Haapy Birthday PLoS

The Public Library of Science did not invent open access, but there's no doubt it took it to the next level:

On the 13th of October in 2003, with the first issue of PLoS Biology, the Public Library of Science realized its transformation from a grassroots organization of scientists to a publisher. Our fledgling website received over a million hits within its first hour, and major international newspapers and news outlets ran stories about the journal, about science communication in general, and about our founders—working scientists who had the temerity to take on the traditional publishing world and who pledged to lead a revolution in scholarly communication (see, for example, [1,2]). It was not only scientists and publishers who wanted to see what this upstart start-up was doing; we had somehow captured the imagination of all sections of society. Not all of the reactions were positive, of course, especially from those in the scientific publishing sector with a vested interest in maintaining the subscription-based system of journal publishing. But thanks in no small part to the efforts of the founders—Pat Brown, Mike Eisen, and Harold Varmus—and an editorial team that included a former editor of Cell and several from Nature, our call for scientists to join the open-access revolution [3,4] did not go unheeded. Five years on, the publishing landscape has changed radically.

But what about the future?

The next challenge—for PLoS Biology, for PLoS and for all open-access publishers—is to demonstrate the utility of open access in advancing science beyond what can be gained from just making the information publicly available to read. The biggest misconception about open access is that it's only about putting online what was in print and removing any toll for access. It's not: it's about having the freedom to reuse that material without restriction [11]. Open-access publishing is therefore a crucial catalyst for a genuine shift in the way we use and mine the literature and integrate it with databases and other means of scientific communication. We are only just beginning to see the start of these: in video-based initiatives such as SciVee (Table 1); in knowledge discovery platforms such as Knewco, OSCAR, and the NeuroCommons (Table 1); with the increasing use of blogging in discourse about scientific research (see, for example, http://researchblogging.org/); and in the emergence of wiki projects in community-based knowledge curation [13,14].

I can't wait. Here's to the next five years.

More Parallel Universes

Some while back I wrote a piece called "Parallel Universes" looking at the surprising similarities between the world of open source and open access. So I was interested to see that there's trouble 't mill over the use and misuse of the term "open access":

I don't know and I don't care what [Nature editor] Maxine means by "open" or "free". I care what the BBB [Budapest-Bethesda-Berlin] Declarations mean. Peter is not defining terms however he likes; he is working with published, widely accepted definitions. He is well within his rights to expect that other people will indeed use the same definitions: that is, after all, the point of having developed and published them. Nature does NOT have "many open access projects and products", it has one (barely) OA journal and the excellent Precedings, together with a number of commendable free-to-read initiatives (blogs, Nature Network, the various free-to-read web special collections, etc). "Open Access" is not a fuzzy buzzword that Maxine is free to define as she sees fit, and if she is going to start abusing it as marketing for Nature then she most certainly does need telling off.

Which is all rather similar to a discussion taking place in the computer world about who has the right to call themselves "open source".

The Nature of the Beast

The journal Nature is a rather ambiguous beast. On the one hand, it represents the acme and epitome of the current science publishing system - and hence everything that is wrong with an analogue, profit-based, traditional access approach - and on the other, it is clearly an organisation that is trying harder than most to be innovative and engage with new ideas flowing from Web 2.0, social networks, virtual worlds and even - whisper it - open access.

One of the people there who seems to get this stuff is Timo Hannay, Head of Web Publishing for the Nature Publishing Group: maybe he's working within the citadel. In any case, this interview with him on the Confessions of a Science Librarian blog is well worth reading for the insights it offers into Nature and its gropings towards openness, and one of the main protagonists prodding things in that general direction.

The Coming Victory of Open Access

In this blog, I've emphasised the parallels between open source and open access. We know that as Microsoft has become more and more threatened by the former, it has resorted to more and more desperate attempts to sow FUD. Now comes this tremendous story from Nature that the traditional scientific publishing houses are contemplating doing the same to attack open access:

Nature has learned, a group of big scientific publishers has hired the pit bull to take on the free-information movement, which campaigns for scientific results to be made freely available. Some traditional journals, which depend on subscription charges, say that open-access journals and public databases of scientific papers such as the National Institutes of Health's (NIH's) PubMed Central, threaten their livelihoods.

