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Biotech Science

New Class of Genes Discovered 106

Posted by michael
from the put-your-new-genes-on dept.
HarryGenes writes "Reuters is reporting that Scientists Find New Type of Gene in Junk DNA. The research from Harvard Medical School describes a discovery in the Yeast Genome of a new class of gene that regulates the neighboring gene through the production of its RNA product. This has much broader implications than the article lets on to. Assuming these same type of genes exist in Humans and other organisms, the whole science behind gene expression and gene mapping will be changed dramatically. This type of mechanism can explain a lot of the 'unexplainable'. This is really exciting. I have been working in gene mapping for years and always felt that the 'junk' was there for a reason."
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New Class of Genes Discovered

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  • by MrIrwin (761231) on Thursday June 03, 2004 @12:35PM (#9326940) Journal
    .....the more you know how little you know.

    And yet there are people prepared to unleash modified genes on the world saying that they **know** there is no risk.

    • No kidding.

      As /. user Colin Smith said [slashdot.org]:

      Who would have thought that evolution would be developing it's own roundup resistance [cropchoice.com]. Damn that Charles Darwin.

      Maybe the Monsanto executives are creationists.
      • We are, hah, weeding out those not resistant to Roundup, of which there will always be some. The Roundup resistance comes with a price: some loss of genetic complexity - or to put it another way, some loss of flexibility. It might be that the resistant weeds survive in a narrower temperature, acidity, humidity or other band, or a specific new weakness might not have an obvious manifestation.

        What this means is that if you throw enough nasty chemicals at the weeds, you will eventually wind up with weeds whic
    • I thought you were from NBC.

      -Cyc
    • by Anonymous Coward on Thursday June 03, 2004 @02:53PM (#9328373)

      And yet there are people prepared to unleash modified genes on the world saying that they **know** there is no risk.

      Every time somebody has a child they "unleash modified genes on the world". When people say that there is no risk, they mean there's no risk above and beyond normal behaviour.

      • context. (Score:2, Informative)

        by gregorsamsa11 (758287)
        I agree. Of course there is some inherent risk in foods modified using modern recombinant DNA technologies, but no more than with conventional breeding, in my opinion.

        Many food producing species have been crossed with outside species (usually closely related, but not always). Crossing with outside species introduces a host of unknown factors, combining genes in a totally unique, unpredictable way. However, this was never a matter of heated public debate. Now if you want to add a single gene culled fro

      • by Anonymous Coward
        Every time somebody has a child they "unleash modified genes on the world". When people say that there is no risk, they mean there's no risk above and beyond normal behaviour.

        When someone has a child in the traditional way, they are unleashing the result of a cross between a human and a human on the world. Several million years of history have shown that the risks involved are relatively low.

        When someone splices a jellyfish gene into a mouse, they are unleashing the result of a cross between a mouse and
        • Parent should be modded UP. Grandparent tries to make the point that there are already cases in nature where humans cross different species. However, such point is not valid, because the type of plant-crossing that humans have been doing for thousands of years is 1) proven to be OK through time, and 2) The species are closely related, or at least both are plants. Now we can mix anything with anything.

          Im not against investigating our new abilities to mix DNA and produce new species, in fact I think it will
        • Several million years of history have shown that the risks involved are relatively low.

          Indeed, several thousands of History have shown that the risks involved in multiplicating humans are relatively high (for both humans themselves and for the other species as well).

      • Every time somebody has a child they "unleash modified genes on the world".

        Barring mutation (which would explain a lot...), each of my genes can be found in one of my parents. They're shuffled, not modified.

      • This is just a nonsensical argument.

        The whole point of fertilization, also known as gametic fusion or (imprecisely) as "sexual reproduction", is for species to make sure there is nothing really novel, nothing unusual, in its genes, hence the need for 2 genomes of independent sources, which need not be identical but they do need to be *compatible*. Otherwise, there is no embryo. How many species of metacellulars do you know that do not practice gametic fusion? I thought so. Even partenogenic species are
    • by Shihar (153932) on Thursday June 03, 2004 @02:56PM (#9328415)
      I don't **know** that the meat I am eating is free of mad cow disease. I don't really care though because I live with one a few billion odds.

      There is certainly a risk involved with genetically modified things. Hell, we know this for a fact because we have been doing it for hundreds of years through more primitive means, and we have screwed up in the past. That said, there comes a point when you need to go over your fear and dive in. We will never know anything for sure, and pretty sure is good enough most of the time. I am pretty sure I am not going to die in a car accident on the way to work each morning and that is good enough for me.

