Amidst the heated discussion about the research, one of the reviewers was identified, along with suggestions that he may have been conflicted because he had published a study showing the opposite finding. Yesterday, the BMJ posted a blog explaining that it was the editors — and not one sole reviewer — who decided to reject the paper: Continue reading In precedent break, BMJ explains why it rejected controversial “weekend effect” paper

Dev Cell paper retracted after author admits to doctoring data

Developmental CellThe authors of a Developmental Cell paper have retracted it after the first author admitted to manipulating and falsifying data and reagents.

The problems came to light after the authors couldn’t reproduce the findings, about a mechanism underlying meiosis. When questioned about the matter, the first author of the paper, Saurav Malhotra, admitted to doctoring data and materials. 

Here’s the retraction notice to the paper, “The Anaphase-Promoting Complex/Cyclosome Is Essential for Entry into Meiotic M-Phase:” Continue reading Dev Cell paper retracted after author admits to doctoring data