I’m rather late getting round to this but, for the record, here is a piece I wrote for Research Fortnight in late November on the challenges that preprints pose to embargoed press releases of research reports.
The tl;dr version (though the piece is only 800 words!) is that the benefits of preprints very likely outweigh the convenience of embargoes.
Posted inScience|Comments Off on ICYMI No. 9: Preprints and Embargoes
“Questions you might want to address are whether you should somehow have to conduct yourself differently? Dress more smartly? Speak more seriously? Do people treat you differently? Does an element of imposter syndrome kick in? And what about workload and direction?
The idea is to give a personal perspective that, nevertheless, gives a few pointers to people who have just become professors.”
This morning I was asked for a comment on the implications of the US presidential election for the scientific world. This was my immediate response:
Unlike the day after the EU referendum vote, when I was bitterly upset, I just feel numb today. I don’t know if that is a kind of despair settling in because despair is precisely the wrong type of reaction to Trump winning the US presidential election. Throughout the campaign he showed himself to be a fascist and racist who bragged about his mis-treatment of women. He showed scant regard for truthfulness and espoused denialist views on climate change. It seems unlikely that the scientific and research prowess of the USA will flourish under such a president, but perhaps the checks and balances built into the US constitution will provide some sort of protection (notwithstanding the fact that the Republicans appear to be in control of Congress and the Senate).
More worrying is the sense of a turn in the tide of history arising from Trump’s victory and the Brexit vote. I’m in my fifties and in my lifetime I have seen Britain join the EU, I have seen the end of the Cold War, and the end of apartheid in South Africa. In my own home nation I have seen the IRA lay down its arms. And yet here we are witnessing the rise of divisive nationalist and xenophobic instincts, which have been deliberately agitated in both recent election campaigns.
Clearly part of the disgruntlement at the status quo is due to the unequal spread of the benefits of globalisation (exacerbated by the lack of consequences for rich bankers in the wake of the 2008 financial crisis). That has to be addressed politically. For researchers, increasingly branded as a self-serving elite that is out of touch with the common people, we need to redouble our efforts to stand up for evidence, and for the intrinisically international nature of what we do. We need to work harder to demonstrate the relevance of our work to the wider population and the values that underpin it. In the UK we are already pretty good at public engagement but I think we may not be good enough for the times that we now find ourselves in.
Science is Vital this week launched a campaign to seek amendments to the Higher Education and Research Bill 2016. The bill is a rather dry and procedural piece of legislation but hidden amongst its many sections and schedules are real threats to the autonomy and independence of UK universities and to the capacity of the research community to guide the research agenda.
The particular issues at stake are summarised on the Science is Vital website and laid out in more detail in a piece I wrote for the Guardian. We hope as many people as possible will write to their MPs to voice their concerns and ask for the necessary amendments to be made. Writing letters is always a bit of a chore so in case it might help some to get over the activation energy barrier, here below I am posting the letter that I have sent this evening to my MP, Mr Bob Stewart, the member for Beckenham. Please feel free to re-work for your own missive.
Dear Mr Stewart
Higher Education and Research Bill 2016
I write as your constituent and as a professor at Imperial College to express my grave reservations about several aspects of the Higher Education and Research Bill 2016, which is currently before Parliament.
As written, the bill removes long-standing legal protections of the autonomy of UK universities and research councils that have been vital to the health these institutions and to the tremendous strength of the UK research base. It is crucial that the bill be amended.
In short, the bill seriously undermines important academic freedoms of universities by giving the Secretary of State the power to give guidance on what courses may be taught, a power that is amplified by creation of an Office for Students with the authority to remove the university status of institutions. On the research front, the bill concentrates further power in the hands of government by giving the Secretary of State the authority to create or abolish research councils and to redirect their research remit. Such decisions will not require consultation or parliamentary scrutiny.
I understand the practical reason behind this shift of power – to enable flexible decision-making in reshaping higher education and research – which on the face of it seems sensible enough. But the loss of parliamentary scrutiny is nevertheless deeply worrying. The present minister Jo Johnson may not have any intention of abusing these powers – and indeed he has tried to offer some verbal reassurances. But who is to say what his successor might do? It would be wiser to build protections into the legislation from the outset.
