The International Association of Scientific, Technical, and Medical Publishers has published, The STM Report: An overview of scientific and scholarly journal publishing, a follow-up to their 2006 report, Scientific publishing in transition: an overview of current developments.

I’m not the biggest fan of this publishers’ organisation, but I think this is a useful report for anyone interested in journals. The press release says that the report “shows that scholarly communications are undergoing profound changes driven by technology and economic factors, while authors’ core motivations to publish remain stable”. Well, you probably knew that already, but it’s hard to give a one-line summary of a 68-page report.

Written by Mark Ware (of Mark Ware Consulting) and Michael Mabe (of stm) the report has a good overview of how journals and scholarly communication work, why researchers publish, the business side of journals, global trends in research publishing, reading patterns and navigation, ethical issues, open access, and new technology. In short, it is a scholarly review of just about everything that has happened in the journals world in the last three years. For anyone who follows these things there is little new, but it’s helpful to have it all in one place and the four page bibliography gives original sources for everything it covers.

This is perhaps an impolite question question to ask in a blog hosted on Nature Network, but I ask in a spirit of enquiry rather than provocation.

I am inspired by an interesting blog post on the Scholarly Kitchen blog that points up the failure of social networking websites to gain many converts in the scientific community. This has been highlighted a few times in recent years so is not surprising. The blog post identifies the problem:

Most networks seem to make two assumptions that doom them to failure: 1) that networking and communication is a central part of a scientist’s day, and 2) that scientists are willing to openly communicate on a wide scale with their communities. The first is a failure of perspective, those building and promoting social networks are “true-believers“, people whose lives revolve around social networking. While communication of results, networking and building collaboration are important for scientists, they’re somewhat peripheral compared to doing actual research. These are things one does in addition to one’s “real” work, performing experiments and seeking funding is often more important as well. Finding collaborators is at best, a sporadic event, not something done often. Any network that asks for regular participation and priority in time and effort will fail for this reason.

This makes a lot of sense to me. I am a bit of a “true believer” – I do join up and try things out. More importantly I think that the social model of information is here to stay. Filtering resource discovery through a network of friends, colleagues or like-minded people is a valuable technique and is something we all do in the real world anyway. Finding a way to do it online is the challenge. I think it will only work when the networks are built into what we already do online, and when there is effectively a single network rather than a series of disconnected networks in different services.

The BBC website also had an article about some new tools for scientists, highlighting the social aspects and mentioning Mendeley, Faculty of 1000 and Google Wave.

Meanwhile, Cell this week has an article about Twitter. They say it has become very popular, yet most scientists are still steering clear of it. The article’s author speaks to some scientists who have found value in tweeting.

Well, if Joanna can post gratuitous pictures of furry animals then so can I. Though mine are funny animals rather than furry animals. Last year I showed some of Liverpool’s superlambananas ; this year I show you a parade of Amsterdam’s elephants.

They are colourful elephant replicas with arty designs and patterns painted on, all in the cause of drawing attention to the Asian elephant and raising money for an elephant charity. The idea has already been in Rotterdam and Antwerp but the Amsterdam version, with 100 elephants, is the largest yet. It will run until 31st October.

This one looks a bit Australian to me

In the style of Matisse, perhaps?

Ah, a bit of Delft-ware

This one has a polar bear on top of it.

And here are a couple of photos of a real-live bird, posing beautifully in Amsterdam’s Vondelpark:

There was an interesting article in Science recently: Strategic Reading, Ontologies, and the Future of Scientific Publishing by Allen H. Renear and Carole L. Palmer, two professors of library science. It reviews some of the literature on scholarly communication in the digital age, but for my taste is a bit speculative in its predictions for the future.

They point out that reading habits have changed in the last 20 years as digital information has grown and surpassed print to a large extent. They suggest that scientists’ aim is to move rapidly through the literature to assess and exploit content with as little actual reading as possible.