The "pit bull" is Eric Dezenhall:

his firm, Dezenhall Resources, was also reported by Business Week to have used money from oil giant ExxonMobil to criticize the environmental group Greenpeace.

These are some of the tactics being considered:

Dezenhall also recommended joining forces with groups that may be ideologically opposed to government-mandated projects such as PubMed Central, including organizations that have angered scientists. One suggestion was the Competitive Enterprise Institute, a conservative think-tank based in Washington DC, which has used oil-industry money to promote sceptical views on climate change. Dezenhall estimated his fee for the campaign at $300,000–500,000.

The Competitive Enterprise Institute, you may recall, are the people behind the risible "Carbon dioxide: they call it pollution, we call it life" campaign of misinformation about global warming.

This is a clear sign that we're in the end-game for open access's victory.

Open Peer Review: Not in Their Nature

One door opens, another door closes: Nature has decided to bin its open peer review experiment:

Despite the significant interest in the trial, only a small proportion of authors opted to participate. There was a significant level of expressed interest in open peer review among those authors who opted to post their manuscripts openly and who responded after the event, in contrast to the views of the editors. A small majority of those authors who did participate received comments, but typically very few, despite significant web traffic. Most comments were not technically substantive. Feedback suggests that there is a marked reluctance among researchers to offer open comments.

Nature and its publishers will continue to explore participative uses of the web. But for now at least, we will not implement open peer review.

I suspect that Nature was probably the worst possible place to try this experiment. Nature is simply the top spot for scientific publishing: getting a paper published there can make somebody's career. So the last thing most people want is anything that might increase the risk of rejection. Public discussion of submitted papers certainly falls into that category, both for the commenter and commented (think scientific mafia).

In a way, this is what makes PLoS ONE so important: it's a tabula rasa for this kind of thing, and can redefine what scientific publishing is about. Nature and its contributors are hardly likely to want to do the same. Kudos to the title for trying, but I bet they're relieved it flopped. (Via Techdirt.)

The Price of Everything, the Value of Nothing

One of the reasons it took a while for people to accept free software is that there is a traditional diffidence in the face of things that are free. After all, if something's free, it can't be worth anything, can it? The same infuriating obtuseness can be seen writ large when it comes to the environment: since the air and sea are all free, they can't be valuable, so polluting them isn't be a problem.

Against this background, it is no wonder that traditional economics pays scant regard to the value of the environment, and rarely factors in the damage caused to it by economic activities. It is also signficant that the seminal work on valuing all of Nature goes back to 1997, when Robert Costanza and his co-authors put the worth of the planet's annual contribution to mankind at a cool $33 trillion per year, almost certainly an underestimate.

So it's high time that this work was updated and expanded, and it's good to see that the Gordon and Betty Moore Foundation is providing some much-needed money to do precisely that:

Over the next year, with an $813,000 grant from the Gordon and Betty Moore Foundation, Costanza and his team will create a set of computer models and tools that will give a sophisticated portrait of the ecosystem dynamics and value for any spot on earth.

"Land use planners, county commissioners, investment bankers, anyone who is interested," Cosntanza said, "will be able to go on the Web, use our new models, and be able to identify a territory and start getting answers."

For example, if a town council is trying decide the value of a wetland--compared to, say, building a shopping mall there--these models will help them put a dollar value on it. If a country wants to emulate Costa Rica's program of payments to landowners to maintain their land as a forest, they'll better be able to figure the ecosystem value of various land parcels to establish fair payments.

This is a critically-important project: let's hope its results are widely applied, and that we can use it as a step towards paying back the debt we owe Nature before it - and we - go environmentally bankrupt. (Via Digg.)

And the First Shall Be Last

It is done: the last unsequenced human chromosome - which happens to be the first in terms of size and hence numbering - has finally been "completed" (to 99.4%). Even more impressive, you can actually read the full Nature report on the subject. The digital code of the human genome, of course, has always been freely available (well, since 1996).

OK, so we've got the source code of us: all we have to do is understand it. Indications are, there will be quite a few surprises.

Open Data in the Age of Exponential Science

There's a very interesting article in this week's Nature, as part of its 2020 Computing Special (which miraculously is freely available even to non-subscribers), written by Alexander Szalay and Jim Gray.

