Yesterday on the train I had a most remarkable experience of synchronicity. I had been at the RIN workshop on the costs of scholarly publishing (more on that later) in London and was heading of to Oxford for a group dinner. On the train I was looking for a seat with a desk and took one up opposite a guy with a slightly battered looking mac laptop. As I pulled out my new Macbook (13” 2.4 GHz, 4 Gb memory since you ask) he leaned across to have a good look, as you do, and we struck up a conversation. He asked what I did and I talked a little about being a scientist and my role at work. He was a consultant who worked on systems integration.
At some stage he made a throwaway comment about the fact that he had been going back to learn or re-learn some fairly advanced statistics and that he had had a lot of trouble getting access to some academic papers, certainly he didn’t want to pay for them, but had managed to find free versions of what he wanted online. I managed to keep my mouth somewhat shut at this point, except to say I had been at a workshop looking at these issues. However it gets better, much better. He was looking into quantitative risk issues and this lead into a discussion about the problems of how science and particularly medicine reporting in the media doesn’t provide links back to the original research (which is generally not accessible anyway) and that, what is worse, the original data is usually not available (and this was all unprompted by me, honestly!). To paraphrase his comment “the trouble with science is that I can’t get at the numbers behind the headlines; what is the sample size, how was the trial run…” Well at this point, all thought of getting any work done went out the window and we had a great discussion about data availability, the challenges of recording it in the right form (his systems integration work includes efforts to deal with mining of large, badly organised data sets), drifted into identity management and trust networks and was a great deal of fun.
What do I take from this? That there is a a demand for this kind of information and data from an educated and knowledgable public. One of the questions he asked was whether as a scientist I ever see much in the way of demand from the public. My response was that, aside from pushing the taxpayer access to taxpayer funded research myself, I hadn’t seen much evidence of real demand. His argument was that there is a huge nascent demand there from people who haven’t thought about their need to get into the detail of news stories that effect them. People want the detail, they just have no idea of how to go about getting it. Spread the idea that access to that detail is a right and we will see the demand for access to the outputs of research grow rapidly. The idea that “no-one out there is interested or competent to understand the details” is simply not true. The more respect we have for the people who fund our research the better frankly.

Posted: December 12th, 2008 under open access, open data, open science.
Comments: 6

I had been getting puzzled for a while as to why I was being characterised as an ‘Open Access’ advocate. I mean, I do adovcate Open Access publication and I have opinions on the Green versus Gold debate. I am trying to get more of my publications into Open Access journals. But I’m no expert, and I’ve certainly been around this community for a much shorter time and know a lot less about the detail than many other people. The giants of the Open Access movement have been fighting the good fight for many years. Really I’m just a late comer cheering from the sidelines.

This came to a head recently when I was being interviewed for a piece on Open Access. We kept coming round to the question of what it was that motivated me to be ’such a strong’ advocate of open access publication. I must have a very strong motivation to have such strong views surely? And I found myself thinking that I didn’t. I wasn’t that motivated about open access per se. It took some thinking and going back over where I had come from to realise that this was because of where I was coming from.

I guess most people come to the Open Science movement firstly through an interest in Open Access. The frustration of not being able to access papers, followed by the realisation that for many other scientists it must be much worse. Often this is followed by the sense that even when you’ve got the papers they don’t have the information you want or need, that it would be better if they were more complete, the data or software tools available, the methodology online. There is a logical progression from ‘better access to the literature helps’ to ‘access to all the information would be so much better’.

I came at the whole thing from a different angle. My Damascus moment came when I realised the potential power of making everything available; the lab book, the data, the tools, the materials, and the ideas. Once you connect the idea of the read-write web to science communication, it is clear that the underlying platform has to be open, accessible, and re-useable to get the benefits. Science is perhaps the ultimate open platform available to build on. From this perspective it is immediately self evident that the current publishing paradigm and subscription access publication in particular is broken. But it is just one part of the puzzle, one of the barriers to communication that need to be attacked, broken down, and re-built. It is difficult, for these reasons, for me to separate out a bit of my motivation that relates just to Open Access.

