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NAND Gate Built From Bacteria

samzenpus posted about 3 years ago | from the squishy-computing dept.

Biotech 63

thodelu writes "Scientists have taken another step towards biological computing, with the creation of logic gates from gut bacteria and DNA. While something similar has been done before, the team says its logic gates behave more like the standard electronic version. They're also modular, which means that they can be fitted together to make different types of logic gates, paving the way for more complex biological processors to be built in the future."

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Did they have to use "gut" bacteria? (1)

s_p_oneil (795792) | about 3 years ago | (#37766752)

Did they have to use "gut" bacteria? I hear it's what gives crap its lovely odor.

Re:Did they have to use "gut" bacteria? (2)

jellomizer (103300) | about 3 years ago | (#37766822)

It would be a fitting platform for {choose your OS that you hate the most} now it can small like it performs.

Re:Did they have to use "gut" bacteria? (5, Informative)

Samantha Wright (1324923) | about 3 years ago | (#37767090)

E. coli is the best-studied bacterium. It's a lot more convenient to work with them.

If it's any consolation, students in past years at iGEM have figured out how to make it smell like mint or bananas with some genetic engineering, if you add the right chemical precursor to the plate. You can even silence the foul-smelling metabolic pathways (which are part of, but not all of, the awful smell of feces) if you're really determined to, but most of the time it's not worth it.

Re:Did they have to use "gut" bacteria? (1)

dkleinsc (563838) | about 3 years ago | (#37767112)

Well, as Stephen Colbert has observed on numerous occasions, your gut is smarter than your brain. Therefor, using gut bacteria here is just attempting to replicate the wonderful thought process of your gut.

Re:Did they have to use "gut" bacteria? (1)

maiki (857449) | about 3 years ago | (#37767562)

Did they have to use "gut" bacteria?

My gut tells me yes.

... which means that at least one of them said no.

Re:Did they have to use "gut" bacteria? (0)

Anonymous Coward | about 3 years ago | (#37770818)

This will give 'My computer is infected' a whole new meaning.

Re:Did they have to use "gut" bacteria? (1)

maxwell demon (590494) | about 3 years ago | (#37771228)

This will give 'My computer is infected' a whole new meaning.

Yeah, now a virus can easily kill your hardware.

Re:Did they have to use "gut" bacteria? (0)

Anonymous Coward | about 3 years ago | (#37773106)

I put some logic in your crap so you can think when you stink.

Intelligent life (0)

Anonymous Coward | about 3 years ago | (#37766780)

Maybe we can use this to create intelligent life! You know, put many of these cells together...

Obligitory Momma Joke (0)

stokessd (89903) | about 3 years ago | (#37766784)

I left half a CPU in your mother last night...

Re:Obligitory Momma Joke (0)

Anonymous Coward | about 3 years ago | (#37767564)

Space docking?

Alaskan pipeline?

Evolution (0)

Anonymous Coward | about 3 years ago | (#37766792)

How much time before the logic gates start revolting?

Re:Evolution (2)

Samantha Wright (1324923) | about 3 years ago | (#37767324)

Knowing E. coli? Probably somewhere between a day and a week. Bacterial DNA replication is really lousy. Anything that doesn't contribute to keeping the cell alive tends to get a little messed up when it's allowed to reproduce freely.

Non-invasive biocomputers! (1)

Commontwist (2452418) | about 3 years ago | (#37766806)

Nice. Next step towards creating genetic symbotes that a person can interact with to mentally self-diagnose, control, and regenerate the body!

Re:Non-invasive biocomputers! (0)

Anonymous Coward | about 3 years ago | (#37766850)

*symbiotes.

Re:Non-invasive biocomputers! (1)

Commontwist (2452418) | about 3 years ago | (#37766874)

Thanks. Noticed but can't edit.

Re:Non-invasive biocomputers! (2)

Samantha Wright (1324923) | about 3 years ago | (#37767186)

None of those functions would do very well in a symbiont. An organism tasked with repairing your tissue would have to be made out of your stem cells. An organism tasked with receiving signals from, or affecting, the nervous system would have to be capable of interacting with nerve endings. Unless you were thinking of manual endocrine signalling (releasing a hormone in response to a thought), which is inherently slow, and would still require a great deal of engineering the human side of things to produce the desired effect.

