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."

Comments

Doesn't this sound like...

[Rog-Mahal]

A recipe for disaster? Sounds like a pretty easy way for people to start making some nasty superbugs. I know all scientific innovation has that kind of risk, but I don't think I want my neighbor hacking E. coli next door.

Re:Doesn't this sound like...

[zappepcs]

Are you kidding? This will revolutionize the world. Your neighbor (not mine), in an attempt to show that you can't even FORCE nature to make a crocoduck will inadvertently create an airborne strain of E. coli that is resistant to any cheap form of treatment: resulting in a solution to rising unemployment and illegal immigration in less than 38 hours. The resulting global changes will be heralded as Allah's revenge against the great satan and simultaneously on the GLBT communities for their crimes against god. In less than a week, big pharmaceutical industry will collapse with the announcement that a 15 year old Korean kid in S.California has created an antidote that can be distributed in the flavor coating on potato chips. Frito Lay purchases several Pharma companies and hires the kid to work on gene therapies to be distributed via Corn Chips. Monsanto sues to block genetically modified material being added to their corn........ sigh

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
Forbes article - DIY Life
MIT TechTV Video - DIY Biology

Fine, I'll think of the children

[jollyreaper]

Biological tinkering has me concerned because we're talking about self-replicating systems. Realistically, we're not going to see nanite swarms or grey goo eating the whole planet as is feared in science fiction. Nanites have to operate within the same laws of physics as anything else and are unlikely to be spectacularly and magically more robust than organics. Hell, at such a small scale they would be more likely to be custom-designed organics.

That being said, organics ranging from viruses to bacteria to algae can cause quite a bit of trouble in our ecosystem. My only concern is that we might create some sort of blight in the lab that gets out. Now I'm not saying she's deliberately working with stuff that's intentionally meant to be lethal like the biological warfare guys in Russia but even those guys who knew they were messing with absolutely lethal bugs still made mistakes and had accidental releases.

Given that we won't know that something is really bad for us in the environment until after it gets out and starts doing terrible things, I would like to suggest we operate with an abundance of caution here. It wouldn't take an accidental flesh-eating bacteria to ruin everyone's day. The next corn smut or citrus canker could not kill a single person and cost the economy billions.

OpenWetWare.org

[ForexCoder]

http://openwetware.org/wiki/Main_Page

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.

Uber Geekery

[Jason Levine]

Now that's what I call Uber Geekery. Instead of the tiring work of brushing your teeth, you get minty fresh breath by hacking the smell of the bacteria in your mouth.

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

[Moraelin]

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.

Basically the same as: I'm not against electricity or nuclear power, but if the neighbour's kid managed to buy ten kilos of plutonium for his science experiment... I'd _worry_.

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

- repeated smallpox outbreaks seem to have been what weakened the Roman empire in the first centuries AD, to the point of near collapse of its economy and army. (Not to mention making everyone disillusioned with the old gods and ways.) There are outbreaks that are estimated to have killed up to 30% of the empire's total population. _Thousands_ of people died daily in Rome alone, for decades straight. (Though later Justinian's Plague killed about ten thousands a day in Constantinople.)

- ask the american indians how well smallpox worked for them later

- bubonic plague outbursts killed a majority of Europe's population back then, with mortality as high as 75% per outbreak in some cities (though not all.)

- we had a killer flu as late as after the first world war

Knowing that everyone can concoct their own cross between flu and aids with just a couple of relevant genes from the noro-virus for extra flavour, doesn't exactly make me sleep easier.

And before someone goes, "omg, but now we have antibiotics": yeah, but curing viruses is still where we suck. Royally.

And at least theoretically it would be possible to concoct even bacterias which don't respond to antibiotics that well. The easy to explain version is to just start from VISA/VRSA (think MRSA with extra resistances) and give it a gene so it multiplies faster. But for something more advanced for true gurus, why not swap out the proteins attacked by the antibiotics in the first place? E.g., give it the ribosome from an animal cell, and you just rendered a whole class of antibiotics impotent at a more fundamental level than normal bacterial resistances. Might need to recode a couple of other proteins for it to work, but that's why I've said it's for gurus only.

Or get creative. Make a bacteria or virus that can live equally well on plants _and_ animals. Now that'll be a royal pain in the arse to completely root out, and it can safely kill its hosts without making itself extinct.