Indeed in some respects Open Access, at least in the form in which it is funded by author charges can be a hindrance to effective science communication. Many of the people I would like to see more involved in the general scientific community, who would be empowered by more effective communication, cannot afford author charges. Indeed many of my colleagues in what appear to be well funded western institutions can’t afford them either. Sure you can ask for a fee waiver but no-one likes to ask for charity.

But I think papers are important. Some people believe that the scientific paper as it exists today is inevitably doomed. I disagree. I think it has an important place as a static document, a marker of what a particular group thought at a particular time, based on the evidence they had assembled. If we accept that the paper has a place then we need to ask how it is funded, particularly the costs of peer and editorial review, and the costs maintaining that record into the future. If you believe, as I do, that in an ideal world this communication would be immediately available to all then there are relatively few viable business models available. What has been exciting about the past few months, and indeed the past week has been the evidence that these business models are starting to work through and make sense. The purchase of BioMedCentral by Springer may raise concerns for the future but it also demonstrates that a publishing behemoth has faith in the future of OA as a publishing business model.

For me, this means that in many ways the discussion has moved on. Open Access, and Open Access publication in particular, has proved its viability. The challenges now lie in widening the argument to include data, to include materials, to include process. To develop the tools that will allow us to capture all of this in a meaningful way and to make sense of other people’s record. None of which should in any way belittle the achievement of those who have brought the Open Access movement to its current point. Immense amounts of blood, sweat, and tears, from thousands of people have brought what was once a fringe movement to the centre of the debate on science communication. The establishing of viable publishers and repositories for pre-prints, the bringing of funders and governments to the table with mandates, and of placing the option of OA publication at the fore of people’s minds are huge achievements, especially given the relatively short time it has taken. The debate on value for money, on quality of communication, and on business models and the best practical approaches will continue, but the debate about the value of, indeed the need for, Open Access has essentially been won.

And this is at the core of what Open Access means for me. The debate has placed, or perhaps re-placed, right at the centre of the discussion of how we should do science, the importance of the quality of communication. It has re-stated the principle of placing the claims that you make, and the evidence that supports them, in the open for criticism by anyone with the expertise to judge, regardless of where they are based or who is funding them. And it has made crystal clear where the deficiencies in that communication process lie and exposed the creeping tendency of publication over the past few decades to become more an exercise in point scoring than communication. There remains much work to be done across a wide range of areas but the fact that we can now look at taking those challenges on is due in no small part to the work of those who have advocated Open Access from its difficult beginnings to today’s success. Open Access Day is a great achievment in its own right and it should be celebration of the the efforts of all those people who have contributed to making it possible as well as an opportunity to build for the future.

High quality communication, as I and others have said, and will continue to say, is Just Good Science. The success of Open Access has shown how one aspect of that communication process can be radically improved. The message to me is a simple one. Without open communication you simply can’t do the best science. Open Access to the published literature is simply one necessary condition of doing the best possible science.

Posted: October 14th, 2008 under Uncategorized, open access.
Comments: none

So BioBarCamp started yesterday with a bang and a great kick off. Not only did we somehow manage to start early we were consistently running ahead of schedule. With several hours initially scheduled for introductions this actually went pretty quick, although it was quite comprehensive. During the introduction many people expressed an interest in ‘Open Science’, ‘Open Data’, or some other open stuff, yet it was already pretty clear that many people meant many different things by this. It was suggested that with the time available we have a discussion session on what ‘Open Science’ might mean. Pedro and mysey live blogged this at Friendfeed and the discussion will continue this morning.

I think for me the most striking outcome of that session was that not only is this a radically new concept for many people but that many people don’t have any background understanding of open source software either which can make the discussion totally impenetrable to them. This, in my view strengthens the need for having some clear brands, or standards, that are easy to point to and easy to sign up to (or not). I pitched the idea, basically adapting from John Wilbank’s pitch at the meeting in Barcelona, that our first target should that all data and analysis associated with a published paper should be available. This seems an unarguable basic standard, but is one that we currently fall far short of. I will pitch this again in the session I have proposed on ‘Building a data commons’.

