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Digital DNA Circuits

Posted by michael on from the synergistic-merger dept.

TheSync writes "ScienceNews has a story about digital DNA circuits. The circuits use proteins that activate or deactivate genes on the DNA for control. Since an inverter and an AND gate have been created, any digital logic circuit can now be done in DNA. Moreover, evolution can help make circuit elements work better. There is even a "databook" of BioBricks circuit elements and BioSPICE for biocircuit simulation."

157 comments

  1. And, not by Anonymous Coward · · Score: 2, Interesting

    But does this mean we can store data in DNA using hundreds of bases (latch), instead of a few bases directly?

    1. Re:And, not by Anonymous Coward · · Score: 0

      DNA likes mystical cheesewedges, or so I've heard.

    2. Re:And, not by Rassleholic · · Score: 0, Offtopic

      No. You cannot store in any base. All your base are belong to us. You storing in base violates DMCA. Death beating with random fish is following.

      --
      Not noteable, IMO a rubbish article.
  2. Oh! by Quasar1999 · · Score: 2, Interesting

    So that's how the neuro-gel packs work in Star Trek... and all this time I thought it was crap!

    Seriously though... what's the delay on these things? Comparable to silica versions?

    --

    ---
    Programming is like sex... Make one mistake and support it the rest of your life.
    1. Re:Oh! by g4dget · · Score: 5, Informative

      Transcription and translation happen at about 45 nucleotides per second in bacteria, meaning it takes at least a few seconds to get a signal through a genetic "gate" or "switch".

    2. Re:Oh! by ciroknight · · Score: 1

      This means mister checkov could have very well been saved by a device placed on his forehead during star trek 4... DUDE!!!

      --
      "Victory means exit strategy, and it's important for the President to explain to us what the exit strategy is." G.W.Bush
    3. Re:Oh! by Alsee · · Score: 1

      Transcription and translation happen at about 45 nucleotides per second in bacteria

      That sounded a bit low to be considering that some bacteria replicate every 20 minutes, so I did a google search. Most popular google report is 500 nucleotides per second in bacteria, plus some reports of specific bacteria running 1000 per sec.

      -

      --
      - - You can't take something off the Internet! That's like trying to take pee out of a swimming pool.
    4. Re:Oh! by The_K4 · · Score: 4, Informative

      Yes, but if you have several trillion copies of your program you can run them all in parellel. Think of cytography....you could make a bioprogram that's designed to find the 128 bit key. There's 2^128 possible solutions. So if you have a whole bunch of these 2^1000 bio-programs in a solution, you can quickly find the 128 bit key. Look here under DNA computing for an example of why this stuff is useful, even if it is slow compared to silicon.

    5. Re:Oh! by Anonymous Coward · · Score: 0

      The acute reaction to attempted patenting of genetic sequences make this a very trick area of research. What company is going to invest the necesssary millions (if not billions) in R&D required to see any of these ideas come to fruition if they cannot assert intellectual property rights? After all, they need to be assured that they can recoup their investments.

      Would DNA circuits infringe on patents of silicon circuits that are otherwise identical? That is just one of many questions that I have.

    6. Re:Oh! by aqkiva · · Score: 3, Informative

      The original post of 45 nt/s is correct for transcription and translation (the speed of RNA polymerase and ribosomes). 1000 nt/s is for replication (the speed of DNA polymerase).

    7. Re:Oh! by Jerrry · · Score: 1
      Yes, but if you have several trillion copies of your program you can run them all in parellel. Think of cytography....

      There's a novel on this subject, "The Paris Option" by Robert Ludlam. Terrorists steal a DNA computer and use it to break all of our encryption codes and wreak havoc on the U.S. military and infastructure.

    8. Re:Oh! by g4dget · · Score: 2, Insightful
      No, you are just confusing lots of issues. DNA computing has little to do with genetic networks. It's also unproven whether DNA computing can actually do anything useful.

      And while DNA is compact, 2^128 and 2^1000 are really big numbers. 2^128 is about 10^38, and 2^1000 is about 10^300. A pound of hydrogen has about 10^27 atoms, so even if you use one hydrogen atom per key, you need nearly a billion tons of hydrogen just to get 2^128 atoms, let alone a billion DNA molecules.

      All this attention from computer scientists to "biocomputing" is mostly hype, and it's probably due to lucrative DARPA grants running out for the old kind of work. There are interesting questions to be asked there and interesting applications to be found, but biologists and mathematicians have been asking those for decades already.

    9. Re:Oh! by g4dget · · Score: 1
      "let alone a billion DNA molecules."

      Oops--that should have read "let alone 2^128 DNA molecules".

    10. Re:Oh! by racermd · · Score: 1

      "There are interesting questions to be asked there..."

      I agree: Would it be illegal to kill (turn off) such a computer? Would it be illegal to overclock with controlled substances?

      In all seriousness, however, there are some pretty amazing things that could be done with a DNA-based computer. The fact that it is actually in base-4 rather than the traditional base-2 allows much more data to be stored along a given chain. (Yes, I'm aware that there are only 2 combinations of the 4 chemicals, but you can arrange either one "upside-down" to offer an additional 2 possible combinations per pair). Data density is relatively fixed as it's just about impossible to shrink DNA strands. Moore's Law won't apply to that facet of DNA computers.

      It seems to me (and without reading the article) that the first major implementation of a DNA comptuer will be for large-scale storage. Processing the raw data will either require a new CPU that can handle "quads" (a value with 4 possibilities rather than 2) or a translation circuit to send data to a traditional binary CPU. Development of either of these solutions will be expensive and will probably first be seen in data storage warehouses as the processing power required in that environment is rather limited, anyway.

      The potential for the immediate term isn't earth-shaking. Long-term development will probably change the way we use computers, though. Either way, it's very interesting and something that I'll be following in the years to come.

      --
      My sources are unreliable, but their information is fascinating. -- Ashleigh Brilliant
  3. Huh? by blackmonday · · Score: 2, Funny

    This one wins my vote for absolute nerdiest post ever!

  4. imagine that by g4dget · · Score: 5, Funny

    And people have known about them only for, oh, a few decades.

  5. but then... by Tuxinatorium · · Score: 3, Interesting

    but then, that's not much more compact than a 90-nanometer transistor. Do you know how huge a polymerase protein is?

    --
    Repeal the DMCA!
    1. Re:but then... by g4dget · · Score: 5, Interesting

      But proteins go into a little 3D bag, while transistors need to be packed near a flat surface with current VLSI technologies.

    2. Re:but then... by Tuxinatorium · · Score: 1

      Do you think polymerase can do 50ghz?

      --
      Repeal the DMCA!
    3. Re:but then... by Mr+Z · · Score: 1

      Imagine the parallelism you could get with a few mL of DNA, though. A DNA CPU would be the ultimate multithreaded computer.

      --Joe
      --
      Program Intellivision!
    4. Re:but then... by g4dget · · Score: 1

      I was merely pointing out that size comparisons alone are meaningless. However, some proteins do work on picosecond timescales.

