Links of note/Science

Probiotics In Future May Be Prescribed For Your Neurological Well-Being – Medical News Today

Posted on by charlie

“The study was led by Professor Mark Lyte and has been published recently in BioEssays. The researchers have proposed that neuroactive compounds if delivered via neurochemical-producing probiotics could help improve a host’s gastrointestinal and psychological health. These probiotics could be prepared for delivery of the compound using a unifying process of microbial endocrinology.”This paper proposes a new field of microbial endocrinology, where microbiology meets neuroscience,” said Lyte.”

I’ve seen a few papers talking about immunoregulation by gut bacteria. Here’s a report on neuroregulation. Pretty cool.

[via @microbeworld]

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Innovation/Links of note/Science/Strategy

Open access comes of age : Nature News

Posted on by charlie

“A study of open-access publishing — published last week in the open-access journal PLoS ONE — has found that the number of papers in freely accessible journals is growing at a steady 20% per year (M. Laakso et al. PLoS ONE 6, e20961; 2011). To many, the growth confirms the health of the free-access, author-pays model. But to a few it is a discouraging sign that open access is not about to take over the world of scholarly publishing.”

This is heartening, and I suppose 20 years is not enough to change a model that is 400 years old. Nonetheless, I saw one figure that 30% of all published science is freely available and open access. Not bad. Especially where there is some good stuff out there. PLoS has been kicking butt, and Nature and some other big groups are starting to step up as well. Let’s see how it goes!

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Links of note/Science

Navy probe descends on bacteria power | SmartPlanet

Posted on by charlie

“The U.S. Navy has enlisted some very tiny sailors to fuel their latest research vessel. Microorganisms are descending into the sea, enabling unmanned pods to gather data beneath the surface. Weeks later, (perhaps even years researchers say), the craft could emerge via power it had generated on board. No batteries required—just bacteria.”

This is cool.

[via @microbeworld]

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Links of note/Science/Strategy/The Narrative

Three Biomedical Funders to Launch Open Access Journal – ScienceInsider

Posted on by charlie

“Three heavyweight, nongovernmental funders of science announced today that they are launching a free online biology journal aimed at publishing the very best papers within a few weeks of submission. But few confirmed details are available about the journal, which doesn’t yet have a name, editor, publisher, or business model.”

These are big organizations, backing an old, but still small, area of science publishing. The good thing is that these organizations bring yet another business model for open access publication, and they have the funds to be patient before the venture funds itself.

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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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