linkstream2 microblog

#Emergent Sensing of Complex Environments by Mobile Animal Groups: Fish swarm into dark patches from speed adjustment
http://www.sciencemag.org/content/339/6119/574.abstract

An interesting discussion of how fish swarms reflect collective behavior. The basic idea is that fish like to swim in dark patches of water as opposed to light patches and one question is how a swarm finds this quickly. It turns out that it is not related to individual fish swimming away from light and dark but rather that the fish in light water swimming more quickly than those in dark water and the fish also trying to stay together as a swarm. The latter acts essentially as almost an axle between two wheels that are moving at different speeds forcing the fish to naturally turn into dark areas. A very intuitive discussion of this topic and a nice comparison to how this type of collective behavior is what one sees in the nervous system as well – One would not want to be making mental decisions on the basis of an individual neuron.

http://www.nature.com/gim/journal/v15/n10/full/gim201372a.html

The RGASP papers are now out, back-to-back:
http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.2722.html http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.2714.html A tour de force.
.@markgerstein Both #rnaseq #RGASP papers list the “RGASP Consortium” as an author. But this comprises different people in the 2 papers!

Some notes from a senior author:

* Due to space constraints unfortunately most of the results are in the supplemental data.

* If it is helpful for testing updates to programs, or to compare the results against future methods not yet considered, the analysis code from each study is on GitHub: https://github.com/RGASP-Consortium.

* The papers are not open access, unfortunately.

http://genome.cshlp.org/content/early/2013/11/05/gr.164806.113.abstract Interesting association of viral integration, relevant to bkpts

#Genomically Recoded Organisms Expand Biological Functions: Changing UAG from stop to a new amino acid in E. coli http://www.sciencemag.org/content/342/6156/357.abstract

Marc J. Lajoie1,2,

Alexis J. Rovner3,4,

Daniel B. Goodman1,5,

Hans-Rudolf Aerni4,6,

Adrian D. Haimovich3,4,

Gleb Kuznetsov1,

Jaron A. Mercer7,

Harris H. Wang8,

Peter A. Carr9,

Joshua A. Mosberg1,2,

Nadin Rohland1,

Peter G. Schultz10,

Joseph M. Jacobson11,12,

Jesse Rinehart4,6,

George M. Church1,13,*,

Farren J. Isaacs3,4,*

Interesting discussion of a protein produced in mice and dog urine that acts as a pheromone. It is called Darcin and was named after the famous character, Mr. Darcy from Jane Austen’s novels, since it makes females very attracted to males.

Pheromonal Induction of Spatial Learning in Mice: Darcin
(#Austen-inspired name) acts as an attractant to females
https://www.sciencemag.org/content/338/6113/1462

Interesting discussion of a sort of aberrant hydrogen atom that has a proton and a muon as opposed to an electron. Since the muon is much heavier than the electron it sits much closer to the proton giving a sense of its shape. One can only imagine what muonic helium would look like with two of these things.

How Big Is the Proton? As determined from muonic hydrogen
http://www.sciencemag.org/content/339/6118/405.summary #physics

Cell division

.@NatureNews on WI-38, a cell line w/ tricky ethics (like #HeLa), from an aborted fetus, but essential for vaccines
http://www.nature.com/news/medical-research-cell-division-1.13273

Interesting discussion of another cell line other than Hela called WI-38 that has some challenging ethical issues. This cell line was taken from a fetus and used to develop important viral medications. The person who originally did this — Hayflick — identified four stakeholders that should really be compensated: the estate of the unborn child, the scientists, the institution and the funders.

In 1962, Leonard Hayflick created a cell strain from an aborted fetus. More than 50 years later, WI-38 remains a crucial, but controversial, source of cells.

http://www.nature.com/news/medical-research-cell-division-1.13273

Interesting discussion of a temporal cloaking device that can hide picosecond timescales. This could potentially be used to obscure communication between two parties — from say the CIA — in a short time period.

Temporal cloak erases data from history. Perhaps useful to foil future #NSA metadata collection.
http://www.nature.com/news/temporal-cloak-erases-data-from-history-1.13141 #privacy

http://www.nature.com/news/temporal-cloak-erases-data-from-history-1.13141

MT @genomematt Astrogenomics: #bigdata, old problems, old solutions: Both propose organizing the data hierarchically
http://genomebiology.com/2013/14/8/129