  6. Motorola anyone??? by Anonymous Coward · · Score: 1, Funny

    This sounds like an ad for Motorola

  7. DNA computing and Cryptography by jwdb · · Score: 2, Interesting

    Does anyone know of any research into DNA computing and cryptography? I'd expect, given the massively parallel capabilities of DNA, it would be a very useful tool for a brute force attack...

    Imagine coding all possible keys as dna, mixing in the message, and pulling out the only possible and logical match -> your decrypt.

    Or am I just dreaming?

    Jw

    1. Re:DNA computing and Cryptography by rwiedower · · Score: 4, Interesting

      Even your body doesn't rely upon chemical reactions to accurately predict certain outcomes. Studies have shown that nerve fibers in your arm will often send a "the ball is coming" signal to your brain well in advance of the actual signal reaching your fingers. This sort of predicative function makes complex tasks like walking and talking much easier, but when it catches up to you (like when you fall on the bottom step of a flight of stairs because you forgot how many steps there were) you crash and burn.

      The point is, that chemical reactions are very slow. If they were faster, your brain (and your neurons in your arm) wouldn't have to guess. Because they're so slow they'd be very poor at brute force attacks, regardless of the sheer number of cells.

      So, yes, you're dreaming.

    2. Re:DNA computing and Cryptography by Code-Ex · · Score: 2, Informative

      Try this page

    3. Re:DNA computing and Cryptography by 42forty-two42 · · Score: 1

      Actually this could be effective - bacteria are von neumann machines ;)

    4. Re:DNA computing and Cryptography by VendingMenace · · Score: 1

      Actually, he is not dreaming. Chemical reactions will (and already have) yeild massive parallel computations. DNA oligamers have already been used to solve for the solution to path problems in graph theory. The trick is designing the system. That is the hard part. The theory is that chemical reactions can be used for parallel processing is ALREADY practice.

    5. Re:DNA computing and Cryptography by Anonymous Coward · · Score: 0

      I think you're missing the point. Even though chemical reactions are slow, using DNA in such a manner would be like using an amazingly dense, massively parallel processor. However, the key thing to remember is that computing with DNA is essentially trading time complexity for space complexity. If there are 2^2048 keys in your search space, you would need at least that many DNA strands times some scalar and a whole bunch of other molecules to aide in the computation.

    6. Re:DNA computing and Cryptography by demonbug · · Score: 1
      The point is, that chemical reactions are very slow. If they were faster, your brain (and your neurons in your arm) wouldn't have to guess. Because they're so slow they'd be very poor at brute force attacks, regardless of the sheer number of cells.


      In this case, it isn't really an issue of the speed of chemical reactions (which oftentimes are not slow at all - they can be nearly instantaneous). The electrical impulse that moves along each nerve is very fast, of course, but the slowdown occurs between nerves - when one neuron talks to another. This is done by the first nerve releasing chemicals, which are then picked up by receptors on the second neuron. It isn' the speed of the chemical reaction that is slow, it is the physical movement of the chemicals from release to uptake that slows the system down. At least, thats what I remember from my Biopsychology class a couple years ago (that was a really cool class, all about nerves and neurons and the chemicals that affect their action and by extension the brain).

    7. Re:DNA computing and Cryptography by Anonymous Coward · · Score: 0

      Propaganda. It works, I use it every day to crack 65536 bit-encrypted messages sent from my neighbor's spy satillite. His FPGA system doesn't work so he can't fix it.

  8. watch out for motorola by steelerguy · · Score: 1

    they have a trade mark on digital dna i believe...i just just seem them getting their attorney's ready. they have to make money somehow! :)

  9. Illuminate Me by rwiedower · · Score: 2, Interesting

    Okay, this may seem short-sighted, but if silicon circuits are so much faster, why not simply design silicon-to-carbon interfaces rather than try to redesign the wheel? Unless there's some level of functionality that's not applicable on the silicon side, I don't see why the results of a process couldn't be approximated. In the article, for instance:

    It's far easier to describe the schematics of these circuits than to build them for operation inside a cell. For instance, to hook up one gate to the next, the amount of protein produced by the first gate must be the right amount to activate the next gate. And at every step, the output protein must be either very high or very low, to avoid false positives or negatives. It's also necessary to tweak many parameters, such as the strength with which the various proteins and the messenger RNA bind to different parts of the DNA sequence.

    If the end result is accomplished simply by having the right protein the right place at the right time, why not build the circuit in silicon and simply train the cell to produce the appropriate protein based on the result of a calculation? Perhaps my ignorance is becoming too glaring...

    1. Re:Illuminate Me by pr0t0plasm · · Score: 1

      Depends what you want to do. If you're looking for autonomous, self-contained agents, Si-C interfaces will be far to large and cumbersome to meet your mobility needs. If, alternatively, you want a sessile colony of living front-ends to an electronic circuit, synthetic ion channels might be useful as an interface.

      --
      - - - Patent applied for and deliver us from evil
    2. Re:Illuminate Me by Mr.+Spectre · · Score: 2, Interesting

      Okay, this may seem short-sighted, but if silicon circuits are so much faster, why not simply design silicon-to-carbon interfaces rather than try to redesign the wheel? If the end result is accomplished simply by having the right protein the right place at the right time, why not build the circuit in silicon and simply train the cell to produce the appropriate protein based on the result of a calculation?

      They are hacking the instructions written the code that cells already understand. This might allow for programming a cell to produce a particular protein only under certain circumstances determined by the hacked code. How is creating a silicon-to-carbon interface going to get a cell to do what you want it to?

    3. Re:Illuminate Me by rwiedower · · Score: 2, Insightful

      I wasn't saying the interface would solve the problem. I was saying that if I designed a cell to respond to an external stimulus with a certain protein production, I'd have a handy interface. Instead of building a cell to light up in the presence of a complex chemical compound, I could then simply have a cell send a protein to a circuit which could then send a signal to a led. Or, vice-versa, I could program a complex series of actions into a processor which would then interface with said S-2-C cell which would produce the proper proteins to achieve the desired effect.

      The article certainly goes beyond the idea of having one cell act a certain way. They implied that multiple cells could be chained together like some sort of rube-goldberg contraption. It's the chaining together that seems inefficient to me, when you could use silicon for the complex stuff and an interface cell to make the conversion. Kind of like a digital-to-analog switch, only between silicon and carbon. You still need to hack the cells, but you don't need to create complex machines. That was all I was wondering.

    4. Re:Illuminate Me by ciroknight · · Score: 2, Insightful

      There are applications of this FAR beyond those of silicon. What if you designed a circuit to detect the presents of certain viruses? You could make chemical/biological weapon detectors the size of CELLS! Also, think of what it can give us in a way of examining solutions to problems in our bodies.. you could design circuits to output certain chemicals/protiens when certain chemicals are in our blood stream. We could build cells that help filter out cancerous elements, PRODUCE INSULIN so that people would never need the shot again. This is just the tip of the iceburg on what all is possible with this new technology.

