Forgot your password?
typodupeerror
Science

Complex Logic Circuit Made From Bacterial Genes 37

Posted by samzenpus
from the feeding-the-machine dept.
another random user writes "Just as electronic circuits are made from resistors, capacitors and transistors, biological circuits can be made from genes and regulatory proteins. Engineer Tae Seok Moon's dream is to design modular 'genetic parts' that can be used to build logic controllers inside microbes that will program them to make fuel, clean up pollutants, or kill infectious bacteria or cancerous cells. The circuit Moon eventually built consisted of four sensors for four different molecules that fed into three two-input AND gates. If all four molecules were present, all three AND gates turned on and the last one produced a reporter protein that fluoresced red, so that the operation of the circuit could be easily monitored."
This discussion has been archived. No new comments can be posted.

Complex Logic Circuit Made From Bacterial Genes

Comments Filter:
  • ...correct me if I'm wrong, but doesn't life, by definition, do this already... but in a nearly-infinitely more elegant, efficient fashion?

    This research strikes me as comparable (scrambling around for a suitable analogy here...) to welding a bunch of pairs of vise-grips into a shape vaguely reminiscent of a pair of pliers and then loudly proclaiming that one has achieved the ability to manufacture impressive tools...

    • Re: (Score:2, Insightful)

      by Anonymous Coward

      Sure, but we don't know how to program life to do what we want. I'm not convinced that implementing digital logic circuits is the way to accomplish his goal, but I'm not convinced that it isn't either. This may be a dead end. Perhaps we will have a much better method later. However, this seems to be an approach that we can investigate now.

      • by pepty (1976012)
        We're already pretty good at programming life to do what we want. It's what molecular biologists have been spending their time doing for 40 years: getting bacteria to express new proteins or express/not express not express proteins in response to certain stimuli. You can buy the modular 'genetic parts' from catalogs like New England Biolabs, complete with digital or analog on/off switches that react to the presence of stimuli such as particular sugars, antibiotics, peptides, or small molecules.

        There are ki

        • by tylikcat (1578365)

          I think it is still up in the air how useful this will be - and not just in the research side of things, though certainly it will be used there first. It doesn't seem that unlikely to me that you want to have finer control over what is expressed when, that you want different things expressed at different times, or that you want a series of things expressed in a particular order under different circumstances.

          This as it stands it pretty rudimentary, but it could be the first step in allowing us to program cel

          • This as it stands it pretty rudimentary, but it could be the first step in allowing us to program cells in a much more defined and complex way than anything we can do yet.

            It's all relative, my 1970's HS biology teacher would have viewed this as "Star Trek" science. This level of detailed understanding [youtube.com] would have made his jaw drop in awe, as it did mine. :).

    • by Belial6 (794905)
      No, it is more like finding a bunch of hammers around, welding them together in the shape of a pair of pliers in a land where no pliers previously existed, and loudly proclaiming that one has achieved the ability to manufacture impressive tools.
      • Stop with the analogies already. That's like trying to fix a radiator leak with WD-40.

        Yes, life does infinitely more complex logical operations than these simple logic circuits. But we can't control that stuff well and we have figured out how to do fairly elaborate things with simple logic gates in hardware. So if you can create such 'easy to program' devices into cells, you can hopefully use them as an interface to the more complex machinery.

        Imagine a Beowulf cluster of E. coli ....

        • Imagine a Beowulf cluster of E. coli ....

          No imagination required, I have a tub of yoghurt in the fridge. I don't actually use the API myself, it gives my tongue a furry feeling.

    • by drinkypoo (153816)

      correct me if I'm wrong, but doesn't life, by definition, do this already

      It's not clear whether anything in our heads actually operates like a classic logic gate. Our brains are analog. There may be digital logic in there somewhere, but it's probably all emulated.

      • Pfft, forget heads. Every cell does this all the time; it's how signalling cascades work. More embarrassingly, projects like this are routinely done by undergraduate students as part of the iGEM competition. To have this story publicised verges on humiliation.
    • by Gorobei (127755)

      ...correct me if I'm wrong, but doesn't life, by definition, do this already... but in a nearly-infinitely more elegant, efficient fashion?

      This research strikes me as comparable (scrambling around for a suitable analogy here...) to welding a bunch of pairs of vise-grips into a shape vaguely reminiscent of a pair of pliers and then loudly proclaiming that one has achieved the ability to manufacture impressive tools...

      Yes, but that is what building abstractions to support higher order systems is all about. The computer I'm typing this post on does about 12 billion ops/sec, many more in the GPU,) and probably trillions of nand gate state changes per second. All that to underline "nand" as a misspelt word to me. Every abstraction layer in a computer (general purpose CPU, VM model, garbage collection, multi-threading, communication protocols, ACID file systems, HLL representations, etc) costs about 10x in terms of terms of

    • Yep, it's like inventing a crappy uneven wheel and proclaiming it's more impressive than the rolling log it came from
  • ... make fuel, clean up pollutants, or kill infectious bacteria or cancerous cells ...

    This list of applications sounds like generic funding BS found in grant applications. As others have pointed out this is a bit nonsensical since we already have organisms that do some of these things. We are unlikely to outperform nature's solution, the organism eating oil in the gulf of mexico for example, its hard to beat millions of years of evolution.

    That said this research could be useful. Perhaps there would be an advantage to organic circuitry. Size, performance, cleaner manufacturing process, ..

    • by pepty (1976012) on Sunday October 14, 2012 @04:37PM (#41651637)
      Actually, we are very likely to outperform nature when it comes to specialized jobs like eating crude oil in the gulf. We would start off with the organisms that are there naturally and optimize them for better metabolism in that specific environment, or hybridize them with other bacteria to make them more efficient in other environments. The trade off is the resulting microbes are crap at living under other conditions, but we don't care about that. Nature makes horses fast but evolution balances speed against fragility. People breeding horses make horses much faster - and then watch in horror as their legs break like matchsticks. When it comes to industrial bacteria, people turn mustangs into the equivalent of eight legged quarterhorses on steroids that keel over just after finishing their first race.

      I don't see Moon's research conferring much of an advantage in industrial, remediation, or medical uses; those are best off with a single control mechanism. Most of the decision making process for those situations will continue to be most efficient if it is done outside of the bacteria. For an analogy: a factory could have four sensors hooked up to four smartphones to tell it how much it has in stock of four diffeerent parts and automatically order more when the levels get too low. Or instead a factory could have a sensor and a smart phone phone attached to each and every individual part to do that job. Each part would have to carry that sensor and phone which would inflate its cost without contributing to its final use. Ditto for distributing the control architecture to the bacteria.

      I think the use for Moon's control architecture will be in research; the rest (like you said) will be hype.

  • Engineer discovers biology, builds elementary genetic circuit, and thinks it's a great breakthrough!

  • This was really interesting. And now I am waiting .... for a first bug report.

  • --- Have a Green Thumb? You too can have the latest in organic computing! --- I will have to stick with silicon based computing, if my basil and rosemary plants are any indication.
  • Very interesting article.. For those that didn't read the article, I really like how Moon emphasizes the difference between what has been done before and what he has done. What was accomplished earlier was the construction of gates, circuits and complex systems from non-living material, silicon... But what he has accomplished is the intellectual breakdown of an already living system, and the use of that knowledge to manipulate and prove that he can control it by reproducing the gates and circuits we use for
  • Wins the award for most meta implementation of a genetic heuristic.
    woooaaah

  • So in Little Alchemy, bacteria + bacteria = computer.

All life evolves by the differential survival of replicating entities. -- Dawkins

Working...