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26 October 2011, 15:05

Open Source, Open Science, Open Source Science

by Glyn Moody

The digital age has added significantly to the tools available to scientific work, but has also introduced new challenges. Glyn Moody describes the present situation, and suggests that we need true openness with respect to scientific software.

One of the key inspirations for the free software movement was the scientific tradition of sharing information and building on the work of others. That arose a few hundred years ago, at a time of rapid scientific progress:

The great scientific advances in the time of Hooke and Newton motivated wealthy patrons such as the government to begin subsidising science as a profession. Much of the motivation came from the public benefit delivered by scientific discovery, and that benefit was strongest if discoveries were shared. The result was a scientific culture which to this day rewards the sharing of discoveries with jobs and prestige for the discoverer.

This cultural transition was just beginning in the time of Hooke and Newton, but a little over a century later the great physicist Michael Faraday could advise a younger colleague to "Work. Finish. Publish." The culture of science had changed so that a discovery not published in a scientific journal was not truly complete.

We take that culture for granted today; and yet, ironically, the core aspects of openness and sharing that supposedly lie at the heart of the scientific method have been undermined in recent years.

For example, the central role of publishing in scientific discoveries has made academic journals key control points. That, in turn, has made the publishers that own them very powerful – and very rich. Until recently, it was the publishers who claimed ownership of the scientific papers published in their titles, and they used the importance of those papers and their control over them to push up the prices for scientific journals to absurd levels – often thousands of pounds a year.

That made it increasingly hard to access scientific knowledge unless you belonged to a well-funded establishment. The old ideal of sharing knowledge freely in order to promote progress had been all but lost. As a reaction to this, the open access movement has been fighting to at least make publicly-funded research – which is most of it – freely available online. Publishers have naturally resisted this move as fiercely as proprietary software companies have resisted open source, but have been forced to recognise the legitimacy of open access's demands. As a result, more and more academic papers are starting to appear online for free.

More recently, another major shift has taken place in science: the rise of digital science. Although it is hardly surprising that computers have started to play an increasing role in the conduct of science, as they have elsewhere, it has had knock-on consequences for openness and sharing that are only now being understood.

Here's a good explanation of the problem:

One of the key features of science is deniability: if you erect a theory and someone produces evidence that it is wrong, then it falls. This is how science works: by openness, by publishing minute details of an experiment, some mathematical equations or a simulation; by doing this you embrace deniability. This does not seem to have happened in climate research. Many researchers have refused to release their computer programs – even though they are still in existence and not subject to commercial agreements. An example is Professor Mann's initial refusal to give up the code that was used to construct the 1999 "hockey stick" model that demonstrated that human-made global warming is a unique artefact of the last few decades. (He did finally release it in 2005.)

The author of that passage – Darrel Ince, professor of computing at the Open University – doesn't mince his words:

So, if you are publishing research articles that use computer programs, if you want to claim that you are engaging in science, the programs are in your possession and you will not release them then I would not regard you as a scientist; I would also regard any papers based on the software as null and void.

Just as the unreasonable power of scientific publishers led to the birth of the open access movement, so this issue of releasing scientific code has prompted the formulation of the Science Code Manifesto by Nick Barnes, who explains the background thus:

I am the author of the Science Code Manifesto, although many others have contributed suggestions. I wrote it for the Climate Code Foundation, initially as a response and contribution to the Royal Society’s policy study on “Science as a Public Enterprise”. It is partly inspired by the Panton Principles, a bold statement of ideals in scientific data sharing. It refines the ideas I laid out in an opinion piece for Nature in 2010.

However, I did not originate these ideas. They are simply extensions of the core principle of science: publication. Publication is what distinguishes science from alchemy, and is what has propelled science – and human society – so far and so fast in the last 300 years. The Manifesto is the natural application of this principle to the relatively new, and increasingly important, area of science software.

(Disclaimer: I am an unpaid member of the Climate Code Foundation's Advisory Board.)

Next: Science Code Manifesto

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