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Biotech Science

Central Dogma of Genetics May Not Be So Central 196

Posted by Soulskill
from the can-we-blame-aol-for-this dept.
Amorymeltzer writes "RNA molecules aren't always faithful reproductions of the genetic instructions contained within DNA, a new study shows (abstract). The finding seems to violate a tenet of genetics so fundamental that scientists call it the central dogma: DNA letters encode information, and RNA is made in DNA's likeness. The RNA then serves as a template to build proteins. But a study of RNA in white blood cells from 27 different people shows that, on average, each person has nearly 4,000 genes in which the RNA copies contain misspellings not found in DNA."
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Central Dogma of Genetics May Not Be So Central

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  • Central Dogma? (Score:3, Insightful)

    by Microlith (54737) on Monday November 08, 2010 @08:23PM (#34168384)

    Who do you think they are, Soulskill, NERV?

    Also, science holds no dogma. If it does, it ceases to be science.

    • Re: (Score:2, Funny)

      by digitig (1056110)

      Also, science holds no dogma.

      Is that a dogma that science holds?

      • Re: (Score:3, Insightful)

        More like a dogma that the philosophy of science holds.

        • Re: (Score:3, Insightful)

          by digitig (1056110)
          No, it's not that. The philosophy of science doesn't hold dogmas, it identifies dogmas. Such as the metaphysical dogma of materialism. All attempts so far to eliminate that dogma from science have failed, and it doesn't look likely that it will ever be eliminated.
          • It may be a dogma that scientists hold, but it is more a presupposition to science than it is science.

            • by digitig (1056110)
              What is "science" if not the collection of presuppositions, working practices and conclusions of scientists?
    • Re:Central Dogma? (Score:5, Interesting)

      by mauthbaux (652274) on Monday November 08, 2010 @08:49PM (#34168584) Homepage
      Actually, as I was taught it (which, I will readily admit, could be wrong), Central Dogma is in fact the proper term, though the definition has been tweaked over time.
      Originally it stated something along the lines of, One DNA gene is transcribed into one RNA transcript, which is then translated into one protein.
      The discovery of antibodies threw that concept out the window. Variability in intron splicing and recombination means that a small handful of genes can yield a huge variety of protein products (See VDJ recombination).
      Yet another twist was added with the discovery of retroviruses which reverse the direction of transcription, turning RNA into DNA. Previously we had thought the central dogma to be unidirectional.
      The more we learn about life's mechanisms, the less surprised we are when exceptions to the rules are discovered. Evolution really is the ultimate hacker; constantly expanding the usefulness of very simple resources.

      Also, kudos on the evangelion reference.
      • by Microlith (54737)

        I'd mod you up but, as you can see, I commented.

        • Re: (Score:3, Informative)

          Here's the full answer:

          "In his autobiography, What Mad Pursuit, Crick wrote about his choice of the word dogma and some of the problems it caused him:

          "I called this idea the central dogma, for two reasons, I suspect. I had already used the obvious word hypothesis in the sequence hypothesis, and in addition I wanted to suggest that this new assumption was more central and more powerful. ... As it turned out, the use of the word dogma caused almost more trouble than it was worth.... Many years later Jacques M

      • Re: (Score:3, Informative)

        by jd (1658)

        There are many, many twists to this sordid puzzle, but you are correct. The concept of a 1:1:1 translation has been dead for a very long time.

      • by Bigjeff5 (1143585) on Monday November 08, 2010 @09:22PM (#34168840)

        The use of the term "dogma" in "Central Dogma" was incorrect from the get-go. Frankly, Francis Crick either chose to misunderstand the word or simply didn't fully grasp its connotations.

        He was just looking for a more dramatic word for "hypothesis".

        "Central Hypothesis" would be the more accurate name for it. It isn't a proper theory, but it does provide a framework for understanding molecular biological functions.

        It's basically this (from WP): 'once information gets into protein, it can't flow back to nucleic acid.'

