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Biotech Science Hardware

MIT Making Computer Parts from DNA 243

Posted by CowboyNeal from the growing-more-storage dept.
Rei writes "Following in the footsteps of Lynn Conway's pioneering work on VLSI that allowed ordinary students to create their own processors, a group of MIT professors have almost completed doing the same thing using DNA, known as synthetic biology. While not all of the components of a basic computer are working yet, there is hope that some day ordinary students may be able to design living computers, producing everything from novel drugs to seeds that sprout into treehouses."
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MIT Making Computer Parts from DNA More

MIT Making Computer Parts from DNA

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  • Humans playing God? (Score:5, Interesting)

    by IO ERROR ( 128968 ) * <error@ioe[ ]r.us ['rro' in gap]> on Monday January 10, 2005 @10:21PM (#11317004) Homepage Journal
    This has been on /. twice [slashdot.org] before [slashdot.org].

    Anyway, it appears that they're actually trying to create synthetic living things, which is way beyond computer parts. If they can pull this off, it will be one hell of a hack. Humans playing God, creating life. Theology may well be shaken to its very foundations.

    • Re:Humans playing God? (Score:4, Funny)

      by orangesquid ( 79734 ) <orangesquid@nOspaM.yahoo.com> on Monday January 10, 2005 @10:33PM (#11317080) Homepage Journal
      I'm just waiting until the DEAMCA prohibits the transfer or publication of any DNA-code which is capable of producing controlled substances...
    • Theology may well be shaken to its very foundations.

      How so? What does it prove that we can "create" life? If anything, it's more proof that some religions are right. The great immitator at work again, man wanting to replace God.

      Pan

      • I don't know.. man creates God, man creates nanotech, nanotech destroys man, aliens laugh at silly carbon-based lifeforms.

      • Re:Humans playing God? (Score:5, Informative)

        by MillionthMonkey ( 240664 ) on Tuesday January 11, 2005 @12:15AM (#11317696)
        There are efforts to construct living creatures (all prokaryotic) de novo from nothing but inert chemicals and information from sequence databases. If these efforts are successful in creating a viable organism from nonliving sources, it should rightly shake our thinking in a number of fundamental ways.
        • First of all, if we succeed in creating life from non-life (and only non-life), we demonstrate that a process of abiogenesis is physically (i.e. kinematically and thermodynamically) possible. Abiogenesis has never been directly observed, only inferred from our existence.
        • If we can demonstrate abiogenesis, we also demonstrate a weaker possibility- if it's possible to create life from chemicals, it's possible to create life from matter that is no longer alive (i.e. dead).
        • We also demonstrate that abiogenesis may have happened before. After all, if we can make a bacterium from scratch, it isn't as farfetched to suggest that bacteria might have arisen from natural processes. Our technology is constrained by nature.
        • There is also a large class of interesting biological questions one might finally answer. For example, your DNA is right-handed and your proteins are levorotary. This is common to all life on earth. Nobody knows if a biochemistry based on left-handed DNA and dextrorotary proteins is viable or not. Some people say things twist the way they do because of chance in the way they evolved; others say things have to be this way because of the weak nuclear force or something. If we can create a "normal" bacterium from dead chemicals off the shelf, we can create a mirror image version, and directly observe how well our mirror-image bacteria digest sugars of either chirality.

        • Re:Humans playing God? (Score:3, Interesting)

          by Anonymous Coward
          What if we create a bacteria that is toxic to us?

          The problem that I have with 'creating life' is that how do we know that what we do is going to be something that doesn't create a plauge?

          I guess that the modivation of most people over there at MIT is that they want to patent something and then live off of it for the rest of their lives. They don't seem to me to actually be concerned about anything more than their next grant or getting tenure and being shown as being so clever.

          So, if the profit motive is
          • Oh, and if they want to play god, then don't do it from a tax-free organization. Also, if they are tax free then all of their patents should be in the public domain.

            Public universities issue patents all the time. They even have foundations [uvapf.org] set up for that very purpose.
        • If we can demonstrate abiogenesis, we also demonstrate a weaker possibility- if it's possible to create life from chemicals, it's possible to create life from matter that is no longer alive (i.e. dead).

          Being able to re-create life from dead things does not mean making them alive again... it just means you create a new life from the remains (inert) of another life form. Let's not get into "Pet Cemetary" like arguments here =)

          IMHO, abiogenesis is inevitably possible. But I also think that that raises an

          • I also happen to think that consciousness is very fundamentally linked with quantum physics and how nothing is deterministic. But that's just really far out there, and people are going to call me crazy...

