Sometime in the middle of 2015, Jennifer Byrne, professor of molecular oncology at the University of Sydney, began her journey from cancer researcher to a scientific literature sleuth, seeking out potentially problematic papers.
The first step was when she noticed several papers that contained a mistake in a DNA construct which, she believed, meant the papers were not testing the gene in question, associated with multiple cancer types. She started a writing campaign to the journal editors and researchers, with mixed success. But less than two years later, two of the five papers she flagged have already been retracted.
Nearly 50 years ago, researchers in Uppsala, Sweden used cells from a patient to establish a brain tumor cell line that has become widely used. But a new study suggests that the most common source of that cell line used by scientists today may not be derived from that original patient’s tumor, raising questions about the results obtained in hundreds of studies.
Researchers are retracting two papers about molecular signalling in plants — including one from the Proceedings of the National Academy of Sciences (PNAS) — after discovering some inadvertent genotyping errors. But that was only after they used the problematic plants for an entire year without realizing they’d made a mistake.
In a pair of refreshingly transparent and detailed notices, the authors explain that the transgenic plants used in the papers included genotyping errors, which invalidated their findings. According to the notices, first author Man-Ho Oh generated the problematic transgenic plants, while corresponding author Steven C. Huber, based at University of Illinois, Urbana-Champaign (UIUC), took responsibility for omitting some critical oversight.
Huber told us that there were only two papers that used the transgenic plants in question, so no other retractions will be forthcoming.
The authors of a paper on a new probiotic strain of bacteria found in pig feces have retracted it from Animal Science Journal after discovering some of the bacteria might have been contaminated.
Readers likely know by now how easy it is for this to happen, as we frequently report on retractions due to similar reasons. Like other instances of mistaken cell identity, the authors of this 2013 paper realized the mistake following further tests of the bacteria used in the experiment.
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 highly cited Nature letter that purported to discover a much sought-after, stable light source from quantum dots, after they realized the light was actually coming from another source: the glass the dots were affixed to.
When the paper “Non-blinking semiconductor nanocrystals” was published in 2009, it received some media coverage, such as in Chemistry World. That’s partly because very small sources of “non-blinking” light could have wide-ranging, big-picture applications, author Todd Krauss, a physical chemist at the University of Rochester, told us:
Off the top of my head, a quantum computer. Quantum cryptography is another one. People want a stable light source that obeys quantum physics, instead of classic physics.
The retraction note, published Wednesday, explains how the researchers found out the effect was coming from the glass, not quantum dots:
A trio of papers on health issues in elderly patients, all sharing an author, have been retracted from Geriatrics & Gerontology International.
The reasons for the retractions range from expired kits, an “unattributed overlap” with another paper, “authorship issues,” and issues over sample sizes.
Tomader Taha Abdel Rahman, a researcher at Ain Shams University in Cairo, is the first author on two of the papers, and second author on the third.
The author of an article mapping the genome of an infectious bacterium is pulling the paper because — well, it wasn’t the bacterium she thought it was.
Study author Celia Abolnik is retracting her paper in Genome Announcements because it didn’t actually map out the DNA of Mycoplasma meleagridis, a bacterium that typically infects turkeys but has recently been found in chickens.
The trouble was, the sequence for Mycoplasma meleagridis in the National Institute of Health’s DNA database, Genbank, was actually a different variety of bacteria — Mycoplasma gallinaceum, another scourge of poultry.
The retracted paper, “Effect of Temperature and Storage Time on Sorbitol Dehydrogenase Activity in Sprague-Dawley Rat Serum and Plasma,” looked to test the durability and stability of sorbitol dehydrogenase, an enzyme used to detect cancerous liver damage in rats.
Researchers are retracting two papers about molecular signalling in plants — 