      Personally I'de love to sit and tinker with them, a cell program that could provide anti-histimenes when they build up in my system would be really nice, never worry about allergys again. Pipedream maybe, but it looks really sound and possible to me.

      --
      "Victory means exit strategy, and it's important for the President to explain to us what the exit strategy is." G.W.Bush
    5. Re:Illuminate Me by rwiedower · · Score: 1

      Wasn't this what nano-technology promised us years ago? We would all have tons of nanites roaming through our bodies, cleaning up the arteries and destroying cancerous cells. So far though, little concrete has been developed.

      I'll believe it when the applications actually arrive. And unlike nanites, these cells depend upon chemical reactions...I'm not sure I'd trust someone to inject tons of living cells into me the same way I'd trust them to inject tons of non-living machines into me.

    6. Re:Illuminate Me by ciroknight · · Score: 1

      The beauty of it is, it wouldn't need to be tons, and they wouldn't have to be injected neccisary. And besides, every day walking through your house you intercept hundreds of thousands of airborne bacteria. This is nothing new to us.

      The other advantage is unlike nanites, these things are very temporary. Our immune systems would nuke them pretty quickly, within a few hours in most cases. But for uses like insulin production, you'de have to develope one that was resistant, or actually lived somewhere else (like the human colon for example). There are billions of germs in us, but for once, we'd actually be making helper germs to combat the ones that hurt us. The ultimate antibodic/antiviral medicine.

      --
      "Victory means exit strategy, and it's important for the President to explain to us what the exit strategy is." G.W.Bush
    7. Re:Illuminate Me by Anonymous Coward · · Score: 0

      How long before they engineer cells that can produce THC? Or LSD?

  10. Death.. by Anonymous Coward · · Score: 3, Funny

    So, now will death be refered to as a power outage?

    1. Re:Death.. by hesiod · · Score: 2, Funny

      > So, now will death be refered to as a power outage?

      Well, it sort of is. As I understand it, death is usually just a lack of oxygen to the brain (explains why guillotine victims seemed to be alive a few moments after being decapitated -- there was still blood/oxygen/power in the head, feeding the brain.

    2. Re:Death.. by Anonymous Coward · · Score: 0

      Or even better, a bluescreen as an abortion? I've been calling MS products that for years!

    3. Re:Death.. by Anonymous Coward · · Score: 0

      No. Just a program exiting...

  11. how much wasted to decimal ? by Anonymous Coward · · Score: 0

    So how much of the potential will be wasted to decimal? Will finally dumping decimal help us see the true potential of this?

    1. Re:how much wasted to decimal ? by hesiod · · Score: 1

      > So how much of the potential will be wasted to decimal?

      Good question(?): none. It's DNA, not math. There is no number base. (Sorta' like "there is no spoon")

  12. [insert supreme being/philosophy etc.] called... by Dutchmaan · · Score: 5, Funny

    He wanted to remind you that he has held the copyright for DNA for billions of years now..

    He's been in contact with his lawyers and is tallying your bill as we speak.

  13. Sounds Good but by Creep73 · · Score: 0, Offtopic

    This idea sounds good but I have to believe that it's not simply a mater of technology advances that will get us to this point. Such modifications to our cells/DNA are bound to cause problems. The body rejecting these cells etc. It's also another thing people can blame for cancer. It's an interesting idea and I hope it can work but I don't believe I will see it within my lifetime. Of course I could be wrong :)

    1. Re:Sounds Good but by Vengeance · · Score: 1

      I suppose that depends on how old you are ;-)

      --
      It was a joke! When you give me that look it was a joke.
  14. You better understand it... by Anonymous Coward · · Score: 0

    Nerds will soon take over (using advanced understanding of math and physics) and kill those who don't understand math and physics.

    1. Re:You better understand it... by ChemicalSpider · · Score: 1

      What about us chemists who only have a rudimentary understanding of math and physics? Aren't we nerdy enough?

  15. Could you program these bacteria� by Anonymous Coward · · Score: 5, Funny

    ... to play the game of life?

    1. Re:Could you program these bacteria� by hesiod · · Score: 1

      That was odd... I didn't find that terribly funny right at first, but I couldn't stop chuckling because of the irony.

  16. Motorola by Anonymous Coward · · Score: 0

    I seem to remember Motorola advertising "Digital DNA" on TV a coupld years back. I assume it is/was just some type of FPGA or something. If they still tout that slogan, this place here might have to change its name, heh.

  17. Self-improving circuits by 16977 · · Score: 5, Interesting

    The most interesting thing about this announcement is that this guy has been able to use evolution to improve his circuits. I don't expect molecular computers to surpass electronic computers, at least right away -- although they could theoretically perform faster than electronic computers in the short term, any advantage is offset by the time needed to convert the information to human-readable form (by finding and correctly reading the DNA sequence). As the article says, it's better to take advantage of the fact that you can "work with" bacteria. But if DNA computers could repair and upgrade themselves, they would have an advantage that electronics currently does not have. Electronics already is under intense artifical selection, and it can reproduce itself after a fashion, but unlike copper and aluminum, DNA computers can be randomly mutated, and the close homology between computers ensures that some of those mutations will be beneficial.

    1. Re:Self-improving circuits by rwiedower · · Score: 2, Interesting

      DNA, maybe. DNA is fairly good at reproducing without errors. RNA, on the other hand, isn't that good with errors, but is much quicker. (Ask any virus.)

      My thought is this: as soon as the process becomes complex, errors introduced into each cell could produce vastly different results. And the debug process would be tortuous. There'd be no guarantee that a single mutation couldn't bring down the whole system.

    2. Re:Self-improving circuits by ocie · · Score: 1

      The problem I see with this is that we assume that the circuits that implement our desired function will be selected for. What if the circuit can be biologically successful without implementing the desired result. After all, we haven't figured out the question to that 42 question yet.

      --
      JET Program: see Japan, meet intere
    3. Re:Self-improving circuits by pyrosoft · · Score: 1
      DNA, maybe. DNA is fairly good at reproducing without errors. RNA, on the other hand, isn't that good with errors, but is much quicker. (Ask any virus.)

      DNA and RNA don't replicate themselves, they need the help of enzymes called polymerases. These biological machines unwind the template DNA or RNA strand and create a complementary copy (A pairs with T, G with C). Along with the template reading and synthesis domains, there is also a proofreading domain, checking to ensure that the right match has been made. However, the more stringent the proofreading, the slower the synthesis. Many viruses (which can have DNA or RNA as their base genetic material) want to replicate quickly, so their polymerase has diminished proofreading capability. HIV is an example of this, and consequently mutates quite frequently as a result of mismatches, deletions, insertions, etc. On the other hand, there are polymerases that are very very stringent with proofreading, and therefore have a very low mismatch (mutation) rate. This is independent of the nucleic acid (DNA or RNA) used as the template. The impression that RNA has a higher mismatch rate possibly comes from the fact that RNAs such as messenger RNA is transient in the cell (half-life of seconds to minutes) while DNA is around much longer (days to years).

