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New Code Discovered in DNA?

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.'"

285 comments

  1. So wait by antifoidulus · · Score: 5, Funny

    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?!

    1. Re:So wait by tomstdenis · · Score: 3, Funny

      That means farking is a DMCA violation. Hmm...

      Tom

      --
      Someday, I'll have a real sig.
    2. Re:So wait by geoffrobinson · · Score: 2, Funny

      The RIAA was right. Life as we know it is endangered by free, unhindered downloads.

      --
      Except for ending slavery, the Nazis, communism, & securing American independence, war has never solved anything.
    3. Re:So wait by JudgeFurious · · Score: 2, Funny

      Exactly and these guys are getting themselves into a world of litigation by trying to break it. My client, known to many of you as GOD ALMIGHTY has retained the services of my firm to protect his substantial investment in your genetic code which I may add you merely licensed from him when you agreed to the EULA by leaving the womb.

      --
      Appended to the end of comments you post. 120 chars.
    4. Re:So wait by DrWho520 · · Score: 1

      Nah, more like private and protected data members. And probably one or five mutex locks.

      --
      The cancel button is your friend. Do not hesitate to use it.
    5. Re:So wait by b17bmbr · · Score: 1

      no, it means a lawsuit from SCO.

      --
      My problem? I was perfectly gruntled, until some numbnuts came by and dissed me.
    6. Re:So wait by 3waygeek · · Score: 4, Funny

      Yeah, right. Where in heaven is God going to find a lawyer?

    7. Re:So wait by IAmTheDave · · Score: 1
      Yeah, right. Where in heaven is God going to find a lawyer?

      God: "Pete, put a temporary override on the lawyer auto-filter. Apparently, I'm gonna need a few."

      --
      Excuse my speling.
      Making The Bar Project
    8. Re:So wait by pla · · Score: 1

      So my body has built in DRM?!

      Well, yeah - You don't want just any ol' genetic fragment (such as a virus) coming along and modifying your code... You only want properly authorized DNA from a compatible player to merge with your own. And don't even think about trying any region unlock codes - We all know that leads to nothing but the big "C".


      Now, if they find that our DNA has a copyright notice, I'll get a tad worried. But DRM can count as beneficial, just not the kind controlled by an evil megacorp.

    9. Re:So wait by baKanale · · Score: 4, Funny

      Yeah, right. Where in heaven is God going to find a lawyer?

      I think you mean to say, "Where the hell is God going to find a lawyer?"

    10. Re:So wait by DigiShaman · · Score: 2, Funny

      No it's not because you're creating a new compilation with another member. ;) Now cloning however...

      --
      Life is not for the lazy.
    11. Re:So wait by Cee · · Score: 2, Interesting
      So my body has built in DRM?!

      No, no, you got it all wrong. Your body is built using the Object Oriented paradigm, by the use of encapsulation/information hiding.
    12. Re:So wait by Anonymous Coward · · Score: 0

      Just let one thing be clear: I will allow no-one to mutex my private members!

    13. Re:So wait by PMuse · · Score: 1
      So my body has built in DRM?!
      You'd darned well had better hope so.
      All the organs of the body were having a meeting, trying to decide who was the one in charge
      • "I should be in charge," said the brain, "because without me, you would not know what to do".
      • "I should be in charge," said the stomach, "because without me, you would starve for energy."
      • "I should be in charge," said the legs, "because without me, we could not go anywhere."
      • "I should be in charge," said the eyes, "because without me, we could not find the things we need."
      • "I am in charge," said the rectum, "And that's final."
      All the other body parts laughed at the rectum and insulted him, so he shut down tight. Within a few days, the brain had a terrible head ache, the stomach was bloated, the legs got stiff, and the eyes got watery.

      Moral: this is how the asshole get to be in charge.
      --
      "We reject as false the choice between our safety and our ideals." --The American President (20.1.2009)
    14. Re:So wait by The-Bus · · Score: 3, Funny

      That's not a surprise. For years, I've been friendly enough to offer sharing my genetic code with any number of buxom, nubile females. I was told the code was "incompatible" and often never even got to the I/O phase.

      --

      Small potatoes make the steak look bigger.

    15. Re:So wait by 0xABADC0DA · · Score: 2, Funny

      My cells factor very large primes, therefore I am

    16. Re:So wait by Anonymous Coward · · Score: 0

      "The DNA you are installing has not passed Frank's Logo testing to verify its compatibility with Frank."

    17. Re:So wait by davidsyes · · Score: 1

      Well, hopefully these extra "wrappers" will stop companies and certain governments from "playing god".

      Unfortunately, if there IS a god out there (the kind that certain people prefer to kill in the name of) he/she/it doesn't seem too interested in keeping certain secrets extremely well-protected. Almost as if allowing humans to go ahead and violate certain aspects of nature, life, mortality...

      Some god...

      Maybe "god" needs an upgrade or two?

      --
      Previously: "Linux... Toward the Sunrise..." Now: "Linux... Toward the-- No, now, part of Every Sunrise"
    18. Re:So wait by doublem · · Score: 2, Funny

      So, you never got past the Handshake phase?

      --
      "Live Free or Die." Don't like it? Then keep out of the USA
    19. Re:So wait by whitehatlurker · · Score: 1

      I had permission to write there.

      --
      .. paranoid crackpot leftover from the days of Amiga.
    20. Re:So wait by c_forq · · Score: 1

      Well one the disciples of Christ was a tax collector, so I think God could find a lawyer. Now if Christ wasn't the messiah we may be screwed...

      --
      Computers allow humans to make mistakes at the fastest speeds known, with the possible exception of tequila and handguns
    21. Re:So wait by Hal_Porter · · Score: 1


      Some god...

      Maybe "god" needs an upgrade or two?


      Looks like he's got mod points though doesn't it?

      --
      echo -e 'global _start\n _start:\n mov eax, 2\n int 80h\n jmp _start' > a.asm; nasm a.asm -f elf; ld a.o -o a;
    22. Re:So wait by thePowerOfGrayskull · · Score: 1

      I was all excited, I thought maybe it would be CPP, but it's still the same old GATC. That language is so dead.

    23. Re:So wait by Fordiman · · Score: 1

      Aren't you thinking "Trusted Computing"?

      --
      110100 1101000 1101000 1100110 0 1101111 1101000 1100011 1
    24. Re:So wait by I+Like+Pudding · · Score: 1

      No, I think this prevents variable capture during macro expansion.

    25. Re:So wait by arashi+no+garou · · Score: 1

      No, farking isn't. Fucking might just be though.

    26. Re:So wait by Anonymous Coward · · Score: 0

      Nope, In Hell, Lawyers are easy to find...

      In Soviet Russia, Lawyers find you...

      In Heaven, finding a lawyer might be impossible ;-)

    27. Re:So wait by pato101 · · Score: 1

      Not really, your genes have built in Unix security model:
      ls genes | grep lung | grep cancer
      -rwxr-x--- human lung lung_cancer_gene

    28. Re:So wait by hicksw · · Score: 1

      My cells factor very large primes, therefore I am

      Call back when they can rapidly factor large non-primes. Someone from NSA could make you an offer you cannot refuse.

  2. DNA DRM? by shadowknot · · Score: 3, Funny
    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?

  3. Midichlorians? by digitaldc · · Score: 3, Interesting

    So did we finally discover the Midichlorians that Qui-Gon was rambling about?

    --
    He who knows best knows how little he knows. - Thomas Jefferson
    1. Re:Midichlorians? by OSS_ilation · · Score: 0, Offtopic

      Low score ... hmmmm... The force was not strong with this comment.

    2. Re:Midichlorians? by syntaxglitch · · Score: 3, Informative

      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.

    3. Re:Midichlorians? by dan828 · · Score: 2, Informative

      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.

    4. Re:Midichlorians? by smellsofbikes · · Score: 2, Informative

      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 mitochondria.

      In other words, bacteria have one source of DNA (or RNA...), animals have two DNA repositories, and plants have three.

      --
      Nostalgia's not what it used to be.
    5. Re:Midichlorians? by syntaxglitch · · Score: 1

      Brain fart. I forgot that plants have mitochondria too. What can I say, I'm not a biologist. :(

    6. Re:Midichlorians? by budgenator · · Score: 1

      Plants also have mitochondria, especial plants with chloroplasts. Mitochondria are what make areobic metabolism possible.

      --
      Apocalypse Cancelled, Sorry, No Ticket Refunds
    7. Re:Midichlorians? by dustman · · Score: 1

      (hence the discussion of 'maternal DNA' since you only get maternal mitochondria.)

      I've heard this before, and it "makes sense"... But just to confirm: Do sperm cells not have mitochondria? Or do their mitochondria not make it into the fetus?

    8. Re:Midichlorians? by 955301 · · Score: 2, Interesting

      It gets destroyed by the egg cell:

      http://en.wikipedia.org/wiki/Sperm

      --
      You are checking your backups, aren't you?
    9. Re:Midichlorians? by B2382F29 · · Score: 1

      Sperm cells have no mitochondria, only the egg has them.

      --
      Move Sig. For great justice.
    10. Re:Midichlorians? by B2382F29 · · Score: 1

      i stand corrected... they have, but they don't get used...

      --
      Move Sig. For great justice.
    11. Re:Midichlorians? by WillAffleckUW · · Score: 1

      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.)

      Not only that, but they function as little power cells, and when they stop working well, you get things like Parkinsons that impact the cells which use more energy the most (e.g. brain cells and muscle cells).

      --
      -- Tigger warning: This post may contain tiggers! --
    12. Re:Midichlorians? by Anonymous Coward · · Score: 0

      ONLY on /. can a comment like the parent be scored 'Interesting'.

    13. Re:Midichlorians? by smellsofbikes · · Score: 1

      I've read a lot of good science that indicates that mitochondrial ageing might be a major driving force for ageing in general. It's not like there's just one thing that makes us age, and as (I believe) JSB Haldane pointed out (and provided mathematical support for), evolution will tend to make all ageing mechanisms run their course at the same pace. But with that said, it's my memory that mitochondria do not have particularly good DNA replication accuracy, and they're also the site of some of the nastiest, most damaging chemistry in the body (ATP synthases and the like) so they undergo irreparable damage fairly quickly. It would be interesting to see what mitochondrial replacement therapy would do.

      --
      Nostalgia's not what it used to be.
    14. Re:Midichlorians? by nwbvt · · Score: 1
      "In plants, chloroplasts fill a similar role."

      Actually, mitochondria in plants fill a similar role as mitochondria in animals. These organelles are actually common to virtually all eukaryotic cells. Chloroplasts in plants and algae end up filling a very different role.

      See, I knew that minor in Biology would come in handy at some point.

      BTW, isn't this old news? I seem to remember hearing about this theory way back in high school... They may have found more evidence for it recently, but I don't think this is a brand new discovery as the article seems to indicate.

      --
      Mathematics is made of 50 percent formulas, 50 percent proofs, and 50 percent imagination.
    15. Re:Midichlorians? by hellergood · · Score: 1

      So how did these pre-mitochondrial animals generate ATP? (IANACellBiologist)

  4. Genes, introns and nucleosomes by Intron · · Score: 4, Funny

    Personally, I think it's God's version of Sudoku.

    --
    Intron: the portion of DNA which expresses nothing useful.
    1. Re:Genes, introns and nucleosomes by cttforsale · · Score: 1

      Well I think it's Sudoku's version of God.

    2. Re:Genes, introns and nucleosomes by Bacon+Bits · · Score: 1

      I'd say it's God's version of sudo.

      --
      The road to tyranny has always been paved with claims of necessity.
    3. Re:Genes, introns and nucleosomes by syousef · · Score: 1

      Didn't Einstein say "God does not play Sudoku"?

