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Biological Computer Created at Stanford

sciencehabit writes "For the first time, synthetic biologists have created a genetic device that mimics one of the widgets on which all of modern electronics is based, the three-terminal transistor. Like standard electronic transistors, the new biological transistor is expected to work in many different biological circuit designs. This should make it easier for scientists to program cells to do everything from monitor pollutants and the progression of disease to turning on the output of medicines and biofuels."

56 of 89 comments (clear)

  1. Synthetic Biologists? by Anonymous Coward · · Score: 4, Funny

    We have synthetic biologists now?!?! What happened to the real ones?

    Reminds me of a quote.. "Synthetic scotch and synthetic commanders..." - Scotty

  2. All your base pairs are belong to us. by Gabrill · · Score: 4, Funny

    Hahahhaha funny.

    --
    Always going forward, 'cause we can't find reverse.
    1. Re:All your base pairs are belong to us. by tokencode · · Score: 1

      The problem is that only 0.01% of the population would understand the joke :(

    2. Re:All your base pairs are belong to us. by mcgrew · · Score: 1

      To those of us to understand the pun it's just too obvious to be funny.

    3. Re:All your base pairs are belong to us. by nemesisfixx · · Score: 1

      Your statistics makes the fallacy worse! Am optimistic more than 50% of /. has already tried some GA hacking in one way or another.

  3. Biological Computer? by hawks5999 · · Score: 5, Funny

    My wife and I have created 4 of those.

    1. Re:Biological Computer? by ackthpt · · Score: 1, Insightful

      My wife and I have created 4 of those.

      And they are regularly infected with virii!

      --

      A feeling of having made the same mistake before: Deja Foobar
    2. Re:Biological Computer? by jones_supa · · Score: 1

      It's viruses, not virii.

    3. Re:Biological Computer? by i+kan+reed · · Score: 3, Funny

      I've made up my mind. I'm going to create a computer virus strain called "virii" just to troll people like you.

    4. Re:Biological Computer? by jones_supa · · Score: 3, Funny

      Do you plan to infect many Windows boxen?

    5. Re:Biological Computer? by Belial6 · · Score: 1

      I was thinking Amiga boxes.

    6. Re:Biological Computer? by sjames · · Score: 1

      We need a series of browser plugin virii that will screw up apostrophes, change all plurals to pseudo-latin form and randomly leave out the harvard comma. It should also transpose all instances of loose and lose.

    7. Re:Biological Computer? by Beorytis · · Score: 1

      like Amigas with benefits?

    8. Re:Biological Computer? by geekoid · · Score: 2

      Yes, troll the educated and intelligent.

      You never really left high school, did you?

      --
      The Kruger Dunning explains most post on /. http://en.wikipedia.org/wiki/Dunning%E2%80%93Kruger_effect
    9. Re:Biological Computer? by OhSoLaMeow · · Score: 1

      We need a series of browser plugin virii that will screw up apostrophes, change all plurals to pseudo-latin form and randomly leave out the harvard comma. It should also transpose all instances of loose and lose.

      Who's side are you on? Their not going to like this.

      --
      They can take my LifeAlert pendant when they pry it from my cold dead fingers.
    10. Re:Biological Computer? by avgjoe62 · · Score: 2

      We need a series of browser plugin virii that will screw up apostrophes, change all plurals to pseudo-latin form and randomly leave out the harvard comma. It should also transpose all instances of loose and lose.

      I think the vast majority of computer users in this world already have that plugin.

      --

      How come Slashdot never gets Slashdotted?

    11. Re:Biological Computer? by i+kan+reed · · Score: 1

      Trolling people who are easy to troll is the whole point of trolling. Also, I love that the definition of enlightened is apparently "caring excessively much about proper pluralization".

    12. Re:Biological Computer? by kur0saki · · Score: 1

      I'm officially searching for a (female) research partner to create biological computers.

  4. Slashdot brings you yesterday's news by damn_registrars · · Score: 1

    This was all over the news ... yesterday. Kudos, though, for linking to the original Science paper instead of some crappy summary of it - even though the Science paper is paywalled.

    --
    Damn_registrars has no butt-hole. Damn_registrars has no use for a butt-hole.
  5. WAR! by Xicor · · Score: 2

    it is a war between building a working biological computer and getting the quantum computers to add 2+2 correctly 100% of the time! who will win? im betting on quantum computers. (especially since i would love to see an ansible sometime in my life)

    1. Re:WAR! by raymorris · · Score: 3, Funny

      2 + 2 is one thing, but when they can correctly compute 4195835 / 3145727 they'll be better than Intel.

