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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."
Isn't this the kind of thing that Bill Joy got all freaked out about...
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.
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.
Kwisatz Haderach
Sell the spice to CHOAM
This Mahdi took Shaddam's Throne
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.
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.
My sci-fi novel, Ghost Thief, is now available from Amazon.com.
It's got to be much less trouble than maintaining access to a real vagina. All the talking and spending, just to taste some poon. It's downright unromantic.
Apart from her crowning achievement of getting bacteria to smell like mint and bananas If we could just get the bacteria cultures that create yogurt to taste like mint and bananas, then we could produce yogurt with no added flavoring!
I've abandoned my search for truth; now I'm just looking for some useful delusions.
As a working biochemist/molecular biologist I cringe at her la-de-da attitude. Making bacteria smell like bananas is cute, so is making a glowing mouse (green fluorescent protein). But abuse is a centimeter away (cloning botulism toxin into the flu virus anyone?) Where I work I have to justify just about everything I do. That's a good thing. If you want to hack biology get into plant breeding... 537
Ok, I know this is a bit off topic, but brainy indian girls are just oh so hot!
Why am I imaging a dystopian world where we are buying genetic 'upgrades' ala bioshock suddenly becoming much closer to reality.
-Ours is the wisdom of Solomon, the magic of Merlyn, the fall of Icaris.
They're my friends, Roy. I made them.
If Slashdot were chemistry it would look like this:Cadaverine
I recall the first application was glow-in-the-dark aquarium fish. But its a mjor tool in bio-marking now. It won Nobel prizes last year.
This years toy is next years Nobel Prize?
Or Kamandi, the last boy on Earth. Whichever post-apoc scenario it is, caused by people playing around with this kind of stuff.
Not that I'm opposed to genetic engineering as a whole, I just realize there's all sorts of consequences to it.
What could possibly go wrong?
Wake me when someone has hacked the THC gene into the tomato. Just imagine the possibilities - a pizza that gets you high AND alleviates the munchies.
In all seriousness though. Wouldn't it pretty much end the marijuana legalization debate if somebody spliced THC genes into something as common and innocuous as the tomato? Or perhaps something invasive (and edible) like kudzu...
[Posted anonymously so I can still pass the Google-test with potential employers.]
(AC, so I'm not as much a karma whore)
http://diybio.org/ - open source hardware, biology, XMLizing lab protocols, the goods.
http://openwetware.org/
http://biopunk.org/
http://syntheticbiology.org/
http://partsregistry.org/
http://igem.org/ (international genetically engineered machines competition)
http://ponoko.com/
http://shapeways.com/
http://thingiverse.com/
http://instructables.com/
lifeboat foundation (AKA "fearmongers click here")
cat * > /dev/trend-spotting-machine
Wait, now we're using that made-up plural form of virus as the SINGULAR form? Great.
Making fun of dumb people since 2009
Shudd'na posted da story here... slashdotters... genes... run for your lives!!
Also, here is a recording from a Computer Chaos Club Congress about messing with DNA. You can get a fairly good grip on this subject if you watch it ;)
http://video.google.com/videoplay?docid=-6950604815683841321&hl=en
Sounds like the plot of Permutation City
...getting bacteria to smell like mint and bananas... I think her real hidden agenda was to get the bacteria that favor warm, moist regions of the human anatomy to smell like anything other than sushi... a male scientist would never have thought of this approach.
I've abandoned my search for truth; now I'm just looking for some useful delusions.
Who do you trust more? A grad student with a budget and vast lab resources, or a guy in his garage with few skills and fewer lab tools?
How does being enrolled in school preclude one from unethical and/or illegal behavior?
How would someone in their garage succeed where state sponsored programs have failed?
We've TRIED to introduce GM organisms into the wild and failed EVERY TIME. Remember when they developed that mosquito that wouldn't transmit malaria?
Its just fancy chemistry. Calm down.
I'd hit it.
Rapid prototyping of biological systems, if it could be done as easier as a prototyping plastic, would be wonderful. Imagine a new disease discovered and resistant human cell/DNA, being manufactured within a couple of weeks. Doubt we'll get that though. What we might get at best is a new economy segment based on brewing, with genetically engineered yeasts be produce pharmaceuticals and other chemicals cheaply. Yeast is the ideal for the purpose because is grows so quickly, and is used in enclosed environments.
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.
A polar bear is a cartesian bear after a coordinate transform.
Soon Windoze will loose its title as number one malware target ... On the other hand, just maybe some of those adds for larger appendages just might work. I don't know if this is bad news or good news. ;-)
She's Indian, she will have H1 in future, she will take jobs from American....she's not brilliant, she's just cheap to hire...
I wonder how long it'll take us to near perfect the cell phone and then decide to add it directly into our ears or something. (Where would be a matter of engineering or style.) Presto techo-telepathy added to the human genome. I think that we could really do it in less than a hundred years.
There are days that I wonder how long it'll take us to do that and then have most of our current tech apparently vanish in landfills and such and not be replaced. Give it a few generations and people would "forget" that we hadn't always had those abilities. (Sort of like how folks forget how that there was life before newspapers, TV, radio, cell phones, or computers.)
