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Biotech Programming Science

Scientists Create Programmable Bacteria 117

Posted by samzenpus from the anti-coding-soap dept.
wilmavanwyk writes "In research that further bridges the biological and digital world, scientists at the University of California, San Francisco have created bacteria that can be programmed like a computer. Researchers built 'logic gates' – the building blocks of a circuit – out of genes and put them into E. coli bacteria strains. The logic gates mimic digital processing and form the basis of computational communication between cells, according to synthetic biologist Christopher A. Voigt."
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Scientists Create Programmable Bacteria More

Scientists Create Programmable Bacteria

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  • Can't resist urge to make bad pun.., (Score:4, Insightful)

    by antifoidulus ( 807088 ) on Monday December 13, 2010 @06:04AM (#34532752) Homepage Journal
    But how will they be able to find "bugs" in their program when the program is all bugs? Thank you, thank you, I'll be here all week, try the fish, the bacteria in it all programmed in Sea.... Oh I did it again!

    I apologize profusely for whatever pain the above might have caused.

    • But how will they be able to find "bugs" in their program when the program is all bugs?

      It works for me!

    • Re:Can't resist urge to make bad pun.., (Score:5, Funny)

      by Metabolife ( 961249 ) on Monday December 13, 2010 @06:43AM (#34532870)

      "Today marks a milestone for the computer science and pharmaceutical industries. Partnering with one of the software industry giants, Roche Pharmaceuticals today unveiled the future of fighting rapidly mutating semi-lifeforms. Thanks to Norton Antivirus, no human body will ever be unprotected again!"

      Please note that losing the ability to run or perform other activities quickly is a known and acceptable side-effect.

      • Great I can program up projectile vomiting over my boss's desk, to get a few days off work as sick leave and then get the Programmable E. coli to stop 2 minutes after I leave the office. :)
        • Comment removed based on user account deletion
          • Wooshh... which ironically is also the sound of wanting the additional benefit from "projectile vomiting over my boss's desk"

            What's a few minutes mild suffering, for some payback that just keeps on giving ;)

            • Re: (Score:2)

              by Urkki ( 668283 )

              Wooshh... which ironically is also the sound of wanting the additional benefit from "projectile vomiting over my boss's desk"
              What's a few minutes mild suffering, for some payback that just keeps on giving ;)

              It's possible to achieve temporary projectile vomiting with lower-tech substances than programmable bacteria. Probably easier to get too, I'm pretty sure every ambulance and emergency room has them, for poisoning cases and such. I'm pretty sure you could come up with something with basic kitchen supplies, such as, I don't know, salt...

        • There are 10 kinds of people in the world... those who understand binary and those who don't.

          0b101100101101000001011110000000000

          out of that many

      • Re: (Score:2)

        by clambake ( 37702 )

        In this case: Norton Virus

      • Of course. What could possibly go wrong. Wasn't this the way Walking Dead started?
    • This will give a new meaning to "My computer has died". Also. What do you call a virus used to kill bacteria computing? "OMG I have an antivirus! Help it's killing my pc".

    • Re: (Score:2)

      by weicco ( 645927 )

      Bacteria is living thing! with feelings! We mustn't program them against their will!

    • Re: (Score:2)

      by Krneki ( 1192201 )
      First you need to split them between good and bad bugs!

    • Re: (Score:2)

      by ameline ( 771895 )

      Those aren't bugs, they're features.

      See how easy that was?

    • Re: (Score:2)

      by hitmark ( 640295 )

      Brings new meaning to spaghetti code...

    • Yo dawg, I heard you like bugs so I put a bug in your bug so you can bug your bug while you debug.
    • Obviously the programming language would be Mono.
  • Does it run Linux?

    Imagine a Beowulf cluster of these

    1. Create Bacteria
    2. program it
    3. ????
    4. Profit!

    In Soviet Russia Bacteria programs YOU!

    Think that covers everything.

    • Re: (Score:3)

      by PRMan ( 959735 )
      Yes. And they have a virus that runs Windows...

    • In Korea, only old people program bacteria.

    • You must be new here . . .

    • Re: (Score:3)

      by Barny ( 103770 )

      Bacteria? Hell in my day we were lucky to have an atom!

