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Biotech Science

DNA So Dangerous It Doesn't Exist 454

Panaqqa writes "A group of researchers at Boise State University is investigating the theory that there are genome sequences so dangerous they are incompatible with life. Greg Hampikian, a professor of genetics, and his team are comparing all possible short sequences of nucleotides to databases of gene sequences to determine which ones don't exist in nature. The New Scientist reports that the US Department of Defense is interested enough in their work to have awarded them a $1 million grant. I for one am not sure I like the possible directions this research could take."
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DNA So Dangerous It Doesn't Exist

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  • by ztransform ( 929641 ) on Thursday January 04, 2007 @06:11AM (#17455926)
    Just like the Monty Python sketch "the Funniest Joke in the World" [wikipedia.org], developing something that kills itself too quickly isn't going to get propagated far without a lot of effort!
    • Re: (Score:2, Informative)

      "developing something that kills itself"

      This is different. Long double-stranded DNA molecules (up to several kilobases) can be synthesized chemically in large quantities without using organisms. These can then be introduced into organisms by transfection. If the organisms die, the DNA is lethal.
    • Re: (Score:2, Interesting)

      by Threni ( 635302 )
      > Just like the Monty Python sketch "the Funniest Joke in the World", developing something that kills itself too quickly isn't going
      > to get propagated far without a lot of effort!

      It reminds me of the book "A Higher Form of Killing" (by Jeremy Paxman (yeah, *that* Paxman) and Robert Harris) which has this quote from a House Appropriations hearing in 1969:

      "Within the next five to ten years it would probably be possible to make a new infective microorganism which could differ in certain important respec
      • But forensic analyses of blood has found cases well before 1969 (the earliest definite is 1959), and current research has the earliest cases at some time in the 1930's.

        So no it doesn't sound like AIDS was manufactured.

      • by MightyYar ( 622222 ) on Thursday January 04, 2007 @08:51AM (#17456782)
        1. Create deadly AIDS virus.
        2. Release to Africa and homosexuals.
        3. Profit?

        Seriously, let's say the US government possessed such a useless weapon as a blood-borne disease. Let's say they decided to use it. They didn't test it on prisoners or Soviets... no, they went to dirt-poor Africa and infected a bunch of folk there. And maybe they went to San Francisco and infected some gay folks, too. Then the government manages to keep this whole operation a secret and never uses this "weapon" again. The government is terrible at keeping even important things secret - to the point where they redact documents by changing their color in a PDF! Do you really think that the US government was able to develop a virus in secret, and then deploy it in secret?

        That violates Occam's razor. A much simpler explanation is that AIDS evolved to exploit weaknesses in the human immune system, just as many diseases that have come before it.
        • Re: (Score:3, Interesting)

          by the_B0fh ( 208483 )
          Actually, there's another viable theory. There was a tv documentary about it. Try looking up polio research and the use of monkey kidneys (simian hiv is not deadly to simians). Good possibility that the polio used in Africa (but not elsewhere, like US) was contaminated with simian hiv, and that mutated.
        • by gordyf ( 23004 ) on Thursday January 04, 2007 @11:17AM (#17458230)
          Just a nitpick, but AIDS cannot evolve as it's not a virus, merely a condition. HIV is the virus that causes AIDS.
        • by Alsee ( 515537 ) on Thursday January 04, 2007 @12:27PM (#17459224) Homepage
          That violates Occam's razor.

          But you're forgetting Occam's Shaving Cream.

          Conspiracy theory is the handy-dandy foaming lubricant for avoiding the harsh cut of Occam's Razor.

          Occam's Shaving Cream says that Conspiracy theories can trade off lubrication vs foam factor. If a conspiracy theory is slick enough, you don't need much foam. And if the initial conspiracy isn't very slick, the harder someone tries to rub it away the harder it foams up.

