Category: doing the right thing

Overlooked virus “generated a mess,” infected highly cited Cell, PNAS papers

When Alexander Harms arrived at the University of Copenhagen in August 2016, as a postdoc planning to study a type of antibiotic resistance in bacteria, he carried with him a warning from another lab who had recruited him:

People said, “If you go there, you have to deal with these weird articles that nobody believes.”

The papers in question had been published in the Proceedings of the National Academy of Sciences in 2011 and Cell in 2013. Led by Kenn Gerdes, Harms’s new lab director, the work laid out a complex chain of events that mapped out how an E. coli bacterium can go into a dormant state, called persistence, that allows it to survive while the rest of its colony is wiped out.

Despite some experts’ skepticism, each paper had been cited hundreds of times. And Harms told us:

I personally did believe in the published work. There had been papers from others that kind of attacked [the Gerdes lab’s theory], but that was not high-quality work.

But by November 2016, Harms figured out that the skeptics had been right.  Continue reading Overlooked virus “generated a mess,” infected highly cited Cell, PNAS papers

Fracking paper overstated size of methane leak from Marcellus Shale, earning retraction

via Greens-EFA

Last spring, a group of environmental scientists reported an impressive finding: Hydraulic fracturing (better known as fracking) in the Marcellus Shale region of the eastern United States was leaking enough methane to power a city twice the size of Washington, D.C. (We didn’t come up with that comparison, apt though it may be.)

Turns out that wasn’t true. Continue reading Fracking paper overstated size of methane leak from Marcellus Shale, earning retraction

“A painful lesson:” Authors retract paper after discovering mislabeled mouse lines

Neuroscientists have retracted a 2016 paper examining the genetic underpinnings of a degenerative motor neuron disease, after discovering that two mouse lines had been accidentally mislabeled.

According to the retraction notice, published in December in Acta Neuropathologica Communications, mice engineered to have a specific genetic mutation were mislabeled as the normal or wild type group.

The notice cites an investigation by the University of Florida; we asked the university for a copy of the report. The university sent us a redacted document, which a spokesperson told us was a self-report from the researchers regarding the mislabeling. The spokesperson explained: Continue reading “A painful lesson:” Authors retract paper after discovering mislabeled mouse lines

They thought they might solve the world’s energy problems. Then they realized they were wrong.

Frederick MacDonnell

Researchers are retracting a 2016 PNAS paper that described a way to create gasoline-like fuels directly from carbon dioxide in the atmosphere.

Senior author Frederick MacDonnell, a professor at the University of Texas at Arlington (UTA), told us he originally thought his team had made a preliminary breakthrough that might “solve the world’s energy problems.” Instead, he said:

It was an elaborate trap we fell into.

In a retraction notice that contains more information than we usually see, MacDonnell and his co-authors wrote: Continue reading They thought they might solve the world’s energy problems. Then they realized they were wrong.

PNAS retraction weakens theory that fish travel with siblings

In 2016, researchers at Oregon State University published a paper in PNAS that surprised the research community. They showed that certain fish species travel with their siblings — even fighting against the currents of the Pacific Ocean to stay together.

Needless to say, the research community was skeptical, given how difficult a feat this would be. And their skepticism appears to have been warranted.

Recently, the authors — led by Su Sponaugle — retracted the paper, saying a re-analysis of their data using newly developed research tools has erased their confidence in the results. According to Sponaugle, the quick reversal was thanks to the new technology and open data sharing, which led their findings to be successfully challenged within months of publication. She said her team conducted the study with the “best available knowledge we had at the time,” including what they thought were the most advanced tools available to them: 

Continue reading PNAS retraction weakens theory that fish travel with siblings

Caught Our Notice: Oops — 10-fold error reverses heart warning for Ghanaians

Via Wikimedia

Title: Ghanaians Might Be at Risk of Inadequate Dietary Intake of Potassium

What Caught Our Attention: Potassium-rich diets are thought to be “heart-healthy,” and after examining the average dietary habits of Ghanaian adults, researchers determined the average potassium (K) intake to be well below global standards.  However, the authors’ calculations of potassium intake per capita were too low by factor of 10, resulting in the incorrect conclusion that the average potassium intake was only 856 mg per day, an amount substantially lower than the World Health Organization (WHO) recommendation of 3510 mg/day.  The new calculations show an average K intake of 8,560 mg/day, well over the WHO guideline.  

We asked the corresponding author, David Oscar Yawson, about the source of the error, and he responded:

Continue reading Caught Our Notice: Oops — 10-fold error reverses heart warning for Ghanaians

Caught Our Notice: A retraction that is “useful for investigators”

Via Wikimedia

Title:  Yeast CAF-1 assembles histone (H3-H4) 2 tetramers prior to DNA deposition

What Caught Our Attention: Informative retraction notices can be infrequent, but rarer still are notices that fulfill an oft-ignored function: To be a source of learning for others in the field. Here, the authors offer a nearly 800-word “detailed description of the issues” with “some observations that may be useful for investigators conducting similar studies.” These authors embraced the retraction process, carefully explaining their findings or the lack thereof, for each figure from their now-retracted paper.     Continue reading Caught Our Notice: A retraction that is “useful for investigators”

”Definitely embarrassing:” Nobel Laureate retracts non-reproducible paper in Nature journal

A Nobel Laureate has retracted a 2016 paper in Nature Chemistry that explored the origins of life on earth, after discovering the main conclusions were not correct.  

Some researchers who study the origins of life on Earth have hypothesized that RNA evolved before DNA or proteins.  If true, RNA would have needed a way to replicate without enzymes. The Nature Chemistry paper found that a certain type of peptide — which may have existed in our early history — made it possible for RNA to copy itself.

Jack W. Szostak—a professor of chemistry and chemical biology at Harvard University in Cambridge, Mass., who shared the 2009 Nobel Prize in Physiology or Medicine with Elizabeth Blackburn and Carol Greider for their pioneering research on aging—told us he was “incredibly excited” when he “thought we had at least a partial solution to this problem,” which researchers have been working on for over 50 years.  

But in subsequent experiments, Tivoli Olsen — a member of Szostak’s lab — could not reproduce the 2016 findings. When she reviewed the experiments from the Nature Chemistry paper, she found that the team had misinterpreted the initial data: The peptide in question did not appear to provide an environment that fostered RNA replication.

The errors were “definitely embarrassing,” Szostak told us: Continue reading ”Definitely embarrassing:” Nobel Laureate retracts non-reproducible paper in Nature journal

Errors in govt database prompt authors to retract and replace paper in JAMA journal

Researchers have retracted and replaced a June 2016 paper in JAMA Internal Medicine after discovering errors in their data.

The paper explored whether Accountable Care Organizations (ACOs) — groups of health care providers who earn more when they deliver high-quality care without boosting costs  — improve care and lower health care costs for Medicare patients. The paper’s corresponding author, Carrie H. Colla, and her colleagues examined Medicare data over five years and found the ACOs provided “ modest savings on average”  and less hospital care.  

But the data from the Centers for Medicare & Medicaid Services (CMS) contained errors. According to Colla, after the paper was published, CMS “let us know in the fall [2016] that there were errors in the files, but weren’t able to give us final replacement files until winter.” Continue reading Errors in govt database prompt authors to retract and replace paper in JAMA journal

Authors retract plant biology paper after they realized sample was contaminated

Plant biologists from China have retracted a 2013 paper in The Plant Cell after discovering that some of the plant material used was “inadvertently contaminated.”

According to the retraction notice, the authors believe the contamination affects the main conclusion of their paper. Continue reading Authors retract plant biology paper after they realized sample was contaminated