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Confusion and Criticism Over ENCODE's Claims 34

As_I_Please writes "In response to the previous report of the ENCODE project discovering 'biochemical functions for 80 percent of the genome,' many scientists have questioned what was meant by 'function.' Ars Technica Science Editor John Timmer wrote an article calling ENCODE's definition of functionality 'broad to the point of being meaningless. At worst, it was actively misleading.' Nature magazine also has a followup discussing the ambiguity surrounding the 80% figure and claims about junk DNA."
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Confusion and Criticism Over ENCODE's Claims

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  • by BMOC ( 2478408 ) on Wednesday September 12, 2012 @01:01PM (#41313773)

    ...and then climate change happened.

    Since then I just started reading abstracts/papers rather than the journalism. It takes a little longer, but at least I'm not being misled by some self-aggrandizing social-science major who chose his degree poorly and is now trying to just pump out stories in time for the weekend.

    /yes, I'm bitter. But seriously, screw science reporters.

    • Don't leave out the researchers. They seem intent to "play the game" right along with the reporters and PR flunkies.
  • by Hatta ( 162192 ) on Wednesday September 12, 2012 @01:03PM (#41313787) Journal

    The idea that junk DNA accumulates on its own, only because of it's propensity to replicate is expected from evolution. If it replicates, and it's not selected against, it will accumulate. Some of it may have a function, and that which does have a function will be preserved, but that doesn't mean it all has a function.

    If it were discovered that every single base pair in our DNA had a function, that would be very strong evidence against evolution by natural selection.

  • I'll agree that the 80% figure is probably just PR hype, but part of the argument seems to be the notion that only 1% of our DNA codes for Proteins and that's the only important part. I believe that notion has already been discredited with epigenetics, and unless I'm mistaken that is the reason for the ENCODE Project in the first place.
    • No, we've known for a long time that some of the 'junk' DNA has instructions for gene activation and deactivation, pretty much since the discovery of 'junk' DNA in the first place. The problem is that ENCODE's 80% figure assumes that any piece of DNA that produces RNA performs a biological function which is extremely misleading. A lot of that RNA will never be used for anything. A lot of it will be immediately destroyed after it's created.

    • by tehdaemon ( 753808 ) on Wednesday September 12, 2012 @01:24PM (#41313955)
      No - it is not hype - it is a misunderstanding of the definition of 'functional'

      I buy a box of bolts at the hardware store. They have no manufacturing defects, and no damage. They are still in the box. Are they functional?

      Yes - If I take a nut and try to thread it on the bolt, it works, if I try to screw it into a hole, it works.

      No - They are not currently holding any parts of any kind together, they don't form any part of any useful machine - they are not functional.

      The ENCODE project is using the first definition. 80% of the DNA produces RNA, or has binding sites that bind to regulatory proteins, or some other function that can have a real impact on the cell. Whether or not the RNA is actually used, or if the regulatory sites actually regulate something, or if it actually has an effect on the cell was not considered - and is probably not known yet for most of that 80%.

      Most people when they hear 'functional DNA' assume that it has an impact on the organism. The ENCODE project is working on a lower level, asking, 'Does this DNA do something on a molecular level?' not 'Does this DNA make a difference to the cell?'. That is of course the next question, but they are not there yet.


      • by cfulton ( 543949 )
        This is the best explanation for the 80% figure that I have seen. I've been reading a bunch of the articles out there about this and none of them made such a clear and useful analogy. Please Mod Parent Up.
  • by crow ( 16139 ) on Wednesday September 12, 2012 @01:07PM (#41313815) Homepage Journal

    So we understand how somewhere on the order of 20% of the DNA works. It encodes proteins. What we don't understand is how things like body structure and aging work. Clearly those are part of the DNA, so it seems obvious that there's some sort of switching process going on using at least some of that other 80%.

    Once we figure out how the chemistry of that programming works, we can start to decode the fractal patterns that define body structure.

    Of course, we will find that there is true junk DNA--think of code blocks that can't be reached. How much evolutionary dead code is left in there may be an interesting academic question.

    • by cfulton ( 543949 )
      We know and have known for a long time about some if not all of the regulatory function in DNA. The first description of non-coding DNA playing key regulatory roles in activation was in 1959 when the Lac operon was discovered by François Jacob and Jacques Monod for which they won the Nobel Prize. Many other regulatory sequences have been discovered since then. Other types of genetic operators such as transposons which are able to transport and duplicate blocks of DNA are known. This is the problem,
      • This is the problem, we know a lot about the complexity and function of DNA.

        No, the problem is, you think you do when in reality you don't know shit. Future generations will look back on your pronouncements of "knowing so much" about DNA to be as laughable as us hearing stories of professors back in the 1930s who claimed all the important stuff had been discovered, and that there is nothing useful left to research into. In other words, dead wrong, ignorant, and stupid.

    • by Anonymous Coward

      So do we really know that it's DNA that does aging?

  • an article calling ENCODE's definition of functionality 'broad to the point of being fully patentable'
    let the human gnome patent trolling begin.

  • "Several researchers took issue with ENCODE’s suggestion that its wobbly 80% number in any way disproves that some DNA is junk. Larry Moran, a biochemist at the University of Toronto in Ontario argued on his blog that claims about disproving the existence of junk gives ammunition to creationists who like a tidy view of every letter in the genome having some sort of divine purpose."

    Translation: I don't believe it because it conflicts with my beliefs. Where have I heard that before?

  • Any time there's a scientific discovery, or some news about what scientists have learned today, you get a wave of people that instantly baulk and assume that the entirety of scientific knowledge was just overturned and that everything that we've ever known was simply wrong. They see the new discovery as proof that the scientists were ignorant prior to the discovery.
    Then you've got the crowd that assumes a discovery applies to 100% of whatever. For example, ENCODE has found function for some of the DNA tha
    • Actually, they've found that some of the DNA that was considered junk is capable of functioning, but won't be activated during any normal operation of the cell. It's still junk.
      Programming analogy:
      while (false) {
      The "var=5" is functional, if called it will set var to 5. It's also junk, since it will never be called.

How many Unix hacks does it take to change a light bulb? Let's see, can you use a shell script for that or does it need a C program?