      --
      These posts express my own personal views, not those of my employer
    4. Re:Genes, introns and nucleosomes by moro_666 · · Score: 1

      I'd rather call the new dna code God's Malware :)

      --

      I'd tell you the chances of this story being a dupe, but you wouldn't like it.
    5. Re:Genes, introns and nucleosomes by justo · · Score: 1

      there is no sudoku

  5. Yes, and by 2names · · Score: 2, Funny

    I'll bet it is controlled by an Active Directory installation.

    --
    "I'm just here to regulate funkiness."
    1. Re:Yes, and by n2art2 · · Score: 5, Funny

      Is that why we have to crash once a day, and it takes 6-8 hours to reboot?

      --
      Self proclaimed wannabe geek. You know how it is. Most of us who read this stuff probably fit in that category.
    2. Re:Yes, and by mgblst · · Score: 1

      Wow, best version of windows ever!

  6. An important reminder by QuantumFTL · · Score: 4, Insightful

    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.

    1. Re:An important reminder by Knuckles · · Score: 1

      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.

      --
      "When I first heard Daydream Nation it quite frankly scared the living shit out of me." -- Matthew Stearns
  7. Intelligent Discovery. by Anonymous Coward · · Score: 0

    "The NY Times is reporting that scientists have found a second code in DNA that goes beyond the genes."

    Man! How long did it take evolution to figure that one out?

    1. Re:Intelligent Discovery. by HTH+NE1 · · Score: 2, Insightful

      Man! How long did it take evolution to figure that one out?

      What time is it?

      (Did you meant figure out how to do it, or figure out how it does it?)

      I'm anticipating the time when we realize that life and evolution is an example of Reflections on Trusting Trust and thus that the origin of some aspects of DNA and life may be unknowable, and yet explicable, and thus not be of divine origin.

      --
      Oh, say does that Star-Spangled Banner entwine / The myrtle of Venus with Bacchus's vine?
    2. Re:Intelligent Discovery. by Anonymous Coward · · Score: 0

      Just because something might be explicable, doesn't preclude it being of divine origin.

      God put a rainbow in the sky to remind man that he would never flood the Earth with water again.

      Yes, we can explain exactly why it appears there using elementary physics and predict exactly where it will appear at any given time of day based on the position of the sun in the sky.

      But that doesn't diminish its divine origin.

      It's not that God works within the laws of physics to accomplish his ends as much as he created those laws in the first place, and it's therefore to be expected that the laws of physics would be amenable to God's intentions.

    3. Re:Intelligent Discovery. by ichigo+2.0 · · Score: 1

      God put a rainbow in the sky to remind man that he would never flood the Earth with water again.

      Yes, we can explain exactly why it appears there using elementary physics and predict exactly where it will appear at any given time of day based on the position of the sun in the sky.

      But that doesn't diminish its divine origin.


      The problem with this silly statement is that it would mean that there were no rainbows before the flood, and that the laws of physics were changed to enable rainbows to appear.

    4. Re:Intelligent Discovery. by whitehatlurker · · Score: 1
      God put a rainbow in the sky to remind man that he would never flood the Earth with water again.

      Yeah, right - were a quarter million people killed by their own imaginations? There are floods even with the fricking rainbows. Read a newer book.

      --
      .. paranoid crackpot leftover from the days of Amiga.
    5. Re:Intelligent Discovery. by Anonymous Coward · · Score: 0

      "flood the earth" != "local or regional flood"

    6. Re:Intelligent Discovery. by Anonymous Coward · · Score: 0

      Yeah, don't bother for a moment to consider whether it might be possible within our (current) understanding of "the laws of physics" for there to have not been a visible rainbow for however long before the flood. It's absolutely guaranteed that there had to have been rainbows before the flood, since their presence is constant now. I mean, I can look out the window right now and see... OMFG!! THE RAINBOWS ARE GONE!!! What could have erased all the rainbows?!?!?!
       
      Oh, wait, maybe the volume/distribution/temperature/form of water in the air isn't exactly right for that relatively rare phenomenon to appear. Whew! That was close; I almost gave up on my entire belief system!

    7. Re:Intelligent Discovery. by Anonymous Coward · · Score: 0

      [...]the flood[...]

      flood?

    8. Re:Intelligent Discovery. by ichigo+2.0 · · Score: 1

      I'm guessing it's the flood with the Noah's ark etc.

    9. Re:Intelligent Discovery. by HTH+NE1 · · Score: 1

      And you trust ancient peoples who didn't even realize that the world was not flat to determine that the entire planet was flooded?

      --
      Oh, say does that Star-Spangled Banner entwine / The myrtle of Venus with Bacchus's vine?
    10. Re: Intelligent Discovery. by Black+Parrot · · Score: 1

      > Just because something might be explicable, doesn't preclude it being of divine origin.

      And that's precisely the problem with supernatural "explanations".

      I dropped my pen and gravity drew it down to the floor, accelerating it along the way. No, wait - pixies pulled it down, and the acceleration was the result of more pixies joining in as it fell.

      When you start invoking supernatural "explanations", evidence becomes irrelevant, and one claim is just as good as any other. Any other.

      --
      Sheesh, evil *and* a jerk. -- Jade
    11. Re:Intelligent Discovery. by Anonymous Coward · · Score: 0

      The Bible affirms that the world is round, actually... it makes reference to the notion in several places, including Job, Psalms, Proverbs, and Isaiah.

    12. Re: Intelligent Discovery. by Anonymous Coward · · Score: 0

      I wasn't offering the supernatural cause as any sort of "explanation".

      I was merely saying that attributing it to explicable processes that are well understood, even if this attribution is correct, does not mean that it is still not caused by divine action. Occam's razor may suggest that a divine entity is not necessary for such a cause, but first of all, Occam's razor is only a rule, and not a law, and second, it only applies to the universe as we know it, of which a supernatural omnipotent entity that originated it by willing it into existence would necessarily not be a part.

    13. Re:Intelligent Discovery. by Anonymous Coward · · Score: 0

      Which was the (make that THE ) flood referred-to by the GGP.

    14. Re: Intelligent Discovery. by HTH+NE1 · · Score: 1

      faith: the capacity to believe what you know isn't true.

      --
      Oh, say does that Star-Spangled Banner entwine / The myrtle of Venus with Bacchus's vine?
  8. Proff of intellijent design!!!11 by Lord_Slepnir · · Score: 3, Funny

    Only Go^H^Han intelligent designer could have implemented DNA with private and protected data. This sort of thing just can't randomly 'evolve'.

    1. Re:Proff of intellijent design!!!11 by Anonymous Coward · · Score: 0

      Don't be so sure. I'm sure Da Vinci must have had a hand in it somewhere.:-)

    2. Re:Proff of intellijent design!!!11 by kesuki · · Score: 1

      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.

    3. Re:Proff of intellijent design!!!11 by wateriestfire · · Score: 0

      for one would everyone stop calling it mechanisms, it is really processes. Now under the processes it seems reasonable that the system, which is the entire body structure, including cognitive thought would access these parts in a way that will maintain the system. By this logic it is easy to beleive that because of the entire system's need for such a crutial element that that element would create itself when the system is pushed far enough. ---- In Chaos there is Order

    4. Re:Proff of intellijent design!!!11 by Bemopolis · · Score: 3, Funny

      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

      --
      "I guess the moral of the story is, don't paint your airship with rocket fuel." -- Addison Bain
  9. Wasn't this a Star Trek: TNG episode? by thomasdz · · Score: 1
    --
    Karma: Excellent. 15 moderator points expire sometime.
  10. software problem by hey · · Score: 4, Funny

    Any software problem can be solved by adding another layer of indirection.
    So apparenlty we are a software problem.

    1. Re:software problem by PMuse · · Score: 1

      You are adaptively self-programming software running on adaptively self-replicating hardware. TFA is more of a hardware issue.

      Me, I'm just another steam engine trying to contain the pressure.

      --
      "We reject as false the choice between our safety and our ideals." --The American President (20.1.2009)
  11. In other news by Anonymous Coward · · Score: 0

    The RIAA has announced that they are suing the entire human race for violation of their client "God"'s intellectual property.

  12. Cue the "irreducibly complex" creationists... by Anonymous Coward · · Score: 0

    What an arrogant, presumptuous argument.

    "I can't figure out how this could evolve, so God must therefore be precluded from creating a universe in which living creatures evolve."

    As if God is limited to what one human can or cannot understand...

  13. Evolution proves totally brilliant once again by realisticradical · · Score: 5, Insightful
    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".

    1. Re:Evolution proves totally brilliant once again by Anonymous Coward · · Score: 0

      While you're correct, given that the comments here are overwhelmingly devoted to yet another round of scientifically illiterate ranting about creationism, the DMCA and stem cells, if anything it would seem that the NYT didn't dumb down the issue nearly enough.

    2. Re:Evolution proves totally brilliant once again by sanclaus · · Score: 1

      Personally I think this is WAY over-hyped, a link between double helix bendability and nucleosome binding was suspected. Inspecting 200 yeast nucleosome binding sites they found certain DNA protein sequences occurred at about 50% of the sites. They thus postulate that these DNA protein sequences allow the double helix to bend.

      This is rather straight forward and is hardly the discovery of a "second code" nor does it shed any light on the mystery of cellular differentiation.

                (i.e. what the cumbersome language of the article calls "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").

      Nice graphics though.

    3. Re:Evolution proves totally brilliant once again by Michael+Woodhams · · Score: 1

      I agree. It is (assuming the claims stand up) a very significant discovery. It is a new layer of subtilty around gene expression and constraints on the DNA sequences. It is *not* a "second code" - there is no extra information, everything can be derived from the genome DNA sequence.

      --
      Quattuor res in hoc mundo sanctae sunt: libri, liberi, libertas et liberalitas.
  14. Random error produces error control mechanism? by geoffrobinson · · Score: 0, Flamebait

    Error control mechanisms, at the very least, would very much run against the flow of blind Darwinian processes.

    Yes, this discovery does not hurt the ID movement at all.

    --
    Except for ending slavery, the Nazis, communism, & securing American independence, war has never solved anything.
    1. Re:Random error produces error control mechanism? by plalonde2 · · Score: 4, Insightful

      Pardon? Your statement is nothing but a bald assertion. Error control mechanisms run in no way against the evolutionary grain. It's easy to imagine that an organism with a little error correction will be more fit in its niches than an organism without. Changing too rapidly, or too randomly, is as dangerous to an organism as not adapting fast enough.

    2. Re:Random error produces error control mechanism? by Darkman,+Walkin+Dude · · Score: 1

      Error control mechanisms, at the very least, would very much run against the flow of blind Darwinian processes.

      You mean like white blood cells?

    3. Re:Random error produces error control mechanism? by Anonymous Coward · · Score: 1, Informative

      Ummm, error control mechanisms are EVERYWHERE in biology and are nothing new. Take a look at:

      kinetic proofreading
      programmed cell death
      nucleotide excision repair
      base-excision repair

      http://en.wikipedia.org/wiki/DNA_repair

      I'm sure a real biologist could point out even more points to note. From an evolutionary point of view, an organism that couldn't control its cell growth or repair damaged DNA strands probably wouldn't last that long!

    4. Re:Random error produces error control mechanism? by syntaxglitch · · Score: 5, Insightful

      Error control mechanisms, at the very least, would very much run against the flow of blind Darwinian processes.

      No, error correction would counter the mutation process. Given that, generally, more mutations are harmful than beneficial, error-correcting genetics would be a short-term benefit in reducing genetic disorders. The downside would come if another species with a higher mutation rate evolves into a more successful form and crowds out the now-obsolete organism with rigid genetics. The overall winners would likely be organisms within some range of error-correction--neither a total free-for-all, nor a very rigid genome. This seems pretty well reflected in real life, unsurprisingly.