      My thought is this: as soon as the process becomes complex, errors introduced into each cell could produce vastly different results. And the debug process would be tortuous. There'd be no guarantee that a single mutation couldn't bring down the whole system.

      The nice thing about working with bacterial systems is that the numbers of individual bacteria is quite high. A milliliter of liquid culture could have 10^7 or more organisms in it. A single mutation in one organism would be drowned out by the rest of the crowd, especially if it led to a lethal condition and was deleted by selective pressure. On the other hand, this also allows for beneficial mutations which increase survival rates to eventually take over (or at least coexist with) the original version.

      --
      Great spirits have always encountered violent opposition from mediocre minds. Albert Einstein
  18. New female DNA logic circut states by Timesprout · · Score: 5, Funny

    YES
    NO
    MAYBE

    --
    Do not try to read the dupe, thats impossible. Instead, only try to realize the truth
    What truth?
    There is no dupe
    1. Re:New female DNA logic circut states by hesiod · · Score: 0, Troll

      Flamebait? Yeah right, that's Funny. Just 'cuz some overly-sensitive woman (or man, I guess) might get all flustered doesn't mean it's not humor.

    2. Re:New female DNA logic circut states by Anonymous Coward · · Score: 0

      and...
      If_You_Really_Loved_Me_You_Would_Know_The_ Answer

    3. Re:New female DNA logic circut states by sacherjj · · Score: 1

      I thought females had 5 state logic:
      YES - Meaning Yes
      NO - Meaning No
      YES - Meaning No
      NO - Meaning Yes
      MAYBE

      The only thing you can be sure of is the MAYBE state.

    4. Re:New female DNA logic circut states by Lemmeoutada+Collecti · · Score: 3, Funny

      Can't be too sure of that MAYBE state either. It posesses the following sub states:

      MAYBE.You should have noticed already
      MAYBE.NO but I don't want to be the one to say it
      MAYBE.You had better know I mean YES
      MAYBE.Let's just be friends
      MAYBE.Are you being sensitive to my needs
      MAYBE.DON'T EVEN THINK OF PLAYING QUAKE RIGHT NOW OR YOU WILL BE SINGLE

      And there are a lot more potential substates yet to be catalogued in the interface.

      --

      You can have it fast, accurate, or pretty. Pick any 2.
    5. Re:New female DNA logic circut states by stor · · Score: 1

      You forgot the "FINE" state, which means "A fatal error has occurred due to invalid user input"

      Cheers
      Stor

      --
      "Yeah well there's a lot of stuff that should be, but isn't"
  19. Great by grub · · Score: 1


    The DNA circuits will be used in mainstream computing hardware.. The DNA wired computing hardware will become Skynet.. The DNA wired computing hardware that becomes Skynet will become self-aware.. You know the rest of the story.

    Where's my tinfoil hat?

    --
    Trolling is a art,
  20. Don't know how 'wow'-ing this really is... by Necromancyr · · Score: 4, Interesting

    Reports of this sort have been coming out for a few years now - basically, all they are doing is a controlled induction of a promoter. It's nothing amazing. Chaining one promoter to express another promoter ad infinitum (or to restrict expression) is already done in nature and used extensively to create transgenic cell lines, bacteria, etc. Hell, they've already developed means to do basic computations with DNA that are more applicable/advanced then this in some respects.

    1. Re:Don't know how 'wow'-ing this really is... by Dutchmaan · · Score: 1

      It has always amazed me that a mere ~60 years ago computers the size of buildings were doing very simple calculations, and the people marveled at this incredible technology....

      What is DNA going to be doing in another ~60 years?

  21. Evolution of Programming Languages? by jdh-22 · · Score: 2, Interesting

    Does this mean that a new bread of modern inovative programming languages will be needed? I am sure that most expirenced programmers would definatily like to do something differently to make the development process more efficient, and faster.

    Any suggestions on what you would like to see if a new language was developed for this platform?

    --
    Every Super Villan uses Linux.
    1. Re:Evolution of Programming Languages? by Anonymous Coward · · Score: 0

      You can of course call this one Pizza, based on Yeast distro using the Sauce processor...

    2. Re:Evolution of Programming Languages? by Mr+Z · · Score: 1

      I thought YeaST was the installer...

      --Joe
      --
      Program Intellivision!
  22. proteins by lazira · · Score: 2, Interesting

    Have there been studies in alternate programming methods/languages for DNA, like there were for quantum computers? DNA logic doesn't need to be sequential- each protein can affect many things at once. It seems rather unwieldy to try to apply conventional logic building blocks, as each gate would require a unique protein and inhibitor- you can't use the same block twice.

  23. Cliff Notes version by Strange+Ranger · · Score: 1

    ...engineers are starting to program microbes to carry out behaviors that nature never dreamed of. // Eventually, the goal is to produce genetic 'applets', little programs you could download into a cell simply by sticking DNA into it, the way you download Java applets from the Internet.

    Not to stir up the scare-mongers and doom-sayers but that is one huge can of strangely colored worms.

    Combine this w/ personalized medicine and you might live to be 600, albeit going to the doctor every week for a Service Pack and virus definition update, losing any remaining autonomy you might have over your mind and body, and wow, just think of the Homeland Security Bill we'll need to contain the threat of body-java applets... Full DNA scan in the lobby every morning... How do we stamp "FDA approved" on these little buggers?

    Damn I am stirring up the doomsayers. Well I guess that's what they're for. Bring it on.

    --

    Operator, give me the number for 911!
    1. Re:Cliff Notes version by Mostly+a+lurker · · Score: 1
      How do we stamp "FDA approved" on these little buggers?

      No problem: just make a few tweaks to the Palladium specifications so MS + CIA own your body in addition to your computer, documents and household appliances.

    2. Re:Cliff Notes version by fireweaver · · Score: 1

      Well, if you -really- want to stir up the fear-mongers, how about customised bacteriological weapons: They'll kill whoever they're programmed for and ignore everyone else (or just make them a little sick instead of dead.)

  24. linkages by ciroknight · · Score: 1

    are your problem. You might be able to use carbon nanotubes, but otherwise I dont see anything that could not rupture the cell and connect to a digital device at the same time. If we could build a silicon chip that could detect the presents of proteins that would be nice, but (pardon this comment if I'm wrong) I don't know of any chip/gate that can change states at the presents of a protein like these cells can.

    --
    "Victory means exit strategy, and it's important for the President to explain to us what the exit strategy is." G.W.Bush
  25. Next up for review.. by bombkit · · Score: 1

    A hefty airtight coolance case to keep your computer circuits from molding.

  26. Nooooo not again... by fireflew · · Score: 2, Funny

    Gives a new meaning to 'my computer died'.