        • by StikyPad (445176)

          I called this idea the central dogma, for two reasons, I suspect. I had already used the obvious word hypothesis in the sequence hypothesis, and in addition I wanted to suggest that this new assumption was more central and more powerful... As it turned out, the use of the word dogma caused almost more trouble than it was worth... Many years later Jacques Monod pointed out to me that I did not appear to understand the correct use of the word dogma, which is a belief that cannot be doubted. I did apprehend th

      • by gringer (252588)

        To throw a further spanner in the works, a large proportion of non-genetic DNA (i.e. the stuff that doesn't get eventually converted into proteins) has functional aspects — it is transcribed into RNA and then used directly for cellular regulation (see here [nih.gov]).

      • Re: (Score:3, Interesting)

        by sd211 (449486)

        You are right about the central dogma. It was formulated in 1958 and states that information flows from DNA->RNA->protein. Since that time it has been ammended many times. Just because it is genereally not true, does not mean it is not useful. For example, Newton's mechanics is generally not true, but it is quite usefull for some applications.

        Just running some numbers (based on the abstract)
        4 x 10^7 reads * 50 b/read = 2 x 10^9 b.
        Error rate (general ballpark for RNA replication/translation, number

        • by BeanThere (28381)

          ... Newton's mechanics ... is quite usefull for some applications.

          Talk about an understatement.

      • by careysub (976506)

        Evolution really is the ultimate hacker; constantly expanding the usefulness of very simple resources.

        "Mother Nature: Überhacker".

        That would make a cool tee-shirt!

      • by mapkinase (958129)

        One would think that any sensible journalist would be cautious throwing titles like "Central dogma of genetics maybe not so central" with the only scientific publication being a conference lecture [ashg.org].

        That's what I thought after reading this ./ post. But then I found (type: "Cheung VG[au] AND Philadelphia" into the search bar)) [nih.gov] that the main author had some respectable publications on the subject.

        Even with respectability of the authors of the original publication established, the sensationalist title in Science

    • Re: (Score:3, Interesting)

      by interkin3tic (1469267)

      Scientists sometimes use "dogma" in a sarcastic manner. As others have pointed out, this dogma is not so much a "universal rule" as it is "a general guideline with more exceptions than you can shake a stick at."

      Stephen Jay Gould talked about the dogma of gradualism. To hear him tell it, evolutionary biologists were telling the fossils that, no, they couldn't possibly be identical to their ancestors from hundreds of thousands of years prior, they had to have made some mistake in where their bones became bu

  • Why is this news? (Score:5, Informative)

    by jd (1658) <imipak@noSPam.yahoo.com> on Monday November 08, 2010 @08:28PM (#34168412) Homepage Journal

    We have known for many years that the same DNA codes to different proteins, with the adjustments given the information in the non-coding regions AND the information in the epigenome. That people have discovered that the intermediate step is also adjusted can hardly be called a shock. The proteins have to get built differently somehow, so some alteration in the intermediate coding was inevitable. Honestly! If geneticists aren't even reading their own bloody papers, maybe the government grants should be issued to those Slashdot readers who do.

    • by Fluffeh (1273756) on Monday November 08, 2010 @08:30PM (#34168442)

      Honestly! If geneticists aren't even reading their own bloody papers, maybe the government grants should be issued to those Slashdot readers who do.

      Tell us how you feel. Don't hold anything back. You are in a SAFE environment here... Now, show me on the dolly where the geneticist touched you...

      Side note: Totally agree with the comment :)

      • Tell us how you feel. Don't hold anything back. You are in a SAFE environment here... Now, show me on the dolly where the geneticist touched you...

        I think you mean, show me on the memory map where the program inappropriately accessed memory.

    • by RobinEggs (1453925) on Monday November 08, 2010 @08:37PM (#34168492)

      That people have discovered that the intermediate step is also adjusted can hardly be called a shock.

      Yes, it is a shock. The prevailing thought was that the RNA was transcribed faithfully and then that perfect transcript of the DNA was sliced up in strange ways. These people have discovered that the transcript may never have been perfect at all.