      Yes, this discovery does not hurt the ID movement at all.

      This is also true; no scientific discovery will hurt the ID movement, since it has precisely nothing to do with science...

    5. Re:Random error produces error control mechanism? by 1cebird · · Score: 1

      Yes, that assertion most definitely lacks hair...?

      --
      -K
    6. Re:Random error produces error control mechanism? by OneSmartFellow · · Score: 0, Flamebait
      ...no scientific discovery will hurt the ID movement, since it has precisely nothing to do with science...

      You obviously haven't been talking to the extremeley conservative Senator Rick Santorum, he thinks it does; and he is hell (pardon) bent on getting it taught as such !

    7. Re:Random error produces error control mechanism? by geoffrobinson · · Score: 1

      I'm not disagreeing with you.

      --
      Except for ending slavery, the Nazis, communism, & securing American independence, war has never solved anything.
    8. Re:Random error produces error control mechanism? by smellsofbikes · · Score: 4, Interesting

      Case in point: the HIV virus. It's an RNA virus. Most enzymes cells use for replicating DNA (called DNA polymerases) have a proofreading skill: if they detect that what they're reading is incorrect they'll rip it out and try again. Most RNA polymerases lack proofreading skill (because it's expensive: it takes a lot of energy, and RNA is, in the grand scheme of things, considered throwaway material, a transition from the data storage system to the actual machinery.) So, the viruses that rely on RNA as their data storage have a much higher rate of mutation. The result is that they have a vastly higher rate of nonviable viral particles, and a small number of extremely viable particles, which have found, by chance, better ways of evading host immune response. It's a main reason that HIV is so difficult to treat or cure.
      Here is some information about reverse transcriptase error rates. In contrast, here is some for one of the DNApolymerases. As I recall, in eukaryotes there are three DNA polymerases, and only DNApolyIII has bidirectional proofreading ability (I may be wrong) so only it can scan finished DNA, but all three can scan DNA while it's being built. In contrast, I don't believe there are any enzymes that can scan finished RNA (since it's not, to my knowledge, found double-stranded in anything we've found, and you'd have no way of determining that there was an error) so the best you can hope for is really good DNA->RNA fidelity, and as I said earlier, there's not much evolutionary pressure FOR that in the rest of nature, while there's some evolutionary pressure AGAINST it (because it's expensive) so if it were to exist, it would only exist in things that would benefit from it, those being small RNA viruses that are much less likely to have either the history, the machinery, or the overhead to afford proofreading replication enzymes. Besides which, if their gain (number of viruses produced for each cell infected) is high enough, they A: don't care about individual viral particle loss from bad fidelity, and B: actually benefit from high mutation rate because of its help in evading host response.
      whew. that was wordy. sorry.

      --
      Nostalgia's not what it used to be.
    9. Re:Random error produces error control mechanism? by jimktrains · · Score: 1

      This is why I always wondered why people fund/do research on if prayer? What good does it do? Now in science, that is never a good attidtude, but... You aren't going to convince anyone of anything and you can't prove anything. When you're dealing with God, all bets are off. I never insert God as a crutch in science. So what is the point?

      OK, on topic:
      This is why I want to go into molecular/computatioal bio. Weird, exciting, important things are always there tobe discovered (ok, so you can make that assertion about any science, but I prefer bio).

      --
      "You will do foolish things, but do them with enthusiasm." - S. G. Colette
    10. Re:Random error produces error control mechanism? by bigbird · · Score: 1
      It's easy to imagine that an organism with a little error correction will be more fit in its niches than an organism without.

      That's what I love about evolution :) It is pretty easy to imagine up an evolutionary advantage about absolutely any biological feature that ever existed. Just read something like New Scientist to see what I mean. Evolution has an answer to everything.

    11. Re:Random error produces error control mechanism? by gilberry · · Score: 0

      Organisms do not evolve. Species evolve. Organisms adapt.

    12. Re:Random error produces error control mechanism? by hdante · · Score: 1

      Mod parent down. He has just screwed a wonderful joke and explained something we already know =)

    13. Re:Random error produces error control mechanism? by csoto · · Score: 1

      Exactly. Evolution is the basic tenet of modern biology. All biological realities are explained by it. It's one of the most successful theories in existence.

      --
      There exists no way of exchanging information without making judgments. --Bene Gesserit Axiom
    14. Re:Random error produces error control mechanism? by csoto · · Score: 1

      Exactly. I have often mentioned that sexual reproduction is essentially an anti-mutational adaptation. Homologous recombination prefers LIKENESS to UNLIKENESS, so the chances that truly "unique" genes wind up in the recombination product (the child genome) is lessened. Sex keeps known working genes around, and largely prevents completely novel genetic information from being passed on.

      --
      There exists no way of exchanging information without making judgments. --Bene Gesserit Axiom
    15. Re:Random error produces error control mechanism? by Anonymous Coward · · Score: 0

      (since it's not, to my knowledge, found double-stranded in anything we've found, and you'd have no way of determining that there was an error)

      double-stranded RNA: tRNA, mtRNA, shRNA, Dicer template processing stages.

      +viral dsRNA

    16. Re:Random error produces error control mechanism? by smellsofbikes · · Score: 1

      Well, clearly I should go reread my college textbooks...
      But I thought that tRNA and mtRNA, while certainly coiled into an enzyme-like shape, were not double-stranded so much as held together by short runs of complimentary sequences. I know, that's splitting hairs, but my understanding was that 80% or so of the structure was held together by 20% or so of complimentary runs, and that's not going to be very useful for proofreading.
      Now, viral dsRNA is entirely new to me. Do you know if there's any evidence of proofreading enzymes that can work with it? It'd be an interesting tactic to use the host cell polymerases to fix your RNA.
      I also seem to remember that the proofreading enzymes rely on methylation of the ribose/phospates to decide which strand to trust for mismatches (aside from obvious errors like thymine dimers and uracils.) Would this hold with RNA? Are there RNA phosphorylases to even provide this functionality? I'm in areas I don't remember well enough.

      --
      Nostalgia's not what it used to be.
    17. Re:Random error produces error control mechanism? by tgibbs · · Score: 1

      Error control mechanisms, at the very least, would very much run against the flow of blind Darwinian processes.

      Error control mechanisms, which have been known for many years to exist, in no way run counter to expectations from Darwinian theory. In the short term, error correction improves fitness, because any given mutation is more likely to be deleterious than beneficial. In the long-run, however, too much error correction would be bad for the species, because the ability to evolve is required to adapt to changing conditions, and evolution depends upon a pool of variation, derived from those mutations that have not turned out to be particularly deleterious. Evolution has no foresight, so in most situations it is unable to produce change "for the good of the species," so one might worry that species might error correct themselves out of the evolution business. However, there is a short-term disadvantage to error correction--it costs metabolic energy that might offer a greater yield in fitness if used for other purposes. So selection supports the evolution of "just enough" error correction, where the fitness benefit in terms of reduced deleterious mutations just balances the fitness cost in terms of poorer energy "mileage."

    18. Re:Random error produces error control mechanism? by Anonymous Coward · · Score: 0

      No, error correction would counter the mutation process. Given that, generally, more mutations are harmful than beneficial, error-correcting genetics would be a short-term benefit in reducing genetic disorders. The downside would come if another species with a higher mutation rate evolves into a more successful form and crowds out the now-obsolete organism with rigid genetics. The overall winners would likely be organisms within some range of error-correction--neither a total free-for-all, nor a very rigid genome. This seems pretty well reflected in real life, unsurprisingly.

      You're assuming error-correction would be perfect or constant. If your error-correction is also encoded in the DNA, it can be disabled by mutations as well, and also participate in natural selection. During times of stable environment, natural selection would keep error-correction high (a sort of second-order selection, avoid mutants). During rough times, where widely varying mutants might be better adapted, these widely varying mutants will also pass on their lack of error correction, even to offsprings who don't necesarilly share their main diference, thereby maintaining a high mutation rate.

      What does this mean for humans in these days of no natural selection? Don't know, and multigeneration studies of mutation rates aren't very likely in the near future.

    19. Re: Random error produces error control mechanism? by Black+Parrot · · Score: 1

      > Yes, this discovery does not hurt the ID movement at all.

      No discovery will ever hurt the ID movement, because it's based on bullshit rather than evidence.

      --
      Sheesh, evil *and* a jerk. -- Jade
    20. Re:Random error produces error control mechanism? by Trogre · · Score: 1

      it [the ID movement] has precisely nothing to do with science...

      That is true IFF you take science==evolution.

      Unfortunately no other theories on species origins can every be considered scientific by that definition.

      For proper objective science that actually looks at evidence without prejudice, ID is significantly more scientific than evolution.

      --
      "Nine times out of ten, starting a fire is not the best way to solve the problem." - my wife
    21. Re:Random error produces error control mechanism? by HeroreV · · Score: 1

      I find your ideas intriguing and wish to subscribe to your religion. Please present more evidence for intelligent design than there is for evolution and I'll begin throwing away my money to your church immediately.

  15. It's a bit like the way you can embed... by exp(pi*sqrt(163)) · · Score: 2, Insightful

    ...a Whitespace 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.

    --
    Doesn't it make you feel good to know that our freedoms are protected by politicans, lawyers and journalists.
  16. Original article by infolib · · Score: 4, Informative

    Abstract and full text PDF. (currently freely available).

    --
    Any sufficiently advanced libertarian utopia is indistinguishable from government.
    1. Re:Original article by BigCheese · · Score: 0, Troll

      Yes, it is an article. There are a lot of words. Since I am not a bioligist (IANAB) that's as far as I got.

      --
      The obscure we see eventually. The completely obvious, it seems, takes longer. - Edward R. Murrow
  17. Precisely. by 2names · · Score: 1

    It is also why humans pass around so many damn virii. And how much junk mail do YOU get each week? We could go on and on, but I think it is fairly obvious that All Our DNA are Belong to Billy G.

    --
    "I'm just here to regulate funkiness."
    1. Re:Precisely. by Anonymous Coward · · Score: 0, Troll

      Viruses. People who say "virii" look very stupid. Don't look stupid, say "viruses".

    2. Re:Precisely. by LiLWiP · · Score: 3, Funny

      I am just waiting for the new book due out soon.... Men are Linux, Women are OSX... I guess that the gay and lesbian population are different versions of windows?

    3. Re:Precisely. by doublem · · Score: 0

      That's very Homophobic.

      --
      "Live Free or Die." Don't like it? Then keep out of the USA
    4. Re:Precisely. by gharris · · Score: 5, Funny

      Nah, they just run the other os in a virtual machine.

    5. Re:Precisely. by Anonymous Coward · · Score: 0

      People who post AC to correct grammar and spelling in funny or sarcastic posts look very stupid. Don't look stupid, change your idiotic behaviour.

    6. Re:Precisely. by Anonymous Coward · · Score: 0

      People who post AC to defend themselves against somebody pointing out their intelligence deficit disorder look very stupid. Don't look stupid, either raise your intelligence or log in to defend your idiocy.

    7. Re:Precisely. by n2art2 · · Score: 0, Offtopic

      people who also complain about people who post AC are no better then those they post about.

      --
      Self proclaimed wannabe geek. You know how it is. Most of us who read this stuff probably fit in that category.
    8. Re:Precisely. by n2art2 · · Score: 2, Funny

      I would say it the other way around. Men are OS X and Women are Linus. (Men are easier to understand, logical. Women on the other hand, require a lot of time massaging and learning just the right way to interact in order to get what you want out of them, and even then sometimes the outcome is unexpected, and requires more massaging.

