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New Code Discovered in DNA? 285

Posted by Zonk
from the we-needed-more-than-one dept.
anthemaniac writes "The NY Times is reporting that scientists have found a second code in DNA that goes beyond the genes. The code is superimposed genetic information and 'sets the placement of the nucleosomes, miniature protein spools around which the DNA is looped. The spools both protect and control access to the DNA itself. The discovery, if confirmed, could open new insights into the higher order control of the genes, like the critical but still mysterious process by which each type of human cell is allowed to activate the genes it needs but cannot access the genes used by other types of cell.'"
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New Code Discovered in DNA?

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  • So wait (Score:5, Funny)

    by antifoidulus (807088) on Tuesday July 25, 2006 @12:04PM (#15776572) Homepage Journal
    like the critical but still mysterious process by which each type of human cell is allowed to activate the genes it needs but cannot access the genes used by other types of cell.

    So my body has built in DRM?!
  • DNA DRM? (Score:3, Funny)

    by shadowknot (853491) * on Tuesday July 25, 2006 @12:04PM (#15776573) Journal
    The code is superimposed genetic information and 'sets the placement of the nucleosomes, miniature protein spools around which the DNA is looped. The spools both protect and control access to the DNA itself.

    Does this mean that DNA has DRM?

  • Midichlorians? (Score:3, Interesting)

    by digitaldc (879047) * on Tuesday July 25, 2006 @12:07PM (#15776592)
    So did we finally discover the Midichlorians [wikipedia.org] that Qui-Gon was rambling about?
    • Re:Midichlorians? (Score:4, Informative)

      by syntaxglitch (889367) on Tuesday July 25, 2006 @12:46PM (#15776846)
      So did we finally discover the Midichlorians that Qui-Gon was rambling about?

      No, we already knew about those. They're called mitochondria, they provide the energy that powers the machinery of our cells, and they're descended from independent microscopic life forms that long ago entered a symbiotic relationship with animals.

      In plants, chloroplasts fill a similar role.
      • Re:Midichlorians? (Score:2, Informative)

        by dan828 (753380)
        In plants, chloroplasts fill a similar role.

        No, in plants, mitochondria do the same thing as the do in the cells of all other eukaryotes. Chloroplasts convert the energy in sunlight into stored energy. Two very different functions.
      • Re:Midichlorians? (Score:3, Informative)

        by smellsofbikes (890263)
        To expand on that a little, mitochondria in animals seem very likely to be bacteria that have been engulfed and now form a symbiotic relationship with the cell, since mitochondria have their own DNA (and a slightly different code for converting DNA -> RNA -> protein) and reproduce themselves independently of the cell's nuclear DNA (hence the discussion of 'maternal DNA' since you only get maternal mitochondria.)

        In plants, chloroplasts have similar characteristics, and *also* so do the plant mitochondr
      • Plants also have mitochondria [wikipedia.org], especial plants with chloroplasts. Mitochondria are what make areobic metabolism possible.
  • by Intron (870560) on Tuesday July 25, 2006 @12:09PM (#15776603)
    Personally, I think it's God's version of Sudoku.
  • by QuantumFTL (197300) * <justin.wickNO@SPAMgmail.com> on Tuesday July 25, 2006 @12:10PM (#15776609)
    I think this kind of thing is an important reminder to all humans how much we really have to learn about this crazy but wonderful world we live in.
    • by PIPBoy3000 (619296) on Tuesday July 25, 2006 @12:48PM (#15776870)
      Over ten years ago, the hot new field in biology was "gene expression". We already knew about DNA, but there was a lot of "junk DNA" that seemed weird, as well as lots of questions around when and how DNA was actually turned into working proteins.

      It turns out there's some vastly complex actions around how genes are actually expressed. Methylization semi-permanently deactivates DNA. Other things control the unfolding of DNA so that they're accessible to be exposed. Much of the "junk dna" is probably not junk, but rather controls gene expression to some degree.

      The bottom line is that DNA is only the bottom rung of how information is stored and manipulated in the nifty little computers that are our cells. This is also a great context to talk about evolution - no sane intelligent designer would make a cell this way. If you think about small changes over billions of years, though, you can see how the warping and twisting of DNA could produce interesting results that are passed down from generation to generation.

      Science is rarely boring.
      • no sane intelligent designer would make a cell this way.

        Of course, it could also be that the Designer's intelligence is so far beyond your own as to be beyond your comprehension. Things which humans cannot comprehend are often labeled as illogical. Until we learn to understand them, at which point they become perfectly logical.