Just wait until I loose my synthetically engineered spelling-nazi bacterii...
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.
Yea I find this both scary and REALLY cool. To read more about these technologies, read this blog post of links to similar stories.
Think Deeply.
oh yeah. stop hacking computers. we got something new for ya. how about these things. you can kill the entire human race, have fun.
I was just at the AAAS conference in Chicago, and there was an entire session on synthetic biology and programming with DNA and RNA. Quite fascinating. Perhaps most intriguing (and promising) is the ability to add logic to RNA sequences, giving clinicians control over cell therapies. I wrote a summary of the session over at Ars if anyone is interested.
Per Square Mile, a blog about density
technological progress marches on
your average middle class high school kid can buy $500 HD editting software and a $1K HD camera and have more power in his rec room than the average major hollywood studio in 1969
plus, biology is not limited like chemistry or physics: you might know how to make nerve gas or plutonium, but you still need very expensive materials and equipment well beyond your means as a middle class kid. but all genetic hacking requires is biochemical manipulations around us in every microorganism, and nutrients as cheap as your breakfast cereal (or, your actual breakfast cereal). only technology is limited today, and that is getting cheaper and cheaper every day. 10 years ago, it was a huge deal to sequence the human genome and it took millions of dollars and months. now they are talking about doing it in a few days and for $5K and doing it for individuals to tailor their drug regimen. extrapolate into the future
it's a little scary to think about a future where "script kiddie" and "hacker" could refer to a high school kid who can cook up smallpox or polio in his rec room
intellectual property law is philosophically incoherent. it is your moral duty to ignore it or sabotage it
So she's invented Shetty mint and Shetty banana. Pretty sweet.
But will she ever bioengineer a Shetty wall? Will the goddamn Mongorians break down her Shetty wall?
In Soviet Russia jokes are formulaic and decidedly non-humorous.
Oh and when that happens I am pretty sure you will get the "warm fuzzies"..right before you die in orgasmic pain.
I do not support "The Man". I also do not support your irrational stupidity
Juan Enriquez talked about this research in his talk at TED this year. Just posted today: http://www.ted.com/index.php/talks/juan_enriquez_shares_mindboggling_new_science.html He argues that the next big evolution in technology -- wetware hacking -- is going to eclipse the financial crisis.
My dad has been in the field of molecular biology for more than 30 years. Renaming an established field of research to something buzzworthy such as 'Synthetic Biology' seems to have piqued the interest of many a news outlet recently. The truth is people have been genetically engineering (the well established term) bacteria (my dad's company has engineered bacteria to produce vitamins as an alternative to chemical synthesis for decades) and other more complex organisms for a long time. And they have also, in cooperation with the government, developed strict regulations and standards to insure that bob-down-the-street doesn't start brewing some weaponized smallpox in his basement. Would you be alarmed if I told you dihydrogen-monoxide is a dangerous poison found in most of the products you consume every day? A rose by any other name...
For my first project, I changed my own blood type. I now have blood type C, a previously non-existent alternative to A or B. Now the Red Cross never asks me to donate blood, since nobody else would be able to receive it!
Cut that out, or I will ship you to Norilsk in a box.
Just wait until I loose my synthetically engineered spelling-nazi bacterii...
The sad thing is that "bacterii" is almost less of a gross bastardization than "virii". Because even if you incorrectly assumed that virus would follow the "replace us with i to form the plural" rule, that would be viri with one 'i'. There is no reason or rule in English that would suggest "and then add an extra 'i' for no reason".
Bacteria may not even end in "us", but at least when you pluralize it as "bacterii" you aren't adding extra letters for no reason.
The only word in English (afik) whose plural ends with double-i is "radii", and that's because the singular word "radius" already has an 'i' just before the 'us'.
Thus why virii is so obnoxious to me. But I feel better now.
The enemies of Democracy are
these aren't projects that people are (realistically) able to do in their basement.
That is exactly what these companies and projects are trying to change. They set up large libraries of genetic components with standardized "connectors". The create plasmids that "just work". Etc. People will be able to try out lots of stuff in their basement at almost no cost. nd sequences they don't have, they can simply order for a few hundred dollars.
This wasn't even hard or costly 20 years ago, and it's even easier now.
I wouldn't worry about it, though. There's no force on earth that can stop this. If it turns out to be easy to create deadly combinations, we're doomed anyway. And if not, well, then we're going to benefit.
http://xkcd.com/419/
In Soviet Russia, articles before post read *you*!
Electricity was considered dangerous once, too. Yet, every household in the First World has it. Why should we not pursue new technology just because there are some potential negative uses?
Wow, where can I get the DNA of my penis hacked to smell like banana?
right under our noses!
Attack India NOW!!
I doubt any computer hacker have ever managed to not cause a kernel panic. Just as I doubt any biohacker is ever going to manage to cause the equivalent in biology (which would be death to self and possible many many more).
I sure hope we'll improve space travel to the level of being able to travel to other habitable planets before this happens. I don't want to be on earth when a billion script kiddies fool around with life.
It's surprising that nobody has pointed out that she's fucking gorgeous.