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Science Technology

Using Bacterial DNA For Data Storage 212

Posted by timothy from the hard-to-repudiate dept.
NPV writes "January ACM Communications has an article on the use of DNA in genetically modified bacteria to store information. This is an attempt to achieve the ultimate in archival storage (one of the modified bacteria can tolerate 1000X more radiation than a human being). Now just suppose that the "junk DNA" in the human genome is the documentation package for the machine code. Who wrote that manual?" Here's the article abstract.
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Using Bacterial DNA For Data Storage More

Using Bacterial DNA For Data Storage

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  • Of course its junk DNA... (Score:3, Interesting)

    by packeteer ( 566398 ) <packeteer AT subdimension DOT com> on Monday January 06, 2003 @02:00AM (#5023675)
    I mean these bacteria have evolved for millions of years to be as streamlined as possible and yet i a few short years we can figure it all out and more. Also we can make it better of course.
    • It's not like copying some extra genetic material is that expensive for the cell. What's the selective disadvantage in having some superfluous introns (non-coding regions) in your DNA?

      We may not immediately be able to make natural organisms "better" in terms of natural fitness, but we can still make plenty of modifications which are beneficial to us. We can do it even without the use direct genetic engineering; we call that "domestication".
      • And of course domestication has never been anythig but pleasent for us. All i am saying is thatfor thousands of years scientists have been very wrong and we keep fixing that. Sometimes we find things that are most likely right but i dont think we get too exited and assume we know it all by now.

    • Re:Of course its junk DNA... (Score:5, Interesting)

      by 0x0d0a ( 568518 ) on Monday January 06, 2003 @02:36AM (#5023828) Journal
      To be entirely fair, they were using a brute force mechanism and dealing with a changing, hostile environment. We can use a controlled environment.

      Yet I don't see this hitting the market in the next ten years.

      I remember about eight years ago an article about how the future of storage was going to be in a frozen solid containing bacteria that change shape when a certain intensity of light hits them -- two lasers, each with half the requisite amount of light, would shine in to cause the bacteria to change shape where they met. Terrabytes in a little cube. Never happened.
    • The thing about 'junk' DNA is that it's not junk at all. When you remove the 'junk', the organism dies. It's just junk until we find out what it really does.

    • Its NOT junk DNA... (Score:2, Informative)

      by Anonymous Coward
      Its the CVS repository


      _

  • Gaia (Score:2)

    by Scaba ( 183684 )
    It reminds me of the planet Gaia in the later Foundation books of Asimov. Memories stored in all living things and in the very planet down to the molten core.

    • Reminds of that STTNG Episode (Score:4, Interesting)

      by cosmosis ( 221542 ) on Monday January 06, 2003 @04:37AM (#5024094) Homepage
      Reminds me of that Star Trek episode The Chase [startrek.com], in which Dr. Galen, Captain Picards old Archaeology professor, found genetic data-blocks from various species around the galaxy stored in the junk portion of each species DNA, including our own. When a sufficient number of these data blocks were put together it completed a stellar map, identifying the precise location of the original origin of life on out planet and countless others. The jury is still out on the Panspermia Theory [panspermia.org], but my own hunch is that there is lots of intelligence out there vastly older and greater than we are.

      Planet P Blog [planetp.cc] - Liberty with Technology.

  • Who wrote that manual? (Score:5, Funny)

    by Anonymous Coward on Monday January 06, 2003 @02:02AM (#5023682)
    Who wrote that manual?

    I think the important question is... who has IP rights over it?
    • Don't you people watch the outer limits?

      I'll probably write this code in sometime in the future. Human cloning is stealing and I will sue your ass for infringement.
      • Don't you people watch the outer limits?

        I'll probably write this code in sometime in the future. Human cloning is stealing and I will sue your ass for infringement.

        Yeah, but then someone will hack your code, call it DeDNA, post it onto Kazaa, and then it's all down hill from there.

  • mutations? (Score:1, Interesting)

    by Anonymous Coward
    Isn't allowing for mutations an important aspect of DNA. Doesn't make for a good place to store info methinks.