            I share that opinion, and so does Penrose. I have a braindump of my thoughts on it here [happy-digital.com], where I deviate from Penrose quite a bit. I'm sure he doesn't care. The first paragraph is the most lucid; the rest goes a little bit into left field.

        • The reductionistic approach of science has been pretty powerful in explaining many of the mechanisms of life and mind and finding remdies for their defects (disease). The construction of operations life from shelf chemicals would seal this argument.

          A scientist, I still have to keep all possible hypothesis in my mind, include that of an unmeasured "life force", unlikely as that seems to be necessary, until shown otherwise.
    • GM stuff isn't playing God? Putting genes from a fungus into a fish is not plaing God?

      There was a story on shashdot a few months ago (can't find it..) indicating that some researchers created a virus or a bacteria from non-living components.

      I think this story is more about creating life for a purpose that we do not find natually. Other than that, it is already here.

    • Why focus on playing god when just as easily you can play the devil with this? If this is for real then your next script kiddie attack might be in your lungs. Well we're either going to live through the next decades of tech evolution with a total genetic makeover but more likely we're going to die because some weird pathogen escaped from a lab or we open sourced bioengineering. I guess you can already buy the basic tools on ebay...
    • I'm going to wait until they build a human being atom by atom, copying the exact electrochemical composition of someone's brain, shock them to life, and "discover" that yes, you get a real person out of that, no different than the birthed one (except of course for any mistakes you make).

      Sacks of chemicals, people. Just interesting sacks.

  • Ha (Score:5, Funny)

    by aendeuryu ( 844048 ) on Monday January 10, 2005 @10:22PM (#11317011)
    While not all of the components of a basic computer are working yet, there is hope that some day ordinary students may be able to design living computers, producing everything from novel drugs to seeds that sprout into treehouses.

    [Slashdot user looks up from sketchpad] What's that? Seeds that sprout into treehouses? Yeah, I suppose that could be useful.

    [Goes back to designing Angelina Jolie X7c]

    • Re:Ha (Score:3, Funny)

      by Spy der Mann ( 805235 )
      [Goes back to designing Angelina Jolie X7c]

      Yeah, so nice and everything, but will it run Linux?

      • Re:Ha (Score:2)

        by addaon ( 41825 )
        Run it, or ride it?
      • "[Goes back to designing Angelina Jolie X7c]"

        Yeah, so nice and everything, but will it run Linux?

        Alright, all you AJ-X7c's into the hot tub. It's time for a Beowulf cluster!

    • [Another loser looks up from MolecularDesigner v0.12b] Oh yeah? I snagged some DNA from Jolene Blalock at the last Star Trek convention! I'm almost done with my T'Pol mods: real vulcan ears; nympho-nnet-brain-1.2; <censored>; >censored>; and green eyes.

      [Gets the 105 pounds of feedstock matter ready for the Molecular Assembler]

  • BOFH on DNA (Score:5, Funny)

    by djupedal ( 584558 ) on Monday January 10, 2005 @10:24PM (#11317026)
    You can't prove that I had any of the fruit or veg that has your IP in it!" the Boss blurts, placing his summons on my desk.

    "You may be right," I say, "but I'm sure that a quick subpoena would sort everything out."

    "Subpoena?" he asks. "What for?"

    "Just a sample of your DNA - to prove that you now contain some of my IP."

    "It won't show anything!"

    "Oh, don't worry, I'd subpoena your tissue again if the first test was inconclusive."

    "And keep on doing it until you find something I suppose?"

    "Oh no. No, we only get two cracks at it - unless you've got three testicles"

    "WHAT!"

    "Yes, Well you realise that if you've absorbed my IP, any children you have would have to be licensed, and of course the only way I can prove absorption would be through your reproductive organs."

  • BMI (Score:4, Funny)

    by halcyon1234 ( 834388 ) <halcyon1234@hotmail.com> on Monday January 10, 2005 @10:26PM (#11317037) Journal
    You RTFA, nerds. At last, those extra pounds will come in handy. No longer is it a beer gut-- it's a new video card. It's not a fat ass-- it's a 200 GB Maxtor hard drive.

    On a side note: ew.

  • Doing DNA at home... (Score:5, Interesting)

    by TheSync ( 5291 ) on Monday January 10, 2005 @10:26PM (#11317038) Journal
    If you want to try this yourself, check out DNA Hack [dnahack.com], the website for Amateur Genetic Engineering
    • Simple DNA manipulations have been undergradate lab projects and now high school science fair projects for years.
      Not that the nerdy kid next door is going to stumble onto a Frankenstein ....

