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Biotech Science

New Genes May Arise From Junk DNA 110

An anonymous reader writes: Junk DNA (or noncoding DNA) is a term for section of a DNA strand that doesn't actually do much. Huge tracts of the human genome consist of junk DNA, and researchers are now finding that it may be more useful than previously thought. "For most of the last 40 years, scientists thought that [gene duplication] was the primary way new genes were born — they simply arose from copies of existing genes. The old version went on doing its job, and the new copy became free to evolve novel functions. Certain genes, however, seem to defy that origin story. They have no known relatives, and they bear no resemblance to any other gene. ... But in the past few years, a once-heretical explanation has quickly gained momentum — that many of these orphans arose out of so-called junk DNA."
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New Genes May Arise From Junk DNA

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  • by dargaud ( 518470 ) <slashdot2.gdargaud@net> on Wednesday August 19, 2015 @11:26AM (#50347101) Homepage
    One of the properties of junk DNA is that it can endure brutal mutations since it's not used for anything. So over time it can change a LOT. Then suddenly another mutation suddenly activates it by mistake and *poof* you have a new magic super-power (more often than not, lethal). Starting from a crucial gene won't work since the slightest modification will reduce your survival rate, since by definition it's crucial.
    • Re: (Score:3, Insightful)

      by argormar ( 2714823 )

      This is completely wrong. It is used for everything! Formerly called Junk DNA by ignorant people, it is now called Regulatory DNA. It is the code that calls the function calls that is the gene DNA. That is why the field is called Genomics now and not Genetics.

      • I think you mean there are many subfields, including Proteomics.

      • Absolutely. It was labeled "junk" because some egotistical scientist could not figure out what it does. If it befuddles him or her, who is no doubt really Smart, then it must be junk.

      • by Cyberax ( 705495 )
        No. Junk DNA is junk DNA. Less than 1% of it turned out to be useful as regulatory DNA. We also suspect that another 3-5% of it might have some function.

        And we definitely _know_ that most of it is junk - just a pile of SINEs, LINEs and other crap.
        • Junk DNA is junk DNA.

          It may be "junk" in the sense that we can't currently ascribe particular functions to many such sequence elements, but it's also "not junk" in the sense that it's energetically expensive presence is at least not selected against (and might be favorable).

          In my opinion, regardless of whether or not the sequences in question have specific functions, the term "junk DNA" is misleading and dismissive of the history of biological science.

          • by Cyberax ( 705495 )
            No, DNA replication is not energetically expensive for eukaryotic cells. Most of the energy in a cell is spent on protein synthesis (i.e. gene expression), so regulatory mechanisms to suppress or promote DNA transcription are very honed and fine-tuned. These mechanism are also co-opted into fighting DNA parasites but they can't be used to edit away junk DNA completely.

            However, for bacterial cells (which are much smaller than eukariotic cells) DNA replication is a significant burden and so they have very l
        • Some of the "Junk" DNA is packet headers with golay error correction codes and crc check codes. Some of it is activation switches. A lot of it is "mothballed" DNA that is saved for emergency situations.

          Biologists need to have at least some network training, these days. 8-)

    • magic super-power (more often than not, lethal)

      As a general rule of thumb, things that insta-kill me in utero generally do not qualify as "super-powers" in my particular dialect of English.

  • I have a suspicion (Score:5, Interesting)

    by Anonymous Coward on Wednesday August 19, 2015 @11:30AM (#50347131)

    I suspect that in the future, scientists will laugh at the notion of "junk DNA" and think of it as just as much of a myth as "you only use 10% of your brain".

    • same thing in other sciences. archeologists say anything unknown was a religious ritual. astronomy it is dark matter or something similar
      • Unless you think General Relativity is completely false, Dark Matter is some form of matter that acts upon visible objects in the universe. So take your pick, is Einstein wrong, or is there just a class of matter we haven't detected yet.

        • by tepples ( 727027 ) <tepples&gmail,com> on Wednesday August 19, 2015 @12:01PM (#50347405) Homepage Journal

          So take your pick, is Einstein wrong

          Science proceeds toward understanding of nature that is less wrong* over time. So it's very probable that Einstein didn't have the whole story.

