Trading Knowledge

Peer review is one of those old chestnuts that people never seem to tire of discussing. Does it work? What is it? Do we like it? Can it be improved? Do we need it? Why won’t it just go away? etc etc
A blurb for the International Symposium on Peer Reviewing: ISPR 2009 digs up some choice quotes:

In a survey of members of the Scientific Research Society, only 8% agreed that ‘peer review works well as it is’.

Far from filtering out junk science, peer review may be blocking the flow of innovation and corrupting public support of science

They conclude:

The almost unanimous agreement about peer reviewing as principle, and the huge disagreement about its current methods, are a clear sign that more efforts are needed … to identify more effective methodologies and support systems … so the real purpose of peer review is better fulfilled.

Meanwhile, in another part of NN, a suggestion for simplifying peer review down to a simple rating system was gently pushed aside, before some clever clogs (ahem) found that a recent conference had used just such a system to rate submitted abstracts.
So I was fascinated to see this morning a press release today about a paper in the International Journal of Technology Transfer and Commercialisation – not my usual breakfast table reading matter. This described the Peer-to-Patent pilot project that used social networking techniques to help deal with the backlog of patent submissions to the US Patent Office (USPTO).

… the USPTO initiated a pilot project that uses social networking software to allow groups of volunteer review experts to upload prior art references, participate in discussion forums, rate other user submissions and add research references to pending applications. The aim was to allow the actual patent examiners to focus on reviewing the most relevant prior art associated with any particular submission and so streamline the overall application process.

This sounds like a very creative application of social networking. It’s not exactly peer review, but perhaps second cousin to peer review. Does this have any relevance to peer review as practised in journals?
To read the original article you will need a subscription to the journal.

I went to another meeting today about UK PubMedCentral . For the first time I began to feel a bit excited about the resource this project is building.
Whenever I hear the phrase “one-stop shop” I groan inwardly. Since bibliographic databases and journals first appeared on the Internet I have heard publishers and database developers talk about their intention to build a “one-stop shop”. To me it betrays an arrogance beyond belief and an ignorance of the nature of information use. Of course it’s an impossible aim. I’m not sure whether UKPMC ever did use that phrase, but I felt that the early information about the project did have a hint of such an ambition, so I thought to myself “here we go again”.
Happily the meeting today eschewed any such notion and I came away feeling that the intention of the UKPMC project participants is to build a truly excellent, useful and usable resource for health science researchers. I also felt confident that the participants have it within them to do the job.
Sophia Ananiadou from NaCTeM explained the work her group has done using text mining techniques on Medline abstracts. This is the third time I’ve heard her talk about this, and it gets more interesting each time. Her aim is to enrich the literature by automatically creating semantic metadata, and thereby to make “undiscovered science” accessible. The MEDIE system is the most vivid example she showed, allowing you to construct a query in the form “subject – verb – object”. For instance, you can ask “what does p53 activate” by searching for subject=p53, verb=activate. Or you can ask “what causes colon cancer” by searching for verb=cause, object=colon cancer. I tried verb=read, object=book but I’m not sure what question that was answering. Currently this MEDIE system is just searching abstracts, but even so it does a pretty good job. It gives a hint of the power of text-mining techniques; I look forward to them being applied to the full-text corpus that is growing in PubMedCentral.
I also enjoyed seeing Peter Stoehr’s demonstration of CiteXplore , that he has developed at the EBI . I’ve heard of it before and looked at it briefly but never properly considered it as a serious replacement for PubMed. Now, partly because of the additional content in it and partly because it is going to be at the heart of the UKPMC search service, I can see that it deserves more attention.
One advantage it has over PubMed is the coverage – CiteXplore indexes about half a million extra references covering plant and animal science (from the Agricola database); plus a large collection of biological patents and abstracts of Chinese biological journals. Other resources continue to be added (e.g. NICE guidelines). The UKPMC project is actively considering other resources to add to enhance the search service.
I was surprised to see that CiteXplore also has citation data. When you display a record it shows the standard bibliographic fields and abstract but it also shows where that article has been cited. And that’s not all: instead of just showing the citing reference it also shows the sentence in which the original article was cited, thus making it easier to interpret the significance of each citation. It would be interesting to compare the number of citations that CiteXplore lists for a given article with the number listed in Scopus and Web of Science, but I’ve not done this.
Finally, CiteXplore has some features that draw on text-mining tools. When you display results you can ask it to highlight proteins in the results. It will then highlight any occurrences of protein names and turn them into links to UniProt. You can do the same for genes or protein-interactions.
Putting all these together and extrapolating the power of the text-mining techniques that Sophia showed, I left the meeting feeling that before long we are going to have a rather special search tool ready to use.
One caveat – all this does presuppose that UKPMC is successful in its aim to gather in the full-text of published research articles. Open Access mandates from the research funders (MRC, CRUK, Wellcome, DoH etc), who are also funding UKPMC, will hopefully help to achieve a high rate of deposition, but it requires the cooperation of biomedical researchers, who have thus far not proved to be very enthusiastic about Open Access. The promise of a better literature search tool may help to persuade them it is worth it.