      Now, there are plenty of reasons to be weary of modified plants and animals, but all of them are patenting and legal issues. As to the raw science of it though, such concerns are negligible with enough foresight. I don't know about you, but I would merrily risk two or three people in an entire population dying because genetically modified super corn gives them an allergic reaction then watch a few hundred thousand people die because their refuse to grow in the barren land that they live.

      People need to put a careful eye to potential risks and rewards. Humans are horribly crafty bastards. Sure, we screw up for time to time, but we are not all that bad at dealing with the consequences. If you need any proof that we fix things more then we break them, you need only look at the average human life expectancy has changed over time.
      • by FlyingOrca (747207) on Thursday June 03, 2004 @04:08PM (#9329123) Journal
        Man, I don't know. Animals are one thing, but plants are quite another. Ever check out plant genetics?

        I'm more of an animal guy, but my ex was into plant biology, and her take on the whole plant genetics thing is nothing less than... very worrisome. Plants swap and adopt chromosomes, hybridize, etc. much more freely than animals.

        The problem therefore is not that the actions of a gene in one species aren't known (though I'm not convinced they're know well enough); it's that the gene can get into other species far too easily. There are bigger nightmares in that scenario than a few allergic reactions.

        I'll be the first to admit I'm no expert in plant genetics - but a fair number of people who ARE experts are concerned. I'm inclined toward caution. I'd suggest that the best thing to do is to clearly label products containing material from GMOs and let the consumers decide, but the shee^H^H^H^Hconsumers are the same folks with unpatched Windoze boxen. Cheers!
        • After reading your post, all that I can think of is

          "Feed me Seymore!!"

          • That was a truly great flick. I went to see it with a couple of women who were die-hard, I mean "dress-up-'n'-shout-alternate-dialogue" Rocky Horror fans, and all three of us walked out of Little Shop of Horrors thinking it was the best horror musical ever. Thanks for the memories!
        • by Canar (46407)
          You think plants are crazy? Check out bacteria. They swap so many genes its unbelievable. And if the genes kill that bacteria, well, it's been selected against. That won't prevent them from picking up genes elsewhere.

          A shovel-full of dirt contains a regular frenzy of bacteria swapping genes not unlike getting fish, birds, reptiles, mammals, and earthworms together for a big bisexual orgy. The only difference is that with the bacteria, it actually works from time-to-time because they haven't specialized as
          • You think plants are crazy? Check out humans. They swap so much bacteria its unbelievable. And if the bacteria kills that human, well, it's been selected against. That won't prevent them from picking up bacteria elsewhere.
        • There are bigger nightmares in that scenario than a few allergic reactions.

          Hah, like the super plants growing out of control and killing everyone? Sounds crazy right? There is a good write up about it here [xs4all.nl] Interesting stuff.
        • If you think of it this way... you can't breed a dog and a cat, or a human and chimpanzee (although the intelligence of some of the locals here suggests it may have happened), but you can graft or crossbreed a lot of different trees.

          Oranges, Apples, most fruits... and they've managed to crossbreed with nicotine plants. Granted that many of these plants are still fairly related... but I've heard of some very interesting crosses in the world of flora. Fauna is a bit behind on that, I think.
      • If you need any proof that we fix things more then we break them, you need only look at the average human life expectancy has changed over time.

        Humans master fire:
        + life expectancy goes up.
        - Number of people being killed (broken) by fire increases dramatically
        - Number of forests destroyed(broken) by fire goes up

        Humans master agriculture:
        + life expectancy goes up.
        - millions of acres of forest are clearcut(broken) for farming land and buildings for farming villages
        - genetic diversity of agricultur

        • Everything you point out is certainly true - if you are a plant or animal. If you are a non-human animal or tree, having humans around sucks. Lucky for us, we are all human here. I care about the environment exactly as much as it has some sort of impact on humans.

          So yes, agriculture has completely changed the face of the world and wiped out many pieces of the environment, but I give agriculture a big thumbs up. Agriculture means that I don't have to go get my own food, and that gives me plenty of time
      • "I don't know about you, but I would merrily risk two or three people in an entire population dying because genetically modified super corn gives them an allergic reaction then watch a few hundred thousand people die because their refuse to grow in the barren land that they live."

        Ahem, are we saying that GMC's are being used as a solution to world famine? I am no expert, but I know in Europe the EU commision has problems curbing production levels because they are too high. So is there any logic introducin

      • Patent and legal issues are the easiest. Foresight is essentially impossible in any practical sense. Identifying potential interactions of genetic modifications is many orders of magnitude more complex than, for example, nuclear waste management. The state space for the interactions between genes has dimensionality (IIRC) 2^2^log(n) for n genes, and each dimension has variance 2^n. For as few as 20 genes, you have a space too large to search for significant interactions.