  • food (Score:4, Funny)

    by twoes00 ( 839980 ) on Monday January 10, 2005 @10:28PM (#11317055)
    Bah, who needs drugs and treehouses. it should say: producing everything from novel sandwiches to seeds that sprout into cakes." :) Now thats an application!
  • I have visions of Superman 3 going through my head... (or maybe a real life version of ExistenZ)

    Curious. The sci-fi approach has always been machine interfacing with man but I don't think too much thought was given to specially engineered organic components that are all wetware but serve non-organic functions. (Well, maybe Giger...)
    • Funny, I had a vision of the first Superman movie when they mentioned seeds that sprout into tree houses. First thing I thought, "or crystals that sprout into ice palaces?" I know it's not ice.
    • Makes for some fun (and mind-bending) RPGs. A good plot device is to have the PCs be a team of researchers searching out hitherto unknown IP, but the Bad Guys want to stop them, or get it first, or are the IP in question. Throw in some corrupt officials, conspiracies, and plot twists, and you're good to go.

  • Flattery'll only get you so far... (Score:5, Funny)

    by Tackhead ( 54550 ) on Monday January 10, 2005 @10:36PM (#11317097)
    So - humans playing God, synthesizing life from its basic components. Hubris, or something better?

    Without stating a position either way on the existence (or nonexistence) of God, what better way to glorify a Creator than by showing Him we've learned some of His tricks?

    (Allow me one assumption here: the assumption that if God exists, He's not a copyright lawyer, and will be flattered by our success, rather than whomping us with a Deistic Millenium Copyright Act violation notice in the form of a 20-mile-wide asteroid.)

    God: I created you by breathing life into dirt.
    Man: Cool trick, God. We've learned to do the same thing.
    God: Cool trick. Now try it from first principles.
    Man: What do you mean?
    God: Well, next time, make your own dirt.

    And before you point out - correctly - that with a sufficiently large energy input we could indeed synthesize all the components that make up "dirt" out of hydrogen, you haven't solved the problem. Ultimately, it comes down to this:

    God: Look, I appreciate the flattery, and I encourage you to keep at it. But read the job description -- you qualify for My job when you derive a universe capable of evolving intelligent life based on the setting of a small number of physical constants, and you can have My job when your resume' includes experimental proof in the form of a portfolio that includes your worshippers.

    We hairless apes still have a bit of work to do.

    • God: I created you by breathing life into dirt.

      Man: Cool trick, God. We've learned to do the same thing.

      God: Cool trick. Now try it from first principles.

      Man: What do you mean?

      God: Well, next time, make your own dirt.

      Man: Hey, God!

      God: Now what?

      Man: I think I figured out that last trick. [composters.com]

      God: Doh.

    • No God, no matter how perverse would allow Windows to run on His creations.

    • And before you point out - correctly - that with a sufficiently large energy input we could indeed synthesize all the components that make up "dirt" out of hydrogen, you haven't solved the problem.

      Indeed. Where would they get the hydrogen and the energy? All methods of energy "production" that we are capable of are really just methods of converting what is already there.

      My personal theory of LUE (Life the Universe and Everything) is that God made man to explore the creation of God of which man is a par

    • God: Look, I appreciate the flattery, and I encourage you to keep at it. But read the job description -- you qualify for My job when you derive a universe capable of evolving intelligent life based on the setting of a small number of physical constants, and you can have My job when your resume' includes experimental proof in the form of a portfolio that includes your worshippers.

      You should read Permutation City, by Greg Egan --- it's a seriously mind-blowing book where the characters do exactly that.

      Exc

    • My job when your resume' includes experimental proof in the form of a portfolio that includes your worshippers.

      Only an insecure deity would want or need worship. Wouldn't it be embarrasing to have a deity with the divine equivalent of acne, a stupid laugh, and no social skills? The only form of worship I'd want is an occasional sapient showing up at the temple and saying things like, "Look! We have invented this excellent thing to do with grains; we call it 'beer'! Want to try some?"

  • finally! (Score:4, Funny)

    by binarybum ( 468664 ) on Monday January 10, 2005 @10:38PM (#11317111) Homepage
    This should push stem cell research to the point where I can grow my own Shakey's right next to the existing one!
  • Who's DNA to use? I suppose linus and gates would be up for it. And of course, linus DNA would be under the GPL... right?