        Not that I am neccisarily arguing for intelligent design, it's just that our universe is infinitely complex. Deeming something "insanely designed" only points out your limited kno

      • It was about 2 months ago, I downloaded BLAST and some Genomes and started playing around on my home computer. At first I was amazed at how fast my lowly little PC, a 700MHz dinosaur, could rip through the genomes of fruit-flies and it started to dawn on me that if an intellegent putz like me was getting close to being able to do real genetic research on a dinosaur machine like I had; It was very probable that there was something we didn't understand. It looks like I was right!
      • as well as lots of questions around when and how DNA was actually turned into working proteins.

        DNA is transcribed into mRNA which is then translated by ribosomes in the cytoplasm. DNA is not "turned into" proteins.

        Methylization semi-permanently deactivates DNA

        Methylation is just one aspect of chromatin structure. It's not semi-permanent, it's dynamic.

        The bottom line is that DNA is only the bottom rung of how information is stored and manipulated in the nifty little computers that are our cell
      • I'm amused by the popular (and scientific) notion that DNA is some kind of logical code just waiting to be deciphered.

        No one designed the way DNA and genetics work to produce a given biologic result. Evolution naturally selected for certain results without concern for the implementation. In short, DNA/genetics is the ultimate "slop code". It has no clean architecture or consistent rules. Making matters even worse, the code not only defines structures, but it defines how to interpret itself, such that you
    • this kind of thing is an important reminder to all humans how much we really have to learn

      And, as I see it, a reminder that we should stop playing with DNA and setting the resulting stuff free as long as we have no fucking clue.
  • by Lord_Slepnir (585350) on Tuesday July 25, 2006 @12:10PM (#15776616) Journal
    Only Go^H^Han intelligent designer could have implemented DNA with private and protected data. This sort of thing just can't randomly 'evolve'.
    • if humanity is your definition of 'intelligent design' then you've got a way to evolve yet. seriously god should have quit at the garden. animals? what was he thinking.

    • But, then we must of course examine our creator/creators.

      The creator(s) are one of:

      1) more complicated than us. So they even more likely created by another being than us. by the "intricate things have a creator" theory.
      2) more complicated than us as a whole. The creator society as a whole created us.(**)
      2) less complicated than us. Our creators used there intelligence, and directed evolution to create us. (***)
      3) we are not allowed to think about this according to our religion, sorry.

      (**) Similar to how a s
    • Only a crappy programmer would fill essential code with this kind of cruft. No wonder it takes the hardware decades to split off daughter processes.

      Come to think of it, a lot of the crappiest programmers I know think they're God -- er, intelligent designers. Anselm would be proud.

      Bemopolis
  • by hey (83763) on Tuesday July 25, 2006 @12:13PM (#15776629) Journal
    Any software problem can be solved by adding another layer of indirection.
    So apparenlty we are a software problem.
  • by realisticradical (969181) on Tuesday July 25, 2006 @12:14PM (#15776639) Homepage
    I'm always thuroughly impressed by the ability of cells to use lots of simple mechanisims to achieve complex results.

    It's not like nucleosomes are anything new though, the real discovery here is that the scientists found a pattern to their binding.

    Biologists have suspected for years that some positions on the DNA, notably those where it bends most easily, might be more favorable for nucleosomes than others, but no overall pattern was apparent. Drs. Segal and Widom analyzed the sequence at some 200 sites in the yeast genome where nucleosomes are known to bind, and discovered that there is indeed a hidden pattern.

    Sadly the times article is filled with a lot of fluff. This isn't really a "second code" nor do I see why it's "hidden".

    • I also found the NYTimes article painful to read. At first I thought they were running a piece on the histone code, something that has been discussed for years now, not this more recent discovery of a system of arranging nucleosomes. Science writing and reporting becomes more and more fluffy as time passes. I know that biology and medical writing for the layman is awful and misleading, but I'm not so much aware of how bad writing for the layman is in fields that are not my own: comp sci, physics, maths,
  • by exp(pi*sqrt(163)) (613870) on Tuesday July 25, 2006 @12:17PM (#15776656) Journal
    ...a Whitespace [dur.ac.uk] program inside a C++ program. The Whitespace program coexists with the C++ program because of the "wiggle room" (to borrow a phrase from the article) that the C++ grammar givess you.
  • Original article (Score:5, Informative)

    by infolib (618234) on Tuesday July 25, 2006 @12:18PM (#15776661)
    Abstract [nature.com] and full text PDF [nature.com]. (currently freely available).
  • by dpbsmith (263124) on Tuesday July 25, 2006 @12:20PM (#15776672) Homepage
    have been discovered to be eighty units long and oriented face down, nine edge first.
  • Metadata (Score:5, Insightful)