          Aristotle was wrong about the relationship between mass and acceleration due to gravity. Galileo Galilei proved him wrong. Galileo was wrong about gravity being independent of location. Isaac Newton proved him wrong. Newton was wrong about the effect of gravity at what we now call relativistic speeds. Albert Einstein proved him wrong. Einstein was still wrong about "God doesn't play dice with the world." Each of them stood on giants' shoulders to become less wrong.

          * Yes, "less wrong" is a thing. Assuming that "wrong" is an ungradable adjective [] like "unique", "perfect", and "parallel" [] is a fallacy [].

          • Aristotle was wrong about the relationship between mass and acceleration due to gravity. Galileo Galilei proved him wrong.

            IMHO, this is the birth of science, rather than an evolutionary step. For example, back in Aristotle's days, projectile motion was understood as straight-line motion, until the object "runs out of steam" (impetus) and drops straight down. The general idea was that knowledge comes from wise men and old books, rather than actually looking at the world. With that kind of a mindset, it's impossible for the knowledge to evolve in an objectively better direction. To me, Galileo's big idea was to try and take the

      • by blueg3 ( 192743 )

        astronomy it is dark matter or something similar

        Dark matter is not some astrophysics catch-all explanation. Dark matter and dark energy separately refer to a specific observed discrepancy for which we don't have an answer yet.

        • so.... a catch-all for what isn't known. Gotcha.

          • by blueg3 ( 192743 )

            No. "Specific" and "catch-all" are pretty different.

            Dark energy, for example, is essentially the discrepancy between the observed expansion rate of the universe and the quantity of detectable matter in the universe.

      • same thing in other sciences. archeologists say anything unknown was a religious ritual. astronomy it is dark matter or something similar

        I can inderstand that, since the public punishes anyone who says the words "I don't know". Even if it is the best truth known...

    • My impression of so-called 'junk DNA' is that they're like some conditional (if/then) statements in a programming language: the condition required to run that code may rarely, if ever, occur, therefore that code sits there 99.9999999999% of the time doing absolutely nothing. Except, of course, for that one time when it does run. We've made much progress in the last 100 or so years with regards to understanding the mechanisms of life, but we're far, far away still from understanding all of it.
      • by Anonymous Coward
        WARNING: Unreachable codon detected
      • Re: (Score:2, Interesting)

        by Anonymous Coward

        A better analogy might be huge blocks of code that's been commented out. It may have been unable once, and may be unable in the future but right now it can't do anything other than get copied along with everything else.

        • Interesting. You're implying then that there's some mechanism doing the editing of the source code?
        • except that it's a physical system, and the commented sections may play a role in spacing, separation, structure, provide binding sites for regulatory proteins etc.

          just because it isn't transcribed doesn't mean it's not critical to proper function.

          • by Cyberax ( 705495 )
            That's about 1% of the junk DNA. The rest is still just junk.
            • :) i'm not about to argue that we know what the rest is. but i'd also argue that our genomes are a bunch of hacked together spaghetti code where even commenting some bit out could end up being super critical to proper function.

              *how the hell did deleting a comment break the fucking program?*
              *i don't know, but it works, so just fuck off*

      • My impression of so-called 'junk DNA' is that they're like some conditional (if/then) statements in a programming language: the condition required to run that code may rarely, if ever, occur, therefore that code sits there 99.9999999999% of the time doing absolutely nothing. Except, of course, for that one time when it does run. We've made much progress in the last 100 or so years with regards to understanding the mechanisms of life, but we're far, far away still from understanding all of it.

        Hmm, Mod Up or Reply, tough choice, but I have to go with reply - hopefully someone else will mod your comment up - because I agree with you completely. The old "90% of the brain is unused" thing is exactly the right comparison to make, one I've been using for a long time whenever the subject of junk DNA comes up. The fact is that nature simply doesn't operate so inefficiently. The idea that evolution would have maintained huge tracts of completely unusable genetic code serving no purpose at all for million

    • by MightyMartian ( 840721 ) on Wednesday August 19, 2015 @11:44AM (#50347263) Journal

      Scientists haven't thought "junk" DNA as junk for years. It's a shorthand expression for genes that have no obvious expression, though they've known for a long time that junk DNA may have regulatory functions, and that most certainly junk DNA is a potential seed bed of evolution because the likelihood of deleterious mutations in junk DNA sequences is much lower.