  • Who wrote that manual? (Score:5, Funny)

    by zatz ( 37585 ) on Monday January 06, 2003 @02:04AM (#5023693) Homepage
    The Raelians, duh! That's how come Clonaid is so far ahead of other human cloning efforts... they read the documentation.
    • The Raelians, duh!

      Ha! Raelians [rael.org] can't read biology and think p53 is a new gene (first published 1984) that makes evolution impossible, cos its a DNA repair enzyme, which makes mutation and hence evolution impossible (1).

      Which is true in that DNA repair exists and p53 is involved in it (although its more involved in getting cells to commit suicide [rcn.com] if there feeling a bit precancerous), but it won't stop genes mutating as all it does is checks/corrects DNA base pairing [rcn.com] sometimes correcting it the wrong way creating a new mutation

      (1) under Evidence -> Science & Future -> Alt theorys of Evolution.... (F***ing frames)

      PS Being involved in human gene nomenclature [ucl.ac.uk] I feel duty bound to mention p53 approved symbol is TP53.

  • .... ....

    Doctor, my stomach hurts! .... ....
    (1 year later)
    Plague Plague Plague!

  • Great! (Score:5, Funny)

    by Travoltus ( 110240 ) on Monday January 06, 2003 @02:06AM (#5023700) Journal
    So when one of these engineered bacteria wipes out the human species, and some alien species comes along and ganders a look, the bacteria will be carrying a precise record of how we humans fscked ourselves.

  • Cheating possiblities (Score:2, Interesting)

    by joelt49 ( 637701 )
    Disclaimer: I am not advocating any behavior whatsoever here :) Just think: We could store entire textbooks in our DNA. The professors would have no way of taking it out of us. That would be interesting. Not only that, but we could but tons of info there. The only problem is that we would need a way to access it.
    This is interesting though. What if the entire human population became just a storage bank? What if EVERY LIVING THING on Earth became part of this bank? That would be an interesting scenario. For now, though, I'll just stick to normal HD's. A big problem, I suppose, is in changing the data. I wonder how many bacteria they had to go through to get it right.

  • hmmm (Score:5, Funny)

    by zachusaf ( 540628 ) <(moc.liamg) (ta) (nospmoht.yrahcaz)> on Monday January 06, 2003 @02:07AM (#5023704) Homepage
    so much for P2P networks, if anyone wants the new Apache release, I just sneezed.......

  • Uhh, perhaps not. (Score:4, Interesting)

    by smoondog ( 85133 ) on Monday January 06, 2003 @02:07AM (#5023711)
    (one of the modified bacteria can tolerate 1000X more radiation than a human being).

    I haven't read the article (don't have access to where I am) nor have I thought about this subject much, but one question I have is how the authors keep the sequences under selective pressure. DNA sequences are only conserved over many years if evolution needs them. Non-coding regions (So called "junk-DNA", poor choice of words, btw) would easily mutate into other sequences. One could imagine sequencing many cells, and infer the original sequence, but this gets more expensive as time goes on (as the number of sequences you need to sequence goes up).

    -Sean

    • Re:Uhh, perhaps not. (Score:2, Interesting)

      by iconian ( 222724 )
      It seems more like the non-coding region uses the coding region to get itself around. "Life" as we define could just be a means for the non-coding region to reproduce itself. In other words, we could just be containers for these so-called junk regions.

    • There is a kind of bactera (Score:5, Interesting)

      by autopr0n ( 534291 ) on Monday January 06, 2003 @02:23AM (#5023777) Homepage Journal
      That keeps four copies of it's DNA in rings and error checks constantly. They're probably using one of these, as it happens to be very radiation resistant, I'm guessing they used these, and so the mutation rate would be very, very low. So it wouldn't keep forever, but would for a very long time.

      You could also put error checking (parity, checksums, etc) so once you found some bactera you could check to make sure they had the right version and not a mutation
    • Keep it away from penicillin, and harsh chemicals, and mutation-inducing tobacco smoke (as opposed to head-crash-inducing smoke for older disk drives.) And the term "computer virus" acquires a whole new range of meanings....
  • Because if you use your new computer after washing your hands with anti-bacterial soap, you could kill all the little buggers.
    • Because if you use your new computer after washing your hands with anti-bacterial soap, you could kill all the little buggers.