  27. Resemblence between programmable DNA and Java by expro · · Score: 1

    I found particularly enlightening the apparent similarity between Java applets and programmable DNA:

    "Eventually, the goal is to produce genetic 'applets', little programs you could download into a cell simply by sticking DNA into it, the way you download Java applets from the Internet," says Timothy Gardner, a bioengineer at Boston University.

    While it would have been better if it resembled something better supported in open source, it is a relief that it is not modelled after the patent-encumbered CLI-based models and that it is Internet-based rather than based on an AOL keyword.

  28. Grey goo theory? Super sperm? by macshune · · Score: 3, Funny
    Will Bill Joy's "grey goo" theory turn out to be just a bunch of DNA-computer-packin' malevolent super sperm?

    Will women have to worry about guys with DNA-computer enhanced sperm, so unprotected sex could mutate a woman into a ninja turtle?

    Will I be able to code myself urine that tastes like apple cider and poop that tastes like swiss chocolate?

  29. Teletubbies not so far fetched... by Billy+the+Mountain · · Score: 3, Funny

    If you could embed this into human cells, I bet you could convert my stomach into a 1280 X 1024 display!

    BTM

    --
    That was the turning point of my life--I went from negative zero to positive zero.
    1. Re:Teletubbies not so far fetched... by Anonymous Coward · · Score: 0

      convert my stomach into a 1280 X 1024 display!

      I haven't had a stomach with that tight resolution since high school. Mine is currently around 1600x1900. It may seem an odd aspect ratio but appears to have stabilized in the horizontal direction with a slow, steady increase in the vertical direction. It may be 1600x2100 by christmas.

    2. Re:Teletubbies not so far fetched... by addaon · · Score: 1

      They don't call you "the Mountain" for nothing, eh?

      --

      I've had this sig for three days.
    3. Re:Teletubbies not so far fetched... by Guppy06 · · Score: 1

      Then the question is "Would people think you're gay?"

  30. NOT gate by Bowling+Moses · · Score: 3, Informative

    Sounds similar to work being done by the Arnold group at Caltech. They've apparently (haven't read the article yet) made a NOT gate using directed evolution. They're more interested in developing and applying the directed evolution technique than in biological computers, it seems. Lab website's here. And the lab website's got their own articles available for free in .pdf form. Screw you, Elsevier!

  31. Spaghetti Code by Obiwan+Kenobi · · Score: 5, Interesting

    I was listening to NPR the other day which focused on DNA as a computer.

    The guy interviewed correllated the DNA genetic map to spaghetti code, a programmers worst nightmare. Apparently all through the genetic make-up of our bodies are "fuction calls" (to put it simply) and pathways that reference other calls and other pathways, over and over upon itself for a hundred million lines.

    Its not the listing of the GTAC code (ie, genetic map) that's really necessary. Though of course it plays a part. Its the understanding of such code, what it does and what it controls, where power lies.

    The guys interviewed all guessed it would be a hundred years or more before we began truly understanding what "functions" do what in the DNA strand and how it affects the organism in question.

    Food for thought.

    1. Re:Spaghetti Code by chmod000 · · Score: 1

      So, what's the codon for "goto"? Do we know that one yet?

      --
      Aptal soru yoktur; sadece merakli aptallar vardir.
    2. Re:Spaghetti Code by einer · · Score: 1

      Java bytecode also doesn't look terribly appealing in a text editor.

      I wonder if we could decompile our VM and reverse engineer DNA back into it's original source code.

      I'm guessing it's something like LISP

    3. Re:Spaghetti Code by Alsee · · Score: 1

      The guys interviewed all guessed it would be a hundred years or more before we began truly understanding what "functions" do what in the DNA strand and how it affects the organism in question.

      Bad guess. If you check google there are plenty of articles about specific projects on track to build a minimal synthetic cell within a few years.

      It will be a while before we work out the functions and subtlties of all genes, but we're off to a decent start.

      -

      --
      - - You can't take something off the Internet! That's like trying to take pee out of a swimming pool.
    4. Re:Spaghetti Code by 42forty-two42 · · Score: 1

      Spaghetti code can work better. Just look at the more successful Corewars programs, especially the evolved ones - they go and modify their code in mid-run, the result being much greater efficiency (and it's more compact, to protect against attacks (or mutations)).

    5. Re:Spaghetti Code by Arakonfap · · Score: 1

      A big question is though:
      Can we use these basic building blocks to help improve our knowledge base of biology? Could this be used as a link to help more efficently understand more biology? Could there be a way of coding biological structures to communicate with a more typical logic-program? The logic-program could help output data in a form we're more accustomed to.

    6. Re:Spaghetti Code by DocDendrite · · Score: 2, Insightful
      The guy interviewed correllated the DNA genetic map to spaghetti code, a programmers worst nightmare. Apparently all through the genetic make-up of our bodies are "fuction calls" (to put it simply) and pathways that reference other calls and other pathways, over and over upon itself for a hundred million line
      This seems a little strange to me. I am a fourth-year PhD student in Molecular Biology and I see a lot of Biology misinformation on slashdot.

      What the NPR interviewee said does appear true. However, be aware its not the DNA that's actually performing any operations. Genetic control sequences (called promoters, enhancers, and silencers) are well characterized. It is the product of other genes (i.e. proteins) that perform the operations on DNA and are subject to regulation via these control sequences.

      Now what is truly complex is that proteins can bind to other proteins and affect their activity. Lengthy circuits of proteins "touching" one another (called signal transduction pathways) becomes incredibly complex with the exponential level of crosstalk and pathway intersections that can occur. That is where true Bioinformatic power lies....not so much the Folding Projects you see on distributed computing systems.

      The design of the "DNA computation" in the original story is contigent upon the aforementioned processes. It does not work on some natural computing power of DNA.

      -DD
    7. Re:Spaghetti Code by Anonymous Coward · · Score: 0

      yes. we do. read a biology book.

  32. Cyborgs by Luigi30 · · Score: 0, Flamebait

    So does this mean we can create robots and stuff?

    --
    503 Sig Unavailable

    The Signature could not be accessed. Please try again later or contact the administrator
  33. Re:Grey goo theory? Super sperm? by SlashdotLemming · · Score: 1

    Will I be able to code myself urine that tastes like apple cider and poop that tastes like swiss chocolate?

    Given some of the fetish videos out there, I'd make that german chocolate

  34. Spectacular? I doubt it. by Asprin · · Score: 0, Flamebait


    After looking at the article for a couple of minutes, a couple of things are clear to me:

    1) being able to encode logic circuts using DNA != being able to program nano-size virus-like bio-bots to follow your instructions. The "processors" that drive life in virii, bacteria and cells do not follow instructions of this sort. Sure, you might be able to produce an organic computer that can 'run the program', but it won't be alive, it won't reproduce and it'll be a hell of a lot slower than a similar computer built on silicon. You can build logic circuits out of water and buckets if you like, but other than the intellectual curiosity, there just isn't much point.

