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Biotech Science

Opposable Thumbs and Upright Walking Caused By "Junk DNA" 215

Posted by Soulskill
from the stranded-pairs dept.
quinnlynn writes "A group of research scientists at Yale discovered that the evolution of opposable thumbs and upright walking in humans is due to changes in the genome in the areas still classified as "junk DNA." Quoting: 'Results from a comparative analysis of the human, chimpanzee, rhesus macaque and other genomes reported in the journal Science suggest our evolution may have been driven not only by sequence changes in genes, but by changes in areas of the genome once thought of as "junk DNA." ... Researchers have long suspected changes in gene expression contributed to human evolution, but this had been difficult to study until recently because most of the sequences that control genes had not been identified. In the last several years, scientists have discovered that non-coding regions of the genome, far from being junk, contain thousands of regulatory elements that act as genetic "switches" to turn genes on or off.'" Yale has also recently completed sequencing the Trichoplax genome. Trichoplax has the simplest known animal genome, and it shares 80 percent of its genes (comprised of 98 million base pairs) with humanity. Professor Stephen Dellaporta was quoted saying, "We are [excited] to find that Trichoplax contains shared pathways and defined regulatory sequences that link these most primitive ancestors to higher animal species. The Trichoplax genome will serve as a type of 'Rosetta Stone' for understanding the origins of animal-specific pathways."
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Opposable Thumbs and Upright Walking Caused By "Junk DNA"

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  • by ColdWetDog (752185) * on Sunday September 07, 2008 @11:40AM (#24910669) Homepage
    Sometimes these factoids scare the coffee out of me ...

    ... still unknown whether HACNS1 causes changes in gene expression in human limb development or whether HACNS1 would create human-like limb development if introduced directly into the genome of a mouse.

    When shall we welcome our furry, opposable thumbed overlords. Could Douglas Adams had been right all along?

  • by MarkusQ (450076) on Sunday September 07, 2008 @11:45AM (#24910715) Journal

    Every time early researchers solve part of a problem they seem to label the part they haven't solved as being unimportant or irrelevant.

    You found out what 10% of the brain does (the sensory/motor areas)? The other 90% must not be used for anything.

    Find out how to read the DNA code used for a few percent of the genome (the codons to protein via RNA parts)? The rest must be junk.

    When will we learn? Writing "Here there be dragons" at least had to benefit that it led future explorers to (correctly) assume that these places might have something interesting in them.

    --MarkusQ

    P.S. I can't do car analogies, but for the last fifty years or so we've known how to extract strings from the data segment and thought we understood "the" genetic code. Now it's turning out that all that "junk DNA" in the code segment actually has a significant regulatory role in deciding which strings get printed, and when. Who would have guessed?

    • by thermian (1267986) on Sunday September 07, 2008 @12:02PM (#24910865)

      Actually its been widely known that 'junk DNA' does have an active role for a long time. The big problem is identifying which bits of it are responsible for regulation/transcription.

      The main problem with the public's perception, and indeed that of some scientists, is the continued use of the term 'junk DNA' when the concept it embodies has been thoroughly discredited.

      For the moment a lot of work does discount area's of DNA for which there isn't enough background information, but that's more to do with the need to make progress on the bits we understand, rather than to avoid looking at the junk.

      This is likely why so many people still think that Junk DNA is a thing that we actively avoid. It isn't.

      • Call it "Dark DNA" (Score:3, Insightful)

        by Colin Smith (2679)

        Apparently 90% of the universe is made of some weird useless stuff. Might as well use the same term for stuff we don't understand.
         

        • And all things that are not yet discovered could be called 'dark inventions'. I can imagine that the extra load of SINEs and LINEs could act to slow the replication process of the cell to make cell replication slower and more stable or that it could change the synchronization of different parts or act to increase the diffusion distance between one part and other.
      • by Cyberax (705495) on Sunday September 07, 2008 @12:35PM (#24911169)

        Not exactly. We _know_ that a large part of DNA (about 40%) is junk, because it consists of simple repeating sequences (LINEs and SINEs).