      Imagine cutting up a loaf of bread: The geneticists were quibbling about how thick the slices were and how to arrange it on the plate, all without paying attention to what kind of bread they used. Now suddenly they've noticed that the recipe for french bread gave them a sourdough loaf while they aren't looking, and it may not be about the slicing as much as about how the right recipe is giving them the wrong thing to cut up.

      • Who thought it was perfect? The only people that thought that, I suppose, were high school students receiving a highly idealized version of cellular protein synthesis (sort of like perfect gasses, etc.) No researchers ever thought it was perfect, because it would be all but impossible to create such a perfect system. If there's any revelation here, it's that protein production is more error tolerant than we once thought, but no one since the discovery of DNA/RNA has ever thought that the system was perfe

        • Re: (Score:3, Interesting)

          by ColdWetDog (752185)
          NOBODY THOUGHT IT WAS PERFECT

          The weird thing (from TFA) is that the imperfections aren't we're they're 'supposed' to be.And there are too many of them.

          Robin Egg's analogy is pretty good. Let me try a car analogy: You're in a BMW factory, on the input side, all the instructions and parts are geared towards making BMWs - maybe different colors, different hood ornaments or whatever.

          Out pop some BMW's as expected. And a couple of Yugos.

          Well, no, that's not right. Go with the baking analogy.
          • Re: (Score:3, Interesting)

            by Artifakt (700173)

            Exactly - there's a difference between getting an occasionally screwed up BMW, with a random seeming defect, and getting an occasional Yugo, or maybe a working Jetpack, or every time the BMW is not to spec it's always because it has only four lug nut shafts on the left rear wheel, and the spacing also adjusts to make them symmetrically placed, rather than you seeing a host of other defects that are theoretically as likely. Or maybe it's something that definitely won't work as well, definitely what would be

      • Re:Why is this news? (Score:5, Interesting)

        by jd (1658) <imipak@noSPam.yahoo.com> on Monday November 08, 2010 @09:08PM (#34168738) Homepage Journal

        Well, no. The transcription cannot be faithful because there are more letters in RNA than in DNA. Even if you ignore that aspect, geneticists knew that there was a data-driven transform somewhere. Assuming that it is in point A rather than looking is not the hallmark of a scientist. That is the hallmark of the incompetent. Never, ever extrapolate further than the data will permit on the assumption that the extrapolation is valid. Extrapolation should only ever be done for the purpose of creating a hypothesis. Leave articles of faith to religion. On second thoughts, the religious tend to extrapolate beyond limits too, so that might not help.

        Anyways, the fact is that there are only two possible places in which a transform could happen (and it could happen in both). This gives you a total of three possibilities. Now, only the DNA-to-RNA step could include information from the non-coding regions. It's possible that either stage could be effected by the epigenome. From this, it follows that two of the three cases involve the DNA-to-RNA step and two of the three methods involve the DNA-to-RNA step. It may be unexpected, in that they may not have considered that possibility sufficiently, but to call it a shock implies that they ignored the mechanisms entirely -- mechanisms the genetic scientists have been studying in depth for a very long time.

    • by mosb1000 (710161)

      Just because other research indicated this might be the case doesn't mean that this was previously known. Do you really think it unnecessary to actually determine if your assumptions are correct? I hope you aren't using and government grant money.

      • Re: (Score:3, Interesting)

        by jd (1658)

        There are four letters in DNA, five letters in RNA. That tells me that something about not copying identically was indeed previously known. The protein encoding was also known for a fact - it wasn't just indicated, it was pretty much accepted by the genetics community as having been sufficiently gone over to be considered standard fare.