Re:Non-invasive biocomputers! (1)

Commontwist (2452418) | more than 2 years ago | (#37832378)

Lovely amount of 'that can't happen' and no 'this might work'. Can you think of something outside the box that might work?

Say, implant/grow something in human body that creates cells akin to white blood cells that 'capture' invaders. When cells go to the place they go when they die have something there that can take in a sample of the 'dummy' white blood cells and analyze it. If it can connect to the brain via nervous system or though chemical transmission then could things be analyzed and self-diagnosed enough to create a counter? I'm trying to be semi-realistic here but, hey, sci-fi is inspiration so it only has to come close.

Re:Non-invasive biocomputers! (1)

Samantha Wright (1324923) | more than 2 years ago | (#37833046)

There's little in a dead cell that can tell you why or how it died, short of performing huge batches of analyses on every molecule inside of it. If an infectious organism is responsible, it's much more feasible to deal with it in advance—and you can rest assured that the body is already aware of it.

And on that note, good luck outperforming the native biology without causing an immune disorder. We currently work by generating all possible pathogen-detecting receptors that (a) target biological molecules and (b) do not target ourselves. If something that matches is found, we amplify that antibody until the disease goes away. In AIDS, the body generates trillions of disease-fighting cells per day, trying it hardest to outpace the infection. This system is so good that all vaccines have to do is tell the body to prepare certain antibodies in advance by giving it a non-infectious sample to target.

Humans don't need augmentation to help them fight disease. That's what they've evolved to do, and they do it pretty well as long as they're healthy. If you want to play with tech like that, focus on improving our lives beyond what they already have the ability to be. Go back to Douglas Engelbart's ideas of intellect augmentation. Brain-computer interfaces are much more useful for creating two-way communication to control and access external information systems.

Re:Non-invasive biocomputers! (1)

Commontwist (2452418) | more than 2 years ago | (#37839962)

Humans don't need augmentation to help them fight disease. That's what they've evolved to do, and they do it pretty well as long as they're healthy.

Yesssss.... Forgive me if I don't go to the local hospital and visit all the AIDS and cancer patients and repeat that.

I'm just throwing out ideas but, again, thy negativeness knows no bounds. If you've already come up with a Wonderdrug/vaccine that can cure every disease ever known and those that will come then I will bow to your wisdom.

And on that note, good luck outperforming the native biology without causing an immune disorder.

That's right, nobody needs artificial hearts! Oh, wait....
And, yes, I know they aren't as good as a real heart or that the body usually tries to reject it. Finding ways to fix that is called 'progress' and 'positive thinking'. Doctors actually do implant things in people in order to try to save them and, yes, they might actually find a way to do what I described--or perhaps they will come up with something else. As long as someone comes up with the ability to help/assist the body automatically defeat new generation of diseases without years of research I'll be happy.

Not looking for that from you though--no imagination.

Re:Non-invasive biocomputers! (1)

Samantha Wright (1324923) | more than 2 years ago | (#37841548)

I promise you I have plenty of imagination! (Try checking out my site!) But I might very well level the same accusation at you, for lingering so much on health problems. Really, though, your probe comes up against some harsh prerequisites: we're still trying to figure out how to deal with cancer and HIV in the lab. When we finally do figure out how to beat them reliably, the most sensible thing to do would be to issue an update to the human genome so it can do the job itself. A symbiont would be a lot riskier.

That being said, I actually did briefly explore the possibility of engineering a pair of symbionts for one of my undergraduate projects. We were looking at the idea of attaching bacteria to the worm C. elegans so that the bacteria could feed the worm a type of gene suppressing-molecule called siRNA. Our main project was making C. elegans easier to engineer, and the bacterium in question (E. coli) is exceedingly well-understood, so we kind of approached the idea as a form of backward compatibility with other engineering projects.

In the end, we abandoned it when we realised that E. coli is one of the major food sources for C. elegans—it was a little like strapping hamburgers to the body of an exceedingly hungry person, in that it was doomed to fail to accomplish anything useful, no matter how delicious it may have been to the worm.