        It might have some indirect functions (like working as a buffer for mutations), but it's junk by itself.

        There's also a fair amount of inactive genes and other junk.

        • Re: (Score:2, Insightful)

          by iNaya (1049686)

          AFAWK

          Until we've correlated every function of the human body to a gene, how can we discredit any part of the sequence as doing nothing?

          • Re: (Score:3, Informative)

            by Cyberax (705495)

            Because we already know some things about the genome as a whole.

            SINEs and LINEs do nothing - they only propagate themselves (http://en.wikipedia.org/wiki/Short_interspersed_nuclear_element).

            Inactive genes are just that - inactive. They can't be transcribed because they lack crucial parts.

            However, some parts of the DNA which were first identified as a junk do have useful functions and are called 'non-coding DNA'.

            • A strange thing happened, I removed the junk data ( sync preamble ) from my floppy disk encoding and it quit working. I agree that SINEs and LINEs are less of a factor than others but a system is responsive to all its parts and until somebody makes a human clone with all the short and long repeats removed I assume that it does something, even if it just makes a different sync preamble or a getter ( to use a radio tube analogy ) for other junk.
              • by Cyberax (705495)

                We have an animal with almost none of DNA junk - it's the famous pufferfish. It seems that it doesn't cause them any problems.

              • by CharlesEGrant (465919) on Sunday September 07, 2008 @08:57PM (#24915139)

                A strange thing happened, I removed the junk data ( sync preamble ) from my floppy disk encoding and it quit working. I agree that SINEs and LINEs are less of a factor than others but a system is responsive to all its parts and until somebody makes a human clone with all the short and long repeats removed I assume that it does something, even if it just makes a different sync preamble or a getter ( to use a radio tube analogy ) for other junk.

                At an abstract philosophical level you have a point, but by the same token you wouldn't let a doctor remove a wart from your finger, because we can't be sure that the wart doesn't play some unknown role in maintaining health. Practically, quite a bit of evidence shows that warts play no significant role in maintaining health, and can be removed safely. There is a LOT of evidence that LINEs and SINEs are simply 'scars' left by a parasitic attack, much like a wart. Large segments of "junk" DNA have been removed from mice [bioedonline.org] with no apparent ill effect to them or their progeny.

            • Re: (Score:3, Informative)

              by lawpoop (604919)

              SINEs and LINEs do nothing - they only propagate themselves.

              C'mon -- you don't really know that they do nothing. Perhaps they're useful when winiding DNA into chromosomes, or have some larger scale structural purpose, rather than just coding genes.

              Here's a quote from the very article [wikipedia.org] you linked to:

              "With about 1 million copies, SINEs make up about 13% of the human genome.[8] While previously believed to be "junk DNA", recent research suggests that both LINEs and SINEs have a significant role in gene evolution , structure and transcription levels[9]. The distributio

        • But if it's useless, it ought to be more prone to mutations, and should by this time end up as random noise.
          Note: i am by no means an expert, I'd just like an answer if anyone out there knows,

          • by Gyga (873992)
            It's no more prone to mutations than the rest of your DNA, it undergoes the same replication process.
            • Re: (Score:3, Informative)

              by HiThere (15173)

              It may be no more prone to mutation, but it's significantly less subject to selection pressure. There's always a tiny pressure, but in non-transcribed DNA it's usually below the noise-level, unless it does something like shape the folding (of the DNA) in a significant way. Even then it can usually be overruled by epi-genetic modifications, so the selection pressure on non-transcribed DNA is trivial.

        • by thermian (1267986) on Sunday September 07, 2008 @01:11PM (#24911533)

          Not exactly. We _know_ that a large part of DNA (about 40%) is junk, because it consists of simple repeating sequences (LINEs and SINEs).

          It might have some indirect functions (like working as a buffer for mutations), but it's junk by itself.

          There's also a fair amount of inactive genes and other junk.