They also state that as scientists search and browse, they are making queries and selecting information in much tighter iterations. This process of dodging around, clicking forward, back and sideways in search of the right answer is compared to channel-surfing on the TV. The article cites David Nicholas, another information behaviour researcher:

In the past, information seeking was seen to be the first step to creating knowledge. Now it is a continuous process.

Other research suggests that scientists now “read” more papers, but devote a shorter time to each paper. Renear and Palmer see this as fitting in with the “channel flicking” phenomenon.

They then briefly review the history of ontologies and mention some text-mining initiatives, including my favourite Textpresso, before exploring how ontologies can support scientific publishing (and reading) as part of the semantic web.

They predict that in ten years’ time:

Scientists will still read narrative prose, even as text mining and automated processing become common; however, these reading practices will become increasingly strategic, supported by enhanced literature and ontology-aware tools. As part of the publishing workflow, scientific terminology will be indexed routinely against rich ontologies. More importantly, formalized assertions, perhaps maintained in specialized “structured abstracts”, will provide indexing and browsing tools with computational access to causal and ontological relationships.

For more than ten years I’ve been reading predictions about how ebooks were going to replace printed books, but we’re still not at that point. There are various ebook reader devices on sale and there are plenty of books in electronic format available, but we have not reached the tipping point where cheap ebook devices are available and enough ebook content is available at an attractive price. The barriers now are as much commercial as technical – for mass adoption the technology and the market must both work together.

A story in yesterday’s Times Higher, reporting a JISC study, says that while library users were “hungry for digital content” librarians found the business models for course text-books were “often inappropriate” and their prices “too high”. Hear hear.

The business model for a print book is simple – hand over the money and the book is yours. For ebooks it is a whole lot more tricky, especially when you are talking about purchasing access to a book that made may be used by hundreds of students. Even in the personal sphere, when you buy an ebook it is not always clear exactly what rights you are buying. If you lose your Kindle you have to get a police report before Amazon will agree to close down the device. And you may also find that a book you have purchased for your Kindle gets deleted by Amazon if they discover they didn’t have the rights to distribute it in the first place.

Ebooks are a strange new world – not everything works quite the same way as it does with printed books. Of course there are plenty of advantages to ebooks too, and as the medium matures (maybe another five years? ten years?) I’m sure we will find new features that transform the experience of reading a book.

The British Library is trying to help us get used to world of ebooks by providing dedicated space for researchers to get to grips with the latest technologies driving the digital reading revolution. I saw this back in May, but they have just added three new e-reader devices to the display: the COOL-ER reader, Sony’s ‘Pocket’ and ‘Touch’ Reader devices. They are also showcasing Bloomsbury Library Online, on the upper ground floor of the British Library from Thursday 3 September 2009. Readers will be able to view electronic content at their local library and remotely via internet enabled devices.

For me the key to expanding ebook use and usability is going to be the availability of a world-beating ebook reader. Trouble is, no-one has yet agreed what such a beast might look like. Is it an iPhone? an Apple Tablet? a Kindle? This lack of consensus came home to me when I read a blog post about the announcement
that Asus, makers of the eeePC netbook, were to launch the planet’s cheapest e-book reader. This was interesting not just because it was cheap but also because it is going to have two screens, facing each other and folding up like a clam shell. My first thought was “Brilliant!”, followed closely by “But why?” The comment thread on that blog post starts to dissect exactly what is needed from an ebook reader (or eeebook as Asus have it). Top of the list came e-ink, the display technology that matches the readability of paper. The Asus device will apparently not use e-ink. Hence it gets the thumbs-down from most of the commenters.

Trying to define the ideal feature list for an ebook reader is a tricky job as books themselves are so diverse. What works for a novel will not work for a coffee table book or an atlas and may not work well for a scientific monograph.

So, what is your feature-list for the ideal ebook reader for scientific books and articles? I’ll assume that we all agree on readability, long battery life and low weight.

How about colour screen, double screen, ability to annotate, ability to display any ebook format (including plain text, html and pdf), wifi/bluetooth/3G, link-in to an ebook store, lack of Digital Rights Management. Anything else?