  • Suicide genes? (Score:2, Interesting)

    Suicide genes that can be activated at a later date?
    I - am - not - a - machi --*Boom*
  • I, for one, (Score:5, Funny)

    by BerkeleyDude ( 827776 ) on Thursday January 04, 2007 @06:16AM (#17455948)
    I, for one, welcome our new incompatible non-existing overlords.
  • Exactly (Score:5, Insightful)

    by WasterDave ( 20047 ) <<moc.pekdez> <ta> <pevad>> on Thursday January 04, 2007 @06:31AM (#17456020)
    I for one am not sure I like the possible directions this research could take.

    Well, quite. Gene replacement therapy with ones that aren't compatible with life. At all. A project run by the US DOD. "Bound to end in tears" doesn't even start to cover it. Great.

    • >"Bound to end in tears" doesn't even start to cover it.
      Both a well deserved insightful AND one of the best lines ever on /. Good work dude!
    • Re: (Score:3, Insightful)

      by Ingolfke ( 515826 )
      A project run by the US DOD. "Bound to end in tears" doesn't even start to cover it.

      You are so totally right because DoD funded projects are always massive failures or horrible weapons. Oh wait... there's the Internet and OpenBSD.
      • Did you even read the summary? Genes that automatically kill the host are a slightly different kind of thing than the internet.
      • by n3m6 ( 101260 )
        There is actually some good that could come out of this project. That is to say, developing immunity to dangerous organisms that have not existed; or finding the possibility space for these dangerous sequences.
  • by sodul ( 833177 ) on Thursday January 04, 2007 @06:36AM (#17456040) Homepage
    When I first read the title I though it was about a new theory of some religious group trying to say that DNA is dangerous because it proves the theory of evolution so some school board declared that it does not exist.

    Maybe there is some DNA that codes for 666 or that translates to "Hell freezes over".

    But I know that DNA is really coding 42.
    • Re: (Score:3, Insightful)

      by Ingolfke ( 515826 )
      Yeah cause it would suck if "some religious" group used science to disprove a scientific theory. Science is science man... it doesn't matter if it's conducted by the most dedicated atheist or a devout Christian. It's the science that matters.
      • Yeah, like those creationist nutjobs give a damn about that.
        • Who cares what "those creationist nutjobs" think. It's you who presumably cares about science right. So if good science is presented the findings should matter, not the source. Or does some person's own willingness to ignore scientific evidence give you justification to do the same?
    • by SRA8 ( 859587 )
      Reminds me of Ice-9 from Cat's Cradle, except biological.
  • A million dollars?? (Score:5, Interesting)

    by teslar ( 706653 ) on Thursday January 04, 2007 @06:49AM (#17456104)
    From TFA:
    To do this, Hampikian and his colleage Tim Anderson, also at Boise, have developed software that calculates all the possible sequences of nucleotides - the "letters" of DNA - up to a certain length, and then scans sequence databases such as the US National Institutes of Health's Genbank to identify the smallest sequences that aren't present.
    So, basically, it's one regexp and a database lookup. Which is fine (how else would you do it?) but all this requires is one afternoon of PhD time followed by a lot of computer crunching. Even if you buy a very shiny very fast dedicated computer for this, where do the remaining 990 000 dollars go?
    • by teslar ( 706653 ) on Thursday January 04, 2007 @06:54AM (#17456138)
      Ah well, reading the rest of TFA (yeah I know, should have done that before, but hey :) ):
      He has already received a $1 million grant from the US Department of Defense to develop a DNA "safety tag" that could be added to voluntary DNA reference samples in criminal cases to distinguish them from forensic samples. Such tags would not necessarily have to consist of lethal sequences, but could be based on primes that would be easy to detect using a simple kit.
      So the /. summary was misleading, the DoD isn't actually after lethal DNA sequences at all and that is not where the money's going.
    • by Ingolfke ( 515826 ) on Thursday January 04, 2007 @07:50AM (#17456450) Journal
      I hope you're not serious that a "shinny very fast dedicated computer" costs $10k. You can easily spend $100k on a good computer and of course science is driving these massive supercomputing clusters that probably cost $10k/day to operate. Anyways... back to your question.

      where do the remaining 990 000 dollars go?

      Salaries to pay the PhDs to process and analyze the data and tune the software and not go to China or Russia or someone else who'd like to know more about this stuff.
      • by Otter ( 3800 )
        1) This project absolutely does not require a supercomputer. The OP's estimate of cost and time is pretty accurate.

