“Seeking to spur drug development, Stephen Friend has launched a daring series of initiatives to make biomedical research more open and effective.”
Interesting fellow. He’s a mover and shaker in the bioinformatics “data must be free” crowd. It’s a very good article. Read it.
“With new sequencing centers in Europe and the United States, BGI hopes its growing clout will help deliver the benefits promised by genomics—and revenue to pay off a mounting debt.”
Genomics at a scale only China could do.
Oh, my.
As a card carrying practical microbiologist, I like making yogurt – cheap and easy to make and very good for your tummy (see here for more on yogurt and a recipe you can use). But I admit I’m not too adventurous: the most I do is try different cultures, flavors, or milks (latest was goat milk).
Furthermore, having spent a lot of time in the lab, I am just not ready to ingest bugs that have been modified through molecular biology, no matter how harmless the transformation – it’s just deeply ingrained in me from years in the lab.
That doesn’t hold back these adventurers. A while back, Meredith Patterson was working on making a yogurt bug that would detect malamine in the milk. Melamine was that nasty chemical Chinese milk producers were using to up their protein readings.
More recently, Cathal Garvey and Tuur Van Balen, two fellas who are not shy about being adventurous, revisit the topic. Of course, hacking yogurt bugs to produce helpful chemicals (Tuur suggests Prozac) would turn yogurt into an even better functional food.
From Cathal Garvey:
“There is a common conceit among we DIYbio enthusiasts, namely to suggest that one could opt to create “glow-in-the-dark yoghurt” using DIYbio-oriented techniques as a nigh trivial matter. Indeed, this conceit led to my recently being queried by twitter and email about the possibility; where are the guides and how-tos, if it is so trivial? While a conceit it may be to suggest that glow-in-the-dark yoghurt would be trivial, that’s not to say it’s at all out of reach to the dedicated biohacker. Here, I will lay out a suggested course of action based on the available literature.”
Check out his protocol for modifying S thermophilus.
Tuur on the other hand, went so far as to actually going to the parts registry, synthesizing some DNA, and transforming L delbruekii (link via Cathal, of course).
Check out the video for Tuur’s demo:
What kinds of things would you want in your yogurt? Would you eat GM bugs? What do you think of all this?
Image from fred_v
“The Earth Microbiome Project (EMP) is the most ambitious attempt to provide a systematic characterization of the microbial world that dominates this planet. The ecosystem services provided by microbes in every environment (including the human body) are fundamental to the survival of life on this planet and the continued economic and physical health of the human race. The pilot study of the EMP started in March 2011 and is now reaching its zenith.”
This session has four interesting talks on handling the data deluge, a field guide, why we should care, and mathematical modeling. Cool. Can’t wait for the speaker notes and the like.
“A mouthwash that kills S. mutans and leaves the rest of the bacteria to take over S. mutans‘s real estate could spell the end of cavities. In a small clinical study last year, one team found that one application of the mouthwash knocked down S. mutans levels, and that harmless bacteria grew back in its place. If the mouthwash pans out, it could join the ranks of an emerging new type of treatment: better living through hacking the microbiome.”
This is really cool. And this article get extra points for the endnotes on probiotics and fecal transplants.
I totally believe we are entering an age where we are going to manipulate our microbiome for health and medicine.
[via @edyong209]“The Original EcoSphere® is the world’s first totally enclosed ecosystem – a complete, self-contained and self-sustaining miniature world encased in glass. Be wary of inferior and lower quality imitations. Easy to care for, an EcoSphere is an incredible learning tool that can provide powerful insights about life on our own planet… and provide a glimpse of technology that’s shaping the future of space exploration.”
So cool. Will have to get one some day. [via @curisma]
An Analysis of the Existing Regulatory Framework and Recommendations for Alternative Frameworks
A team of researchers at the University of Maryland Baltimore is studying federal regulation of probiotics under a grant from NIH’s Human Microbiome Project (HMP). A portion of HMP funds were set aside to study the Ethical, Legal, and Social Implications (often referred to as the ELSI issues) of the Project’s scientific goals. The probiotics project is an interdisciplinary collaboration between faculty members from the University of Maryland Schools of Law, Pharmacy and Medicine.