        The question was WHERE the change happened - DNA to RNA, or RNA to protein? That wasn't established. Two possibilities, one (or both) could be possible. That gives two out of

        • by Artifakt (700173)

          The four bases in DNA aren't the same as codons in the code - there are 64 codons set up as triplets of bases in DNA, even though of those, 61 are used to code for only 20 amino acids and the remaining 3 code for a STOP bit. Messenger RNA uses the same number of codons by the model, including also having three ways to express a STOP. There are some already known exceptions, mostly some uncommon organisms use one or two of the three STOP bits to code for an amino acid instead. Incidentally, the START bit (AU

    • This is the important part of the article, everything else is comparatively irrelevant:

      The researchers don’t yet know how the RNA misspellings happen. They could be substitutions made while the RNA copy is being made, or the changes could happen later. The consequences of the misspellings are also unknown.

      Not knowing why this is occurring so frequently is what is truly interesting about this, at least from my point of view as a biochemist.

      • Re: (Score:3, Insightful)

        by jd (1658)

        Now that is very different. Not knowing why is indeed very interesting. The consequence of the misspellings depends on whether they ARE true misspellings versus data-driven modifications from non-encoding genetic material. If they are deliberate transforms, then to call them misspellings is flawed, since the spelling would then be precisely what the DNA coded for (when considering all other types of data). Likewise, when U is used in RNA, it is not considered a mis-spelling, even though that would not be th

    • by enderwig (261458)

      Don't forget, we've known about RNA editing for over a decade now...

    • Re: (Score:2, Informative)

      I agree that we've always suspected that transcription isn't a high fidelity process. In fact, there is evidence that leads us to this conclusion (ex. the lack of a 'spell-checker' mechanism). However, just because we have evidence that points to an effect doesn't mean that it shouldn't be tested. The thing is, we've been surprised before. We've had evidence of other phenomena/behaviour should exist but when actually tested, it turned out that it was not as expected. For example, in the past it was thought

      • Re:Why is this news? (Score:5, Informative)

        by Artifakt (700173) on Monday November 08, 2010 @11:23PM (#34169682)

        I don't see why you claim there isn't a spell checker. Using DNA for the long term storage itself increases fidelity over RNA. Putting the DNA in a nucleus to protect it from some chemical processes that can cause data malformation also means an increase in fidelity. Multicellularity means (admittedly among other things), moving the reproductive cells deep in the organism so they are again protected from some more sources of copying errors. Simultaniously, it allows apoptosis (as there's no advantage for cell death in a single celled organism), and that's a second spell checker of sorts for multicelled organisms only. A lot of the more complex organism's defenses against diseases such as cancer could all be described as spell checkers (for example, P53 tumor suppressor). The form of DNA polymerase used in the complex organisms itself improves copying accuracy by about 100fold over what's possible for the non-eukarotes and even some of the fairly complex bacteria, and it's been described in operation as 'wiggling the part it has just put together to make sure it hasn't allowed the wrong base to pair before it moves on to the next bit, and having a digestive capability to strip out such mistakes when it finds them'. (See "Our Molecular Nature", by David Goodsell for more on this). Then there's snRNPs (Small Nuclear Ribonucleoproteins, which are formed to snip out introns from RNA copies for those RNA strands that aren't self splicing ribozymes (and of course rybozymes themselves even in organisms too simple to have snRNPs). It looks to me like most of the major changes in organic complexity are also spell checkers of one sort or another. I don't really like to anthropomorphise evolution as having long term goals, but it's probably at least as fair to say evolution is trying to produce totally accurate transcription, as it is to say it is trying to make organisms more ideally suited to their environments.

        • And sexual reproduction also count as a form of spell checking. It allows you to introduce random errors in the DNA, and get back perfect DNA from other individuals when you reproduce. (Muller's ratchet, which to my mind sufficiently explains why we have sexual reproduction, and which I was sad to find that somebody else had thought of before me.)

    • by Artifakt (700173)

      The problem is, that Natural Selection requires, in theory, that there be some pretty strong limits on blending. The classic Mendelian model implies a code that is pretty reliably non-blending and that in turn is one of the things that makes NS count as science. That is, it had predictive power - Darwin's original work caused him to predict that when the code was discovered, it would allow, at most, only very limited blending. * "One DNA sequence yields one protein, now and forever" also works to make blend

  • by Anonymous Coward on Monday November 08, 2010 @08:29PM (#34168420)

    What it does in fact say is that information flows from DNA to RNA to proteins, and not the other way around: proteins can't write DNA.

