"People are trying things; kettles are exploding. Everyone’s attempting magic right and left."

February 12, 2010 8:06 PM

Do-It-Yourself Genetic Engineering at iGEM

Lab to be first 'open-source' for genetic parts - (BIOFAB)

DIYbio - DIYbio NY (and their YouTube channel) - DIY BIO 4 Beginners

Previously.

posted by brundlefly (23 comments total)

*wraps house with Saran Wrap and duct tape*
posted by ZenMasterThis at 8:12 PM on February 12, 2010

Cuba's way ahead of you.
posted by clarknova at 8:40 PM on February 12, 2010 [1 favorite]

I love underdog stories like this. Really inspiring.

I'm hoping that there will be a book in the near future about synthetic biology that reads like this article. Something like "Soul of a New Machine" or "Where Wizards Stay Up Late".
posted by hanoixan at 8:53 PM on February 12, 2010

(I was talking specifically about the NY Times iGEM story)
posted by hanoixan at 8:54 PM on February 12, 2010

Ladies and gentlemen, I give you New Superhero Ground Zero.
posted by The Whelk at 8:56 PM on February 12, 2010

missing a whatcouldpossiblygowrong tag
posted by empath at 9:31 PM on February 12, 2010 [4 favorites]

I give you New Superhero Ground Zero.

By day, Tommy Tolsen is a mild-mannered community college student -- but at night, he becomes "Glows Slightly In the Presence of Certain Environmental Toxins Man."
posted by empath at 9:34 PM on February 12, 2010 [9 favorites]

Do-It-Yourself Genetic Engineering

posted by brundlefly

Do I have to? No I don't think so.
posted by Splunge at 9:41 PM on February 12, 2010 [6 favorites]

"The team had done some more research and discovered that there are species of bacteria that already have holes in their cell membranes through which sugar passes; those bacteria all use the holes to let food in, but they could, theoretically, be made to do the reverse. It was exactly the design feature that Team City College needed to give its R. Palustris. They had already made multiple attempts to first pull that particular gene out of one bacterium and tweak it in a specific way to turn it into an easily connectable BioBrick part. Then they would try to insert that into R. Palustris."

Christ. We are now living in the future.
posted by Kraftmatic Adjustable Cheese at 10:01 PM on February 12, 2010

Something something intelligent design
posted by kcds at 5:32 AM on February 13, 2010

"With the proper ethical and scientific approach, BIOFAB’s founders say, the synthetic biology will flourish."

Well, that fills me with hope. Still missing the whatcouldpossiblygowrong tag.
posted by sneebler at 6:56 AM on February 13, 2010

clarknova: biotechnology != synthetic biology.
posted by gene_machine at 9:53 AM on February 13, 2010

hanoixan: Ahem... (please forgive the self-link).
posted by gene_machine at 9:55 AM on February 13, 2010

Sounds more like "Try to do it yourself, but fail, because you don't have access to a sterile environment"
posted by delmoi at 10:54 AM on February 13, 2010 [1 favorite]

delmoi: "Sounds more like "Try to do it yourself, but fail, because you don't have access to a sterile environment""

You're probably thinking of cell culture, which requires a "biological safety cabinet", a.k.a. a hood. Bacteria can be handled on an open bench, using aseptic technique. A Bunsen burner also helps, because the updraft from a hot object makes it harder for airborne contaminants to fall right down into your sample.
posted by d. z. wang at 12:39 PM on February 13, 2010

gene_machine: biotechnology != synthetic biology.

But synthetic biology is a major component/subset of biotechnology.
posted by porpoise at 12:44 PM on February 13, 2010

You're probably thinking of cell culture, which requires a "biological safety cabinet", a.k.a. a hood. Bacteria can be handled on an open bench, using aseptic technique. A Bunsen burner also helps, because the updraft from a hot object makes it harder for airborne contaminants to fall right down into your sample.

It might be theoretically possible, but these kids (Well, not all kids, technically) weren't able to do it. The problem is, according to article, anyway you need to pull of 50 or so steps without any contamination of the genetic material in any of the steps. Even if you can do one step with 98% probability, the chances of doing 50 steps in a row without failure drop to just 36%.

If you can pull it off one step with 95% probability, then your chances of success in 50 steps drops to 7%. And so on.
posted by delmoi at 1:53 PM on February 13, 2010

But synthetic biology is a major component/subset of biotechnology.

I wouldn't really say that, yet. I've been keeping an eye on the field since taking one of the early classes on the topic six or seven years ago. The hope is, essentially, to have a system where you can take BioBricks and use them like electrical components. Choose a promoter of strength foo, add upstream sequence bar to make sure that transcription factor baz binds. Everything quantified and easy to insert into a plasmid cassette using common restriction enzymes. But there are few parts that we actually understand in a sufficiently complete and quantitative fashion, and so things inevitably end up being more complicated - to extend the E.E. example, it's as if we have to fabricate all of our own components, instead of popping a 22 ohm resistor into a breadboard.

So, synthetic bio's definitely inspiring stuff - like the iGem research. But the stuff that shows up at iGem, as nifty as it is, provides new BioBricks but generally involves a lot of custom cloning and modification. It's providing the basis for future synthetic biology, and it's definitely focused on making new systems, but it's still using traditional bio/biotech methods. So it's only halfway there.

[Benchtop work with bacteria using aseptic technique] might be theoretically possible, but these kids (Well, not all kids, technically) weren't able to do it.

Well, judging by the NYTimes article, the team was having trouble with cloning, not with bacterial growth. Specifically, the article says: "Hunter was now working with the P.C.R. machine for hours at a time in a storage closet, the only space she could consistently find available." The journalist's descriptions make it a little difficult to tell what was going on. However, it does mention that they were trying to "copy a gene," and that they didn't successfully make any BioBricks. So:

My guess is that they were having trouble amplifying the sugar pore gene from the genomic DNA (or possibly cDNA) of whatever bacterial species has those pores naturally. PCR is usually fairly straightforward (I'm not sure where you got the impression it's a 50 step process), but if you're starting out with genomic DNA (or cDNA), reactions tend to be much more finicky. Plus, the bacterial species might not have a sequenced genome, making it harder to check to make sure that their primers weren't too similar to some other unrelated bit of the genome. DNA contamination happens occasionally, but isn't likely to be the source of months of problems, and it's only likely to be a problem during the PCR bit of cloning. There're a variety of troubleshooting methods that they were probably trying (or would have tried, had they had more time), but some of the methods were probably out of reach for this team, due to the limitations of their equipment and the lack of lab space. So yeah, their problems probably would not have been solved by a cell culture hood.
posted by ubersturm at 3:21 PM on February 13, 2010

Oh. Sweet. Now all I need is some of those bubonic plague thingamajigers and some of those macrobiotic resistant whatchamacallits and we'll call it good.
posted by Skwirl at 4:22 PM on February 13, 2010

Oh it's called antibiotic resistance? Sure send me somma that, too.
posted by Skwirl at 4:24 PM on February 13, 2010

Paing Dr. Frankenstein. I find this equally fascinating and horrifying.
posted by blue shadows at 12:32 AM on February 14, 2010

oh god, a little bit of knowledge
posted by rxrfrx at 4:26 PM on February 14, 2010

In 50 years, the HURF DURF WHATCOULDGO WRONGERS in this thread are going to look as hilarious as those old OMGROBOTSFROMMARS pulp covers.
posted by DU at 4:29 AM on February 17, 2010