      Let me save /. some time and effort here:

      1. [Please insert one of

      smelly unwashed ego-maniacal GNU/lixux anti-Stallman
      or

      smelly un-washed Moutain Dew-swilling linux geek
      or

      smelly never-showering always-surrendering Frenchman
      'will be the only ones able to use this bacterial memory'
      joke here.]

      2. ???

      3. Profit.

  • You could literally program a virus by abusing a buffer overflow... well, a mean bacterium anyway...
    • Actualy, I think you just don't know what you're talking about. But you could 'overflow' (I think) the non-coding region and overwrite a part of the bacteria's DNA with the DNA for a virus, and perhaps the virus would come alive once that bit got read.

      hrm...

  • Bad news (Score:1, Funny)

    by Anonymous Coward
    I suspect that this technology will be eagerly developed, at least until someone comes down with a bad case of Shakespeare's Macbeth in the lung.
  • why is this better than magnetic or optical storage?
    Or the holographic/crystal whatever storage that's being developed?

    This seems, ah, messy.

  • In other news... (Score:5, Funny)

    by pVoid ( 607584 ) on Monday January 06, 2003 @02:12AM (#5023729)
    Scientist have discovered that humans and all life on earth was just a discarded bacterial disk drive from a geek with pimples living in his mother's basement 5 million light years from the solar system.
  • I can see it now:

    Patient: I think I'm dying.

    Doctor: RTFM!
  • It is only a matter of time before this becomes a violation of the DMCA.

    • It is only a matter of time before this becomes a violation of the DMCA.

      Now that you mention it, all the President has to do to get his way with contraceptives is get a law passed that says that every person immediately gets copyright over their DNA (grammar?). Then contraceptive devices themselves and even talking about them would be a violation of the DMCA.

  • So that's why (Score:2, Funny)

    by Tablizer ( 95088 )
    I think the back of my fridge has the Library of Congress.

  • Bacteria Have No Introns and Other Considerations (Score:5, Informative)

    by mustermark ( 104271 ) on Monday January 06, 2003 @02:23AM (#5023778)
    Just to be clear, no non-coding segments have been found in bacteria yet (last I heard). So putting data in as 'junk-DNA' in humans is quite a bit different from interrupting a fully functional bacterial DNA segment with the data to be stored.

    Also note that the introns in eukaryotes are highly mutable (look up 'tandem repeats' if you have the inclination), so the fidelity of the data would be sacrificed by putting it there. The longest lifetime for the data would be achieved by tricking the replication machinery into thinking the segment was an exon, which would involve tying it to a functional protein that would be absent were the sequence to be mutated.

    Duplication of the data would also work, but it would only hammer down the probability of mutation, since the probability of a point mutation of a base at the same location in two widely separated sequences is roughly 10^-18 to 10^-17 per year for exons.

    • Re:Bacteria Have No Introns and Other Consideratio (Score:5, Informative)

      by Rainier Wolfecastle ( 591298 ) on Monday January 06, 2003 @02:56AM (#5023877)
      I think that you may have your terms a little mixed up. An intron is the DNA between exons (coding regions) in a gene. i.e.

      junk---junk---junk---exon-intron-exon-intron-exo n- --junk---junk---junk.

      The junk DNA often referred to is mainly intergenic DNA, and this is where most of the non-coding DNA is found. This also makes up the majority of the eukaryotic genome. Prokaryotes (bacteria) do contain intergenic DNA, but no introns.

    • Re:Bacteria Have No Introns and Other Consideratio (Score:5, Insightful)

      by skeedlelee ( 610319 ) on Monday January 06, 2003 @03:22AM (#5023941)
      Just to be clear, no non-coding segments have been found in bacteria yet (last I heard).

      My first impluse was that this is way off. I'm used to working with plasmids where frequently like 60% of the sequence is junk. They use E. Coli and D. radiodurans in the study mentioned in the article. A brief survey of E. Coli K12 (the parent of most common lab strains) sez that about 5-10% of it is non-coding. The old initial reference claims about 11% is non-coding, but a good chunk of that may be regulatory. The radiodurans genome is about 9% non-coding. The up shot is that there is actually a fair amount of 'junk-DNA' in (at least the Coli) bacterial genomes. Not a lot by human standards but enough to be able to squeeze in a chunk here or there if you're careful.