    2. Re:WAR! by leonardluen · · Score: 1

      low latency is often more important than network speed

    3. Re:WAR! by Xicor · · Score: 1

      ethernet speed is limited by the speed of light. thus, it is not an ansible. technically, if we can get quantum computers to work, we wont need fiber optic cable, because qubits are quantumly entangled, and their information travels instantly.

    4. Re:WAR! by geekoid · · Score: 1

      No information can move faster then the speed of light.

      --
      The Kruger Dunning explains most post on /. http://en.wikipedia.org/wiki/Dunning%E2%80%93Kruger_effect
    5. Re:WAR! by Xicor · · Score: 2

      this is actually incorrect... it has been proven without a shadow of a doubt that entangled particles share information faster than the speed of light. we assume it is instantaneous information, however, like pointed out above, we have no way to prove that it is indeed instantaneous and not just a huge amount times faster than the speed of light.

    6. Re:WAR! by HiThere · · Score: 1

      I think that this depends on how you define information. ISTR that while data is available, calling it information is questionable. E,g,, you may measure somthing and measure it as, say, spinning up, and this will allow you to assert that whenever you opposite number performs the equivalent measurement it won't say spinning down...and that the time could be either before when you measured or after in some particular reference frame. But calling this a tranfer of information is a bit questionable. E.g., you don't know who measured first, and thus determined the signal...or if that's even a meaningful statement.

      --

      I think we've pushed this "anyone can grow up to be president" thing too far.
    7. Re:WAR! by colinrichardday · · Score: 2

      Travels instantly with respect to what reference frame? Infinity is not Lorentz invariant.

    8. Re:WAR! by Xicor · · Score: 1

      correct, but to say it will remain impossible to do this is silly.

  6. Simulated vs. Real results by girlinatrainingbra · · Score: 5, Informative
    There's a good picture of the "simulated results" vs. the results they really got in that Science magazine preview for an AND gate, and a relevant paragraph of the summary : http://news.sciencemag.org/sciencenow/assets/2013/03/28/sn-circuit.jpg
    The Stanford team then showed that they could line up multiple transcriptors to carry out logical functions, creating standard logical circuits called AND gates, OR gates, XOR gates, and so on, which combine signals according to certain rules. (A computer's processor is a vast assemblage of such gates.) They also showed that their novel biological circuit designs were adept at producing signals with large amplification and that they could be used to up the expression of a variety of genes, such as the production of fluorescent signals that made it simple to detect cells that were carrying out their programming.

    I wonder exactly how they "assemble" the circuit and keep the components from diffusing or floating away, thus diassembling the circuit. What keeps the "circuit" of DNA strands in place?

    1. Re:Simulated vs. Real results by Biotech_is_Godzilla · · Score: 3, Informative

      Read TFA for the components of this circuit. The DNA part of the circuit is most likely integrated into the cellular genome, so is effectively stationary in the nucleus. The RNA polymerase component is probably the naturally occurring version of the protein that already exists in the cell. RNA polymerase randomly diffuses around in the nucleus, but there's not just one molecule of RNA polymerase around, there's loads of them, and they can all do the same job. With help from other proteins, they bind to sequences in the genomic DNA that mean "make this gene under this condition", and transcribe the DNA into RNA, which then gets made into protein.

      The conditions under which RNAP binds and transcribes can be dependent on the cell receiving certain signals from other cells, or a gene may be transcribed 'constitutively', meaning it is always transcribed unless the cell changes state/gets a signal from other cells. That's probably what they're using here - RNAP will transcribe what it can transcribe under all conditions, its just that you change what it's allowed to transcribe (see below). The odds of RNAP hitting the DNA part of the circuit are going to be high, and once they do hit the 'promoter' sequence in the DNA part of the circuit, they will lock onto it and start transcribing. They can't transcribe the interesting bit (the 'signal') unless it has been switched on by the third component of the 'circuit', integrase, which removes (and puts back) the "STOP" control for transcription (by cutting at defined sequences, specific to the integrase, either side of the STOP control).

      So the integrase is acting as the gate, and the 'signal' represents electrons flowing to the drain... or whatever. IANACS.

      The method of control for these circuits is probably on the level of the whole cell - the researchers will be adding signalling chemicals to the cells that switch on production of / alter the cellular location of the integrase so that it can either do its job or not. The rest of the circuit doesn't have to be directly controlled as it will constitutively do its job.

      The potentially interesting bit comes from making the 'signal' that's produced be the chemical signalling molecule that controls expression/localisation of integrase in other cells. The problem they'd then immediately run into is that you can't stop the signalling molecule from also acting on the cell that's generating it, locking it into an "on" state, unless the other cells use a different signalling molecule to control their integrase/ use integrases that act at a different specific defined sequence. They could do that, but it would then be difficult to control the placement of cells containing the different flavours of transistor.