      --
      Self proclaimed wannabe geek. You know how it is. Most of us who read this stuff probably fit in that category.
    9. Re:Precisely. by LiLWiP · · Score: 2, Funny

      Yeah, you are right. With women if their dependencies aren't met then they shut down on you and you get NOTHING out of them.... I agree..

    10. Re:Precisely. by Fordiman · · Score: 0, Offtopic

      You're a moron.

      Be more fucking direct.

      --
      110100 1101000 1101000 1100110 0 1101111 1101000 1100011 1
    11. Re:Precisely. by Jesus_666 · · Score: 1

      I would say it the other way around. Men are OS X and Women are Linus.

      No. Just... no.

      --
      USE HOT GRITS WITH STATUE OF NATALIE PORTMAN (NAKED AND PETRIFIED)
  18. Zawinski's law by PhilipOfOregon · · Score: 1

    That's the part that lets us read email.

  19. And in further news, the histones... by dpbsmith · · Score: 2, Funny

    have been discovered to be eighty units long and oriented face down, nine edge first.

  20. How the hell does *that* follow? by Anonymous Coward · · Score: 1, Interesting

    Error control mechanisms, at the very least, would very much run against the flow of blind Darwinian processes.

    Why? Why couldn't DNA evolve error control mechanisms over billions of years? Because you don't want it to?

    Seems to me a mechanism to make the genes encoded into DNA more stable and reproduceable would produce enormous benefits to an organisms ability to rapidly and accurately reproduce and thus would have enormous evolutionary pressure behind it.

    1. Re:How the hell does *that* follow? by geoffrobinson · · Score: 1

      Well, it seems like you are saying that if organisms are more prone to blind Darwinian processes that would make organisms less prone for survival. And putting the brakes on mutations and changes which are at the heart of the Darwinian mechanism would make an organism more prone to for survival.

      So if Darwinian processes produce the survival of the fittest, the first thing those processes have to do is protect an organism from random mutation and error.

      I'll go with that and agree with you.

      --
      Except for ending slavery, the Nazis, communism, & securing American independence, war has never solved anything.
    2. Re:How the hell does *that* follow? by The+Only+Druid · · Score: 1

      You seem to misunderstand how "error correction" benefits a creature. In order for evolution to work, you need natural selection, i.e. a pool of creatures (generation-n) who have slightly variable features due to mutation, which is then reduced by natural selection factors (e.g. predation, limited resources, etc.). The survivors then reproduce (generation n+1).

      Now, each generation needs to have some variability. After all, if everyone is identical, then there will be no adaptability. But, they need to have a much more significant sameness, i.e. lack of variability. After all, they need to be able to breed (among other interrelationships). Moreover, like all course-corrections, it's always better to move in small steps instead of big leaps (at least, almost always).

      Error correction in genetic material would help curtail big leaps, while making small steps more viable (by reducing the number of critical mutations that kill the individual).

      Of course, every now and then, environmental pressures would mean that lower error correction might be beneficial - consider the near-extinction of the Cheetah's ancestor to apparently fewer than 50 individuals - because you need a larger population of genetic variation. Such situations would result in some species having more or less "correction" built in. Species that never had such a bottle-neck would be expected to have more error-correction, most likely.

      --
      "Stumble before you crawl"
    3. Re:How the hell does *that* follow? by geoffrobinson · · Score: 1

      I would agree with all that.

      The point of contention is whether a blind, error-reliant process can do it.

      If you consider the genetic information as a big cark deck, then I would consider each organism to get a different hand based on the shuffle. More shuffles may produce better results. Maybe not.

      I'm just not going to expect a net increase in information based on new cards appearing.

      The Darwinian mechanism, which *produces everything*, has become a just-so story with no consideration to whether the everything in the narrative is consistent with it. It produces new things by random errors. It prevents errors by random errors.

      It has no predictive value either. Anything that is is consistent with the Darwinian mechanims otherwise we wouldn't see it.

      It is consistent with gazelle populations. It isn't consistent with producing an error-control mechanism.

      --
      Except for ending slavery, the Nazis, communism, & securing American independence, war has never solved anything.
    4. Re:How the hell does *that* follow? by tgibbs · · Score: 1

      If you consider the genetic information as a big cark deck, then I would consider each organism to get a different hand based on the shuffle. More shuffles may produce better results. Maybe not. I'm just not going to expect a net increase in information based on new cards appearing.

      Why not? After all, if you play enough hands of poker, you'll eventually gain information as to what hands are good and what hands are bad, even if you started out not knowing the game. The notion that information cannot increase by random processes is fundamentally foolish--a great deal of information can be acquired by random trial and error.

    5. Re:How the hell does *that* follow? by rtb61 · · Score: 2, Insightful
      The biggest driver for evolution is not the slow process of natural selection but natural disasters. A major event will clear an enviroment and create a low competition enviroment allowing more mutations to survive and fill the various vacant ecological niches within that enviroment.

      Consider the very first round of evolution, the original species over used the enviroment to such an extent that they produced a mass extinction event, terra formed the planet and rendered it suitable for previously disfunctional mutations.

      Error correction is required not so much for us reproducing as a collective organism but for the individual cells in our bodies to continue reproducing. You are continuously dying and being reborn every day and you don't want some of your cells evolving and becoming dominant within the eco system of your own body (cancer).

      --
      Chaos - everything, everywhere, everywhen
  21. It's worse than that! by /dev/trash · · Score: 1

    We're C++ code

    1. Re:It's worse than that! by Alexandra+Erenhart · · Score: 1

      I always thought we were made out of some like assembly. G-T-A-C based code doesn't seem very high lvl language to me :P

    2. Re:It's worse than that! by Anonymous Coward · · Score: 0

      G-T-A-C?

      Go-Try-Anonymous-Coward? ;)

    3. Re:It's worse than that! by tomjen · · Score: 1

      Not exactly:

      I was taught assembler
      in my second year of school.
      It's kinda like construction work --
      with a toothpick for a tool.
      So when I made my senior year,
      I threw my code away,
      And learned the way to program
      that I still prefer today.

      Now, some folks on the Internet
      put their faith in C++.
      They swear that it's so powerful,
      it's what God used for us.
      And maybe it lets mortals dredge
      their objects from the C.
      But I think that explains
      why only God can make a tree.

      the rest or sung

      --
      Freedom or George Bush
    4. Re:It's worse than that! by ConceptJunkie · · Score: 1

      Only 4 instructions. People are RISC!

      --
      You are in a maze of twisty little passages, all alike.
    5. Re:It's worse than that! by Physics+Dude · · Score: 1

      More like 20 instructions (Amino Acids). The 4 nucleotides aren't the instructions themselves, but are more like two-bits or a single base_4 digit. Each amino acid is coded for by three nucleotides (a codon). This covers the coding of 20 amino acids with some redundancy.

    6. Re:It's worse than that! by ConceptJunkie · · Score: 1

      Thanks for the clarification. I knew I wasn't being correct but it was just a joke and this is just /. :-)

      However, I have been reading "Darwin's Radio" by Greg Bear and wondering where the science stops and the science fiction begins. It's incredible how much there still is to learn about how this stuff works.

      And finally, 20 instructions is still pretty RISCy.

      --
      You are in a maze of twisty little passages, all alike.
  22. Metadata by Aladrin · · Score: 4, Insightful

    I find it interesting that god/evolution/the great green arkleseizure/FSM/whatever invented metadata LONG before we did. Not surprising, just interesting.

    --
    "If you make people think they're thinking, they'll love you; But if you really make them think, they'll hate you." - DM
    1. Re:Metadata by Trails · · Score: 1

      I think this proves what we've innately known all along: Tim Berners Lee is God, and metadata is His message.

    2. Re:Metadata by realisticradical · · Score: 1

      Err, you may have missed the pattent number at the end of chromosome 19q24. The number of pattent suits coming out of this "God" company is going to put all other pattent holders to shame.

  23. C'mon baby... by NotQuiteReal · · Score: 4, Funny

    I have a lot of good code, ready for re-use!

    --
    This issue is a bit more complicated than you think.
    1. Re:C'mon baby... by jfengel · · Score: 5, Funny

      And like any good programmer, you're willing to share the source for free.

      Just don't expect you to maintain it.

  24. Breaking News!! by Anonymous Coward · · Score: 1, Funny

    Hidden message deciphered in nucleosomes: WE ARE SORRY FOR THE INCONVENIENCE.

  25. How exciting can it be? by butterwise · · Score: 0

    FTFA: "I think it's really interesting," said Bradley Bernstein, a biologist at Massachusetts General Hospital.

    If this guy is so pumped, shouldn't we all?

    --
    If a baby duck is a "duckling," why would anyone want to eat "dumplings?"
  26. New Discovery by Phillip2 · · Score: 0

    NYTimes is reporting a new discovery. However, because neither their journalists couldn't be bothered to understand or imaginatively report the discovery, they have instead decided to simplify it to the point that it appears to be exactly the same as something that biologists. It's hoped that in future, reporting will improve. This could revolutionise newspapers to the point where they are actually useful.

    Phil

    1. Re:New Discovery by dan+dan+the+dna+man · · Score: 3, Insightful

      I'm not entirely sure this is a problem. We have a heirachy of media that cascades, simplifying down at each stage. In this case we normally have something like Nature article (for the practicing biologist) -> Nature News and Views (for the lazy people who read Nature but can't be arsed to read the article) -> New Scientist article/comment (for the interested layman) -> traditional news media (the proletariat). At each stage something is lost. I don't expect the public to care about a prediction method for the sequences involved in higher ordering of chromatin structure, but the fact they might find out that DNA does more than just 'make genes' I think is a relevant point.

      The headline however, is unnecessarily sensationalist..

      --
      I don't read your sig, why do you read mine?
    2. Re:New Discovery by Phillip2 · · Score: 1

      Pah.

      I can't be bothered to read Nature and Science these days. The damn articles are so long and hard to read. I mean, have you any idea at all how busy I am? How am I supposed to do any science if I spend all my days reading papers.

      Phil

    3. Re:New Discovery by autophile · · Score: 1
      In this case we normally have something like Nature article (for the practicing biologist) -> Nature News and Views (for the lazy people who read Nature but can't be arsed to read the article) -> New Scientist article/comment (for the interested layman) -> traditional news media (the proletariat)

      ... -> someone's blog (for the wide-eyed mouth-breather) -> another someone's blog (even wider eyes) -> Slashdot (YOU) -> Slashdot comment (ME).

      --Rob

      --
      Towards the Singularity.
    4. Re:New Discovery by Anonymous Coward · · Score: 0

      Well, this is Nicholas Wade we are speaking of here. He is a shill and will output to the public whatever is input into him. Sorta like a walking printer.

  27. Post to piss off conservatives by aussersterne · · Score: 0, Offtopic

    Evolution! Natural Selection! Darwin! Condoms! Abortion! Diplomacy! Secularism! Science! France! Hollywood! Palestine! Environmentalism! Global warming! Nudity!

    Hahahahahahaha!

    --
    STOP . AMERICA . NOW
    1. Re:Post to piss off conservatives by WilliamSChips · · Score: 0, Offtopic

      There are now 14 assassins trying to kill you. Let's move.

      --
      Please, for the good of Humanity, vote Obama.
  28. Great Ammo For bush by elzurawka · · Score: 1

    "God uses DRM, SO CAN YOU!"

    --
    -EL
  29. First DNA virus hackers? by farker+haiku · · Score: 2, Interesting

    When am I going to see my first wetware virus that uses an "escalation of privileges" type attack?

    --
    Your sig(k) has been stolen. There is a puff of smoke!
    1. Re:First DNA virus hackers? by plalonde2 · · Score: 3, Insightful

      Think of cancer as a fandango on core followed by a DOS/fork bomb.

