ISMB 2008: micro-blogging at its best

Probably like many others, I have often been puzzled by the phenomenon of ‘micro-blogging’, which consists in posting very short messages on the web (typically via sites such as Twitter) with the goal of providing an instantaneous description of the activity, state of mind or thoughts of the writer. The last few days, a small group of bloggers attending the ISMB 2008 Conference in Toronto used a form of collective micro-blogging on FriendFeed in an intensive way to cover many of the talks held at the conference.  Read more

The impact of online publishing

“I haven’t browsed a table of content in ages; I find all my papers by Pubmed searches anyway”. We have probably all heard this remark, which reflects a general trend as how online publishing has changed the way we retrieve scientific publications. In a study published today in Science, Evans (“Electronic Publication and the Narrowing of Science and Scholarship”, Evans, 2008) presents data on citations patterns showing that the appearance of electronic publications has been accompanied by a decrease in the number of citations and a progressive restriction of citations to recent papers:  … Read more

Fascinating correlations or elegant theories?

Chris Anderson, Editor-in-Chief of Wired , wrote a few weeks ago a provocative piece “”http://www.wired.com/science/discoveries/magazine/16-07/pb_theory”>The End of Theory: The Data Deluge Makes the Scientific Method Obsolete“, arguing that in our Google-driven data-rich era (”The Petabyte Age”) the good old “approach to science —hypothesize, model, test — is becoming obsolete”, leaving place to a purely correlative vision of the world. There is a good dose of provocation in the essay and it was quite successful in spurring a flurry of skeptical reactions in the blogosphere, FriendFeed-land and lately in Edge’s Reality Club.  Read more

2007 Impact Factor

2007 Impact Factor

The 2007 Impact Factors were published yesterday by Thompson Reuters. The Impact Factor of Molecular Systems Biology for 2007 is 9.954 This represents a substantial increase over last year’s Impact Factor (see chart) and we would like to warmly thank all our authors and reviewers who have contributed to this success. We will continue to work very hard to maintain the high standards of the journal and promote innovative and insightful research in systems biology. The significance of Impact Factors suffers from intrinsic limitations (see Ian’s post) and interpretation of this metric is subject to much discussion (Rossner et al  … Read more

Google Health, Biomedical Mutual Organizations and Open Consent

Google Health, Biomedical Mutual Organizations and Open Consent

Google Health, the new service offered by Google is now online (via bbgm, Life as a Healthcare CIO, GTO). This service helps users to store, organize and share their health profile and medical records, to use a variety of health-related online services and to search for medical information. Understandably, Google places great emphasis on data security and confidentiality. In this regard, I thought it might be worth highlighting several recent and thought-provoking discussions around the issues of data privacy and participative medical investigations. In a provocative editorial (Bains, 2007, see also Nature Medicine News article), William Bains advocates that collectives  … Read more

Rewiring E. coli transcriptional network

Rewiring E. coli transcriptional network

Research highlight by Kazuharu Arakawa and Masaru Tomita, Institute for Advanced Biosciences, Keio University, Japan Gene duplications and mutations are central driving forces in the evolution of genomes. Genomes must be robust to such changes in order to be evolvable, and many studies have probed genome robustness using systematic gene knockouts or overexpression experiments. In a recent paper, Isalan et al. (2008) took a new approach to test the robustness of Escherichia coli gene circuitry by reconstructing gene duplication events by shuffling the promoter-ORF pairs for about 300 transcription factors and introducing 598 recombined pairs one-by-one into E. coli to  … Read more

ESF-UB Conference on Systems Biology

ESF-UB Conference on Systems Biology

The ESF meeting on Systems Biology, organized by Luis Serrano and Ruedi Aebersold, took place last week in Sant Feliu de Guixols, Spain. A lovely location (I took this picture with my iSight directly from my room…) for a small conference with a list of outstanding speakers. Together with the influence of the Mediterranean-Latin ‘cultural jet lag’ (understand: go to bed very very very very late), the stage was set for intense networking among the participants.  Read more

Contrasts: Craig Venter and NSABB on synthetic biology

Contrasts: Craig Venter and NSABB on synthetic biology

Two rather contrasting videos on synthetic biology this month. In the first videocast, released by TED, Craig Venter exposes his grand vision of synthetic genomics. He insists on the notion of ‘combinatorial genomics’, that will combine the power of large scale DNA synthesis (‘robots that can make a million chromosomes a day’) with a database of 20 million genes, ‘the design components of the future’. This approach, a pragmatic mixture of rational function-oriented design and empirical large-scale selection, is envisioned to prepare a modern ‘Cambrian explosion’ of new synthetic species. It is good to see Craig Venter laughing when announcing  … Read more

A refreshing model: peppermint terpenoids

A refreshing model: peppermint terpenoids

Research highlight by Doron Lancet, Crown Human Genome Center, Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel Living cells are typically asymmetric, having tens of thousands different biopolymers (proteins and polynucleotides), but merely <1000 types of small molecules, such as amino acids and lipids. An exception is certain plant cells that harbor members of ~40,000 strong group of low molecular weight terpenoids, often displaying a complex compositional balance essential for plant growth and survival (Aharoni et al, 2005). Understanding the intricacies of biosynthesis and interconversion of such unusual cellular components appears to require the full power of Systems  … Read more