castanyes blaves

Random ramblings about some random stuff, and things; but more stuff than things -- all in a mesmerizing and kaleidoscopic soapbox-like flow of words.



Green races

BBC NEWS | Technology | Green tech in 'Formula Zero' race
Green tech in 'Formula Zero' race Formula Zero karts Delft University's Greenchoice leads the newly established table The world's first international hydrogen-powered motorsport race was held in Rotterdam this weekend. Dubbed the Formula Zero championship, the contest pitted teams from five countries against each other in a zero-emissions go-kart race. Each team's entry was powered by a commercial fuel cell that produces electricity from hydrogen.



US elections in two and a half months

BBC NEWS | World | Americas | Obama picks Biden as running mate

In two months and a half, November 4th, the United States citizens will be able to decide who they want their president to be. Obama has chosen Biden as the running mate to complement his young profile. Biden as Obama is a "you can make it if you try" kind of person. Biden's work in the Senate: violence against woman act, college tuition affordable for all, lock down chemical weapons. Obama to the stage with U2. Biden to the stage with Bruce Springsteen. Biden: no more tax cuts after tux cuts; being able to pay the bills; energy policy shouldn't be written by and for oil companies; these times require more than a good soldier, they require a wise leader.

Maybe McCain will pull it out, who knows. The idea of fighting in Iraq for 100 years is doesn't make any sense. Healthcare is not going to move any forward with McCain, but towards more privatization. Obama has inspired millions of americans.



Biological Sciences Cyberinfrastructure

Towards a cyberinfrastructure for the biological sciences: progress, visions and challenges : Abstract : Nature Reviews Genetics
Towards a cyberinfrastructure for the biological sciences: progress, visions and challenges

Lincoln D. Stein

Very interesting read about what composes the biological sciences cyberinfrastructure today, and what can be done to improve it. Some random thoughts:

  • A lot of these concepts are present in day-to-day conversations here at the WTGC.
  • The "community annotation hubs".
  • An example of community annotation: the approach taken by Reactome is in my opinion a very clever one: active attract experts on the field, and manually curate the information of their expertise.
  • An example of a large community for manual annotation: the Havana group at the Sanger. Lots of people nowadays (with a big push from the ENCODE consortium).
  • There still are some gaps or disconnections between sources of knowledge and centralized databases. For example, there is a lot of gene-by-gene work done that could be easily put together in a Reactome-style way. Many of these cases are something like: "I've done my PhD on the characterization of gene XYZ and here are the corrections to the annotation in your online database". A lot of this stuff is still disconnected at the moment of creation, and when it gets published and the investigator moves forward, the momentum gets lost. Then an extra manual curation/text mining effort is needed a few years down the road.



More RNA-seq results

A Global View of Gene Activity and Alternative Splicing by Deep Sequencing of the Human Transcriptome -- Sultan et al. 321 (5891): 956 -- Science
A Global View of Gene Activity and Alternative Splicing by Deep Sequencing of the Human Transcriptome

This is another very interesting paper that uses the RNA-seq method to produce a very fine map of Alternative Splicing in the human genome. In this case, they've sequenced poly(A) RNA from human embryonic kidney cells and B cells. The authors use the term "digital transcript-counting approach":

Digital expression levels were normalized (NE values) by taking into account the theoretical number of unique 27-mers (sequences that are 27 bases long) contained in each exon and the total number of reads generated in each experiment.

which in my mind translates to: sequence a shitload of 27mers (Illumina), map them to the reference genome, and count the amount of reads that stack up to the coding exons. If they don't map to currently predicted exons (about 25% of the reads), then have a look and see what is that region. A high proportion of these previously unknown exons were unique to one cell type and likely to be differentially expressed.

Some alternative splicing summary numbers: average of 7.2 junctions per gene with a mean density of 3.8 reads per junction (not that much?). The most common AS event is exon skipping, with events mostly affecting one or two exons.

