A massive comfort : Nature : Nature Publishing Group

“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…

Fuel From Waste? – ScienceNOW

“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…

Pause for station identification

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

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

“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…

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

“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…

Bacterial physiology: Bacteria get old : Nature Reviews Microbiology

“A new study using data from earlier work that had generated conflicting results now reveals that bacteria do indeed age, but aging and rejuvenation occur simultaneously. Aging appears to be related to inheritance of the old pole.”

Seems interesting to think of bacteria aging. But aging is not really about the decay of normal systems over time through accumulated damage. Is it not? Would be nice to have read through this paper. Will need to seek out this CLOSED ACCESS journal article.

Read this article…

Viral infection: The gut microbiota: friend or foe? : Nature Reviews Microbiology

“We normally think of the gut microbiota as the ‘friendly’ bacteria that carry out many beneficial functions, including protecting us from infection. But two studies now identify a different side to the gut microbiota, showing that it can actually facilitate viral infection and promote transmission.”

Another interesting review that is in a CLOSED ACCESS paper. The barrier to casual reading is too high.

Read this article…

Microbiology puts food on the table : Nature Reviews Microbiology

“During the upcoming holidays, many events will involve traditional foods, such as turkey at Thanksgiving and Christmas. That microorganisms can spoil any of these foods, and thereby the entire party, is well known, but perhaps less obvious is the fact that microbiological processes are involved in the production of nearly all types of food. … As made clear by the recent Position statement on food security and safety … microbiologists can have a pivotal role in this important field. The position statement outlines nine research themes through which microbiologists can participate in food safety and security, including the investigation of microorganisms that cause food poisoning or kill crops and livestock, as well as research into the ways in which microorganisms can improve food production.”

Interesting overview of the impact of microorganisms in food production and safety.

Read this article…

PLoS Pathogens: Microbial Spy Games and Host Response: Roles of a Pseudomonas aeruginosa Small Molecule in Communication with Other Species

“In their constant battles with competitors and the host immune system, (opportunistic) microbial pathogens have developed sophisticated cell–cell communication systems termed quorum sensing (QS) that allow exchange of critical information. In return, competing microbes, as well as the host immune system, have developed means to intercept and decode these messages. The information obtained by this molecular espionage is used for their benefit, either to win the war (microbe against microbe), or to prepare for an upcoming battle (microbe against immune system).”

Not surprising, but quite fascinating.

Read this article…

Research at Janelia: Life on the farm : Nature News & Comment

“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…