    2) I'm getting a little tired of this sort of "soon we'll be able to re-program living organism" articles. Talk about a God complex!

    Look at it this way: is the paper aware of the circuit diagram I've drawn on it?

    Methinks somebody needs to lay off the LSD for a while.

    --
    "Lawyers are for sucks."
    - Doug McKenzie
    1. Re:Spectacular? I doubt it. by 42forty-two42 · · Score: 1

      If they don't do these tricks, they don't get funding. Simple as that. 'intellectual curiosity' is all well and good, but nobody's paying for it ;)

    2. Re:Spectacular? I doubt it. by Asprin · · Score: 1


      Wow, that's ironic. My first draft concluded with "... sounds like somebody wants their funding increased."

      Maybe we should start a club, eh? :)

      --
      "Lawyers are for sucks."
      - Doug McKenzie
  35. Re:[insert supreme being/philosophy etc.] called.. by Cobralisk · · Score: 2, Funny

    http://www.copyright.gov/circs/circ15a.html#durati on Sorry dude, its expired

    --
    Waiting for ad.doubleclick.net...
  36. I have firsthand experience by Jerry+Jigglenuts · · Score: 0, Flamebait
    I dabbled with digital DNA chemistry for about 2 years at Carnegie Mellon. It has extreme potential in aiding cancer patients and stroke victims, and shows tremendous promise in preventing Down Syndrome births. We (Craig Curtis, head of Biotech research and myself, an aspiring Biotech student) immediately saw it's vast and influential potential, and immediately set to work on digital DNA.

    However, our work became sidetracked when Craig developed an unusual affinity for horse sex. While the applications of the common horse penis in regards to a human are precaurious, to say the least, Craig nevertheless remained determined to not only engage in rapid, pulse pounding horse sex, but to somehow also increase it's efficiency. Craig quickly utilized the powers of digital DNA to aid him in his ghastly crusade.

    After Craig was caught with a horse that he named "El Chancho the long when limp", 8 gerbils, a shrink wrapped box of OpenBSD, a lengthy printout of recent Kuro5hin.org posts, and an Xbox, funding for the project was cut.

    1. Re:I have firsthand experience by Anonymous Coward · · Score: 0

      ROTFLMAO!!!!!!!!

      That is the funniest post i've evarrr read on $la$d0t.

      Mod Parent up, mod grandkids down.

    2. Re:I have firsthand experience by Anonymous Coward · · Score: 0

      Hilarious! This has got to win, like, troll of the week or something.

  37. Re:serious question, please answer! by Clockwurk · · Score: 1

    Nope, its happening to me too. Still function as links, just they are only 1x1.

  38. The article link by Obiwan+Kenobi · · Score: 2, Insightful

    Is right here. Highly suggested reading/listening.

  39. Parallel by dsanfte · · Score: 1
    The point is, that chemical reactions are very slow.


    So run them in parallel. A billion DNA strands can fit on the head of a pin. More could fit in a beaker.
    --
    occultae nullus est respectus musicae - originally a Greek proverb
  40. Re:Could you program these bacteria? by Alsee · · Score: 1

    I predict this will be the first large-scale software to be implemented.

    -

    --
    - - You can't take something off the Internet! That's like trying to take pee out of a swimming pool.
  41. When will this be available by Boyceterous · · Score: 1

    at Radio Shack?

    1. Re:When will this be available by NoMoreNicksLeft · · Score: 0, Flamebait

      Radio Shack might be a good subject for such a stupid trollery, except that even the most heinous trolls are disgusted by Radio Shack's utter lack of any sort of electronic or computer equipment. This is offtopic, flamebaitish, and perhaps even actionably libelous on my part so get your -1 mods ready, but Radio Shack is incredibly worthless, misnamed and quite likely 'gay' in the literal homosexual sense of the word. They remind me of those ghetto beauty salons you see where the proprietor has no business sense or vision, and starts selling hubcaps as a "side business" in the lobby... only distilled to 99.999% purity. It would be more honest to rename the franchise "Cell Phone Shack" or possibly "Battery Nazis". I have mustered all the contempt that I can, far more than is safe for any 12 humans put together, and it still isn't enough to express just how low they've sunk, and the speed at which they hit bottom. Fuck, it ignores the fact that when they hit bottom, they simply punched a hole through the floor, and contionued sinking. With any luck, they will somehow be connected with terrorism, and Bush will have no choice but to invade Cell Phone Sha... I mean, Radio Shack. After a 2 month bombing campaign, he'll then send in the ground assault of 220,000 troops, who will beat, kill and rape the store managers (in that order). I sometimes fantasize about some demented Marine Corp sargent stomping on some retard clerk's face while screaming at the top of his lungs "YOU'VE GOT QUESTIONS, WE'VE GOT ANSWERS!!!" and then laughing maniacally. Alas, I will not be that lucky. Nor will you. The painful decades will drag by, with clueless people at other stores suggesting "Radio Shack" even though they haven't carried anything remotely cool since the late 70s. You'll be looking for some #4 sheet metal screws at Home Depot, and some hick asshat will say "Maybe you should try radio shack". Wallmart will be out of 9v 400ma DC adapters, and the pimple faced goth slut working the electronics dept will tell you to "go to Radio Shack" rather than check the back stock room for you. This will continue to happen until you go fucking postal, foaming at the mouth and making spastic seizure like movements of your arms, face and legs.

      Radio Shack, what did I ever do to you? Is it so much to ask that you stock some 74xx IC's in at least every other store? Will you at least hire a decent fucking ad agency? Something, anything?

      *weeps* Have you no mercy, no pity? What kind of monsters are you?!?!?!?!?

  42. Re:Grey goo theory? Super sperm? by macshune · · Score: 1

    Yah, poot eet een mein arse.

  43. Microsoft, too. by Anonymous Coward · · Score: 0

    Anybody remember Microsoft Windows DNA?

  44. woot brand recognition... by Anonymous Coward · · Score: 0

    thanks!

  45. Documentation by Psiren · · Score: 1

    The guys interviewed all guessed it would be a hundred years or more before we began truly understanding what "functions" do what in the DNA strand and how it affects the organism in question.

    These developers, they never document anything. Would a few comments really have been all that difficult?! ;-)

    1. Re:Documentation by Anonymous Coward · · Score: 0

      There is akind of ducumentation of sorts. It is in the so called "Junk DNA" they don't code for any proteins, yet are essential in DNA repair. In a since the cell uses them as an maintainance manual. They make up a vast majority of the DNA. (Some of it, are introns though so used to code for something, like commented out code)

  46. GCC Engineering by Anonymous Coward · · Score: 0

    So does this mean that if i don't like my current girlfriend, i can recompile her from source?

    1. Re:GCC Engineering by Anonymous Coward · · Score: 0

      But i can dream!!

      Maybe we should start an Open Source Girlfriend Project..... a place where geeks can develop thier ideal Girlfriend Source Code. Can you imagine some of the features?