    2. Re:First DNA virus hackers? by Anonymous Coward · · Score: 0

      There already is one, it's called Cancer. That's when cells start making proteins they're not supposed to and go haywire.

    3. Re:First DNA virus hackers? by Ginnungagap42 · · Score: 1

      Correct me if I'm wrong, but doesn't HIV "turn off" the T-helper cells in the immune system?

    4. Re:First DNA virus hackers? by dilvish_the_damned · · Score: 1

      Usually shen your seven or eight.

      --
      I think you underestimate just how much I just dont care.
  30. Nicely coded. by Fuzzums · · Score: 1

    "...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."

    Personally I think some of these genes are not declared as 'public', but rather 'protected' or 'internal'.

    --
    Privacy is terrorism.
  31. The most important question... by __aaclcg7560 · · Score: 0, Troll

    Can you program your DNA with PHP?

    1. Re:The most important question... by Anonymous Coward · · Score: 0

      I can't believe this is modded Troll!
      Who could possibly find this post offensive?

    2. Re:The most important question... by chris_eineke · · Score: 1

      I don't think that PHP is the best solution here. If you want sequence processing, you will need... wait for it... wait for it...

      Lisp! :D

      --
      "All you have to do is be fragile and grateful. So stay the underdog." Chuck Palahniuk, Choke
    3. Re:The most important question... by __aaclcg7560 · · Score: 1

      I think the moderator failed to learn PHP during an introduction programming class. Such incidents usually leads to a life of bitterness for falling so short on something so easy to learn. Not everyone has the ability to re-program their DNA with PHP.

  32. Survival of the Fitness to Print by Doc+Ruby · · Score: 0, Troll

    Geneticists have already found a "second code" in DNA, called methylation. And that NYTimes article also reduces the basebair redundancy to "wiggle room".

    The underlying research, published in Nature magazine, is extremely interesting and valuable, no doubt valid. The NYTimes coverage is oversimplified into wrongness out of reporter ignorance, and an insult to both readers and scientists.

    --

    --
    make install -not war

    1. Re:Survival of the Fitness to Print by Doc+Ruby · · Score: 0, Offtopic

      Moderation -1
          100% Troll

      Pathetic SlashStalkers.

      --

      --
      make install -not war

  33. New Code Discovered in DNA by Anne_Nonymous · · Score: 5, Funny

    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

    1. Re:New Code Discovered in DNA by Anonymous Coward · · Score: 0

      ahaahaahaahaa

    2. Re:New Code Discovered in DNA by ichigo+2.0 · · Score: 1

      Interesting Perl script.

    3. Re:New Code Discovered in DNA by smellsofbikes · · Score: 1

      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.

      --
      Nostalgia's not what it used to be.
  34. OOPS, encapsulation by vasanth · · Score: 1

    wow we have discoved that genes use encapsulatio now.. OOPS is the way to go... no wonder it cant access private members of other classes erm.... genes..

  35. I don't know much about DNA... by Anonymous Coward · · Score: 0

    ...but is this anything like the Hot Coffee mod?

  36. Contact? by soxos · · Score: 1

    If you put the new code together correctly will it form the plans for a dimensional portal?

  37. Old "News" by DrKyle · · Score: 1

    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.

    1. Re:Old "News" by FellowConspirator · · Score: 3, Informative

      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.

  38. Some of this isn't terribly new by PIPBoy3000 · · Score: 3, Interesting

    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.

    1. Re:Some of this isn't terribly new by d3ac0n · · Score: 1
      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 knowledge. I prefer to acknowledge that the complexity of DNA is a fascinating mystery which we have yet to fully unravel.
      --
      Official Heretic from the "Church of Global Warming". Proven right thanks to whistle blowers. AGW = Flat Earth Theory
    2. Re:Some of this isn't terribly new by DigiShaman · · Score: 0, Flamebait

      That's Slashdot for you in that some people here think they know of a "better" solution against something that's worked for billions of years. It's called hubris. It runs rampant on this forum.

      --
      Life is not for the lazy.
    3. Re:Some of this isn't terribly new by budgenator · · Score: 1

      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!

      --
      Apocalypse Cancelled, Sorry, No Ticket Refunds
    4. Re:Some of this isn't terribly new by c0d3h4x0r · · Score: 3, Interesting

      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 can't change one without changing the other. The whole mess is ridiculously intertwined and compounded and pointed back in on itself to the point of being beyond human understanding.

      Changing one bit of a gene inevitably has compounded, far-reaching, unexpected effects that cannot be completely controlled or predicted. You can't think of any part of DNA as having any specific isolated effect on the result, and you can't really hope to create an accurate or complete blueprint of how it gets interpreted to produce the result.

      You can't reverse-engineer something that wasn't engineered in the first place. The design follows from the function, nlike engineering where the function follows from the design. The best way to work with DNA/genetics is to create an environment that selects the desired result, let it run for as long as it needs to generate that result, and then create a "patch" from the diff of the before-and-after DNA.

      --
      Moderator hint: a comment is neither "Flamebait" nor "Troll" if it is true.
    5. Re:Some of this isn't terribly new by The+Mad+Debugger · · Score: 1

      Well, it is one of the three great virtues of a programmer..

  39. Even better idea... by Chabil+Ha' · · Score: 1

    "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" that fills the human g-nome.

    --
    We're all hypocrites. We all have hidden parts, it's the contrast between them that make us more a hypocrite than others
    1. Re:Even better idea... by espressojim · · Score: 1

      I don't buy junk DNA. The reason? There's lots of regions that are not in coding regions, but are conserved (read: the same) with other organisms much higher than chance would predict. These regions have been tested, and found that they are being kept the same under via selection.

      Want to know more? Read Nat Genet. 2006 Feb;38(2):223-7.

      In the interest of full disclosure: I'm one of the authors, and I'm sick of reading about 'junk dna'.

  40. Nobel by Glog · · Score: 1

    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.

    1. Re:Nobel by Jerry · · Score: 1
      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.

      --

      Running with Linux for over 20 years!

  41. you are probably correct by GodWasAnAlien · · Score: 1

    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 single person cannot build a jumbo jet, but thousands of people can.
    (***) Note that we can create machines that can make calculations faster than any human. Note also that we can use software evolution to create efficient algorithms.

    1. Re:you are probably correct by Anonymous Coward · · Score: 0
      blah, blah, blah Our creators used there intelligence, and directed evolution to create us blah blah blah


      What is this "there intelligence"? Is that intelligence that's somewhere else? Over there?
       
      Ah, their certainly using there intelligence over they're, aren't they?
  42. DNA code read backwards ! by Anonymous Coward · · Score: 0, Interesting

    As if superimposing two codes into the same gene (the way the article describes) was not enough, DNA has extra surprises for us. There are genes that code one protein when read normally and another different protein when read backwards. And that's not all. Some genes code for a different second protein when read using different frames (starting points). And yet other genes code for another new protein when the complementary strand is read !

    Our view on life mechanisms was so simplistic at the beginning of our scientific quest for origins. That's why we ended up accepting a theory that postulates mutations as the generator of genetic information ! Knowledge advances incrementally but our mind is so unprepaired and suspicious to the real answer: We've been created ! In an wonderful way...

    1. Re:DNA code read backwards ! by nytes · · Score: 2, Funny

      If you play my genes backwards, you hear a car accident and then someone says "Paul is dead. Paul is dead."

      --
      -- I have monkeys in my pants.
  43. Reproducing accurately and rapidly by Anonymous Coward · · Score: 0

    If you assume error-correcting DNA allows more accurate and rapid reproduction because cell division can be faster and offspring are more likely to be viable (I think those are probably pretty safe assumptions - at least on the single-cell organism level), I'd venture to assert that even a small advantage in reproductive rates would utterly outweigh any lost advantages from any loss of potential genetic variability.

    In other words, having the potential for large evolutionary leaps isn't much help in outcompeting a similar organism that can outbreed you.

  44. Duh!! by Billosaur · · Score: 2, Funny

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

    --
    GetOuttaMySpace - The Anti-Social Network
  45. Just beginning to understand by PineHall · · Score: 1

    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.

  46. For large values of second by iabervon · · Score: 2, Interesting

    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.

    1. Re:For large values of second by cnettel · · Score: 1

      But, if your harddrive was part of an evolving system of self-replicating harddrive, it's fully possible that it would evolve irregularities in the sector markings, as there is no specific "penalty" into moderating a bad gene in that way versus any other, more direct, "method".

    2. Re:For large values of second by madrigalscientist · · Score: 1
      iabervon, your analogy that this new "code" is just a property of the storage medium is true, but you fail to understand why.

      A nucleosome (the bundle of proteins that the authors found tend to attach to certain DNA sequences) is modified in many ways that turn the underlying DNA "on" or "off". The modifications (acetylation and methylation) are critical control points for regulation of gene expression. This is what is refered to as epigenetics http://en.wikipedia.org/wiki/Epigenetics/.

      The code of acetylation and methylation that determines if the underlying DNA is able to be transcribed has been under heavy research for almost a decade. What these author's found is the "code" that determines whether a gene will be placed under this particular form of epigenetic control. Important, but certainly not in the same league as the "code" coined by Francis Crick when he determined which nucleotides translate to which amino-acids.
  47. Epigenetics is the future by Anonymous Coward · · Score: 0

    Those cold, dead sequences of DNA that everyone has been sequencing are only the starting point, not the endgame that some were promising. Those dead letters do not exist like that in living cells. Everything is epigenetic. It is in the runtime. It exists in the living, breathing cells, and not in the literal dead sequences. These histone manifolds are just one piece of the puzzle along with chromatin remodeling and DNA methylation that have been discovered and yet-to-be discovered. Many systems control the runtime expression of genomes, build endogenous stem cell lines and sex cells, and control the growth from embryos to adults. The methylation mysteries started showing up in clones, when nothing in the raw DNA sequence could explain what was different in the cloned adults. Turns out the imprinting (which gene gets expressed - mom or dads? Or even both!) is not stored in the DNA, but in the DNA's methylation patterns. And this pattern can be inherited. Will turn out to be one of many mechanisms.

  48. The answer is... by christianT · · Score: 1

    42

  49. To heck with the code... by kybred · · Score: 1

    What we need to find are the comments!

          if (replication_count < MAX_REP_COUNT){
                  childcell = new Cell;
                  replication_count++; // FIXME: should check for overflow here!
          }

  50. answer from my PhD thesis... by DrKyle · · Score: 1

    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 transposon has gone from genomic invader to a productive member of the gene pool it is said to be domesticated. Over long periods of time (hundreds of millions of years) a lot of the copies of the transposons, which are not necessary, and therefore not selected for, are allowed to mutate, degenerate and appear to be "junk".

  51. God-in-the-Gaps by ACQ · · Score: 5, Insightful

    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.

    --
    Currently theta testing the prototype "Event Horizon" server-scaled desktop box with a 50 Gigameg of Ram.
    1. Re:God-in-the-Gaps by Anonymous Coward · · Score: 0
      there's a surge of morons shoving the word "god"

      ...not to mention the morons that go around calling other people morons for their religious beliefs...

      Just so you know, belief in "god" is a matter of faith, since his existence can neither be proved nor disproved. Your guess on the matter does not constitute justification for passing judgement on others as being "morons". In fact, your willingness to do so very much qualifies you as a moron.

    2. Re:God-in-the-Gaps by Anonymous Coward · · Score: 0

      If it was just about the belief or not of some invisible sky fairy then yes I agree. Sadly its (religion) mostly about ritualistic nonsense and hierarchies of power.

      (I'm not the grandparent btw, just an anonymous coward).

    3. Re:God-in-the-Gaps by ACQ · · Score: 1

      I'm just thankful that the scientific method excludes god(s) and anyone who doesn't is hardly a scientist (namely yourself).

