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.
Although many scientists fear putting their data to the test of replication efforts, due to the embarrassment they’d feel if their findings couldn’t be repeated, a new study suggests those fears are unfounded.
The paper, published last week in PLOS ONE, found that scientists overestimate how much having non-replicable data will hurt their careers, and the community values those who are honest about what went wrong.
Authors of a paper on the origin and function of a family of transmembrane proteins have retracted it after an investigation at the University of Florida revealed that an author had falsified some results.
This is the third paper with falsifications that Chi Leung, a former UF postdoc, is responsible for; this summer, we reported on a retraction and a partial retraction of two other papers on which Leung was a co-author. The case is currently under investigation by the U.S. Office of Research Integrity National Science Foundation, a UF spokeswoman tells us.
The problems in the paper, “Phylogenetic, expression, and functional analyses of anoctamin homologs in Caenorhabditis elegans,”occur in a figure that compares mRNA levels in control and experimental populations of C. elegans. The paper was published in the American Journal of Physiology, and has been cited eight times, according to Thomson Scientific’s Web of Knowledge.
The retraction note explains that, according to the other authors, much of the data in the paper are valid:
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).
In this article we report a method to fabricate 2D TiO2–WO3 composite inverse opal films via a mechanical co-assembly route with a template of polystyrene spheres. Upon repeating the experiments described, we found that this was not an effective method for forming the films; often the film was broken or did not form at all.
The note also explains why the experiment didn’t work:
Look at the selection criteria for any major funding agency, and you will find it aims to support research that is “ground-breaking,” “innovative,” “high-risk,” and “at the frontiers of knowledge.”
But are these criteria delivering the best science? Think about the “reproducibility crisis,” familiar to many Retraction Watch readers: Evidence is growing that a high proportion of published research findings are not robust. This is bad news for funders; irreproducible research is a waste of money, and actually impedes scientific progress by filling the literature with irreproducible false-positive findings that, once published, never die.
A major source of irreproducibility comes from research that is funded but never reported. As I have noted previously, many researchers have a backlog of unpublished findings. All too often, they sit on a mountain of data that is unpublished simply because it is not the most exciting thing on their desk, and they need to be working on a new project in order to remain competitive. Negative results – e.g. where a promising treatment shows no effect, or an anticipated association between a genotype and phenotype fails to emerge — are likely to end up in the file drawer. By lingering in obscurity, they contribute to publication bias and the consequent distortion of the truth.
In October, the Academy of Medical Sciences (AMS) published a report considering reasons for irreproducibility in biomedical research and ways to overcome them. It was clear that the problem was not down to any one cause, and that a range of solutions needed to be considered — some bottom-up (such as better training of researchers), and some top-down, driven by institutions, publishers and, the focus of this post, funders.
An article about a dietary plan to help people lose weight has been retracted after other researchers raised concerns, and the authors failed to provide the data that supported their findings.
Waseda University has revoked the doctorate degree of the first author on the now-retracted Nature papers about a technique to create stem cells.
The technique — which claimed to provide a new way to nudge young cells from mice into pluripotency — was initially described in two 2014 Nature papers, both first-authored by Haruko Obokata. However, the papers were soon mired in controversy, corrected, then retracted later that year due to “several critical errors,” some of which were categorized by a RIKEN investigation as misconduct.
A disability journal is “paying significant attention” to papers authored by Anna Stubblefield, a former Rutgers researcher recently convicted of sexually assaulting a disabled man who participated in her research.
Stubblefield was convicted of sexually assaulting “DJ,” a man in his thirties with cerebral palsy who was “declared by the state to have the mental capacity of a toddler,” according to a lengthy piece in the New York Times. Stubblefield and DJ published papers in Disability Studies Quarterly; in one, Stubblefield describes a controversial technique which she claimed helped DJ communicate. But when she eventually used the technique to say DJ was in love with her, his family took her to court, and she was convicted of aggravated sexual assault.
Researchers in Germany have retracted their 2011 article in the Journal of Bacteriology after another lab pointed out a fatal error in the paper.
