A Cancer Cell paper that caused a flurry of activity on the website PubPeer is under investigation, after the last author announced on the site that he’d requested a correction from the journal.
The 2012 paper sparked a lively dialogue last month on the post-publication discussion site, as commenters questioned Western blot images in which some bands appeared to be duplicates. The last author responded, noting he had alerted the journal to a “mishap,” and a correction would be forthcoming. However, some commenters remained unsatisfied, and questioned why the correction was taking so long to appear, as well as the explanation for what went wrong.
A spokesman from Cancer Cell confirmed to us the paper is under investigation:
This latest correction, to a paper on the mechanisms behind RNA silencing in Arabidopsis, was published in RNA. The 2007 paper has been cited 101 times, according to Thomson Scientific’s Web of Knowledge. The corrigendum modifies three figures in total.
Science has retracted an August paper on an interesting electric current researchers observed in a kind of material called a topological insulator. Well, a current the researchers — based at Stanford and MIT — thought they had observed.
A magnetic field with particular attributes reported in the paper seemed to provide evidence of the current. But the researchers soon discovered that the field might have been, in part, an artifact of the very device they used to detect it. The authors, along with a few other researchers, have published that subsequent finding on the physics preprint server, arXiv.
Researchers in Germany have retracted their 2011 article in the Journal of Bacteriology after another lab pointed out a fatal error in the paper.
The article, “Escherichia coli Exports Cyclic AMP via TolC,” came from a group at Tübingen University led by Klaus Hantke. The paper focuses on the crucial role of the membrane channel TolC in exporting cyclic AMP (cAMP)-cAMP receptor protein (CRP) complex, which regulates nearly 200 E. coli genes. According to the abstract:
The data demonstrate that export of cAMP via TolC is a most efficient way of E. coli to lower high concentrations of cAMP in the cell and maintain its sensitivity in changing metabolic environments.
A group of astrophysicists has notched a pair of corrections for papers on galaxy clusters, thanks to an error that affected several figures in the papers, but not the overall conclusions.
The errors came in the catalog of “mock” galaxies that first author Fabio Zandanel, a postdoc at the University of Amsterdam, created to model features that are found in clusters of galaxies. Two mistakes canceled each other out “almost perfectly,” says Zandanel, making the changes that resulted from them subtle.
If you could help reduce the waste of tens of billions of dollars per year in research spending, you’d do it, right?
This is the second in a series of two guest posts about the havoc misidentified cell lines can wreak on research, from Leonard P. Freedman, president of the Global Biological Standards Institute. Freedman who published a paper last summer detailing the financial costs of non-reproducible research — namely, tens of billions of dollars per year. Some of that non-reproducible research is due to the use of contaminated or misidentified cell lines. He writes about one key step to tackling the problem: Ask every scientist to use a relatively inexpensive technique to validate the identity of their cell lines.
Meanwhile, we have to deal with the issue of all the previously published papers that relied on problematic cell lines, now contaminating the scientific literature. Scroll down to the bottom of the post to take a poll on what you think should be done about those papers.
Leonard Freedman
As new frontiers of science emerge, from Pluto to proteins, the very cornerstone of the scientific process—reproducibility—has also reared its head as a huge problem. Estimates of irreproducibility rates of published peer-reviewed papers range from 51% to 89%. An analysis that two colleagues and I recently published in PLOS Biology suggests the U.S. spends $28 billion per year on non-reproducible preclinical research; global spending could be up to $60 billion per year. This lack of reproducibility typically results from cumulative errors or flaws in one or more of the following areas: biological reagents and reference materials, study design, laboratory protocols, and data analysis and reporting. Given the size, scale, and especially the complexity of reproducing preclinical research, there is no single magic bullet fix. This is a difficult issue for scientists to own up to, and for the public to grasp.
What if we told you that approximately 1 in 6 researchers working with human cells are using the wrong cell line? In other words, they believe they are studying the effects of a drug on breast cancer cells, for instance, but what they really have are cells from the bladder. That is the unfortunate reality in life science research today, affecting hundreds of labs. It’s a major source of problematic papers which cannot be replicated, wasting scientists’ time and funding.
We’re pleased to present a guest post from Amanda Capes-Davis, chair of the International Cell Line Authentication Committee (ICLAC), a voluntary scientific committee created to improve awareness of misidentified cell lines. She also collects news about cell line and culture contamination. This is the first in a series of two posts from guest authors about how problematic cell lines are contaminating the scientific literature, and how we can clean it up.
In 2010, I worked alongside Ian Freshney of Glasgow University and other colleagues to publish a list of cross-contaminated or otherwise misidentified cell lines in the International Journal of Cancer. This database of false cell lines is now curated by the International Cell Line Authentication Committee (ICLAC).
Authors have retracted a large meta-analysis claiming that rising levels of carbon dioxide don’t always reduce nutrients in plants.
After commenters on PubPeer raised concerns, the authors say they found several unintentional errors in their data that could “significantly change conclusions” of the paper in Plant Ecology, according to the retraction note.
The paper found that the impact of rising CO2 depends on many factors — in some cases, extra amounts of this greenhouse gas could actually increase plant nutrients. Trouble is, some of the papers that cited the now-retracted article came to the opposite conclusion: Increased carbon dioxide levels do decrease plant nutrients.
The retraction note for “CO2 effects on plant nutrient concentration depend on plant functional group and available nitrogen: a meta-analysis” explains some of the specifics of the errors, and says that there was “no evidence of bias:”
A new project does the relatively straightforward task of comparing reported outcomes from clinical trials to what the researchers said they planned to measure before the trial began. And what they’ve found is a bit sad, albeit not entirely surprising.
As part of The Compare Project, author and medical doctor Ben Goldacre and his team have so far evaluated 36 clinical trials published by the top five medical journals (New England Journal of Medicine, the Journal of the American Medical Association, The Lancet, Annals of Internal Medicine, and British Medical Journal). Many of those trials included “switched outcomes,” meaning the authors didn’t report something they said they would, or included additional outcomes in the published paper, with no explanation for the change.
Here are the latest results from the project, according to its website:
An incorrect proof has felled a math paper. There’s not too much to say in a straightforward situation like this one, which we’ve seen before — the result of honest errors, not any malfeasance.
In this paper, we give an affirmative answer to Mbekhta’s conjecture (Mbekhta, 1990) about the pseudo Fredholm operators in Hilbert space. As a consequence, we characterize pseudo Fredholm operators and we prove that the generalized Kato spectrum satisfies the spectral mapping theorem in the Hilbert spaces setting.
The paper — published in the Journal of Mathematical Analysis and Applications — has been cited twice, according to Thomson Scientific’s Web of Knowledge.
A group of astrophysicists has notched a pair of corrections for papers on galaxy clusters, thanks to an error that affected several figures in the papers, but not the overall conclusions.