        2) Wherever that million dollars is going, it's certainly not to the stipends of Idaho grad students and postdocs.

        3) There is zero weapons potential to this work.

    • The article implied that they were going to try to synthesize the sequences that they find. This is where the interesting science would come from; some of those sequences may not be valid DNA strings - syntax errors if you will. Others may create proteins that are deadly - understanding the difference between the two would be a major advance in understanding the encoding that DNA uses.

      Writing some perl to skim through a database of genes and pull out the entries that aren't there is fairly trivial. Doing it
    • It would be better to make a table of flags. Initialize all of them to zero. Scan the genome only once and set the flag corresponding to each sequence that is present. Then scan for flags that are still zero. This would be much faster than searching the whole genome for the presense of each possible sequence. It would probably run to completion in a few minutes. Heck, replace "flag" with "counter" and see which sequences are most common at the same time...
  • stupid (Score:5, Insightful)

    by mapkinase ( 958129 ) on Thursday January 04, 2007 @06:50AM (#17456110) Homepage Journal
    He is presenting his results at the Pacific Symposium on Biocomputing in Maui, Hawaii, this week.
    That is pathetic claim to importance. The only reason it reached the top /. page is paranoia prevalent at /. The whole research smells pseudo-science at the distance between Hawaii and East Coast (where the government are, but they do not smell it, of course).

    Especially stupid are searches for amino-acid sequences. Some of the sequences do not make structural sense, obviously.

    And what about "dangerous"? Obviously, if the sequence is so crappy that it makes the working conformation of every structural RNA or protein disfunctional then it won't be reproduced. Never.

    More interesting would be to find out why some sequences are not encountered also in non-coding areas. But "danger"???

    Give me a break. This is as stupid as stupid goes.
    • Pathetic resume [nih.gov] of the PI.

      5 references in PubMed! First reference in 1986! Come on. I have more references. And none of his references are him being first or last author.

      In twenty years - 5 publications relevant to the field?

      • More here [boisestate.edu]. Considering his MS in Genetics was awarded in 1986, I would have been surprised to see references from much earlier than that, although maybe when he was an RA in Dermatology he could've done something.
    • ... when the first DNA weapon makes you grow donkey ears and a tail. Of course this will be to reflect your political views. Could be worse, you could grow an elephant trunk and ears!
  • by EvoDevo ( 951991 ) on Thursday January 04, 2007 @06:59AM (#17456178)
    First of all, I am doing research in computational biology. I just read the paper linked from his webpage at http://biology.boisestate.edu/hampikian [boisestate.edu] and I have to say that this is one of the worse papers I have ever read. First of all, I can literally write a program to do all that he proposed in about 10 minutes. Give me the $1 mil, I'll do the research. Although the idea of systematically finding nullomers can have practical applications, there is ABSOLUTELY ZERO evidence that they are incompatible with life. And wow, isn't this the eye catching title that we see on /. The numbers of nullomers that he found in the human genome, for example, looks like they are in line with expectation given a genome genome that is AT rich (more A and T nucleotides than G / C nucleotide). Because the human genome is finite (only about 3 billion nucleotides), of course you are going to find DNA sequence even at only 11 bases long that do not exist in the human genome. Just do the math! 4^11 = 4.2 billion. It makes me so furious that our government wastes so much money on useless stuff.
    • You're just jealous because you didn't think of this idea to get a $1mil grant :)
    • by cowscows ( 103644 ) on Thursday January 04, 2007 @09:32AM (#17457084) Journal
      You missed the last paragraph, obviously. This new DNA will be created out of anti-matter, creating what is essentially anti-DNA. This anti-DNA will annihilate on contact with normal DNA, and release incredible amounts of energy.

      The DOD's goal is to eventually breed entire anti-DNA animals. Imagine an anti-rat, which could infiltrate an enemy building through the sewer lines or hide in a packaging crate or whatever. Once it's entered the compound it would emerge from hiding, and natural instincts would drive it to attempt mating with other rats. Since it's likely that most of the rats it may find will be of the normal, non-anti-matter variety, the commencing of the mating process will result in mutual annihilation of both rats, and the release of ridiculous amounts of energy. So a hugemongous explosion.

