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The Seven Stones details
Listing ID: 377
Title: The Seven Stones
Description: The blog of Molecular Systems Biology, the open-access journal published by the Nature Publishing Group and EMBO.
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listed on: May 01, 2008 08:25:22 AM
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| The role of neutral mutations in the evolution of phenotypes - Tue, 25 Nov 2008 23:23:16 +0100 |
Research highlight by Pedro Beltrao, University of California, San Francisco
Using this model, Wagner describes how highly robust phenotypes can lead to faster exploration of the genotype space. He further proposes that evolution of innovation occurs via cycles of exploration of nearly neutral spaces (dubbed neutralist regime) followed by a reduction in diversity once a new phenotype of higher fitness is discovered (selectionist regime). Although these models and ideas were mostly developed using models of sequence to structure relationships, Wagner cites several examples suggesting that these concepts are equally valid for cellular phenotypes that depend on molecular interactions (ex. gene expression patterns). As Wagner points out, in order to understand the evolution of innovation we must fully understand the mapping between genotypes to phenotypes. This is why it is important to continue to develop richer evolutionary models to link changes at the DNA level with changes in molecular structures, interactions and ultimately phenotypes with a quantifiable impact on fitness. This is an area where systems biology should play an important role. Models of RNA and protein structure stability upon mutation have existed now for some time (Hofacker et al. 1994, Guerois et al. 2002). More recently the study of large amounts of genomic information and/or systematic interactions studies are providing us with accurate models for different types of molecular interactions (Berger et al. 2008, Burger & van Nimwegen 2008, Chen et al. 2008). In parallel to these, theoretical analysis has been use to aid in the understanding of cellular phenotypes (i.e. cell-cycle, signaling pathways etc) (Tyson et al. 2003). Connecting these different layers of abstraction is an important challenge that will allow us to better understand the origins of biological innovation. Berger MF et al. (2008). Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences. Cell 133:1266-76 Burger L & van Nimwegen E (2008). Accurate prediction of protein-protein interactions from sequence alignments using a Bayesian method. Mol Syst Biol 4:165 Chen JR et al. (2008). Predicting PDZ domain-peptide interactions from primary sequences. Nat Biotechnol 26:1041-5 Guerois R, Nielsen JE & Serrano L (2002). Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations. J Mol Biol 320:369-87 Hofacker IL et al. (1994). Fast folding and comparison of RNA secondary structures. Monatshefte für Chemie / Chemical Monthly 125:167-188 Tyson JJ, Chen KC & Novak B (2003). Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell. Curr Opin Cell Biol 15:221-31 Wagner A (2005). Robustness and Evolvability in Living Systems. Princeton University Press Wagner A (2008). Neutralism and selectionism: a network-based reconciliation. Nat Rev Genet 9:965-974 |
| RECOMB Systems Biology Conference - Thu, 30 Oct 2008 14:49:45 +0100 |
The RECOMB Satellite on Regulatory Genomics, RECOMB Satellite on Systems Biology, and DREAM reverse engineering conferences are currently held jointly at the MIT, in Boston. Some of the talks are currently 'live-blogged' on FriendFeed and can be followed below or in the "Recomb-Sat/DREAM 08" room. |
| SciFoo: scientific fireworks - Mon, 18 Aug 2008 10:30:00 +0100 |
SciFoo is a so-called 'unconference': there is no program or more precisely, as Timo Hannay explained during the opening of the conference, the attendees are the 'program'. The actual schedule was defined only on the first evening in a purposefully chaotic process by anyone who wished to organize a session on any topic. For the next two days, in a festival of parallel sessions, astrophysicists, 'googlers', technologists, molecular biologists, taxonomists, game designers, flying car constructors, publishers, thinkers and (some) dreamers discussed and exchanged ideas with great enthusiasm and a rare intensity and openness. Needless to say that deciding which session to attend was close to impossible... In any case, I ended up following three types of talks: a series on systems biology related topic (data integration, machine learning, personal genomics, baroque structure of the transcribed genome), several (of many) sessions focused on the theme of open data/science and finally some more eclectic sessions (only from my standpoint, of course) on diverse topics such as the foundations of the concept of time in physics, on some demonstration of very simple yet powerful Python scripting exercises to analyze text and the potential of game design to harness our 'cognitive surplus'. I cannot possibly summarize all the talks, interactions and impressions gathered at this meeting, but here are a few subjective excerpts:
The meeting ended with some final scientific fireworks, when some of the speakers gave a series of brilliant 2 min summary talks, providing a colorful overview of the many sessions we inevitably had missed. I have to admit that I like fireworks and I would certainly have enjoyed having a little more of this final kaleidoscopic view of science. Clearly, the authentic value of this conference lies in the unique and direct human interactions, but I wish there would be nevertheless some way–perhaps by using this last session in some form of outreach action–to disseminate this pure joy of scientific diversity and curiosity to a broader audience. Credits: illustrations from Bob Lee, Flickr, some rights reserved |
In a recent opinion piece,
In his list of eight 'generative' values (