      This is all speculation as I haven't got access to the full article, but from the abstract I'm fairly confident that's what these guys have done. It's not about to lead to anything remotely resembling a proper computer any time soon. As I biologist I automatically think of anything associated with 'synthetic biology' as being sensationalist rubbish, and I don't think this is an exception, sadly.

  7. This is not a computer by Anonymous Coward · · Score: 1

    The summary has nothing to do with the headline. A transistor does not a computer make. To have anything worth talking about (as far as computers go), you would need to have a stupendous amount of these so-called "transistor"s interacting. This is no small leap- there is a significant amount of engineering work that goes into a processor even at higher levels of abstraction than gates.

    This is like saying that someone's made a car, when all they really did was make a gear or something. It's just sensationalist BS that belittles the work of actual computer engineers.

    1. Re:This is not a computer by bluefoxlucid · · Score: 3, Insightful

      You're wrong. A small computer can be assembled from a few hundred vacuum tubes. I designed a CPU when I was in high school, on paper, turing complete. 4 bits, 16 instructions. Not a lot went into that.

    2. Re:This is not a computer by i+kan+reed · · Score: 4, Insightful

      A transistor is a computer. It just computes exactly one function on exactly one set of inputs. It's a simple finite state machine.

    3. Re:This is not a computer by SloWave · · Score: 1

      A transistor is a computer. It just computes exactly one function on exactly one set of inputs. It's a simple finite state machine.

      So transistor is a finite state machine is a computer. Well I've got a jar of pennies where each one is a finite state machine and therefore each one is a computer. Or else maybe they should start teaching more engineering and less computer science.

    4. Re:This is not a computer by spire3661 · · Score: 2

      Well then their definition is wrong. An abacus is a literal computation device, a computer.

      --
      Good-bye
    5. Re:This is not a computer by i+kan+reed · · Score: 2

      If someone is going to argue that something is untrue, and there is an understood interpretation of words that makes it true, they are being obstinate. Such semantics should only be argued when someone is holding 2 mutually exclusive definitions at once.

    6. Re:This is not a computer by CanHasDIY · · Score: 1

      Correction: an abacus with a human operator is a calculator. Without the human an abacus does nothing.

      There's a "guns don't kill people" joke in here somewhere, I just know it...

      --
      An enigma, wrapped in a riddle, shrouded in bacon and cheese
    7. Re:This is not a computer by Belial6 · · Score: 1

      The common person does not use "computer" to mean anything other than a device running Windows or maybe OSX. We all happen to know that "computer" means more than that.

    8. Re:This is not a computer by Logger · · Score: 1

      A penny can have more than one state, but a finite count of them. A transistor can have one state unless you add a method to change it, such as a sine wave generator or another transistor. Then it is a transistor + input generator make a computer. The penny has itself and a small image (signal) that make it a computer.

      You're confusing transistor with flop-flop or flash cell or something which is slightly more than just a transistor. Which by the way, a transistor does not have a finite number of states. Transistors are analog devices with continuously infinite number of states. It just happens that digital computers use them in arrangements of multiple transistors where we generally only use 2 states.

    9. Re:This is not a computer by phantomfive · · Score: 1

      Sequential logic isn't the problem, it seems they've found a good way to propagate the signal. Neither is clock skew, there are ways to deal with that, and even clockless computer designs.

      The biggest question is whether they can feed a signal back into a circuit, a flip-flop. A secondary question is reliability, whether you can use the same circuit repeatedly without it self-destructing. Once you've got that (and assuming their signals propagate as well as they think), then you have no problem building a computer. Will it be fast? Probably not, but it can still have uses.

      --
      "First they came for the slanderers and i said nothing."
    10. Re:This is not a computer by geekoid · · Score: 1

      No it isn't.
      It's like saying one of your cells is you. i.e. stupid.
      A computer need to ..compute.
      A transistor does not use a set of instructions.

      --
      The Kruger Dunning explains most post on /. http://en.wikipedia.org/wiki/Dunning%E2%80%93Kruger_effect
    11. Re:This is not a computer by geekoid · · Score: 1

      yes, an abacus is a manual power computer.
      But a transistor isn't a computer any more then one bead from an abacus is a computer.

      --
      The Kruger Dunning explains most post on /. http://en.wikipedia.org/wiki/Dunning%E2%80%93Kruger_effect
    12. Re:This is not a computer by geekoid · · Score: 1

      There in no requirement on the power source to call something a computer.

      --
      The Kruger Dunning explains most post on /. http://en.wikipedia.org/wiki/Dunning%E2%80%93Kruger_effect
    13. Re:This is not a computer by geekoid · · Score: 2

      " Transistors are analog devices with continuously infinite number of states."
      You could have just said you don't know how a transistor works. I mean, sure that sentence conveyed the same information, but is seems like a round about way to show off your ignorance.