      Of course, by breaking this story, slashdot has probably saved millions of lives. Had the pentagon kept this secret as they had hoped, they'd be able to hide their attacks right in public view. Imagine the generous donation by a US "Charity" of a full grown elephant to the Beijing zoo. Little would the chinese government expect that this is actually an anti-elephant, and when it interacted with the normal elephants they already had...let's just say that China wouldn't be challenging the US economy any time soon.

      • I was unaware that most buildings had sewer lines that were magnetically isolated from other matter (might be an interesting grant opportunity right there--antimatter sewer lines, stop pollution and provide alternative energy).
  • Run for the hills (Score:5, Interesting)

    by Adam J Stone ( 1018520 ) on Thursday January 04, 2007 @07:01AM (#17456182)
    There may also be some that are lethal in some species, but not others. We're looking for those sequences.

    This article reminds me of a doomsday hypothesis I once read. Daniel Pouzzner [mega.nu] posted this some time ago on his website:

    It is quite likely that the Endangered Species Act and similar policies will continue to be enforced, setting large areas of land (and associated natural resources) out of the reach of interested industries. Corporations in these industries will create a demand for black market genetic bullet engineering, by which obstacle species can be purged, freeing the land for industrial exploitation. The profit motive is overwhelming; the resources at issue are worth trillions of today's dollars annually. An engineer who can target species on demand can obviously target humans, or even subsets of humans, if he wants to. Black markets by definition are not subject to regulatory scrutiny, and of course tend to be populated by unsavory and low characters. The environmentalist extremists (many of whom are well-financed or independently wealthy) will retain the services of some of these black market operators, to "fight back" (as they see it) on behalf of the species being targeted for/by the corporations. This will probably culminate in a doomsday bug.
  • DNA makes protein. Let's say there are DNA sequences which lead to protein so poisonous no cell can take it. Implant the DNA in a creature (plant/cell/animal). Whaaaw, now we have a creature which... kills itself??? It is not like there are no proteins available which are lethal to man but can be tolerated by other creatures: snake venom, certain plant extracts. The whole point of this is that no creature can take it.
    • by xero314 ( 722674 )

      The whole point of this is that no creature can take it.

      The problem lies in what this research can lead to. Once you know what DNA sequences are incompatible with life, therefor killing anything that has this particular sequence, you could design a virus, probably a retrovirus, which could contain an RNA sequence which when reverse transcription to a host cell takes place causes one of these incompatible sequences in the Host cell. This could even be designed so that it would only produce the incompatibl

  • I'd like a grant to theorise about a few things:

    1) the "Rabbit that is so dangerous it can cut your head off"
    - I believe most of my research will be around the castle Aaaaaargh.
    2) The "Chuck Norris move that's so dangerous that it doesn't exist"
    - Even chuck norris would perhaps have to spend more than 20 minutes researching it.
    3) the "solution to the iraq war which is so useful it doesn't exist"
    - and now I've passed from the plausible to the ridiculous, sorry about that.

  • As mankind reaches closer to controlling reality as a computer program, perhaps it is necessary for all countries to sign on a global contract on what should be allowed and what not. It may not ultimately save us from eugenic wars, but it will minimize the risk of someone toggling the life switch off at will.
    • Did someone say "Eugenic Wars?" You know where that leads,"KKKKKKhhhhhhhhhhhhhhhaaaaaaaaaaaaaaaaaaaann nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn"
  • scientists will have solved the riddle of extending life to 1000 years and will sequence all of our genes so we die at age 72 because it's too expensive to offer state run healthcare to people over the age of 72.
    • Well, you've already got end part right. Just skip the first part and get that middle part done.

      P.S. - if you can come up with a modification that will reduce the age to under 6, there's a massive DOD contract in your future.
    • by argent ( 18001 )
      They already made that movie [imdb.com].
    • Re: (Score:3, Interesting)

      by TheLink ( 130905 )
      Why do that? Govs can just stop being stupidly trying to ban people from smoking and just keep taxing tobacco heavily.

