David Willetts speaking at the Big Society policy launch, Coin St, London. (Photo credit: Wikipedia)

Yesterday David Willetts, the UK Science and Universities Minister gave a speech to the Publishers Association that has got wide coverage. However it is worth pulling apart both the speech and the accompanying opinion piece from the Guardian because there are some interesting elements in there, and also some things have got a little confused.

The first really key point is that there is nothing new here. This is basically a re-announcement of the previous position from the December Innovation Strategy on moving towards a freely accessible literature and a more public announcement of the Gateway to Research project previously mentioned in the RCUK response to the Innovation Statement.

The Gateway to Research project is a joint venture of the Department of Business Innovation and Skills and Research Councils UK to provide a one stop shop for information on UK research funding as well as pointers to outputs. It will essentially draw information directly from sources that already exist (the Research Outputs System and eVal) as well as some new ones with the intention of helping the UK public and enterprise find research and researchers that is of interest to them, and see how they are funded.

The new announcement was that Jimmy Wales of Wikipedia fame will be advising on the GTR portal. This is a good thing and he is well placed to provide both technical and social expertise on the provision of public facing information portals as well as providing a more radical perspective than might come out of BIS itself. While this might in part be cynically viewed as another example of bringing in celebrities to advise on policy this is a celebrity with relevant expertise and real credibility based on making similar systems work.

The rest of the information that we can gather relates to government efforts in moving towards making the UK research literature accessible. Wales also gets a look in here, and will be “advising us on [..] common standards to ensure information is presented in a readily reusable form”. My reading of this is that the Minister understands the importance of interoperability and my hope is that this will mean that government is getting good advice on appropriate licensing approaches to support this.

However, many have read this section of the speech as saying that GTR will act as some form of national repository for research articles. I do not believe this is the intention, and reading between the lines the comment that it will “provide direct links to actual research outputs such as data sets and publications” [my emphasis] is the key. The point of GTR is to make UK research more easily discoverable. Access is a somewhat orthogonal issue. This is better read as an expression of Willetts’ and the wider government’s agenda on transparency of public spending than as a mechanism for providing access.

What else can we tell from the speech? Well the term “open access” is used several times, something that was absent from the innovation statement, but still the emphasis is on achieving “public access” in the near term with “open access” cast as the future goal as I read it. It’s not clear to me whether this is a well informed distinction. There is a somewhat muddled commentary on Green vs Gold OA but not that much more muddled than what often comes from our own community. There are also some clear statements on the challenges for all involved.

As an aside I found it interesting that Willetts gave a parenthetical endorsement of usage metrics for the research literature when speaking of his own experience.

As well as reading some of the articles set by my tutors, I also remember browsing through the pages of the leading journals to see which articles were well-thumbed. It helped me to spot the key ones I ought to be familiar with – a primitive version of crowd-sourcing. The web should make that kind of search behaviour far easier.

This is the most sophisticated appreciation of the potential for the combination of measurement and usage data in discovery that I have seen from any politician. It needs to be set against his endorsement of rather cruder filters earlier in the speech but it nonetheless gives me a sense that there is a level of understanding within government that is greater than we often fear.

Much of the rest of the speech is hedging. Options are discussed but not selected and certainly not promoted. The key message: wait for the Finch Report which will be the major guide for the route the government will take and the mechanisms that will be put in place to support it.

But there are some clearer statements. There is a strong sense that Hargreave’s recommendations on enabling text mining should be implemented. And the logic for this is well laid out. The speech and the policy agenda is embedded in a framework of enabling innovation – making it clear what kinds of evidence and argument we will need to marshal in order to persuade. There is also a strong emphasis on data as well as an appreciation that there is much to do in this space.

But the clearest statement made here is on the end goals. No-one can be left in any doubt of Willetts’ ultimate target. Full access to the outputs of research, ideally at the time of publication, in a way that enables them to be fully exploited, manipulated and modified for any purpose by any party. Indeed the vision is strongly congruent with the Berlin, Bethesda, and Budapest declarations on Open Access. There is still much to be argued about the route and and its length, but in the UK at least, the destination appears to be in little doubt.

