Notes from the biomass

The hypothesis behind the research of preference for heavy metal music amongst gifted teens in the UK remains obscure in this report in the Telegraph;  A comprehensive study of the last.fm profiles of researchers would be more representative and I would not be surprised if an aged matched sample would find a preference for music that some people would classify as “heavy”. After all, Dream Theater or Rush are ideal to cancel the deafening silence of an office out and with Arcade Fire et al. abound, no one should worry about the lyrics of Mastodon.

Konrad was the first this morning to hint at release of Venters effort of providing  environmental sequencing samples from the world oceans. The data is backed by several papers in PLoS Biology and the new camera database. Other bloggers have followed and the main stream media will pick it up soon.
What to add on a busy day like today? The results might not breathtaking but that was as true for the release of the release of the human genome project back in 2000. Sequencing the human genome was a necessity - but the environmental samples provide a complete new picture of our planet, even if our initial view is warped and noisy and our ways of understanding the data is limited.

About time to mention Re:publica here, open for registration since the weekend.The ununconference on blogging, social media and the rest, organized by the unmissable Berlin-based bloggers Johnny Haeusler and Markus Beckedahl will take place in Berlin from April 11th - 13th 2007, halfway between my flat and the institute. Nice.
Science wise, the hard blogging scientists will host a “plug in” - not so sure what that is yet, I’ll attend anyway. If you are interested in blogging in the natural sciences, drop me a note.

Philica is an attempt at academic publishing with very few restrictions. Journalology (my source) is critical as is Archaeoastronomy. I too doubt whether the initiators do much good to academic publishing by releasing work on divination methods.

The newly founded company Metaweb recently announced Freebase, an effort to organize the world’s information by creating meaningful connections between the different data sources. The data base will be released under a Creative Commons by-attribution license.
The major difference to Google Base from what little I can see at this point is that the company actively takes place in integrating the different data and creating a meaningful way to navigate rather than search it. Freebase already incorporates Wikipedia and other smaller projects and should allow future content to be connected to this resource in a controlled manner. However, as the database is early alpha and only open by invitation, it’s premature to discuss the use on hard scientific data.
There’s more on the matter in Konrad’s post and comprehensive coverage on bbgm.

Update: An informative sneak preview and the news that BioMedCentral content will be incorporated.

Friday’s my literature review day; the most noteworthy one from today’s lunch break reading is Functional Taxonomy of Bacterial Hyperstructures in the current issue of Microbiology and Molecular Biology Reviews. The work by Vic Norris and many others discusses the notion of hyperstructures, the principle, large scale organization of cellular processes in bacteria.

The review is not at all a patch work of the latest research on particular subject areas. Instead, it revisits modern concepts of well characterized structures and processes such as transertion, the physical interplay of transcription, translation and secretion, which is happing in physical proximity in bacteria. Other hyperstructures discussed are related to the heavily discussed bacterial cytoskeleton and processes like glycolysis and cell division.

Despite a philosophical inclination, the review it does not wander off into a quasi-esoterical musings and I would recommend it to anyone working with prokaryotes as an update of our view of the bacterial cell. Besides, they show that they don’t have to do the buzz word ride: systems biology is never mentioned.

Infections caused by Mycobacterium tuberculosis kill 2 million people each year; tuberculosis is the most important disease caused by a bacterium. Despite the introduction of vaccines in the 1920s and promising antibiotics in the 1950s, it remains one of the major health issues in developing countries.

News@nature has a special, summarizing the current state of research, accompanying the current issue of Nature Medicine that focuses on tuberculosis. The extensive material is both introduction and overview, helpful to those new in the field (like me).

Rob Carlson from the synthesis blog and author of the New Economy forthcoming book “Biology is Technology” suggests to use Open Biology rather than Open Source Biology and admits in a recent post:

Despite unleashing the phrase “Open Source Biology” on the world six years ago, at this point I no longer know what Open Source Biology might be. Perhaps Drew Endy still has a useful definition in mind, but as I try to understand how to maintain progress, improve safety, and keep the door open for economic growth, I think the analogy between software and biology just doesn’t go far enough. Biology isn’t software, and DNA isn’t code.

The following analysis highlights why we have not seen biohackers tinkering with bugs as we have hackers tinkering with computers abound today.