From the DIUS website :
The Football Association has today confirmed Ian Watmore as its new Chief Executive. Mr Watmore is currently Permanent Secretary at the Department for Innovation, Universities and Skills (DIUS). He will take up his new post in June.
It’s good to see people involved in the highest echelons of UK science policy being promoted to positions that really matter.

I’ve been struggling to think of something to say about Darwin or evolution. And then, walking down to the coffee area, I passed this sculpture that I pass every day and thought – aha!

Example 10, by Emily Wardill (2003).
(Apologies for my clumsy attempt to take a photo – I cut off the right hand edge of the sculpture. I’ll try and take a better version next week).
Emily Wardill spent a three-month residency at NIMR some years back and produced this sculpture as a result. Rather than endeavour to explain it myself I will just quote the description on the NIMRart website

…to illustrate how science, and biology in particular, has undertaken a paradigm shift in order to progress. It was argued that rather than science being forced to regress to childhood in order to understand nature, science had actually given birth and was attempting to emulate its offspring. In order to clarify this idea a debased model of Darwin’s famous evolutionary walk was proposed. In this, the progression of man was manipulated to comprise of ape; man; scientist; pregnant scientist; and finally a scientist on all fours crawling next to their new-born.

This set me to thinking about art and evolution and my thoughts turned to the Mutators Research Group who held an exhibition at NIMR a year or so ago. They have produced a couple of videos on evolutionary themes.

I’m sure there must be many more examples of evolution represented by art.

You probably have too much to read about Darwin already, but as a Librarian I feel strangely obligated to burden you with still more reading material on this topic. So here are a few bits and pieces. I make no claims to its being at all comprehensive nor to having selected the best bits. It’s just there.
Some newspaper features and journal special issues:

• Another Nature special on Darwin
• Guardian features on Darwin
• Biology Letters – special feature on brain evolution
• International Journal of Biochemuistry and Cell Biology special issue on Molecular and cellular evolution
• American Psychologist special issue
• Biochemical Journal special issue

• The Biochemist special issue

Some resources from libraries:

• The complete work of Darwin online
• Online exhibition from UCL Libraries

• Natural History Museum catalogue – search the world’s greatest natural history library for works about Darwin. Try searching for “charles darwin biography”

Some more articles and miscellanea:

• What Darwin learned in medical school. Eldredge N. Lancet . 2009 Feb 7;373(9662):454-5
• 200 years after Darwin. Rosenberg RN, Stüve O, Eagar T. _Arch Neurol _. 2009 Feb;66(2):153-5
• Happy birthday, Mr. Darwin. Introduction. Sugden A, Ash C, Hanson B, Zahn L._ Science_ . 2009 Feb 6;323(5915):727
• Assessing evo-devo in the Darwin year. Raff RA. Evol Dev . 2009 Jan-Feb;11(1):1-2
• Darwin misunderstood. Shermer M. Sci Am . 2009 Feb;300(2):34
• Darwin’s Originality. Bowler PJ._ Science_ . 2009 Jan 9;323(5911):223-6
• Darwin 200: A natural selection. Nature . 2009 Jan 1;457(7225):40
• Darwin in disguise. Derry JF. _Trends Ecol Evol _. 2009 Feb;24(2):73-9. Epub 2008 Dec 25
• A letter to Darwin. Gannon F. EMBO Rep . 2009 Jan;10(1):1
• Darwin’s influence at UCL