          No, we have no idea what a lot of it does, but its not junk, its just not fully understood. The term junk implies we know that it does nothing, but we do not know this for sure, and a lot of what we were sure was inactive now turns out to be active after all.

          Also, we don't even know for sure if 'inactive' genes are really inactive or not. Its fiendishly hard to tell an 'active' gene from an 'inactive' one as it is. Inactive in this case meaning that it is sufficiently different in form from what we understand as being an active gene that we believe it may be one longer in use, or we haven't detected expression from it.

          In fact there is no method currently capable of telling active genes from inactive ones with greater than 80/12 accuracy.

          This means that when 80% of genes, in fact the promoter element, which is what we look for, have been correctly identified, 12% of DNA which is known not to be Genes have been incorrectly identified as being Genes.

          And that's with labeled data that has been carefully prepared. Even allowing for labeling errors, that's not great accuracy, although its pretty good that we can do that well.

          Applying the same technique to unlabeled DNA (such as a straight end to end search of someones DNA sequence), and its likely your level of accuracy will drop even more.

          • Re: (Score:2, Insightful)

            by Cyberax (705495)

            But some parts of genome are completely understood. SINEs and LINEs are retrotransposons - they just try to replicate inside your genome and they make the bulk of 'junk DNA'.

      • Some of the "junk DNA" is transcribed into non-protein-coding RNA. RNA does its business, then decays in minutes. New technologies are discover its new roles.
    • by jdrugo (449803) on Sunday September 07, 2008 @12:06PM (#24910903)

      You found out what 10% of the brain does (the sensory/motor areas)? The other 90% must not be used for anything.

      This old myth actually never had its origin in science, but was created and then spread through popular media [washington.edu]. Please don't help it survive - it's time to let it die.

    • Re: (Score:2, Interesting)

      by zappepcs (820751)

      junk dna
      theory of evolution
      master/slave systems

      People get pissy when I insist they use proper terminology when conveying ideas and information. I think those people ignorant, yet here we are suffering (again) because of bad terminology.

      While the theory of evolution is correct, the multiple uses of the word theory give rise to confusion if not downright misinformation. I'm amazed that those involved with genetic research can know of the theory of evolution on the one hand and on the other assume that there i

      • by ColdWetDog (752185) * on Sunday September 07, 2008 @01:59PM (#24911943) Homepage
        Somebody else is beating you up about the 10% brain issue (although when you deal with people on a regular basis it's not hard to believe that 99.9995% of a human's brain isn't used much), you Darwinism leads me to jump on you about another pet peeve of mine.

        If Darwin was right about evolution, then all that DNA stuff has to be there for a reason.

        Charles Darwin was amazingly right on the broader picture of speciation and evolution. Not surprisingly, he got some stuff wrong. But nowhere does ol' Charley - or any other serious tract on evolution - require the perfection that your statement implies.

        Many people (biologists included) look at highly evolved structures (and by this I am specifically not including television producers) and wonder about the complexity and intricacy of it all and use these concepts as some sort of metric for perfection. Evolution doesn't require this at all. All you have to do to be successful is to produce more of you than dies off for whatever reason. If you carry large quantities of DNA (or adipose tissue or whatever) that doesn't do anything useful but doesn't do anything harmful, then that's OK. If said stuff is a selective disadvantage, then it's not so OK but it might not be a problem in terms of the ability to create progeny. Stuff doesn't have to be there for a "reason". It can be neutral or only mildly deleterious and the critter survives.

        That said, it may be that these piles of repetitive sequences interspersed with sequences that used to code for something but currently don't create a gene product or are used as a control sequence, serve as evolutionary reservoir to get spliced and diced by random processes and eventually create something that does help the organism survive.

        Evolution only requires that the organism muddle through better than some other organisms. It doesn't require perfection and grace.