The schedule for today is up as a googledoc spreadsheet with many difficult decisions to make. My current thinking is;

1. Kaitlin Thaney – Open Science Session
2. Ricardo Vidal and Vivek Murthy (OpenWetWare and Epernicus).  Using online communities to share resources efficiently.
3. Jeremy England & Mark Kaganovich – Labmeeting, Keeping Stalin Out of Science (though I would also love to do John Cumbers on synthetic biology for space colonization, that is just so cool)
4. Pedro Beltrao & Peter Binfield – Dealing with Noise in Science / How should scientific articles be measured.
5. Hard choice: Andrew Hessel – building an open source biotech company or Nikesh Kotecha + Shirley Wu – Motivating annotation
6. Another doozy: John Cumbers - Science Worship / Science Marketing or Hilary Spencer & Mathias Crawford – Interests in Scientific IP – Who Owns/Controls Scientific Communication and Data?  The Major Players.
7. Better turn up to mine I guess :)
8.  Joseph Perla – Cloud computing, Robotics and the future of Science and  Joel Dudley & Charles Parrot – Open Access Scientific Computing Grids & OpenMac Grid

I am beginning to think I should have brought two laptops and two webcams. Then I could have recorded one and gone to the other. Whatever happens I will try to cover as much as I can in the BioBarCamp room at FriendFeed, and where possible and appropriate I will broadcast and record via Mogulus. The wireless was a bit tenuous yesterday so I am not absolutely sure how well this will work.

Finally, this has been great opportunity to meet up with people I know and have met before, those who I feel I know well but have never met face to face, and indeed those whose name I vaguely know (or should know) but have never connected with before. I’m not going to say who is in which list because I will forget someone! But if I haven’t said hello yet do come up and harass me because I probably just haven’t connected your online persona with the person in front of me!

Posted: August 7th, 2008 under Friendfeed, Meeting, biobarcamp, data commons, open access, open science, scifoo, talk, workshop.
Comments: 7

I’m in Barcelona at a satellite meeting of the EuroScience Open Forum organised by Science Commons and a number of their partners.  Today is when most of the meeting will be with forums on ‘Open Access Today’, ‘Moving OA to the Scientific Enterprise:Data, materials, software’, ‘Open access in the the knowledge network’, and ‘Open society, open science: Principle and lessons from OA’. There is also a keynote from Carlos Morais-Pires of the European Commission and the lineup for the panels is very impressive.

Last night was an introduction and social kickoff as well. James Boyle (Duke Law School, Chair of board of directors of Creative Commons, Founder of Science commons) gave a wonderful talk (40 minutes, no slides, barely taking breath) where his central theme was the relationship between where we are today with open science and where international computer networks were in 1992. He likened making the case for open science today with that of people suggesting in 1992 that the networks would benefit from being made freely accessible, freely useable, and based on open standards. The fears that people have today of good information being lost in a deluge of dross, of their being large quantities of nonsense, and nonsense from people with an agenda, can to a certain extent be balanced against the idea that to put it crudely, that Google works. As James put it (not quite a direct quote) ‘You need to reconcile two statements; both true. 1) 99% of all material on the web is incorrect, badly written, and partial. 2) You probably  haven’t opened an encylopedia as a reference in ten year.

James gave two further examples, one being the availability of legal data in the US. Despite the fact that none of this is copyrightable in the US there are thriving businesses based on it. The second, which I found compelling, for reasons that Peter Murray-Rust has described in some detail. Weather data in the US is free. In a recent attempt to get long term weather data a research effort was charged on the order of $1500, the cost of the DVDs that would be needed to ship the data, for all existing US weather data. By comparison a single German state wanted millions for theirs. The consequence of this was that the European data didn’t go into the modelling. James made the point that while the European return on investment for weather data was a respectable nine-fold, that for the US (where they are giving it away remember) was 32 times. To me though the really compelling part of this argument is if that data is not made available we run the risk of being underwater in twenty years with nothing to eat. This particular case is not about money, it is potentially about survival.

Finally - and this you will not be surprised was the bit I most liked - he went on to issue a call to arms to get on and start building this thing that we might call the data commons. The time has come to actually sit down and start to take these things forward, to start solving the issues of reward structures, of identifying business models, and to build the tools and standards to make this happen. That, he said was the job for today. I am looking forward to it.

