Popular neuroscience book suggestions

Neuroscience isn’t really my thing, so when my teenage daughter came asking for suggestions of a good popular book on the subject I took to Twitter. Several people kindly made suggestions, while others asked to be notified of the outcome of my quest. It seems to be a popular subject.

Here, in no particular order are the titles that were offered.

Graham Steel, one of my OA buddies, was first off the mark and ‘highly recommended’ Barry Gibb’s The The Rough Guide to the Brain (2012). 

Dorothy Bishop, an Oxford professor of psychology suggested Eric Kandel’s In Search of Memory (2007) as ‘autobiography with historical account, so you appreciate where understanding came from’.

Steve Black, a friend from my college days, offered Vilayanur Ramachandran’s The Emerging Mind (which are his 2003 Reith Lectures and are available from the BBC website) and his earlier Phantoms in the Brain (1999).

I myself had been thinking of David Eagleman’s Incognito (2012), which science writer Amy Harmon told me she is presently reading. Eagleman chimed in on Twitter* to confirm the sagacity of this choice.

Many thanks to all who made recommendations. If you have read any of these titles (or others not listed), please let me know what you thought. My daughter will be much obliged.

 

Update 1 (15 Sept; 08:52): After posting this, several other suggestions have come in through the comments (see below) and on Twitter.

Steve Royle enjoyed The War of the Soups and the Sparks (2007), which focuses on the discovery of neurotransmitters.

Ron Reid felt Christof Koch’s The Quest for Consciousness (2004) to be worthy of consideration even if it is a bit more academic. He also recommended various titles by Oliver Sacks, including The Man who Mistook his Wife for a Hat, Awakenings and Uncle Tungsten; Nicole Slavin would add Musicophilia to that list of Sacks favourites.

Mirco Musolesi called Sebastian Seung’s Connectome (2013) ‘a great read’, a view with which Amy Harmon concurred.

John Tweedle declared Paul Broks’ Into the Silent Land (2004) to be ‘brilliant’.

And finally (for now), Peiro Raimondi recommended Ramachandran’s The Tell Tale Brain (2012) as a ‘beautiful compendium of all his other works (see above).

 

Update 2 (15 Sept; 21:17): The recommendations have kept on coming, so here is another slew.

Tom Pollard (and several others) judged the graphic novel approach taken by Matteo Farinella and Hana Ros in Neurocomic (2013) to be ‘beautiful’.

As an undergraduate, Matthew Apps was inspired by Daniel Dennett’s Consciousness Explained (1993).

As a PhD student, Narender Ramnani was influenced by Steven Rise’s The Making of Memory (2003). 

Ned Jenkinson recommended Neuroscience: an historical introduction (2014) by Mitch Glickstein. The single reviewer on Amazon also seemed to be impressed.

Aidan Horner thought Charles Ferneyhough’s Pieces of Light: the new science of memory (2013) was great. It was shortlisted for the Royal Society Winton Prize 2013 and the 2013 Best Book of Ideas Prize — and recommended by Frank Norman in the comments below.

Divija Rao mentioned (but did not assess) Rhythms of the Brain (2011) by Gyorgy Buszáki. However, Amazon reviewers called it ‘scholarly’ and ‘dense but readable’. Science writer David Dobbs declared it to be ‘an amazing book’. But it may be a bit pricey for the casual reader.

Olga Rodriguez recommended Michael Gazziniga’s Who’s in charge (2011) but, cryptically, not for teenagers who she thought would be better off with the works of Oliver Sacks (see above for titles).

For Shane O’Mara Carl Sagan’s Broca’s Brain (1988) was the book that hooked him on psychology.

And finally for now, @eegrapher really enjoyed the bite-sized chunks in Mo Costandi’s 50 Human Brain Ideas You Really Need to Know (2013).

Thanks again to all who took the trouble to share their favourites. Now, which one shall I get for my daughter…?

 

*I would have embedded some of the tweets I got but can’t seem to get Twitter to play with WordPress tonight. 
 
Posted in Book Review | Tagged , , , | 10 Comments

Advice on presentations: I’m not as clever as you think

I spent the last two days in Leicester at Translation UK, a two-day conference that is an annual gathering for scientists working on all aspects of translation — the protein synthesis kind. The conference is friendly and informal. It is kept short so that it is cheap enough for labs to send postdocs and PhD students who dominate the roster of speakers.

As one of the older heads at the meeting I was collared on arrival to act as a judge of the oral presentations. This I was glad to do. It’s just the sort of discipline I need to make me pay full attention for the entirety of the proceedings.

The standard of talks was pleasingly high. Most people seem to have mastered the elements of PowerPoint and if any of the speakers were nervous, it didn’t really show. But there were a few elements of inexperience on display which I wanted to address while my impressions are still fresh.

Your title: compose with care — ask a question or make a statement — and make sure to refer to your title right at the beginning of the presentation. Don’t just tell the audience they can read it off your first slide, even if they can.

Your introduction: establish right at the start of the talk, especially if it’s a short one, the problem that your work is addressing. Outline the background and context to set the scene, and then tell the audience what your work is aiming to achieve. If you are feeling bold, state your conclusion right up front. This will help the audience keep on track for the rest of your talk, though it may reduce your scope for a dramatic reveal of a surprising result. That one is up to you but remember that the main purpose is to convey information effectively.

Your results: Less is more. This is perhaps the hardest lesson of all, one I still struggle with. Yes, you may have been labouring for a year or more on the results that you are about to present but you won’t have time in a short talk — 10 or 12 minutes is typical these days — to do them complete justice. So you have to give edited highlights. Pick out the most important findings and the most important pieces of data that support them. A talk is not a paper so you do not have to present every single piece of data that supports your thesis. Some people think they need to cram in all the data to make their talk seem substantial — though some crammers are just showing off — while others believe they are flattering the audience’s intelligence by presenting complex data at a galloping pace. But let me tell you this: I may be a professor but I am not as clever as you think I am. I would rather be taken through selected data with care. If my interest is sparked, I’ll ask you for more information after the talk. Trust me.

