Links of note/Strategy/The Narrative

University of Massachusetts Amherst creates 12,000 square foot food garden — City Farmer News

Posted on by charlie

“The story of a group of University of Massachusetts students who set out to initiate the construction of the school’s first permaculture garden a year ago is a remarkable one, but it’s only the beginning of a worldwide movement.”

This is really interesting. Small-scale farming was killed by industrial farming to feed huge masses. But could it be that small-scale farming, like it used to be, to feed a local group, say a family or a cafeteria, is making a comeback? That would be cool.

Question: does technology and science help make us better “micro-farmers”?

Read this article…

Image of the garden from the article linked above.

Strategy/The Narrative

Trend: Probiotics, and a commentary

Posted on by charlie

When I lived in the US in the 90s, it was hard to find live-culture yogurt in supermarkets (you could find them in natural food stores, of course). The only one I could find was Stonyfield yogurt.

When I lived in Finland, not only were there a bunch of live-culture milk products, but there was one in particular “Valio A+” that was specifically recommended for women to balance their flora.

Now back in the US, it’s hard not to find live-culture yogurt, and some are specifically marketed, yes, for women to balance their flora. Furthermore, the use of live bacterial cultures for health purposes, called probiotics, has become mainstream enough that you can find probiotic supplements for children in the supermarket.

What does this mean?

It means that folks are becoming aware of functional foods, of the importance of microorganism in their diet, and that the feeding desire to find a short cut (a pill rather than eating wholesome yogurt) is always a good business.

I’ve been seeking out all these probiotic products to get an idea of what’s out there, what the message is, and, for me, always on the look out for practical use of microbes, I’ve been trying to understand what microorganisms are in fashion.

OK, so the science behind probiotics is still in progress, so I will not go into that right now.

But, going on the premise that yogurt is the gold standard for beneficial live (with microorganisms) food, then my standard for all probiotic products used for digestive health is Stonyfield’s yogurt. Stonyfield’s has 6 bacteria (S thermophilus, L bulgaricus, L acidophilus, Bifidus, L casei, and L rhamnosus). I’d say that most of the products I have seen have one or more of these bugs. There are some proprietary sub-species and I’ve been pleased to see a few products with S salivarius or some other bacteria.

For me, the type, variety, and number of bacteria in a probiotic food or supplement is key. And I think it’s just snake oil if the product only has one bug.

Nonetheless, I think as probiotics go mainstream, buyers will be more astute as to what they are looking for. Also, I hope that new applications show up, beyond gut and vaginal flora health (I can think of a few).

What I do know, is that doctors are starting to suggest probiotics to patients on antibiotics or with digestive issues such as colitis or C diff.*

And that’s great.

Do you eat probiotic foods or take supplements? Send me pics of the ones you see or take! I could/should create a database of products and attach reviews or commentary. Hm…. not another project….

*Ego boost: A gastroenterologist aked me recently what probiotics I recommended. Ha! My first probiotic consulting gig?

Innovation/Science/Strategy/The Narrative

Fortify your poop – Transfaunation

Posted on by charlie

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!)

Innovation/Links of note/Science

Domestic-use in-vessel composters – really cool

Posted on by charlie

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

 

Innovation/Links of note/Science/The Narrative

Health benefits and health claims of probiotics: bridging science and marketing – BJN

Posted on by charlie

“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…

Links of note/The Narrative

A massive comfort : Nature : Nature Publishing Group

Posted on by charlie

“Widely described as the point of no return, the event horizon of SgrA* would be the largest in our skies, but still just 30 microarcseconds across — the apparent size of a tennis ball on the Moon when viewed from Earth. To capture its image would be a stunning technical achievement in itself, but it would also open the door to further studies of how black holes spin and gather material, as well as probing some fundamental aspects of space-time and general relativity. And the first picture taken of our local supermassive black hole — the most enigmatic and charismatic of all the wonders of the Universe — would surely be one of the defining images of the time. It might even knock everyday trouble and strife from the front pages, and perhaps even, for a while, from people’s minds.”