    by Aladrin (926209) on Tuesday July 25, 2006 @12:24PM (#15776693)
    I find it interesting that god/evolution/the great green arkleseizure/FSM/whatever invented metadata LONG before we did. Not surprising, just interesting.
  • by farker haiku (883529) on Tuesday July 25, 2006 @12:29PM (#15776731) Journal
    When am I going to see my first wetware virus that uses an "escalation of privileges" type attack?
  • by Anne_Nonymous (313852) on Tuesday July 25, 2006 @12:37PM (#15776785) Homepage Journal
    New Code Discovered in DNA

    b-e-s-u-r-e-t-o-d-r-i-n-k-y-o-u-r-o-v-a-l-t-i-n-e
    • Interesting Perl script.
    • I wish I could find a web ref, but a communcation published in the journal of biologic chemistry a few years back indicated that... okay, let me back up. There are twenty (ish) proteins making up people. For sake of brevity, they've been assigned one-letter names. Since the human genome is now known, we can read all possible proteins that would be produced by the DNA. So the aforementioned communication said that "ELVIS" appears many times, but "LIVES" very few.
  • The placement of histones on DNA is something I learned about 10 years ago in my genetics textbooks. This is merely a slight addition to our current knowledge of which sequences histones are likely to bind.
    • Re:Old "News" (Score:4, Informative)

      by FellowConspirator (882908) on Tuesday July 25, 2006 @01:29PM (#15777198)
      When I was in graduate school, one of my thesis advisor's friends at Weizmann (not the cited author, but a colleague) was developping HMMs for nucleosome binding prediction. It worked, though not very well at the time. That was about 10 years ago.

      This isn't a "new code" of any sort, but rather a pattern of stacking properties in the binding regions. There are other similar physical phenomenon that are well know, but poorly characterized (that is to say, you know it happens and you've a good idea why, but coming up with a model that is strongly predictive is very tricky).

      This "discovery" is not that the signature exists, but that we've finally got the statistical sampling good enough to build a computer model of that signature that can be used to predict/identify the sites. Interesting and good work, but a fundamental shift in our understanding of biology it is not.
  • "The discovery, if confirmed, could open new insights into the higher order control of the genes."

    Perhaps this may provide additional information as to the usefullness of the supposed "junk DNA [wikipedia.org]" that fills the human g-nome.

    • The short answer is this: "selfish" DNA like transposons invade a genome, they replicate and produce many copies, some preferentially insert near genes. These transposons over time degenerate but their ability to create mutations, including using their own proteins to control expression of some genes leads to diversity = better ability to cope to environmental pressures. This leads to a better capacity for evolution than waiting for single base mutations from cosmic radiation and the like. When a transpo
  • by Glog (303500)
    From TFA: A histone of peas and cows differs in just 2 of its 102 amino acid units.

    Mmmm, a histone of peas... Seriously, let me be the first to say: I smell a Nobel prize for this one.

    • by Jerry (6400)
      Seriously, let me be the first to say: I smell a Nobel prize for this one.


      That was my first thought after reading the article!

      But, at the speed at which Nobel winners are chosen probably 10-20 years will pass before they are so honored. Assuming, of course, that the research is proven correct.

  • Duh!! (Score:3, Funny)

    by Billosaur (927319) * <wgrother@HORSEop ... minus herbivore> on Tuesday July 25, 2006 @12:55PM (#15776923) Journal

    Everybody knows there's a hidden code in our DNA... Leonardo DaVinci put it there!

  • I find it fascinating how cells are amazingly complex, and yet are able to reproduce of themselves. It is like there is a whole world found in a cell, and it is able to transfer all this needed information accurately to the next generation. I think we are just beginning to understand cells and there is a lot more complexity to be discovered.
  • by iabervon (1971) on Tuesday July 25, 2006 @12:58PM (#15776946) Homepage Journal
    This isn't a second code. The second code is the binding sites for proteins that activate and inhibit gene expression. Then there are a number of other codes already known that affect replication or expression in various ways.

    This is way down on the list of discoveries of patterns in DNA, and it's really more a storage medium property than a code. This is more like sector markings on a hard drive platter than anything to do with data or filesystems. It's important, but because it will tell us where DNA is likely to get damaged, but these sequences are not functional components of the actual use of DNA.
  • God-in-the-Gaps (Score:5, Insightful)

    by ACQ (966887) on Tuesday July 25, 2006 @01:04PM (#15777000)
    In response to a small percentage of posts, I can't help but make this comment: As usual, when there's a new scientific discovery that proves nature is more "complex" (a totally subjective word in and of itself) than we once thought, there's a surge of morons shoving the word "god" in where the words "I personally have no explanation" should be used instead.
  • by posterlogo (943853) on Tuesday July 25, 2006 @01:04PM (#15777003)

    FTA: "Biologists have suspected for years that some positions on the DNA, notably those where it bends most easily, might be more favorable for nucleosomes than others, but no overall pattern was apparent. Drs. Segal and Widom analyzed the sequence at some 200 sites in the yeast genome where nucleosomes are known to bind, and discovered that there is indeed a hidden pattern."