However, if it is symbiotic organisms that get your mind going, one application would be in using siRNA in humans to get around the whole "icky genome patching" issue, which is sure to garner complaints from lots of people. At present, RNA interference experiments in humans typically involve syringes; pills don't work since our digestive systems are much too acidic. siRNA also doesn't last very long. Using so many syringes would be an unpleasant way to keep oneself protected—but having an on-board organism that could release the appropriate RNA under specified times might be highly practical. It does have has its limitations, however, in that it can only turn genes off, not supplement them. Such a guest organism would most likely have to be a genetically population of leukocytes, since there are few ideas in medicine worse than "let's put undetectable bacteria into the bloodstream and watch what happens!" However, this would allow for a "detection –> silencing" cycle for dealing with genetic disorders, cancers, and even particularly vexing viruses like HIV.

Re:Non-invasive biocomputers! (1)

Commontwist (2452418) | more than 2 years ago | (#37841776)

I promise you I have plenty of imagination! (Try checking out my site!) But I might very well level the same accusation at you, for lingering so much on health problems. Really, though, your probe comes up against some harsh prerequisites: we're still trying to figure out how to deal with cancer and HIV in the lab. When we finally do figure out how to beat them reliably, the most sensible thing to do would be to issue an update to the human genome so it can do the job itself. A symbiont would be a lot riskier.

Wasn't so much the idea as the tone of your initial counter-argument that had me 'linger' so much on this possibility. All I initially said was that the topic was the next step towards something like a possible symbiotic anti-disease creation not that it could be done using technology right now. My reaction was 'huh?!' when I saw your response. For all we know a medical breakthrough or two could allow it to be done fifty or a hundred years from now... or it could not. We don't know. You don't know... even if you are a biologist. I dared to dream of the future and got slapped down.That's why I got mildly annoyed at the negative vibe I got.

That being said, I actually did briefly explore the possibility of engineering a pair of symbionts for one of my undergraduate projects. We were looking at the idea of attaching bacteria to the worm C. elegans so that the bacteria could feed the worm a type of gene suppressing-molecule called siRNA. Our main project was making C. elegans easier to engineer, and the bacterium in question (E. coli) is exceedingly well-understood, so we kind of approached the idea as a form of backward compatibility with other engineering projects.

In the end, we abandoned it when we realised that E. coli is one of the major food sources for C. elegans—it was a little like strapping hamburgers to the body of an exceedingly hungry person, in that it was doomed to fail to accomplish anything useful, no matter how delicious it may have been to the worm.

You tried, you failed, and that's a good example if an odd visualization. If you'd mentioned this in the beginning I'd've been less annoyed for the info's sake alone.

However, if it is symbiotic organisms that get your mind going, one application would be in using siRNA in humans to get around the whole "icky genome patching" issue, which is sure to garner complaints from lots of people. At present, RNA interference experiments in humans typically involve syringes; pills don't work since our digestive systems are much too acidic. siRNA also doesn't last very long. Using so many syringes would be an unpleasant way to keep oneself protected—but having an on-board organism that could release the appropriate RNA under specified times might be highly practical. It does have has its limitations, however, in that it can only turn genes off, not supplement them. Such a guest organism would most likely have to be a genetically population of leukocytes, since there are few ideas in medicine worse than "let's put undetectable bacteria into the bloodstream and watch what happens!" However, this would allow for a "detection –> silencing" cycle for dealing with genetic disorders, cancers, and even particularly vexing viruses like HIV.

Symbiotic organism? Not really. Ways to permanently defend against all diseases, past to future, would be more accurate. The current human immune system might be excellent but there is obviously a need to improve detection of diseases. White blood cells can do a lot but they need to learn how to identify some invaders better without wiping out their host. It sounds like figuring out how to defend against AIDS is doing better and cancer the same way (ironically using the former's methods).

It would be nice if one could program the current immune system with a broad range identifier would eliminate all but the rarest of virus infections. Then the next step would be to somehow analyze foreign invaders to give scientists advance warning. Then a way to create fixes automatically. David Weber gave a shot at imagining something like that but with alien tech implants and nanotech in his Troy series. Some DNA rewriting in the first book as well. How accurate he was I leave to you.

Re:Non-invasive biocomputers! (1)

Samantha Wright (1324923) | more than 2 years ago | (#37876050)

White blood cells can do a lot but they need to learn how to identify some invaders better without wiping out their host. It sounds like figuring out how to defend against AIDS is doing better and cancer the same way (ironically using the former's methods).