  • Imagine the greater system possibilities! (Score:4, Interesting)

    by theblacksun ( 523754 ) on Monday January 10, 2005 @10:44PM (#11317144) Journal
    Integrate these biological components into a electrical/electronical/mechanical system and you can get some neat toys.

    How about a tree designed specifically to hide wireless cameras/microphones?

    Home biological garbage disposals, like a fast-paced compost pile.

    How about some easily controlled flying insectoid? You could tap into its optical system and save yourself the power of the cameras, just have the transmitter.

    Of course I am ignoring the possibilities of abuse. They are both endless and quite horrifying.
  • Seeman's NYU lab is at the forefront of DNA "machine" synthesis. They might even produce working "Wang Carpets", intelligent "machines" made entirely of DNA, a la Greg Egan's fictional inventions.
  • ...seeds that sprout into treehouses

    Was any part of design done by students living in hollow tubes under the ocean, having sex to let nanoprobes in their blood exchange information [wikipedia.org].
  • Aren't "living computers" basically what we are?
  • While not all of the components of a basic computer are working yet...
    They are still trying to figure out how to make a printer, a floppy drive, and a mouse out DNA. Definitely promising technology though.
  • seeds that sprout into treehouses

    The only novel I've seen this in is Forge of the Elders [amazon.com] by L. Neil Smith. Awesome book, if, like me, you don't mind the libertarian propaganda. :)
  • Ordinary students can't even design computers that don't crash like a burning treehouse. Hell, teams of engineers can't do that, either. How can we expect teams of engineers to unleash genetic engineering tech that won't burn the Earth, the treehouse we all live in? Advances like these make the space program look more and more essential.

  • Carlson Curves (Score:3, Funny)

    by thedustbustr ( 848311 ) on Monday January 10, 2005 @11:38PM (#11317428)
    From TFA:
    One of Endy's friends at MSI, Rob Carlson, charted the rates at which various biotechnologies were improving. The DNA-reading machines used by the Human Genome Project were doubling in efficiency every 18 months. DNA synthesis was accelerating even more quickly. If reality kept up with these "Carlson curves," then by 2010 a single lab worker would be able to synthesize a couple of human genomes from scratch every day.
    Moore's Law [wikipedia.org], anyone? I shall now generalize this concept, establishing TheDustbustr's theorem: The efficiency of the product of any emerging technology will double every 18 months, until fundamental theoretical limits in the technology are approached.

    • Re:Carlson Curves (Score:3, Interesting)

      by Rob Carlson ( 848359 )

      As the Carlson in question, let me add the following thoughts.

      First, to what physical limits are you referring? It's worth considering what the physical limits of biological technology might be. I don't think the answer is simple.

      Second, a note on "Carlson Curves" (this is Oliver Morton's phrase, not mine): The plots were meant to provide a sense of how changes in technology are bringing about improvements in productivity in the lab, rather than to provide a quantitative prediction of the future. I am

  • A practical consequence of "Playing God" is that you open the doors to a scary problem. It is the problem where if we can make replacements for humans we lose our humanity. Its more then just the philosophical question of where we lose our humanity. What if a group wants to replace the goverment leaders by clones which they control? ok, maybe it would be an improvement, but it is still a problem.
    • What if a group wants to replace the goverment leaders by clones which they control? ok, maybe it would be an improvement, but it is still a problem

      Doesn't sound like a problem to me.

      At least in the US, we are *supposed* to have politicians that we control... with our votes. But after a couple of centuries of American citizens dumbing down, that system is now corrupt. The politicans are now able to effectively control the majority of the population with negative campaign ads.

      If the best scientific minds

  • What, still not here? (Score:2, Interesting)

    by Mex ( 191941 )
    I read about DNA based computers about 10 years ago from a "Popular Science" type magazine here in Mexico.

    I thought they'd ALREADY be, at least, close to releasing one.

    It's interesting how many technologies take so much, much longer to come about than we'd like.