The key amendments required can be summarised as follows:
Remove the provision (Part 1, Sections 2(2) & 2(4)) allowing the Secretary of State to give guidance to the Office for Students on what courses may be taught by universities.
Change the provision (Part 1, Section 43(1)) allowing the Office for Students (a body appointed by the Secretary of State) to revoke the right of institutions to grant degrees and retain the name ‘university’, so that each such decision requires parliamentary assent.
Change the provision (Part 3, Section 87(5)) allowing the Secretary of State to create or abolish a research council, or to alter their remits without parliamentary assent.
Without these amendments there is a real risk that this Parliament will preside over a serious weakening of the independence enjoyed by our universities and our research base. As a university professor, clearly I have a conflict of interest in this matter, but this is not special pleading. Important cultural institutions are at stake – as well as the national interest.
While the academy might occasionally have butted heads with governments on a range of issues over the years, I hope you will agree that such disputes are an essential part of the life-blood of an open democracy. Ideas have to be tested to destruction if sound decisions about the best interests of the country are to be made.
I would be grateful if you could find the opportunity to relay these concerns to the Minister for Universities and Science and, if possible, to communicate them on the floor of the house.
I would be more than happy to meet in person to discuss these issues in greater detail.
It is the weekend and I have been treating myself to some time with the paper. Usually, I buy the Saturday Guardian. On occasion I will also get The Observer on a Sunday but most weekends I don’t have the time to absorb both. Sometimes even one newspaper is too much.
The book review section is a particular favourite and one of the reasons I have switched away from the digital version of the paper that is served on the web. Not only does this afford the nostalgic and tactile pleasures of the paper paper, but it also releases me from the linear tether of online searches into the comradely hands of the editors, on whom I rely each week to dish up a collection of the new and the unexpected.
I am rarely disappointed, but the joy of novelty is almost invariably accompanied by sweeping feelings of helplessness amid a rising tide of “yet more stuff”. Not only does each fresh volley of book reviews bring new titles to add to my list of the unread, but the reviews invariably also refer to earlier books and authors previously unknown to me. Worse still for my self-confidence, the reviews tend to be written by people whose learning embraces whole movements and epochs of human history, and whose judgement of the achievements of humankind down through the ages rings with cast-iron assurance. Am I the only reader drowning in information who gawps at such a firm grasp of the world? So much knowledge on show makes me uneasy. It compounds my fear of being a dilettante – flitting here and there across the periphery of the world of ideas without really understanding the centre.
In truth this isn’t so serious fear because it doesn’t put me off my weekend read. I can tolerate the discomfort for the sake of the rewards. Such as last weekend, when, in Mary Beard’s review of James Stourton’s new biography of art historian Kenneth Clark, I was once again pleased and disconcerted to have my ignorance taken by surprise. Although I had thrilled at Clark’s Civilisation, his beautiful 1969 television documentary on the importance of European art, I guess I should have expected that not everyone was so impressed. The teenage Mary Beard was also delighted by it on first viewing but learned quicker than I did to mistrust the “great man” approach to history. And nor was the critic John Berger, whose own later documentary, Ways of Seeing, Beard noted in her review as a important critical response to Clark (who nevertheless still has his defenders).
I had never heard of Berger or his 1972 television series which, it turns out – why did I expect anything else? – is widely regarded as a seminal piece of work. Nevertheless, I was sufficiently intrigued to seek out Ways of Seeing online. All four of the 30 minute episodes are available on YouTube.
As was the style of the time the presentation is rather static – large chunks of each episode consist of Berger in a studio, standing in front of a plain screen, just talking. His patterned shirt and 70’s hairstyle strike a more relaxed tone than Clark’s buttoned-up tweediness, but to my ear the accent was no less posh and the story he had to tell no less riveting.
I would need to watch Civilisation again to triangulate precisely for points of opposition. Although there are clear references to Clark’s interpretation of the meaning of art and, in particular, the nude, Berger’s agenda is radically different. His aim is not history per se, but to interrogate the process of looking.