  • Huh? (Score:5, Interesting)

    by MightyMartian ( 840721 ) on Wednesday August 19, 2015 @11:37AM (#50347187) Journal

    What is heretical about novel new genes arising out of junk DNA? Molecular biologists have known for many years that so-called "junk" DNA played a number of roles; regulatory, and that most certainly novel genes could arise.

    Oh, I get it, this is the idiotss otherwise known as "scientific journalists" hyping up a rather unremarkable finding, and fixating on the word "junk" much as they, in ignorance and the need to sex up stories, concentrated on the word "God" in the "God particle"

    • Re:Huh? (Score:4, Interesting)

      by ShanghaiBill ( 739463 ) on Wednesday August 19, 2015 @11:45AM (#50347275)

      What is heretical about novel new genes arising out of junk DNA?

      Labeling it "heresy" is just bad journalism. Biologists have long suspected that new genes could arise from "junk" DNA. The news is that now there is some actual evidence, rather than just conjecture.

      • Re:Huh? (Score:4, Informative)

        by MightyMartian ( 840721 ) on Wednesday August 19, 2015 @11:47AM (#50347289) Journal

        As I said, it's a fairly unremarkable finding. I remember references to junk DNA sequences having the potential to be expressed in the early 1990s.

        • by narcc ( 412956 )

          This is part of the problem of the public understanding of science.

          You hear idle speculation 20 years ago and, with clenched fists and tears welling up in your eyes, whisper "it's gospel truth" and go around believing, wholeheartedly, unsubstantiated nonsense.

          Now, far off in the future, someone says "hey, here's some evidence that indicates that this idea may have some merit" you scoff and complain that this is "unremarkable" old news.

          You'd be amazed at how many "scientific" beliefs people have that are no

    • "God particle" appears to have originated in Dell Publishing's censorship of "goddamn particle", which was originally chosen because of the difficulty faced by particle physicists in producing an excitation of the Higgs field. Had the title of the book [] instead been The G.D. Particle, there probably wouldn't have needed to be as much "sex[ing] up".

    • by tlambert ( 566799 ) on Wednesday August 19, 2015 @12:57PM (#50347877)

      What is heretical about novel new genes arising out of junk DNA? Molecular biologists have known for many years that so-called "junk" DNA played a number of roles; regulatory, and that most certainly novel genes could arise.

      There is a small percentage of biologists which really, really would like acquired traits to be heritable (as a work study job in college, I worked in the lab of one of them, and we were cautioned not to talk about his theory outside the lab).

      Every so often, one of the proponents of the idea of heritable changes due to environmental pressure, or more formally, either Lysenkoism or Lamarckism, tries to find a mechanism that could make it work. Even though it's never been demonstrated (the biologist in the lab I worked at was attempting experiments with, among other things, chelodina longicolis diets, to force physical changes, which he hoped the offspring would inherit, even though not on that diet).

      This theory is what's known as "soft inheritance".

      The main premise for its development in the first place was that Joseph Stalin was all pissy about genetic being a non-Soviet idea, and wanted an nice, Soviet alternative that better fit the ideology he put forth. This actually influenced a lot of decisions in Soviet agriculture that didn't work out badly enough that they ended up importing wheat from the West.

      The last go-round was trying to use introns as a mechanism whereby he introns were involved in making traits heritable (and before that, it was endogenous viruses, such as PERV - Porcine Endogenous Retro Virus). Those were the main ones. The've also tried to explain it with varying degrees of gene methylation, and so on. Todays flavor is non-coding DNA (the correct scientific name for "junk genes").

      Unless the can demo it in plants, mice, or fruit flies, etc., don't expect that the idea will go anywhere directly.

      The sad part is, if they had concentrated on the punctuated equalibria model, which the article mentions, instead of trying to explain it as a short scale inheritable phenomenon, the might have had a really great argument.

      (Yes, I am in the 90% who are skeptical about this, without further evidence and perhaps a demo).

