My body is my thesis: The 2009 AAAS Science Dance Contest

The 2009 AAAS Science Dance Contest is for hidden artists disguised as scientists, nerds and shameless self promoters who are tempted to dance their PhDs, upload it to YouTube and enjoy microcelebrity. A real thesis live, non-profit but for fun and a one and only chance to make a fool out of you.

This is a perfect match for John Bohannon, The Gonzo Scientist (whom I introduced you back in 2007) who is an organizer, chronicler and participator of the contest and I must say I liked the rather-theatrical-performance-than-simple-dance version of his thesis, entitled The role of the WSS operon in the adaptive evolution of experimental populations of Pseudomonas flurescens SBW25 (here).

But what to think of the performance of a professor with a thesis title: “Analysis of thymic nurse cells in the chicken”? Artist, nerd, self promoter, did I miss something?

Here are the details of how to enter the contest and don’t miss to read about the prizes too (guests at the 2009 AAAS Annual Meeting in Chicago):

The contest is open to anyone who has (or is pursuing) a Ph.D. in any scientific field, Continue reading

PITTCON, 2008: bioDIY questions, RFVials, and Science’s new web hirings

pittconchildAs a local New Orleans face (my colleagues just call me Mitoman in the lab) I had the chance to just simply walk into the grandiose PITTCON exhibiton at the Ernest N Morial Convention Center and I liked it. In addition to getting answers to some strictly lab related questions concerning filters and fuges (nevermind), I satisfied my 2 major side interests: the older bioDIY and the brand new RFID.

1. I surprised every biotech vendor - some of them laughed, others were meditating a bit - with the question: ok, but what is the cheapest gadget you have for somebody who wants to set up his basic DNA private lab at his backyard?

In my coming series to help launch a grassroots biotech DIY movement I’ll put together concrete suggestions on what to buy, but according to the experts:

- the price of a new benchtop centrifuge (6-8000 x g) is $800-1200, but the manufacturer is simply not interested in individual service and recycle used machines for low-throughput hobbyist end-users

- liquid nitrogen: 24 liter tank around $5000 (you can get it lower), LN itself is not that cheap but it’s worth storing your cells in a local repository bank instead, at least an expert guy told me

- a laminar hood for sterile work with cells is also around $5000, way too much for garage biofreaks, but you can still build your own out of a household air purifier

2. Have you ever thought of tracking, reidentifying your eppendorfs and tiny PCR tubes in the lab instead of the almost impossible hand marking? Well, we are not there yet, but Baytek developed an RFID kit for glass GC or HPLC vials. Continue reading

The conditions of a mass biotech DIY movement

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The idea of doing biological experiments with current biotechnological methods and conducting research projects at home is quite new. There are already many names in use referring to the same concept: bioDIY, home biology, biotech DIY, garage biology.

We have a detailed case example which can be considered as the first registered, high profile biotech DIY activity starting the era of useful garage biology: Recently Hugh Rienhoff amplified his daughter’s DNA at home to help doctors figure out her genetic disorder. From the Nature cover article:

“So he bought a used PCR machine, a microcentrifuge, some small-volume pipettes and a brand new gel box. All told, the equipment cost him about $2,000. With these simple tools and some sequence-specific DNA primers of his own design, he could pick the relevant genes out of his daughter’s genome and amplify them enough for sequencing. Freezing the samples and packing the tiny tubes on ice, Rienhoff sent them off for sequencing at about $3.50 a pop. He prepared upwards of 200.”

Another suggested project was the How to isolate amniotic stem cells from the placenta, at home! but so far I haven’t heard of anybody who really did that at home and I only isolated the cells at the lab.

In my coming series I’d like to examine the following conditions of a mass biotech DIY movement: acquiring skills, affordable kits, tools, hardware, motivations, business opportunities and impact.

acquiring the how to skills:

- good education tools, protocols, videos, howto-s on the web

- short intensive academic or industrial lab courses available for every citizen

- self-education in community: forming Homebrew Biotech Clubs

available, affordable tools, hardware:

- cheap kits: based on the Rienhoff example, a very basic home lab can be set up out of 2-3000 dollars, which is the price of a good laptop.

says Mr. Rienhoff in an email: I bought all the equipment used from a local vendor who buys equipment at auction and from universities. All the gear is at least ten years old so it was very used and low throughput. But given that my project was incredibly focused I did not need the more sophisticated equipment.