I will attempt to do some updates via twitter/friendfeed (cameronneylon on both) but I don’t know how well that will work. I don’t have a roaming data tariff and the charges in Europe are a killer so it may be a bit sparse.

Posted: July 17th, 2008 under data commons, data formats, economics, ethics, linking papers to open data, ontologies, open access, open access for the developing world, open data, open notebook science, open science.
Comments: none

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Following on from the discussion a few weeks back kicked off by Shirley at One Big Lab and continued here I’ve been thinking about how to actually turn what was a throwaway comment into reality:

What is being generated here is new science, and science isn’t paid for per se. The resources that generate science are supported by governments, charities, and industry but the actual production of science is not supported. The truly radical approach to this would be to turn the system on its head. Don’t fund the universities to do science, fund the journals to buy science; then the system would reward increased efficiency.

There is a problem at the core of this. For someone to pay for access to the results, there has to be a monetary benefit to them. This may be through increased efficiency of their research funding but that’s a rather vague benefit. For a serious charitable or commercial funder there has to be the potential to either make money, or at least see that the enterprise could become self sufficient. But surely this means monetizing the data somehow? Which would require restrictive licences, which is not at the end what we’re about.

The other story of the week has been the, in the end very useful, kerfuffle caused by ChemSpider moving to a CC-BY-SA licence, and the confusion that has been revealed regarding data, licencing, and the public domain. John Wilbanks, whose comments on the ChemSpider licence, sparked the discussion has written two posts [1, 2] which I found illuminating and have made things much clearer for me. His point is that data naturally belongs in the public domain and that the public domain and the freedom of the data itself needs to be protected from erosion, both legal, and conceptual that could be caused by our obsession with licences. What does this mean for making an effective data commons, and the Science Exchange that could arise from it, financially viable? Read more »

Posted: May 11th, 2008 under Collaboration, academic credit, data commons, data formats, funding, linking papers to open data, open access, open data, open-science-charter, osci-protocol, science21.
Comments: none

Perimeter Institute by hungryhungrypixels (Picture found by Zemanta).

Sabine Hossenfelder and Michael Nielsen of the Perimeter Institute for Theoretical Physics are organising a conference called ‘Science in the 21st Century‘ which was inspired in part by SciBarCamp. I am honoured, and not a little daunted, to have been asked to speak considering the star studded line up of speakers including, well lots of really interesting people, read the list. The meeting looks to be a really interesting mix of science, tools, and how these interact with people (and scientists). I’m looking forward to it. Read more »

Posted: April 8th, 2008 under open access, open data, open notebook science, open science, science21, talk.
Comments: 3

Ok, having flagged up two surveys in my previous post I have now done the second one. It seems to be for anyone worldwide but I wanted to bring it to people’s attention because it further clouds the definition of Open Access, whether deliberately or through ignorance I can’t say.

Fairly early on we have the following question:

6. What do you understand by the term ‘Open Access’? (Tick all those that apply)

• Journals that are free to the reader
• Journals that are free to the author
• Journals that charge the author
• Copies of journal articles freely available online (other than in the journal itself)
• Not sure
• Never heard the term
• Other (please give details)

BBB doesn’t seem to even exist as an option!
And then in the following panel;

Full Open Access (OA) journals are generally defined as journals that are free for everyone to read immediately on publication, whether the costs of publication are defrayed through author-side charges, or in some other way

Now, we can (and have) argued for a long time over definitions of OA and the role of BBB etc. But to not mention it at all does not seem helpful. Might I humbly suggest that all those who feel it appropriate do the survey and put something in the ‘Other’ box for Question 6?

The survey is at: http://www.surveymonkey.com/s.aspx?sm=O8NxxhwFB2DQwDUvW183nw_3d_3d

I am assuming fair use for the purpose of criticism (this is significantly less than 5% of the full text of the survey).

Posted: January 16th, 2008 under open access.
Comments: 2

UK PubMedCentral, a UK mirror of PMC and a growing project at the British Library is soliciting responses to a survey:

Dear Colleague,

As you will know, UKPMC provides free access to an extensive repository of biomedical research literature, as well as an easy way for researchers to submit newly published work to meet the UKPMC Funders Group members’ Open Access requirements. The vision is for UKPMC to be much more than that!