And a prize for anyone who tell me when all these features are going to come together into one handy device that costs under GBP100!

Competition is a wonderful thing. 18 months ago who ever would have thought that there was room for a general chemical journal? Then back in April along came Nature Chemistry and won some applause (sometimes mainly for its colour ). It was noteworthy since chemical journal publishing is dominated by two large society publishers (the Royal Society of Chemistry and the American Chemical Society), and it was also a new direction for Nature Publishing Group.

Now I receive news from the Royal Society of Chemistry of another new journal: Chemical Science will apparently be dynamic, unique, and a leader. It will provide

A dedicated home for findings of exceptional significance from across ALL the chemical sciences. In a break with tradition, the journal will give authors the freedom and flexibility to publish more extensive accounts of their novel research without page restrictions

It is due to launch in 2010, with free access for existing RSC customers for the first one or two years.

Am I too cynical in seeing this as a response from the old guard (RSC) to the new chemical kids on the block (NPG)?

As summer draws to a close and the new autumn season looms, it’s that time when librarians start to think about subscriptions for the next calendar year. (Actually we now think about them all year round – I just had a licence from one publisher to sign for our 2009 subscriptions and we started thinking about another publisher’s 2010 subscriptions back in April).

In a good year we can just renew everything without any worries, perhaps trimming or adding at the edges. In a bad year we have to try to make more major changes and often that means some kind of major review.

This year for the first time I have tried using usage statistics as the principal means of identifying titles to go on the hit list. This is not perfect – minority subjects may get unfairly targeted and groups where there has been some staffing hiatus will also show low usage. So I also ask all PIs for comments on the proposed list. Here is the message (slightly amended) that I have just sent out. It’ll be interesting to see what response I get.

Journal subscriptions account for about 90% of this library’s consumables budget. In the last few years the annual price increases have been less steep (about 7% p.a.) than previously but the recent weakness of the the Pound is going to cause problems for 2010 as many publishers quote their prices in US dollars or in Euros.

We are proposing to make changes to our subscriptions for 2010, saving about £15k in total and helping us to continue to pay for the remaining journal subscriptions and packages.

Low usage
We have been looking at usage figures for all our subscribed titles and comparing them with the cost of the journals, and have arrived at a list of journals that appear to be providing poor value for money. Twelve titles are suggested for cancellation.

Reducing print
We have already reduced the number of print journal subscriptions substantially in favour of online-only access, and we will go further down that route in 2010. We will keep print subscriptions only for the weeklies with news content and for general titles. Some titles that do not allow an online-only subscription may also have to be retained in print for now. We plan to keep just ten print titles.

Note that due to the way that UK VAT works, switching from print to online only does not usually save money

What is a subscription?
Journal business models have changed hugely over the last 15 years. Many of the online journals that are listed in our catalogue and e-journals list are free, partly free or come as part of a package deal where we pay a single price for a large collection of titles from one publisher. These package deals give us access to a large range of titles including some of high interest, some of low interest and some of no interest at all. Overall they are good value but they do make it harder to say what the cost of an individual title is. Publishers offering package deals also insist on no-cancellation clauses, so reducing our options to cancel titles.

Open access
Open Access is slowly having an effect on access to journals. Full open access titles such as PLoS Biology require no subscription. Titles with open backfiles (usually after 12 months) are useful but we still need subscriptions for current material. The growing number of articles archived in PubMedCentral and elsewhere are also useful but many of these are delayed by 6 or 12 months, so we still need subscriptions to key titles. At present Open Access gives fringe benefits but is not a complete replacement for subscription-based access.

I have spent most of the week fiddling about with details of publications and grant codes in Excel, in an effort to make us look good present an accurate picture of my Institute’s publications and matching them up with our research programmes over the last three years. These will all go into MRC’s new e-Val system (also now on Twitter ).

