Hacking With Synthetic Biology

blackbearnh writes "If you've gotten tired of hacking firewalls or cloud computing, maybe it's time to try your hand with DNA. That's what Reshma Shetty is doing with her Doctorate in Biological Engineering from MIT. Apart from her crowning achievement of getting bacteria to smell like mint and bananas, she's also active in the developing field of synthetic biology and has recently helped found a company called Gingko BioWorks which is developing enabling technologies to allow for rapid prototyping of biological systems. She talked to O'Reilly Radar recently about the benefits and potential dangers of easy biological design, why students should be hacking wetware, and what's involved in setting up your own lab to slice genes."

OpenWetWare.org

[ForexCoder]

http://openwetware.org/wiki/Main_Page [openwetware.org]

This is the info sharing site for bio-hackers. Has everything from courses for the gene-script kiddies to protocols and other neat stuff. It's a better resource then the corporate site for those who want to know about it.

Re:Doesn't this sound like...

[xplenumx]

I can't say I'm terribly concerned about your proposed scenario. Unlike computer programming, bioengineering takes quite a bit more capital. Let's say you want to insert a protein into a bacteria - first you need to create the cDNA (you'll need a PCR machine or water baths (heh), expensive enzymes, the ability to pipette uL amounts, random primers, and a source of mRNA), then you'll need to isolate the protein's cDNA, next you'll have to clone out the gene (do you have access to a sequencer?), and put the gene in a plasmid that will express the protein (you'll have to buy one as you won't be able to reasonably make one). Let's see, you'll also need amp/kan, LB plates, a warm room, some media, and a shaker (unless you want to use sub-sub-optimum conditons). After this, you'll have to express your plasmid in the bacteria - did I mention that, typically, bacteria that express the protein will be at a selective disadvantage? Wait, you want to stably integrate your protein into the bacterial genome? That's a whole, more difficult, can of worms. So you want to modify a virus... where are you planning on getting the viral vector? What type of virus are you attempting to modify? Some are very difficult to work with. Making one can be a PhD thesis in and of itself. Infecting eukaryotic cells is not easy either - a lot of money is being spent on trying to increase the efficiency for anti-cancer therapy.

Unlike computer programming, these aren't projects that people are (realistically) able to do in their basement. Often we give the simplest experiments (just the cloning part), where all the reagents are present and the knowledge base is easily available, to summer students - and often times they fail. I don't worry about the rogue 'biohacker' next door (all the more power to them - maybe they'll learn something about science). I worry about rogue governments - particulary ones that believe God will protect them.

Re:Doesn't this sound like...

[cd.rubysocks]

I like how she responded to this issue with the word 'democratization'. She doesn't seem to be so worried about some crazy terrorist getting access to this technology, as governments monopolizing it for biowarfare development. And I'm inclined to agree that we should be just as worried about the latter as the former. A few links about this scientist/entrepeneur:
Her Bio [openwetware.org]
Forbes article - DIY Life [forbes.com]
MIT TechTV Video - DIY Biology [mit.edu]

In Forbes months ago

[olddotter]

She was in Forbes magazine months ago (unless I get Forbes and Wired confused). Nope, google confirms it was Forbes and it was Aug. of 2008. [forbes.com]

Yea I find this both scary and REALLY cool. To read more about these technologies, read this blog post [blogspot.com] of links to similar stories.

Re:Doesn't this sound like...

[shipbrick]

You're making it sound quite difficult and expensive, but I don't think it's really that expensive or difficult. You laugh at water baths, but that would work just fine for PCR, and Taq Polymerase really isn't that expensive (~$100 for lots of rxns). Sure all the kits us biologists use are easy and expensive, but if someone is doing it for a hobby, they can bypass kits and do things "old school" style (where one actually knows what they are doing instead of adding reagent A to reagent B). Also, if someone knew that they are able to this, they could just ask a lab for a plasmid, which the lab might gladly send for shipping cost only (they may have to pretend or imply they have a PhD and lab though). A sequencer is not needed for cloning, you could simply use agarose gels and go by size for cloning (agarose=cheap and a power source could be made easy). You can get pipettes (ul) on ebay for not too expensive (few hundred). Bacteria do NOT need to be shaken either, or even grown at 37C... I've commonly grown e.coli at room temp without shaking (sometimes even to *optimally* express a protein), they just won't grow as fast. Ampicillin and LB isn't very expensive... My university has a surplus store where old or broken equipment goes to be sold for pretty cheap. One could get a fair amount of specialty equipment there, especially if another hobby was fixing equipment. I would guess you could do a cloning for less than $2000 easy (which is cheaper then some computers)...

Re:Doesn't this sound like...

[olddotter]

Did you even think about reading the article? The ultimate goal of this is to make sure that people can do it for little cost. I listen to researchers in the area complain that they can't get grad students to work on a project if there isn't an easy off the shelf kit you can buy to do the work.

A few $1000, eBay, and you can equip a basement lab. This time is to bioscience what the 1970's were to Steve Jobs and Woz. See this ebay search: http://shop.ebay.com/items/_W0QQ_nkwZsequencerQ20dnaQQ_armrsZ1QQ_fromZR40QQ_mdoZ [ebay.com]

Re:It's less about "evil" as about "safeguards"

[interkin3tic]

I don't think anyone cringes at exploring technology per se, but at doing so without much safeguards if any. The potential for mass harm is great, and while nobody proposes to outlaw it as such, it would be nice if it stayed only in proper labs and you at least had to tell someone your idea before even starting on it. You know, sorta like the XKCD idea of having your comment read out loud to you so you get a second chance to spot if it sounds bloody stupid.

If you work in a lab, you obviously have to tell your boss what you're up to. If you have your own lab, you're too busy telling the NIH what you've done and why they need to give you more money, to be doing this on the side. If you run into a problem you can't solve, the first thing you do is ask your colleagues for advice. In other words, people know what you're working on, we already talk to each other and hopefully would be able to tell if our colleagues were about to create a supervirus (which, by the way, is unlikely to happen by accident, although it's always good for a horror/scifi movie).

And here we're talking about something which has historically caused more harm than a nuke before.

All the examples you provided were diseases that had natural origins (the smallpox was intentionally spread, but was not created or spread by scientists), which highlights something key here: if there is going to be a killer virus, it's going to be natural. If someone catches an airborn form of ebola and is infectious while in a major international airport... goodnight. Don't worry about the amateurs, the most dangerous and evil biologist is nature itself.