What Open Source Can Learn From Open Access

Peter Suber's indispensable SPARC Open Access Newsletter, whose latest issue has just appeared, contains some interesting thoughts of relevance to the open source world.

For example, here are Suber's thoughts on the important NIH open access policy, which, though amazingly mild in OA terms, is being fiercely resisted by publishers:

The NIH policy covers so much literature in biomedicine (80,000 peer reviewed articles per year), and the compliance rate is climbing so quickly, that its opponents have little time left before even they will have to accommodate it. Its success is moving up the dinosaur moment when TA publishers must adapt or refuse to publish NIH-funded research. Most have already adapted, of course, a fact that tends to be lost in the protests of the publishing lobby. But the clock is ticking for those who hate the idea of adapting. This matters. While publishers have the money to lobby against government OA policies forever, the question is becoming moot as the policy's friends grow in number and power and as its opponents revise their own policies to live with it.

The lesson here is that it's very hard to argue against something that is manifestly successful. This makes projects like Firefox critical showcases for free software, to say nothing of GNU/Linux.

Even before the crisis, library budgets were growing more slowly than inflation and much more slowly than journal prices. Now they will slow further or shrink. Libraries will cancel larger percentages of their serials subscriptions than they have in decades. That will reduce access to the TA literature, which will strengthen the case for OA among researchers, librarians, and administrators.

At the same time, it will reduce revenues for TA publishers and strengthen the case for OA on their side as well. It may not cause many TA journals to convert to OA, in 2009, but it will add pressure. The more library budgets are constrained, the more it looks like a losing game to compete for shrinking library dollars, especially to society journals excluded from the nearly impervious big deals. If TA publishers found OA journal business models unattractive a few years ago, one reason was that subscription models still looked better. But the balance of attraction has to change as the odds of survival under a subscription model decline, roughly the way clean and renewable sources of energy become more attractive as oil becomes more expensive. Moreover, a few years ago OA publishers were too new to be profitable, and today at least three are reporting profits, including BMC (even before the Springer acquisition), which is based in expensive London. When contemplating their options in the face of declining subscriptions, publishers can no longer dismiss the OA alternative as untested or insufficient.

Replace "libraries" by "companies", and "publishers" by "software companies", and the parallels with the world of enterprise open source are clear. Again, the lesson is that once there are established successes in the world of open source companies, the hypothetical problems raised begin to look pointlessly theoretical.

Overall, then, the message is that in the world of openness, it gets better as things get better. Heartening stuff.

Open Access's Big Win

Now here's a nice way to end the year - and to start the next:

The Director of the National Institutes of Health shall require that all investigators funded by the NIH submit or have submitted for them to the National Library of Medicine's PubMed Central an electronic version of their final, peer-reviewed manuscripts upon acceptance for publication to be made publicly available no later than 12 months after the official date of publication: Provided, That the NIH shall implement the public access policy in a manner consistent with copyright law.

That's just been signed into law in the US, and even though the choice of 12 rather than six months is slightly pusillanimous, it's still a huge win for open access in the US. It will also have a knock-on effect around the world, as open access to publicly-funded research starts to become the norm.

For more details see Peter Suber's post, with links to more details and background.

The Power of Open Genomics

The National Human Genome Research Institute (NHGRI), one of the National Institutes of Health (NIH), has announced the latest round of mega genome sequencing projects - effectively the follow-ons to the Human Genome Project. These are designed to provide a sense of genomic context, and to allow all the interesting hidden structures within the human genome to be teased out bioinformatically by comparing them with other genomes that diverged from our ancestors at various distant times.

Three more primates are getting the NHGRI treatment: the rhesus macacque, the marmoset and the orangutan. But alongside these fairly obvious choices, eight more mammals will be sequenced too. As the press release explains:

The eight new mammals to be sequenced will be chosen from the following 10 species: dolphin (Tursiops truncates), elephant shrew (Elephantulus species), flying lemur (Dermoptera species), mouse lemur (Microcebus murinus), horse (Equus caballus), llama (Llama species), mole (Cryptomys species), pika (Ochotona species), a cousin of the rabbit, kangaroo rat (Dipodomys species) and tarsier (Tarsier species), an early primate and evolutionary cousin to monkeys, apes, and humans.

If you are not quite sure whom to vote for, you might want to peruse a great page listing all the genomes currently being sequenced for the NHGRI, which provides links to a document (.doc, alas, but you can open it in OpenOffice.org) explaining why each is important (there are pix, too).

More seriously, it is worth noting that this growing list makes ever more plain the power of open genomics. Since all of the genomes will be available in public databases as soon as they are completed (and often before), this means that bioinformaticians can start crunching away with them, comparing species with species in various ways. Already, people have done the obvious things like comparing humans with chimpanzees, or mice with rats, but the possibilities are rapidly becoming extremely intriguing (tenrec and elephant, anyone?).

And beyond the simple pairing of genomes, which yields a standard square-law richness, there are even more inventive combinations involving the comparison of multiple genomes that may reveal particular aspects of the Great Digital Tree of Life, since everything may be compared with everything, without restriction. Now imagine trying to do this if genomes had been patented, and groups of them belonged to different companies, all squabbling over their "IP". The case for open genomics is proved, I think.