    Flying car, I miss you :(

  • nice first step, but... (Score:4, Insightful)

    by ctalnh ( 542227 ) on Monday January 10, 2005 @11:59PM (#11317572)
    Their approach is pretty cool, where the activity of each gene corresponds to one bit (actually one analog "voltage", but I digress) that can be independently controlled. Unfortunately each cell in their "computer" is expected to behave similarly, so the approach won't scale. The problem is that each gene is gonna be at least 1000 base pairs, roughly. Compare that to a typical bacterial genome (~5,000,000 base pairs) or the human genome (~3,000,000,000 base pairs), keeping in mind that large portions of those genomes are there to, well, keep the organism alive. Right now they're not even talking about taking over whole entire genomes here, just plasmids and viruses. That'll get you in the ballpark of 100,000 base pairs, or 100 bits, at most. Oh yeah, for each transition in a circuit here you'll have to make a new batch of proteins. That'll take minutes to hours. Not exactly stellar clock speeds. Which of course begs the question of how nature gets anything done at all. It's still pretty mysterious actually, but part of it comes down to the fact that your cells use feedback in a much more nuanced way than just "on" and "off". There's also lots of parts re-use, but probably the most important thing of all is communication and coordination *between* your cells. Like the fact that each neuron in your head does something different, and all of them put together make up something interesting and useful (hopefully). Rudimentary cell-cell communication circuits are already being constructed, and I'd like to see these scientists incorporate some of that into their work.
  • Soilent XP! It's made from people! It's made from people!

  • It's not just MIT .... (Score:3, Informative)

    by Salis ( 52373 ) on Tuesday January 11, 2005 @12:36AM (#11317820) Journal
    The Slashdot post makes it seem like the people at MIT invented the idea of synthetic biology. Well, I'm sure the good guys over at MIT would agree that the hallmark papers that started the craze didn't originate from MIT...they came from Princeton & Berkeley and there's plenty of other institutions who are making major contributions (some greater than MIT's), especially on the science end.

    That being said, their idea of Biobricks is very innovative and they did host the first conference on the topic. So the popular press can be easily misled.

  • Genetic Programming Languages / Frameworks (Score:3, Interesting)

    by JPyObjC Dude ( 772176 ) on Tuesday January 11, 2005 @12:38AM (#11317831)
    I spent a bit of time the last couple of weeks checking out the exibits at the Ontario Science Center on genetics which is probably one of the best exibits they have ever put together. In looking at the concepts of DNA/RNA/... A thought came to me - Why not build a programming language coding framework that is based on the strict constructs of genetics. The language/framework would implicitly have serializability of all structures and could allow for generation of truly extensible components. The basic concepts of highly structured data frameworks is growing (ie. http://nakedobjects.org) but why not pull these constructs one step away from the business data and bring it to the business logic or core application coding level.

    Anybody know of such coding or at least theortical hacks out there?

    JsD
  • ...there is hope that some day ordinary students may be able to design living computers...

    ...bringing a whole new meaning to BSOD.

  • The 1954 novella "The Houses of Iszm" by Jack Vance postulated custom-grown treehouse homes. From Rich Horton's review [sff.net]:

    I didn't like

    The Houses of Iszm quite as much [as "Son of the Tree"], though by and large it's fairly comparable in quality. It even shares a trope -- trees big enough to live in. The planet Iszm controls the supply of these trees by strictly preventing the export of female trees. Ailie Farr is a botanist who comes to Iszm and eventually gets involved in a scheme to steal a female tree, w

  • "...some day ordinary students may be able to design living computers, producing everything from novel drugs ..."

    Ok, so it's not novel, but what's wrong with just growing your own cannabis? It's much easier ! ;-)

  • You guys are really hyper-paranoid for no reason at all. While the original post says "While not all of the components of a basic computer are working yet," it would be more accurate to say, "We hope that in a year or so, we may be able to build a full-adder*." Seriously, the only parts that work reliably are NOT and OR gates, and you can only use about three of each in your system before cumulative stochastic error makes it fail. (Not to mention that you can't use the same gate twice -- if you've got two N

  • Can I make a clone of Kelly LeBrock? (Score:3, Informative)

    by Slur ( 61510 ) on Tuesday January 11, 2005 @06:07AM (#11319160) Homepage Journal
    That's what I would do as a young student with a DNA machine.
  • Heh. The word debugging now takes on a whole new world of meaning!

  • ...if I downloaded Britney Spears' DNA?

    Would they consider that stealing if someone just happened to be sharing it with me?

  • Synthetic biology is not as new as /.ers think it is,but it is clearly pre-critical mass -- something like Linux was before Linus.

    The critical thing to understand is that this is OPEN SOURCE BIOLOGY ... bringing the same resources, intellectual curiosity and viewpoint fostered by the open source software community. There's not a biological GPL yet, but I believe there will be.

    On the Dark Side, open source software's Darth Vader -- Bill Gates -- is an early player in synthetic biology. Check out that, th

  • seeds that sprout into treehouses? Sounds like Stephenson's Seed Technology from The Diamond Age.

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