  • ... is declaring something you don't understand "junk". I always found the concept of junk DNA to be unbelievably short-sighted.
  • Well no shit... (Score:4, Informative)

    by KlomDark ( 6370 ) on Wednesday August 19, 2015 @11:38AM (#50347203) Homepage Journal

    That's always been the key to genetic evolution. This is somehow new??

  • Genetic spare parts? (Score:4, Interesting)

    by gstoddart ( 321705 ) on Wednesday August 19, 2015 @11:39AM (#50347213) Homepage

    So basically there's a bunch of spare stuff laying about which, under the right circumstances, can actually change into something new and unexpected.

    This is good, because it means we have more potential than what we already have. It also explains why organisms aren't constrained by things which came before them.

    I still get the impression we still don't understand how all this works. Which is good. Because people start thinking science has answered everything, only to find out there's tons more to go.

    • Re: (Score:2, Interesting)

      by Anonymous Coward

      We don't. We have laboriously identified the purpose of specific areas, but you can't a priori deduce the function of arbitrary DNA turned into a protein, and you can't currently simulate the working environment of the enzyme, or understand the full extent of the "reactome" chain of related processes and consequences of a particular change.

      Lots of what we have learned is transferred from in vivo experiments of gene suppression. Fortunately the massive similarity between many living organisms allows us to po

    • by Cyberax ( 705495 )
      Not a "bunch" but "perhaps tens or hundreds of places out of several million". People really underestimate the amount of junk DNA - it's 95% of the genome, around 3 billions base pairs. In all this junk we sometimes find a few kilobases here and there that actually have some useful functions. Just for reference - all the known regulatory non-coding sequences amount to less than 20 megabases out of that 3 gigabases.

      Is it likely that there are more hidden gems out there? Sure. Is it likely that a significa
    • I'm just waiting for the x-gene to activate among people all around the world... ;)
  • I know that there's a big difference between "hey, i've got a cool idea" and actual scientific proof, but as is usually the case in such things there were a lot of precursors to this "once-heretical" idea gaining traction. Greg Bear's Darwin's Radio [] is one of the more famous SF examples (though certainly not the only, and quite possibly not even the first) of speculation that junk DNA could actually be useful for something. It came out in 1999, and although i don't know if he based his ideas on any research
  • by Anonymous Coward

    The term Junk DNA is a laughing stock within the scientific community for ages now.

    It was 'blank slate' and 'we are all the same under the skin' retards pushing for such an ignorant assumption.

    We have known for a while now that essentially all non transcribing DNA is highly used as "regulator factors". This is the DNA that controls the transcribing DNA. You can think of the 'gene' DNA as function calls. The 'junk' DNA is the code that calls those function calls, where and when! It is the most important DNA

  • That's what happens when we eat too much junk food.
  • by Jesrad ( 716567 ) on Wednesday August 19, 2015 @12:18PM (#50347547) Journal

    ... is that hybridization might play a very big role in the appearance of new species [], in several different ways:
    - apomixis, producing some (most often aneuploid) news organism (which then clones itself indefinitely by fragmentation, budding or parthenogeny, becoming a distinct species all by itself)
    - polyploidization, where the different DNA sets just add up and coexist side by side (like in pretty much every angiosperm on the planet, and many other plants, as well as many fish, reptile and salamander species - like Ambystoma platineum)
    - symbiotic association, as seen in lichens and also in how mitochondria fused with bacteria into eukaryotes
    - recombinational stabilization (a.k.a allohomoploid nothospeciation), where the slightly mismatched chromosomes from different DNA sets of compatible but different species pair up into complex heteroduplexes that end up fragmenting or fusing chromosome segments when the first generation of hybrids starts mating - which very well might be how two chimpanzee's chromosomes fused into our own bigger Chromosome 2.

    In the cases mentioned of TFA some of the 'exotic' genes may be explained more simply as introgressions from a past hybridization event with a different species followed by backcrossing [].

  • big surprise (Score:4, Interesting)

    by holophrastic ( 221104 ) on Wednesday August 19, 2015 @12:20PM (#50347567)

    so I'm not carrying all this stuff for nothing. I'm so glad to be a member of a species that thought otherwise for so long. I like my appendix too, by the way, also the other 80% of my brain, thanks very much.

