Science in the 21st Century

Perimiter InstitutePerimeter 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. Continue reading “Science in the 21st Century”

Biosciences Federation Survey on Open Access – Please do this survey!

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).

Some surveys you may wish to fill out

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.

Open Science and the developing world: Good intentions, bad implementation?

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.

Some New Year’s resolutions

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!

A big few weeks for open (notebook) science

So while I have been buried in the paper- and lab-work there has been quite a lot of interesting stuff going on. Pedro Beltrao has started an Open Notebook style project at Google Code which he describes in a post on Public Ramblings. This in interesting, because once again someone is using a different system as an Open Notebook. We have Wiki’s, Blogs, TeX based documents, and now, software version repositories being used. As Jean-Claude Bradley has said and we have discussed we have a lot to learn from exploring different systems, both in terms of understanding the benefits and limitations of specific systems on the way to designing and implementing better ones, but also from the perspective of what this tells us about how we do our science, and how this differs from discipline to discipline. Indeed, there already seems to be a place where this discussion has started in Pedro’s system. It is great to see this going forward and also great to see other members of the community, including Bill Hooker and Michael Barton already getting in and getting their hands dirty. I only wish I could contribute a bit more on the science itself.

Also good is the publicity that Open Notebooks and Open Notebook Science are getting. An article in Chemistry World, the member’s journal of the Royal Society of Chemistry, features UsefulChem, and discussion from Peter Murray-Rust, Steve Bachrach and others. Our efforts at Southampton even get a mention! What is good about this is not so much the personal publicity but that the mainstream ‘industry’ journals are increasingly starting to pick up the story. Not so long ago there was the article in Wired; Chemistry World has also recently discussed the issues associated with openness in a reasonably balanced manner (see also Peter Suber and Peter Murray-Rust’s commentaries).

In addition there is good coverage on the web. Rosie Redfield’s lab pages got featured by David Ng on World’s Fair on Science Blogs which was also picked up at BoingBoing (thanks to Neil Saunders for bringing this to my attention). Momentum is building as Neil says. The issues are becoming mainstream and the benefits are starting to flow through in specific cases. This is how things start to change. The challenge is in maintaining this forward momentum as it builds.

e-science for open science – an EPSRC research network proposal

The UK Engineering and Physical Sciences Research Council currently has a call out for proposals to fund ‘Network Activities’ in e-science. This seems like an opportunity to both publicise and support the ‘Open Science’ agenda so I am proposing to write a proposal to ask for ~£150-200k to fund workshops, meetings, and visits between different people and groups. The money could fund people to come to meetings (including from outside the UK and Europe) but could not be used to directly support research activities. The rationale for the proposal would be as follows.

  • ‘Open Science’ has the potential to radically increase the efficiency and effectiveness of research world wide.
  • The community is disparate and dispersed with many groups working on different approaches that do not currently interoperate – agreeing some interchange or tagging standards may enable significant progress
  • Many of those driving the agenda are early career scientists including graduate students and postdocs who do not have independent travel funds and whose PI may not have resources to support attending meetings where this agenda is being developed
  • There is significant interest from academics, some publishers, software and tool developers, and research funders in making more data freely available but limited concensus on how to take this forward and thus far an insufficient committment of resources to make this possible in practice

The proposal would be to support 2-3 meetings over three years, including travel costs, and provide funds for exchange visits. What I would like from the community is an expression of interest, specifically the committment to write a letter of support saying you would like to be involved. It would be great to get these from tenured academics, early career academics, graduate students and PDRAs, publishers (NPG? PLoS?), library and repository people (UKOLN, Simile, others?) and anyone else who is relevant.

The timeline is tight (due Tuesday next week) but if there is enough interest I will push through to get this done. I propose to write the grant in the open and online so will post a Google Doc or OpenWetWare page as soon as I have something to put up. Any help people can offer on the writing would be appreciated. In the meantime please drop comments below. I will be pointing to this page in the grant proposal.

Variations in reproduction charges – the results are in!

I blogged the other day about the way charges for reproducing figures in review articles appear to have gone ballistic. At that stage I only had the cost for J Biol Chem which was a whopping $USD73 to reproduce a figure. I had three other images I was using and was expecting around $20 for them, based on the website that Science Direct points you at for permissions. Well I was wrong, they have now come back at $USD3 each. So J Biol Chem, $73, Structure and J Mol Biol $3. Question is, what am I paying for from J Biol Chem (apart from my own lack of organisation in getting similar but copyright free figures). The other question is why through one website is it $3 whereas the one at Science Direct said it would be $20. Especially seeing as they both seem to be run by the Copyright Clearance Center!

Limits to openness – where is the boundary?

I’ve been fiddling with this post for a while and I’m not sure where its going but I think other people’s views might make the whole thing clearer. This is after all why we believe in being open. So here it is in its unfinished and certainly unclarified form. All comments gratefully received.

One issue that got a lot of people talking at the Scifoo lives on session on Monday (transcript here) was the question of where the boundaries between what should and should not be open lie. At one level it seems obvious: the structure of a molecule can’t really have privacy issues whereas it is clear that a patient’s medical data should remain private. The issue came up a lot at the recent All Hands UK E-science meeting where the issues were often about census data or geographical data that could pinpoint specific people. It seems obvious that people’s personal data should be private but where do we draw the line? I am uncomfortable with a position where it is ‘obvious’ that my data should be open but ‘obvious’ that personal medical or geographical data should not be. Ideally I would like to find a clear logical distinction.

Continue reading “Limits to openness – where is the boundary?”

Variations in reproduction charges for figures in a review article

Interesting morning negotiating the problems of getting permission to re-produce figures in a review I am currently writing. I wanted to reproduce figures from four papers, two from J Mol Biol (Elsevier), one from Structure (Cell Press), one from J Biol Chem (ASBMB). I could request permission for all three journals from copyright.com and as I’m in a rush I did this. Looking back at the journal websites now it appears that I should have gone to copyright clearance centre for the J Mol Biol ones and for the article in Structure.

At copyright.com the JBC article was charged at USD73 to reproduce a figure and at the copyright clearance centre it seems that the others are around USD23. Putting aside the issues of the price differential here I am wondering when these charges came in. The last time I wrote a review like this there was an administrative charge of $1.50 (I think) on one of the images I borrowed. Admittedly that was a couple of years ago. These are mostly representations of the structure of biological macromolecules so there is a clear creative aspect in generating the original figures.

Anyway, I’m tied in now, so will report back what the final charges are. I did consider asking the authors of the original papers for different, non-copyright, versions of the pictures but for most of these I feel I am reviewing the paper and should therefore reproduce the image. Anybody got an alternative view on this? I already took the decision that I woudn’t refer to any papers that I couldn’t view from my desktop (if I restricted myself to open access I wouldn’t have had anything to write about) but would I be better off leaving the pictures out?