Tag: Peer-Reviewed Literature

Faculty of 1000 going arXiv

So Azimuth tells us:

In math and physics we have the arXiv, but nobody referees those papers. In biology and medicine, a board called the Faculty of 1000 chooses and evaluates the best papers, but there’s no archive: they get those papers from traditional journals.

Whoops—never mind! That was yesterday. Now the Faculty of 1000 has started an archive!

• Rebecca Lawrence, F1000 Research – join us and shape the future of scholarly communication, F1000, 30 January 2012.

I’m all for giving this a try, but I still have a hard time seeing how some type of arXiv thing would work in the life sciences, simply because the life sciences are so damn big. Life scientists in academic research make up more than one third of all academic scientists. There are more than twice as many academic life scientists as physical scientists, and more life scientists than all academic physicists, mathematicians, computer scientists, chemists, and earth scientists combined. As far as I can tell by my anecdotal observations, life scientists publish many short papers, as opposed to fewer and longer papers, which is the norm in other fields.

Gene Networks and Natural Selection

This was originally posted at Adaptive Complexity, but it might be of interest to our patrons here at The Finch and Pea.

Life can be brutal for yeast in the wild. You don’t know where your next meal is coming from or what form it’s going to take. The key to being a successful yeast is to be metabolically agile, able to switch your metabolic state quickly based on the food source that’s currently available on the bark of an oak tree or in the leaf litter of a forest floor.

So yeast, especially the set of species related to baker’s yeast, have various networks of genes that specialize in making a meal out of different sugars. A yeast has to detect, pump in, and break down various sugars like sucrose, galactose, maltose, and glucose. Each of these sugars has different chemical properties, and therefore yeast requires different sensors, transporters, and enzymes to use each as a food source. Continue reading “Gene Networks and Natural Selection”

More than just a pretty shell

Researchers at UC Berkley exploited an interesting property of extant species of the mollusk genus Conus. Apparently, the patterns on the shells of these little buggers is a reflection of activity patterns in their neurons.

Continue reading “More than just a pretty shell”

Scientists scooped by evolution

It turns out that your classic experimental trick to mimic protein phosphorylation by mutating serines and threonines to aspartate or glutamate at phosphorylation sites was not first discovered by humans. Pearlman, Serber and Ferrell argue that many phosphorylation sites in proteins evolved from negatively charged amino acid residues, which means that phosphorylation evolved to mimic the effects of glutamate and aspartate. This, of course, occurred long before human scientists discovered in 1987 that you could replace phosphorlated serines and threonines with negatively charged amino acids and still get a functional protein.

“A Mechanism for the Evolution of Phosphorylation Sites”, Samuel M. Pearlman, Zach Serber, James E. Ferrell Jr., Cell Volume 147, Issue 4, 11 November 2011, Pages 934–946 Continue reading “Scientists scooped by evolution”

Single cell gene expression linkfest

Gene regulation is an old field, but gene regulation at the single cell level is a whole new ball of wax. Some of us in the lab are trying to get up to speed in this field, and I need to pick out five good papers for consideration.

The place to begin is with this great review, and then work through the references:

Central dogma at the single-molecule level in living cells, Gene-Wei Li and X. Sunney Xie, Nature 475, 308–315 (21 July 2011)

Picking selectively, I ended up with the list below, and unfortunately I need to somehow narrow this down to five… and preferably all five won’t be from Sunney Xie’s group. Any suggestions?

Quantifying E. coli Proteome and Transcriptome with Single-Molecule Sensitivity in Single Cells, Yuichi Taniguchi, Paul J. Choi, Gene-Wei Li, Huiyi Chen, Mohan Babu, Jeremy Hearn, Andrew Emili and X. Sunney Xie, Science 30 July 2010: Vol. 329 no. 5991 pp. 533-538 Continue reading “Single cell gene expression linkfest”