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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."

21 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.

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

    My wife and I have created 4 of those.

    1. 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.

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

      Do you plan to infect many Windows boxen?

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

      Yes, troll the educated and intelligent.

      You never really left high school, did you?

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      The Kruger Dunning explains most post on /. http://en.wikipedia.org/wiki/Dunning%E2%80%93Kruger_effect
    4. 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.

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  4. 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 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.

    3. Re:WAR! by colinrichardday · · Score: 2

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

  5. 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.

  6. 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.

  7. 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.

  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.

  9. 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.

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  10. 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.

  11. 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.

  12. Synthetic Biologists by commodore73 · · Score: 2

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

  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.

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