        Now, expand that space to accoun
      • As to the raw science of it though, such concerns are negligible with enough foresight

        Like the foresight we used when we put lead in gasoline? Or put CFCs in aerosol cans? Or started using fission for electrical power generation without a plan for storing nuclear waste? When profits enter the picture, foresight is a rare commodity.

        I don't know about you, but I would merrily risk two or three people in an entire population dying because genetically modified super corn gives them an allergic reaction t

      • but I would merrily risk two or three people in an entire population dying because genetically modified super corn gives them an allergic reaction then watch a few hundred thousand people die because their refuse to grow in the barren land that they live.

        Sorry to burst your bubble, but I Call For Bullshit(R) here

        The agricoltural assets are just about enough to feed every living person on this planet, given a fair redistribution of those assets (in fact, in the EU, the goverments pay the farmers not to

    • And yet there are people prepared to unleash modified genes on the world saying that they **know** there is no risk.

      Genetic engineering consists of moving DNA for a reason - i.e. its done with the sequences that we know well how they work. No-one is creating commercial GMOs out of 'junk' DNA today - but now our understanding is growing, some of that junk isnt junk any more, and when it *is* understood, it probably will feature in future biotechnological innovation.

      It's only in Nature that you see huge chu

    • there are people prepared to unleash modified genes on the world

      It's so scary. After all, genes have gone unmodified since the beginning of time, no one knows what could happen if you change them from their original, perfect form.

      I mean, if anyone had different genes, they're libel to become zombies or something. Hasn't TV taught us anything?

      OK, ok. I was tempted to stop here, and have a nice little troll, but some of what we hear about as "genetic engineering" really is little more than the selective

  • Yeah, But (Score:4, Interesting)

    by 4of12 (97621) on Thursday June 03, 2004 @12:51PM (#9327124) Homepage Journal

    I have been working in gene mapping for years and always felt that the 'junk' was there for a reason.

    Sometimes, too, the gene may have moved into the junkyard for a good reason.

    Just imagine reactivating some junk human genes to see what happens:

    Human females have a more pronounced season of going into and out of heat.

    Get an extra furrowed forehead to better protect vision during rainstorms and intense heat on veldt.

    Get large hairy ears to better pick up on approaching predators like lions.

    Given the current rate of change in human environment due to social and cultural changes, I'd venture to guess we have a lot more junk DNA that needs to exit (eg, propensity to develop diabetes if not on a hunter/gatherer diet) than we have need to reactivate old junk DNA.

    If we could engineer useful new DNA, probably creating a visual transmitter capable of expressing information more quickly than voice or hand movement would be high on the list. I would call this the Teletubby gene...

    • Mmm, sexy. (Score:5, Funny)

      by mopslik (688435) on Thursday June 03, 2004 @01:03PM (#9327222)

      Human females have a more pronounced season of going into and out of heat.
      Get an extra furrowed forehead... [and] large hairy ears

      Well, those two should help cancel each other out, no?

    • Actually all of these would be good things if you ask me:

      Knowning when the ladies are in heat... that can't be bad at all. Evolution took this out because we don't need it to survive.. what we need and what we want aren't always the same thing.

      Extra furrowed forehead which gives better vision, better vision sounds good. The cosmetic affect after all is irrelevant, when everyone has this it won't "look bad" anymore.

      Improved hearing, this is bad?

      • by Patrik_AKA_RedX (624423) <patrik.vanostaeyen@NOspam.gmail.com> on Thursday June 03, 2004 @01:50PM (#9327701) Journal
        Improved hearing, this is bad?
        If you live in a flat with thin walls, I say it is.
      • Knowning when the ladies are in heat... Evolution took this out because we don't need it to survive.

        Actually, "Evolution" probably took it out for a positive reason, not just because we didn't need it.

        There are a number of other species in which the female estrus is weak or nonexistent and females are sexually active much of the time. These species have a number of characteristics that they share with us humans: They are mostly social species in which the males contribute a great deal to the raising of
        • Re:Yeah, But (Score:3, Interesting)

          by s0l0m0n (224000)
          Knowning when the ladies are in heat... Evolution took this out because we don't need it to survive.

          Actually, "Evolution" probably took it out for a positive reason, not just because we didn't need it.


          I don't think that it's gone. Your lady may want to have sex with you on a regular basis, but she is most fertile on certain days of her cycle. The natural planning method of birth control would work, except for the fact that sperm are able to live for quite some time whilst looking for an egg to fertil
        • Re:Yeah, But (Score:3, Interesting)

          by shaitand (626655) *
          Females are sometimes in heat and sometimes not NOW. Being in heat being more pronounced won't make them want sex any less or less often, our species mates for recreation as well as breeding.