- used equipment network: Continue reading

Biotechies at O’Reilly ETech, March 3 – 6, San Diego

The O’Reilly Emerging Technology Conference (ETech) is on and this year they had a growing number of biotech related sessions. Fellow SciFoo Campers like Hugh Rienhoff and Timo Hannay, Makers like Phil Torrone and Limor Fried, Brain Hackers like Ed Boyden are visiting and many more.

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Bubble City’s South Park: geek tourism

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Finally back from my Bay Area trip, the workshop I participated turned out to be very stimulating in terms of people and ideas. Also visiting The Blood Knot performance at the American Conservatory Theater and having a drink with Monya&Dan were absolutely delightful. I missed my flight on Saturday, so I slept in LA (and missed my wife) and discovered the city to the amount of a Taco Bell dinner near to the La Quinta Hotel. Also I did a little geek tourism and visited the South Park area in San Francisco (but forgot to check the Wired headquarters) which was so nicely described in Aaron Swartz‘s unfortunately unfinished (but not unfinishable) Bubble city:

Downtown San Francisco is a world of carefully-gridded streets and looming skyscrapers, but hidden behind a gas station on Third is a place that almost looks like another world. The sun shines brightly upon a park with green grass and tall shady trees and vibrant swings with children. The park is an oval and the perimeter is lined with small, pastel-colored buildings. Here and there are a smattering of small cafes and restaurants. And the other buildings are filled with startups. Twitter here. Adaptive Path there. Even Yahoo, when it wanted to encourage its employees to be more startup-y, opened up an office in the neighborhood. Sit on the grass and chances are you’ll sit near a friend from another company or bump into them in line at a cafe. The place crawls with companies and back on the street, surveying the scene with a distant but watchful eye, lie the journalists, whose publications cover with awe the rumblings of those below. It was here that Newsflip made its home.

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The Spittoon: the eminent corporate blog of 23andMe and Consumer Enabled Research

ceramicspittoonpictureThe personal genomics service 23andMe just launched publicly a corporate blog called The Spittoon that has been internally up for a few weeks. It is a new chapter in biotech corporate blogging. Just like the web page of 23andMe, The Spittoon’s WordPress blog platform, the concept and design is excellent: amongst others you can find scientific blog posts written by Matt Crenson science writer and posts written by founders Linda Avey and Anne Wojcicki in the name of radical transparency. As Wired fellow Clive Thompson wrote:

Radical forms of transparency are now the norm at startups – and even some Fortune 500 companies. It is a strange and abrupt reversal of corporate values. Not long ago, the only public statements a company ever made were professionally written press releases and the rare, stage-managed speech by the CEO. Now firms spill information in torrents, posting internal memos and strategy goals, letting everyone from the top dog to shop-floor workers blog publicly about what their firm is doing right – and wrong. Jonathan Schwartz, the CEO of Sun Microsystems, dishes company dirt and apologizes to startups he’s accidentally screwed. Venture capitalists now demand that CEOs be fluent in blogspeak.

Radical transparency could be standard in the case of Silicon Valley tech startups but in the Biotech Industry the standards are light years away from that. For instance the 23andMe research team communicates publicly on the biparental inheritance of mitochondrial DNA which is a sensitive issue concerning their genealogy service. The reason why Spittoon is so web-friendly and uptodate and is in fact a paradigm corporate blog for every other biotech company in the future is its web-based business model and Google-like corporate culture thanks to its networking background.

For instance, Anne Wojcicki co-founder introduces the concept of Consumer Enabled Research in her introductory blog post The Power of We:

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Our goal at 23andMe is to enable individuals to form communities around shared interests and to empower those communities to be actively involved with research. We call it Consumer Enabled Research. We don’t just want communities to have a voice, we want to provide a platform for them to collectively aggregate their genetic information. One of the significant bottlenecks in research is the lack of data. Researchers and physicians rarely have enough of it to really understand a disease or how to treat it. Our goal is to change that.

After registration readers can make comments and I strongly hope that the comment system will not be shut down (just like in the past at BoingBoing), but for that commenters should be on-topic and moderate. I’ve just commented Wojcicki’s post, but I’d like to share it with you here too: Continue reading

Working without a personal assistant on the top of the big G…is fun!

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I’m on my way to a Friday comprehensive exam from stem cell and mitochondrial biology which gives me no time to immerse into blogging this week. I mostly think of big holes in my knowledge like mitochondria and Ca2+ signalling. That’s why I can only offer soft things like the following quote from a fresh New Yorker article by Ken Auletta called The Search Party on Google:

Continue reading