Notes from the Biomass

More than once, I critized PLoS for changing only the access to publications rather than offering an enhanced way of scientific communication. At least one of the standard features of most content management systems - the ability to add comments - will now be used for all PLoS journals. The aim is to add real correspondence, not just "I like this papr. Good vork. Yours Schnuffelfred", hence the "electronic letters" will undergo editorial screening. As of now, you have click links in the sidebar to find out whether there are "eLetters", which is a little annoying but I am sure there will be enhancements. A selection of letters is supposed to appear in the monthly journal.
The editorial of the current issue has more details and specifically mentions blogs as an influence.

[N.B.: Of course, there is a page to see all eLetters.]

After Nature, my favourite scholartainment magazine, started blogs (which I fail to find after the recent site redesign), offered a toolbar and the social reference manager Connotea, the podcast, which was started with the current issue, was a foreseeable extension. I have not much use for podcasts - I don't listen to the radio much at all and I usually cycle to work, when most people listen to it, I guess. Anyway, I downloaded the hefty 20 minutes and listened. The 'cast is presented by the ungooglable Dr Chris Smith. We get reviews of recent scientific publications, commented and explained in a rather light hearted manner and augmented with interviews with the scientists. I like the personal note of the interviews really. The selection of topics is suitable to a wide audience of scientists but I was surprised that the Nobel prizes that were announced on Monday and Tuesday were not part of the Wednesday show - I guess, the medium needs a little more independence and more spontaneous action - announcement of the prizes caught somebody by surprise.
Let's see how it develops - 20 minutes is a little long for my attention span, so a handful of shorter podcasts, spread over the week would suit me better. May be I should also buy that iPod Nano finally.

Many people criticized the current state of publishing in the life sciences, in particular Eugene Koonin, whose views on peer review and the long delays that go with it made it into Nature. The launch of Biology Direct, a new BioMed Central journal for everything around biology and bioinformatics (with an initial focus on the latter) offering href="http://www.biology-direct.com/default/10078-aims.htm">novel open peer review might actually change the system. This is going to be very interesting - the launch of PLoS forced many publishers to go open access - let's see what happens to the ill-mannered closed peer review.

Some days back, the archive of Proceedings of the National Academy of Sciences (of the USA) was extended back to 1915. Browsing the back issues tells much about how science was done back then. Publication style changed quite a bit over the years. The canonical methods/results/discussion separation was not enforced back in the 20s and the publications read more like letters that the highly standardized, specialized publication we get today.
Also, the short titles of the single author papers show how it was possible to be achieve much without running being part of larger group.

It would be nice if all journals would open their archives this way. Nature is (only) going back to 1950 and requires special licenses for issues from 1996 back. Science has not made his back issues available before 1997 - if you want to read about the genome of Haemophilus influenzae, you'll have to order it.

For the bioinformatic text miners, the character recognition and access to the whole corpus might remain an issue. It will be nice to have the whole corpus of scientific publications under one roof - it won't take much more than a couple of years to complete.

As we discuss whether a open, online system could replace how we judge the impact of a publication today, many people question aspects of the current system, run entirely by Thompson ICI.
In the editorial of the current edition of PLoS Biology, Hemai Parthasarathy, its managing editor reviews oddities in the way the impact factor is calculated for PLoS Biology.

Is the impact factor of a journal really that important? We all know that it only captures part of the importance of a journal. I really never understood the scientists who did not want to consider PLoS because the impact factors were not established and I would not be surprised to learn that those will now refrain from publishing in PLoS because of its low impact factor.

Will exaggerating the impact factor ever stop in the awareness driven economy of the sciences? Probably not. How about a more transpararent alternative?

Research groups from Texas A&M and the University of Illinois studied the chromosomal rearrangements in the evolution of mammals. Their study appeared in Science.

Rates of chromosome evolution within mammalian orders were found to increase since the Cretaceous-Tertiary boundary. Nearly 20% of chromosome breakpoint regions were reused during mammalian evolution; these reuse sites are also enriched for centromeres.

Nice paper ... and 124 pages supplementary material.

The current issue of Bioinformatics starts of with the very useful review of the evaluation of clustering results.

Clustering is easy: You always get a result that can be called a success by one measure or the other. The authors of the review consider mathematical properties of the solutions and show how to compare them amongst each other.

It is a handy reference for your next clustering problem - with all the high (and medium) throughput data pouring out of the labs into the bioinformatics offices, there is a steady interest in such techniques. Even if clustering often fails to explain much of the data.

The first issue of the latest journal - PLoS Computational Biology - was launched by Public Library of Science. Will be interesting to see whether it can become the prime bioinformatics journal - it certainly has the potential.