Who Can Put the "Open" in Open Science?

One of the great pleasures of blogging is that your mediocre post tossed off in a couple of minutes can provoke a rather fine one that obviously took some time to craft. Here's a case in point.

The other day I wrote "Open Science Requires Open Source". This drew an interesting comment from Stevan Harnad, pretty much the Richard Stallman of open access, as well as some tweets from Cameron Neylon, one of the leading thinkers on and practitioners of open science. He also wrote a long and thoughtful reply to my post (including links to all our tweets, rigorous chap that he is). Most of it was devoted to pondering the extent to which scientists should be using open source:

It is easy to lose sight of the fact that for most researchers software is a means to an end. For the Open Researcher what is important is the ability to reproduce results, to criticize and to examine. Ideally this would include every step of the process, including the software. But for most issues you don’t need, or even want, to be replicating the work right down to the metal. You wouldn’t after all expect a researcher to be forced to run their software on an open source computer, with an open source chipset. You aren’t necessarily worried what operating system they are running. What you are worried about is whether it is possible read their data files and reproduce their analysis. If I take this just one step further, it doesn’t matter if the analysis is done in MatLab or Excel, as long as the files are readable in Open Office and the analysis is described in sufficient detail that it can be reproduced or re-implemented.

...

Open Data is crucial to Open Research. If we don’t have the data we have nothing to discuss. Open Process is crucial to Open Research. If we don’t understand how something has been produced, or we can’t reproduce it, then it is worthless. Open Source is not necessary, but, if it is done properly, it can come close to being sufficient to satisfy the other two requirements. However it can’t do that without Open Standards supporting it for documenting both file types and the software that uses them.

The point that came out of the conversation with Glyn Moody for me was that it may be more productive to focus on our ability to re-implement rather than to simply replicate. Re-implementability, while an awful word, is closer to what we mean by replication in the experimental world anyway. Open Source is probably the best way to do this in the long term, and in a perfect world the software and support would be there to make this possible, but until we get there, for many researchers, it is a better use of their time, and the taxpayer’s money that pays for that time, to do that line fitting in Excel. And the damage is minimal as long as source data and parameters for the fit are made public. If we push forward on all three fronts, Open Data, Open Process, and Open Source then I think we will get there eventually because it is a more effective way of doing research, but in the meantime, sometimes, in the bigger picture, I think a shortcut should be acceptable.

I think these are fair points. Science needs reproduceability in terms of the results, but that doesn't imply that the protocols must be copied exactly. As Neylon says, the key is "re-implementability" - the fact that you *can* reproduce the results with the given information. Using Excel instead of OpenOffice.org Calc is not a big problem provided enough details are provided.

However, it's easy to think of circumstances where *new* code is being written to run on proprietary engines where it is simply not possible to check the logic hidden in the black boxes. In these circumstances, it is critical that open source be used at all levels so that others can see what was done and how.

But another interesting point emerged from this anecdote from the same post:

Sometimes the problems are imposed from outside. I spent a good part of yesterday battling with an appalling, password protected, macroed-to-the-eyeballs Excel document that was the required format for me to fill in a form for an application. The file crashed Open Office and only barely functioned in Mac Excel at all. Yet it was required, in that format, before I could complete the application.

Now, this is a social issue: the fact that scientists are being forced by institutions to use proprietary software in order to apply for grants or whatever. Again, it might be unreasonable to expect young scientists to sacrifice their careers for the sake of principle (although Richard Stallman would disagree). But this is not a new situation. It's exactly the problem that open access faced in the early days, when scientists just starting out in their career were understandably reluctant to jeopardise it by publishing in new, untested journals with low impact factors.

The solution in that case was for established scientists to take the lead by moving their work across to open access journals, allowing the latter to gain in prestige until they reached the point where younger colleagues could take the plunge too.

So, I'd like to suggest something similar for the use of open source in science. When established scientists with some clout come across unreasonable requirements - like the need to use Excel - they should refuse. If enough of them put their foot down, the organisations that lazily adopt these practices will be forced to change. It might require a certain courage to begin with, but so did open access; and look where *that* is now...

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In Praise of that Damn' Richard Poynder

I hate Richard Poynder. Well, not exactly "hate". I'm just continually miffed that he not only keeps interviewing the very people in the open access world that I vaguely had in mind to talk to, he has the temerity to do it better than I would have done.

Unfortunately, it seems that there are some benighted individuals that are *really* less than well inclined towards Richard. The situation is so serious that the grown-ups of OA have been forced to step in to sort things out:

Trying to suppress Richard Poynder's investigations through threats of legal action is contemptible. We hope that the friends of open access in the legal community will attest to the lawfulness of his inquiries and that all friends of open access will attest to the value and legitimacy of his investigative journalism.

Oh, OK: I attest, I attest.

What's in a Name? Strong and Weak Open Access

A few months ago, I had the temerity to suggest the following:

Definitions matter. If you want to see why, compare the worlds of open source and open access. The very specific definition of what is open source - having an OSI-approved licence - means that it is relatively easy to police. Open access, by contrast, does not have anything like a tight, "official" definition, with the result that less scrupulous publishers try to pass off their wares as open access if it's vaguely open or vaguely accessible.