          The only difference would be that you'd have women walking up to you at various times and rubbing their bodies against yours.

          Actually however, our social structure isn't really a superior way to propogate the species. The males sticking around is really a bad thing.

          The purpose of a species of course is perpetuate,
    • Re:Yeah, But (Score:3, Interesting)

      by isotope23 (210590)
      "I'd venture to guess we have a lot more junk DNA that needs to exit (eg, propensity to develop diabetes if not on a hunter/gatherer diet) than we have need to reactivate old junk DNA."

      I was struck by this as it is connected with something I have been thinking about for awhile.
      Namely the impact of Race and DNA on diet.

      We know that issues such as lactose intolerance are regional :

      http://www.gnxp.com/MT2/archives/001681.html

      I would suspect that tolerance of other foods are as well, given the differing ava
      • Re:Yeah, But (Score:3, Interesting)

        by 4of12 (97621)

        With the above, it surprises me that instead of things like Atkins, there is not a more racial approach to diet. I.E. A "northern european" diet heavier on dairy, an asian diet heavier on fish etc.

        Actually, there is.

        A while back people started coming out with the notion that the ideal diet (and, for that matter, entire lifestyle including exercise regimen) depended on blood type [about.com], which roughly characterizes some racial features.

        • Blood type (Score:3, Interesting)

          by isotope23 (210590)
          Interesting idea, but from looking at blood type distribution it does not seem to closely related to differing areas of the world. The blood types seem to be rather evenly spread.

          My thinking is that the prehistoric people regardless of blood type would have all had to survive on the available local foods. I would think that the lack of choice, i.e. "rabbit or nothing" would have killed off those in the region incapable or less well suited to digesting most of the local quisine.

          The question for me is are t
  • bad article (Score:5, Insightful)

    by merdark (550117) on Thursday June 03, 2004 @01:02PM (#9327212)
    As usual, the quality of a mainstream news outlet reporting on science news is bad. This really has nothing to do with 'junk DNA' from what I can tell. Also, the term 'junk DNA' is terrible.
    There are repeats (sometimes referred to as 'junk DNA') and there are introns and intergenic regions with no *known* function (also referred to as 'junk DNA').

    So while it is technically true that the gene was found in 'junk DNA', it's also true that EVERY new gene is found in junk DNA. That is not what is interesting here at all.

    Basically, they found a gene that turns another gene on or off via it's RNA product. This is what the intereseting news is.
    • Good article (Score:5, Informative)

      by cariaso1 (674515) on Thursday June 03, 2004 @01:34PM (#9327532) Homepage
      Until this article was published, 'junk dna' would be considered the correct term for this region. Broadly speaking, the term suggests that there is no known function for the region. We don't know much beyon "is a region is a coding region?" and "is a region regulatory?". Now this region can be classified as regulatory, but it uses a mechanism never before observed. That is news.

      Much more information can be found in this article taken from pubmed.

      Stealth regulation: biological circuits with small RNA switches [genesdev.org]

      • Re:Good article (Score:3, Insightful)

        by merdark (550117)
        Sorry, but I still think it's a bad article. What do they mean by 'junk DNA'? Is it a repeat (turns out no), intergenic, intron? Junk DNA is a terrible term to use. As I said in my previous post, every new gene or regulatory region is found in so called 'junk DNA'. This is nothing new.

        The important part of the article is that this is a new never before seen *type* of gene. That's the news here, not this sillyness about junk DNA. That part should have been completely left out IMO.
        • Junk DNA is a terrible term and should be phased out. It would be analogous to calling unexplored parts of the earth "garbage dumps" simply because we haven't explored them yet and don't know what's there.

          I hereby propose DUFF - DNA of Unknown Form and Function.
      • I am with you on this one, cariaso.

        While my specific area of interest is not genetics or molecular biology- it is mathematical and computational ecology- I do have the basic knowlege of genetics required of anyone in a college biology program.

        I have always heard the term "junk DNA" refer to sequences of genetic code that appear to have no use, oftentimes appearing just to be big repeating patterns of nonsense and outside of a coding region.

        What interests me especially about this article is that since I f
    • Re:bad article (Score:2, Insightful)

      by HarryGenes (772322)
      This is novel and interesting for the fact that the gene was found in 'intergenic space' and does not have all the normal features and functions of a gene. You are taking the reference of Junk DNA far to personally. It is not to say the DNA has no purpose. If it is there for nothing else, it minimizes the odds of mutating important genes. If the genome was just one gene stacked end to end, then every time a mutation occurred, it would be in a gene. Since 95% of the material has no known function, at th
      • But most new genes are found in 'intergenic space'. That it has a different structure is interesting for sure, but I just don't see the focus of being found in 'intergenic space' to be all that important.