Your slides: Less is more. Try not to stuff too many results onto a single slide. By all means build up a complex figure piece by piece but make sure to give yourself the time to talk about every element that you show. Don’t put things on slides that you are not going to talk about as this will only distract the audience. And don’t forget to explain your figures; it is all too common to assume that the audience is as familiar as you are with your data formats — figures, photos, gels, etc. — but they will thank you for taking the time to make their meaning clear.

Your voice: Speak slowly and with feeling. If you pack in too many results you will feel pressured from the off to talk quickly for fear of running out of time. This is counterproductive. Give yourself the time to punctuate the talk with emphasis on the most important points, or those that make you most excited. Genuine excitement is infectious and audiences love it.

Your eyes: Try to spend as much time as possible speaking to the audience rather than to the screen. Look at them — make eye contact when driving your message home.

And that’s all there is to it, apart from forcing yourself to rehearse in front of a critical friend, of course. I look forward to these lessons being universally adopted at next year’s meeting, though feel free to take issue or to suggest additional pointers in the comments. There is an element of personal taste in all this.

Finally, for those with the time (27 minutes, to be precise), a more detailed video version of this little sermon is available on YouTube.

 

Posted in Science | 8 Comments

Australia Tour 2014

It’s funny how one thing leads to another. The video of my Friday Evening Discourse at the Royal Institution last year caught the attention of a former colleague and produced an invitation to contribute a lecture to her plans to celebrate the International Year of Crystallography at the University of Western Australia in Perth this summer.

And then, because my wife has family in Brisbane whom we have never visited, the organisers of the International Biophysics Congress, which will be held there this August, were good enough to offer a slot for a public lecture in their opening program.

And then, to help justify the expense of the trip, which is being part funded by the Society of Crystallographers of Australia and New Zealand, stopovers in Sydney and Melbourne were added to the itinerary. (Update, 23/07/14: after this was originally posted, I got a further invitation to talk at Hobart, which has now been added to the itinerary). All in all it is going to be quite a month for me and my family.

Australia Map

The four five talks are all free and open to the public, so if you find yourself in the area next month, please do come along. I hope to offer an eye-opening answer to the question, “What is X-ray Crystallography and how did it transform our view of the world?”

The tour dates (I am sotempted to have t-shirts printed) are:

We are looking forward to the trip immensely. Never having visited Australia, we would be glad to have suggestions of things that we must see or do.

Posted in Protein Crystallography, Science | Tagged , , , | 4 Comments

The REF: what is the measure of success?

Science has been extraordinarily successful at taking the measure of the world, but paradoxically the world finds it extraordinarily difficult to take the measure of science — or any type of scholarship for that matter.

That is not for want of trying, as any researcher who has submitted a PhD thesis for examination or a manuscript for publication or an application for funding will know. Assessment is part of what we do and not just at the level of the individual. The UK research community has just prostrated itself for the sake of Research Excellence Framework (REF), an administrative exercise run by the Higher Education Funding Council for England (HEFCE) that has washed a tsunami of paperwork from every university department in the country into the hands of the panels of reviewers now charged with measuring the quality and impact of their research output.

The REF has convulsed the whole university sector — driving the transfer market in star researchers who might score extra performance points and the hiring of additional administrative staff to manage the process — because the judgements it delivers will have a huge effect on funding allocations by HEFCE for at least the next 5 years. The process has many detractors, though most might grudgingly admit that the willingness to submit to this periodic rite of assessment accounts at least part for the high performance of UK research on the global stage. That said, the enormity of the exercise is reason enough to search for ways to make it less burdensome. So before the current REF has even reached its conclusion (the results will be posted on 18th December), HEFCE has already started to think about how the evaluation exercise might itself be evaluated.

 

The metrics review

As part of that effort and at the instigation of the minister for science and universities, David Willetts, HEFCE has set up an independent review of the role of metrics in research assessment. The review is being chaired by Prof James Wilsdon and, along with eleven others from the worlds of academia, publishing and science policy, I am a member of its steering group (see this Word document for the full membership list and terms of reference).

Metrics remain a tricky issue. In 2009 a pilot of a proposal to supplant the REF (or rather, its predecessor, the RAE) with an assessment that was largely based on bibliometric indicators concluded that citation counts were an insufficiently reliable measure of quality. How much has changed since then is a question that will be considered closely by the steering group, although this time around the focus is on determining whether there are metrics that might be used meaningfully in conjunction with other forms of assessment —including peer review — to lighten the administrative load of the assessment process. There is no appetite for a wholesale switch to a metrics-based assessment process. To get an overview of current thinking on metrics from a variety of perspectives, I would recommend this round-up of recent posts curated by the LSE Impact blog.

One thing that has changed of course is the rise of alternative metrics — or altmetrics — which are typically based on the interest generated by publications on various forms of social media, including Twitter, blogs and reference management sites such as Mendeley. The emergence of altmetrics is very much part of the internet zeitgeist. They have the advantage of focusing minds at the level of the individual article, which avoids the well known problems of judging research quality on the basis of journal-level metrics such as the impact factor.

Social media may be useful for capturing the buzz around particular papers and thus something of their reach beyond the research community. There is potential value in being able to measure and exploit these signals, not least to help researchers discover papers that they might not otherwise come across — to provide more efficient filters as the authors of the altmetrics manifesto would have it. But it would be quite a leap from where we are now to feed these alternative measures of interest or usage into the process of research evaluation. Part of the difficulty lies in the fact that most of the value of the research literature is still extracted within the confines of the research community. That may be slowly changing with the rise of open access, which is undoubtedly a positive move that needs to be closely monitored, but at the same time — and it hurts me to say it — we should not get over-excited by tweets and blogs.

