Some links worth checking out regarding suppressing publishing and bioterrorism

Just a quick one here with some links worth checking out regarding the recent discussion of suppressing some parts of a paper on engineering flu viruses

Difficult times in predicting flu evolution suggested by recent paper

There is a potentially controversial and very interesting article in the journal PLoS Pathogens on Flu Evolution. The study was led by Edward Holmes at Penn State, and co-authored by many researchers including colleagues of mine at my former institution TIGR. They performed a detailed evolutionary analysis of the cmplete genomes of 413 influenza A viruses of the H3N2 type (the H#N# system refers to the subtypes of Hemaglutanin and Neuraminidase genes).

The virus genomes were sequenced at TIGR using a high throughput flu viral genome sequencing protocol originally developed at described by Elodie Ghedin and colleagues here and here. The viruses they selected were from across New York State as part of a surveillance program.

Using a variety of evolutionary analyses including phylogenetic reconstructions and examination of substitution patterns, they come to a surprising conclusion – that

stochastic processes are more important in influenza virus evolution than previously thought, generating substantial genetic diversity in the short term

This may seem somewhat uninteresting to many out there but if true it is critically important in fighting flu and in understanding viral pathogen evolution. Right now there are substantial efforts to try and predict what future dominant flu strains will look like. These predictions tend to rely on assumptions that positive selection of viruses is critical in generating and maintaining diversity. If stochastic processes are as important as Holmes et al conclude, it would mean that more intensive monitoring of flu is needed in almost real time (since predicting random events tends to be, well, very hard).

I confess I have not tried to evaluate whether or not I think their conclusions are correct, but on first glance they seem sound. This just goes to show that general genomic surveys that try to be relatively unbiased in their sampling can reveal substantial novel patterns not seen before in highly target genome sequencing projects.

Flu Evolution Revisited and Biology Direct’s Foray into Open Peer Review

Anyone interested in scientific publishing and/or the flu should check out a new paper in the journal Biology Direct. The paper suggests a new way of thinking about flu evolution. Whether you agree with the authors or not (I am still not sure), what is most interesting about this to me is that the reviews are posted online as are the authors responses. See the paper here and some stories about it here and here.

Biology Direct is an Open Access journal that is experimenting with the peer review system. Their experiment is quite intriguing in its methods. For details see here and here.
Basically, the author is charged with selecting reviewers and then getting the reviews. Then the paper can be published along with the reviews, whether they were positive or negative. The author can make changes based on the reviews or can choose not to. Thus someone could publish complete crap, but since the reviewers will be named publically, hopefully the reviews will indicatethat it is crap. The key to this is that the author has to select people from the Editorial Board that then select the reviewers. So as long as the Editorial Board is reasonable, the review process should be OK (note – I am on the Editorial Board although I have not been asked to do anything yet).

Do I like this system? I am not 100% sure. But I admire Eugene Koonin and colleagues for trying something different and giving the world an example of a possible way to get around the flaws of the current review system. Of course, to me, the most important thing is that the journal is Open Access, which means that anyone out there can get a fascinating look at peer review for free.

For example, people should really check out the paper and the reviewers comments and the authors responses. Or even better check out some other papers in the journal. It makes for a good read.