        The article almost makes it sound like this is about junk DNA. It's not though, it's about this new type of gene. That's why I feel it's a bad article. And it would have been nice if they at least provided a reference to the lab or paper.
      • by jc42 (318812)
        There is a fair amount of precedent in science and math for this sort of terminology.

        For example, a few centuries ago some mathematicians started studying the funny numbers like the diagonal of a unit square, and proved that they weren't the ratio of two integers. The idea that there were such numbers was widely ridiculed. The mathematicians' reaction was to say "We need a name for these new numbers. People are calling us irrational for talking about them. Why don't we just call them `irrational' numbe
        • For example, a few centuries ago some mathematicians started studying the funny numbers like the diagonal of a unit square, and proved that they weren't the ratio of two integers. The idea that there were such numbers was widely ridiculed. The mathematicians' reaction was to say "We need a name for these new numbers. People are calling us irrational for talking about them. Why don't we just call them `irrational' numbers?" And so it was.

          Actually, irrational numbers are so named because they can't be forme

        • For example, a few centuries ago some...irrational....

          This is some weird combination of revisionist history (the ancient Greeks knew about irrational numbers) and just plain making shit up (irrational means it can't be expressed as a ratio of integers). See Mathworld's definition of irrational number [wolfram.com] for one more credible, and more researched, version.

          Some time later, in the 1800's... imaginary....

          Imaginary numbers under a variety of names were discussed at least as early the 16th and 17th centuries a

    • I don't quite follow why that's even so interesting, though. RNA inhibition is a pretty hot topic; we've known about antisense RNA [rcn.com] (which is produced by DNA to complement mRNA and inhibit translation) for about 30 years now, RNAi [sirna.com] for about five, and microRNA for probably two (the latter two, again, regulate gene expression by interfering with mRNA, though RNAi cleaves the mRNA in the process and microRNA doesn't).

      Of course, most people reading a Reuters article probably don't even know what RNA is, much l

  • by JGski (537049) on Thursday June 03, 2004 @01:04PM (#9327225) Journal
    Irrational enthusiasm expressed by too many biotech execs (I used to be in the business - my sister and brother-in-law are "wheels" in the business) is concerning.

    This article is about is genomics knowledge which is one of the best understood areas of biotechnology and molecular biology, yet it's always bugged me that PhDs in biology would simply dismiss what didn't fit into their neat little model as "junk DNA". That "junk DNA" was conserved gave serious doubts about it being junk. That it has to be a "control system" component has pretty obvious.

    Until recently though, math and systems theory have not been strengths of biologists in general - when I was in school, biology was what people took to be able to do science without a lot of math. Ask a biologist about Laplace, Linvill or Liapunov and you'll get a blank stare - which is truly scary if they're mucking around with living feedback systems being spread into the broader environment. There's still a generation that probably needs to be purged before the profession can be deemed "systems theory aware".

    What's scarier: the whole knowledge-base of proteomics and enzyme/metabolic circuitry is far more primitive that genomics, yet this area represents far more of the biology activity in cells than genomics. Which makes plunging head-long into rolling out things like Monsanto safflower extremely dubious and dangerous.

    That said, I'd be the last to advocate ceasing this type of genetic research and technology development - only it is different from most every potentially dangerous technology humanity has developed, so considerable caution and process safe-guards are needed.

    • Until recently though, math and systems theory have not been strengths of biologists in general - when I was in school, biology was what people took to be able to do science without a lot of math. Ask a biologist about Laplace, Linvill or Liapunov and you'll get a blank stare - which is truly scary if they're mucking around with living feedback systems being spread into the broader environment. There's still a generation that probably needs to be purged before the profession can be deemed "systems theory a

      • Good reply, but those of us without Nature subscriptions can't view the actual article. What does the actual research say? The original Reuters article doesnt really supply enough information to understand.
        • Transcription by RNA polymerase II in Saccharomyces cerevisiae and in humans is widespread, even in genomic regions that do not encode proteins. The purpose of such intergenic transcription is largely unknown, although it can be regulatory. We have discovered a role for one case of intergenic transcription by studying the S. cerevisiae SER3 gene. Our previous results demonstrated that transcription of SER3 is tightly repressed during growth in rich medium. We now show that the regulatory region of this gen

      • Sorry, No. When I said "school", I meant college, undergrad and graduate. High school is about as distant as kindergarten from my point of view. A few graduate degrees will do that. Perhaps you see the past differently.