    Honestly, many of us biologists are kind of giggling at how the NYT (and I guess Slashdot) have been hoodwinked by hot headlines. We have known for decades that histones bind DNA and organize it (into nucleosomes), periodically, all along its length. Now, this group has identified some concensus sequences where the nucleosomes are most likely to form. Turns out, yeah, it's what we thought, with the little twist that precise positioning of nucleosomes could help regulate gene expression (also heavily predicted and fully expected). There are new articles about DNA organization weekly. I think the NYT just picked one and labeled it as a "code beyond genetics", which is absurd, since the organization of DNA is controlled ultimately by DNA sequences. Also, if you want to talk about codes beyond genetics, there is a whole field of study called "epigenetics" [wikipedia.org], which is "the study of reversible heritable changes in gene function that occur without a change in the sequence of nuclear DNA".

  • by Anonymous Coward on Tuesday July 25, 2006 @01:15PM (#15777079)

    The existence of nucleosomes is well known. It is not a secondary dna, simply a packing/folding mechanism for DNA, and it may have a role in regulating gene expression.

    http://en.wikipedia.org/wiki/Nucleosome [wikipedia.org]

    The paper itself is as bad as the press reporting it. Slashdot is hardly the avenue to discuss the fine points of a research, but here is something to chew on: note how the authors claim that they predict 54% of nuclesomes ... yet a little later note how by random chance this so called "prediction" would yield a 39% accuracy anyhow. I guess that 54% accuracy is a whole lot less impressive.

    Behind the mumbo-jumbo, p-values, Komolgorov-Smirnoff tests, Boltman partition functions, etc all they do it match a set of 146 bp (start,end) intervals to another one. They are very-very skilled at hiding the simplicity of what they do behind a whole lot of fancy plots and words.

    Nature should be ashamed of themselves ... the literature on this subject goes back many decades, besides doing more experimental work none of this is new, novel or even interesting. I also expect a significant backslash from people that are far more knowledgeble than I am in the matter.

  • by Improv (2467) <pgunn@dachte.org> on Tuesday July 25, 2006 @01:58PM (#15777455) Homepage Journal
    With much fear, surprise, and surprise for some of the scientists, they began to read the new code... it began:

    #!/usr/bin/perl -ane ......

    One scientist looked at the other, and said "This explains everything!"
  • by kzinti (9651)
    Darwin's Radio? (Greg Bear)
  • Organic Software (Score:3, Interesting)

    by Scottux (985006) on Tuesday July 25, 2006 @02:44PM (#15777857) Homepage
    I find this akin to a computer trying to reverse engineer itself. For instance: I am a software program (mind) that is running on organic hardware (body). Whatever designed me probably coded me in Jah++, I can compile Jah++ natively, but I don't really know what any of it means - because I only understand binary. Is it even possible to understand how we are coded? I mean we can see that there is input and it is n characters long, and it affects the eyeballs. But can we really fully understand why? Why were we coded this way in the first place, and how are we able to understand what little bit we can? Finding comments and metadata etc. in our DNA should come as no surprise to anyone here. We have crudely reproduced the most basic inner workings of animal deduction in modern PCs. We didn't invent the PC, we observed and deduced things that occur naturally. PCs are built the same way we are, foreground processes (listening, watching, reading, consciousness) running on top of background processes (breathing, blood circulation, subconsciousness) inside of a case that cools and provides structure. There are input and output devices, microphone, camera, scanner, printer, speaker, etc. We are the creator's computers. We are a part of a grand design for a self contained network of evolving machinery. As far as our computers go, we are building the dinosaurs and hard shelled organisms, slowly we will evolve into making organic computers that are made out of the same stuff we are and can reason - way beyond AI, I am talking about proper intelligence being built into an organism. Arms being recreated, lungs being grown for implants, brains being repaired after car accidents. It is not a far fetched sci-fi scenario. We are able to interface brain to computer right now. Give us time and we will have a Data, we will not know the difference between man and machine. Just my observations. I could be wrong.
  • by espressojim (224775) <eris@NOsPam.tarogue.net> on Tuesday July 25, 2006 @03:49PM (#15778563)
    When I read articles about biology, especially molecular biology/genetics, I see lots of interesting "facts" about the field given by various members of the slashdot crowd. I'm not a leader in the field, but I feel knowledgeable enough working in the field to know just how wrong these "facts" are, yet get modded insightful.

    What scares me are all the articles about topics that I'm not an expert in, where I can't judge the veracity of comments. I've realized that if you guys are so terribly wrong here, that you're probably not believeable anywhere else, either.

    Not that this news to anyone. It just depresses me everytime I see this type of story come up.

    *sigh*

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