      --
      Currently theta testing the prototype "Event Horizon" server-scaled desktop box with a 50 Gigameg of Ram.
    4. Re:God-in-the-Gaps by Maximilio · · Score: 1
      Just so you know, belief in "god" is a matter of faith, since his existence can neither be proved nor disproved.

      It doesn't need to be disproved. As long as it remains unproven, it can be safely dismissed from any real discussion on the subject.

      Theists often assume that they can play faith on both sides of the argument but forget that non-theists have asserted nothing. They have simply failed to incorporate a fictitious quantity into their world-view. It is not two sides of the same coin.

    5. Re:God-in-the-Gaps by sgt_doom · · Score: 1
      The existence of existence proves the existence. So where does it rain?????

      [If the intelligent were meant to design, there wouldn't be programmers...]

    6. Re:God-in-the-Gaps by mrpeebles · · Score: 1

      I disagree that the non-theist asserts nothing. Certainly the existence of "God" (whatever particular Incarnation you mean, of course, hehe) cannot be proven or disproven. And maybe if you are going to simply take an abstract theological position of "weak agnosticism", then you aren't asserting anything. But if "God exists" were simply an academic question, it would be confined to academia. "God exists" is also a fully religious question, and religion is really about the frailty of the human condition, and personal transformation in light of that frailty. And I think to be a human being, you have to take a position on that, which, incidentally, is why religion has been used so successfully throughout history to control people. The reason that the statement "the Christian God exists" is interesting is that it is an answer for human frailty. It is a promise that there is morality, redemption, and hope despite a world that allows suffering. This may not be the non-theists answer. But to live his (or her) life, he has to have some answer. And even if that answer is as simple as despair, it cannot be based entirely on deductive logic, or on scientific facts, because it is going to be subjective, and logic and science are not subjective. It will depend on something akin to faith, or at least on imagination.

    7. Re:God-in-the-Gaps by Maximilio · · Score: 2, Insightful
      I disagree that the non-theist asserts nothing

      Without going into too much detail, you're wrong.

      OK, some detailBut if "God exists" were simply an academic question, it would be confined to academia.

      It's not an academic question. It's a fundamental assertion regarding the nature of the universe. Theists assert that it was created by God. Non-theists don't. We aren't replacing a logical quantity (GOD) with another quantity. That's something you just don't seem to be able to grasp.

      And I think to be a human being, you have to take a position on that, which, incidentally, is why religion has been used so successfully throughout history to control people.

      No, I don't. My position is, that being's existence isn't real. I don't have to prove anything. I'm not even asserting anything. I'm simply failing to nod my head in agreement when that fictional being's existence is asserted by someone else. The real world is sitting right there in front of us, and it operates just fine whether you believe in God or not. There are a good number of glurge-y myths, often promulgated by 700-club devotees and others, that assert that atheists live some sort of dark, miserable life and are ruinously unhappy and unsuccessful in life but quite frankly they are a load of bull.

      It is a promise that there is morality, redemption, and hope despite a world that allows suffering.

      People choose their moral compass first and then twist their beliefs to fit their actions. And, bluntly, suffering is an unfortunate condition but no one's prayer has ever alleviated it in the slightest -- except in their own minds. If you choose to imagine that the Big Sky Fairy will fix things for you, you may be missing out on the opportunity to take action for yourself, and I am pretty sure many people do.

      But to live his (or her) life, he has to have some answer. And even if that answer is as simple as despair, it cannot be based entirely on deductive logic, or on scientific facts, because it is going to be subjective, and logic and science are not subjective. It will depend on something akin to faith, or at least on imagination.

      I invite you to read the book in my .sig. You can listen to it for free on podiobooks.com if you like. Because that's what it's allllll about.

    8. Re:God-in-the-Gaps by mrpeebles · · Score: 1

      Theists assert that it was created by God. Non-theists don't. We aren't replacing a logical quantity (GOD) with another quantity. That's something you just don't seem to be able to grasp.

      To simply state "God created the universe" is a boring statement. The real argument is over what this statement means. What sort of "God" created the universe. Does He care about human beings? Is He rational? Does answering these questions twist our concept of God so profoundly that it isn't really relevant to ask the question anymore? And you seem to want to divide the world into "theists" and "non-theists". And your division of everybody into "theists" and "non-theists" seems very artificial to me. Where does Einstein, a pantheist, fall into your categorization? He believed in God as the Universe, which I think must be intimately connected with his dream of a single, unifying equation of physics. Or the enlightenment Deists?

      We aren't replacing a logical quantity (GOD) with another quantity. That's something you just don't seem to be able to grasp.
      I agree with this statement. What I'm saying is that the expression "God exists" is really only interesting because it is only a kind of short hand for a lot of other statements.

      No, I don't. My position is, that being's existence isn't real. I don't have to prove anything.
      My statement was that you have to take a position on the frailty of the human condition, not on the existence of God. Hell, the logical positivists would (I think) claim that the existence of God isn't even a meaningful question, so they certainly haven't taken a position of the existence of God (which doesn't even mean anything if you are a logical positivist, since it doesn't have any empirically observable implications.) My points is that no human being can really simply say "God doesn't exist." This is just shorthand for another set of answers, typically a sort of scientific-reductionist kind of humanism, which is fine.

      If you choose to imagine that the Big Sky Fairy will fix things for you, you may be missing out on the opportunity to take action for yourself, and I am pretty sure many people do.
      Yes, Christianity believes in a "Big Sky Fairy" that orders its people to commit genocide, sacrifices its own son on the cross, and condemns people to eternal fire for enjoying a piece of fruit. As you might be able to guess, I think this is a terrible misrepresentation of Christianity. If nothing else, Christianity is a great work of art that tries to wrestle with why life can be so wonderful and so terrible. You might disagree with its answers (assuming it offers any), but you cannot escape its questions. It is a testament to the power of Christian imagery and language that a Christian can seem to sum up all his answers to these many questions with the statement "I believe in God, and in Jesus." But the non-Christian cannot also answer all those questions with the statement "God does not exist." So after he makes that statement, he still must answer these other questions which are not in the "yes or no" format (like, for example, in light of all the pain we experience in life, where do we draw hope?). Incidentally, I understand that atheism doesn't necessarily lead to despair.

      I can't find what book you are talking about (I guess I don't know how to read your .sig) so I have no idea if you are agreeing with me or not :-P

    9. Re:God-in-the-Gaps by Anonymous Coward · · Score: 0

      I can't help but make this comment: As usual there's a surge of can't get a longs shoving the word "morons" in where the words "To each his own" should be used instead.

      Please tell me Mr. Smarty Pants, how is it humans singularly (came to be) (evolved)
      above all other creatures?

      Yea, Yea, Science has the answer for everything...

      Science is just the study of things we don't understand.

    10. Re: God-in-the-Gaps by Black+Parrot · · Score: 1

      > there's a surge of morons shoving the word "god" ...not to mention the morons that go around calling other people morons for their religious beliefs...

      I don't think it was a dig at religious beliefs per se, but at the foolish notion that this or that discovery is evidence for a religious belief.

      > Just so you know, belief in "god" is a matter of faith, since his existence can neither be proved nor disproved.

      So you seem to share the same sentiment.

      --
      Sheesh, evil *and* a jerk. -- Jade
  52. A new "twist" in an OLD OLD story... by posterlogo · · Score: 5, Informative

    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", which is "the study of reversible heritable changes in gene function that occur without a change in the sequence of nuclear DNA".

    1. Re:A new "twist" in an OLD OLD story... by Anonymous Coward · · Score: 0

      >We have known for decades that histones bind DNA
      >and organize it (into nucleosomes), periodically, all along its length.

      Your parties are kind of dull, and you come off as condescending. If you want a rockin' party, hang out with the Physicists.

    2. Re:A new "twist" in an OLD OLD story... by Malacca · · Score: 1
      DNA topology has long been a subject of study as has Knot Theory as it pertains to DNA strand topology. The idea being that more exposed DNA is more likely to be active. DNA doesn't really exist in cells in 'naked' form but attached to nucleosomes which are a sort of scaffold. Segal et al.'s work appears say that based on DNA sequence, they can predict which bits of DNA are associated to nucleosomes. Bear in mind that their model isn't (yet) complete (emphasis mine):

      "Our results demonstrate that genomes encode an intrinsic nucleosome organization and that this intrinsic organization can explain approx 50% of the in vivo nucleosome positions.

  53. Epigenetics by jbeaupre · · Score: 1

    Personally, I find epigenetics http://en.wikipedia.org/wiki/Epigenetics more interesting than this article. It also explains the "mysterious process" of cell types.

    --
    The world is made by those who show up for the job.
  54. Re:Don't worry by Anonymous Coward · · Score: 0

    Secretary: Mr. President, it's God on the red phone.
    Bush: Make him hold.
    *ten minutes later*
    Bush: Yeah?
    God: Sorry to interrupt. I just wanted to call and ask if you could stop killing innocent people.
    Bush: F&"! You!
    God: C'mon, it's not nice to kill innocent people and provoke wars around the world. Could you at least back up a bit?
    Bush: *hangs up the phone*

    You don't mess with higher powers. Bush is above law, above God and you should not speak against him. (Or you end up in some distant resort and learn some new hobbies like waterboarding.)

  55. junk press, junk science by Anonymous Coward · · Score: 4, Interesting

    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

    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.

    1. Re:junk press, junk science by Anonymous Coward · · Score: 0

      This reminds me of something called the "finger print of god" that I read a while ago. Something about a secondary sequence in DNA that explains something using toruses and vortex.

      What? Go Google it.

    2. Re:junk press, junk science by Anonymous Coward · · Score: 0

      Hear, hear! (We're giggling too)

  56. Evolution, Schmevolution, let's just talk science by chloroquine · · Score: 2, Insightful
    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, and so on. If it is as bad, then we should all go with our pitchforks and torches and demand that the monster be delivered to us so we can fix the problem.

    The only way this code was hidden was that we didn't know about it before. It took a whole bunch of yeast work and number crunching to see it.

  57. :o by supermegadope · · Score: 1

    "There are about 30 million nucleosomes in each human cell. So many are needed because the DNA strand wraps around each one only 1.65 times, in a twist containing 147 of its units,..."

    1.65 hmmmmm thats awfully close to .....1.618 The Divine Proportion....damnit i was soooo close to finding the meaning of life this time!

    SMD
    over and out

    1. Re::o by Anonymous Coward · · Score: 0

      add pi/100 to the divine proportion and you've got it.

  58. Link o the original Nature paper by Anonymous Coward · · Score: 0
  59. Strawman by geoffrobinson · · Score: 1

    The argument those of us are making is more complex than "we don't understand it, therefore God."

    The arguments are closer to "the more you understand, the better our case is."

    --
    Except for ending slavery, the Nazis, communism, & securing American independence, war has never solved anything.
    1. Re:Strawman by ACQ · · Score: 1

      If your argument stems from the complexity of such things as proof of a higher being(s), then I must quote Werner Heisenberg: "We have to remember that what we observe is not nature herself, but nature exposed to our method of questioning." Our method of questioning has invented complexity as a benchmark for comparison. Our problem is that our minds are extremely limited and that makes us go "oooh look at that, where'd it come from?!" The universe just is the way it is and we're temporarily here for the ride. We believe what we want whether it's correct or not. Scientific facts are all we have to go on.

      --
      Currently theta testing the prototype "Event Horizon" server-scaled desktop box with a 50 Gigameg of Ram.
    2. Re:Strawman by bmajik · · Score: 1

      You should take a peek at the book "A new kind of science", by Wolfram (yes, that Wolfram). I picked it up on the dollar shelf at B&N and it has been pretty interesting.