        My biology-majoring school (I mean, university) friends, both in undergrad and graduate school did, in point of their own words, pick biology because of the minimal math. Those people are now runnng biotech and pharma companies today. Statistically significant? - well, a dozen data po

    • by mz2 (770412)

      What I hate the most in scientific debates are those people whose arguments are both heated and unknowledgeable. Junk DNA is something of a junk word if you ask from a real geneticist, as many examples of regulatory and other types of function have been attributed to the non-protein-coding regions of the genome.

      This is because your personal DNA sequence is not just the blueprints for all your components, it also works as a script to trigger synthesis of these components at a right place and time -- as a re

    • Very ironic (Score:2, Interesting)

      by hung_himself (774451)
      I think you are looking at the wrong sample. You could probably say the analogous things about computer execs. The real algorithmic research of course happens at the universities and similarly that's were the real biology research is happening - not at the biotechs.

      You are correct that nowadays biology and mathematics are intertwined, attracting more quantitative people. Where you are mistaken is your implicit assumption that the naivete is on the biologists side. There is a lot of knowledge that needs t
  • Boy, I can't wait till they find out that genes are multi-dimensional, the same way a fugue is. :)

    --
    The fallacy of government is that it assumes everyone needs to be told how to live, but the fact remains it is unconstituational to homogenize community by its own standards. When it passes more laws until it makes everyone a criminal it has made the mistake of placing the intent on the "Letter of the Law" over the "Spirit of the Law."
    "The more corrupt the republic, the more numerious the laws" -- Tacitus,
    • Re:Multi-dimensional (Score:3, Informative)

      by Coos (580883)
      Boy, I can't wait till they find out that genes are multi-dimensional, the same way a fugue is.

      Sorry, but they already are!

      A single gene can contain up to three overlapping reading frames, and some virii and bacteria can generate three completely different and functional proteins from the same gene sequence by this method. Add to that that certain gene products may be broken into subunits at different points along their sequence, and a highly-evolved (or carefully designed) gene could encode >10 protei

  • by RobertB-DC (622190) * on Thursday June 03, 2004 @01:08PM (#9327266) Homepage Journal
    Reading the article, it was fun to substitute "Junk DNA" with "-1, Troll posts". The concept is similar: troll postings serve no useful purpose, but they do modify the discussions in subtle ways. Referring to any particularly offensive link as "goat-related" is one of the obvious examples.

    Since I'm bored today, I'll try my hand at rewriting the Reuters article.

    Slashdotters Find New Type of Moderation in Troll Postings

    LONDON (Reuters) - Troll posts may not be so useless after all.

    Slashdotters coined the term to describe the textual wasteland within the Slashdot database, or book of posts, which consists of long uncharted stretches of text for which there is no known function.

    But researchers from Hard Vard Medical School in Jamaica said on Wednesday that within troll postings in the Science database they have discovered a new class of post.

    Unlike other posts, the new one does not produce an Insightful or Interesting comment to carry out its function. But when it is browsed at -1, it moderates a neighboring post.

    "This doesn't explain all troll posting. It gives a potential use for some troll posting," Professor Red Finster, who headed the research team, said in a made-up Slashdot posting.

    "I cannot think of another regulatory post such as this one," he added.

    There are about 3,000,000 to 4,000,000 posts in the Slashdot database. Much of the database consists of troll postings which scientists are trying to decipher to determine the causes and potential treatments for boring, inane discussions.

    The new troll called GOAT1 blocks the function of the adjacent posting in the Science database. Finster and his team, who reported their finding in the science journal UnNature-al, believe other trolls could work in the same way and in other databases including the main database.

    "We found one example of a type of troll posting that hasn't been found before that might alert investigators to look for it in other offtopic discussions," Finster said.

    "This type of moderation may occur in other cases throughout the message board kingdom," he added.

    The new troll works by making Frustration, a cousin of Interest, which causes down-moderation or turning off the adjacent post.

    "When people are looking to understand the regulation of posts from whatever database -- main, games, Apple, science -- they cannot just look for messages that are acting there. It might be that it is simply the act of moderating that is causing regulation," said Finster.

    The Moderation alphabet consists of several moderations -- Flamebait and Troll to Insightful and Informative -- which carry instructions for making all databases. The sum of the moderations carries the score. Each set of moderations corresponds to a single comment score, which join up in many different combinations to make discussions.