Related articles

• Key questions in the UK’s shift to open-access research(blogs.nature.com)

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• Crossing the Rubicon – Is the UK Going to Enable Open Access for All Taxpayer-Funded Research by 2014? (scholarlykitchen.sspnet.org)
• UK Government on open access: better than I could have hoped (svpow.com)
• Willetts’ Speech on Open Access: Analysis (reciprocal space)

• Attempts by a variety of big pharma to replicate disease relevant results published by academic labs failed in ~80% of cases (see for instance this story about this commentary in Nature[$])
• When a particular blood cancer group was asked what factor about their disease was most to them, they said gastro-intestinal problems. No health professional had ever even considered this as a gastro-intestinal disease.
• Jamie Heywood spent $25M of his own money on attempting to replicate around 500 published results that were therapeutically relevant to ALS and could not repeat the findings in a single case.
• A cancer patient, advocate, and fundraiser of 25 years standing said the following to me: “We’ve been at this for 25 years, we’ve raised over $2B for research, and new patients today get the same treatment I did. What’s the point?”

In a room full of very smart people absolutely committed to making a difference there were very few new ideas on how we actually cut through the thicket of perverse incentives, institutional inertia, disregard for replicability, and personal ego-stroking which is perpetuating these problems. I’ve been uncertain for some time whether change from within our existing structures and systems is really possible. I’m leaning further and further to the view that it is not. That doesn’t mean that we can’t do anything – just that it may be more effective to simply bypass existing institutions to do it.

Related articles

• Sage Congress: The synthesis of open source with genetics (radar.oreilly.com)

PLoS: The Public Library of Science (Photo credit: dullhunk)

As a child I was very clear I wanted to be a scientist. I am not sure exactly where the idea came from. In part I blame Isaac Asimov but it must have been a combination of things. I can’t remember not having a clear idea of wanting to go into research.

I started off a conventional career with big ideas – understanding the underlying physics, chemistry, and information theory that limits molecular evolution – but my problem was always that I was interested in too many things. I kept getting distracted. Along with this I also started to wonder how much of a difference the research I was doing was really making. This led to a shift towards working on methods development – developing tools that would support many researchers to do better and more efficient work. In turn it lead to my current position, with the aim of developing the potential of neutron scattering as a tool for the biosciences. I got gradually more interested in the question of  how to make the biggest difference I could, rather than just pursuing one research question.

And at the same time I was developing a growing interest in the power of the web and how it had the potential, as yet unrealized, to transform the effectiveness of the research community. This has grown from side interest to hobby to something like a full time job, on top of the other full time job I have. This wasn’t sustainable. At the same time I’ve realized I am pretty good at the strategy, advocacy, speaking and writing; at articulating a view of where we might go, and how we might get there. That in this space I can make a bigger difference. If we can increase the efficiency of research by just 5%, reduce the time for the developing world to bring a significant research capacity on stream by just a few years, give a few patients better access to information, or increase the wider public interest and involvement in science just a small amount, then this will be a far reader good than I could possibly make doing my own research.

Which is why, from July I will be moving to PLoS to take up the role of Advocacy Director.

PLoS is an organization that right from the beginning has had a vision, not just of making research papers more accessible but of transforming research communication, of making it ready for, making it of the 21st century. This is a vision I share and one that I am very excited to playing a part in.

In the new role I will obviously be doing a lot of advocacy, planning, speaking, and writing on open access. There is a lot to play for over the next few years with FRPAA in the US, new policies being developed in Europe, and a growing awareness of the need to think hard about data as a form of publication. But I will also be taking the long view, looking out on a ten year horizon to try and identify the things we haven’t seen yet, the opportunities that are already there and how we can navigate a path between them. Again there is huge potential in this space, gradually turning from ideas and vaporware into real demos and even products.

The two issues, near term policy and longer term technical development are inextricably linked. The full potential of networked research cannot be realized except in a world of open content, open standards, APIs, process, and data. Interoperability is crucial, technical interoperability, standards interoperability, social interoperability, and legal interoperability. It is being at the heart of the community that is working to link these together and make them work that really excites me about this position.

PLoS has been an engine of innovation since it was formed, changing the landscape of scholarly publishing in a way that no-one would have dreamed was possible. Some have argued that this hasn’t been so much the case in the last few years. But really things have just been quiet, plans have been laid, and I think you will find the next few years exciting.

Inevitably, I will be leaving some things behind. I won’t be abandoning research completely, I hope to keep my toe in a range of projects but I will be scaling back a lot. I will be stepping down as an Academic Editor for PLoS ONE (and apologies for all those reviews and editorial requests for PLoS ONE that I’ve turned down in the last few months) because this would be a clear conflict of interest. I’ve got a lot to clear up before July.

I will be sad to leave behind some of those roles but above all I am excited and looking forward to working in a great organisation, with people I respect doing things I believe are important. Up until now I’ve been trying to fit these things in, more or less as a hobby around the research. Now I can focus on them full time, while still staying at least a bit connected. It’s a big leap for me, but a logical step along the way to trying to make a difference.

Image via Wikipedia

…although some are perhaps starting to see the problems that are going to arise.