• Darwin’s student days

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A colleague sent me the latest issue of Research Trends – a bi-monthly newsletter from Elsevier with short features on bibliometrics. Cynics might say it was a thinly veiled marketing ploy to help embed their Scopus database as a worthy tool for bibliometric work, but it is useful nonetheless.
Actually a study commissioned by HEFCE and published last year found that Scopus should be considered as a potential alternative to the Web of Science for the purposes of the REF, though given the recent purchase of Evidence Ltd (the company setting up the REF system) by Thomson Reuters (the company who publish Web of Science), perhaps Elsevier still have worries on this score.
Anyway, Research Trends is just 8 pages long and is quite a good read even if you’re not that interested in bibliometrics. This issue has articles about

• the various recent studies into the reading and citing behaviour of scientists that seem to indicate they are reading more widely but citing more narrowly
• studies into the productivity of female scientists versus male scientists

• the need for robust business intelligence data to help institutes win funding

Finally a clutch of more predictable items on Nobel laureates and country rankings.

I’m rather proud of my Science Blogging 2008 T-shirt. Brown isn’t my favourite colour, but the logo looks good and I wear it in the knowledge that it’s a pretty exclusive brand. So I spent a day last month parading it around midtown Manila. I don’t know what I expected but it didn’t attract any attention (well, except for the usual invitations to buy a Rolex or some Viagra).
Although SMS texting is the number one preoccupation in the Philippines, blogging does seem quite popular too. I read one article in the Manila press commenting that a series of recent corruption exposes had shown the power of political bloggers there in rooting out wrong-doing.
Science blogging seems still to be in its infancy though. I found a list of Filipino science blogs but it has just nine blogs and most of them cover science only incidentally, that is hardly at all.
More interesting is the Filipino Voices blog where I found a post about the problems of Filipino science . Professor Flor Lacanilao, a respected Pinoy scientist, has drawn attention to the lack of meritocracy in Philippine science, criticising the National Academy of Science and Technology.
Lacanilao stresses the importance of publication in peer reviewed journals. He says that in the Philippines poor research practice contributes to the lack of a publication culture and severely compromises graduate training and education. It’s good to see forthright views being expressed so freely.
Finally, I am happy to see that there is a Filipino librarian blog

I spent Christmas and New Year in the Philippines. It was lovely to be somewhere warm and lovely to enjoy being somewhere quite different, but also strangely familiar. Relics from their colonial history (first Spain and then USA) makes the Philippines less of a culture shock than many other countries in southeast Asia.
I attended a midnight mass on Christmas eve, in a church in Peace Village, a suburb of Antipolo City. The service was entirely in Tagalog which meant the sermon was mostly incomprehensible except for one sentence in English that took me by surprise: Man is the highest animal, but still an animal. I didn’t understand the next sentence except for the name Charles Darwin.
It’s good to know that, in a small suburban chapel in the Philippines, the work of Charles Darwin can be celebrated at one of the busiest church services of the year.
Perhaps I shouldn’t have been surprised. The Philippines is very proud of its education system, modelled on that of the USA, and boasts the oldest University in Asia (University of Santo Tomas ). Though the country is not known for science, they can lay claim to being the source of erythromycin and are also host to IRRI, the International Rice Research Institute . They have also recently announced plans to reinvigorate the science base.
Later in my holiday I paid a visit to the library unit at the Philippine Council for Health Research and Development (PCHRD) and learnt more about the structure of research in the Philippines. PCHRD is one of the Philippine research councils – currently there are five but they are being reorganised into just three: Health; Energy and emerging technology; Agriculture, environment and oceans. All three are part of DOST – the Dept of Science & Technology – which recently celebrated its 50th anniversary.
PCHRD itself is just 25 years old. It puts great emphasis on nurturing a culture of research across the country and has a strong regional agenda. They fund research projects – focusing on applied research related to national needs e.g. medicinal chemistry and phytopharmaceuticals. They do not have any intramural research institutes, though there is the National Institutes of Health , based in the University of the Philippines, Manila.
I was interested to learn about local publishing practices. There are about 180 locally published health journals (many non-peer reviewed) but only about 30 of them publish regularly. The proliferation of local journals is recognised as a problem and so more support is being given to the more regular journals. Another problem is that not all researchers are accustomed to publishing, preferring to prepare unpublished reports. DOST is trying to change this situation, but it will take time and, I expect, money. I didn’t have the time to really look into the financial aspects of being a researcher in the Philippines but I would hazard a guess that funding is hard to come by and there is little incentive to put in the effort to craft a well-honed manuscript for publication.
It will be interesting to see whether the efforts to boost science and technology in the Philippines will pay off, and what effect they have on publication practices.