      • Re: (Score:3, Interesting)

        by JebusIsLord (566856)

        Lets say a feature evolves, and then is adapted for another use later on (feathered wings for catching insects, probably later evolved to aid in flight). Some of those insect-catching genes are now useless, so they either disappear or are simply turned off. Having a few extra genes doesn't hurt the host, so they don't disappear in later generations.

        Another hypothesis is that much of the "junk" is actually left-over DNA from all the retroviruses our ancestors became immune to (and made it into their reproduc

        • Re: (Score:3, Interesting)

          by zappepcs (820751)

          I read a story the other day where it is posited that about 8% of our DNA is retrovirus leftovers.

          On the evolution and it not requiring perfection comments, lets look at it this way. Whether we see a reason for it's existence, it is there for a reason. Mother nature is rather good at not creating useless junk everywhere. If it is left over DNA and not actively used at this point in our being, you might think of it as junk in relation to what we require of our DNA right now, or at least as far as we know, b

      • by HiThere (15173) <charleshixsn&earthlink,net> on Sunday September 07, 2008 @04:37PM (#24913321)

        I don't think that you understand the theory of evolution.

        Evolution predicts that much junk will be generated during the process of evolution...and that it will be cleared away at a rate related to how expensive it is to continue it's existence. It also predicts that this will be a stochastic process.

        At a more basic level the question becomes "What is the proper theoretical level to assign the role of replicator?" Traditionally this was considered to be either the individual animal or the population. Recently (20 years) strong arguments have been made that the proper level is the gene. This has been confirmed, though not proven, by the discovery of transposons and various other genetic elements that appear to act as parasitic genes. Also by virus genes embedded into the DNA that appear to have melded into the normal code to produce useful-to-the-organism genetic code, and others that do things like alter the sex ratios in a manner that facilitates their propagation of multiple copies.

        It's hard to see what proof would be possible. Confirmation is offered by some predictions based on that theory being confirmed and on many other observations that are more simply explained by considering the genetic code itself as the level at which evolution is occurring.

        One would think that genetic programming might offer some clues, and, indeed, it does. In genetic programming one of the big problems is clearing away junk genetic codes as the generation progress. I'm not current, but when I last checked this problem had not been solved satisfactorily.

    • Re: (Score:3, Insightful)

      You found out what 10% of the brain does (the sensory/motor areas)? The other 90% must not be used for anything.

      Find out how to read the DNA code used for a few percent of the genome (the codons to protein via RNA parts)? The rest must be junk.

      You'd have a good point ... except that no serious researcher in neuroscience or genetics has ever claimed either of those things.

      • by julesh (229690)

        You found out what 10% of the brain does (the sensory/motor areas)? The other 90% must not be used for anything.
        [...]
        You'd have a good point ... except that no serious researcher in neuroscience or genetics has ever claimed either of those things.

        Yep. This should be modded up.

        For example, the "unused brain" thing has never been reliably attributed to a real scientist. Basically, it was made up by the media.

        OTOH, I do believe that many geneticists did originally believe that the so-called junk DNA served n

      • Re: (Score:3, Interesting)

        by MarkusQ (450076)

        You found out what 10% of the brain does (the sensory/motor areas)? The other 90% must not be used for anything.

        Find out how to read the DNA code used for a few percent of the genome (the codons to protein via RNA parts)? The rest must be junk.

        You'd have a good point ... except that no serious researcher in neuroscience or genetics has ever claimed either of those things.

        Nuts. Galen, widely recognized as the father of modern medicine, thought the brain was used to cool blood (like a radiator). There

    • I am no Biologist but I have often wondered at thew high levels of successful evolution mammals can do compared to the relatively slow levels that reptiles and insects seem to have. The idea of "Junk DNA" being merely unused DNA would make a lot more seance then it just being nothing. I wouldn't be surprised if our ability to digest rotten meat, or our spine structure being different, or our forearms being longer were all still there. It would allow for much faster adaption if instead of reinventing new str
      • by philspear (1142299) on Sunday September 07, 2008 @04:06PM (#24913043)

        I am no Biologist but I have often wondered at thew high levels of successful evolution mammals can do compared to the relatively slow levels that reptiles and insects seem to have.