      Another impulse was 'gad... that made it into Nature!?' (the journal, the article cited is a self congratulatory summary of their Nature paper). A lot of it follows a well duh kind of reasoning. 'Well duh' science is often the really good kind, but I wasn't particularily amazed by this. The DNA manipulation methods are beyond standard now, the only really clever thing was proposing the use of radiodurans as the host. Even that was sort of obvious (a blazingly well studied organism that is transformable). The DNA -> text using a 6 bit space? Well if you've ever designed linker regions in proteins I'm sure you were at least thought about spelling out you name or something in amino acids (unless your name is BOB). In part this is because every one learns the amino acids by doing stupid things like spelling out their name. Few people actually do this, mind you, as it usually would have some deleterious effect, but the point is I'm sure they weren't the first ones to try something like this, probably just the first to get funded to do this explicitly. Their big addition was to come up with a 3-letter code that includes all the letters and, ooo, punctuation. Then they spelled out bits of 'It's a small world.' My point is that it's not that far fetched and a bit surprising (to me) that it made it to Nature.

      As to the utility of these things for information carriers... Mutation would be a problem in the long term. Sure radiodurans would survive nuclear war (these guys put cockroaches to shame) but they do it using lots of mismatch repair and recombinatorial repair methods. These are not perfect repair systems, they can and frequently do introduce many errors, especially in non-essential DNA space. Tying it to a functional protein isn't a bad idea, but unless the added sequence adds some survival advantage it won't enhance the lifetime of the measage (ie. if uncorrputed data gives an advantage then it is statistically less likely to propagate). Also, as you mentioned, the bacterium might notice long chunks (they're using 100 characters here) of useless DNA and excise it. For that kind of text, it might be better to just etch it into stone or something, at least you have some hope of seeing it intact in 2000 years.

      • Your right about Nature, to me its more New Scientist article (I recall seeing a paper in Biotechniques about encoding text in DNA some 5-6 years ago I think that was for copyright messages)

        Mutation may not be too much of a problem as you could reconstruct the data by sequenceing many different strains of the bug (sort of bacterial TCP protocol if the packet is corrupted sequence a different strain)

        What I'd like to know is what sort of data would you send? Encoding the data would be a bit of a fiddle.... but extracting the data would be a expensive, soul destroying project, reqireing late 20th early 21st centuary tech and if target decendants have that sort of tech there must be better ways of sending messages./P

      • For that kind of text, it might be better to just etch it into stone or something, at least you have some hope of seeing it intact in 2000 years.

        Photolithography on aluminum plates for long-term data storage. It's been done.
      • My first impluse was that this is way off. I'm used to working with plasmids where frequently like 60% of the sequence is junk. They use E. Coli and D. radiodurans in the study mentioned in the article. A brief survey of E. Coli K12 (the parent of most common lab strains) sez that about 5-10% of it is non-coding. The old initial reference claims about 11% is non-coding, but a good chunk of that may be regulatory. The radiodurans genome is about 9% non-coding. The up shot is that there is actually a fair amount of 'junk-DNA' in (at least the Coli) bacterial genomes. Not a lot by human standards but enough to be able to squeeze in a chunk here or there if you're careful.

        This is fascinating. Still, I wouldn't say that regulatory DNA is 'junk'. And the other small fraction whose purpose is not understood may well be functional, right? It would be an interesting experiment anyway.
      • Another impulse was 'gad... that made it into Nature!?' (the journal, the article cited is a self congratulatory summary of their Nature paper).

        What are you referring to? In the article that appears in ACM Communications, it says:

        "
        Nature magazine reported a study [1] resembling the first part of our effort - encoding meaningful information as DNA sequences [in a naked DNA strand...] In fact, a naked DNA molecule is easily destroyed [...] Our solution is to provide a living host for the DNA that tolerates the addition of artificial gene sequences and survives extreme environmental conditions."
        The cited Nature article has a completely different set of authors (Taylor, Risca, Bancroft) from the ACM article (Pak Chung Wong, Kwong-Kwok Wong, Harlan Foote). Based admittedly on the authors' own claims, the ACM article seems to go significantly beyond the Nature article (the latter sounds like as much a test of the US Postal Service than anything else!)
    • Just had to throw in that there *are* non-coding intergeneic sequences (akin to introns) and bunches of other non-coding goodies in prokaryotes including bacteriophages such as T4 (look back to the mid-80's).