That said, I think it’s still OK to be excited by altmetrics; it’s just that the proponents for these new forms of data capture need to get down to the serious work of determining how much useful information can be extracted. That has already begun, as reported in a recent issue of Research Trends and I look forward to finding out more through the work of the steering group. Though I have already written a fair amount about impact factors and assessment, I don’t feel that I have yet come close to considering all the angles on metrics and claim no particular expertise at this juncture.

That’s why I would encourage people to respond to HEFCE’s call for evidence which is open until noon on Monday 30th June. The review may have been set up at the behest of the minister but it remains very much independent — as I can attest from the deliberations at our first two meetings — and will take a hard look at all the submissions. So please make the most of the opportunity to contribute.

 

Beyond the review

Although the remit of the review is strictly limited to consideration of the possible role of metrics in future assessment exercises, I can’t help wondering about the wider ramifications of the REF.

The motivation behind the process is undoubtedly healthy. The validation of the quality of UK research and reward of those institutions where it is done best, instills a competitive element that drives ambition and achievement. But however the evaluation is performed, the focus remains on research outputs, primary among which are published papers, and that narrow focus is, I think, problematic. I hope you will indulge me as I try to pick apart that statement; my thinking on this topic has by no means fully matured but I would like to start a conversation.

I know from my time making the arguments for science funding as part of Science is Vital that it is hard to measure the value of public spending on research. As shown in classic studies like those of Salter and Martin or the Royal Society The Scientific Century report, this is in large part because the benefits are multi-dimensional and hard to locate with precision. They include the discovery of new knowledge, realised in published papers, but within the university sector there are many other activities associated with the production of those outputs, such as training of skilled graduates and postgraduates, development of new instruments and methods, fostering of academic and industrial networks, increasing the capacity for scientific problem-solving and the creation of new companies.

There is a whole mesh — or is it mess?  — of outputs. The latest incarnation of the REF has made a determined effort to capture some of this added value or impact of UK research but has wisely taken a pragmatic route. Realising that a metrics-led approach to measuring impact presents too many difficulties, not least for comparisons between disciplines, HEFCE instead asked departments to produce a set of impact case studies, which give a narrative account of how published research has impacted the world beyond academia. Although there has been much carping about the introduction of impact agenda, which many see as boiling the research enterprise down to overly utilitarian essentials, the retrospective survey of the wider influences of UK research output embodied by the REF has been a surprisingly positive experience, not least because it has unearthed benefits of which many university departments were previously unaware. Collectively, the case studies might even provide a rich resource with which to argue for continued and increased investment in the research base.

Even so there are other problematic aspects to the REF. In the past year, as well as generating all the paperwork needed for our REF submission, our department has undergone an external review of its undergraduate teaching. As the current Director of UG Studies (DUGS) I was required to take a leading role in preparing the voluminous documentation for this further assessment exercise — a 58-page report with no fewer than forty appendices — and organising a site visit by our assessors involving many different staff and students. As with the REF, the process is administratively onerous but the exercise nevertheless has significant value: it provides an opportunity to take stock and serves as a bulwark against complacency.

But the question that now looms in my mind is why are these assessment exercises separated? The division appears arbitrary, even if it makes some kind of logistical sense, given the strains that they place on university departments. From that perspective it might be difficult to argue for any kind of unification but there is a fundamental issue to be addressed: is it sensible to isolate research performance from other valuable academic activities?

These other activities include not just UG teaching but also postgraduate training, mentoring of young postdoctoral scientists, peer review of research papers, grant and promotion applications, institutional administration, the promotion of diversity, and involvement in public discourse. Arguably the separation (which in reality means the elevation) of research from these other activities is damaging to the research enterprise as a whole. It creates tensions within universities where staff are juggling their time, more often than not to the detriment of teaching, and is responsible for a culture that has become too dependent on publication. This distortion of the academic mission has been worsened by the reification of journal impact factors as the primary measure of scientific achievement.

Evidence published last Tuesday shows that, in biomedicine at least, the most important predictor of ’success’ for an early career researcher is the number of first-author papers published in journals with high impact factors. The measure of success here is defined narrowly as achieving the independent status of principal investigator running your own lab (usually by securing a lectureship in a university or a long-term post at a research institute). It should come as no surprise that the well-known rules of the game — publish or perish — should produce such an outcome. But what is missing here is consideration of the negative impacts of the artificial separation of research from other facets of the job of academic.

In recent months I have spoken to more that one young researcher who has abandoned the dream of leading their own research group because of their perception of the extreme intensity of the competition and the sure knowledge that without a high-impact paper they are unlikely to make it in such a world. A ‘pissing contest’ is how one memorably described it. Is anyone counting the cost of those broken dreams? Should not these losses be counted in our research assessment processes?

It has often struck me that an academic career is a tremendous privilege; it offers the chance to follow your curiosity into uncharted territory and to share your love of your discipline with the next generation. There are still plenty of people who derive great satisfaction from their work in the academy — even I have my good days — but I detect increased levels of stress and weariness, particularly since becoming DUGS. The responsibilities of that position have had some impact on my own research output but I was willing to take it on because I believe in the multifaceted role of ’the academic’ and in the broader value of the institution known as the university*. However, it has not been an easy task trying to promote the value both research and teaching in a culture — promoted in part by the REF — that places such a supreme value on research output. In such an environment, research cannot do other but conflict with teaching and that is ultimately to the detriment of both. And to the student experience. And to the quality of life for staff.

