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"The electric eel inspires a new type of battery"
10 November 2009
08 November 2009
DIYbio at iGEM 2009
It was nice to see the easy flow of ideas and decisions. As with iGEM, this group is in a very early stage. But already some things are becoming clear as to what it's going to take to keep growing.
One more thing (and I might be inviting a flame war): there is clearly some friction between the iGEM folks and the DIYbio folks. Part of this resides in prejudices towards amateur biologists (unfounded), part in worries about safety (well founded), part in the small difference in culture.
DIY home base
One of the things that happened is that iGEM required teams to be affiliated with an institution. That was a way to ensure safety concerns (indeed, the FBI was a sponsor of the Jamboree, go figure). Independently, the DIYbio groups in Boston and NYC (and I) realized that, while it would be nice to actually do kitchen biology, groups need some sort of entity with which they can buy supplies, teach safety and techniques, and, of course, enter into iGEM.
I'm all for it. In the past months, reading and following and talking to DIYbio folks, my thoughts on hack-spaces has evolved to include more than just a bench, but also seminars, safety certification, mini-grants, and even a store (check out Pearl Biotech).
I was also glad to finally meet Mac, one of the leaders in DIYbio. He's recently purchased a lab trailer, full of equipment. He's now looking for space (too bad my ample backyard is so far from town). His goal is to build this out as a hack-space, also hoping to mix novice and experience biologists, to get some culture and skills transfer.
That's super. I look forward to getting more involved. Mac has a ton of projects in mind and could use some help. And I want to learn from the DIYbio NYC folks who recently formed a non-profit and are acquiring space so that they can get out of their living rooms and get a nice space to play around in.
This is going to be fun.
And here's a video of the folks at the meeting:
07 November 2009
06 November 2009
05 November 2009
Report on iGEM 09, from a newbie
This iGEM was my first. I'd read about it, talked about it, but this is the first time I've been immersed in it.
OK, so I wasn't part of a team, so I told folks I was a "lurker." That was out of the ordinary, since most folks were either staff, team members, or volunteers (which is what I should have done to save the registration fees - maybe).
Clever little undergrads
I'm not going to go into details as to how the teams got to the Jamboree. Suffice it to say that anyone who wanted to come, came; also, the teams were undergraduates who thought long and hard on what they would build and then built everything over the summer.
I was impressed with the creativity the teams showed. There was light-induced vanillin production (for the aroma), electrically-induced light production (creating pixels - see video below), various detectors (for toxic metals and mines), and inducible pigment production (to free us of the boring tyranny of all the usual fluorescent reporter proteins).
While some might call for something applied to come out of all this, I am content to see the participant's enthusiasm; their learning of how to solve problems, think, and communicate results; the multi-disciplinary nature of teams, mixing engineers, biologist, sociologist, designers, mathematicians, physicists, artists, and programmers; and the gathering of like spirits to exchange information and dream up even more exciting things.
Keeping up with the E colis
For me, it was heaven. I had not been immersed in this field in so long. It was good to try to figure things out, talk about how decisions were made, and learn all the clever techniques and solutions folks came up with.
Of course, at the end, I started dreaming up some of my own "machines." Who knows if I might be able to build one someday.
E. chromi
I was particularly pleased with the winning team - Cambridge - for their creation of inducible pigmentation in bacteria. Through a network of connections, I had met the irrepressible Daisy Ginsberg, a designer from London who has been exploring the future world where synthetically engineered biological organisms are established and integrated into society. Daisy coined the term Kingdom Synthetica to add to the Eucarya-Bacteria-Archaea Kingdoms that we already have.
Daisy, and her partner in design-crime, James King, worked with the Cambridge team to help them explore the sociological and design aspects of what the team was building.* They got the team to think of a future that had colored bacteria and what that would mean. For example, one team talked about color-poachers killing rare wild-life for color genes; or, global battles over patenting of colors (for example, the Dutch if China were to patent Orange).
The best example of the future was colored poop, formed by these color producing bacteria detecting metabolic states and reporting it through color production, say green for an ulcer or red for vitamin deficiency (see picture). This colored poop was the sensation of the Jamboree. James and Daisy walked around with a silver valise, telling their whole story and ending with opening the valise, much to the surprise of their audience.
It was very fun.
Naming gaming
Daisy christened the Cambridge bacteria as E chromi (@echromi on Twitter). And they presented their colored poop to the MOMA in NYC, so don't be surprised if the valise ends up there.
Other teams also named their bugs, as in Essencia coli (Team KU Leuven) and GlueColi (Team ULB-Brussels).