        I am a biologist, you've got that totally backwards (it's okay though, it's for counterintuitive reasons). By most evolutionary standards, the bugs own this planet. A famous geneticist named Haldane was asked once "knowing what you do about nature, what can you tell me about God?" He said "He has an inordinate fondness for beetles." They're incredibly diverse compared to mammals. Insects dramatically outnumber us and out breed us. And their evolution rate is extremely fast due to their extreme proliferation. Pioneering studies of genetics and evolution almost always involve Drosophila flies because you can get tens of thousands of generations in a research career (and genetic change to match that) wheras you could probably get at most two human generations and only hundreds of mice generations. As one last testament to the (evolutionary) superiority of insects: cockroaches have been here before we have and will undoubtedly survive after we have nuked ourselves off the planet, they might slow down for a generation, but they've far outspecialized mammals.

        Keep in mind that evolution doesn't mean higher, smarter, faster, it just means more fit to their niche. A bigger brain has given us the power to make a civilization and big buildings, but evolutionary fitness is actually measured in how many offspring you have, since that's the goal ultimately in evolution, and bugs have us whipped there.

        It would allow for much faster adaption if instead of reinventing new structures at random all our bodies had to do was express other "Junk" genes at random.

        That is an accepted theory, one which the current results do support (I think, I haven't read the article.) It's also worth noting that plenty of times, non-junk DNA gets co-opted for different purposes. What appears to have happened fairly often is that a gene that's needed for something gets copied, so some organism has two functional copies of it, and then one is free to be changed slightly to different purposes. I don't know the statistics, but there are huge families of closely related genes which have different purposes but were at one point probably carbon copies that now do other things.

    • There is good reason for us to theorize that large portions ARE junk. We have useless vestigial organs (appendix, in-vitro gills and tails etc), because there is harmless genetic code for these things even though they're useless. It is an educated hypothesis that much of our DNA is similarly useless but harmless enough not to be selected against evolutionarily.

      But agreed - a lot of it is just an "I don't know what this does". Lots of it WILL be found to be functional.

    • Every time early researchers solve part of a problem they seem to label the part they haven't solved as being unimportant or irrelevant.

      Maybe it's different for different sciences, but in cell or molecular biology that is not the case. Most papers I read specifically adress the unknowns in the discussion section, usually a one line thing that amounts to "we don't understand why this happened in our experiments, but it is very important" or "This helps but it isn't the complete picture, we still need to do X, Y, and Z." Other times they suggest hypotheses or models that are not supported yet by the literature and say those should be tested

  • by Ralph Spoilsport (673134) * on Sunday September 07, 2008 @11:46AM (#24910729) Journal
    I'd love to see the results of removing Junk DNA from a human's genome, and then pump it into an egg and grow it up all normal like and see what kind of walking cancer emerges.

    Junk DNA doesn't exist. It's just DNA we don't understand.

    RS

    • Junk DNA doesn't exist. It's just DNA we don't understand.

      As far as I understand it, the term was a complete misnomer. Maybe the people that coined the term used it as specific jargon meaning something, if so, they didn't seem to understand how it might be misleading.

    • Yeah, that would totally rock. You'd end up with some hideous blasphemy, like a sort of cross between Sarah Palin and Cowboy Neil. Or perhaps Cthulhu.
    • by RDW (41497) on Sunday September 07, 2008 @12:38PM (#24911185)

      'I'd love to see the results of removing Junk DNA from a human's genome, and then pump it into an egg and grow it up all normal like and see what kind of walking cancer emerges.'