      Get off my lawn!

    • 1. Programmable bacteria may not injure a human being or, through inaction, allow a human being to come to harm.
      2. Programmable bacteria must execute any program given to them by human beings, except where such execution would conflict with the First Law.
      3. Programmable bacteria must protect their own existence as long as such protection does not conflict with the First or Second Law.

      • Re: (Score:1)

        by jlf278 ( 1022347 )

        1. Programmable bacteria may not injure a human being or, through inaction, allow a human being to come to harm. 2. Programmable bacteria must execute any program given to them by human beings, except where such execution would conflict with the First Law. 3. Programmable bacteria must protect their own existence as long as such protection does not conflict with the First or Second Law.

        how do express that in c# as executable code?

    • Re:Yes but... (Score:5, Funny)

      by Ihmhi ( 1206036 ) <i_have_mental_health_issues@yahoo.com> on Monday December 13, 2010 @10:19AM (#34533748)

      Does it run Linux?

      Yes, but as a side effect it causes open sores.

    • Re: (Score:2)

      by ignavus ( 213578 )

      Think that covers everything.

      bacterium.speak("Hello, world!\n");

      ERROR: method "speak" not found in class Bacterium.

  • That leads to a joke (Score:5, Funny)

    by Chrisq ( 894406 ) on Monday December 13, 2010 @06:23AM (#34532822)

    What do the University of California E-coli research team and Microsoft have in common?

    They are both full of shit programmers

    • I thought your joke was going to go down the E. coli is another name for bugs route. At which point everyone can then make up their own bug/Microsoft jokes.

  • Killer app (Score:5, Funny)

    by Anonymous Coward on Monday December 13, 2010 @06:25AM (#34532828)

    Finally we're gonna see a decent implementation of Conway's Game of Life!

    • Finally we're gonna see a decent implementation of Conway's Game of Life!

      I built a set of logic gates using 5 and 6 year olds. (Human children, that is.)

      We also simulated Conway's game of Life.

      It was a lot of fun for the kids and the geeks, but most of the parents didn't get it.

  • Antibiotics? (Score:4, Interesting)

    by MichaelSmith ( 789609 ) on Monday December 13, 2010 @06:29AM (#34532838) Homepage Journal

    Say you could tailor a bacteria to attack or compete with a bacteria which you needed to control. As the target mutates your attack vector could be reprogrammed accordingly.

    Or how about extending the idea to build a programmable immune system? If the patients immune system has crashed you just feed in tailored bugs to keep infection under control.

    • The article isn't very informative. As far as I know, you can have communication from parents to their children with genetic code. with viruses, you can also broadcast something horizontally to all individuals. From the article I get that they're trying to formalize a programming language that can control 1 individual bacteria.
      Honestly, it's a bit sad that I don't have time to look into the details, even if I don't know a lot about biology.

      However, I will start worrying when they start designing systems of

      • Re: (Score:2)

        by Rand310 ( 264407 )
        They're inserting synthetic genetic code (with known function) into E. coli that will allow individual bugs to respond in predictable ways to other bugs' chemical signals. So, for example, there is a known DNA sequence that encodes a protein that 'recognizes' signal. There is another sequence that encodes a second signal recognition protein. There is a third sequence that encodes a scaffolding that binds the two signal proteins (an AND gate), and it produces some chemical or enzymatic output. This outpu

    • Re: (Score:2)

      by thms ( 1339227 )
      Sorry to rain on your Computer Scientists discover the Wonders of Biology parade, but...

      tailor a bacteria to attack or compete with a bacteria which you needed to control

      This already exists in the from of a virus which attacks bacteria, also known as a Bacteriophage [wikipedia.org]. It doesn't even have to be programmed from the outside to keep up with the evading, evolving bacteria; it just evolves as well. And even if you wanted to "program" this feature, you'd have to deal with the nasty problem of protein folding in silico. Better to leave this entire process highly parallel in wetware.

      programmable immune system

      Also known a

      • Re: (Score:2)

        by Rand310 ( 264407 )

        And even if you wanted to "program" this feature, you'd have to deal with the nasty problem of protein folding in silico. Better to leave this entire process highly parallel in wetware.

        there is no need to deal with protein folding in silico - we know a LOT about proteins and how they work just from standard biochemical assays. There are literally tens of thousands of characterized molecules with known DNA sequences from which we can pick and choose useful sets - slightly modify if need be - and then recombine in novel ways inside a cell. And we can do it directly - without having to rely on some kind of directed evolution - which is quite slow. It is very hard to program a specific wel

    • Or how about extending the idea to build a programmable immune system? If the patients immune system has crashed you just feed in tailored bugs to keep infection under control.