  • by sam_handelman (519767) <skh2003@columbi a . e du> on Monday November 08, 2010 @08:29PM (#34168422) Homepage Journal
    This is not nearly as earth-shattering as the journo makes out.

      When DNA is copied to make new DNA, you get a certain number of copying errors, called mutations - most of them harmless. I assume everyone knows about those.

      When DNA is copied to make a temporary-working-copy RNA, you get a larger number of these copying errors because, in general, they are one-shot non-critical deals. The need for stringency is much lower, the selective advantage for stringency is not so great, so it comes as no surprise that the level of proof-reading is also reduced.

      Now, it's also possible that there are mechanisms by which these RNA molecules can be purposefully edited. As mentioned in the article, significant post-transcriptional editing (including in eukaryotes the readaction of big chunks, which are called "Introns".) But this finding doesn't speak much to that, although the rate is a *sconch* higher than I might expect for random errors. Even so, this doesn't shake the central dogma of molecular biology in any meaningful way, as for example Reverse Transcriptases did.
    • RTFA. These are not errors. They happen the same way in every strand of RNA.

      • by afidel (530433)
        Doesn't mean they aren't errors. Just because a high percentage of people are improperly encoding the RNA for this protein doesn't mean that it's not just a common defect. For all we know this is a defect holdover that at one point conveyed some advantage like sickle cell anemia providing a partial immunity to malaria.
    • by semiotec (948062)

      Not to mention that a whole bunch of stuff happens between transcription (DNA -> RNA) and translation (RNA -> protein).
      The ends have to be capped and modified, in eukaryotes the transcript is only a precursor and has to be spliced into the mature sequence, then the whole thing is exported from the nucleus to the cytoplasm.
      Plus there's a whole bunch of stuff happening that we don't really know about, like pseudouridylation and methylation of specific sites.
      Not to mention, there's always the good

  • Slashdot (Score:5, Funny)

    by BitHive (578094) on Monday November 08, 2010 @08:29PM (#34168426) Homepage

    News for nerds who never took a biology course and are deeply suspicious of the so-called "sciences"

    • by chebucto (992517)

      News for nerds who never took a biology course and are deeply suspicious of the so-called "sciences"

      They didn't even read The Economist [economist.com]. In 2007.

  • by RobinEggs (1453925) on Monday November 08, 2010 @08:31PM (#34168446)
    The summary and the abstract really say almost nothing other than to confirm that the misspellings aren't random and don't seem like lab artifacts.

    I'd be interested to know how conservative these mistakes tend to be. If the mistakes generally replace amino acids with very similar ones it might be a programmed method of prodding just how much variation a structure can take while remaining functional. Weird and random events, which can be only so weird and so frequent before everything breaks entirely, are necessary for evolutionary adaptation, and these weird protein errors might be a previously unknown mechanism of exploring slightly different structures for proteins and seeing how far an organism can push the envelope.
    • by Alsee (515537)

      I'd be interested to know how conservative these mistakes tend to be.

      They must be very conservative.
      I've been seeing a lot of mistakes among the Tea Partiers.

      -

  • No Surprise (Score:2, Insightful)

    Any engineer should find this to be perfectly intuitive. When the DNA itself replicates to produce a new cell entirely, there are a lot of extra safeguards to ensure as near-exact copying as possible, as mutations can easily be fatal. For RNA copying, there is no need for this sort of precision, because even if the resulting protein is useless, the cell remains alive, and a new RNA strand can easily be produced if needed.
    • Engineers are probably the absolute worst people to be judging complex biological processes like reproduction. In fact, even during meiosis and mitosis, there are all sorts of flaws. It's one of the driving forces of evolution, creating at least a certain fraction (just what that is is still up for debate) of the variation in any population's genome.