These issues are not new, and have been addressed previously by the likes of Peter Lawrence and Ron Vale. The San Francisco Declaration on Research Assessment, which has just celebrated its first anniversary (please sign up), is the latest attempt to rein in the mis-measurement of research achievements. But while there may be local efforts to hire and promote staff based on performance across the whole range of academic activities, research remains an international business involving the exchange of people and ideas across national boundaries, so a coordinated effort is required to solve these problems, or at the very least to identify and promote instances of best practice.

To that end, what are the chances that the REF might take a lead — perhaps even by using metrics? If we are going to take some account of citations or downloads in discussions of research quality, why not consider adding other measures designed to capture the student learning experience, or staff satisfaction, or good academic citizenship, to create a basket of measures that might rebalance the incentives for universities and their staff? There are huge and obvious problems with such an approach that need careful consideration; I am not proposing that we submit thoughtlessly to the whims of student satisfaction surveys, but am intrigued by how measures of workplace quality might play a role).

There are no easy answers. I anticipate some will argue that switching the tight focus of the REF away from research risks undermining the power of the UK research base. But to those tempted to follow that line, please evaluate the cost of not doing so and report back.

 

Footnote

*Though I cannot deny that my motivation for applying for a lectureship back in 1995 was to secure a permanent foothold that would enable me to start a career as a PI. At the outset I was prepared to pay the quid pro quo of teaching hours demanded but was advised not to get over-enthusiastic about teaching if I wanted to get promoted.

 

 

 

 

Posted in Scientific Life | Tagged , , | 17 Comments

Mars Attacks (the senses)

Last night on Twitter someone posted a ‘selfie’ taken by the Mars Curiosity rover.

It’s quite a photograph, particularly since it captures a fantastic piece of human technology amidst the landscape of another planet. The detail is what makes the picture. If you click to get a larger view you can see the nuts and bolts holding the rover together and the waves of sand on the Martian surface. My reaction was immediate.

 

And it set me hunting for even higher resolution pictures, which didn’t take very long at all. The one below from the Wikipedia page on the Curiosity rover and was taken in November 2012 on a nice sunny sol.

Curiosity Self-Portrait

Curiosity Self-Portrait. Image courtesy of NASA/JPL-Caltech.

 

The picture is a composite of several photographs which I think explains why it appears to have been taken by someone standing to one side of the rover. Better still, the original is a huge image of over 5000 by 7000 pixels so if you click here you can zoom in and have it fill your entire screen. It’s not quite the same thing as being there but is still a breath-taking visual feast. Enjoy.

Posted in Astronomy, Science | Tagged , | Comments Off

Get out of the laboratory

The Society for General Microbiology (SGM) kindly awarded me this year’s Peter Wildy Prize Lecture, which I delivered at their Spring meeting in Liverpool just a few weeks ago.

The prize is given for “an outstanding contribution to microbiology education and/or communication in order to stimulate interest and understanding in the subject”. It sounds rather grand, but please don’t be put off. As I tried to explain in my lecture, I didn’t feel entirely worthy. All I had done was to start writing a science blog and then react to some of the things that happened to me because I was writing a science blog.

Nevertheless I am grateful to the SGM for the honour and very glad that they have given some recognition to science blogging, and to science communication in general (the Peter Wildy Prize Lecture has been going since 2001). I was particularly pleased to have the opportunity to give a lecture on the topic to an audience of several hundred scientists. If you have forty-five minutes to spare, please have a look — it seemed to go all right on the night.

I took as my title “Science communication: a communicable disease?” My main message was simply to encourage more of my colleagues, young and old, to look beyond the laboratory every now and then. Plenty already do, of course, but public engagement is still too often viewed as problematic within academia, as Jonathan Eisen recently revealed. Even among those who take up the challenge, it can sometimes be for box-ticking, self-serving reasons. As Valeria Souza observed, this is known as ‘doing it wrong’ and it’s a point I touched on in my talk (that bit starts at 4:50). I think you have to find the intrinsic values — plural — in talking with the public about science and, as I tried to argue, these aren’t so hard to locate.

Despite some residual resistance, I look to the future with optimism. After my lecture I talked with several young scientists, at least two of whom, Sarah Caddy and Lauren Parker, have been encouraged to get into blogging since the meeting (though in Sarah’s case it was more a matter of ’taking it to the next level’). Why not have a peek at what they’re up to? If you like what you see, maybe you could say so in their comment threads.

And my erstwhile colleague, Dan Davis (now at a parish in Manchester), has also been using the pages of Nature Immunology Reviews to exhort his fellow immunologists to take science communication more seriously. That’s the way to do it with scientists: catch ‘em unawares; put a bit of stick about. Shoo them out of the laboratory.

 

Posted in Communication, Scientific Life | Tagged , , , | 8 Comments

Losing my virginity and the Café Scientifique Reading List

Last night I lost my virginity.

To be precise, I lost my Café Scientifique virginity because I gave a talk about science in a café in Portsmouth at the kind invitation of local organiser Maricar Jagger. It was a really good evening. I gave a short talk about my research and how I see my role as a scientist in modern Britain to a varied and interested audience who proceeded to ask lots of questions. I very much enjoyed the occasion — I left feeling we’d had a good discussion and was sorry I couldn’t stay longer.

I’d recommend these events to scientists (as possible speakers) or to anyone who looking to have an interesting conversation about science. The Café Scientifique is a world-wide organisation that was started in 1998 by Duncan Dallas (who sadly passed away earlier this month) so there may well be a venue near you.

In my introduction I talked about how I got into science, about my current research work on the structural analysis of proteins involved in the ‘life-cycle’ of RNA viruses such as foot-and-mouth disease virus and human noroviruses (aka the winter vomiting bug), about campaigns for science funding and about the importance of open access (natch).

