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Archive for the ‘Research integrity’ Category


A recent article on bioarchiv “Amending published articles: time to rethink retractions and corrections?” puts forwards ideas on how we might change the way we deal with retractions and corrections. (more…)

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I am a fan of PubPeer, as it provides a forum for discussion between authors and the wider community, something I have discussed in a number of posts (two examples being here and here). Two days ago, My colleague Mike Cross came by my office, having just delivered a pile of exam scripts for second marking (it’s exam and marking season), asking if I had seen a comment on our paper on PubPeer. I had not – too many e-mails and too busy to look at incoming!
So I looked at the question, which relates to panels in two figures being identical in our paper on neuropilin-1 and vascular endothelial growth factor A (VEGFA) – indeed they are labelled as being identical.
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Discussion surrounding post publication peer review (previous post here seems to be growing and one issue that is frequently raised is anonymity. In a PLOS Medicine editorial Hilda Bastian argues that current post publication peer review is over focussed on what apparently is wrong in papers and that anonymity is a threat to effective post publication peer review.
A PubPeer thread takes issue with these and some other points and I have also joined in (I am Peer2). We should remember that any notion of power has nothing to do with scientific capability – indeed there may even be an inverse relation. So providing those with the least power (so the most disenfranchised) a means to participate in post publication peer review is essential. Though we have no data on PubPeer, PubMed Commons is a venue for the established. There are some critiques, there is also a fair amount of hagiography too. I would hazard a guess that PubPeer is far more diverse in terms of the career stage of participants and in terms of their gender/social group. Certainly my anecdotal evidence suggests as much, and that is all I have to go on. (more…)

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Leonid Schneider has a guest post on Retraction Watch “What if universities had to agree to refund grants whenever there was a retraction?” that has generated a lot of discussion. My own comment became so long that I am posting it below. For those who are not aware, in the USA, the Office of Research Integrity (ORI) has the power to reclaim from institutions grant funding acquired through fraudulent means, e.g., manipulated or made up data, though there is a time limit and this is only exerted in a fraction of the cases investigated by ORI. No other country has a similar or analogous mechanism.

I like Leonid Schneider’s idea. (more…)

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Gel (see footnote at end for a brief description of gels aimed at non-biologists) splicing is a term that describes the cutting and pasting of images of lanes (where 1 lane = 1 sample) and placing the images of the lanes in a different order or even combining lanes from different gels. A more extreme form is to simply shift the subsection of the lane, corresponding to the probed molecule, from one lane to the next.
This is wrong and it always has been. However, in post publication peer review on PubPeer, it is often defended, particularly for “older” papers, from a decade or more ago. This then raises arguments about what was acceptable then and are we shifting the goalposts of scientific integrity? The matter has even been a “Topic” on PubPeer. (more…)

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The question relates to what Langmuir termed “Pathological Science”, simply put “people are tricked into false results … by subjective effects, wishful thinking or threshold interactions“. There is a lot of pathological science and I only use the examples below, because I am most familiar with them; for nanoparticles, I have a personal interest in understanding these materials, since I use them to try to make biological measurements, e.g., here.
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I need a “Bullshit-O-Meter”, which would determine the purity of bovine excrement that at times heads my way. In a previous post, “Why doesn’t the sun go around the earth?”, I put forth my views on the case brought by Fazlul Sarkar that aims to lift the anonymity of PubPeer. This led to an e-mail from Weishi Meng, which starts (note I have redacted the co-addressee).

“Dear Drs. XXX and Fernig, (more…)

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