Cool.

Read this article…

Innovation/Links of note/Science/Strategy

Fuel From Waste? – ScienceNOW

Posted on by charlie

“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…

Announcements

Pause for station identification

Posted on by charlie

I seem to be overdue for a station identification. And, all the more urgent, as I was recently mentioned in an article in the NYT (why, oh, why do I always miss these traffic spikes?).

So, hello, all of you who still stick around here to read my ramblings. And, hello, to all of you who wonder who the heck Charlie Schick is and how did he manage to get his name in the NYT?

Practical microbiology (and then some)
My name is Charlie Schick. I am Director of Marketing, for Big Data and Warehousing products at IBM. My focus is Healthcare and Life Sciences (I have a PhD, by the way). I thoroughly enjoy this job, as it allows me to talk science and healthcare, while working for an amazing tech leader.

Prior to that I was at Children’s Hospital Boston (as fundraiser and as scientist and faculty – though roles separated by a decade), and Nokia (total hack in marketing and product management). If you’re interested in knowing more of my tenure at those two places, feel free to invite me to lunch or beer.

Thinking rather than doing
Throughout my life, I have dabbled in many things – building things from bio-molecules to web publications to communities. I am always happy to get deep into the tech (bio or otherwise) and get my hands dirty and tinker. In the past few years, I’ve returned to my first love – biology – and have been studying the practical uses of microbiology, such as probiotics, functional foods, physiology, and the like (just see the things I’ve been posting and commenting on here on this site and on Twitter).

Alas, I have a wide range of interests (see my About page) and I have a very active family, so I’m more of a thinker than a doer. I suppose one day I’ll find the right doer for my thinking and we’ll have a blast. Until then, I’ll keep writing (I managed to complete NaNoWriMo last year) and fermenting foods.

As I said before, if you want to learn more, I’m in the Boston area and always welcome a free beer.

Where does DIYbio come in?
I’m more of a lurker and booster. That’s all. Attended a few meetings, really haven’t used the wetspace yet (it’s 30 miles from home). But I provide input where I can and let everyone know all the great stuff going on. For example, Happy Birthday Genspace!

DIYbio also gives me an excuse to talk bio with enthusiasts. How great is that?

Do you DIYbio? Have you ever DIYbio?

And of course, my standard disclaimer (riffing off of Cringley)
Everything I write here on this site is an expression of my own opinions, NOT of my employer, IBM. If these were the opinions of IBM, the site would be called ‘IBM something’ and, for sure, the writing and design would be much more professional. Likewise, I am an intensely trained professional writer :-P, so don’t expect to find any confidential secret corporate mumbo-jumbo being revealed here. Everything I write here is public info or readily found via any decent search engine or easily deduced by someone who has an understanding of the industry.

On the flip side, this is my personal site. Please don’t flood me with ideas that you think IBM might be interested in. There are other channels for such biz dev, and this site is not part of them.

Image from Rising Damp

Links of note/Science/Strategy

Ecology drives a global network of gene exchange connecting the human microbiome : Nature : Nature Publishing Group

Posted on by charlie

“Horizontal gene transfer — the exchange of genetic material between different species or lineages — is an important factor in bacterial evolution. A study of human microbiome data comprising more than 2,000 full bacterial genomes shows that this environment is a hotbed of horizontal gene transfer: pairs of bacteria isolated from the human body are 25-fold more likely to share transferred DNA than pairs from other environments. Thus microbial ecology — rather than phylogeny or geography — is the most important driver of the patterns of horizontal gene exchange. Further analysis revealed 42 unique antibiotic-resistance genes that had been transferred between human and agricultural isolates, and 43 transfers across national borders.”

This paper sets me spinning due to it being about microbes, microbes on humans, human microbial ecology, and horizontal gene transfer. The other thing that is intriguing about this paper is the mention of unique antibiotic-resistance genes.

Read this article…

Innovation/Links of note/Science/Strategy

The quest for the $500 home molecular biology laboratory >> Medical Laboratory Observer December 2011

Posted on by charlie

“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…