It would be nice if one could program the current immune system with a broad range identifier would eliminate all but the rarest of virus infections. Then the next step would be to somehow analyze foreign invaders to give scientists advance warning. Then a way to create fixes automatically.

This is where the problems are. In some diseases, there are no distinguishing features for immune cells to lock onto. They can only see what's on the surface, after all; there's no one "broad range identifier" that works. Trying to create one is as problematic as trying to come up with a universal identification for computer malware without an uninfected 'reference' copy: how do you even know if what it's doing is bad? In computers, we always have the "if it's modifying the boot sector, that's bad" excuse, but (a) the human genome is more than 6.2 billion bytes in size, and (b) it changes all the time on its own. There are even things in our bodies that are repurposed viruses, nearly indistinguishable from normal ones except by surface features our immune system already has a handle on. The only really good way to tell if something's diseased is... if it dies.

Re:Non-invasive biocomputers! (1)

Commontwist (2452418) | more than 2 years ago | (#37876220)

True enough, yet the body holds together despite all this complexity and figures a lot of all this out on its own. Like I said before, who knows how much more we will learn about the human body and its mechanics in the next 50 to 100 years? Maybe we can find a way to distinguish those diseases using something supplementary to the white blood cell. Perhaps (and I'm just tossing out ideas) something small (artificial protein?) that can be 'added' to all normal cells as an enhanced early warning device when something that gets by the white blood cells? *shrug* I don't know how feasible that is *right now* but maybe some time in the future when we finally know all the stuff the body is doing. Heck knows viruses manage to take over entire cells so adding minor tattletale 'features' might be possible.

Re:Non-invasive biocomputers! (1)

Samantha Wright (1324923) | more than 2 years ago | (#37883322)

Perhaps (and I'm just tossing out ideas) something small (artificial protein?) that can be 'added' to all normal cells as an enhanced early warning device when something that gets by the white blood cells?

That's how it works now, actually. They're mostly sugar groups, though. HIV is a problem primarily because it steals one of the body's normal tags and coats its virus particles in it, making it look like one of our cells.

Re:Non-invasive biocomputers! (1)

Commontwist (2452418) | more than 2 years ago | (#37911096)

Not possible to create a new sub-set that prevents that? (You'd know more than I.) Who watches the watchers?

Re:Non-invasive biocomputers! (1)

Samantha Wright (1324923) | more than 2 years ago | (#37911358)

It's possible, but it would be an arms race. Certain kinds of viruses, like the mimivirus [wikipedia.org] , which infects amoebae, are capable of stealing genes from their host organisms. HIV, by contrast, mutates and reproduces at a rate so high that it has a reasonable likelihood of inadvertently developing such a protective glycoprotein over the course of a few infections, akin to how superbugs develop from conventional bacteria.

(Also, I may have been a little bit in error in describing exactly how HIV functions before; it's not that it presents human surface proteins, although there are viruses that do this, HIV is primarily a nuisance because of its fast pace of evolution, and tendency to target the cells that are supposed to be cleaning up after it.)

Re:Non-invasive biocomputers! (1)

Commontwist (2452418) | more than 2 years ago | (#37913454)

I'd say the arms race has been ongoing for quite some time with occasional heavy casualties on the human side (Black death, HIV, etc.)
The arms race was the reason why I attempted to come up with a real-time anti-virus defense. Hopefully something that can adapt as fast as HIV, or at least cover a very large range of possible mutation possibilities, can be thought up. Even if it's something that can only last for a week or two you could eliminate vectors of infection.

Anyway, I think I'll stop the thread here. We're getting pretty long. lol.

Re:Non-invasive biocomputers! (1)

Commontwist (2452418) | more than 2 years ago | (#37841928)

Went to see your page. All was forgiven when I saw the entry on politicians of the world--heartily agree.

Re:Non-invasive biocomputers! (1)

gr8dude (832945) | about 3 years ago | (#37780540)

Actually, you may have coined an interesting term: symbot - a symbiotic robot programmed for a specific purpose to be fulfilled inside the body of a host.

Circuit bugs (0)

Anonymous Coward | about 3 years ago | (#37766840)

Sorry, I think my logic has a bug in it!

Hmmm... (1)

broginator (1955750) | about 3 years ago | (#37766878)

I think there's some fuzzy logic growing in my fridge right now.