      Get your source at www.girlfriend.org

  47. One flaw in that question. by Anonymous Coward · · Score: 0

    Geeks don't have girlfriends (and I mean real ones).

  48. On account of using GCC... by Anonymous Coward · · Score: 0

    you must mean boyfriend.

  49. Keep working by smittyoneeach · · Score: 2, Insightful

    I don't think we'll have serious applications in bioware in the next decade.
    The sequencing work done to date is phenomenal. Not trying to sell anyone short. However, the complexity when you move from the genome to the proteome can be fairly described as staggering, so I'm weighing in on the conservative side on this one.

    --
    Get thee glass eyes, and, like a scurvy politician, seem to see things thou dost not.--King Lear
  50. Entertaining cross-reference by descil · · Score: 1

    Here's a nice salon.com (fictional) story about this topic, fast forwarded and given a bigger picture.

  51. Woman Are Quantum Computers by ari_j · · Score: 2, Funny

    Women actually have these three states (yes, no, and maybe), but here are the correct definitions: YES - a superposition of maybe and no
    NO - a definite no
    MAYBE - a superposition of yes and no

    1. Re:Woman Are Quantum Computers by mOdQuArK! · · Score: 1

      Dunno about these definitions - in my experience (in a not-sexual context) when a woman says YES, she means maybe, NO means maybe and MAYBE means either YES or NO (but you're expected to be able to figure out which one she meant - and if you guess wrong, you'll be in hell for an indefinite period of time).

  52. Something went terribly wrong... by Anonymous Coward · · Score: 0

    Somehow I ended up with a NAND gate instead of aN AND in my DNA and ended up with one of the shortest tubes in North York. If we can finally build logic gates out of organic matter, does this mean I won't have to go through life as stumpy the wonder fuck? Penis enlargement made for real?

  53. How would speeds be compared? by kireK · · Score: 1

    Calories per second?

  54. BioBricks - Pretty laughable really by Angry+Toad · · Score: 1

    I had a look at the "BioBricks" site - anyone out there who does molecular biology work should do the same if you're looking for a laugh.

    It reads rather like a treatise on basic cloning written by someone who had a look through Maniatis (Sambrook for the newbies) and pretty much understood most of it.

    The plasmids with "ampecillin" resistance genes, and their MCS with an "Echo RI" site, good lord...

  55. Re:[insert supreme being/philosophy etc.] called.. by demonbug · · Score: 1
    He wanted to remind you that he has held the copyright for DNA for billions of years now..

    He's been in contact with his lawyers and is tallying your bill as we speak.


    UPDATE:
    He/She/They/It has sued for control of her/his/their/its intellectual property, which the judge granted. He/She/They/It may order return of all IP active immediately, or up to 100 years from this date at the parties discretion. Due to the omnipotent power of the suing party, no other legal enforcement has been deemed necessary.

  56. Origins of this stuff by WillWare · · Score: 3, Informative
    Tom Knight and some other MIT people were talking about this kind of stuff in 1996-97. This was the same group interested in amorphous computing at the time. They saw it all as one big research agenda, and amorphous computing fell under the DOD funding umbrella for autonomous battlefield surveillance widgets.

    These guys were poking around with some genuinely interesting ideas. Their idea was that if you relaxed the requirements on manufacturing quality, you could make nodes that were super-cheap with a modest (but today-considered-unacceptable) failure rate. They set forth a collection of programming axioms that treated a sea-of-nodes as a continuous computational "gunk". Very cool stuff.

    --
    WWJD for a Klondike Bar?
  57. I dont see what's new by Anonymous Coward · · Score: 0

    Since all they are doing is basically the same as doing a litmus test .... either it turns fluroscent or not based on the presence of some organic chemicals. I am quite sure that most medical test involves something like this anyway.
    Maybe this is a case of reinventing the wheel.

  58. Oh, the irony... by nickgrieve · · Score: 4, Insightful

    In the course of her work with Watson and Crick, Rosalind Franklin had to do a serious amount math by hand (Patterson analysis to create Patterson maps). Later, after her work on DNA she was forced to hire a computer (an 18yr old girl) to do the leg work on the data she gathered on the Tobacco Mosaic Virus.

    Today I read here http://www.sciencenews.org/20030426/bob11.asp (Computer circuits made of genes may soon program bacteria)

    "Silicon circuits perform complex operations using a handful of simple components known as logic gates. Genetic- circuit engineers are now building the same devices inside cells."

    I wonder, what she would have thought, to know that very thing she was studying could some day be used to do the math that took up so much of her time.

  59. genetic algorithms are somewhat flaky by Trepidity · · Score: 1

    First of all, this is just an issue of genetic algorithms, which don't require you to explicitly have a logic circuit coded in DNA -- there's many other analogous ways of "evolving" software or circuits.

    Secondly, they do come up with very interesting results (sometimes), but often these results are not really what you'd want. I can't seem to recall details (if anyone has a reference I'd appreciate it), but I recall about a decade ago someone evolved a timing circuit that used something like 20% fewer gates than the standard human-engineered design. The catch? It used weird interactions between unconnected components, so it only worked in the exact environment (temperature, humidity, surrounding magnetic/electrical fields, etc.) it was evolved in, and stopped working entirely when the conditions changed.

    For complex circuits, it's very difficult to make sure your evolving circuit is not "cheating" and making any assumptions that will cause it to break unexpectedly when those assumptions are no longer true.

    --
    10 PRINT CHR$(205.5+RND(1)); : GOTO 10
  60. great... by j0se_p0inter0 · · Score: 1

    i just finished digital circuits, and now here come digital DNA circuits. i imagine the lab fees will be pretty high for that one. i suppose i'll have to buy a biological protoboard too. d'oh!

  61. Why does this post have a SPAMish link? by Anonymous Coward · · Score: 0

    The link to the journal Science News (www.sciencenews.org) actually points to a moronic spam page at www.sciencenews.COM ... well at least it wasn't www.scientology.com!

  62. "DNA computers can be randomly mutated" by da5idnetlimit.com · · Score: 1

    FPGA.

    They can do the same, auo mutate, compare circuits topology using the game of life rules and "automatically" reconfigure and evolve to compare their results to an etalon measure.

    => Seem to remember a FPGA test where the goal was tone recognition. The FPGA was programmed to try and get a wave analysis and recognition tested against set rules.

    After X generation, not only did the processor perform the deed asked, but had modified it's gate in a way even the engeneer that designed it didn't envision, separating itself in two separate and specialized components on the same chip.

    Also to be noted that the interpretation of how the fpga actually worked could only be determined after the experiment by copyng the gates configuration and is still a matter of puzzlement... It was on slashdot last year, search yourself 8p

    --
    It takes 40+ muscles to frown, but only four to extend your arm and bitchslap the motherfucker
  63. No wow at all by bfinuc · · Score: 1

    This article was designed to amaze people that don't know anything about genetic regulatory systems. The hugely complex bodies of all organisms are "computed" by the the genes of the original fertilized egg. there are plenty of examples of genes that switch other genes on and off, and AND and OR are all over the place.