    • Re:big surprise (Score:5, Interesting)

      by ledow ( 319597 ) on Wednesday August 19, 2015 @01:05PM (#50347939) Homepage

      Almost everything you can summarise in a line is bollocks news headlines. Science is, unfortunately, a lot more complicated than that.

      We (probably) use all our brain. Just not all on conscious intellectual thought. It's not hard to see that - cut into the brain and you ALWAYS lose something, it just might not be immediately obvious what.

      The appendix may well be a store of gut bacteria that reseeds the gut in the case of illness. Which kinda makes sense, the same way you save some of the cheese by-products to help make the next cheese. And also explains why when it blows it's quite so serious - it's basically an inactive mini-gut getting infected and exploding.

      It's just that it's hard to prove these things definitively because they were never DESIGNED to do that. They just happen to do so. And so they may be doing ten jobs well or one job badly or no jobs at all and it's incredibly difficult to say which for a global population at any static point in time.

      Similarly "junk" DNA is as it says - noncoding. We think. But it might be doing other stuff. Hell, it may just be purely structural, or it may be remnants of old coding, or it may just have got mixed in the same way you accidentally mix in insects into basically every foodstuff you eat (yes, literally) but because it "just works" and nobody notices, it doesn't really matter.

      Or, maybe, it's coding is not as simple as we expect. Nobody's every really SEEN things like DNA do their jobs. You can look at it, you can simulate it, but nobody really knows exactly what's going on in the millions of full strands inside a HUMONGOUS cell that replicates billions of times over in the space of a matter of months.

      The problem is that science is so complicated that you can't understand it, and headlines are all you pick up. How many moons does the Earth have? Depending on which scientists you ask, and which definition of "moon" you use, it can be zero, one, two, twenty-seven or hundreds. Nothing is as simple as you can explain in one sentence. Or even one article. Or even one research study and paper. Or even one field of expertise.

  • by peter303 ( 12292 ) on Wednesday August 19, 2015 @12:33PM (#50347689)
    Its just poorly understood DNA sections. The ENCODE project studied non-coding DNA and estimated that up 80% could be important. Some codes for RNA which until recently was hard to measure because it decays so rapidly. Some may encode for epigentic control like methlyation locations. Some may control the folding of histone-DNA complexs, forcing sections sections DNA to be nearly one another for reasons we dont understand yet.

    Clever biochemists will figure these out soon enough.
  • It seems pretty simple, if a gene was useful in the past at some time, it is possible it might be useful in the future. Therefore it is handy to write down old unneeded sequences just in case. How many you write down would be related to the desire to facilitate mutations or prevent them as the case may be. FYI this was actually hinted at by creationist who pointed out the probability of gene sequences spontaneously forming being astronomically low. Clearly biology was cribbing from previously useful seq
  • by Anonymous Coward

    The first rule of intelligent tinkering is to keep all the pieces.
    -- Aldo Leopold.

    • The first rule of intelligent tinkering is to keep all the pieces.
      -- Aldo Leopold.

      Good point.
      Biological systems are very wasteful in many ways, but very conservative in others. It is quite possible that those are kept "just in case", so to speak. 8-)

  • Uh oh, now I am afraid an HERV [] will suddenly get activated, pop out, and start infecting people.
  • Basically, it's a frame shift method of writing code. If any of you had ever had to use old style 4 bit encoding schema to store data, you'd know that.

    It allows one set of instructions to adapt for different environmental conditions. We don't just bootstrap our DNA, we use it to fold and generate proteins when we need them, and then we discard it when we don't need it. But the instructions are still there.

    Now, that said, some of it is inserted viral code from infections, or instructions on how to grow gills

  • by WindBourne ( 631190 ) on Wednesday August 19, 2015 @04:39PM (#50349687) Journal
    Mosquitoes carry viruses between mammals. Some of these virus are mammal specific, but a number of unknown virus are transmitted regularly, that have cut sections of DNA from organism A and then inserts it into organism B via arthropod borne viruses. Interestingly, we do not look for these because they are asymptomatic. But, they still transfer large DNS sequences , with some genes, between us.

fortune: cpu time/usefulness ratio too high -- core dumped.