That's great (0)

Anonymous Coward | about 3 years ago | (#37766890)

Soon not only do you have to buy a new computer every 2 years, you have to buy a new one every time you take a really big crap.

This is cool but... (0)

jellomizer (103300) | about 3 years ago | (#37766892)

This is a really cool exercise and I would love to see how complex they can go...
But is there any really good application for this? Aren't current electronics have gates that are smaller and faster then bacteria, and faster then they could ever really get to be. Then you need to keep the bacteria alive and operating.

Re:This is cool but... (1)

Anonymous Coward | about 3 years ago | (#37766954)

These would likely be more useful for long time-scale things- e.g. environmental sensors etc. where the bacteria would have less upkeep than a conventional computer or possibly for uses like drug delivery or production

Re:This is cool but... (2)

Infiniti2000 (1720222) | about 3 years ago | (#37767106)

From TFA:

Devices could include sensors that swim inside arteries, detecting the build up of harmful plaque and delivering medications. Other sensors could perhaps detect and destroy cancer cells inside the body.

Re:This is cool but... (1)

maxwell demon (590494) | about 3 years ago | (#37771248)

E. coli in your blood? Doesn't sound very healthy to me ...

fitted (0)

Anonymous Coward | about 3 years ago | (#37766928)

What is wrong with 'fit', as in "can be fit together"? These extra "ed"s that seem to be pasted on the end of verbs by engrish speakers (putted, inputed, hitted) are annoying.

Nice, but not small (1)

dtmos (447842) | about 3 years ago | (#37766952)

Even the smallest bacteria are around 300 nanometers in diameter [wikipedia.org] . State-of-the-art silicon processes have a minimum feature size around 22 nm or so [wikipedia.org] -- plus or minus a generation or two -- so the transistors made in these processes (less than 100 nm in diameter) are significantly smaller than the smallest bacteria. It would depend on the layout rules in the specific process, but it's likely that one could make a NAND gate (4 transistors) in a modern process, fit within a 300-nm circle -- including contacts.

Of course, "the interesting thing about a dancing bear isn't how well he dances, but that he dances at all." Biological computing is interesting and valuable for reasons other than the size of the devices. It's just a never-ending source of amazement (at least to me) that we've gone beyond bacterium-size and are now into virus-size transistors -- and the inorganic molecule-size transistors are on the horizon.

Re:Nice, but not small (2)

vlm (69642) | about 3 years ago | (#37767070)

Yeah but if you analyze reproduction, the 22 nm transistor and the 22 acre process plant must mate and share the work of raising the next generation of transistors and plants. I suppose the minimum size required for a complete industrial system (like a biosphere for industry) including raw material, power plants, warehouses, petrochemical facilities, is more like 22 square miles rather than 22 acres. So the average size of that "reproductive pair" is 22 miles for the big momma + 22 nm for the litte guy / 2 = about 11 miles. Pretty big.

On the other hand, a "reproductive pair" of 300 nm bacteria is pretty small, like 300 nm or so.

Re:Nice, but not small (1)

dtmos (447842) | about 3 years ago | (#37767246)

Yeah, good point. Plus you won't need the $4 billion to make the fab in the 22 acres, to make the "reproductive pair" of 300 nm bacteria. A few generations from now one will need the Gross National Product of Peru to make a new fab.

Re:Nice, but not small (2)

rnaiguy (1304181) | about 3 years ago | (#37768184)

However, this NAND gate comes with a suite of chemical sensors attached. Many of which can be used as inputs to the gate. I doubt that can be fabricated in a 300nm circle.

NAND is functionally complete (2)

hplus (1310833) | about 3 years ago | (#37766994)

Since NAND gates can be combined to make AND, OR, and NOT gates, this means that bacteria could theoretically realize any logic circuit. Cool stuff.

Re:NAND is functionally complete (0)

Anonymous Coward | about 3 years ago | (#37769654)

I wonder if evolution (which takes place on a more rapid scale with single cell organisms) would cause offspring of these components to fail.

That said, it'd be neat to have computers that can "self heal" the way our bodies do, I just don't want to change my CPU's diaper!