      --
      The Kruger Dunning explains most post on /. http://en.wikipedia.org/wiki/Dunning%E2%80%93Kruger_effect
    14. Re:This is not a computer by CanHasDIY · · Score: 1

      I don't get it - is that the setup, or the punchline?

      --
      An enigma, wrapped in a riddle, shrouded in bacon and cheese
    15. Re:This is not a computer by mattack2 · · Score: 1

      The other summary posted, http://science.slashdot.org/comments.pl?sid=3595685&cid=43312417, says they have created "standard logical circuits". That summary doesn't mention NOR gates, but it does mention OR gates, and I'm making the leap that they have an inverter.

      So wikipedia says you can make a flip flop with NANDs or NORs.

      Where is the flaw in my logic (no pun intended) that they likely (my inverter leap) have enough parts to make a flip flop?

    16. Re:This is not a computer by phantomfive · · Score: 1

      The flaw is you're depending on what you read in Slashdot comments. Why don't you go read the article and figure it out? Better yet, read the paper.

      --
      "First they came for the slanderers and i said nothing."
    17. Re:This is not a computer by mattack2 · · Score: 1

      The comment was just quoting from the same article. (Though I admit I didn't check that at the time.)

    18. Re: This is not a computer by Logger · · Score: 1

      Try using google my friend.

  8. Good point, but a dozen can run vmware by raymorris · · Score: 3, Informative

    Perhaps the headline should have said "logic gates" instead of "computer". It didn't say "Core i7" either, though. Babbage's machine was a computer. Programing graphics processors with punch cards dates to the early 1800s, so "computer" doesn't imply a modern desktop.

    I suspect you'd agree that any processor capable of running Windows is a computer. Therefore, any machine that can run a hypervisor, which in turn runs Windows, is a computer. You probably know where I'm headed - Turing machines. Any Turing machine can emulate a Core processor, and is therefore a computer. Wolfram's Turing machine requires only a few gates, so these researchers can probably build a biological Wolfram Turing computer today.

    1. Re:Good point, but a dozen can run vmware by Belial6 · · Score: 1

      A C64 or Apple II are not practical either. That doesn't mean they are not computers.

    2. Re:Good point, but a dozen can run vmware by raymorris · · Score: 1

      A Core i7 emulator running on an Amiga, or on a Picaxe, is also not realizable in a practical way. Most certainly an Amiga is a computer.
      The core functionality of a simple PIC micro is a few thousand transistors. IO is several thousand more. If they already have gates with six transistors or so each, combining a dozen gates into modules and a dozen modules into a simple CPU is not a huge leap. It's not a computer, yet, but it's a couple of incremental steps away.

  9. This will change the terminology by Oloryn · · Score: 2

    So, is this going to bring a new meaning to the term "computer virus"? As in an actual biological virus might affect the hardware.

  10. Synthetic Biologists by commodore73 · · Score: 2

    I think it is more interesting that we have created synthetic biologists (as per the summary).

  11. An Abacus is a series of registers, not a computer by girlinatrainingbra · · Score: 1

    An abacus may be seen to be a series of registers. Each string holds beads and the positioning of the beads on the string sets the value of the register.
    :>)
    The human operator of the abacus is the executor of the machine code: it's the human that:
    -- reads the value of a register (by looking at it)
    -- stores a numeric value in a register (by sliding beads)
    -- performs the carry when overflow occurs by carriage returning the beads in one row and moving an extra bead in the next (above or below depending on your own definition) string
    -- transfers values from paper or mind onto the string
    .
    So obviously an abacus merely is a large temporary variable allowing a human being to perform calculations without holding all of the digits in their own memory: the abacus is a set of registers holding integer numeric values, an abacus by itself is not a computer, but just part of a computing system. It requires an agent, a human "computer" (or a sufficiently programmed and capable (vision + motion) robot !!!) actor in order to be a full computing system.

  12. An Abacus is a series of registers, not a computer by girlinatrainingbra · · Score: 1

    An abacus may be seen to be a series of registers. Each string holds beads and the positioning of the beads on the string sets the value of the register. :>)

    The human operator of the abacus is the executor of the machine code: it's the human that:
    -- reads the value of a register (by looking at it)
    -- stores a numeric value in a register (by sliding beads)
    -- performs the carry when overflow occurs by carriage returning the beads in one row and moving an extra bead in the next (above or below depending on your own definition) string
    -- transfers values from paper or mind onto the string
    .
    So obviously an abacus merely is a large temporary variable allowing a human being to perform calculations without holding all of the digits in their own memory: the abacus is a set of registers holding integer numeric values, an abacus by itself is not a computer, but just part of a computing system. It requires an agent, a human "computer" (or a sufficiently programmed and capable (vision + motion) robot !!!) actor in order to be a full computing system.