Links of note/Science

Biosphere 2 Gets New Owner, Funding – ScienceInsider

Posted on by charlie

“The future of Biosphere 2 as a scientific facility is on a firmer footing, thanks to two major gifts announced this week. On Friday, the University of Arizona (UA), which has managed the iconic glass pyramids as a tourist destination and research venue since 2007, will become the owner of the property.”

Heh. I remember when this was a dream and then followed the drama throughout the decades. It was ambitious, but was foiled by over-simplicity and human foibles. I suppose it’s now one gargantuan greenhouse and after so long and so many changes to the scientific and political landscape, might be used in a new and useful way for ecological and climate studies. Should be interesting. Finally.

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Links of note/Science

Rediscovered glowing mushroom could shed light on bioluminescence (Wired UK)

Posted on by charlie

“Researchers believe that fungi make light just as the firefly does, using a chemical mix of a compound called luciferin and an enzyme luciferase. However, scientists haven’t yet identified the luciferin and luciferase in fungi which glow at all times rather than in bursts as fireflies do”

Dang. When I read this title, I was hoping it was some symbiotic bacteria that was glowing and there’d be some cool story as to how the fungi take up the bacteria. Alas, the fungi produces its own glow. But then, quite interesting that its done with luciferase, like fireflies. A quick look at Luciferase in Wikipedia <http://en.wikipedia.org/wiki/Luciferase> shows that luciferase is found in quite divergent organisms.

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Innovation/Links of note/Science/Strategy/The Narrative

Eurekometrics: Analyzing the Nature of Discovery: PLoS Computational Biology

Posted on by charlie

“Despite the great strides in automated discovery and digitization of data that is currently occurring, however, there are limits to eurekometrics. The most important limitation is how to determine what constitutes a “discovery.” Quantifying what constitutes a discovery is never an easy proposition: Is each publication a discovery? Or do only certain ones rise to meet that definition? Furthermore, even if we can list discoveries, it needn’t necessarily be possible to quantify their properties. For example, while it’s possible to quantify the properties of minor planets and extrasolar planets, it is not nearly as easy to quantify the properties of methodological innovations made in computational fields.”

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Announcements/Science/The Narrative

“DIYbio: hackspaces, open source & f*ck yeah ethics” a proposed SXSW session

Posted on by charlie

I’ve done it. I’ve submitted a proposal to SXSW.

Alas, I was only able to submit one, despite all the ideas I had (anyone going to submit others, want to coordinate?)

I can edit this until 05 August, then I guess the voting begins. Next step for me is to determine if it’s a panel or solo or what. I don’t think I represent a typical DIYbiologist enough to go solo, so hence my preference for leading a panel with some of you hot-shots (you know who you are).

See current proposal below (with comments):

Title: DIYbio: hackspaces, open source & f*ck yeah ethics
Event: SXSW Interactive 2012
Organizer: Charlie Schick
Description: Humanity has been messing with biology for millennia. In the last 50 years, the tools have advanced to where we can design new remixes of organisms to make things for us, such as fuel, drugs, and the fresh smell of rain. What’s more, the open source and hackspace tinkering culture of the tech world has spilled over to create a nascent and vibrant community of do-it-yourself biologists. this session bring you up to speed with what DIYbio is, how you can get involved, and what are the resources available. [CS: Obviously I need to flesh this out. If this is a panel, I have a list of folks I’d like to be on it to represent the community (see supporting material below). If this is a workshop, then it’ll be a about tinkering.] Questions answered:

1. What is DIYbio?
2. How can I get involved in DIYbio?
3. What are the resrouces I can access – info and instruction, space, pepole, events?
4. What is the future of making things thorugh biology?
5. Why is this important to the SXSWi crowd?

Level: Beginner
Supporting material: http://diybio.org, http://genspace.org/, https://www.facebook.com/BioCurious, http://openpcr.org/
Category: Emerging Technology / Mobile [CS: Best category I could find. Not sure why mobile is still considered “emerging”.] Tags: diybio, hackerspaces, science

And, hat tip to @100ideas and the folks from the DIYbio Continental Congress for the “f*ck yeah ethics” in the title.