    "We want to understand the psychology behind the regulation (of the postings). It is a previously unidentified type of moderation and if we could understand how it is controlled, we will learn more about Slashdot moderation," said Finster.
  • so let's see... (Score:3, Interesting)

    by MoOsEb0y (2177) on Thursday June 03, 2004 @01:57PM (#9327773)
    Does this mean DNA has parity bits for error correction?
  • by jchenx (267053)
    Coincidentally, I just finished reading Greg Bear's [wikipedia.org] Darwin's Radio and Darwin's Children novels. They use the premise that "junk DNA" is not junk at all, but is used to drive evolution.
    • Coincidentally, I just finished reading Greg Bear's [wikipedia.org] Darwin's Radio and Darwin's Children novels. They use the premise that "junk DNA" is not junk at all, but is used to drive evolution.

      Just in case someone wants another opinion on this: I've read Darwin's Radio [barnesandnoble.com] but haven't picked up Darwin's Children [barnesandnoble.com] yet. I highly recommend the first book. As the parent post says, the major premise is that the so-called "junk DNA" is really a latent genetic disease that causes sudden, drastic changes i

  • OK, is anyone else having trouble finding the actual paper? Winston, in Nature, at Harvard. I went on Pubmed and searched for him, no hits. He has a faculty webpage [harvard.edu] at Harvard, but I can't find this paper through Pubmed or from Nature's website.

    Anybody know where I can get this paper? I hate reading news blurbs on research. I want the meat!!!

  • Maybe junk DNA is like a bucket of lego-like building blocks that are randomly cut out and reinserted elsewhere during recombination, maybe they have *evolved* to be error prone in this way. If ACTG are the letters of the DNA alphabet, maybe the stuff in the Junk DNA sections are the words in the DNA dictionary ( or even common sentences ). Maybe having Junk DNA around made up of sequences that tend to be useful when an organism needs to adapt over multiple generations via evolution is worth conserving.
    • Or maybe they are just the adjectives, connectives, or articles in the DNA dictionary. (OK, so I have no idea what I am talking about. This is /., isn't it?)
  • Computer Parallels (Score:4, Insightful)

    by photon317 (208409) on Thursday June 03, 2004 @03:27PM (#9328704)

    The more I heard about genetic codes, the more they resemble certain thigns in the computer world to me. Probably convergent evolution of sorts. Sounds like they've been staring at an incomprehensible data-set they were examining byte by byte to understand where the data was stored in what format. They found isolated bits that matched up and identified their purpose, but large amounts of the code remained a mystery. Then with this discovery, they just realized that they're actually staring at a huge peice of mixed data and code (probably in some cases dual-purpose bits which are both data and code) - just like in the computer case. Well, not so much in a high level language's case, but remember when people used to write ultra-compact self-modifying code/data in asm? When you think about it, for any given computing problem that can be solved by some chunk of code and data, the most space-efficient hyper-optimal way to do it usually ends up being self-modifying assembler "code", which re-uses code for data and data for code where possible.

    It is of course mind-bogglingly complex to write code in this fashion for any sufficiently complex software, which is why we only tend to have examples of this on very small scales (tiny little DOS programs and simple virii back then).

    But.. if that's the most efficient way to pack the functionality into a small space - and if writing DNA is similar in nature to writing assembler code - then evolution would naturally gravitate towards this method of encoding, eventually becoming such a complex self-modifying code/data mess that it causes us all these problems trying to unravel it.
    • Very true, I would agree. Though, I'm sure we will have computer to reverse engineer DNA code through some form of emulation software. Once we are able learn how and what DNA sequences are needed to make cells, we will be able to artificially make life.

      Imagine coding a machine or chemical factory in source code. Then, compiling that source code into a DNA sequence rather then binary. From there, you can make the DNA chain synthetically and grow the product. Of course, with any tool there is a dark side. I'
    • I wonder how much of the Junk DNA is just part of a data segment? Most of it will never even get looked at but some tiny bit of that junk might describe how to make the inside bit of a big toe.

      Many of the people I know that were involved with the early stages of the human gome project also where involved in the theoritcal computer science.
  • On the other hand... (Score:4, Informative)

    by Indomitus (578) on Thursday June 03, 2004 @03:49PM (#9328903) Homepage Journal
    New Scientist [newscientist.com] has an article about some scientists who removed pretty huge chunks of a mouse's "junk DNA" and the mouse was just fine in every way they could measure.

    So the moral is, we have a lot to learn about DNA.

    • by mopslik (688435) on Thursday June 03, 2004 @04:21PM (#9329239)

      ...the mouse was just fine in every way they could measure.

      I think that might be the crucial factor there. After all, how can we effectively measure things that we're just starting to discover?

      • Oh yeah, I don't think anybody's willing to start cutting out the "junk" in our DNA or anything yet. It's an interesting finding though.