Love them or hate them – and most people hate them – research impact indicators Ref¹ are a feature of today’s research world. John Suslston may say that journal-based metrics “are the disease of our times” but funders still insist on research impact and have devised systems to gather in data. There has been a buzz for more than a year around the RAE being replaced by the REF and adopting a bibliometric approach. Recently it was revealed that HEFCE are backing away from bibliometrics in the REF, but this doesn’t seem to have stemmed the tide of interest in metrics. I mean, indicators.

A little while back Richard blogged on this topic, generating a very interesting comments thread. he mentioned the recent ALPSP meeting on research impact. Richard will be co-presenting a session on this topic at the Science Online meeting on Saturday.

The one indicator that seems most significant to me is the amount of publisher interest in developing indicators. Thomson of course have long been the great wizards of bibliometrics and continue to be major players, particularly since their acquisition of Evidence Ltd. I have had presentations recently about two new or forthcoming products from newer entrants into this market – Elsevier’s SciVal Spotlight and NPG’s still gestating Nature Trends. Both promised interesting new ways to look at research outputs (i.e. publications). They are aimed at Universities rather than specialist research institutes, though NPG’s product looked to be the more flexible. Whether I could ever justify spending scarce funds on these kind of products is another matter. I believe that Richard is also working on some kind of research impact project over at F1000. He has hinted this but not explicitly said as much. It would certainly make a lot of sense for F1000 to move into that territory.

Next on my agenda will be helping to prepare for our QuinQuennial Review (QQR), which starts this autumn. I just downloaded the Publish or Perish programme and tried it out. It looks fun, providing all kinds of magic numbers in an instant. Unfortunately it will take me about two days to figure out what all the different numbers mean, if they mean anything at all.

¹ Note I call them indicators not metrics, following Jonathan Adams’ usage – he insists that “metrics” is a misnomer.

I usually quite enjoy filling out surveys. If the topic of the survey is something that I am concerned about, answering some questions and (especially) filling in the free-text bits can be a good way to vent my feelings. I recently enjoyed telling the powers that be (anonymously of course) what I thought about the room booking system here.

Now I’m seeing it all from the other side – I have created an online questionnaire and have started getting some responses. I realise that sometimes survey responses tell you more about the responder than about the question they are answering.

It is an internal survey to ask our researchers how they use the library and library services, what they think of it and what they need from it in future.

We do have a rough plan – reducing the space given over to print storage; increase the amount of study space; develop more ways to help staff get the best out of information tools; continue to provide as much online access to everything as we can possibly afford – but we want to fine tune it with some input from the users, and verify that there is a body of users who do value what we are proposing.

Of course different people have different needs or even no needs and we are realistic enough to expect quite a range of responses to questions about “Would you value help in setting up subject alerts?” or “Is the Library blog useful?”. But one or two responses made me see red. I had to go away and sit down quietly for a bit to recover my composure.

One respondent suggested that we had a library blog just because someone thought it was “cool”, but that’s not what blogs are for and we are all out of touch with the real world and the internet. I know that petulance is never an attractive character trait, but this response made me want to stamp my little foot and say “Up yours Mr Clever-clogs-know-it-all!” But I’m much too professional to give in to such feelings. I’ll just blog about it instead, even though I’m out of touch with the real world and the internet.

Well, I have recovered now (I think), and feel a bit sorry for that respondent in their splendid state of unknowing. As more survey responses have come in we are seeing a more well-rounded picture emerge, and my faith in human nature has been restored. What that response has taught me though is that I need to put still more effort into communicating about what the Library offers its users – though perhaps not via a blog.

Talking of new topics emerging , synthetic biology seems to be popping up all over the place these days. OK, it’s not exactly new any more but I keep seeing announcements from quasi-official bodies indicating an interest in looking at the ethics of, public interest in, or broader implications of synthetic biology. When the froth rises to the top it suggests there’s a lot brewing down below.

