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(US) New eLife editor Michael Eisen wants to shake up scientific publishing – Berkeley News (Robert Sanders | April 2019)0

Posted by Admin in on January 24, 2020
 

The University of California system’s recent decision to walk away from negotiations with scholarly journal publishing giant Elsevier highlights once again the many problems within the scientific publishing business, a $10 billion-per-year worldwide enterprise that is the bedrock of modern science. Publishers like Elsevier, Springer — which publishes the high-impact journal Nature —and dozens of other for-profit companies and nonprofit scientific societies are an essential part of the give-and-take of science, offering a place to publish and share new results. But they also charge for scientists and the public to read those results, much of which the public originally funded through federal agencies such as the National Institutes of Health (NIH) and the National Science Foundation (NSF). The UC most recently paid Elsevier $11 million for a year’s worth of access to its journals, which include the well-known medical journal The Lancet and more than 2,500 lesser-known titles, from Poetics to Fungal Biology.

Michael Eisen, a professor of molecular and cell biology and a Howard Hughes Medical Institute investigator, has done his part to disrupt the stodgy business, which he thinks not only takes advantage of authors and universities, but distorts the process of science. As a founder 19 years ago of the first open access journal, PLOS (Public Library of Science), he sought to establish a new business model where scientists pay to publish, while anyone can view the results for free. Other journals slowly moved in that direction, but even today, only about 20 percent of all published research is open access, and almost none of the papers appearing in high profile publications like Nature, Science and PNAS(Proceedings of the National Academy of Sciences) can be read by the public without charge.

Appointed last month the editor-in-chief of the open access journal eLife — Berkeley Nobel Laureate Randy Schekman is stepping down as founding editor — Eisen has a new platform to shake up the field of science publishing and help make it serve scientists and the public.

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Eleven tips for working with large data sets – Nature (Anna Nowogrodzki | January 2020)0

Posted by Admin in on January 22, 2020
 

Big data are difficult to handle. These tips and tricks can smooth the way.

Big data are everywhere in research, and the data sets are only getting bigger — and more challenging to work with. Unfortunately, says Tracy Teal, it’s a kind of labour that’s too often left out of scientific training.

“It’s a mindset,” says Teal, “treating data as a first-class citizen.” She should know: Teal was until last month the executive director of The Carpentries, an organization in Oakland, California, that teaches coding and data skills to researchers globally. She says there’s a tendency in the research community to dismiss the time and effort needed to manage and share data, and not to regard it as a real part of science. But, she suggests, “we can shift our mindset to valuing that work as a part of the research process”, rather than treating it as an afterthought.

Here are 11 tips for making the most of your large data sets.

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Meta-analysis study indicates we publish more positive results – ARS Technica (John Timmer | December 2019)0

Posted by Admin in on January 13, 2020
 

Meta-analyses will only produce more reliable results if the studies are good.

While science as a whole has produced remarkably reliable answers to a lot of questions, it does so despite the fact that any individual study may not be reliable. Issues like small errors on the part of researchers, unidentified problems with materials or equipment, or the tendency to publish positive answers can alter the results of a single paper. But collectively, through multiple studies, science as a whole inches towards an understanding of the underlying reality.

Similar findings have been found before, but it’s important to rearticulate the value of negative results to science and practice.  This speaks to poor research culture and training. University education, and even high and primary school, do not acknowledge that failure is part of discovery. The rewards for ‘success’ are high and it is very tempting for students that can lead to research misconduct.

A meta-analysis is a way to formalize that process. It takes the results of multiple studies and combines them, increasing the statistical power of the analysis. This may cause exciting results seen in a few small studies to vanish into statistical noise, or it can tease out a weak effect that’s completely lost in more limited studies.
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But a meta-analysis only works its magic if the underlying data is solid. And a new study that looks at multiple meta-analyses (a meta-meta-analysis?) suggests that one of those factors—our tendency to publish results that support hypotheses—is making the underlying data less solid than we like.

Publication bias

It’s possible for publication bias to be a form of research misconduct. If a researcher is convinced of their hypothesis, they might actively avoid publishing any results that would undercut their own ideas. But there’s plenty of other ways for publication bias to set in. Researchers who find a weak effect might hold off on publishing in the hope that further research would be more convincing. Journals also have a tendency to favor publishing positive results—one where a hypothesis is confirmed—and avoid publishing studies that don’t see any effect at all. Researchers, being aware of this, might adjust the publications they submit accordingly.

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Russian journals retract more than 800 papers after ‘bombshell’ investigation – Science (Dalmeet Singh Chawla | January 2020)0

Posted by Admin in on January 11, 2020
 

Academic journals in Russia are retracting more than 800 papers following a probe into unethical publication practices by a commission appointed by the Russian Academy of Sciences (RAS). The moves come in the wake of several other queries suggesting the vast Russian scientific literature is riddled with plagiarism, self-plagiarism, and so-called gift authorship, in which academics become a co-author without having contributed any work.

The RAS commission’s preliminary report documenting the problems and journals’ responses to them is “a bombshell,” says Gerson Sher, a former staffer at the U.S. National Science Foundation and the author of a recent book on U.S.-Russia science cooperation. The report, released yesterday, “will reinforce the suspicions and fears of many—that their country is not going down the right path in science and that it’s damaging its own reputation,” says Sher, who applauds RAS for commissioning the investigation.
Russia’s roughly 6000 academic journals, the vast majority published in Russian, are popular among the country’s academics. A 2019 study found that Russian authors publish far more in domestic journals than, for instance, their counterparts in Poland, Germany, or Indonesia. But standards are often low. In March 2018, for instance, Dissernet, a network aimed at cleaning up the Russian literature, identified more than 4000 cases of plagiarism and questionable authorship among 150,000 papers in about 1500 journals.
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