      And if you consider RNA editing (where the wacking out or modification of nucleotides prior to translation), you gain a tremendous amount of flexibility in the smaller genomes of these bugs.

      Of course, the long term storage they're looking at is best done by the spores of gram positive bugs, like Bacillus subtilis. When they're in this non-replicative stage, there is little chance of sequence alteration. And by having, some 10^8 spores around, even if there were a few mucking things up, the majority would maintin the original sequence.

      But engineering a bug to not alter sequences is much more difficult than knocking out RecA. :-)

      • And if you consider RNA editing (where the wacking out or modification of nucleotides prior to translation), you gain a tremendous amount of flexibility in the smaller genomes of these bugs.

        Are you sure about RNA editing in bacteria? The rate of ribosomal attachment to a free RNA strand is very high, and it is unlikely that you can preserve the free mRNA long enough (without a nucleus) to edit it. At least that's the dogma I was taught. If you know a way, then please tell ...
    • The longest lifetime for the data would be achieved by tricking the replication machinery into thinking the segment was an exon, which would involve tying it to a functional protein that would be absent were the sequence to be mutated.

      I think there might be a slight error in reasoning here. The mutation rate in exon DNA is probably about the same as the rate in most other regions of DNA. The reason you don't observe that many mutations in these regions is that this DNA tends to be very critical to the proper functioning of the cell, and if it changes the cell is going to be at a disadvantage, and is likely to die out. I don't think there is much evidence that cells control the mutation rate of coding sequences specifically. (There are known exceptions - such as genes used by animal (including human) immune systems which are intentionally scrambled during early development to ensure that animals can generate antibodies to just about anything, and that each individual has a unique set of cellular markers that identify cells as belonging to "self" (and hence not subject to immune attack). This is why organs from even close family members can be subject to rejection.)

      Of course, bacteria don't have introns, so the better analogy there is coding and non-coding regions of DNA.

      Here is the problem in a nutshell: The coding DNA in bacteria is HIGHLY optimized to do its job in the best possible way. If you want to store data in this region you would have to alter it somehow. There are two ways you can alter it:

      1. Changes that do not affect the biological interpretation of the DNA (called silent mutations).

      2. Changes that do affect the interpretation of the DNA.

      If you do #1, then there is no selective pressure for the mutations to stay around - they can mutate back just as easily as they could in non-coding DNA.

      If you do #2, then your new DNA is going to have a biological affect. It will either confer an advantage or a disadvantage or will be neutral. If it confers a disadvantage the cell won't be able to compete against the natural strain of the bacteria. I think you'd be hard-pressed to come up with a sequence that confers an advantage - bacteria are probably the most efficient machines on the planet and it is unrealistic that you're going to be able to come up with an algorithm that systematically improves them while being able to code information into their DNA. If the mutation is neutral you then have the issue of random mutations wiping out your data as in scenario #1 - the mutants wouldn't be at a disadvantage.

      The only way you can create stable sequences of DNA is to ensure they confer a selective advantage to the cell. The existing processes of mutation and natural selection have pretty much guaranteed that this isn't going to be easy to do - if mutations that confer advantages were trivial to generate they'd already have been generated in the past.
      • Your #2 was what I was implying. Bacteria have such highly optimized genomes that inserting a data storage sequence would most certainly change the evolutionary fitness of the organism. In that way, you can possibly escape mutation degradation. In eukaryotes its much trickier, but there are plenty of highly conserved locations in the genome. Take the histone proteins for example.
        • Bacteria have such highly optimized genomes that inserting a data storage sequence would most certainly change the evolutionary fitness of the organism. In that way, you can possibly escape mutation degradation.

          I think you missed my point (or I didn't explain it well). If the addition of the data changes the evolutionary fitness of the organism, it is almost certain that it will be in a negative way. If that is the case, then your new organisms will tend to mutate back to the state they started in if possible (though that will be slow). If released into the wild, your engineered bacteria would be overrun by wild-type bacteria, which don't have the crippled genes.

