The real problems of post publication peer review

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.

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A milestone

Sometime last night this blog received its 50,000th page view. I write this blog because I like to. That others find the content worth reading at times is lovely, thank you.

What has been read the most and the least?

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Should universities refund grants based on retracted papers?

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.

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REF 2014 and all that (II): Continuous progress

REF 2014 is the fourth assessment in a row where we have made real progress, and this is very pleasing.
In RAE 1996 the newly formed School of Biological Sciences attained a grade 4, which equates to research of national standard, with some research of international standard.
In RAE 2001 44/65 staff were returned, attaining a grade 5B. This equates to over 50% (and we were only just over the 50% bar on this one) of returned staff producing research of international standard. In RAE 2008 terms (and in REF 2013) this (more or less) corresponds to 2* to 4*. Though difficult to compare between different grading systems, a guesstimate of the School of Biological Sciences RAE 2001 performance in RAE 2008 terms is ~ 35-40% 2*-4* research, with the balance of 65-60% at 1*.
In RAE 2008 all 65 staff were returned, with 40% 4* and 3*, 45% 2*, 15% 1*, and, as I mentioned in the previous post in REF 2014 we are at least up to 65% of all staff having 3* and 4* outputs.
So progression in score. This also reflects real change, it isn’t cosmetic. It would be obvious to anyone visiting the School/Institute over the 20 years 1994-2014 that the place has changed and there is a far greater buzz about.
This begs a question, which I will turn to in the future post: Was it RAE/REF that drove these changes or something else, and so is RAE/REF worthwhile?

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Science does not exist without post publication peer review

An excellent article on the coming of age of post publication peer review by Emma Stoye is up at Chemistry World
She quotes me (correctly) as stating that “Science does not exist without post publication peer review. If anyone wants to follow the quote up, my own posts can be found here.

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2014 REF and all that (I)

Now that the dust has settled, institutions have posted their interpretations of the results of the 2014 Research Excellence Framework (REF), and people have gone through the results and institutional interpretations in various blogs, I thought it time to put my oar in. This is the first of a series of posts that will look at the REF 2014 score of the Institute of Integrative Biology, how RAE/REF scores for this academic enterprise have fared over time, and whether REF/RAE is of any use.

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Why gel splicing is not OK

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.

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An accidental discovery

Changye and Yong’s first paper, up as a preprint at PeerJ
in accord with my 2015 and 2014 New Year resolutions describes an accidental discovery. One of their co-authors, Sarah Taylor, was exploring HaloTag as an alternative means of labelling protein to green fluorescent protein, and I thought it would be good to be able to have a pure in vitro system to validate labelling. So Changye and Yong made some recombinant HaloTag fibroblast growth factor-2 (HT-FGF2). When they showed me the gel, they noted that HT-FGF2 did not seem terribly promising, because there was quite a lot of protein in the bacterial pellet.

It is at this point that the professor earns his keep,

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