Open notebook science.

I haven't been blogging lately because my supervisor, Dr.Add'EmUp, has an NIH grant due and things have been quite busy. First of all, I'm trying to finish kicking the monkey. As I write this blog, I have R in the background running analysis on my data. Thank god for the new computer - this never would have worked on TheRelic (although I defended my PhD in 2007, I wrote my thesis on a computer that dated back to the bronze age). Secondly, I'm learning all kinds of new things on the fly in an effort to try and get some fabulous preliminary data that will strengthen the grant application. Dr.Add'EmUp is a mathematician, who has started his own lab. This will be the second mathematician I have worked under who has started their own lab. (Apparently all the cool kids are doing it.)

It's strange how I am drawn to mathematicians...there must be some Freudian reason I seek them out. Perhaps unconsciously, I'm trying to come to terms with being traumatized by math as a child. Instead of car games like "I spy" my mom always would ask me stupid math problems, like "A car is travelling 60 km/hr beside a train that is travelling 120km/hr..." (Who cares how fast that train goes, mom. Listen, I spy with my little eye something that is...pink.)

The fact that we are applying to NIH made me think about this an article I read recently in PLoS Biology by John Willinsky. At first, I found the issue slightly confusing, but then as I dug a little deeper, I realized that this was more than just about copyright law.

The backstory is this:

Last year NIH endorsed legislation that would ensure the public has access to research funded by government agencies like NIH. Public access was because NIH requires scientists, who are funded by NIH, to submit final peer-reviewed journal manuscripts to the digital archive at PubMed Central.

This caused malcontent among STM publishers. STM Publishers are an international association of publishers. If you read their webpage, they claim to be responsible "for more than 60% of the global annual output of research articles" and "over half the active research journals and the publication of tens of thousands of print and electronic books, reference works and databases." (I wonder what the reference is on this? I'd like to read the article if it was open access...)

These guys didn't like the legislation so at the end of last year, they tried to pass a bill called the "Fair Copyright in Research Works Act” (Want to read the text of HR 6845?).

So what does the Fair Copyright bill propose? It would prevent federal agencies like NIH from holding any claim to the research articles, even if the work was government funded. The Act was seen as a way to prevent the government from interfering with the publisher's exclusive ownership over research. At the time this was being voted on, there were some serious swellheads. For example, Allan Adler, Association of American Publishers, vice president for legal and governmental affairs, stated that,

"Government does not fund peer-reviewed journal articles—publishers do," and that the bill [Fair Copyright in Research Works Act] would "preserve the incentives for peer-review publishing."

(Wow, so Allan, where do we obtain grant applications?)

The bill was fundamentally an attack on the right to the public to have access to a public good. I think Paul Courant, a university librarian at the University of Michigan, said it best when he responded to the bill saying it was "an odious piece of corporate welfare wrapped in a friendly layer of doublespeak."

Furthermore as Willinsky rightly states in his article,

The scholarly publishing market depends on government interference in the first instance. The government allows publishers to exercise monopoly rights over this research through copyright law, a form of market interference warranted by the works' contribution to “the progress of Science and useful Arts,” as the United States Constitution puts it [4]. And if that were not enough, the government also funds directly and indirectly the production, authoring, and reviewing of the content.

Although the bill didn't pass, according to Willinsky (2009) and Suber (of The Open Access News) we haven't seen the last of it.

In my mind, this is a serious concern for scientists and educators alike because ultimately, it asks the question: who has the right to knowledge? For publishers - it is an economic argument - they want the right to control the distribution of the works they publish. The funding agencies say they want to maximize the return on that investment for the public, and for scientists. So who owns knowledge ends up in a demilitarized zone (DMZ), a strip of land heavily guarded by both sides, but, one that no one occupies.

As it stands, some publishers require library subscriptions in order to access to certain journals. This means the smaller universities in North America where library budgets are constrained, scientists and students will not have access to all the scientific knowledge. Let alone universities in developing nations, who are already at a serious disadvantage. The rich get smarter and poor stay dumb.

This DMZ, I think, has ignited open access publishing. But lately some scientists have taken the idea and philosophy of open access one step further, in what is called, the open notebook science. Wikipedia has an excellent description here. Essentially it's like a blog, but written by scientists doing science online. Chemists like Jean-Claude Bradley and Cameron Neylon are using it to discuss experiments and then post results in real-time. Mathematicians, like the dude who won the Fields Medal, Terence Tao, are talking math and sharing ideas online. (Oh, you bet I visited the website. I spy with my little eye, something that is...pink).

So why are no biologists sharing? Archiving and sharing protocols and data is an amazing idea because it can save time. I mean who really wants to invent a square wheel when clearly the round one works better. And recently we had a discussion about starting something similar in our lab. But there was some serious concern about the consequences of sharing data. The main issue, of course, is "the trauma of getting scooped." The second issue not discussed but a problem for the open notebook science idea, is that the science isn't peer-reviewed. And in the world where we conduct our scientific business in the currency of publications, it can matter.

So can we have our cake and eat it too?

Willinsky is advocating,

constant, if not increased, vigilance on behalf of those with an interest in the openness of science.

Yeah, only in once-upon-a-time land.

We can't expect, on the one hand, to have an interest in sharing and openness in science, and yet with our other hand, foster a community where the currency of publications, reigns supreme.

This is simply a friendly layer of scientific doublespeak.