linkstream2 microblog

http://cacm.acm.org/magazines/2015/1/181614-distributed-information-processing-in-biological-and-computational-systems/fulltext

http://cacm.acm.org/magazines/2015/1/181628-in-search-of-bayesian-inference/fulltext

http://www.nytimes.com/2015/01/25/nyregion/sheldon-silvers-link-to-a-bonanza-and-a-cancer.html?_r=0

The Superorganism Revolution
http://www.americanscientist.org/issues/num2/the-superorganism-revolution/1 The lack of distinction between ecological v evolutionary change for the #microbiome

QT:{{”
This distinction between ecological and evolutionary timescales appears fundamental, but may not apply when dealing with the microbiome. For many if not all members of the human microbial fauna, generation times are measured in hours or even minutes. These short generation times, coupled with the large population sizes of many bacteria, effectively elide the boundary between ecological and evolutionary time (this attribute also accounts for the fiendish ability of viruses to outrace both the immune system and efforts to combat viral infections).
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Bioinformatics (2015) 31 (1): 33-39. doi: 10.1093/bioinformatics/btu615

Making novel proteins from #pseudogenes
http://bioinformatics.oxfordjournals.org/content/31/1/33.short Outcomes in 16 cases where one gets stable & functional translated products

http://bioinformatics.oxfordjournals.org/content/31/1/33.short

http://www.nytimes.com/2015/01/24/opinion/this-cold-house.html?smid=tw-nytopinion&_r=0

The Many Guises of Aromaticity
http://www.americanscientist.org/issues/pub/2015/1/the-many-guises-of-aromaticity #Resonance is hyped; hence, many proposals for compounds w/ it that aren’t benchstable

QT:{{”
Today, an inflation of hype threatens this beautiful concept. Molecules constructed in silico are extolled as possessing surfeits of aromaticity—“doubly aromatic” is a favorite descriptor. Yet the molecules so dubbed have precious little chance of being made in bulk in the laboratory. One can smile at the hype, a gas of sorts, were it not for its volume. A century and a half after the remarkable suggestion of the cyclic structure of benzene, the conceptual value of aromaticity—so useful, so chemical—is in a way dissolving in that hype. Or so it seems to me.
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Bench-Stable, Bottleable

Computers made the determination of the structure of molecules in crystals easy—what took half a year in 1960 takes less than an hour today. They also made computations of the stability of molecules facile.

Whoa! What do you mean by stability? Usually what’s computed is stability with respect to decomposition to atoms. But that is pretty meaningless; for instance, of the four homonuclear diatomic molecules (composed of identical atoms) that are most stable with respect to atomization, N2,C2, O2, and P2, two (C2 and P2) are not persistent. You will never see a bottle of them. Nor the tiniest crystal. They are reactive, very much so. In chemistry it’s the barriers to reaction that provide the opportunity to isolate a macroscopic amount of a compound. Ergo the neologism, “bench-stable.” “Bottleable” is another word for the idea. A lifetime of a day at room temperature allows a competent graduate student at the proverbial bench to do a crystal structure and take an NMR scan of a newly made compound. Or put it into a bottle and keep it there for a day, not worrying that it will turn into brown gunk.

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Here is a link for some helpful information on the new NIH format for biosketches:

http://grants.nih.gov/grants/policy/faq_biosketches.htm.

QT:{{”
What biologists should appreciate, what was on offer in Mumford’s obituary, and what mathematicians can deliver to genomics that is special and unique, is the ability to not only generalize, but to do so “correctly”. The mathematician Raoul Bott once reminisced that “Grothendieck was extraordinary as he could play with concepts, and also was prepared to work very hard to make arguments almost tautological.” In other words, what made Grothendieck special was not that he generalized concepts in algebraic geometry to make them more abstract, but that he was able to do so in the right way.
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http://liorpachter.wordpress.com/2014/12/30/the-two-cultures-of-mathematics-and-biology/

http://en.wikipedia.org/wiki/Jonathan_Ive