Each episode is a short essay. The first discusses the importance of context, remarking specifically on how modern reproductions of works in print and on television easily detach them from the artist’s intention. The second brings a thoughtful, feminist perspective to the nude and how such paintings reflect the power imbalance between men and women. The third discusses the development of oil painting as a particular way of representing real objects, especially possessions that denote the wealth and status of those who commissioned works of art. And the last episode shows how colour photography has largely supplanted this function of oil painting, but also altered it through widespread use in advertising to create images that, rather than showing achieved wealth and status, foment modern anxieties of aspiration.
But that is just a potted summary. I will leave you to discover for yourself. As Berger himself says in closing the documentary, everything “must be judged against your own experience.”
Today sees the publication on bioRxiv of a revised version of our preprint outlining “A simple proposal for the publication of journal citation distributions.” Our proposal, explained in more detail in this earlier post, encourages publishers to mitigate the distorting effects on research assessment of journal impact factors (JIFs) by providing a simple method for publishing the citation distributions that are so incompletely characterized by the JIF.
Since it was first published on 5 July 2016, the preprint has been downloaded well over 11,000 times. It was widely reported in various news outlets and has generated a large volume of commentary on social media (see metrics tab for the article at bioRxiv). As an exercise in post-publication peer review we could hardly have wished for a better response.
In revising our preprint, we have tried to take on board the most substantive criticisms raised online and in follow-up emails from a number of people. These criticisms and our explanation of how we have addressed them are laid out in the Responses to Comments document that is published today alongside the revised preprint (as Supplemental File 4). We are extremely grateful to all those who took the trouble to engage in these discussions and believe that the new version of the preprint provides a much clearer explanation of the rationale behind our work.
We discussed the option of submitting the revised preprint to a peer-reviewed journal but decided in the end not to do go down this route. This decision is primarily motivated by the fact that the preprint has already received extensive peer review from more than a dozen commentators and is unlikely to be altered significantly by further scrutiny. We also feel, given the core message of the article (which is in any case more of a policy paper than a research paper), that there is symbolic value in sticking with a publication venue that does not have an impact factor. However, that choice should not be taken to imply any veiled criticism of the more traditional practices of publication through a scholarly journal, in particular also of work previously posted as a preprint. The mores and modes of academic publishing may currently be the subject of lively discussion but that is a debate for another time and another place.
Finally, we hope that our preprint will continue to be read and discussed, and that its recommendations will be implemented widely by research journals to improve clarity in reporting citation metrics (as some of the journals associated with the undersigned have already done). This is the last revision that we intend to post (barring corrections for any residual errors of fact), so it should be treated as the version of record. Like any traditional journal article, our preprint must now stand or fall on the merits that it has today, the moment of publication.
Vincent Larivière, (Université de Montréal, Canada)
Véronique Kiermer, (PLOS, USA)
Catriona J. MacCallum, (PLOS, UK)
Marcia McNutt, (National Academy of Sciences, USA)
Mark Patterson, (eLife, UK) Bernd Pulverer, (The EMBO Journal, Germany)
Sowmya Swaminathan, (Nature Research, USA)
Stuart Taylor, (The Royal Society, UK)
Stephen Curry, (Imperial College, UK)
In case you missed it last week, I had a segment in the Naked Scientist’s 15th anniversary radio show. Or rather, three segments, based on a day-in-the-life-of-a-scientist piece that I wrote a few months back on the Guardian, that were woven into an hour-long programme devoted to (and titled) Scrutinizing Science.
If you have the time I’d recommend listening to the complete show because the whole is very much greater than the sum of its parts, most of which, I’m bound to say, are better than my contribution.
For the program I reworked my original article to pull out themes linked to scientific careers,scientific publishing and dealing with the media – and recorded them in a studio at the university (the links take you to the audio and text for each segment). The pieces don’t quite have the lightness of touch of the original. Plus, I’m not a huge fan of my own voice and winced here and there at my phrasing, but your mileage may vary.
