Tuesday, March 13, 2007

Global Ocean Sampling Expedition - Update

(via Konrad and Jonathan Eisen) The first results of Craig Venter's boat trip are now packaged and presented in PLoS Biology. There is going to be a webcast today at 10:00 AM Eastern time, 15:00 GMT. I am still skeptic of the usefulness of such datasets. Right now I still think that metagenomics, with current analysis methods, looks more promising at a smaller scale, to analyze smaller bacterial communities were the impact of perturbing the bacterial community could be studied. Of course this can be just my naive view of someone that never actually did any work with these datasets. In any case, many groups are likely throwing a lot of computing power at making many more interesting findings from the data. Also, this is just the first part of the trip. The full voyage can be seen in their website. I wonder what they will do with the rest of the data.

Any concrete questions on metagenomics can be directed at the blogs of the experts :). Konrad works with metagenomics in the Bork group and Jonathan Eisen is one of the authors in some of the papers, so he might know a thing or two about this stuff.

Craig Venter might be a controversial figure but he has surely been one of the few that has so strongly generated enthusiasm in science. He has been involved in the sequencing race to finish the human genome draft, a great metagenomics sampling voyage around the world (inspired by the British Challenger expedition) and some initiatives on the personal genome and biofuel production. His actions are propagated in the media and bring biology closer to the people that pay for us to do this work.

(image adapted from Gross L (2007) Untapped Bounty: Sampling the Seas to Survey Microbial Biodiversity. PLoS Biol 5(3): e85 doi:10.1371/journal.pbio.0050085)

Update - The webcast mentioned above has started. It looks like a bit of marketing hype event. The fact that we need windows media player might scare some people away. There is an email address in the site to send in questions. I will try to liveblog it for a while.

14:18 GMT -A PLoS editor is up explaining why open access publication is such a good match to this work.
Many of genome papers are not freely available. Venter decided to publish in PLoS making not only the data but the papers describing them are available.

14:20 GMT - Venter is up again. It took them 6 months of peer review to get the papers trough so we should not confuse open access to easy access. 18 000 40 000 new species after 1 my of sequences from the Sargasso sea. The question was to continue sequencing Sargasso sea or going to other places. This why the the expedition was set up. Part of the motivation for the voyage was also to promote science to the main public. Some of the areas were they passed they had some political problems because they are contested by different countries. There is a very large divergence from site to site (but this we can read in the papers anyway).
He suggest it would be possible to tell were a ship came from by analyzing the microbial diversity in the boat. There is strong geographical preference for the light sensitivity for the foto-receptors. Another surprise was trying to map the diversity obtained in the voyage to known genomes. They could observed co-existence of organism with very large sequence diversity for the same species (not sure I got this right but it is in the main paper). New gene and protein families are being discovered in linear fashion and therefore we are still not near saturation.

14:30 - Introduction of the CAMERA database to host the data. Genomic and environmental on a big cluster, currently doing blasts . There are huge problems with a database of this size so they are (i think) making different copies of the database in the US.

14:40 - Venter is up again to answer Q&A. I'll end the liveblogging here.