Re:NAND is functionally complete (2)

hawk (1151) | about 3 years ago | (#37769830)

IOW, an ulcer is Turing complete . . .

hawk

Will this be efficient? (1)

Hentes (2461350) | about 3 years ago | (#37767054)

Does genetic computing have a chance of getting faster than traditional circuits? It seems to me like something too big and complicated to be quick.

Re:Will this be efficient? (2)

Samantha Wright (1324923) | about 3 years ago | (#37767254)

The primary application of this kind of biological computing tends to revolve around the negligible energy requirements: just throw some sugar water on it, and you're done for the next while; no electricity required. Other than that, there's a lot of theoretical interest in these systems for their comparability to neurons, but to be honest they're comparatively useless. We have great respect for DNA computing (which is very different from turning bacteria into transistors) and the potential of exploiting enzyme kinetics for computing applications, but projects like this are relatively fluffy and conceptual.

Re:Will this be efficient? (1)

countertrolling (1585477) | about 3 years ago | (#37769964)

Useless? That would depend on how well it ferments, and tastes.. I wouldn't mind if it's a little slow if it produces a nice brandy, or similar

UNIX uptime and gut bacteria (0)

Anonymous Coward | about 3 years ago | (#37767174)

Can gut bacteria cause constipation under a heavy load?

You ever wonder sometimes... (1)

Haedrian (1676506) | about 3 years ago | (#37767196)

Now we have organic computers, and we use bacteria to make stuff for us like insulin and plastics and stuff...

Ever wonder whether we're all a giant part of a large computer?

Re:You ever wonder sometimes... (0)

Anonymous Coward | about 3 years ago | (#37767262)

for a slashdot reader, you dont read much..

Re:You ever wonder sometimes... (1)

uncanny (954868) | about 3 years ago | (#37767312)

42

Cool, Slant (1)

honestmonkey (819408) | about 3 years ago | (#37767630)

"Slant" by Greg Bear had just such a computer in it. Actually, it also had bees and I think other forms of life as well (worms, other insects). I guess everything in science-fiction comes true at some point.

Inerface Can B. A ... (0)

Anonymous Coward | about 3 years ago | (#37769172)

"Liquid Life" (1936) by Ralph Milne Farley
http://www.xenology.info/Xeno/6.2.htm

Slavery? (0)

Anonymous Coward | about 3 years ago | (#37769268)

I see a dim future when we force lesser creatures to compute for us.

Only need NAND (0)

Anonymous Coward | about 3 years ago | (#37769342)

As I recall, it's possible to build all computer logic by using only NAND gates.

Re:Only need NAND (1)

Osgeld (1900440) | about 3 years ago | (#37770124)

yes but its not the most efficient use of space

for example it takes a couple of transistors and a couple resistors to make a nand gate, using a couple of them you can make them into a and gate. In contrast you can make an and gate with 2 diodes.

similar research (1)

gargeug (1712454) | about 3 years ago | (#37769926)

There is a professor named Eric Klavins at University of Washington who was doing this like 2 years ago. I toured his lab and I think he already had all the basic logic gates working, and they were working on getting an oscillator going. Here is his site in case you are interested. http://depts.washington.edu/soslab/mw/index.php?title=Main_Page [washington.edu]

This is meaningless (0)

gweihir (88907) | about 3 years ago | (#37769996)

You can easily build "AND" gates with mechanics. This never did scale. Also modern circuitry is mostly constrained by interconnect, not logic gates.

I call this a "funding stunt".

Yea great (1)

Osgeld (1900440) | about 3 years ago | (#37770108)

now get 42 million of them in less than a quarter inch square at 180nm thick, then you would be up to a decade old pentium 4

Next Generation of Computer Viruses (0)

Anonymous Coward | about 3 years ago | (#37770784)

.. made from real bacteria.

Viruses and Bacteria -- WE ARE THE BORG!!!! (1)

Ramin_HAL9001 (1677134) | about 3 years ago | (#37788988)

So writing a computer virus could involve either hacking the software running on the bacteria NAND circuits... or could involve writing a bacteriophage that attacks the circutiry itself.

Or what if a bacteria learned how to colonize and take-over a human brain? Just like the Borg!!! I'm in your brain, hacking your dreams.

As if it wasn't bad enough worrying about computer viruses, now we have to worry about computer bacteria too, and computer bacteria viruses (bacteriophage hacking).

Oh well, this is still cool as hell.
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