I’m not really selling this, am I? It’s probably just a bout of impostor syndrome and everything’s fine. Anyway, my thanks to producer and presenter for Graighagh Jackson for the chance to contribute to the Naked Scientists’ anniversary programme.
It is a truth universally acknowledged that a researcher in possession of interesting experimental results, must be in want of a journal with a high impact factor.
It is also true – and widely understood – that journal impact factors (JIFs) are unreliable indicators of the quality of individual research papers. And yet they are still routinely used for that purpose, despite years of critique, despite the San Francisco Declaration on Research Assessment (DORA), despite the Leiden Manifesto, and despite The Metric Tide report.
But today sees the arrival of a new initiative to challenge the mis-use of JIFs in research assessment. I have joined forces with bibliometrician Vincent Larivière, and co-authors from PLOS, eLIFE, the Royal Society, EMBO Journal, Science, and Springer Nature, and together we have published a new paper, “A simple proposal for the publication of journal citation distributions,” on the BioRxiv preprint server.
The JIF, calculated each year as the mean number of citations to papers published in a journal in the previous two years, is the metric that will not go away. Its longevity has at least two sources. First, it is beloved of journal publishers (despite the criticisms often voiced by journal editors), who see it as a valuable tool in brand management. The good opinion of authors and readers is, quite reasonably, good for business. Second, the JIF is easily elided with prestige in the minds of researchers and their institutional managers. Pride in our reputations matters to us, and for good reason – science is quintessentially a human endeavour. But that elision confers on the JIF a seductive legitimacy in research assessment, giving rise to the well-known prejudices with regard to its influence on career progression.
Our proposal aims to bring some cool reason to this troubled situation. We are asking journals to publish the citation distributions that underlie the JIF (using the simple protocols detailed in the paper). The move is avowedly pragmatic: we recognise the reality of impact factors but, by facilitating the generation and publication of journal citation distributions, we aim to raise awareness of the broader picture that JIFs conceal. In doing so, we want to focus the attention of assessors on the merits of individual research papers.
I have already laid out the reasons for publishing citation distributions in threepreviousposts, so won’t repeat the details here. In any case, the argument is summarised in our brief preprint, which I would very much like you to read.
There is nothing especially new or original in our approach – except, and this is something that gives me particular pleasure and stirs my expectations, that it is the product of a constructive collaboration with several well-known publishers. I hope their example will soon be followed by others.
We harbour no illusions about this paper quickly neutralising the distorting pull of JIFs on research assessment. Nevertheless, our proposal is simple, transparent and reasonable. It is a feasible step in the right direction one that – with luck – will soon be universally acknowledged as such.
P.S. Our paper is a preprint and we would very much welcome critical comments and suggestions as to how it might be improved. Please comment at bioRxiv.
I have just posted a preprint of a book chapter on the interactions of open access and public engagement with science. It’s called “Open Access: the beast that no-one could – or should – control?” and is my contribution to an upcoming book – “‘Here be monsters’: Science, politics and the dilemmas of openness” which is being edited by Brigitte Nerlich, Alexander Smith, Sarah Hartley, and Sujatha Raman. The book is one of the major outputs of a Making Science Public project funded by the Leverhulme Trust and directed by Brigitte at Nottingham University.
You can download my chapter from figshare. I hope that you will because I would be glad to have your feedback to help me rework it in time for the July 1st deadline for submission of the final version.
I should have done this weeks ago when I completed my draft chapter. After all, I have been banging on about preprints for a while now and adopted preprint publication as standard practice in my lab for my structural biology research. But this felt different. It was a book chapter and part of a project being led by someone else.
However, given the subject matter (open access, public engagement) and given the increased intensity of discussions on preprints in the life sciences in the past few months, the move to publish as a preprint makes perfect sense. If I am honest I suspect the publication on Monday of a preprint from Cameron Neylon, Martin Paul Eve and colleagues on the meaning (or lack of it) of research ‘excellence’ provided a timely stimulus – see how one thing leads to another in this open access world?