      Well, Nature has (sort of) done this experiment already. The Fugu (pufferfish) genome has a highly 'compressed' genome, with about the same number of genes as mammals, but a much smaller complement of non-coding DNA:

      http://genomebiology.com/2002/3/9/comment/1012 [genomebiology.com]

      So it's certainly possible for an 'advanced' species to survive without the 'burden' of much of this material (obviously the regulatory elements are still required, but a lot of the highly repetitive stuff seems to be dispensable). Of course the 'junk DNA' may still confer evolutionary advantages (as the linked article put it: 'it may in fact be the clay from which evolution fashions morphogenetic changes'), and perhaps it says something that mammals have in general evolved in what most of us would regard as a much more interesting way than pufferfish...

      • by mikael (484)

        Would being underwater shield fish (and their DNA) from the mutation causing effects of radiation and other factors in the environment? Although, there was a research study that showed there were something like a million virus particle per litre of sea water.

    • by mpe (36238) on Sunday September 07, 2008 @01:00PM (#24911433)
      I'd love to see the results of removing Junk DNA from a human's genome, and then pump it into an egg and grow it up all normal like and see what kind of walking cancer emerges.

      Unless you also modified the host's DNA as well it might well do nothing. Chickens have genes for growing teeth and long tails, which are simply switched off.

      Junk DNA doesn't exist. It's just DNA we don't understand.

      Some of it probably is actually junk. Where DNA performs no function at all there is no evolutionary effect to weed out harmful mutations. Though it's possible that many mutations of an "obsolete" gene may result in something useful.
      If DNA is observed which dosn't vary much between individuals (or even species) then that tends to imply that it functional (possibly even very important). Even if we currently have no idea what that function actually is.
    • I agree. It's a pretty stupid term that was probably never intended to be an official name, or whatever you call it. I wish they would hurry up and change it to something more meaningful, because it's one of those things that is going to cause a huge amount of misconception (if it hasn't already).

    • Re: (Score:3, Informative)

      by jannesha (441851)

      I'd love to see the results of removing Junk DNA from a human's genome, and then pump it into an egg and grow it up all normal like and see what kind of walking cancer emerges.

      Would you be satisfied if it was done in a mouse instead? Because that's already been done. [doe.gov] These researchers removed 2.3 million bases from the 2.7 billion-bp genome, and could find no defects in the resulting mice. I totally agree that "we don't know what it does" != "it has no function". But some of it, clearly, really is just junk. --jjj.

  • DNA fingerprinting (Score:5, Interesting)

    by Anonymous Coward on Sunday September 07, 2008 @11:51AM (#24910769)

    In defense of DNA fingerprinting it is often stated that the databases only store non-coding DNA, so there is no risk that someone might be able to centrally deduce possible health problems and other traits which could negatively affect the individual. How does that argument hold up now?

    • by brit74 (831798)
      Anonymous coward is right: DNA fingerprinting doesn't store or show genetic sequences. It would be impossible to determine a person's exact genetics or genetically-based health problems based off of a DNA fingerprint.
    • by julesh (229690) on Sunday September 07, 2008 @02:48PM (#24912371)

      In defense of DNA fingerprinting it is often stated that the databases only store non-coding DNA, so there is no risk that someone might be able to centrally deduce possible health problems and other traits which could negatively affect the individual. How does that argument hold up now?

      I'm not sure where the statement you're questioning came from, but my understanding of DNA fingerprint databases is that they don't actually store DNA base-pair sequences at all, but merely a list of the distances between certain marker sequences. Imagine taking a text document, counting the length of each paragraph, and summarising it by saying how many of each length there is. With long enough documents you're unlikely to find exact matches, but the numbers don't tell you anything actually useful about the contents of the file.

  • monkeys DO have opposable thumbs.
  • Well he must do if all this junk is getting through and messing with his creations.

    So anyway god, I suggest you start using spamhous's new 'creation guard' anti DNA spam list. Its the state of the art for protecting all your 'miracles of life'(tm).

  • by pushing-robot (1037830) on Sunday September 07, 2008 @11:58AM (#24910839)

    In the last several years, scientists have discovered that non-coding regions of the genome, far from being junk, contain thousands of regulatory elements that act as genetic "switches" to turn genes on or off.

