Notes from the Biomass

Free Association is a blog, accompanying Nature Genetics with commentaries in papers therein and in other journals, editorial policies, announcements of editors at meetings, and covering genetics in the media, including blogs. The commentaries by authors are really required for the usual Nature Genetics two-pager that solely consists of numbers and links to the supplementary material.

Free Association is a "real blog", with identifiable authors, trackbacks, comments and a very clean, unNatural layout free of advertisment, all powered by Movable Type. I appreciate its low tone really and prefer this way of commenting to the letters to the editor at BMJ or PLoS Biology.

Comments are reviewed as most publishers gone blogging do. Let's see what happens when things go controversial. I hope that the editors pick up good traditions from the blogs, such as identifying your sources and providing links to content other than your own, which I often miss in the media coverage.

Most likely, this is one of the first blogs that many geneticists will see - and it will a powerful influence for the A-list of science blogs. It might also be helpful in establishing blogs as a serious form of communication in science - that alone would be a good thing.

[Via nodalpoint.org]

Associated with and inspired by the Creative Commons, the Science Commons project is providing standardized licenses to spread open access and facilitate the exchange of data and publications. It is backed by an impressive group of scientists. I like the separation into data, publishing and licensing, providing a distinction between experimental information, hypotheses and resources such as cell lines.
The Creative Commons website presents the Science Common in depth.

[via netzpolitik.de (requires German but never registration )]

Dear SVP of a Boston based PR company,

You are new in the email spamming business, aren't you? Otherwise you would have noticed that sending unsolicited email to bloggers is a mildly silly idea, even more so when signed personally by a "senior vice president". They can simply put the name of the company you would like to promote on their site together with defamatory statements (such as hires "PR companies to send unwanted emails"). Get that blogger issue from Forbes and tremble a little, I can't be asked to take any further actions here and won't even disclose your name here. You've got mail.

Roland

Looks like the biotech spammers are as inexperienced as the biotech spammees. And thank twoday.net for taking care of comment spam.

Many European scientists consider creationism a purely American issue and Kansas (e.g. as described at Pharyngula) won't happen here and there is hardly any need for a campaigning to defend basic scientific principles.

Recently there were several articles in the media (none in English afaics) about the invitiation of a know criticizer of evolution, the munich based microbiologist Siegfried Scherer, by the head of the state of Thüringen.
Our designated minister for education and science, Annette Schavan, studied catholic theology (as well as philosophy and education) and is a member of the "Christian Democratic Union" , the major right wing party (interesting for a laicistic state, eh?). However, few (including me) fear a similar discussion for German class room. I suspect that the issue will come up in near future nonetheless as technology and science are seen critical by the German public and that the discussion won't be easily dismissed.

American trends used to take about months to establish themselves in Germany - now we get both creationists issues and the church of the flying spaghetti monster at about the same time. There is certainly a lot of science criticism across the German political spectrum - christians on the right, a strong technology criticism on the left and with the greens. Our tight stem cell regulations were supported by critics of all parties. I just hope that the latent criticism in the general public stays with reading horoscopes and does not manifest in (more) overregulation. What's worse in the long run: a few creationist wingnuts or established beaurocrats?

[Afterhoughts: Well, substantial cuts in funding is obviously worse. And I am not going to mention that president.]

I've been bad and considered Nature infotainment before. I have to repeat myself and link to this very cool (but practically useless) rendering of RNA interference available from the Nature website. Finally, science looks like in the movies. Now back to my Emacs window.

[Via F&L]

Pedro Beltrao noted that a table of the 10 most highly cited papers include the bioinformatics applications BLAST, ClustalW and MFOLD. This even more surprising in that the set is not limited to life science publications.

The work from Julie L Morrison and colleagues from the university of Glasgow, recently published in BMC Bioinformatics, is interesting in several ways. GeneRank: Using search engine technology for the analysis of microarray experiments. describes the application of the PageRank algorithm used by Google to "boost" the rank of genes in a list that are e.g. differentially expressed.

This idea naturally extends to analysing the results of a microarray experiment, where we would like a gene to be highly ranked if it is linked to other highly ranked genes, even if its own position is lower, e.g., due to measurement variability.

Algorithmically, the work is solid and the application of such algorithms seems a smart way of making use of interaction networks and expression data and I got a nice introduction to the PageRank algorithm with it. The algorithm includes a weighting parameter, you can solely rely on the underlying network for detecting groups or rely only marginally on the use of GeneRank algorithm off.

For me, there is one big caveat: Are the genes that are highly connected really important, pivotal genes? Morrison et al only use a network obtained from Gene Ontology. For integration, it might be more useful to use the rich resource we have in protein-protein interaction data, particular when analyzing data in yeast. However, given the many false positives and the fact that the highly connected proteins generally display unspecific binding, I wonder whether we would anything out of such analyses. Obviously, this applies to all interpretation of networks.

If you create the interaction map of the parts of a machine or study the human body and count the interaction of its structures - are the "important" parts the ones that are highly connected?

Other Mac users wondered that I ran Firefox on my Powerbook instead of using Safari - it was slow and not the great experience that you got from Firefox on Windows boxes. I only realized how "bad" it really was until I installed the Firefox 1.5 Release Candidate 1 yesterday. Now, surfing the internet is pure bliss again.

[N.B. I was this close to include a smiley in this post]

I always wondered how the motto of the German Federal Ministry for Research and Education for the "elite university programme"- Brains Up! - would resonate with somebody whose native tongue is English. Tacky was a good guess, or?