I am loving all these RNA-seq experiments!



The future of electricity generation

Energy alternatives: Electricity without carbon : Nature News
Electricity generation provides 18,000 terawatt-hours of energy a year, around 40% of humanity's total energy use. In doing so it produces more than 10 gigatonnes of carbon dioxide every year, the largest sectoral contribution of humanity's fossil-fuel derived emissions. Yet there is a wide range of technologies — from solar and wind to nuclear and geothermal — that can generate electricity without net carbon emissions from fuel.

In the solar energy section, a striking statistic: even under the best conditions, the efficiency of photosynthesis barely reaches 1%. In comparison, most solar panels can nowadays reach 15% efficiency, with the most efficient reaching 40%.
On the other hand, other renewable sources of energy, like wind, have great potentials, but other great downsides. So it seems that it's all a matter of combining the best of each world. At the end, what is sought for is efficiency, reliability, possibilities of expansion, etc.



Samsung Puts a Little Corn Into Its Cellphones - Bits - Technology - New York Times Blog
Samsung is hoping to steal a little of the Olympic spotlight in Beijing on Thursday as it unveils its latest “eco-phone.” The E200 Eco is the third phone Samsung has introduced this year with parts made from bioplastics — materials extracted from corn. It is the first, however, in which the entire case is bioplastic.




Spanish shopkeeper finds Homer Simpson euro | U.S. | Reuters
Spanish shopkeeper finds Homer Simpson euro



Methane-producing meat versus kangaroo meat

BBC NEWS | UK | Eat kangaroo to 'save the planet'
Switching from beef to kangaroo burgers could significantly help to reduce greenhouse gas emissions, says an Australian scientist.

The Australian scientific body, CSIRO, is very interested in the possibilities of a more productive and greener farming. The use of sheep and cows immunized against methane would make adequate changes in the digestive flora.

Genomics are also contributing to the understanding of digestive ecosystems. The methagenomics analysis of the termite's midgut has revealed the large possibilities that these tiny ecosystems have for the development of the next generation (third? fourth?) of biofuels.



Next-generation sequencing

Cost of the machine (454/Solexa/Solid) ~ $500k
Cost per run:
  • 454 ~ $5000
  • Solexa/Solid ~ $3000


Better catalysts for energy storage

CHEMISTRY: New Catalyst Marks Major Step in the March Toward Hydrogen Fuel -- Service 321 (5889): 620 -- Science
New Catalyst Marks Major Step in the March Toward Hydrogen Fuel
Robert F. Service

Climate change concerns, high gas prices, and a good deal of international friction would fade if scientists could learn a trick every houseplant knows: how to absorb sunlight and store its energy in chemical bonds. What's needed are catalysts capable of taking electricity and using it to split water to generate hydrogen gas, a clean fuel. Unfortunately, the catalysts discovered so far work under harsh chemical conditions, and the best ones are made from platinum, a rare and expensive metal.

No more. This week, researchers at the Massachusetts Institute of Technology (MIT) in Cambridge led by chemist Daniel Nocera report online in Science a new water-splitting catalyst that works under environmentally friendly conditions ( More important, it's made from cobalt and phosphorus, fairly cheap and abundant elements. The new catalyst needs improvements before it can solve the world's energy problems, but several outside researchers say it's a crucial development.

"This is a great result," says John Turner, an electrochemist and water-splitting expert at the National Renewable Energy Laboratory in Golden, Colorado. Thomas Moore, a chemist at Arizona State University in Tempe, goes further. "It's a big-to-giant step" in the direction of powering industrial societies with renewable fuels, he says. "I'd say it's a breakthrough." Meanwhile, on pages 671 and 676, other groups report related advances--a cheap plastic fuel cell catalyst that converts hydrogen to electricity, and a solid oxide fuel cell catalyst that operates at lower temperatures--that affect another vital component of any future solar hydrogen system.


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