    ...Biologists discover "flags". Seriously, these guys should just bring a programmer on-staff — preferably assembly, as decoding the arcane secrets of all Earth life should be a breeze for anyone whose day job involves the x86 instruction set.

    • Re: (Score:3, Funny)

      by $RANDOMLUSER (804576)
      Heh. Good point. I know that a lot of my code that's been around for a long time may contain as much as 30% commented out code, not to mention all the stuff in #ifdef blocks.
      • Re: (Score:3, Insightful)

        by julesh (229690)

        a lot of my code that's been around for a long time may contain as much as 30% commented out code, not to mention all the stuff in #ifdef blocks.

        You know, getting rid of all that stuff is what version control systems are for.

    • by Daniel Dvorkin (106857) * on Sunday September 07, 2008 @12:28PM (#24911101) Homepage Journal

      Biologists discover "flags". Seriously, these guys should just bring a programmer on-staff -- preferably assembly, as decoding the arcane secrets of all Earth life should be a breeze for anyone whose day job involves the x86 instruction set.

      [Sigh] Every time a biology story is posted on /. it seems like we get a bunch of posts along the lines of "dumb biologists, any techie would have figured that out a long time ago!"

      Please don't confuse the reality with the dumbed-down versions that appear in the popular press or the even more dumbed-down summaries. Bioinformatics, which is what I do, has been an established science for over a decade, and I can assure you that computer scientists have been working with biologists for a lot longer than that. Most of the obvious computational analogies have already been thought of -- and most, unfortunately, have had to be discarded. Despite some of the superficial similarities, genomes are not programs, at least not in the way CS people use the word. They're more like a collection of heuristics, and even that way of thinking about things breaks down when you start looking at the details.

      I'm more on the CS/math/stat side of things, and my colleagues on the bio side are often mystified by what I do -- but I'm equally often mystified by what they do. Both CS and biology are tremendously complex fields, and if you think you can arbitrarily apply lessons learned from one field to the other, you will almost always turn out to be wrong. Biologists and computer scientists can learn a lot from working with each other; work in one field very often leads to advances in the other; and by all means (he says, with a healthy dollop of self-interest) the areas of collusion should continue to grow. But thinking that there's some natural equivalence in one field to what you know from the other is simply a mistake.

      • For what it's worth, I was aiming for funny — not insightful.

        But as time goes on, I predict that the two fields will become very closely linked, as we continue to develop machines that imitate biology (and vice versa).

        • Re: (Score:3, Interesting)

          Fair enough, and I admit I'm a bit touchy on the subject.

          No doubt there will be a close link, but I think the division will always be a pretty strong one. I'm deeply skeptical about the potential of "DNA computing" and the like (although I'd be happy to be proven wrong!) and I suspect we will mostly be analyzing biological data with computers, rather than doing computational things that produce direct biological results, for quite some time. The fundamental difference, of course, is that biological system

    • by oldhack (1037484)

      ...Biologists discover "flags". Seriously, these guys should just bring a programmer on-staff -- preferably assembly, as decoding the arcane secrets of all Earth life should be a breeze for anyone whose day job involves the x86 instruction set.

      Let's not use a $10M cruise missile to knock out a $10 tent.
      (Damn, I wish that wasn't a BS.)

  • "Junk" DNA (Score:4, Informative)

    by quinnlynn (1343325) on Sunday September 07, 2008 @12:00PM (#24910853)
    I probably should have clarified in the post but "Junk" DNA is a misnomer though still the most commonly used term for the part of the human genome (over 90% of it) that we don't know the uses for. The word "junk" isn't used in the sense that the DNA there is worthless and should be discarded. More like a junk drawer. There's a bunch of stuff over there that doesn't seem to belong to anything but we know that a lot of it probably does, so scientists keep testing around in there to see what goes where.
    • Re: (Score:3, Informative)

      by wisebabo (638845)

      Hmm... I thought the term "Junk" DNA referred to the fact that a lot of it (all?) seems to be made up of long repeating sequences like AAAAAAAAA or ACACACACAC or something else that seems pretty 'worthless" like ending sequences that aren't at the end of anything. Also I thought that they saw "skeletons" of viruses (from retrovirii that became permanently embedded in our DNA) and broken and incomplete copies of functional genes. But then IANABiologist.

