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Biotech Science Technology

Researchers Build Logic Gates With RNA 58

Posted by Soulskill
from the finally-a-use-for-that-pesky-rna dept.
Ars Technica reports on research out of Cal Tech where scientists were able to create logic gates out of RNA molecules. Thus far, they've demonstrated AND gates and OR gates, with work proceeding on more complicated systems. The work shows promise for ability to easily detect the presence of particular chemicals. The abstract from the scientists' paper is available at Science. Quoting Ars: "Detecting tetracycline isn't especially interesting, but RNA that binds to specific small molecules is actually relatively easy to make; repeated rounds of amplification and selection for binding can evolve these RNAs in a couple of days. This means that, in a matter of days, researchers can grow yeast colonies that glow in response to a variety of chemicals, or even to combinations of chemicals. More complicated circuits should be possible if the ribozymes are inserted into messenger RNAs that encode transcription factors, which could, in turn, regulate genes that encode yet other ribozymes."
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Researchers Build Logic Gates With RNA

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  • Nice... (Score:5, Funny)

    by Anonymous Coward on Saturday October 18, 2008 @05:24AM (#25422831)

    But how long before it runs Linux?

  • I guess this means skynet will be part-biological.
    • Re:Uh oh... (Score:5, Insightful)

      by Cylix (55374) on Saturday October 18, 2008 @05:47AM (#25422873) Homepage Journal

      Completely wrong track I'm afraid.

      Skynet is more cell phones, cash registers and anything with a system.

      Matrix was more humans are batteries, but in this case we get to be both networked pods and large D cells.

      Yes, it could be said that the matrix villains are far more green then the terminators. Marketing research shows that hippies prefer matrix type overlords.

  • even my stupid neighbour has plenty of intelligence!
  • by The Clockwork Troll (655321) on Saturday October 18, 2008 @05:48AM (#25422875) Journal

    Perhaps the results of this research can be used to create biological instances of the satisfiability [wikipedia.org] problem.

    If satisfiability can be reduced to DNA transcription in polynomial time, then we could genetically engineer colonies of randomly poisoned cats in boxes to solve NP-complete problems.

  • If this can (after more research) be used as a basis for cell 'monitoring', that, in itself would be amazing

    Our ability to transmit information to and from living systems, and to process and act on information inside cells

    From that quote I would guess that, yes, it can be extended; but I am at home and cannot read the whole Science article. More interesting is the possibility of cell manufacturing... factories that churn out cells with particular attributes and particular reactions on demand. That might be a bit far into the future though and the process may need to branch and include DNA. Nonetheless, this research is

    • by Moraelin (679338) on Saturday October 18, 2008 @06:26AM (#25422957) Journal

      1. Actually, I don't know if they really need a cell.

      Even from the viewpoint of life evolution on Earth, it all started with some self-replicating ribosyme that "lived" perfectly well in the soup of aminoacids and nucleotides around it. The cell was just an increasingly complex test tube around that reaction, complete with increasingly complex ways of regulating the exact composition of the contained drop of sea water.

      I can see how that was an advantage to evolve, in a primordial soup that was hit and miss anyway and probably (very slowly) degrading in quality over time. But in a lab, we can do that regulating artifficially. Admittedly, using a cell might be cheaper, but we can do without it too.

      And indeed there is plenty of organic stuff we already do without a cell. E.g., detecting certain DNA sequences is done via enzymes which bind exactly to one sequence, and start replicating it until it's enough to be detected. We don't really build specialized cells for that.

      2. Actually, to me another aspect is more interesting there: the fact that it's all done with RNA.

      Proteins already _do_ exactly what these guys seem to do: bind only to certain mollecule configurations, but not to others. You can see it as logic operations and whatnot, but really it's all chemistry and that's all it does: bind only to certain mollecules, but not to others. It's a bit like saying that a keyring with two keys is a mechanical OR gate: it unlocks a lock that matches either key 1 or key 2. It's simultaneously technically true, and a bit misleading.

      But there's a more interesting aspect to it: your body usually uses proteins for that, and DNA/RNA is just a way to encode a protein which will actually do the matching. E.g., those enzymes I mentioned, are proteins. They do all the heavy duty chemistry, from processing the cell's "food", to regulating what goes in or out, to destroying all chemicals which are non-polar and pass right through the cell wall instead of being regulated by the protein valves on the wall, to movement, to DNA repairs, to regulating what other proteins are built and where do they go.

      As long as that's all the model we know, that needs a rather complex initial configuration for the start of life. You need something that's capable not only of replicating itself, but also of encoding proteins. It's already a bit too big an incredible machine, and appearing out of nowhere, even after billions of years and trillions of tries per second, still is a damn improbable event.