This site is chock-full of info on probiotics policy, regulations, and science. Really good stuff.
“Artificial two-dimensional biological habitats were prepared from porous polymer layers and inoculated with the fungus Penicillium roqueforti to provide a living material. Such composites of classical industrial ingredients and living microorganisms can provide a novel form of functional or smart materials with capability for evolutionary adaptation. We demonstrated a design of such living materials and showed both active (eating) and waiting (dormant, hibernation) states with additional recovery for reinitiation of a new active state by observing the metabolic activity over two full nutrition cycles of the living material (active, hibernation, reactivation). This novel class of living materials can be expected to provide nonclassical solutions in consumer goods such as packaging, indoor surfaces, and in biotechnology.”
Hm. Some really practical uses of microbes – impregnating fabrics to provide bioactive activity.
A bit of history:
I experienced a huge brain- and world-expanding time during my Nokia Lifeblog years (2004-05). Early on, we paired up with Six Apart (via Marko Ahtisaari and Joi Ito), and I spent a lot of time under Loïc LeMeur’s wing promoting blogging, Six Apart, and Lifeblog, and meeting some of the key movers in the nascent Web 2.0 (thank you, Loïc).
In those days, I pushed for the fusion of web and mobile, started seeing how everything was coming in as streams, and how people started exuding their own lifestreams. The next logical idea was how to bring that together.
In 2006, the poster child was NetVibes. But I though we could do better. Some started talking about personal aggregators, Digital Lifestyle Aggregators, the widgetization of everything.
Morsels:
For me, the sweetspot was to be the one holding all the morsels (He who hold the morsels, holds the experience. “The structure holding the morsels becomes the experience” – Fabio Sergio), a dynamic dashboard where all my social streams come in, where I could mix and match, and then send all the things of note out back into the streams.
This was my original vision of what should have become Ovi.com. Alas, I could point to so many places where the harpoon was sunk and twisted into me (and into those who stayed on), but I had been given a huge wad of cash to do it, and I f-ed it up by not channeling my inner-Jobs and insisting we stay true to vision.
Lesson learned. Enough self-pitying. I had my chance and blew it.
In the time since, I have seen attempts to create similar services, and even some blatant suggestions from some great thinkers as to what was missing in this age of lifestreams (which I thought would be in 2008). But nothing really took hold (though I think Seesmic desktop shows promise).
Bottlenose:
And, lo, on comes a new service. And from a brilliant semantic web guy with a track record of actually coming out with things that I thought approached what I wanted to see.
“Bottlenose is a new social media dashboard for influencers of all stripes. But it’s not just for posting and reading; it helps you filter and manage your networks with semantics and machine learning. It’s all Web-based, written in HTML 5 and Javascript. It does the data crunching on the browser side (for the non-pro users), so you get native performance behind these major operations reading and parsing your stream.”
Read this article from Read Write Web
I signed up and have been checking it out. Of course, I’m sure this is better than whatever I would have built in 2007, given how the Web and mobile world have changed since then. I think one issue that could come to bite is any deviation from the usual UI folks are accustomed to for scanning info and streams. The weirder, the less likely someone will use it without feeling geeky.
In any case, I’m excited to play with it. If you check it out, let me know what you think of it.
One more thing:
I’ve also evolved my thinking since 2007 and think Bottlenose should be a P2P system. Take back the Cloud!
Image from the Read Write article on Bottlenose.
“Now, a new study by Eric Martens, David Bolam, and colleagues has looked into how a pair of the most common species of gut bacteria metabolize polysaccharides, showing that each bacterium is highly specialized. Using a high-throughput system for feeding the bacteria dozens of kinds of carbohydrates, one at a time, and tracking the bacteria’s gene expression, they were able to see how these microbes have tailored themselves to fill specific niches in the gut.”
This is a really good study. For me, a better understanding of the gut metabolic ecology will allow for the development of better probiotics. One interesting finding in this study is that some bug don’t grow well on simple sugar because their sensors are built for complex sugars. Made me think of folks in developed world and what effect eating more simple sugars (high-fructose corn syrup) has on gut flora and any consequential obesity.