        One of the theories about the junk DNA is that it's there to help reduce the chances that a mutation could cause catastrophic harm to the organism. If you've got 5 times as much stuff to hit with a cosmic ray, for example, you're more likely to hit the "padding" than the useful stuff. If that's correct, you would see exactly what they're seeing with this mouse, until an im
    • New Scientist has an article about some scientists who removed pretty huge chunks of a mouse's "junk DNA" and the mouse was just fine in every way they could measure.

      I forget where I saw this analogy, but... imagine you're reverse-engineering a car by removing parts of it and seeing what stops working. You remove the windscreen wipers and the headlamps and hey, nothing's wrong! They're junk components.

      At least, until you drive at night in the rain.

      The argument was that junk DNA might contain contingen

  • by Anonymous Coward on Thursday June 03, 2004 @04:55PM (#9329568)
    I have been working in gene mapping for years and always felt that the 'junk' was there for a reason."

    Nature is a pack rat. Get used to it...

  • I remember reading an article in New Scientist I think that talked about research that had been done on so called junk dna and they found that it worked as a repair mechanism. Essentially they found that dna can transmit electrons and what was happening was when something tried to damage an area of dna by giving it an extra electron, if it didn't need it it could pass it down the line so to speak till it reached one of these areas where it would cause no real harm. Likewise areas that were robbed of an el
  • I am a firm believer of Darwin's theory of evolution, and as you all know the main point of this theory is survival. This implies that in contrast to what some previous posts here mentioned, there is no need for "optimal", "efficient" or "errorchecking (-free)" coding in the neuro-bio-chemical-whatever way DNA does this coding. Just the fact that it works is enough, you will live, hopefully survive, and pass on this "working" code to your offspring (well, at least pieces of it). One scientist once said: "DN
  • Total Genome size (Score:2, Insightful)

    by Coos (580883)
    The Human Genome Project surprised us by finding far fewer genes than were theorised to be neccessary for life: perhaps if a significant amount of the regulatory function is carried out by DNA-previously-known-as-junk, a new genome annotation exercise might produce a figure closer to the estimate. It can't be long before ampaper along these lines is published...
  • by dnaboy (569188) on Friday June 04, 2004 @10:40AM (#9334607)
    Researchers have been discovering these genes for some time now. They're generally extremely short (~21 nucleotides) and in their endogenous form are referred to as micro RNAs (miRNA).

    Interestingly, the mechanism was actually understood before functional miRNAs had been discovered. Back in the 90s there was an upswelling of new biotech companies (Isis, for one) looking at antisense technology. Basically, the idea is that if you insert a complementary RNA strand to a messenger RNA (mRNA- The RNA's which code for proteins), you could block the expression of that gene into protein. The problem was that these weren't very specific (relative to what people would expect, since it was the exact complement of the gene sequence). Also, it's a bitch to get a full length RNA strand into cells reliably, short of using viruses. Generally a bad stigma.

    Over time, people started realizing that these antisense targets being inserted were being cleaved into really small (~20 to 25 nucleotide) pieces by an enzyme group called the RISC complex (It's a lot more complecated than that, but whatever). This explained one thing. ~20 nucleotide chunks are much more likely to stick to another gene. There's a much better chance that the 20 bases are identical to 20 bases in another gene, than several hundred to several thousand being repeated. What it didn't answer is what was going on.

    It was assumed that the complex that large antisense targets made blocked translation into protein. 20 base pieces were much less likely to do that. What people came to realize is that another enzyme called DICER was chomping up the genes where these ~20 nucleotide pieces stuck. This technique isa called RNA interference, or RNAi, and these ~20 nucleotide sequences were called short interfering RNAs or siRNAs. The sweet thing is these, relative to their much longer antisense couterparts are relatively trivial to insert into cells.

    Anyway, to make a long story short, researchers didn't really know why this worked at first, and consensus was that it was either an evolutionary legacy, a mechanism to fight RNA viruses, or a fluke (which generally, very few things in biology end up being).

    Anyway, this article points out what researchers all over are finding which is that these little guys appear to be present all over the human and other genomes. They are much more likely to be a mechanism for regulating gene expression. For more info, google 'micro RNA'.

    Cheers

  • This is exciting but not unexpected news to me. Two of my children have a flaw in one of these junk areas that causes dramatic effects for them. Their symptoms range from mild mental retardation to muscular effects throughout every muscle type. Its amazing, given the many known diseases that result from flaws in junk DNA, that its taken them this long to come close to admitting there is no such thing as junk DNA. So called "scientists" have a remarkable blindness to the facts that they can't explain tha

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