I had the pleasure of interviewing Gray a couple of years back. He's a Grand Old Man of the computing world, with a hugely impressive curriculum vitae; he's also a thoroughly charming interviewee with some extremely interesting ideas. For example:

I believe that Alan Turing was right and that eventually machines will be sentient. And I think that's probably going to happen in this century. There's much concern that that might work out badly; I actually am optimistic about it.

The Nature article is entitled "Science in an exponential world", and it considers some of the approaching problems that the vast scaling up of Net-based, collaborative scientific endeavour is likely to bring us in the years to come. Here's one key point:

A collaboration involving hundreds of Internet-connected scientists raises questions about standards for data sharing. Too much effort is wasted on converting from one proprietary data format to another. Standards are essential at several levels: in formatting, so that data written by one group can be easily read and understood by others; in semantics, so that a term used by one group can be translated (often automatically) by another without its meaning being distorted; and in workflows, so that analysis steps can be executed across the Internet and reproduced by others at a later date.

The same considerations apply to all open data in the age of exponential science: without common standards that allow data from different groups, gathered at different times and in varying circumstance, to be brought together meaningfully in all sorts of new ways, the openness is moot.

Will Data Hoarding Cost 150 Million Lives?

The only thing separating mankind from a pandemic that could kill 150 million people are a few changes in the RNA of the H5N1 avian 'flu virus. Those changes would make it easier for the virus to infect and pass between humans, rather than birds. Research into the causes of the high death-rate among those infected by the Spanish 'flu - which killed between 50 and 100 million people in 1918 and 1919, even though the world population was far lower then than now - shows that it was similar changes in a virus otherwise harmless to humans that made the Spanish 'flu so lethal.

The good news is that with modern sequencing technologies it is possible to track those changes as they happen, and to use this information to start preparing vaccines that are most likely to be effective against any eventual pandemic virus. As one recent paper on the subject put it:

monitoring of the sequences of viruses isolated in instances of bird-to-human transmission for genetic changes in key regions may enable us to track viruses years before they develop the capacity to replicate with high efficiency in humans.

The bad news is that most of those vital sequences are being kept hidden away by the various national laboratories that produce them. As a result, thousands of scientists outside those organisations do not have the full picture of how the H5N1 virus is evolving, medical communities cannot plan properly for a pandemic, and drug companies are hamstrung in their efforts to develop effective vaccines.

The apparent reason for the hoarding - because some scientists want to be able to publish their results in slow-moving printed journals first so as to be sure that they are accorded full credit by their peers - beggars belief against a background of growing pandemic peril. Open access to data never looked more imperative.

Although the calls to release this vital data are gradually becoming more insistent, they still seem to be falling on deaf ears. One scientist who has been pointing out longer than most the folly of the current situation is the respected researcher Harry Niman. He has had a distinguised career in the field of viral genomics, and is the founder of the company Recombinomics.

The news section of this site has long been the best place to find out about the latest developments in the field of avian 'flu. This is for three reasons: Niman's deep knowledge of the subject, his meticulous scouring of otherwise-neglected sources to find out the real story behind the news, and - perhaps just as important - his refusal meekly to tow the line that everything is under control. For example, he has emphasised that the increasing number of infection clusters indicates that human-to-human transmission is now happening routinely, in flat contradiction to the official analysis of the situation.

More recently, he has pointed out that the US decision to base its vaccine on a strain of avian 'flu found in Indonesia is likely to be a waste of time, since the most probable pandemic candidate has evolved away from this.

The US Government's choice is particularly worrying because human cases of avian 'flu in North America may be imminent. In another of Niman's characteristically forthright analyses, he suggests that there is strong evidence that H5N1 is already present in North America:

Recombinomics is issuing a warning based on the identification of American sequences in the Qinghai strain of H5N1 isolated in Astrakhan, Russia. The presence of the America sequences in recent isolates in Astrakhan indicates H5N1 has already migrated to North America. The levels of H5N1 in indigenous species will be supplemented by new sequences migrating into North America in the upcoming months.

Niman arrived at this conclusion by tracking the genomic changes in the virus as it travelled around the globe with migrating birds, using some of the few viral sequences that have been released.