      But that everything can be done via RNA only, that opens a whole new possibility. We already know that RNA can replicate itself. If it can also take the functions of a protein, offers a much simpler initial configuration for life. It's entirely possible that assembling proteins came later, as a better replacement, much like DNA later replaced RNA as the encoding of choice. The first cells could have been RNA-only, but could still have a metabolism and be able to regulate themselves well enough.

      I find that fascinating.

      • I don't know if they need a cell either. What I find interesting is that this may become a way of monitoring cell processes. I.e. a way of monitoring that can do more than we currently can. You said it:

        But there's a more interesting aspect to it: your body usually uses proteins for that, and DNA/RNA is just a way to encode a protein which will actually do the matching. E.g., those enzymes I mentioned, are proteins. They do all the heavy duty chemistry, from processing the cell's "food", to regulating what goes in or out, to destroying all chemicals which are non-polar and pass right through the cell wall instead of being regulated by the protein valves on the wall, to movement, to DNA repairs, to regulating what other proteins are built and where do they go.

        _That_ is what I am interested in seeing elucidated more than current technology can. I don't know if this research can do it, but it, certainly, seems like it's along the right path.

      • RNA world hypothesis [wikipedia.org]

      • Re: (Score:2, Informative)

        by Anonymous Coward

        IAACB (I Am A Chemical Biologist), and your enthusiasm is great, but there are just a few gaps in your understanding that modern biochemistry is just starting to fill in...
        The classical idea that RNA is nonfunctional has really more and more fallen by the wayside, especially since the crystallization of the eukaryotic ribosome. More and more, we understand that RNA, while not as robust at doing chemistry as proteins, is really a very powerful tool within the body and life in general. One recent discovery

      • The whole point of the article is that they can (possibly)construct synthetic RNA that would regulate gene expression. The fact that they have linked computation to gene expression means they can use computer logic to synthesize RNA that would either express a gene or suppress it; and there is an exact method for doing that now.

        Before this, it was a kind of guessing game where they could inhibit a gene but it would turn on expression of some other gene like "violent aggression". I assume this will eventua
      • by Bazer (760541)

        I find that fascinating.

        I disagree.

        Personally, I find that completely awesome.

  • ANDs and ORs are nice, but what about a NAND (Not AND)? Give me a NAND, and I can implement any Boolean equation.
    • by tsjaikdus (940791)

      In any other industry you don't need logic gates perse to build something that does arithmetic. It's the electronics industry that defines the NAND gate as the primary building block, because chips are made with that specific technology.

      It's really all about shifting bit from one place to the other. Gates are only a convenient way to do this.

      • Re: (Score:3, Informative)

        by Anonymous Coward

        You didn't really get it.

        With a NAND (or a NOR), you can implement any logic function.

        NOT(x) = NAND(x,x)

        Now that we have a NOT gate using NAND only, we can use it to implement AND:

        AND(x,y) = NOT(NAND(x,y))

        Using AND and NOT (which only use NAND), you can implement a OR:

        OR(x,y) = NOT(AND(NOT(x),NOT(y)))

        You can't do this with AND, OR, or combinations of the two. Specifically, you can't use them to implement a NOT.

        • by tsjaikdus (940791)

          I'm just adding that gates are not a prerequisite for building something that can calculate. People often 'prove' that once you have your basic gate(s), you can thus also build a computer. The thing is that in the chip making industry gates are very useful. But in other fields of industry (biological, chemical, mechanical) gates may not be the best building block.

          • by ricegf (1059658)

            Of course. In high school, I created a gate-less electrical calculating device for a science fair project. But according to the summary, the article is about building logic gates with RNA. I was commenting in that vein.

            Another way to calculate with RNA is to construct a living creature. Humans calculate, for example (well, at least some of us). So do chickens, dolphins, and various primates, or so I read. I bet my dog could, if some roasted meat was involved. :-)

            • by RockDoctor (15477)

              Another way to calculate with RNA is to construct a living creature.
              [SNIP]
              I bet my dog could, if some roasted meat was involved. :-)

              Why roasted ... ah, your dog has never encountered raw meat. Or at least, never encountered it in the context of "food".

              Which is sadly plausible.
              I remember being astonished the first time I encountered two kids (my sister's first two step kids) who didn't recognise a lump of coal. I wouldn't have been surprised that they didn't recognise it's significance (as part of t

              • by ricegf (1059658)
                Huh? I live in Texas - my dog kills and eats a variety of wildlife. But she prefers her meat roasted. Don't you??
                • by RockDoctor (15477)

                  Huh? I live in Texas - my dog kills and eats a variety of wildlife.