      They should still keep educating them on the dangers of smoking and make it illegal for kids to start or be sold cigs to.

      But other than that, if you know the dangers and you still like to smoke a few packs a day: "Thank you citizen for your contribution and sacrifice!"

      If you die soon after your productive years or retirement, you are no longer a drag to healthcare - while there's your last 3
  • by Mixel ( 723232 ) on Thursday January 04, 2007 @07:44AM (#17456400) Homepage
    Nature generally selects proteins that fold well, because it leads to some stable function. Nature therefore selects DNA sequences that code for such proteins. Rare/nonexistant DNA sequences code for rare/nonexistant proteins that are unlikely to have a stable fold. It is probably worth investigating just in case a few of those have interesting function. The research equivalent of going through someone's garbage. $1 million doesn't go very far these days, so it sounds about right. Why is this in the headlines, again?
  • It's like scientifically searching for EVIL(TM).

    Over a couple of Beers at the pub an interesting discussion, but NOT something one should really engage in.
  • Afraid? (Score:5, Interesting)

    by RAMMS+EIN ( 578166 ) on Thursday January 04, 2007 @07:56AM (#17456476) Homepage Journal
    ``I for one am not sure I like the possible directions this research could take.''

    You mean that it could be used to manufacture new weapons? I don't know if having n+1 ways to kill is really much worse than having n ways, given that n is already as large as it is.
  • by highacnumber ( 988934 ) on Thursday January 04, 2007 @07:58AM (#17456490)
    Just like in DNA, there are words so dangerous that they don't exist. Here's one of them: sdlnfnerooij. Use it with care and send me the check. Most DNA does something, or is a slightly mutated version of a sequence that does something (like endogenous retroviruses). So its like a language with some spelling mistakes - of course there are lots of sequences that won't be there. And if you look at long enough strings, there have to be some missing.
  • Could this be used to attack cancer cells?
  • by Rogerborg ( 306625 ) on Thursday January 04, 2007 @08:30AM (#17456646) Homepage
    What are the DoD going to do; shoot me with a bullet impregnated with a mutagen?
  • I can take a guess as to what strand might be incompatible with life... Here's one famous one:

    H-H-S-O-O-O-O (repeating)

    If I recall, the first test case was the famous "Little Johnny" who was, after the test, a Little Johnny no more.
  • >"I for one am not sure I like the possible directions this research could take."

    not sure? possible directions?

    well then get back to us when you ARE sure about something and maybe we'll listen to your opinion then. otherwise sit down and stfu.
  • Program an organism to self destruct before it becomes a permanent danger.
  • ...that the U.S. D.O.D. would be interested in this. There are people in this world who are completely wrong in the head; ...to the point where having NO survivors in an all out war would be considered a victory. "Yeah, no one would survive. But at least the enemy would be eliminated". That is the only thing a weapon (bio, nuclear, chemical, etc...) that assures complete destruction of all life would be useful for.
    • Re: (Score:3, Insightful)

      by geekoid ( 135745 )
      Jeez, don't be an idiot.
      The DOD funds many pieces of research without the idea that it wouold kill people.
      Yes, they also fund research that kills people.
      If You have been paying attention you would note that the DoD focuses on smaller strategic strikes with maximum impact.

      What's the DoD hoping to find? I way to rearange someones genetic structure so the magically turn to goo? There are better, faster, cheaper, and realistic ways of actually killing someone.

      You people knee jerk reaction to these articles is m
      • Re: (Score:3, Informative)

        by eno2001 ( 527078 )
        Oh I'm well aware of the fact that they research things that aren't used for killing. You're using the fruits of some of that research right now to attack me. ;P (RAR!!!) I'm not saying the D.O.D. is evil. I'm saying that there are some very warped people who work at various levels of our government who are very interested in the ultimate killing technologies. Especially solutions that would exterminate all life on Earth if necessary just to win an ideological argument. Considering how you went off on

Overload -- core meltdown sequence initiated.