  • by Laxori666 (748529) on Sunday September 07, 2008 @12:09PM (#24910919) Homepage
    We'll eventually discover that DNA is just instruction tape for a type of turing machine which generates our entire body as its output. As we all know, Turing machines require lots of repetitive instructions to operate because they're so limited in their actions.
  • by moxley (895517) on Sunday September 07, 2008 @12:21PM (#24911023)

    Saying that any DNA is "Junk DNA" is like saying that all dark matter in the universe (which we don't quite yet fully understand) is "Junk Matter."

    It's the sort of misnomer that has no place in science IMO.

    It always blows my mind when I think about things like this, how people think that at this point in our development that humans are the be all end all, that we understand everything there is to understand - it's such bullshit. I am not saying that our science and advancements aren't incredible and amazing; they are - I am only saying that it is incredibly foolish to think we know everything..about anything really... (in the natural world especially).

    • by Pedrito (94783)

      Saying that any DNA is "Junk DNA" is like saying that all dark matter in the universe (which we don't quite yet fully understand) is "Junk Matter."

      You're absolutely right. Right now, the term "junk DNA" is just sort of a way of filing it as "unknown function", but the term "non-coding DNA" is probably the more accurate term to describe it.

      It's been hypothesized for some time that some of this non-coding DNA is used for morphological guidance of development. That is, some of the coding specifies why we look

  • Trichoplax has the simplest known animal genome, and it shares 80 percent of its genes (comprised of 98 million base pairs) with humanity.

    I get the impression by this that the 80% or so roughly defines the basic "building blocks", things like how to make a kidney or blood cell or even a midochondria, and the remaining 20% is more of a blueprint of how to take the blocks to build a given animal in shape and behavior. The shape of the skeleton, layout of the circulatory system, etc.

    • Re: (Score:3, Informative)

      by tehdaemon (753808)
      You need the Wikipedia entry on Trichoplax [wikipedia.org]. They are really simple.

      Also, this is 80% of Trichoplax's DNA is also in human DNA, not the reverse. Trichoplax's DNA is about 98 million base pairs, humans are around 3 billion... 80% of 'hello world' is also in the linux kernel, for a comparison...

      T

  • Finally. (Score:4, Funny)

    by ari wins (1016630) on Sunday September 07, 2008 @12:31PM (#24911127)
    I'm glad I can now scientifically justify why I like a little junk in the trunk.
    • "I'm glad I can now scientifically justify why I like a little junk in the trunk."

      There should be a moderation option, "-1, Too Much Information".

  • Lovely... (Score:4, Funny)

    by DelitaTheFridge (912659) on Sunday September 07, 2008 @12:55PM (#24911377)
    Our DNA has a goddamn registry.
  • ... another man's ... well... umm... man.

  • wasn't George Carlin that said

    "ever notice how your junk is stuff and everyone elses stuff is junk?"

  • Maybe life uses those "junk DNA" sequences as experimental. The most radical changes could be included at the end of the strands, and those would cease to be copied first, killing only a few.

  • Every time I see DNA stuff discussed I think it looks more and more like a program. There are areas that are "code" and there are areas of "data."

    The "junk DNA" may simply be static constants or variables used by the rest of the DNA. If you were to look at the static load area on an embedded system you'd call it junk because it seems to do nothing. It has illegal operands. But it has a purpose, it turns things on/off, defines their behavior, etc. Sound familiar?

    I think biologists focusing on DNA should take

  • Given the current state of affairs how is anyone surprised that the piece that separates humans is considered "junk"? Seems perfectly logical to me.

"Only the hypocrite is really rotten to the core." -- Hannah Arendt.

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