    • For RNA copying, there is no need for this sort of precision, because even if the resulting protein is useless, the cell remains alive, and a new RNA strand can easily be produced if needed.

      The problem with thinking that way is that these "errors" are not random like transcriptual errors usually are.

  • Thought I read somewhere that when the first cells started to form in the primordial soup they were more RNA than DNA since that gave them rapid mutations, the ability to adapt quickly and evolve.

    Later on as Cells and organisms became more complex, DNA took over since it was more stable but mutates / evolves at a slower rate...

    • Re: (Score:3, Interesting)

      by MightyMartian (840721)

      It seems likely that the earliest replicators (they may not even have been cells, per se) probably did not use RNA and DNA at all. RNA would have been a somewhat later innovation, like lipids being used to produce simple membranes to create a semi-permeable barrier to protect replication and protein synthesis. At that point we would have had simple cells.

      • Re:Mutations (Score:4, Informative)

        by rnaiguy (1304181) on Monday November 08, 2010 @09:14PM (#34168780)
        It's actually believed that the earliest forms of biochemical life consisted almost entirely of RNA. It is the only molecule we know of that can act as both information storage/transport and chemical catalyst (all proteins made by modern life are in fact polymerized by a reaction catalyzed by RNA). There is some disagreement as to whether this "RNA world" came before or after lipid membranes.
        • That's not my understanding. RNA world is not the starting point, but at some point further along. But perhaps we need to clarify the terminology. The most primitive replicators may not have been life in the sense that we apply.

    • by Artifakt (700173)

      DNA definitely has a lower mutation rate. That doesn't mean it evolves more slowly. Complex species actually seem to give way to new species more rapidly than simpler ones. There's some arguments that a high enough mutation rate actually slows evolution down:

      1) Most mutations are bad
      2) Of the few that are good, most give only a small improvement, since most organisms are pretty well adapted to their environments.
      3) So a successful mutation usually means an organism has on average, say 1.01 offspring while i

  • by zach_the_lizard (1317619) on Monday November 08, 2010 @08:48PM (#34168570)
    I for wun du not mind the speling erorz. So long as they kan reed it, wut difurinc duz it maek? Itz not liek thuh bodee iz a speling Notzee.
  • Thanck God! (Score:4, Funny)

    by T Murphy (1054674) on Monday November 08, 2010 @08:48PM (#34168572) Journal

    nearly 4,000 genes in which the RNA copies contain misspellings

    I new my bad speling wasnt my falt- its just genetic. Finaly I can prove it to my teacher! I hope scientists next fined genes with bad grammar,

  • Not news. (Score:2, Informative)

    by pesho (843750)
    How is this news? RNA editing has been known for so long that it is already in the textbooks.

    From the article: The most common of the 12 different types of misspellings was when an A in the DNA was changed to G in the RNA. That change accounted for about a third of the misspellings.

    This is a textbook example of RNA editing by adenosine deaminase. It will convert the Adenosine bases ('A') to Inosine ('I'). When they try to sequence the RNA the first step is to make a DNA copy. During the process the pos

  • The 'dogma' concerns the direction of information flow (DNA <-> RNA -> proteins), not about how perfect it is.

  • by Caerdwyn (829058) on Monday November 08, 2010 @09:22PM (#34168842) Journal

    So here's a question.

    Suppose that this "error" that happens every time nonetheless yields the same original DNA sequence?

    dna half-strand ACTG ----> rna TATTCGAGATATAC ---> dna half-strand ACTG

    It's been a very, very long time since I took my college biology, so be kind if I'm wrong. My point is that these might not be "errors" at all, just alternate intermediate steps that generate the same ultimate results. The assumption to date seems to be "one, and ONLY one, amino acid on RNA yields one, and ONLY one, corresponding amino acid on DNA". Is that necessarily the case, every time? I'm quite sure about ohhhh, a billion molecular biologists have already thought about this. I just don't know the answer.