Links of note/Science

Widespread RNA and DNA Sequence Differences in the Human Transcriptome

Posted on by charlie

We compared RNA sequences from human B cells of 27 individuals to the corresponding DNA sequences from the same individuals and uncovered more than 10,000 exonic sites where the RNA sequences do not match that of the DNA. These differences were nonrandom as many sites were found in multiple individuals and in different cell types, including primary skin cells and brain tissues. These widespread RNA-DNA differences in the human transcriptome provide a yet unexplored aspect of genome variation.”

We regularly talk about errors in replication, much less so about errors in transcription. This is indeed an unexplored aspect of genome variation. Furthermore, we have no easy way to visualize errors in translation, either. Right now, so many of our tools look en-masse and only see averages. With advances in single-cell techniques, might we start seeing individual molecules and understand the effect of chance and variability in life? I hope so, don’t you?

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Links of note/Science/Strategy/The Narrative

Breast Cancer Drug Gets a Unanimous Thumbs Down – ScienceInsider

Posted on by charlie

“Some members of the advisory committee pointed to a downside in today’s decision to strip the drug of its breast cancer label: This could undermine the accelerated approval process under which Avastin first got FDA’s blessing. Accelerated approval is a way to get drugs to the sickest patients more quickly, with less clinical data. It’s virtually unheard of for FDA to reverse such an approval. In this case, FDA did so, agency officials said, after subsequent studies showed that the benefit was much less than initially thought.”

I’ve been following pharmacoepidemiology quite a lot lately, mostly because one of the product we sell (and I market) is used to look the effectiveness of drugs, help understand if there might be some off-label uses, and help drugs like Avastin succeed in their selected market and others that might also work. Of course, I’m now going to see how this deregulation can be avoided with better data analysis.

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Links of note/Science

Predicting a Human Gut Microbiota’s Response to Diet in Gnotobiotic Mice

Posted on by charlie

“A model community of 10 sequenced human gut bacteria was introduced into gnotobiotic mice, and changes in species abundance and microbial gene expression were measured in response to randomized perturbations of four defined ingredients in the host diet. From the responses, we developed a statistical model that predicted over 60% of the variation in species abundance evoked by diet perturbations, and we were able to identify which factors in the diet best explained changes seen for each community member. The approach is generally applicable, as shown by a follow-up study involving diets containing various mixtures of pureed human baby foods.”

Another great report I can’t read at the moment (no subscription). This sounds like a nice analysis of something everyone has been seeing. Looking to see effect of other diets, beyond the baby food tested.

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Innovation/Links of note/Science

DARPA to Offer $30 Million to Jump-Start Cellular Factories – ScienceInsider

Posted on by charlie

“Approved barely a month ago, the $30 million Living Foundries program should be sending out a request for proposals in the next few weeks and making awards several months from now. With its investment, over the next 3 years DARPA will support academic and corporate researchers for developing and applying an engineering framework to biology for biomanufacturing.”

Here’s a nice summary of the DARPA announcement made at the synthbio conference a few weeks back. Good to see the government funding agencies starting to pick up interest in synthbio and the practical uses of synthbio. The next 5 years should be quite interesting for those who are already doing synth bio. Also, big investments like this will get lots of students and post-docs flocking to synthbio, with a strong impact in 5-10 years. Yup. It’s gonna be great.

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Links of note/Science

anti-mega at Interesting 2011

Posted on by charlie

“The nature of the day was participatory, so instead of doing a presentation on stage (as I did at Interesting 2007), this time I attempted to get all 200ish people in the room trying, making and tasting things. By-the-by, this is also one of the hardest things I’ve done in years – scaling to 200 people took an awful amount of thinking and prep. Apologies if I’ve seemed scatty in the last few weeks.”

Always something fun and interesting from this guy. He’s a practical microbiologist too!

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