Last week I spoke at a Question Time style event held at Oxford University and organised by Simon Benjamin and Victoria Watson called “The Scientific Evolution: Open Science and the Future of Publishing” featuring Tim Gowers (Cambridge), Victor Henning (Mendeley), Alison Mitchell (Nature Publishing Group), Alicia Wise (Elsevier), and Robert Winston (mainly in his role as TV talking head on science issues). You can get a feel for the proceedings from Lucy Pratt’s summary but I want to focus on one specific issue.

As is common for me recently I emphasised the fact that networked research communication needs to be different to what we are used to. I made a comparison to the fact that when the printing press was developed one of the first things that happened was that people created facsimiles of hand written manuscripts. It took hundreds of years for someone to come up with the idea of a newspaper and to some extent our current use of the network is exactly that – digital facsimiles of paper objects, not truly networked communication.

It’s difficult to predict exactly what form a real networked communication system will take, in much the same way that asking a 16th century printer how newspaper advertising would work would not provide a detailed and accurate answer, but there are some principles of successful network systems that we can see emerging. Effective network systems distribute control and avoid centralisation, they are loosely coupled, and distributed. Very different to the centralised systems for control of access and control we have today.

This is a difficult concept and one that scholarly publishers simply don’t get for the most part. This is not particularly suprising because truly disruptive innovation rarely comes from incumbent players. Large and entrenched organisations don’t generally enable the kind of thinking that is required to see the new possibilities. This is seen in publishers statements that they are providing “more access than ever before” via “more routes”, but all routes that are under tight centralised control, with control systems that don’t scale. By insisting on centralised control over access publishers are setting themselves up to fail.

Nowhere is this going to play out more starkly than in the area of text mining. Bob Campbell from Wiley-Blackwell walked into this – but few noticed it – with the now familiar claim that “text mining is not a problem because people can ask permission”. Centralised control, failure to appreciate scale, and failure to understand the necessity of distribution and distributed systems. I have with me a device capable of holding the text of perhaps 100,000 papers It also has the processor power to mine that text. It is my phone. In 2-3 years our phones, hell our watches, will have the capacity to not only hold the world’s literature but also to mine it, in context for what I want right now. Is Bob Campbell ready for every researcher, indeed every interested person in the world, to come into his office and discuss an agreement for text mining? Because the mining I want to do and the mining that Peter Murray-Rust wants to do will be different, and what I will want to do tomorrow is different to what I want to do today. This kind of personalised mining is going to be the accepted norm of handling information online very soon and will be at the very centre of how we discover the information we need. Google will provide a high quality service for free, subscription based scholarly publishers will charge an arm and a leg for a deeply inferior one – because Google is built to exploit network scale.

The problem of scale has also just played out in fact. Heather Piwowar writing yesterday describes a call with six Elsevier staffers to discuss her project and needs for text mining. Heather of course now has to have this same conversation with Wiley, NPG, ACS, and all the other subscription based publishers, who will no doubt demand different conditions, creating a nightmare patchwork of different levels of access on different parts of the corpus. But the bit I want to draw out is at the bottom of the post where Heather describes the concerns of Alicia Wise:

At the end of the call, I stated that I’d like to blog the call… it was quickly agreed that was fine. Alicia mentioned her only hesitation was that she might be overwhelmed by requests from others who also want text mining access. Reasonable.

Except that it isn’t. It’s perfectly reasonable for every single person who wants to text mine to want a conversation about access. Elsevier, because they demand control, have set themselves up as the bottleneck. This is really the key point, because the subscription business model implies an imperative to extract income from all possible uses of the content it sets up a need for control of access for differential uses. This means in turn that each different use, and especially each new use, has to be individually negotiated, usually by humans, apparently about six of them. This will fail because it cannot scale in the same way that the demand will.

The technology exists today to make this kind of mass distributed text mining trivial. Publishers could push content to bit torrent servers and then publish regular deltas to notify users of new content. The infrastructure for this already exists. There is no infrastructure investment required. The problems that publishers raise of their servers not coping is one that they have created for themselves. The catch is that distributed systems can’t be controlled from the centre and giving up control requires a different business model. But this is also an opportunity. The publishers also save money  if they give up control – no more need for six people to sit in on each of hundreds of thousands of meetings. I often wonder how much lower subscriptions would be if they didn’t need to cover the cost of access control, sales, and legal teams.