I was a bit concerned that I might have ranged to widely and too superficially to prompt interrogation from the audience but I needn’t have worried. There was no shortage of questions, on all the topics that I had covered. I hope I gave a decent account of myself and useful answers to the various points of inquiry but, almost inevitably, as I sat on the train back to London I kept thinking of things I should have added or explanations I could have phrased differently. Oh well, I guess that is the nature of the beast.

Out of the corner of my eye during all this interrogation I noticed someone taking a note after I had mentioned Nick Lane’s Life Ascending as a good read for anyone wanting to find out more about current thinking on the origins of life on Earth. Given my retrospective frustration at not having answered every question quite how I would have wanted, I thought it might be useful to note down a few more suggestions for further reading — for last night’s audience and anyone else who might be interested.

Returning to the question of the origins of life, those looking for a breezier read that Nick Lane’s rather detailed account should  pick up Adam Rutherford’s Creation, which in its first half, covers much the same ground (with the added bonus of being sprinkled with cryptic film references). The second half of Rutherford’s book considers how our modern understanding of the molecular and genetic basis of life is enabling us to think in completely new ways about biological engineering.

To follow up the question of scientific funding and the interaction between public investment in basic research and subsequent economic development, I would recommend Marianna Mazzucato’s slim and accessible volume The Entrepreneurial State (PDF) an interesting and accessible (see my previous review).

And finally, for those wishing to learn a bit more about the tortuous subject of Open Access, let me point you to this recent summary by Eva Amsen at F1000 or, if you are looking for more detail, Peter Suber’s handy overview. If you really get a taste for it, then grab a free copy of Peter’s book.

Posted in Book Review, Communication, Science, Scientific Life | Tagged , , | 2 Comments

Open Access — yes you can

For researchers who have never dipped a toe into the debates on open access that surge across the blogosphere it is all too easy to imagine that they need not get involved. For sure, people are increasingly aware that a decision of some sort needs to be made about OA once their paper is accepted for publication but that’s about as far as it goes. The complexity of the issue is off-putting — who has the time? — and there is in any case a vague sense that funding agencies (RCUK, HEFCE, NIH, the Wellcome Trust and the like) have the matter in hand so any sense of involvement or responsibility is, with little effort, shrugged off.

But to do so misses the real significance of the changes seeping through academic publishing. Worse, it overlooks the capacity the individual researcher to influence them.

The changes in train are as much cultural as technological: while the high-speed connectivity of the internet is enabling us to re-imagine publication by spreading research results faster and further than ever before, at the same time it is providing the democratic empowerment needed to challenge the status quo. Established publishers naturally seek to protect the advantages of hegemonies built up before the web came along; but these are not always aligned with the movement towards open access and it is now possible for each of us, working singly or in web-linked groups, to make a real difference.

In this post I want to go through a number of recent examples — some of them pretty straight-forward — that show how simple it can be to take part in the push for open access. The more of us that push, the faster we will get to where we want to be.

Push

Get what you pay for: Last December I noticed that the PDF of a 2012 paper in Elsevier’s Journal of Virological Methods on which I am a co-author and which was supposed to be OA was marked “Copyright © 2012 Elsevier B.V. Published by Elsevier B.V. All rights reserved.” The paper was clearly denoted as OA on Science Direct but there was no indication of this on the PDF. Since we had paid a hefty Article Processing Charge (APC) for the hybrid OA option to make our paper freely available in a journal that normally requires a subscription, this didn’t seem like very good service.

Through Twitter, and then in email exchanges, Elsevier’s Alicia Wise agree to attend to the defect and within about a month the PDF had been altered. The text now reads “© 2012 Elsevier B.V. This is an Open Access article under Elsevier’s open license: http://www.elsevier.com/open-access/userlicense/1.0/”. Alicia spent some time in our email exchanges explaining how tricky it had been to amend the PDF after publication; while I was grateful for the effort made, I couldn’t help pointing out that the trouble would have been avoided if the article had been marked up correctly in the first place, especially given the charge levied for Elsevier’s OA option. I understand several other problematic OA articles by Imperial College authors like myself have been brought to Elsevier’s attention by Chris Banks, our Director of Library Services, and have now been attended to. I recommend that you check your own OA papers are clearly marked as such; if not, please contact your publisher to insist on a fix.

Get behind me, paywall: I am not the only one who has been having technical difficulties with my OA papers of late. The Wellcome Trust, in an admirable move towards openness and transparency, recently published the details of their spending on open access publishing on Figshare. To be precise, they published the data as an Excel spreadsheet that was immediately digested, assimilated, annotated and improved by a variety of OA advocates, including Peter Murray-RustCameron Neylon, Ernesto Priego and Michelle Brook (of the Open Knowledge Foundation).

As Wellcome’s Robert Kiley subsequently reported, one of the key things this open, collective effort revealed was that some OA articles for which an APC had been paid remained behind paywalls or had not (as promised by the publisher) been deposited in PMC or Europe PubMed Central repositories or had not been marked up with the appropriate Creative Commons licences. As in my case, the problems are most likely due to processing errors but given the high fees levied for OA services by major publishers such errors are simply not acceptable. This episode underscores the need for openness and for community action to drive performance levels in OA publishing.