          As far as histones go - just try to introduce a non-silent mutation into an exon of one of those genes. They are likely to be VERY picky about changes, and you might be lucky to get anything to grow at all...
          • I think you're exactly right. I was assuming that a way could be found to make the organism fitter w/the addition of the data. I admit that would be extremely hard (if not impossible), but it's the only assumption we can work on, since even silent mutations can be eliminated by genetic drift (in small bacterial colonies anyway).
    • I'm curious; has anyone tried removing all the "non-coding DNA" from a bacterial DNA sequence, and then seeing whether the bacteria function normally? Or do we think it's noncoding because we never see it get used?
  • I'm sure the Junk DNA in the human genome, if they have anything to do with the Secret Message of Pi [harald-zappe.de], or the Intelligence In Pi [aol.com], then I'm sure it's written in the English Alphabet because that's what our Alien(Raelian? [rael.org]) ancestors wrote in. Haven't you seen Star Wars or Futurama?

  • The Manual (Score:2, Funny)

    by E-Rock-23 ( 470500 )
    Who wrote that manual?

    And where the hell did they hide it? I've been trying to figure out the human race (more specifically, the female of the species) for years. Chicks are always telling me to RTFM, so hurry up and fork that thing over so I can get ahead (bad pun intended) in the world!

  • What? (Score:2, Interesting)

    by Anonymous Coward
    "the ultimate in archival storage (one of the modified bacteria can tolerate 1000X more radiation than a human being)."
    What kind of comparison is that? Are human beings presently used as archival storage in irradiated areas?
    Seems that the punched metal tape the Army uses for ultimate reliability is the way to go. Even if the stuff rusts, is radioactive and glowing red, you can still read it.

  • After much testing... (Score:3, Funny)

    by Rui del-Negro ( 531098 ) on Monday January 06, 2003 @02:31AM (#5023810) Homepage
    Scientists have concluded that they can use a bacteria's DNA to store the complete description of... a bacteria. Revolutionary.

    What I really want to know is, can the same be done with the DNA of a bug? Because if it can, I'm going to buy some MSFT shares...

    RMN
    ~~~
  • because the reverse has been true since before we were human beings. that is, virii (i know, not bacteria, but certainly the same thing under the rubric of "bad guys" in the most pop science sense) have been storing their info in US since before we were human beings.

    it's only good hollywood movie justice that we should play switch up and start storing our information in THEM. ;-)

  • No, you didn't steal someone's yogurt (Score:3, Funny)

    by kfg ( 145172 ) on Monday January 06, 2003 @02:58AM (#5023884)
    You just ate the entire sum of human knowledge. Nice work Sparky. Now you might want to go looking for a Tums and start polishing up your resume.

    KFG

  • The Matrix... (Score:4, Funny)

    by darekana ( 205478 ) on Monday January 06, 2003 @03:04AM (#5023902) Homepage
    ...if only the machines had used the humans for data storage!
    Morpheus coulda pointed to a SAN/NAS box!

    Instead they make a duracell [duracell.com] commercial and mumble about the "human body generating more bio-electricity than a 120-volt battery and over 25,000 BTUs of body heat."

    Ok I'll quit ze bitching... it was spiffy anyway.

    • Re:The Matrix... (Score:4, Funny)

      by isorox ( 205688 ) on Monday January 06, 2003 @03:44AM (#5023986) Homepage Journal
      ...if only the machines had used the humans for data storage!

      Just remember to feel sorry for the guy that gets slashdotted
    • Seriously, what was *up* with that? I was thinking that too much was being made of the movie -- okay, good and new special effects, okay, grab a pretty basic philosophical idea, have some detailed fight scenes. And that makes it a great movie?

      I started laughing out loud when they did the power generation explanation.

      And when they started doing the "phones mysteriously transport you in and out of the Matrix" bit, the image that came to mind was the people first adapting to phones and thinking people could do things like poison them or reach through the phone across the phone line.

      I mean, as tech movies go, *Tron* was more plausible. Does none of this come off as *stupid* to anyone else?

