Notes from the biomass

The current issue of Nature Biotechnology contains a commentary on protein-protein interaction networks that nicely reflects the view of the informed end of the community. The only thing that I would criticize in their treatment is the lack of differentiation between the methods. Only by checking the references, you’ll notice that the lack of overlap they cite is between the now very dated data sets by Uetz and Ito. If you compare the high-confidence interactions (not the complete sets) of the 2006 studies by Krogan et al. and Gavin et al. you’ll notice that they are in good agreement, even if we are nowhere close to what we are used to from studying genomic information.

Our new paper in BMC Bioinformatics is about the only one that is not “highly accessed”. Next time we’ll take care to put “human cancer interaction” in the title.

The current issue of EMBO Reports contains a short analysis, which shows that the number of retractions of scientific publications increases dramatically. The authors give two possible explanations: Competitions amongst scientists lowers the quality of published research. It might also mean that scientists are more aware of other people’s mistakes and that “the self-correction of science is improving”.

While both alternative are plausible, my favourite suggestion is that online publications have made it feasible to retract papers and there is an incentive for the journals to show that they take care of possible misconduct. A large number of the retractions might be of heavily flawed works rather than fraud (a blogger’s assumption, I have not checked enough retractions myself). Earlier, the community would know that a particular work is not reproducible, but the retraction process was cumbersome and consumed too much time, so it was only pursued in the grossest instances.