Get to know your Institutional Repository*: My December run-in with Elsevier must have sensitised my antenna. While I was following the green route to OA by depositing our first paper of 2014 (published in Elsevier’s Bioorganic & Medicinal Chemistry Letters) in Imperial’s Digital Repository I took the time to read the copyright notice that the publisher insists on attaching to the entry. It says (with my highlighting):

“© 2013 Elsevier Ltd. All rights reserved. NOTICE: this is the author’s version of a work that was accepted for publication in Bioorganic & Medicinal Chemistry Letters. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published in BIOORGANIC & MEDICINAL CHEMISTRY LETTERS, Vol.: 24, Issue: 2, (2014) DOI: 10.1016/j.bmcl.2013.12.045”

Since the version I was permitted to deposit was the final accepted manuscript, which has been revised in the light of peer-review and contained no significant differences from the version published in Bioorg. & Med. Chem. Letters, the catch-all statement highlighted in red seemed inaccurate and likely to undermine the confidence of the reader in what they would get from this download. The statement in blue was true but only in the trivial sense in this case that some minor stylistic changes may have been made by the journal. To counter this, I added the following statement to the front page of my PDF:

“This version of the paper, which contains all the modifications made to reviewers’ comments, is the one that was accepted for publication. Essentially, it differs only in matters of formatting from the final published version.”

I also raised the matter with Alicia Wise and was glad to learn that Elsevier is working to re-phrase the boilerplate statement that it applies to deposited post-prints. I look forward to reading the re-drafted text. It is important that precise language is used so that the very real value of work made available through repositories is clear to users. If we can’t get this from publishers, we will have to work with our repositories to eliminate all sources of confusion.

Get to know your rights: A question of language was also raised by Kevin Smith, Scholarly Communications Officer at Duke University in the US who recently observed that the licence to publish used by Nature Publishing Group (NPG) required article authors to waive their moral rights. This was a demand too far in his view since, as he put it, moral rights are broadly understood to include “the right of attribution and the right to preserve the integrity of one’s work”.

NPG’s Grace Baynes countered that the publisher had no intention of undermining authors’ rights of attribution but was seeking to preserve its ability to make corrections to papers (as is sometimes necessary), so as to maintain the integrity public record. I’m pretty sure that’s genuine, but you have to ask why the publisher couldn’t have come up with a more refined form of words in the first place to acquire the legal authority to preserve the academic literature without threatening authors’ right of attribution. And I don’t just mean that as a figure of speech. You have to ask — as those commenting beneath Grace’s statement have done. It’s an important part of the process and, thanks to NPG’s commenting facility, easy to do. So far, we have yet to see any undertaking by the publisher to amend the wording of their licence to publish but now that the matter is out in the open I hope it will be resolved. But this is only likely to happen if the community remains vigilant.

Get value for money: The analysis of the Wellcome Trust’s data on the charges it pays to different publishers for open access publishing articles highlighted high cost of hybrid OA, an issue that was also raised in a recent assessment of the OA publishing market by Bo-Christer Björk and David Solomon. Their report, commissioned by a consortium of funders that included the Trust (Disclaimer: I was on the steering group that oversaw the preparation of the report), revealed that the average fee for hybrid OA (~$2,700) was almost twice the average cost of publishing in a ‘born-digital’ full open access journal (~$1400).

These numbers should give researchers and funders pause for serious thought. Contrary to what was first envisaged, hybrid OA funding has not been used by publishers as a mechanism for flipping their journals to full OA. Instead it is increasingly seen as an additional revenue stream for publishers that does not deliver value for money to the research community. Concerns about double-dipping expressed by the UK House of Commons and Science Minister David Willetts have for the most part yet to be credibly addressed. In part that’s because the resolution is technically difficult but Harvard’s Stuart Shieber has analysed the matter with typical incisiveness and correctly diagnosed the root of the problem: publishers are reluctant to lubricate the transition to OA because it should create a functioning market for publication services that in the long run is likely to reduce revenues (PDF).

Get with the groove (of the new): As far as possible therefore (within the constraints of ongoing collaborations), I shall be avoiding the hybrid OA route and aim instead to publish with fully OA titles that offer a good service at a competitive price. My group’s most recent paper was submitted to one of the newest kids on the block, PeerJ, an online-only, fully OA journal established by Peter Binfield, Jason Hoyt and Tim O’Reilly that opened for business in 2012.

I’ve written before about PeerJ’s ground-breaking pricing models (which start with a one-off ‘membership fee’ of $99 that permits an author to publish one paper a year) but this was the first time I had tried the journal myself. It was an interesting and positive experience. For a start I took advantage of their recent offer to publish peer-reveiwed papers for free if they were first submitted as a pre-print to PeerJ PrePrints. Like the recently established BioRxiv (of which I am an affiliate), this is a laudable attempt to tempt researchers in the biomedical and life sciences to get into the habit of rapid and early publication that has long been the norm in several sub-disciplines of physics, mathematics and computer science through the ArXiv.

The preprint submission was slightly nervy — old habits die hard — but I was assuaged by the knowledge that our preprint would immediately be subjected to peer review. Even so, because the manuscript was going straight into the public domain**, I found myself fretting more than ever over possible errors.

As it turned out our preprint, which reported the solution and crystal structures of the polypyrimidine tract binding protein, didn’t take long to become a full-fledged paper. Submitted on 20th Jan 2014, we had an editorial decision — accept with minor revisions — by 3rd Feb that was based on three reviews. The reviewers were thorough and professional; one pointed out a technical problem with our crystallographic data analysis that we had overlooked and when we looked again it turned out they were correct. Those who might like to have a look at the details can do so because we and the reviewers agreed that our correspondence should, like the paper, be made freely available online.

Having made our corrections the revised manuscript was re-submitted and accepted on 14th Feb and shepherded into publication on 13th March. The online layout of our paper is clean and clear, as is the PDF that you can freely download. Needless to say, it is clearly marked as being distributed under a CC-BY 4.0 licence, the copyright having been retained by the authors. I take Richard Poyner’s point that OA advocates should be careful not to ally themselves to particular publishers, for fear ceding strategic control of the developing OA market (see page 21 of his recent interview (PDF)), but I nevertheless applaud the innovation and professionalism of PeerJ’s operation. I will certainly be submitting papers there again and think that in an open market, they will win a decent share.