As a service manager, my first impulse is always to give people what they want. My primary objective is to keep the customer happy (yes, I’m afraid even in Libraries these days we have started to call our users ­customers). To keep information-hungry researchers happy is simple: just provide access to everything, everywhere. The only snag is that I also have to stay within a budget, so I have to make choices about what access to purchase. Most of my budget is spent purchasing journals, so journal selection is always a major concern. I try to keep to a steady state, maintaining the same range of journals with only small tweaks (individual additions and deletions), but there are periodic hiccups (cancellations at times of budget crisis).
I was interested to see in a recent report that “Publishing companies, especially the large and commercial ones, are launching journals at a higher rate than in 2005”. New journals are the best way for a publisher to attract new subscriptions, so it’s not surprising that new launches are increasing. The report, from the Association of Learned and Professional Society Publishers (ALPSP), also found that publishers are closing more titles.
Requests from library users for new journals are a mixed blessing. On the one hand, it’s very useful to know what people want to read. On the other hand, I can’t satisfy all requests as the budget will not stretch that far. How do I decide when a subscription is justified? I look at the brand (Nature Publishing and Cell Press titles usually go to the top of the list), and at the topic of the journal (not interested in Nature Geoscience here but translational medicine is a hot topic). If the journal is not completely new then I do some data analysis (counting up how many times NIMR authors have published in it, cited it, asked the Library for articles from it). Finally I look at who is asking for it (a lone postdoc voice or a group of PIs?).

When Science STKE changed to Science Signalling and started to publish primary research articles, then I got messages from three heads of division plus another two PIs telling me they must have access, and I knew that I must add the title to our deal with the publishers, AAAS.
When another senior scientist forwarded an email from the editor of two journals he was connected with, I took less notice. The email begged him to recommend his librarian to start subscriptions to the two titles, but he later sheepishly admitted “I am not quite sure why I agreed to be on the editorial board – but so far this is the first thing they have asked me to do”. My analysis showed there had been no previous interest in the titles and I decided to do nothing further.
A couple of lone voices asked for two other titles. Both were in core subject areas for NIMR, but had not been heavily requested or cited by NIMR authors. I put them in the category of “nice to have, not essential”, so the result is no action. One of the titles may be part of a “big deal” later on, which is the other complicating factor in choosing whether to subscribe.

Occasionally I will take the initiative myself. When the Company of Biologists (CoB) announced their new journal Disease Models & Mechanisms I knew the topic was one we had to be interested in. Translational research is being pushed by the government and all biomedical research funders so this title, aiming to publish “across the entire spectrum of disease research, including basic, translational, and clinical research” looks unmissable. The range of topics in the first two issues seemed a good match for NIMR interests and CoB have a good track record in producing high-quality journals. (As an aside, I see fellow blogger Heather has just published there). After a bit of consultation I agreed to try a subscription for a year or two. However, just like buses, two translational journals have come along at the same time.

We also have EMBO Molecular Medicine due to start in 2009, with a very similar set of aims and impressive-looking editorial board. The good news is that they are offering free access to all content for the first two years of publication, so I can delay making the decision to part with any money just yet.