      The complete immune system is to complex to be treated this way, but read up on Phage Therapy. Short form: we don't have the technology yet, but stuff like this is a step in the right direction.

    • ...and how long before someone starts claiming that this has already happened and this is why we have Atlantis myths and the Black Plague? Actually, sounds like a good science fiction story for someone to write.

  • Tinfoil Hat (Score:4, Interesting)

    by Aldenissin ( 976329 ) on Monday December 13, 2010 @06:30AM (#34532840)

    No matter how tight I wear my tinfoil hat, unless it is actually a full body suit and electrified on the outside, I think this will obsolete it. Imagine, cells turn cancerous if your black, gay, white, short, don't have any certain genetic or set of genetic markers. If you leave a certain atmospheric pressure, like come down off your mountain prison it reacts to a change in your body. If you pass or leave a magnetic field (or it accidentally loses power) you're a goner. I could go on and on.

      While I can also think of the wonders this could allow, I think more of what could easily go wrong. When you have American scientists laughing because they gave the Russian's leukemia on accident with an early vaccine test, this doesn't make me feel any better.

    • It's a Dean Koontz book, to be sure. Science goes unexpectedly wrong in horrific ways. Being a Koontz book it would also need the compulsory pet dog and a strong woman the (loner/damaged) hero gets attached to.

    • Re: (Score:2, Insightful)

      by Anonymous Coward

      Take a deep breath.

      People have been poisoning each other with both chemicals and bacteria for thousands of years; what you describe is no different.

      Even the race thing. Each race is statistically more or less resistant to a given disease than others. Think smallpox in the Americas. And if you can't find a suitable genetic marker, just distribute your poison at a suitable gathering.

      Police state devices can already be created with electronics.

      As for these things taking over the world, they'd be out-competed b

  • Comment removed based on user account deletion

  • So ... are zombies the seg. fault? Broken pipe? Shit man, programming just got real.

  • So, they'll still be prone to bacteriophage viruses right?

    • Re: (Score:2)

      by clambake ( 37702 )

      So, they'll still be prone to bacteriophage viruses right?

      I think those will now be referred to as patches.

  • Has to be the worst layman analogy, ever. (Score:3)

    by pinkushun ( 1467193 ) on Monday December 13, 2010 @07:36AM (#34533008) Journal

    “At some point, Microsoft Word had to have been converted to 1s and Os. It's the same way with cells," Voigt said. "What we've done here is created a fundamental language to show that they can work in bacteria. We still have a lot fewer circuits that you could use in computers."

    *chuckles*

  • Trek becomes Reality (Score:5, Funny)

    by Anonymous Coward on Monday December 13, 2010 @07:40AM (#34533030)

    In the TNG episode "The Chase", it's discovered that aliens seeded the oceans of various planets with life and placed part of a computer program into the DNA distributed on each planet. When the various races (humans, vulvans, cardassians, etc) put the code together a billion years later they find an ancient race has left us a holographic message of goodwill and peace.

    We Must do this! Except we change the message to play "Never gonna give you up", Rick Astley built right into the DNA of all living beings forevermore. Just waiting to be found in a billion years. Most epic troll ever.

    • Its a bit odd, but it too can be construed as a message of peace.

      Never gonna give you up
      Never gonna let you down
      Never gonna run around and desert you
      Never gonna make you cry
      Never gonna say goodbye
      Never gonna tell a lie and hurt you

      • Re: (Score:2)

        by ghmh ( 73679 )

        Or to quote Radiohead:

        You do it to yourself, you do
        and that's what really hurts
        You do it to yourself, just you
        you and no-one else
        You do it to yourself
        You do it to yourself

        That being said, pain can be a great teacher.

    • WTF? Vulvans? Wow! I assume they must be all female and use cloning as there means of reproduction.