Let's hope for the sake of everyone that WHO and the other relevant organisations see the light and start making all the genomic data available. This would allow Niman and his many able colleagues to monitor even the tiniest changes, so that the world can be alerted at the earliest possible moment to the start of a pandemic that may be closer than many think.

Update: In an editorial, Nature is now calling for open access to all this genomic data. Unfortunately, the editorial is not open access....

Open Data - Good; Open Access - Bad?

Great story in Nature about data mashups - the mixing together of data drawn from disparate sources to create a sum greater than the parts.

This approach is not new: it lies at the heart of open source software - where chunks of code are drawn from the specialised databases known as hackers' brains and stitched together - and open genomics. Indeed, bioinformatics represents a kind of apotheosis of the mashup - see, for example, the way in which data from many researchers is pulled together in a genome browser like Ensembl.

Data mashups are more recent, and have started to gain popularity thanks to Google Earth. This provides a useful and conceptually simple scaffolding for other data to be brought together and displayed - like Nature's own avian flu mashup.

A pity, then, that this paean to the virtues of open data is not itself freely available under an open access licence. (For the benighted, the indispensable Open Access News has a long quotation that conveys the essence.)

Wellcome Moves

The news that the Wellcome Trust has reached an agreement with three publishers of scientific journals to allow Wellcome-funded research published in their journals to be immediately available online and without charge to the reader is good news indeed.

Good because it will make large quantities of high-quality research immediately available, rather than after the tiresome six-month wait that some journals impose when providing a kind of pseudo-open access. Good, because it shows that the Wellcome Trust is willing to put its money where its mouth is, and to pay to get open access. Good, because by making this agreement with Blackwell, OUP and Springer, the Wellcome Trust puts pressure on the the top science publisher, Elsevier, to follow suit.

In fact, thinking about it, I was probably unkind to describe Nature as the Microsoft of the science world: that honour clearly belongs to Elsevier, both in terms of its power and resistance to opening up. Moreover, Nature, to its credit, now gets it about Wikipedia - it even made subscriber-only content freely available. And the conceptual distance between wikis and open access is surprisingly small; so maybe we're seeing the start of a historic shift at Nature.

Going to the Dogs

My heart leapt last week upon seeing the latest issue of Nature magazine. The front cover showed the iconic picture of Watson and Crick, with the latter pointing at their model of DNA's double helix. A rather striking addition was the boxer dog next to Crick, also gazing up at the DNA: inside the journal was a report on the first high-quality sequencing of the dog genome (a boxer, naturally).

This is big news. Think of the genome as a set of software modules that form a cell's operating system. Every change to a genome is a hack; like most hacks, most changes cause malfunctions, and the cell crashes (= dies/grows abnormally). Some, though, work, and produce slight variants of the original organism. Over time, these variations can build up to form an entirely new species. (In other words, one way of thinking about evolution is in terms of Nature's hacking).

Mostly, the changes produced by these hacks are small, or so slow as to be practically invisible. But not for dogs. Humans have been hacking the dog genome for longer than any other piece of code - about 100,000 years - and the result can be seen in the huge variety of dog breeds (some 400 0f them).

Getting hold of the dog genome means that scientists have access to this first Great Historical Hack, which will tell us much about how genomic variation translates to different physical traits (known as phenotypes). Even better - for us, though not for the dogs - is that all this hacking/interbreeding has produced dogs that suffer from many of the same diseases as humans. Because particular breeds are susceptible to particular diseases, we know that there must be a strong genetic element to these diseases for dogs, and so, presumably, for humans (since our genomes are so similar). The different breeds have effectively separated out the genes that produce a predisposition to a particular disease, making it far easier to track them down than in the human code.

That tracking down will take place by comparing the genomes for different breeds, and by comparing dog genomes against those of humans, mice, apes and so on. Those comparisons are only possible because all this code is in the public domain. Had the great battle over open genomics - open source genomes - been lost at the time of the Human Genome Project, progress towards locating these genes that predispose towards major diseases would have been slowed immeasurably. Now it's just a matter of a Perl script or two.

Given this open source tradition, and the importance of the dog genome, it's a pity that the Nature paper discussing it is not freely available. Alas, for all its wonderful traditions and historic papers, Nature is still the Microsoft of the science world. The battle for open access - like that for open source - has still to be won.