      Wolfram's fundamental premise (so far -- it's a huge book that i've barely gotten into) is that science, and observational knowledge in general, seems to be filled with the idea that apparently complex behavior requires complexity in the underlying rules.

      Wolfram uses analysis of cellular automata and other "programs" to show that this is grossly inaccurate - that certain systems with trivial rules generate tremendous complexity.. (others generate apparent "randomness" but the most interesting are neither random nor repetitive.. but somewhere inbetween.. a structure that you could't predictively determine without simply running the program to completion, and when you are done, the result has clear indications of intelligence or informational coding, but yet remains unpredictable)

      I happen to be a religious person but my faith is not hinged on any particular version of a story about how the universe works. I beleive that we were given senses to learn about the world around us, and i beleive that while certain "scientists" may have anti-theistic motives and biases, that in aggregate, there is not a grand unified conspiracy to distort the truth in the name of non-theistic goals. If "evil", such as it is, had the power to aggregately distort all of mans senses, then axiomatically, nothing can be beleived in.

      Finally, where there lies an apparent contradiction beween observed science and biblical accounts of the same or related phenomena, i temper my own analysis with the following guiding principles:

      - God designed our senses, and the rules of the universe
      - There is a high correlation between the importance of something and the frequency and non-subtlety with which its specific details show up in the religious text
      - Our observations, measuring devices, and theoretical models about our world are simply that - approximations, observaions, and models. They continue to converge on reality, but are never quite there.
      - I don't think God has stacked the deck against us - intentionally making things seem one way when they're really something quite different.
      - In the history of mankind's battle between "science" and "religious dogma", more harm has been commited on the side of those in religious power that claim to have the sole interpretation of scripture than those that claim to have the sole interpretation of physics. I'll continue to bet on the physicists.

      It is not my life mission to resolve apparent contradictions between observational science and reading scripture. The number of human-perceivable-time-units over which the earth was formed has no bearing on how i live my life, so if I am a little confused about it taking 5 billion years, 6 days, or something else entirely, I figure I'll either die confused and my skin cells wont much care as thev're turned into worm food, or it will be "Standard Question #938230" on a poster in the waiting room outside of Heaven.

      So, I'm not going to sweat it, and I'm not going to rely on a "God of the Gaps".

      --
      My opinions are my own, and do not necessarily represent those of my employer.
    3. Re: Strawman by Black+Parrot · · Score: 1

      > Wolfram's fundamental premise (so far -- it's a huge book that i've barely gotten into) is that science, and observational knowledge in general, seems to be filled with the idea that apparently complex behavior requires complexity in the underlying rules.

      Wolfram doesn't seem to understand science. The whole history of science has been an attempt to explain complex phenomena by means of relatively simple rules.

      --
      Sheesh, evil *and* a jerk. -- Jade
    4. Re:Strawman by geoffrobinson · · Score: 1

      There is a difference between complexity and intelligence.

      Simple solutions are sometimes the most elegant, beautiful, and intelligent.

      Also, complexity in and of itself does not mean it is a sign of intelligence. A big pile of rocks could be arranged in a complex way. A smaller pile of rocks which say "Welcome to Hollywood" may be less complex but conform to a pattern which we recognize as being caused by an intelligent agent.

      I would also add that if you are theist, simplicity, beauty and intelligence going together (and the fact they are all immaterial concepts) should come as no surprise.

      --
      Except for ending slavery, the Nazis, communism, & securing American independence, war has never solved anything.
  60. Don't try to rehash the 2nd law of thermodynamics by Anonymous Coward · · Score: 0

    I'm just not going to expect a net increase in information based on new cards appearing.

    Repeat after me until it sinks in:

    "The Earth is not a closed system."

  61. Re:Don't try to rehash the 2nd law of thermodynami by geoffrobinson · · Score: 1

    I wasn't referring to the 2nd law of thermodynamics. I was referring to information.

    --
    Except for ending slavery, the Nazis, communism, & securing American independence, war has never solved anything.
  62. Correction by Aqua_boy17 · · Score: 1
    Mmmm, a histone of peas... Seriously, let me be the first to say: I smell a Nobel prize for this one.
    Obiviously this would be a Nobel Peas prize.

    Some jokes just write themselves.
    --
    What if the Hokey Pokey really is what it's all about?
  63. New code found by Improv · · Score: 3, Funny

    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!"

    --
    For every problem, there is at least one solution that is simple, neat, and wrong.
    1. Re:New code found by Improv · · Score: 1

      Errmmm, I mean delight to replace the last "surprise". So much for humour. Damn.

      --
      For every problem, there is at least one solution that is simple, neat, and wrong.
    2. Re:New code found by MadCow42 · · Score: 1

      Please, oh PLEASE God, don't tell me I'm written in Perl! I would like to think that I'm maintainable by someone other than just the original coder on a good day.

      --
      I used to have a sig, but I set it free and it never came back.
  64. Hmmm... by kzinti · · Score: 1

    Darwin's Radio? (Greg Bear)

  65. Too randomly by phorm · · Score: 1

    Changing too rapidly, or too randomly, is as dangerous to an organism as not adapting fast enough

    As in cases of cancer, mutation, and other such things. We want our bodies to adapt, but not necessarily mutate (and I don't mean in the X-men way)

  66. Re:Don't worry by shaitand · · Score: 1

    Sounds like a legitimate point, not a troll.

  67. Ever get tired of spewing bullshit? by Maximilio · · Score: 1
    Knowledge advances incrementally but our mind is so unprepaired and suspicious to the real answer: We've been created ! In an wonderful way...

    I mean, honestly. The creationist tactic of taking plausible-sounding premises and coming up with utter bullshit conclusions is frustrating, amusing, and finally just boring. You've said nothing of actual useful interest here, and it's a good solid bet that 90% of the premises you've put forward are complete garbage anyway. You numbskulls do not now and never will understand what science is actually about. Real knowledge is real power. Fake knowledge will give you the illusion of power, and the moment the sand shifts under your feet you will have nothing except a bunch of people laughing at what jackasses you are.

    1. Re:Ever get tired of spewing bullshit? by Anonymous Coward · · Score: 0
      it's a good solid bet that 90% of the premises you've put forward are complete garbage anyway

      Please refrain from betting against your chances because the premises are simply true and backed by the experimental science. Multiple coding in some particular genes (the ways described above) is a scientific reality. I mean, you're selling experimental truths for an unexperimented hypothesis. And then you talk about fake knowledge, the "illusion of power" and the sand shifing under someone else's feet.. Strange !
  68. Redundant? by Anonymous Coward · · Score: 0

    That's a little unfair considering the posts came in within one minute of each other.

  69. Re: Rainbows, God, and Physical Laws by Anonymous Coward · · Score: 0
    The problem with this silly statement is that it would mean that there were no rainbows before the flood, and that the laws of physics were changed to enable rainbows to appear.
    I don't really care to argue this one way or the other, particularly on Slashdot of all places, but if one presupposes an external being capable of creating the entire universe and comprehending every bit of it past, present, and future, it's not really much of a stretch to presume that being is also capable of manipulating physical laws as it sees fit. There are "Christian science" (I know, I know) explanations involving things like a pre-flood "vapor canopy" that would've prevented rainbows from being observed, but really, an omnipotent God doesn't need to play by the universe's rules.

    If you want to argue properly against the existence of God, you'll need to at least do a little reasoning.
  70. Ummmm... by Seoulstriker · · Score: 1

    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 cells.

    DNA is the fundamental unit of information, which is the source of all gene regulation. If the DNA wasn't what it was, nothing would work in the cell. Afterall, "junk DNA" as you call it is not junk and is responsible for gene silencing (microRNA) other forms of gene regulation.



    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.

    To claim that you are smarter than the creator of the universe is pure hubris. Who are you, o little man? You are but a speck in the ocean of the universe.

    --
    I am defenseless. Use your button. Mod me down with all of your hatred.
  71. Argument from Personal Incredulity by jpetts · · Score: 2, Informative

    This is called the argument from personal incredulity, and is a favourite of the IDers. See http://www.millerandlevine.com/km/evol/design2/art icle.html for an excellent example of how this argument fails spectacularly with the nature-evolved wheel, the eubacterial flagellum.

    --
    Call me old fashioned, but I like a dump to be as memorable as it is devastating - Bender
    1. Re:Argument from Personal Incredulity by jpetts · · Score: 1

      Apologies: Miller's article refutes the argument from irreducible complexity, not personal incredulity: the latter hardly needs refuting.

      --
      Call me old fashioned, but I like a dump to be as memorable as it is devastating - Bender
  72. Quantify by Maximilio · · Score: 1
    Let's break this one down, shall we? The argument you claim you've made (which is actually nothing more than a categorical assertion that something is true), goes like this: as we increase our understanding of DNA encoding, we increase the amount of evidence in favor of an Intelligent Encoder. Is that what you're trying to say? In that case you've got some hidden premises to explain which, I think, brought out in the open would shrivel like bugs on a hibachi grill.

    Without being able to view your premises I can only guess at what they are, but I assume they include ideas like "irreducible complexity" which has been violently debunked a number of times now.

    Also there's the simple matter of a testable hypothesis, which by the very definition that is given is impossible. In the meantime, real scientific knowledge advances despite all Creationist efforts to prevent it. I find it variously hilarious and very irritating (as I've posted before) that Creationists try to glom onto every new scientific fact before it can get out into the world and cast it as some sort of religious revalation. The problem is, and has been, that if you come up with bogus conclusions and are later trumped by reality, you end up looking just plain stupid.

    But that's a choice you make for yourself. Filling in the gaps with God has been the tactic for centuries and we can always look back into the past and see that in those gaps were always more revealing and far more compelling real-world explanations than the unimaginative God-obsessed dullards could ever come up with. Fake knowledge is fake power. Real understanding leads to real illumination. I always prefer the real thing.

  73. Some clarification by PIPBoy3000 · · Score: 1

    I suppose by "semi-permanent", I meant that methylization was a fairly sturdy structure compared to other methods of blocking transcription. This is in comparison to RNAi, which is fairly temporary.

    DNA is the fundamental unit of information
    I suppose we could go over semantics forever. Lots of stuff carries information. I'd argue that everything carries information in some form or another. Prions, viruses, and raw RNA seem to do just fine without any DNA. What I was trying to get across is that there were lots of biological mechanisms that carried and processed information, not just DNA.

    To claim that you are smarter than the creator of the universe is pure hubris.
    Guilty as charged. :)
    I am tempted to summon Occam's Razor in this case. It's sort of like the "Little Man in the Coke Machine" argument. Sure, the Coke cans might be dropped down by a little man inside the vending machine when I put in my money. The simpler mechanical answer is more likely, though.

    In this case, I'd argue that a super-intelligent being might take pity on me and make DNA that didn't fall apart and get cancer, make my knees non-screwed up, and my sinuses drain outside my body instead of down my throat.

    Who knows? Maybe the universe was created by a Book of Job God who likes to punish us to teach us to be good. I never did understand the part about Job being okay with getting a new wife after God killed off his old one, but maybe Job was a swinger or something.

    Sorry for wandering off topic. I blame the coffee.

    1. Re:Some clarification by cagle_.25 · · Score: 1
      I never did understand the part about Job being okay with getting a new wife after God killed off his old one, but maybe Job was a swinger or something.
      It doesn't actually occur in the book of Job. He loses his kids, but the wife lives. Ironically, she is one of his sources of stress (Job 2.7 - 10).
      Who knows? Maybe the universe was created by a Book of Job God who likes to punish us to teach us to be good.
      That part doesn't happen, either. Job never finds out why he has been singled out for smackery. In fact, his friends articulate the view that suffering is either punishment for your past sins (Job 18) or else a way to teach you a lesson (Job 22). They are positive that Job must have done something to deserve it all. But in the end, God is angry at them for their blasphemy and (more irony) makes them ask Job to pray on their behalf so that God won't smack *them* (Job 42.7 - 9).
      --
      Human being (n.): A genetically human, genetically distinct, functioning organism.
  74. Organic Software by Scottux · · Score: 3, Interesting

    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.