      I for one welcome our new Vulvan overlords!

    • Re: (Score:2)

      by Trip6 ( 1184883 )

      No way - Boom Boom Pow rules my DNA.

  • Does he pass the Voigt-Kampf test?

  • This sounds like one of those Greg Egan novels I read recently.. What was It... Steve Fever.... http://www.technologyreview.com/Infotech/19534/ [technologyreview.com] Yep, thats it!

  • Mom! (Score:1)

    by bobgap ( 613856 )
    Timmy keep using my lunch to feed the computer! Not fair!
  • So, now I can be sued for copyright infringment after catching a cold?

    1. make programmable bacteria

    2. release bacteria

    3. people get infected

    4. sue the infected people for copying the bacteria

    5. profit!

  • Red Dwarf anyone? A programmable virus? We need never peel potatoes again!

  • This was being done at MIT 10 years ago.
    http://people.csail.mit.edu/rweiss/ [mit.edu]

  • possible original source (Score:3, Informative)

    by anonymousNR ( 1254032 ) on Monday December 13, 2010 @09:39AM (#34533450) Homepage
    Robust multicellular computing using genetically encoded NOR gates and chemical ‘wires’ [nature.com]
    I am not a Biologist. Can some one verify if this is the original paper?

    • Robust multicellular computing using genetically encoded NOR gates and chemical ‘wires’ [nature.com] I am not a Biologist. Can some one verify if this is the original paper?

      It certainly looks like it. One interesting feature that was left out of the /. summary is that the 'wires' in the circuit are quorum sensing molecules - or signalling molecules that are sent and received by all the bacteria in a group. Except that the abstract refers to 'orthogonal' quorum sensing receivers and producers, so I guess each colony make one compound and senses another? Interesting stuff.

      • Re: (Score:2)

        by Rand310 ( 264407 )
        The orthogonal refers to the fact that the molecule is not naturally part of the E. coli sensing system - and so the synthetic 'message' is not convoluted or otherwise disturbed by the natural processes already taking place in the E. coli. So yes, this would allow individual cells or populations to pass different bits. You cold have as many bits of information as you found 'orthogonal' signaling molecules.
  • concerned about this? Oh sure, it won't get out of hand...just like the creation of the A-bomb didn't get out of hand. This one is more scary because it is bacteria. I thought we outlawed germ warfare (even though we know both sides kept up the research).
  • Instead of having bugs in our programs, we are going to have programs in bugs. What would happen if it supports recursion? Is it possible we humans have been looking down the call stack instead of up? OMG indeed. OMG is just one step up the call stack! OMG'sG!!!!
  • Let me be the first to welcome our programmed bug overlords in Soviet America where bugs have programs in Beowulf cluster.
  • I wonder how long till Intel starts marketing Petri dishes!
  • - but my news ticker gave me a virus...

  • I remember reading an ACM journal article back in 1984 or '85 about the possibility of doing this. And now, 25 years later, here we are.

       

  • Is there a cross-compiler for it yet?

  • Programmable bacteria are all well and good, but I would rather hear more about this synthetic biologist. Can he use contractions?

  • This is definitely news for nerds, but this phrase in the summary got me wound up:

    'logic gates' -- the building blocks of a circuit...

    Aargh! Surely someone who doesn't know what a gate is wouldn't be reading slashdot?

  • bacteria with builtin Bluetooth?
  • The ability to encode arbitrary information in DNA has applications in security and encryption.

    Let's say Alice wants to send a plaintext message to Bob. Except with DNA it's always Bob sending plaintext DNA to Alice. OK I have to correct a little bit and replace "Alice" with "Bob" and "Bob" with "Alice"... eh, that didn't work because it replaced all the strings with "Alice".... ctrl-Z ctrl-Z ok let's do this right... first replace "Bob" with a swap like "Sue"... replace "Alice" with "Bob"... wait a seco

  • I've seen a lot of shitty software in my time

  • Is that the biologist Christopher A Voigt?
  • One of the lines had the "mad scientist's" mum asking why on earth he'd want to make bacteria smart? The hero asked his mother, "Why are you so worried?" She answered, "Ask anyone that's ever cleaned a toilet bowl."

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