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Biotech United Kingdom

NAND Gate Built From Bacteria 63

Posted by samzenpus
from the squishy-computing dept.
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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NAND Gate Built From Bacteria

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

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

    • by Samantha Wright (1324923) on Wednesday October 19, 2011 @03:58PM (#37767090) Homepage Journal
      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.
    • by dkleinsc (563838)

      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.

    • by maiki (857449)

      Did they have to use "gut" bacteria?

      My gut tells me yes.

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

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

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

    • 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
      • 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 en

        • 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 molecule

          • 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 f

            • 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 riski

              • 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 i

                • 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,

                  • 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 s

                    • 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.

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

                    • 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;

                    • 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

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

    • by gr8dude (832945)

      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.

  • 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.

    • by Anonymous Coward

      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

    • 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.

  • 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

    • by vlm (69642)

      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 /

      • by dtmos (447842) *

        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.

    • by rnaiguy (1304181)
      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.
  • by hplus (1310833) on Wednesday October 19, 2011 @03:49PM (#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.
  • 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.

    • 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 en
      • 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

  • 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?

  • "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.
  • 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]
  • 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".

  • 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

  • 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

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