Once again, these names just point out that this Jamboree is more than a bunch of geeks building gadgets, but a whole way of thinking and mixing and creating. This is all so embryonic and what will come out of it no one really knows. But what is sure is that mixing folks from different background in a fertile playground with no dominant player is a sure way to come up with lots of interesting things.
Now I'll go off and start building my E coliroid (hm, what might that be?).
Here are some images and video that I took at iGEM:
*One nice feature of the competition was a thorough list of judging criteria, nudging the team to do more than just building something. Most interestingly, teams were encouraged to do a sociological survey around ethics, society, and synthbio. This added non-scientists to the teams. One of the most interesting findings (as these we mostly qualitative, due to experimental design constraints) was that folks were against genetically modified organisms (GMO) in general, but were fine with GMO use in humanitarian work, such as toxic waste or mine detection.
04 November 2009
31 October 2009
30 October 2009
29 October 2009
28 October 2009
26 October 2009
Vestiges of the past in our tools: Fruit fly culture bottles
In a previous post, I discussed how we've forgotten techniques and instruments of the past. These techniques and instruments could come in handy as garage scientists try to build their labs.
In that post, I mentioned that folks keep fruit flies in plastic bottles that look like milk bottles (well, only if you know what a milk bottle looks like, otherwise, it's just another oddly-shaped bottle). In case you're wondering, the use of milk bottles goes back to the days of Thomas Hunt Morgan, the genetics genius who chose the fruit fly as a model organism. Somehow, he and his contemporaries did a ton of great science without the kits and super equipment we have today.
What do you think?
I think these vestiges are really cool and I like seeing them wherever I can (and I have a ton of stories about these vestiges).
Do you know of any more?
Image from wikipedia.
23 October 2009
Oh, what we've forgotten...
In this new era of natural philosophers (neo-natural philosophers?), where the cost of buying science kits and instruments can be an obstacle to amateur science, I keep thinking back to how science was done many years ago. What were the tools used? What were the different reagents of the day? How can this lost knowledge be applied today to circumvent barriers to modern reagent and instrument access?
I remember when I was a tech at MIT, back in the late 80s. There was an old Worthington molecular biology catalog with reagents and enzymes. For restriction enzymes, there were two: EcoRI and BamHI. Talking around the lab, our PI told me how "in the day" everyone had to purify their own restriction enzymes.
To me, that was fascinating. By the late 80s, the New England Biolabs catalog was already full of a ton of enzymes and kits. And, huh, it was so easy to sequence DNA by doing nested deletions of M13 vectors and using the kit's primers. And then you could purify plasmids with CsCl gradients and gobs of Ethidium Bromide in milligram balanced tubes and a wicked cool ultra-centrifuge.
State of the art, man!
As the junior tech in that lab at MIT, I was also responsible for keeping the fly stocks alive, transferring them on a regular basis from old bottles to new bottles. As per fruit fly science convention of the time, the flies were kept in small glass milk bottles, with cardboard plugs. I wonder how old our bottles were, but I was told that it was getting harder to find the bottles or even the cardboard plugs.
When I went over to the Whitehead to do some experiments, I saw that they all had plastic containers - in the shape of a milk bottle. It was the future, but in the image of the past. I wonder if folks today know why they still use such oddly shaped bottles to store flies in.
Straddling the past and future, that lab was a treasure trove of old stuff. I once opened a drawer at the lab and found a ton of capillary tubes with different color markings and sizes. These were actually glass micro-pipettes, calibrated and used with a mouth adapter (oh, my!), and eventually replaced by Gilsons with disposable plastic tips.
In summary, there are a ton of techniques and tools that have been knocked aside by kits and newer instruments, mostly for convenience (because I am a science history enthusiast, I have a ton of these stories). For those enterprising neo-natural philosophers, if you long for some kit or instrument, imagine back to the day when you got your hands dirty and didn't just buy your reagents. You might find some ideas how to create your own reagents and tools.
Image of pigments from hyperscholar, to remind you that "in the day" artists ground and mixed their own pigments to make paint. No kit for them!
22 October 2009
17 October 2009
My writings
- Cognections - site
Precognition, cognition, recognition - photos and writings. - Life blog - site
Thoughts and actions ranging from biomedicine, molecular manipulations, indiscriminate writing, the long now and a post-electronic age, various forms of performances thespian and corporate, and philosophizing on the fusion of Internet and mobile devices. - One night
A global story of one night in the mobile life. Written for Vodafone'sreceiver magazine. Made into a podcast, too. - chillin'
Deep thinking while up in the stratosphere. - The Depths of Thought and the Inquiry into Our Spirit
Something I wrote eons ago, wondering at the difference between humans and other animals.