    --
    -Scottux
  75. Re:So wait ... wait wait... don't TELL me... by davidsyes · · Score: 0, Troll

    the mod who gave me 0, troll must be a hyper-reactionary religious nutcase, or must be an employee or benefactor of the pharma/biomeds, or both... or something else...

    Any astute person would realize a wee bit of irony and sarcasm (and poor wit, too) in my previous post: IF "god" didn't want humans to access the DNA, then "god" would have used his/her/its hand to keep humans out.

    Now, I'll chance the bush-clan reaction:

    IF "god" is allowing scientists to access the "wrapper" or second DNA layer just (supposedly just) discovered, then the administration has no fucking business calling the shots. Fortunately, OTHER countries are seeing fit to exploit this information. I just hope the exploitation is for the GOOD injured/defect-affected and not JUST the PROFIT of some businesses.

    Shee, some people need to get some sex (or, to borrow a phrase from the auto-checkout thread... some "electron-auto-erotic strangulation stimulation) and lay off the 0, troll mod power...

    --
    Previously: "Linux... Toward the Sunrise..." Now: "Linux... Toward the-- No, now, part of Every Sunrise"
  76. Re: Rainbows, God, and Physical Laws by Anonymous Coward · · Score: 0

    For God to "play by the universes" rules means that God isn't what he says he is.* The thing about evolution and chance, is that there isn't as much failures as you'd expect given the time scope.

    *Side note. If there's no God, doesn't that mean there's no Devil too? I don't see too many fights breaking out over that aspect of the issue.

  77. At last! by Seroster · · Score: 1

    Message finally revealed to be: "All your bases are belong to us..."

  78. suggested reading ... by madhippy · · Score: 1

    any biologists have any recommended reading / courses for this kind of stuff ... ie what's the best starting point etc

    I've been reading a lot of Richard Dawkins - find it interesting - gave up biology at GCSE level (exam in UK we take at 16yo) - but could do some OU (www.open.ac.uk) courses etc.

    1. Re:suggested reading ... by drunken_boxer777 · · Score: 2, Interesting
      If you had some basic biology, have an interest in learning more, and aren't afraid of a little chemistry, then I recommend "Molecular Cell Biology" by Harvey Lodish et al. (This was one of my college textbooks.) A new edition is pricey (~US$120), but you can buy the old edition (1999) on Amazon.com for cheap (as low as US$2.20!), which should suffice.

      The book starts off describing cells, their components, and some chemistry involved. It goes on to discuss genetics, cell energetics, and cell-cell communication. The authors use and explain the scientific terminology (unlike the NYT), but don't get bogged down in detail that will confuse someone 'new' to biology, IMO.

      If you read and understand a book like this, then you will be able to read and understand any science article in a newspaper or lay magazine easily. You'll probably be able to understand the original scientific articles, to some degree.

    2. Re:suggested reading ... by madhippy · · Score: 1

      cheers for that - I've added it to my favourites in amazon - from the uk it's about 47pounds ... only a little cheaper used ...

  79. Re:Don't try to rehash the 2nd law of thermodynami by The+Only+Druid · · Score: 1

    The 2nd Law of Thermodynamics is that closed systems move towards greater states of entropy, i.e. disorder. The appearance of more order in an isolated area of a closed system (i.e. more information) is not problematic so long as the sum entropy of the whole system is not reduced.

    The point is that the 2nd law is about information.

    --
    "Stumble before you crawl"
  80. Re:So wait ... wait wait... don't TELL me... by Anonymous Coward · · Score: 0

    from the mod: I didn't mod you down for your point (which, reading between the lines, was somewhat insightful), I modded you down because fully half the post was trite, off-topic, and deliberately inflammatory: "the kind that certain people prefer to kill in the name of", "Some god...Maybe 'god' needs an upgrade or two?"

  81. Publicity Stunt by mdm001 · · Score: 1

    With loose hanging comments like: "I think it's really interesting," said Bradley Bernstein, a biologist at Massachusetts General Hospital. and a link to the hospital web site, I think this article was for publicity purposes and nothing else. It really says nothing new, nothing that matters and nothing for nerds. Who let this one through the editorial process?

  82. OO by kushboy · · Score: 1

    So it's like Object Oriented Genetics?

  83. As my spelling Nazi cousins I feel the need to... by CyberLord+Seven · · Score: 1
    ...correct you. There is no such thing as an "egg cell". Human females produce Oocytes. They are not considered to be cells because they do not have a complete genetic package. Human males produce spermatocytes. They are not cells either for the same reason.

    While I'm on the subject, there is no such thing as a red blood cell or white blood cells. These objects are corpuscles, or bodies, not cells because they have no genetic material.

    Now, what kind of a Nazi am I?

    You're not allowed to bring up Goodwin's Law. :)

    --
    We have always been at war with Eurasia!
  84. Re:So wait ... wait wait... don't TELL me... by Anonymous Coward · · Score: 0

    Making a point that isnt understood by all will only get you in trouble faster.
    Although i had a good laugh at that one. Good job from me^_^

  85. [OT] I must be new here by espressojim · · Score: 2, Insightful

    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*

    1. Re:[OT] I must be new here by Eivind+Eklund · · Score: 1
      We need a "Wrong" moderation. Seriously. Moderators do not read the replies, so replying with an explanation do not work.

      Preferably, it would also be possible to post an explanation of why it is wrong at the same time, without that "Cannot post and moderate" restriction.

      Eivind.

      --
      Doubting the existence of evolution is like doubting the existence of China: It just shows that you're uninformed.
  86. Re:Don't worry by Anonymous Coward · · Score: 0
    Sounds like a legitimate point, not a troll.


    Yeah, it's a valid point, but it's also against Bush and therefore violates Patriotic Act, I love USA Act, We Praise George W Bush Act and All Your Base Are Belong to US Act.

  87. Re: Rainbows, God, and Physical Laws by ichigo+2.0 · · Score: 1

    Isn't that similar to the ID argument? How the hell can we use science to deduce if a external being has changed the laws of our universe and is able to manipulate time at will? I was just pointing out that it doesn't matter if we could scientifically deduce how rainbows could have been created by god, because we first have to make a faith-based assumption that god did create rainbows.

  88. Wonderment by rayk_sland · · Score: 1

    Wheels within wheels, code within code. How much more intricate can it get?

    --
    Jedis are stupid. If they were so powerful, why couldn't they handle counseling for a kid who missed his mom?
  89. Inquire here for information by Henge · · Score: 1

    I actually did a short research rotation in Jon Widom's lab at the beginning of grad school, 3 years ago. If anyone has any more specific questions regarding the implications of this work, let me know and I'll post something useful.

  90. I take your point but... by Any+Web+Loco · · Score: 1

    I'm not a biologist, and as much as I'm interested in this kind of thing I don't have the time, inclination or background to keep up with such old, old stories.

    Sure, it's a hot headline & ./ may have been hoodwinked by it, but I don't really mind - one of the great things about /. is that when you get an article like this, folks who actually *do* know what they're talking about will chime in with links to better info, better commentary, explanations of their own... which means that I get to vaguely edumacate myself over lunch.

    It's not like it's another "Google releases x beta" story - it's a starting point for discussion. Just my £0.018

    1. Re:I take your point but... by posterlogo · · Score: 1

      Touche!

  91. Sounds like C++ by gravy.jones · · Score: 0

    The paraphrase sounds like it could be describing a C++ class with protected members and friend classes.

    --
    Where's the 0xBEEF
  92. Histones are nothing new by BluSteel · · Score: 1

    I am a Molecular Biology major. Biologists have known about histones (that's what they are called) for years now. I don't see how the NYtimes can play this up as something new.

  93. Re:So wait ... wait wait... don't TELL me... by davidsyes · · Score: 1

    I am DEFINITELY on the wrong planet...

    --
    Previously: "Linux... Toward the Sunrise..." Now: "Linux... Toward the-- No, now, part of Every Sunrise"
  94. thank you by Anonymous Coward · · Score: 0

    thank you for reading my useless post.
    thank you for pointing out "their". please inform the editors.

  95. dna (tagging beta) by Bruce+Losis · · Score: 1

    Did anyone else think this was a perfect summary of TFA?

    --
    Don't believe the nonsense, unless you hear it from me directly.
  96. Self-encapsulating DNA ? by themoneyish · · Score: 0
    "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."

    Sounds like data security and C++ encapsulation ;)
  97. Junk DNA isn't really Junk by vivin · · Score: 1

    To add to what you said, I read an article in Scientific American a few years ago (The Hidden Genetic Program of Complex Organisms, John S. Mattick, Scientific American, October 2004, p62).

    It seems that the "junk DNA" may actually code for RNA molecules that perform a bunch of regulatory functions. Removing some of this "junk DNA" seems to have ill effects on some organisms.

    There's also more here.

    --
    Vivin Suresh Paliath
    http://vivin.net

    I like
  98. We'll Return, After This Message by KlaymenDK · · Score: 1

    My first thought was "oh my $DEITY, they *ACTUALLY* found it". But thun again, of course I've been reading too much sci-fi. It's just that this one story ....... well, here it is:

    "We'll Return, After This Message" by John Walker, December 1st, 1989
    http://www.fourmilab.ch/documents/sftriple/gpic.ht ml

  99. Re:As my spelling Nazi cousins I feel the need to. by VdG · · Score: 1

    Whilst (mature) red blood corpuscles don't have nuclei, I was under the impression that white blood cells are genuine cells, and do have nucleii.

  100. Oh bad! by ebvwfbw · · Score: 1

    Looks like all that time they took to map the human genome could be a waste of time. They may have to do it all over again.

  101. I dont believe in junk DNA by peter303 · · Score: 1

    Nature wouldn't evolve as system as wasterful as 2-3% useful DNA (0.1% in some amoebas). The other stuff is doing something, either rarely used or relatively transient.

  102. Amen. by 2names · · Score: 1

    Also Wik.

    --
    "I'm just here to regulate funkiness."
  103. Re:Don't try to rehash the 2nd law of thermodynami by geoffrobinson · · Score: 1

    No. It is about entropy, not information. They are different categories.

    --
    Except for ending slavery, the Nazis, communism, & securing American independence, war has never solved anything.
  104. Re:As my spelling Nazi cousins I feel the need to. by 955301 · · Score: 1

    Let me correct your correction then. Once the sperm enters the Oocyte it is then considered a cell. It's after this point that the mitochondria introduced by the sperm is destroyed. Clearly it wouldn't have happened before because the mitochondria wasn't in the Oocyte. The embryo is the egg cell I speak off, not the precursory elements of it.

    --
    You are checking your backups, aren't you?
  105. Explains genetic code redundancy? by barakn · · Score: 1
    From the article:

    In the genetic code, sets of three DNA units specify various kinds of amino acid, the units of proteins. A curious feature of the code is that it is redundant, meaning that a given amino acid can be defined by any of several different triplets. Biologists have long speculated that the redundancy may have been designed so as to coexist with some other kind of code, and this, Dr. Segal said, could be the nucleosome code.

    Except that the amino acid code existed in Bacteria long before the Eukarya and Archaea, and Bacteria don't have histones, the core feature of nucleosomes. There may be another code that explains the redudancy, but it's probably not a nucleosome code.
    --
    "I'm so moist I'm sticking to the leather." -Kermit the Frog on The Late Late Show