This brought down upon me the wrath of Mr Open Access himself, as the comments to the above post bear witness. Happily, I survived the thunderbolts, and therefore lived to see the following declaration from the same presiding OA oracle:

The term "open access" is now widely used in at least two senses. For some, "OA" literature is digital, online, and free of charge. It removes price barriers but not permission barriers. For others, "OA" literature is digital, online, free of charge, and free of unnecessary copyright and licensing restrictions. It removes both price barriers and permission barriers. It allows reuse rights which exceed fair use.

There are two good reasons why our central term became ambiguous. Most of our success stories deliver OA in the first sense, while the major public statements from Budapest, Bethesda, and Berlin (together, the BBB definition of OA) describe OA in the second sense.

As you know, Stevan Harnad and I have differed about which sense of the term to prefer --he favoring the first and I the second. What you may not know is that he and I agree on nearly all questions of substance and strategy, and that these differences were mostly about the label. While it may seem that we were at an impasse about the label, we have in fact agreed on a solution which may please everyone. At least it pleases us.

We have agreed to use the term "weak OA" for the removal of price barriers alone and "strong OA" for the removal of both price and permission barriers. To me, the new terms are a distinct improvement upon the previous state of ambiguity because they label one of those species weak and the other strong. To Stevan, the new terms are an improvement because they make clear that weak OA is still a kind of OA.

On this new terminology, the BBB definition describes one kind of strong OA. A typical funder or university mandate provides weak OA. Many OA journals provide strong OA, but many others provide weak OA.

This was partly what I was trying to get across, in my own, 'umble and clearly not very successful way: the fact that "open access" was being used for quite different things - now named "strong" and "weak" open access - which confused matters no end, not least for people who were coming to the concept for the first time.

As a result of this new nomenclature, we now have precisely the "tight" definitions I was looking for:

"Weak OA" literature is digital, online, and free of charge. It removes price barriers but not permission barriers. "Strong OA" literature is digital, online, free of charge, and free of unnecessary copyright and licensing restrictions. It removes both price barriers and permission barriers. It allows reuse rights which exceed fair use.

There, that wasn't too hard, was it?

The Open Research Web

Aside from the strong moral arguments for open access - based on the fact that much of the research published in journals has been paid for by the public, who therefore have a right to see the stuff - there are also strong utilitarian grounds for making materials freely accessible.

A group at Southampton, including the irrepressible Stevan Harnad, have put together an excellent discussion of some of the amazing things that thoroughgoing open access will permit in the future.

Many of them - there are 28 in all - are positively gob-smacking, and make explicit the way in which the open access revolution will render ordinary impact factors, one of the great bugbears of academic research, obsolete by bringing in far richer metrics for measuring influence and achievement.

This is the sort of stuff that will make traditional publishers break into a cold sweat at night; but it will warm the cockles of the growing band of OA supporters because it breaks the vicious circle of "high-impact" journals being favoured by top researchers simply because they are "high-impact", not because they are the best vehicles.

Beyond Parallel Universes

One of the themes of this blog is the commonality between the various opens. In a piece I wrote for the excellent online magazine LWN.net, I've tried to make some of the parallels between open source and open access explicit - to the point where I set up something of a mapping between key individuals and key moments (Peter Suber at Open Access News even drew a little diagram to make this clearer).

My article tries to look at the big picture, largely because I was trying to show those in the open source world why they should care about open access. At the end I talk a little about specific open source software that can be used for open access. Another piece on the Outgoing blog (subtitle: "Library metadata techniques and trends"), takes a closer look at a particular kind of such software, that for repositories (where you can stick your open access materials).

This called forth a typically spirited commentary from Stevan Harnad, which contains a link to yet more interesting words from Richard Poynder, a pioneering journalist in the open access field, with a blog - called "Open and Shut" (could there be a theme, here?) - that is always worth taking a look at. For example, he has a fascinating interview on the subject of the role of open access in the humanities.

Poynder rightly points out that there is something a contradiction in much journalistic writing about open access, in that it is often not accessible itself (even my LWN.net piece was subscribers-only for a week). And so he's bravely decided to conduct a little experiment by providing the first section of a long essay, and then asking anyone who reads it - it is freely accessible - and finds it useful to make a modest donation. I wish him well, though I fear it may not bring him quite the income he is hoping for.

Open Access, Open Source, Open Dialogue

One of the most important facets of the blog world is the rapid and intelligent dialogue it allows. A case in point is the interview that appeared on Richard Poynder's blog "Open and Shut?". As you might guess from its title, this is a kindred spirit to the present site, and is highly recommended for anyone interested in following the latest developments in the open access and circumjacent domains.

The interview is a fairly specialist one, and concerns the some open access nitty-gritty. But what caught my attention was the response to points made there by Stevan Harnad in his own blog, which has the rather lumbering title "Publishing Reform, University Self-Publishing and Open Access" but the wonderful sub-title "Open Access Archivangelism". This is rather appropriate since if anyone has the right to be called the Archivangelist of Open Access, it is Harnad, who is probably the nearest thing that the movement has to Richard Stallman (also known as Saint IGNUcius).

In his response to the interview, Harnad comments on a point made in the Poynder interview about moving from the Eprints to a hosted system called bepress. Eprints is open access archiving software that not only proudly sports GNU in its name, but runs principally on GNU/Linux (with the odd bit of Solaris and MacOS X thrown in for good measure), but notes "There are no plans for a version to run under Microsoft Windows." Defiantly open access and open source: how right-on can you get?