I went to a very interesting talk a few months back given by Thomas Murray president of the Hastings Center, which has an ongoing investigation into ethical issues in synthetic biology. He was invited over here to give the Nuffield Council on Bioethics Public Lecture 2009 and his talk was titled “New genetic recipes: are we cooking up trouble with synthetic biology?” A video of the lecture is available.

Dr Murray explained that ethics begin with facts, so he gave us a few definitions of synthetic biology. Essentially it entails the application of engineering principles to the fundamental components of biology. He also reminded us that as yet synthetic biology is mostly aspirational. Those in the field hope that they can use it for biological production, drug creation or bioremediation, but it’s still a hope.

Drawing on a recent review in Bioessays Dr Murray highlighted three major strains of synthetic biology, each of which may raise different ethical issues:

• protocell creation
• DNA-based device construction
• genome-driven cell engineering

He also noted that with its mix of biology and engineering, synthetic biology brings together two fields with different attitudes to ethical issues. He suggested that biologists are more engaged in ethical debates about the consequences of their research than are engineers. This point was disputed by a representative of the Royal Academy of Engineering who was in the audience (oops!), who maintained that ethics are now part of engineers’ training, but I’m inclined to think that Dr Murray had a point.

He then looked at the very different approaches taken in the UK and the USA to the debates about a) GMOs and b) stem cells. In examining these differences he teased out the idea that some of our beliefs are based around “interests” (financial, personal, family) and some are based around “identities” (deepseated beliefs such as religion or politics). If a position is based on interest then there can be trade-offs and compromises and it is acceptable for there to be public and commercial interests. If a position is based on identity then there are no compromises and the two sides of an issue are probably mutually unintelligible. That certainly sounded like a familiar situation – just think of debates about the use of animals or hybrid embryos in research. Dr Murray thinks that this way of looking at bioethical debates could prove useful.

He talked a little of the potential benefits and risks of synthetic biology. I liked his term bio-errorism (sic). He dissected the precautionary principle (when in doubt, pause) and contrasted it with the pro-actionary principle (when in doubt, go ahead), asking “Who bears the burden of uncertainty?”.

Finally, Dr Murray commented that synthetic biology may be seen as a continuum with genetic engineering, and it may lead us to re-examine our ethical approach to genetic engineering. If we feel that synthetic biology has an impact on how we see ourselves we may treat it as an “identity” issue. He suggested that the debate needs compelling narratives of synthetic biology scenarios as well as philosophical arguments.

The lecture didn’t provide any answers, but it did provoke a good deal of interesting thoughts.

Here is my evidence of the synthetic biology froth:

• Two Research Councils, BBSRC and EPSRC, have set up a steering group of independent members to “advise them on how to gauge and understand the public’s perceptions, aspirations and concerns around synthetic biology”.

• The Royal Society have established a Synthetic Biology Policy Coordination Group which aims to “track and stimulate policy activities and processes to encourage the responsible and responsive development of synthetic biology”.

• The National Endowment for Science, Technology and the Arts (NESTA) and the
  Royal Society of Chemistry (RSC) are designing a series of workshops that will engage an interdisciplinary cross-departmental group of academics who are interested in developing new research ideas in synthetic biology.

• Back in May Nature ran a story about the Centre for Synthetic Biology and Innovation at Imperial College, London, highlighting the fact that social scientists will be a key part of the Centre.

• Also in May the Royal Academy of Engineering (RAE) report looked at practical, regulatory and ethical issues in synthetic biology

• The RAE later issued another report that gauged public attitudes to the field.

• Meanwhile, in Germany, a joint policy paper from the DFG and the Leopoldina academy looks at safety and ethical issues raised by synthetic biology.

• I just noticed that there has been a special issue of EMBO Reports on this topic, in their Science & Society section.

Finally, a couple of books:

• The ethics of protocells edited by Mark A. Bedau and Emily C. Parke – moral and social implications of creating life in the laboratory

• Synthetic Biology by Markus Schmidt
  - a comprehensive overview on relevant societal issues of synthetic biology

p.s. see also Pamela Ronald’s post on genetic engineering.