So here it is. I am grateful to Brigitte for the go ahead. To summarise briefly: my chapter looks at the rise of open access and recent policy developments and tries to examine how these were shaped by and are shaping the interactions of the research community with society at large. The effects, so far as I can discern them, appear relatively modest, though there are murmurings of great potential. Please have a read for yourself. And if you think there are points I have missed or over-emphasised or misconstrued, let me know in the comment thread below or, if you prefer, privately by email.
Update (04 July 2016):My thanks to Bev Acreman, Laurence Cox, Richard Fisher, David Mainwaring, and Richard Poynder for comments on the first posting of this preprint. A revised version is now available.
This weekend’s Guardian has a quite wonderful feature comprised of letters to Britain from European writers about the decision to be made in the upcoming referendum. It offers a fresh and little-heard perspective on a debate that has become worn out and embittered over the past few weeks. I urge you to read it.
What you will read is that every contributor – from France to Bulgaria – has a vision of a vibrant but flawed European community that is desperate for Britain to remain part of the family. I was surprised how often the war was mentioned – in relation to the terrors and the bloodshed that the EU has helped to heal, but also in gratitude that Britain was prepared to stand firm in the face of Nazi aggression (see especially Jonas Jonasson’s contribution).
Ireland’s Anne Enright, married to a Brit, and with two daughters of complex loyalties (given that the family relocated from Britain to Ireland) gives a lovely pen portrait of the UK that resonates also with this emigrant:
“I like Britain very much. I mean, I like whatever Britain is – a shifting thing, a landscape, a language, a library full of astonishing books, a mosaic of peoples stalled in one migration or another, from the raw Saxon faces you see in East Anglia, to the sari shops of Bradford, to the eyes of my two children, who came from God knows where.
They like the trees, by the way. Also, and in this order: curry, cousins, Yorkshire pudding, “the way that everything is better funded”, the BBC, Bristol, sarcasm, the pub, AFC Wimbledon, Edgar Wright, Topshop and “how the politicians seem very polite but are really furious”. So now you know.”
And then there is Yanis Varoufakis from Greece who pleads with Britain to stay despite the EU’s poor handling of the crisis in his home country.
“Rather than escaping the EU, Brexit will keep you tied to a Europe that is nastier, sadder and increasingly dangerous to itself, to you, indeed to the rest of the planet.”
Amid all the acrimony of the present debate these missives from across Europe made me think that more than ever, it is time for Britain to roll up its sleeves and plough once again into the theatre of conflict (not so bloody this time around, thankfully); to stand beside our European friends and family in defending democracy – yes, this will require some reform of EU institutions – and to help point the way to a brighter future for the continent.
For some of my own musings on the scientific side of the EU referendum, try these twopieces in the Guardian.
I was sneered at on Twitter yesterday for sneering at people taking pictures of the Impressionist paintings on display at the Musée D’Orsay in Paris.
Fair enough perhaps. I had adopted an exaggerated version of the pontifical tone that comes so readily when composing tweets and not everyone saw the funny side. But behind my mock outrage was a genuine note of annoyance.
I don’t have a strong objection to people taking pictures. Indeed I took a few myself. But it was odd to observe those who only took pictures. Those who paused in front of a work with their smartphone or tablet or – more rarely – an actual camera just long enough (quite a while in some cases) to focus and compose the shot before moving on.
Thankfully these were a minority. But then there is the crowd that does not know how to turn off the flash on their phone, or the red light that some cameras use to aid focusing or the fake shutter noises that digital devices insist on retaining as a default setting. As a result, even if you can mentally block out the phones constantly being thrust into you peripheral field of vision, the viewing experience is degraded by random illumination and manufactured mechanical noise. It is a marked change from a couple of years ago.
Our guide book had advised us that photography was strictly forbidden at the Musée D’Orsay in order to prevent bottlenecks forming in what is clearly a popular attraction – we had queued for 40 minutes to get in. This seemed like a sensible restriction, one that serves a greater good.
But clearly the museum has abandoned this policy, ceding defeat to the inexorable rise of digital technology. This technology is undoubtedly a boon in many other areas of life but I wish the museum managers had found a better accommodation, perhaps allowing photography during a happy-snappy hour each day. Because much as I enjoyed my visit yesterday, the abiding memory is one of digital interference.