    More interesting are the abstract pattern creation systems. Think about the following example.

    Fly legs have precursors in maggots which are flat disks. The disks are concentric circles of precursor cells. The "toes" are in the middle and the "hips" are on outside. The whole thing swells up into a leg when it gets switched on.

    Butterflies often have "eye spots" on their wings, which are concentric circles of different colored scales. The scales "know" what color to be based on the genes expressed in the circle.

    Think about it. The concentric circles are abstract - the same genetic machinery creates both patterns and then the patterns are applied to completely different applications.

    All this is based on NOTs and ANDs.

    --
    I bragged about my Karma at a job interview but I didn't get the job.
  64. HIT ME! by Anonymous Coward · · Score: 0

    I would love to be able to give my brain an IP address...

    maybe work an 802.11 transmitter into my forehead. or emulate genisis games on my forearm

  65. Digital DNA Citcuits by Captain+Ed · · Score: 0

    http://www.eugenics.net/papers/gw002.html REPRODUCTION TECHNOLOGY FOR A NEW EUGENICS Paper for The Galton Institute conference "Man and Society in the New Millennium" 16 - 17 September 1999 at The Zoological Society of London Regents Park, London NW1 4RY Published as: Whitney, G. (1999). Reproduction technology for a new eugenics. The Mankind Quarterly, XL, #2, 179-192. Introduction The first century or two of the new millennium will almost certainly be a golden age for eugenics. Through application of new genetic knowledge and reproductive technologies the Galtonian Revolution will come to fruition. This new revolution in the new millennium, which I call the Galtonian Revolution (Whitney, 1995; 1997a) will be more momentous for the future of mankind than was the Copernican Revolution or the Darwinian Revolution. For with the Galtonian Revolution, for the first time, the major changes will not be to ideas alone, but rather the major change will be to mankind itself. In order to briefly discuss some of the reproductive technology ...........

  66. A new kind of science by nounderscores · · Score: 1

    A lot of people are saying "Nothing new here, these are just gene feedback loops," "this will pale in comparison to the power of sillicon" and "when can I customise my own bizarre pet."

    They're missing the point.

    I think that the most exciting thing about this research thrust to make packages of genes that you can plug into a genome and expect to see it work is that it is concurrant with Stephen Wolframs's A New Kind of Science.

    Sure Wolfram claims to have invented everything from Mathamatica (fair enough) to Occam's Razor (at one point he sagely counsles us to use simpler cellular autonoma to get the desired result and forget the more complicated ones), but the exciting thing is that the book does give interesting examples of how to use cellular autonoma to solve real world problems which are poorly suited to math.

    The cellular autonoma that he proposes operate by looking at their ancestor cell and the cells which surround them and then looking up a table of rules to determine what properties they will have. We can do this now with real cells using short range hormones and making the output something like turning on a Green Fluroescent Protein gene.

    Wolfram is trying to use a computer with one or two processors to simulate an exponentially growing colony of cells. this means that he runs out of computing resources at an ever increasing rate.

    With real cells, the processing power grows with each iteration, because each new cell takes care of its own housekeeping. Just add nutrient.

    So borrow the book, read it and then you can see the revolution on your hands if we manage to produce something as dumb as non-motile procaryotes which are able to take the average of the hormonal output of their three nearest cells and then change colour.

  67. Evolution by NeoXero · · Score: 1

    Evolution is a flawed theory. If you believ in evolution you should read this book "The Evolution Cruncher". It disproves virtually every aspect of the theory of evolution. An excellent read.

    1. Re:Evolution by fireweaver · · Score: 1

      So tell us, what is the -right- answer?

  68. shiny my Interweb computer screen by Eotnak · · Score: 1

    sciencenews.com is certainly MY preferred search engine

  69. DRM DNA by LegendOfLink · · Score: 1

    It's only a matter of time until the RIAA tries to put restrictions on the intellectual copyrights of downloading MP3's into your genes. Who will be the first to be sued for absorbing the new Madonna single?

    --
    IGB: More fun than eating oatmeal!
  70. First application sensors? by Doctor+Hu · · Score: 1
    I'd started to compose a 'funny' about computers that worked about 8 orders of magnitude slower than the calculator in my mobile phone and mutated to give unreliable results at the end of the guarantee period, then looked at the article.

    This isn't (yet?) an attempt to build a bio-computer (although from the article they've apparently already reached the Blinkenlichts level: The result was a population of gently twinkling cells like flashing holiday lights, Elowitz says. "It was very beautiful," he says).

    Rather, as far as practical results are concerned, the researchers appear to be taking a cue from electronic logic circuitry, and anticipate ways to use that field's rules to make new and sensitive measurement mechanisms. Again from the article, speculating about what might be possible: "If you spread cells around . . . they will form a fluorescent ring around the [chemical], and the middle of the bull's eye is where the bad guys are," Weiss says. It's an interesting approach for very specific bio-sensors.

    I'm not too sure I like the idea of E. coli of all things being manipulated to flash in different colors, but there you go.

  71. If your experimental circuit dies... by MMHere · · Score: 1

    ...you can feed it to your cat.

    Remember that not all mutations are beneficial to the organism.

  72. I do this... by Salis · · Score: 1

    One thing they didn't mention is that Gene circuits can not only exhibit bistable behavior (bits), but multistable behavior (trinary, etc). Because chemical species exist in concentrations and not 'on' or 'off, there's quite a bit of additional complexity that can be utilized to perform added functions.

    Differentiating stem cells in the body take a signal (concentration of a chemical species) and differentiate into different cell types (more than two different cell types).

    Sometimes, it's like an 'if then' statement => If received X signal, differentiate into cell type A, else B. If received signal Y (after having received X), differentiate into cell type C, else D.

    Or, it might receive a 'low' signal of X and go A. Medium => B. High => C. None => D.

    There's different mechanisms that can be employed to give the gene this behavior. But, the cell must be able to effectively distinguish between 'none', 'low', 'medium', and 'high'..even in a highly fluctuating environment. So it's not simple nor has it ever been studied rigorously before.

    Yes, scientists have played with gene circuits and have created some interesting designs. But, it's becoming an engineering discipline whereby the engineer should know _exactly_ what will happen if the microbiologist assembles the specific components together in a cell.
    That'll take a decade or more, but it's getting there.

    Howard Salis
    Chemical Engineer
    University of Minnesota

    If you want to read a great paper, read Adam Arkin's paper on the Stochastic simulation of Lambda-Phage infection of E. coli. It's from 1998 (I think). The fact that one can simulate exactly what occurs inside cells is amazing. The next step is to _predict_ what will happen. This is what engineers do.

    How many times do you see buildings spontaneously collapse? :)

    --
    Favorite /. tagline: "On the eighth day, God created FORTRAN." And it was good.