Responding to questions raised on PubPeer

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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REF 2014 and all that (III): is RAE/REF a driver or passenger of change?

Reading my colleagues’ papers, a key step in our evaluation of outputs, was very, very useful. I learned many new things and also understand the research across my Institute and indeed large parts of the Faculty much better. The University has yet to use this knowledge accumulated by its REF Wallahs – it would make sense for these people to inform research policy, they have read a lot of papers.

The Faculty Clinical Medicine subpanel meetings were fun – my colleagues on this panel are a great bunch to work with and their injection of humour into proceedings eased the pain.

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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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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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Onwards and upwards

Last year’s resolution was: I will only referee papers from Open Access or Learned Society journals. This I more or less stuck to, except in a couple of cases where it really had to be me.

In 2015 I will follow the resolution 100%, but will add two further resolutions:
1. Papers where I am PI will only be published in Open Access journals (something I achieved in 2014)
2. All the above papers and for as many of those where I am co-author as possible will also provide Open Data. This is something started in late 2014 and which will continue in 2015.

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