There, I’m done (for now). Your turn.

 

*Update (22-4-14): Another good reason for those in the UK to get to know their institutional repositories is that HEFCE has announced that to be eligible for the next Research Excellence Framework exercise, essentially all publications will have to be deposited in an institutional or subject repository on acceptance for publication. This new policy kicks in from 1st April 2016 but you might as well get into the habit now.

**Update (22-4-14): Mike Taylor pointed out to me that ‘public domain’ can technically be taken to imply publication under a CC0 licence, which permits reuse without attribution. That is not the case here since our preprint was made available under a CC-BY licence. This licence stuff is complicated.

Posted in Open Access | Tagged , , | 25 Comments

Open Access – reasons to be cheerful: a reply to Agrawal

A opinion piece by Anurag Agrawal that was rather skeptical about some aspects of moves toward open access was published in the March issue of Trends in Plant Sciences. I felt several of the arguments advanced by Agrawal were rather weak and was glad to have the opportunity to write a rejoinder which has now been published in the April edition of the same journal. I am grateful to the editor, Dr Susanne Brink, for the opportunity to write for the journal’s regular readership.

I think my piece may be freely available from the journal web-site. From home, outside the privilege of my university’s subscription access, I was to be able to download it via the PDF link on the table of contents, but the situation seems a little confused because after clicking the ‘Full-text HTML’ link, I ran straight into the paywall at Science Direct.

I imagine others may be experiencing similar difficulties or confusion so, in the interests of furthering the discussion, I am posting the author accepted manuscript here (PDF). This version differs in no significant respect from the version published in the journal. When I get a chance, I will also deposit it version in my university repository.

Posted in Open Access | Tagged , | 4 Comments

Moon Boy

After splashdown at 4:51 pm on 24th July 1969 the Apollo 11 astronauts returning from the first moon landing  had to don full-body Biological Isolation Garments before they could leave the conical command module that was bobbing in the Pacific Ocean. Having transferred to the dingy that had come to meet them, Neil Armstrong, Buzz Aldrin and Michael Collins then had to scrub one another’s suits with diluted bleach.

From the dingy the astronauts were helicoptered to the aircraft carrier USS Hornet and immediately sealed inside a windowed metal box, the Mobile Quarantine Facility, in which they were cocooned for the voyage back to Hawaii and the flight to the Manned Spacecraft Center in Houston. There they could finally move into the much roomier quarters of the Lunar Receiving Laboratory but were still sealed off from the outside world until August 10th, fully 21 days after Armstrong and Aldrin had quit the lunar surface. It was an ignominious end to an amazing journey.

All of these precautions were to protect the Earth’s population from any infection that might have returned with them from the moon. But NASA’s quarantine measures were only partially successful. The planet may not have succumbed to some unknown lunar disease but I certainly got infected with something, and I suspect many others of my age did too.

I have been living with the condition over forty years now. The symptoms are largely benign — a low-level compulsiveness that means I have to take at least a passing interest in every rocket-powered foray into space. That I can cope with. But every so often there is a flare-up and I find myself yielding to a full-blown obsession. This time it was triggered by reading Carrying the Fire, Michael Collins’ account of his time as an astronaut with NASA. Once I started I couldn’t stop. It’s the oldest cliché in publishing but, just like an object in zero gravity*, the book was unputdownable.

Carrying the Fire

Of the three Apollo 11 astronauts Collins comes across as the most approachable. Armstrong was famously reclusive after his return to Earth while Aldrin suffered bouts of depression and battled with a drink problem. Though he wrote a candid account of his voyage to the moon and his struggles to re-adjust to life after the Apollo program, I found Aldrin’s book a bit of a mess. Collins is more level-headed. You get a good sense of the man from his contributions to the 2007 documentary, In the Shadow of the Moon, and the same friendly acuity comes across from the pages of his book.

Carrying the Fire gives a straight-forward account of Collins’ graduation from Air Force test pilot to NASA’s astronaut program in 1963 (having failed on his first attempt). He details the preparations and experiences of his first flight into space on Gemini 8, a program that aimed — among other things — to work out docking procedures in Earth orbit. The second half of the book is devoted to the historic Apollo 11 mission. It’s not a book for the casual reader looking for a story engineered to be dramatic. There is no shortage of tension and excitement but it emerges unadorned from the narrative. Collins combines a keen eye for detail with a disarming and sometimes brutal frankness when assessing himself and his crew-mates.

For me it was access to the sheer complexity of the planning and execution, and the many unexpected twists and turns, of the Gemini and Apollo missions that gripped the most. The story has a compelling blend of unimaginable risk-taking in a hostile environment with the camaraderie and jealousies that pushed and pulled at NASA’s first spacemen. In my mind it forged a new connection to the astonishing ambition of the moonshot, an event that hugely expanded humankind’s sense of itself. Collins is at his best when recalling the strange nitty-gritty of spaceflight but struggles to convey what the trip really meant for himself, Aldrin and Armstrong and is only partially successful in doing so. He observes wryly that it may have been odd to assign humankind’s greatest voyage of exploration to a bunch of macho and taciturn test pilots.

But he does at least try and I am grateful for that. I wonder if my generation connects more intensely with the moon landings because we lived through them. Even though my memories are faint and immature — I was only five years old in the summer of 1969 — it is an event that still resonates with inspiration. Within not so many years all the astronauts will be dead and not long after those who witnessed it on TV will be gone too. When that time comes, I hope that Collins’ book might still keep the flame alive.