As we enter the next stage of developing UKPMC into an innovative and useful resource for UK researchers we want to ensure that your needs and ideas are heard and incorporated at the outset. Please help us by completing our online questionnaire.

It should only take a few minutes and, as our way of saying thank you, all respondents will be entered into a prize draw to win an all-expenses paid weekend for two in London.

Click here to be taken straight to the survey page:

http://www.bl.uk/surveys/ukpmc/ukpmc.htm

Much of the survey asks questions about what additional tools you use for scientific search etc and what features you would like to see in UK PMC. This worries me as it seems like duplication both of effort and the creation of yet another del.icio.us/Facebook/Google/whatever for scientists. We don’t need another one, we need integration between the existing ones and improvement of user interfaces, interoperability, and useability. This wonderful video on the data portability initiative, which I saw featured on Deepak’s blog, tells the story. That’s my view anyway. Feel free to take the survey and disagree with me!

In addition the UK Biochemical Society has also commissioned some research and is looking for people to fill out another survey;

The Biochemical Society, in collaboration with other members of the Biosciences Federation (www.bsf.ac.uk), is conducting research into your experience of Open Access; I am writing to ask you to participate in this, by completing a brief questionnaire that should take no longer than 15 minutes.

The survey can be found here and the deadline is 1 February.

Posted: January 16th, 2008 under open access, tools.
Comments: none

I spent last week in Cuba. I was there on holiday but my wife (who is a chemistry academic) was on a work trip to visit collaborators. This meant I had the opportunity to talk to a range of scientists and to see the conditions they work under. One of the strong arguments for Open Science (literature access, data, methods, notebooks) is that it provides access to scientists in less priviledged countries to both peer reviewed research as well as to the details of methodology that can enable them to carry out their science. I was therefore interested to see both what was available to them and whether they viewed our efforts in this area as useful or helpful. I want to emphasise that these people were doing good science in difficult circumstances by playing to their strengths and focussing on achievable goals. This is not second rate science, just science that is limited by access to facilities, reagents, and information.

Access to the literature

There is essentially no access to the subscriber-only literature.  Odd copies of journal issues are highly valued and many people get by by having visiting positions at institutes in the developed world. I talked to a few people about our protein ligation work and they were immensely grateful that this was published in an open access journal. However they were uncertain about publishing in open access journals due to the perceived costs.  While it is likely that they could get such costs waived I believe there is an issue of pride here in not wishing to take ‘charity’. Indeed, in the case of Cuba it may be illegal for US based open access publishers to provide such assistance. It would be interesting to know whether this is the case.

Overall though, it is clear that acccess to the peer reviewed literature is a serious problem for these people.  Open Access publishing provides a partial solution to this problem. I think to be effective it is important that this not be limited to self archving, as for reasons I will come back to, it is difficult for them to find such self archived papers. It is clear that mandating archival on a free access repository can help.

Access to primary data

Of more immediate interest to me was whether people with limited access to the literature saw value in having free access to the primary data in open notebooks. Again, people were grateful for the provision of access to information as this has the potential to make their life easier. When you have limited resources it is important to make sure that things work and that they produce publishable results. Getting details information on methodology of interest is therefore very valuable. Often the data that we take for granted is not available (fluorescence spectra, NMR, mass spectrometry) but details like melting points, colours, retention times can be very valuable.

There were two major concerns; one is a concern we regularly see, that of information overload. I think this is less of a concern as long as search engines make it possible to find information that is of interest. Work needs to be done on this but I think it is clear that some sort of cross between Google Scholar and Amazon’s recommendation system/Delicious etc. (original concept suggested by Neil Saunders) can deal with this.  The other concern, relating to them adopting  such approaches, was one that we have seen over and over again, that of ‘getting scooped’. Here though the context is subtley different and there is a measure of first world-developing world politics thrown in. These scientists are, understandably, very reluctant to publicise initial results because the way they work is methodical and slow. Very often the key piece of data required to make up a paper can only be obtained on apparatus that is not available in house or requires lengthy negotiations with potential overseas collaborators. By comparison it would often be trivially easy for a developed world laboratory to take the initial results and turn out the paper.