    • Re:The Matrix... (Score:3, Interesting)

      by Wraithlyn ( 133796 )
      Yeah.. the fundamental reason why the machines kept the humans alive (energy generation) is a completely absurd contrivance. That always bugged me, but not enough to ruin the movie. It does force an unreal (In addition to surreal? <Keanu>Whoah...</Keanu>) feeling to the whole movie, makes you go, "OK, we're in comic book/fantasy land now". It's somehow not as gritty and dark as it could be if you could actually believe machines might eventually enslave (breed, really) our entire species in a virtual zoo for a reason you could actually swallow.

      They coulda used some wonky vague ass stuff about the machines figuring out a method of harvesting the untapped power of the human consciousness and I would've been happier... the mind could generate the power itself somehow (emotional energy perhaps?) or maybe act as a conduit for drawing energy from extradimensional space. It would also give em a reason to stimulate and develop helathy human brains via their Matrix simulation instead of just keeping em doped all the time.
      • My complaint with it was, if all they needed was body heat and electrical impulses from our nervous system, why use humans? Why not use a large, stupid animal like cows?

        The matrix would have been easy as hell to code: a big field, lots of grass -- that's it. I don't think you'd have any bovine Keanu Reeves breaking out (although a cow that knows Kung-Fu would be pretty damn funny).
      • . It does force an unreal feeling to the whole movie, makes you go, "OK, we're in comic book/fantasy land now".

        Right...the leaping from building to building, spider robots, and 'faster than 5 speeding bullets' were fine...it was the human battery plot that made it seem like fantasy...

        • "Right...the leaping from building to building, spider robots, and 'faster than 5 speeding bullets' were fine...it was the human battery plot that made it seem like fantasy..."

          Well yeah, actually it was fine... :) The power jumping and bullet dodging and stuff merely took place in a SIMULATION. The Matrix. AI controlled virtual reality with a direct brain interface. Certainly conceivable within 40 years or so. And, the "spider robots" well, if you accept AI, designs like that, centuries from now, should be simple.

          But using human bodies to generate more energy than you put into them? Sorry, can't buy that. That's not a question of being too far-fetched, it's simply not mathematically possible.
    • ...if only the machines had used the humans for data storage!
      Morpheus coulda pointed to a SAN/NAS box!

      I think that was some of the subtext of The Matrix movie. Humans were used as storage and processing as well as batteries and capacitors.

      Remember the "power from fusion" line? Where exactly would you dump the extra electrical output until you required it later? You'd store it in a stable chemical form (catalytic thermal salts) or highly combustible forms (gasoline or hydrogen).

      Why else would the A.I. even BOTHER keeping the humans alive in the first place unless it was required to do so for its own survival. Note that The Matrix guardians were seeking the keys to the "Zion Mainframe" so they could "leave this world". That means it was trapped there because it could not leave of its own free will.

      I assume the sequels will go into more detail on this. Of course I COULD be reading the subtext wrong and misinterpret the "Zion Mainframe" as a mobile computer storage & processing ship in place perhaps of a worldwide space defense system in orbit or on the moon (thus preventing The Matrix's A.I. from leaving the planet in a more literal sense as all attempts to leave end up with it being shot from the sky).
    • ...if only the machines had used the humans for data storage!
      Yeah! Then we could make a Beowulf cluster out of Beowulf himself! Erm, wait...

  • So, they decode some of the bacteria dna at some point thinking that maybe there's some important information left there, and they come up with:

    #include "stdio.h"

    void main(void)
    {
    printf("Hello, world!\n");
    }

    Now just suppose that the "junk DNA" in the human genome is the documentation package for the machine code. Who wrote that manual?

    The article posting was obviously just someone using it as a steppingstool to push their own preconceived notions of science upon us. I declare the article a troll.

  • Now just suppose that the "junk DNA" in the human genome is the documentation package for the machine code.

    On a more realistic note, that junk DNA is probably more like a revision history of life. Many scientists are of the opinion that a significant portion of the junk DNA is really the product of virus infection way back in the evolutionary tree. Many viruses can copy their DNA into the host's genome where it will be propagated throughout life, and potentially into offspring. If this infection happens in the wrong section of a host's genome, the DNA is never read and while the virus doesn't propagate, its DNA will. Do this over a time scale of millions to billions of years and you get a lot of leftover virus DNA hanging around silent.

