On open-access and peer review

We've covered this topic often on both this blog and on the podcast but it may be time to revisit it one more time. Open access (OA) publishing has won the heart of most scientists. By definition our work only gains value by sharing, and sharing is easier when it's free. As an author of papers, I can also retain copyrights over my own work so that I am free to do whatever I please with it, including reproducing it in my thesis or posting it on my blog. I mean what's not to love. Well some people actually oppose it, obviously people who have a vested interest in the multi-million dollar publishing business. PLOS, one of the pioneers in open-access, has basically proven that not only can the idea work, but it can make for a high profile journal. But with the introduction of PLOS-ONE it may have shown its Achilles' heel. See the opponents of open-access always pointed out that openness would destroy peer review. Obviously a ridiculous assertion, since peer review is already open and free. But with PLOS ONE peer review was changed from outside "random" assigned expert to "in-house" academic editors. In fact I strongly suspect that Nature's precedings, was built to fail, an exercise in futility, to show how openness equals lack of peer review and craptacular creationist papers published. And while the opponents of open access like PRISM might have an axe to grind, they also make a good point, what is peer review, and who oversees peer reviewers?

First lets check out what they say one their site: what's at risk?

• undermining the peer review process by compromising the viability of non-profit and commercial journals that manage and fund it;

• opening the door to scientific censorship in the form of selective additions to or omissions from the scientific record;

• subjecting the scientific record to the uncertainty that comes with changing federal budget priorities and bureaucratic meddling with definitive versions; and

• introducing duplication and inefficiencies that will divert resources that would otherwise be dedicated to research.

The first point could have been better formulated. But what I think they are trying to say is "hold-on you guys can't police yourself, you need publishers to manage peer review". I mean they don't actually fund peer review since it's free but they do manage it. I don't see why editors of OA journals can't do the same, but it does raise the need for a peer-review watchdog (more on that later)

The second point is even more asinine. They're saying "Hold-on you can't choose what can and cannot be published, that's censorship, let corporations do that job". This is ironic since the purpose of journals like PLOS ONE is to let people publish based on the quality of the science not the importance of the findings. Importance is subjective, and often Nobel winning discoveries like PCR or antibodies were rejected from publication.

The third argument is also flawed because funding shouldn't affect OA journals, they are run by the publication costs defrayed by the authors. In fact one could argue that traditional private publishing is at the mercy of investors, stock market crashes and economic conditions.

Finally duplications could actually be a problem, especially for journals like PLOS ONE. If papers are not discriminated upon the basis of importance, very small incremental findings could be published which do not really lead the field forward. That being said, I would rather have more information than less. In fact if information is freely available, perhaps you would be less likely to unknowingly duplicate someone's work that was published in an obscure journal to which your institution doesn't have access.

Then what's the answer?:

Well one big step in the right direction was the creation of BPR3 an acronym coined by none other than Kevin Z (of bayblab podcast fame). Bloggers for peer review reporting aims to overview the peer review process, and check out their take on PLOS ONE. Ultimately we need some kind of watchdog, a "peer-review watch", and that it could be born in a blog just shows you the power of web 2.0 and openness.

In the mean time, why not check out this spoof of PRISM (the axis of evil publishers), called PISD (I think it is pronounced [piss]-t):
"We don't believe it's a publisher's place to make the value judgment that dissemination of scientific information is a greater social good than the increase in capital associated with charging higher subscription rates. That judgment should be made by politicians, ethicists, economists, and other valuable members of society. If you would like to know more, we suggest you consult review articles on the theory of utility or the laws of supply and demand. If your institution doesn’t provide access to such articles, we'll be happy to sell them to you at a reasonable price."

Bugs in PLOS ONE

PLoS ONE is the sujet du jour in the bay today. The quality of the submissions in PLoS has been increasing, but how long will that last? We had a journal club concerning a new report in PLoS about P53 mutations in ovarian cancer suggesting that patients with mutated p53 actually respond better to chemotherapy, probably because they have a harder time repairing damage, but can still undergo apoptosis in a p53-independent manner. The findings are not as novel as they might sound since it's been known for a while that in some instances, the oh-so-famous p53 tumour supressor can misbehave. P53 loss of function renders cells suceptible to DNA dammage and p53-mediated senescence of stromal cells may be required for the initiation of certain types of tumour. At the end of the talk, some of the PIs expressed their mistrust of this free-for-all that is PLoS ONE. Is this a generation gap in science? Are we just so used to the wikipedia, facebook, youtube, digg, blog sharing networks that we think science should be freed, liberated. I think if we've learned anything from the internet, it is that the masses are generally less intelligent than the individuals that they are comprised of.

Take the latest hot paper in PLoS ONE, "Order in spontaneous behavior". In that paper they hooked up fruit flies to a flight simulator, and because the fly can generate erratic patterns of flight that are endogenous to their neuronal circuitry at that instance, and not merely pre-wired, the authors concluded that they have a form of free will. Free will as the author points out, is an oxymoron: "the term ‘will’ would not apply if our actions were completely random and it would not be ‘free’ if they were entirely determined. So if there is free will, it must be somewhere between chance and necessity - which is exactly where fly behavior comes to lie."

This echoes what Einstein believed: "I don’t believe in the freedom of the will. Schopenhauer’s saying, that a human can very well do what he wants, but can not will what he wants, accompanies me in all of life’s circumstances and reconciles me with the actions of humans, even when they are truly distressing. This knowledge of the non-freedom of the will protects me from losing my good humor and taking much too seriously myself and my fellow humans as acting and judging individuals".

Which leads me to the quality of the reviewers on PLoS. Most PI's are obviously too busy to give free time to peer-review stuff on the internet that wont get them any type of recognition. Furthermore it blurs the line between "expert in the field" peer review and "random degenerate grad student" review. And really, when the best young minds are free to write anything on the internet, what comes out is probably "I for one welcome our new cyborg fruit fly overlords". What we lack is accountability and a positive reward in your career from contributing to peer-review, or publishing in non-traditional journals (is it even a journal?).

On the one hand some of the reviews appear quite adequate, yet some seem to be overly philosophical, probably because they were written from out-of-field scientists and not experts: "The findings actually have nothing to do with free will. Free will is a feeling I have (when I do something deliberately) that I am doing what I am doing because I feel like it: a feeling that my willing it is the cause of my doing it. It is undeniably true that that is what it feels like to do something deliberately. But whether what feels like the cause -- feeling -- is indeed the cause of my doing is an entirely different matter. The real cause might, for example, be a fractal order mechanism of the kind reported by Maye et al. But that mechanism is the causal mechanism it is irrespective of whether it happens to be accompanied by (or generates) feelings. And it certainly does not explain how or why we (let alone the fruit fly) feel anything at all. And without feeling there is no free will, just mechanisms, whether deterministic or nondeterministic -- unless we are ready to believe in telekinesis."

But what really took me over the edge, is this blog spamming on that paper's annotations. It's one thing for the bayblab to spam digg, but this is a taste of what's to come to the scientific discussion and peer review process if it remains open...