The usual flip side argument holds here; by placing an initial result in the public domain it may be easier for them to find a collaborator who can finish of the paper but I can understand their perspective. These are people struggling against enormous odds to stake out a place for themselves in the scientific community. The first world does not exactly have an outstanding record on acknowledging or even valuing work in developing countries so I can appreciate a degree of scepticism on their part. I hope that this may be overcome eventually but given that the assumption of most people in my own community is that by being open we are bound to be shafted I suspect we need to get our own house in order first.

The catch…

All of this is well and good. There are many real and potential benefits for scientists in the developing world if we move to more open styles of science communication. This is great, and I think it is a good argument for more openness. However there is a serious problem with the way we present this information and our reliance on modern web tools to do it. Its a very simple problem: bandwidth.

All of our blogs, our data, and indeed the open access literature is very graphics heavy. I actually tried to load up the front page of openwetware.org while sitting at the computer of the head of the department my wife was visiting (the department has two networked computers). Fifteen minutes later it was still loading.  The PLoS One front page was similarly sluggish. I get irritated if my download speeds drop below 500K/second, at home, and I will give up if they go down to 100K. We were seeing download rates of 44 bytes/second at the worst point. In some cases this can even make search engines unuseable making it near impossible to track down the self-archived versions of papers. Cuba is perhaps a special case because the US embargo means they have no access to the main transatlantic and North American cables, in effect the whole country is on a couple of bundles of phone lines, but I suspect that even while access is becoming more pervasive the penetration of reasonable levels of bandwidth is limited in the developing world.

The point of this is that access is about more than just putting stuff up, it is also about making it accessible. If we are serious about providing access, and expanding our networks to include scientists who do not have the advantages that we have, then this necessarily includes thinking about low bandwidth versions of the pages that provide information. I looked through PLoS One, openwetware, BioMedCentral, and couldn’t find a ‘text only version’ button on any of them (to be fair there isn’t one on our lab blog either).  I appreciate the need to present things in an appealling and useful format, and indeed the need to place advertising to diversify revenue streams. I guess the main point is not to assume that by making it available, that you are necessarily making it accessible. If universal accessibility is an important goal then some thought needs to go into alternative presentations.

Overall I think there are real benefits for these scientists when we make things available. The challenges shouldn’t put us off doing it but perhaps it is advisable to bear in mind the old saw; If you want to help people, make sure you find out what they need first.

Posted: January 14th, 2008 under open access, open access for the developing world, open notebook science, open science.
Comments: 9

I don’t usually do New Year’s resolutions. But in the spirit of the several posts from people looking back and looking forwards I thought I would offer a few. This being an open process there will be people to hold me to these so there will be a bit of encouragement there. This promises to be a year in which Open issues move much further up the agenda. These things are little ways that we can take this forward and help to build the momentum.

1. I will adopt the NIH Open Access Mandate as a minimum standard for papers submitted in 2008. Where possible we will submit to fully Open Access journals but where there is not an appropriate journal in terms of subject area or status we will only submit to journals that allow us to submit a complete version of the paper to PubMed Central within 12 months.
2. I will get more of our existing (non-ONS) data online and freely available.
3. Going forward all members of my group will be committed to an Open Notebook Science approach unless this is prohibited or made impractical by the research funders. Where this is the case these projects will be publically flagged as non-ONS and I will apply the principle of the NIH OA Mandate (12 months maximum embargo) wherever possible.
4. I will do more to publicise Open Notebook Science. Specifically I will give ONS a mention in every scientific talk and presentation I give.
5. Regardless of the outcome of the funding application I will attempt to get funding to support an international meeting focussed on developing Open Approaches in Research.

Beyond the usual (write more papers, write more grants) I think that covers things. These should even be practical.

I hope all of those who have had a holiday have enjoyed it and that all those who have not are looking forward to one in the near future. I am looking forward to the New (Western, Calendar) Year. It promises to be an exciting one!

I am now off to cook lots of lovely Chinese food (and yes I know that is calendarically inappropriate - but it will still taste good!). Happy New Year!

Posted: December 31st, 2007 under open access, open data, open notebook science, open science.
Comments: 2