We are increasingly going to see these kinds of failures. Legal and technical incompatibility of resources, contractual requirements at odds with local legal systems, and above all the claim “you can just ask for permission” without the backing of the hundreds or thousands of people that would be required to provide a timely answer. And that’s before we deal with the fact that the most common answer will be “mumble”. A centralised access control system is simply not fit for purpose in a networked world. As demand scales, people making legitimate requests for access will have the effect of a distributed denial of service attack. The clue is in the name; the demand is distributed. If the access control mechanisms are manual, human and centralised, they will fail. But if that’s what it takes to get subscription publishers to wake up to the fact that the networked world is different then so be it.

Image via Wikipedia

It’s one of those throw away lines, “Before we can talk about a github for science we really need to sort out a TCP/IP for science”, that’s geeky, sharp, a bit needly and goes down a treat on Twitter. But there is a serious point behind it. And its not intended to be dismissive of the ideas that are swirling around about scholarly communication at the moment either. So it seems worth exploring in a bit more detail.

The line is stolen almost wholesale from John Wilbanks who used it (I think) in the talk he gave at a Science Commons meetup in Redmond a few years back. At the time I think we were awash in “Facebooks for Science” so that was the target but the sentiment holds. As once was the case with Facebook and now is for Github, or Wikipedia, or StackOverflow, the possibilities opened up by these new services and technologies to support a much more efficient and effective research process look amazing. And they are. But you’ve got to be a little careful about taking the analogy too far.

If you look at what these services provide, particularly those that are focused on coding, they deliver commentary and documentation, nearly always in the form of text about code – which is also basically text. The web is very good at transferring text, and code, and data. The stack that delivers this is built on a set of standards, with each layer building on the layer beneath it. StackOverflow and Github are built on a set of services, that in turn sit on top of the web standards of http, which in turn are built on network standards like TCP/IP that control the actual transfer of bits and bytes.

The fundamental stuff of these coding sites and Wikipedia is text, and text is really well supported by the stack of web technologies. Open Source approaches to software development didn’t just develop because of the web, they developed the web so its not surprising that they fit well together. They grew up together and nurtured each other. But the bottom line is that the stack is optimized to transfer the grains of material, text and code, that make up the core of these services.

When we look at research we can see that when we dig down to the granular level it isn’t just made up of text. Sure most research could be represented as text but we don’t have the standardized forms to do this. We don’t have standard granules of research that we can transfer from place to place. This is because its complicated to transfer the stuff of research. I picked on TCP/IP specifically because it is the transfer protocol that supports moving bits and bytes from one place to another. What we need are protocols that support moving the substance of a piece of my research from one place to another.

Work on Research Objects [see also this paper], intended to be self-contained but useable pieces of research is a step in this direction, as are the developing set of workflow tools, that will ultimately allow us to describe and share the process by which we’ve transformed at least some parts of the research process into others. Laboratory recording systems will help us to capture and workflow-ify records of the physical parts of the research process. But until we can agree how to transfer these in a standardized fashion then I think it is premature to talk about Githubs for research.

Now there is a flip side to this, which is that where there are such services that do support the transfer of pieces of the research process we absolutely should be  experimenting with them. But in most cases the type-case itself will do the job. Github is great for sharing research code and some people are doing terrific things with data there as well. But if it does the job for those kinds of things why do we need one for researchers? The scale that the consumer web brings, and the exposure to a much bigger community, is a powerful counter argument to building things ‘just for researchers’. To justify a service focused on a small community you need to have very strong engagement or very specific needs. By the time that a mainstream service has mindshare and researchers are using it, your chances of pulling them away to a new service just for them are very small.

So yes, we should be inspired by the possibilities that these new services open up, and we should absolutely build and experiment but while we are at it can we also focus on the lower levels of the stack?They aren’t as sexy and they probably won’t make anyone rich, but we’ve got to get serious about the underlying mechanisms that will transfer our research in comprehensible packages from one place to another.

We have to think carefully about capturing the context of research and presenting that to the next user. Github works in large part because the people using it know how to use code, can recognize specific languages, and know how to drive it. It’s actually pretty poor for the user who just wants to do something – we’ve had to build up another set of services at different levels, the Python Package Index, tools for making and distributing executables, that help provide the context required for different types of user. This is going to be much, much harder, for all the different types of use we might want to put research to.

But if we can get this right – if we can standardize transfer protocols and build in the context of the research into those ‘packets’ that lets people use it then what we have seen on the wider web will happen naturally. As we build the stack up these services that seem so hard to build at the moment will become as easy today as throwing up a blog, downloading a rubygem, or firing up a machine instance. If we can achieve that then we’ll have much more than a github for research, we’ll have a whole web for research.

There’s nothing new here that wasn’t written some time ago by John Wilbanks and others but it seemed worth repeating. In particular I recommend these posts [1, 2] from John.