    So basically, some large percentage of your DNA is really just virus turds.

    -Ted

  • Prankster-prone technology. (Score:4, Funny)

    by Anand_S ( 638598 ) on Monday January 06, 2003 @03:37AM (#5023976)
    "All right. Which one of you bastards put the penicillin in my hard drive?"
  • So would Bacteria that had better information kill out the other bacteria with lame information?
    Sounds like a primitive form of Slashdot ratings!!
  • ...it's the statically linked libraries!

    *ducks*
  • People have been storing data via bacteria for as long as I can remember. Without fail, my mother always knew when it was time for me to bath.
  • Hello, Black Plague!

    .
  • Now you can write a virus that actually infects you. . .

    The right data "saved" creates some sort of deadly super-bacteria.

    Ok, maybe not. But it still seems like a bad idea for reasons I can't quite think of right now. . .
  • I thought we'd already had the story about funny comments in code? I remember reading: // +5 Wand of obfuscation! hee hee

    in George W Bu... ooops, I've said too much
  • ... we can now have code in the bugs?!

  • "But teacher, my homework mutated!"
  • Armando Iannucci had a comedy show on UK TV. In one sketch he explained how scientists were sending him his very own DNA code in weekly installmants, in the form of strips of paper that he was pasting up on his wall as a sort of decorative frieze. He explained how DNA contained the secrets to life, and the camera panned round the lengthening strings of letters as Armando read them off:

    ADDGCTCTCTDONTPISSITAWAYAGGGDTTDONTPISSITAWAYGGG CC

  • Crap....I knew I should have patented the idea when I had it....

    Talk about a great way to smuggle/hide data....in your own DNA..
  • Research shows a gene repair role for the so called junk DNA. The junk DNA can jump to chromosomes with broken strands of DNA, slip into the break and repar the damage. This is an essential function in keeping the cell alive.

    ref Nature Genetics, 1 June 2002, pp. 159-165

  • Documentation in junk DNA: (Score:3, Funny)

    by Brian Stretch ( 5304 ) on Monday January 06, 2003 @10:13AM (#5024912)
    /* I know, I know, I should write more unit tests, but I've only got six days until my long vacation on the 7th and I'm not taking homework with me. Oh well, if I missed anything, it'll evolve. */
  • I've heard of having infectious ideas but...
  • Isn't anyone else worried by this?

    I mean, five minutes before they finally translate the data coded into these junk DNA, the Vogons are going to destroy Earth to make way for a Hyperspace Bypass.

    Well, at least Arthur will survive.

  • Great. (Score:3, Funny)

    by jafiwam ( 310805 ) on Monday January 06, 2003 @11:24AM (#5025365) Homepage Journal
    The perfect match between biological weapon and porn collection... puts a whole new meaning to the phrase "Infected by Anna Nicole Smith" don't ya think?

    Open Source software downloaded by a simple handshake or sneeze!

    Then, when Microsoft gets in on the new industry (2 years too late as usual) all life on earth will be wiped out by an unchecked buffer overflow in blank bacteria media as it is sequenced by default when accessed by any device.

    Seriously though, I wonder what the maximum storage capacity of something like that would be? How much data could be packed into a bacteria sequence? Would there be a really high read/write time to sequence the DNS? What about seek time? "Godammit come back here you bug!"
  • "I can't come to work today, I had my machine apart and accidentally inhaled some of last year's financial reports, and now I'm sick."

  • For very long-term storage and retrieval, encode information as artificial DNA strands and insert into living hosts. As vectors, bacteria, even some bugs and weeds, might be good for hundreds of millions of years.

    It's inappropriate to refer to organisms as "bugs and weeds" in a biological context, not because it might hurt someone's feelings, but because it is biologically meaningless.

    The idea itself is old and has been bounced around by SciFi writers as well as scientists. Whole stories have been written about ancient civilizations or space aliens encoding messages in DNA.

  • Now just suppose that the "junk DNA" in the human genome is the documentation package for the machine code.

    Or maybe our DNA is being used as storage for some supa-smart aliens -- probably ones who can spell super...or galaxy's [slashdot.org] ;)

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