                  That wasn't present in your posting ; from the characters on screen you could just as well have been living on the 17th floor of a tower block in the heart of a big conurbation - like Houston, for example - with your neighbour having a de-clawed cat who's never been out of the apartment.

                  But she prefers her meat roasted. Don't you??

                  NULL - no preference. It's food. It all comes out (of me) the same.

        • by tsjaikdus (940791)

          As an example, Babbage invented an anticipatory carriage that added all carries (40 or 50 in his machine per register) simultaneously. In electronics they use something similar which is called a look ahead carry. But it will typical add 4 carries at once (some other techniques exist to speed up things, but in the end you'll always use some translation mechanism that ripples a carry). Babbage's mechanical solution really did not ripple. It was later also used by Wiberg's difference engine.

    • Re: (Score:3, Insightful)

      by cryptor3 (572787)

      Why restrict them to discovering a nand implementation? I was going to ask how close they were to implementing "not".

      I'd rather ask the less restrictive question of how close they are to implementing a functionally complete set of gates in their process technology.

      So for example this could be any of {nand}, {nor},{and,or,not}.

      After all, it could be that in the RNA domain, building things out of all NANDs just isn't as efficient (in whatever sense they mean) as in static CMOS.

  • Why are they working on more complex systems? If they already have AND and OR, all they need is a NOT and they can make any other type of gate
    • I would imagine that NOT is implicit already (i.e. if A || B == false then it's !A and !B)
      • My last comment is obviously wrong. All that can be said is that it's NOT A and NOT B. But my original meaning still stands... they can infer NOT, and I can imagine the research easily implenting the NOT operator.
        • Re: (Score:3, Funny)

          by eric-x (1348097)

          > My last comment is obviously wrong.
          > But my original meaning still stands.
          1.post theory and proof
          2.retract proof and state that the theory is still valid.

          Interesting concept you have there...

  • 3D Processors, Quantum Computers, DNA/RNA based Computers. A lot of progress is being made in these fields, it seems. But how many of them will actually make it into usable devices, if any?
    • > But how many of them will actually make it into usable devices, if any?

      They're irrelevant until they speak x86.
      • by tsjaikdus (940791)

        You're right, we should stop all R&D right now. Until we know for sure that some usable devices will come out of it. Like the IKEA Three-seat sofa with long cover white.

  • A similar technology is DNA stem-loop logic gates [unm.edu]. Theye were used to make MAYA and MAYA II [wikipedia.org], a DNA computer that could play tic-tac-toe.

  • Do you run linux?
  • by Anonymous Coward

    Yes, yes, it looks and sounds cool and that's precisely why it was accepted into Science, but if you look closer at the results then you'll be greatly disappointed.

    Why? Their RNA switches don't really perform as logic gates. When we think of logic gates, we think that the "signal" -- voltage in the case of electronic circuits or the production of a reporter gene in this case -- will have a clear difference between the "ON" and "OFF" states... 1 and 0. Electronic circuits are designed so that the voltages th

    • by Intron (870560)

      "When the RNA switch is ON, then the gene expression reporter will have an output of (for example) 1030. When the RNA switch is OFF, then the reporter will output 1000."

      So you are saying that a reporter has a great deal of bias? What else is new?

  • We already have DNA-based computing. Google "bacteria computer" or "bacterial computer". These are based on building DNA sequences which get up-regulated or down-regulated in the presence of certain chemicals. By joining these sequences together with sequences which produce the chemicals, they form logic gates. Researchers have been doing this for several years.

    So what's the advantage of using RNA to build circuits? The article doesn't seem to explain what the point of this is, how it would be applied,

  • OT Rant (Score:1, Informative)

    by Anonymous Coward

    Gaah! This pisses me off every time I see it. I've got two degrees from the California Institute of Technology, and it's Caltech, dammit, not "Cal Tech". Get it right!

  • "What's that glow?"

    "Um...did I mention that I have a bit of a yeast infection?"

  • by unassimilatible (225662) on Saturday October 18, 2008 @03:02PM (#25425549) Journal
    This means that, in a matter of days, researchers can grow yeast colonies that glow in response to a variety of chemicals, or even to combinations of chemical

    As a homebrewer, there are lots of chemicals that show up in beer, some good, some bad. It would be great to modify a strain of yeast that would glow when diacetyl or some other chemical was present.

Computers are unreliable, but humans are even more unreliable. Any system which depends on human reliability is unreliable. -- Gilb

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