*Strictly, ‘zero-gravity’ is the wrong term and I should say ‘free-fall’ but frankly zero-gravity is a better descriptor and I’m sticking with it.

Posted in History of Science, Technology | Tagged , , | 8 Comments

The horror is in the detail

I recently came across a film on YouTube called ‘Unedited footage of the bombing of Nagasaki (silent)’. It is one of the dullest and most horrific things I have ever seen. The film shows US servicemen on Tinian island performing the banal tasks needed to prepare the Fat Man bomb before it was dropped on Japan. We see men, stripped to their waists in the summer heat, desultorily spraying the bomb with a water-proofing agent to keep the innards dry during its plunge through the atmosphere; we see them load the bomb onto a trailer, cover it with a tarpaulin (to hide the casing design from prying eyes) and follow it in slow procession to the airfield; we see it lowered gently into a pit and the pilot of the B29 Superfortress reverse his plane so that the bomb can be hoisted into the belly of the aircraft.

The film then cuts to footage of the plane gleaming in the sun on its final approach to Nagasaki. And then quickly cuts to a view of the ground beneath, where a mushroom cloud is already blooming and rising slowly into the morning sky. No details are visible on the ground so there is no sense of scale, and no notion of the hell that has just been unleashed on the unsuspecting population. Forty thousand souls obliterated in an instant and thousands more who will soon be dead through blast injuries and fire.

We know of the horror, because we have seen films — I find them almost unwatchable — of the devastation of the city and the blank, uncomprehending faces of the injured, their burnt skin detaching from their bodies like so much tissue paper.

But there is no sense of this in the film of the preparation. The men are almost casual as they go about their business. Some stand around while others work. The bomb has been signed by many of them. One wag has added the sardonic acronym ‘JANCFU’ (Joint Army and Navy Command Fuck Up), not realising, I imagine, quite how badly Fat man was going to fuck things up. But occasionally, in the course of an ordinary day, we change the world.

Posted in History of Science | Tagged , , | 3 Comments

Impressions of Turner

I may not know much about art but I know what I like and I like the work of Joseph Mallord William Turner — all the more so now that I have seen the Turner and the Sea exhibition at the National Maritime Museum. The artist painted a variety of landscapes over the course of a long life but is probably best known for his seascapes (though I can’t be entirely sure since I don’t know much about art). In any case those are the works that most appeal to me, an aficionado of Patrick O’Brian’s Aubrey-Maturin novels. O’Brian’s writing brings the sea vividly to life in the imagination but the Turner exhibition is a chance to revel in it splashed over canvas.

‘Splashed’ is the wrong word. Turner’s application of paint was of course supremely artful and the real delight of the works on show in Greenwich is to be able to see how his artistic vision developed.

Born in 1775, Turner’s talent became evident in his teenage years; he exhibited his first oil painting at the Royal Academy in London in 1796. Fishermen at Sea displays considerable skill at rendering the play of light on water though I didn’t care for this early picture so very much — the colour and composition seemed too forced.

I preferred the darker mood of The Shipwreck painted nearly 10 years later. Strangely, however, if you look closely, the evident drama of the scene is somewhat undermined by the way the people holding on for dear life depicted — the figures have the simplicity of a child’s story book. Perhaps it’s unfair to look too closely but in some ways the engravings from his Liber Studorium seem to use his skill to better effect — they have an almost photographic immediacy.

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The Shipwreck (1805) — from the Tate Collection (click link for a larger view)

 

That said, the exhibition is dominated by the paintings — and rightly so. Turner’s The Battle of Trafalgar, 21 October 1805 is particularly dominant; at 3.6 m x 2.6 m it is by far the largest painting in the show. Nelson’s flagship, HMS Victory, commands the scene but is surrounded by and succumbing to the bloody and smoky chaos of battle. 

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The Battle of Trafalgar, 21 October 1805 (painted 1824) — National Maritime Museum

 

It’s a complex composition; there is action in every corner and the painting repays prolonged viewing though, truth be told, I found Stanfield’s HMS ‘Victory’ Towed into Gibraltar more moving and Pocock’s earlier and simpler painting, Battle of the First of June more dramatic and arresting.

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 Battle of the First of June (1794) — National Maritime Museum

 

Ultimately it was Turner’s later works that impressed the most, as he strived less to render the precise form of the sea and more to capture the sense or feeling of it. One of my favourite paintings in the exhibition is Fishing Boats Bringing a Disabled Ship into Port Ruysdael, which was first shown in 1844. There is a melding of land, sea, sky and boats that is a bold attempt to convey the whole experience of being at sea.

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Fishing Boats Bringing a Disabled Ship into Port Ruysdael (1844) — Tate Collection

 

The blurring of boundaries foreshadows the emergence of impressionism and is seen also in a work from the same period, Waves breaking against the wind. As the caption put it, the picture was an attempt to portray the endless repletion but infinite forms of the waves beating against the shore. It is a painting of mesmerising, almost puzzling beauty. It baffles me that the image breaks down completely as you move in to examine the application of paint. And what is it about that wash of yellow at the upper right that is so appealing? I’ve never seen a sky that colour and yet it still has me convinced.

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 Waves breaking against the wind (1840) — Tate Collection

 

And finally (in this mini-tour), there is Snow Storm Steam Boat off a Harbour, which is even more impressionistic. There is a clear artifice in the way that Turner’s bolder strokes bind the sea and sky together as the elements swirl around the struggling steamboat; and yet, again, it works.

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Snow storm steam boat off a harbour (1842) — Tate Collection

 

But please don’t take my word for it, or rely too heavily on the miniature renditions included in this post for an impression of Turner’s art. Go and see the exhibition for yourself. You have until April 21st.

Posted in Science & Art | Tagged , , | 14 Comments