“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]
Read this article…
“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.
Read this article…
 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.
 As you know, I’m always looking for practical uses of microbes. One that I stumbled upon a long while back was “transfaunation”, or, seeding one person’s gut with microbes from another’s. Yes, transfering poop microbes from one to another.
Be an adult. Don’t get grossed out. I’ve read some great papers on the process how our guts get colonized after birth. Also, there are some really interesting papers on how our gut microbes (or lack thereof) are involved in various intestinal disorders. And there are some promising papers on how diet affect the bacterial ecology in the gut. [Sorry, I'll link to the papers in a larger gut related set of posts at some point in the future - you can also just search for gut and microbes in my posts.]
Here’s the basic idea. People suffering from the hardy C. diff bacteria are generally prescribed a powerful antibiotic. Problem is, the drugs don’t just kill the invaders; they also wipe out much of the beneficial bacteria in the gut. With these “good” microorganisms out of the way, any C. diff stragglers have a much easier time regrouping for a second bout of illness. If there were some way to respawn the beneficial bacteria in the intestines, such re-infections could be warded off. Some people, like Ruth, turn to expensive probiotic supplements. (At one point she was spending $350 on them every week.) But in certain cases, a patient who has lost nearly all of her good bacteria will find it nearly impossible to get them back. A fecal transplant seems to work as a sort of mega-probiotic, allowing doctors to repopulate a patient’s intestines with the appropriate microorganisms by placing a robust sample directly into her gut.
Slate had a nice article on the subject (quoted above). It’s a serious subject and for many, the only hope to get a better and healthier bacterial gut fauna (hence the term, transfaunation).
My wife’s a vet and she’s not only heard of this procedure, but performed it on animals. It’s not uncommon to jumpstart an animal’s ability to digest grass by grabbing bugs from one animal and putting it in the right place. And, did you know, some animals eat poop on purpose for this very reason – rabbits, capibaras, hamsters, elephants, termites, pandas, koalas, and hippos – to colonize their gut?
And really, folks eat yogurt to populate their gut with good bacteria. Why not poo bacteria as probiotics? I actually think, as we learn more about our gut fauna, this will be come a more accepted course of action for folks with nasty bowel infections, colitis, or inflammatory bowel diseases.
What do you think?
Image of Kristen Paulson’s Anatomy and Guts Embroidery Hoop Art on Etsy (get your own!)
 I stumbled upon domestic-use in-vessel composters (on a lead from @harvestpower, of course).
I had heard of in-vessel composting, but never realized that at least two companies created machines that you plug in, feed with your organic waste (with addition of saw dust), and out comes compost.
As far as I can tell, the process is very fast, so it’s immature compost (composting has a final curing step). But I’m sure the raw stuff that comes out of these machines is pretty good. And to me, one could use this machine for the first step and have a larger separate bin for the curing step.
The two are:
- NatureMill Automatic Compost Bin is from San Francisco (it’s the silver box in the pic on right*)
- And GreenGood are the North American distributors of the Oklin (Korea) in-vessel composter. The interesting thing about the Oklin composters is that they use a special thermophile (called “acidulo” bacteria).
I am so tempted to buy one. Maybe the manufacturers could “lend” me a machine for review and comparisons (hint hint)?
Alas, my wife suggested I build one myself. Gah. Not happening soon.
Image from Nature Mill
*The picture cracks me up. It’s such a Euro-couple. And she’s smiling at him as he dumps an almost full plate of food in the bin. Perhaps it was some bad cooking? Only, whose – his or hers? Sheesh.
“Health claims for probiotics are evaluated by the Panel on Dietetic Products, Nutrition and Allergies of the European Food Safety Authority. Despite a substantial amount of basic and clinical research on the beneficial effects of probiotics, all of the evaluated claim applications thus far have received a negative opinion. With the restrictions on the use of clinical endpoints, validated biomarkers for gut health and immune health in relation to reduction in disease risk are needed. Clear-cut criteria for design as well as evaluation of future studies are needed. An open dialogue between basic and clinical scientists, regulatory authorities, food and nutrition industry, and consumers could bridge the gap between science and marketing of probiotics.”
Not sure what to make of this other than the comment that ‘clear-cut criteria’ will be needed to actually turn claims into science.
Read this article…
“A team led by Jay Keasling, a bioengineer at the Joint BioEnergy Institute in Emeryville, California, worked to extend the strategy to make more commonly used fuels. They used Escherichia coli, a bacterium into which it’s relatively easy to insert new genes. They started by creating two strains of E. coli, inserting genes for breaking down cellulose in one and genes for breaking down hemicellulose in the other. They then split each of these two strains into three groups and to each group added genes for one of three different metabolic pathways that allow the microbes to make chemical precursors for either gasoline, diesel, or jet fuel.”
Nice step towards making this happen.
Read this article…
“Molecular diagnostics and molecular biology in general are becoming more pervasive every day in a range of applications but are still seen by many as being an arcane science. Many undergraduate science curricula cover only the basics of theoretical components without exposure to laboratory practice, due to perceived cost and complexity of laboratory facilities needed. With this in mind, I recently set out on a quest to see whether a non-specialist, $500 complete molecular biology laboratory was possible.”
Hm. Quite interesting. Sure got me searching on eBay for some stuff. Quite amazing.
Read this article…
“But what happens next? Can Janelia Farm do ‘great science’ during the next 5 to 10 years? Will it pass Rubin’s deletion test? Can it rewrite the introductory biology texts (Cech’s favourite definition of great science), or foster “a couple of programmes that create a whole new direction” (Tjian’s favourite)? That is the great unanswerable question. As Simpson says, “you can’t engineer great science. You just have to create the conditions that make it possible, and see what happens.””
Great overview of the current state of HHMI’s experiment in cross-disciplinary collaboration. I say, step back and let it happen. Heck, it’s only been five years.
But also, 1) don’t measure it against traditional measures; 2) serve a an inspiration, if not model, for other privately (foundation) funded institutes. The government is at its limit and we’re all fretting. We need new funding models. The HHMI and Jenelia is one.
Read this article…
“In summary, the Tara Oceans project leverages powerful new technologies and analytical tools to develop the first planetary-scale data collection effort that links biogeography with ecology, genetics, and morphology. Guided by the cross-disciplinary philosophy the pay-offs can be immense, considering the massive number of samples and data that have been collected, archived, and interconnected for scientific study, only half-way through the expedition. A lesson from this project is that, when it comes to addressing broad and complex issues of general interest to mankind, competition between scientists may not be the best model. The Tara Oceans project is a pioneering enterprise towards a truly worldwide, systems-level characterization of the largest and most fundamental ecosystem on our planet.”
Cool. In my current job, we spend a lot of time talking to people who are combining huge and disparate sources of data and correlating, analyzing, and exploring the connections. Now, I see this happening everywhere. While the 80s-00s could be the Information Age, I’d like to call the new age we are entering the Age of Data (or something like that – it’s all about Data Analysis, innit?)
Read this article…
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