    • by gringer (252588)

      > Suppose that this "error" that happens every time nonetheless yields the same original DNA sequence?

      I'm not convinced your example ACTG ----> rna UAUUCGAGAUAUAC ---> dna half-strand ACTG matches the article [with tyrosine changed to uracil], because it sounds like they're talking about substitutions, rather than insertions, in this article (i.e. ACTG ----> rna TATC (although if substitutions are happening, an insertion/deletion may also be possible).

      Anyway, there are certain RNA codons that pr

  • The article has nothing to do with how faithfully the DNA is copied; it is about a well known process where a faithfull RNA copy is changed in a specific manner. In any event, the idea of the central dogma has been dead at least since the discovery of retroviruses (early 70s) not to mention splicing (late 70s) I don't know how well the accuracy of making RNA copies (RNA pol II transcription error rate) has been studied (with nods to cairns and starvation induced mutation in the lac system) but the error ra
  • Not so Surprising... (Score:5, Interesting)

    by Genda (560240) <mariet@@@got...net> on Monday November 08, 2010 @10:08PM (#34169130) Journal

    The fact that the "errors" are consistent, suggest this is not an error at all. There was a famous experiment utilizing genetic algorithms to build an optimal circuit with the least possible number of components. It was a simple circuit, and the optimal circuit was well understood. It was an attempt to prove that the genetic methodology would quickly yield this optimal circuit. To everyone's surprise, the process yielded a circuit with fewer parts than the theoretically optimal circuit. What the designers of the experiment hadn't taken into consideration was that the genetic algorithm didn't care about theory, only outcome. It had discovered a heretofore unknown capacitive reactance on the closely spaces lines of the experimental circuit board, and found a way to use that capacitance to reduce the number of parts in it's design. Given the nature of the system, evolution found a clever way to engineer around the believed limitations of the experiment, and utilize any and all real world resources to create a solution transcending of the point of view of the experimenters.

    Likewise, there's something interesting going on here with the RNA, well outside of the obvious perspective of the researchers. Bring in biochemists, theoretical physicists, and maybe a couple applied organic chemical engineers. Let them figure out what's happening at the quantum and molecular level to have this outcome be the result. Start doing simulations. Look at topologies and protein folding.

    Look at CJD (Creutzfeldt-Jakob Disease) or BSE (Bovine Spongiform Encephalopathy) the causative agent is a prion. A vital protein that in its normal state is essential to neurological function, which can fold in more that one way, and folded the wrong way destroys brain tissue and ultimately causes dementia and death. I'll bet dollars to donuts, that there is some funny quantum state, or a protein folding problem, or some simple nonbiological chemical process whose probable result is a code misspelling in protein formation. Its an interesting problem, but not at all surprising. We are complex systems, and trying to force the world processes that make us possible into a box is at once myopic and foolish.

    • Re: (Score:2, Interesting)

      by wanax (46819)

      That reminds me of an anecdote about genetic algorithms that Rick Riolo (U. Michigan) told during a complex systems seminar. He was part of a team in the 80s that was trying to use GA's to find the most fuel efficient autopilot possible for a specific airplane. They configured an industry standard simulation environment with a realistic gamut of weather conditions, etc etc. and left the GA running for a few weeks. When they came back, they were surprised to find all the surviving autopilots had more fuel th

  • RNA actually IS a copy of the DNA. The apparent misspellings are the genetic equivalent of backslash-escaped backslashes and other meta-characters. :)

  • Typically, DNA is thought to be transcribed into RNA in an exact copy of the DNA minus random errors that occur due to poor fidelity of the polymerase that makes it. However, it's been well known for more than 10 years that RNA can be altered systematically through (still mostly mysterious) mechanisms called RNA editing [wikipedia.org]. This is a well known phenomenon that is pretty much universally believed by all biologists. However, RNA editing was thought to be a mostly rare process that only affected a handful of gene
  • That mRNAs are edited post-transcriptionally has been known for some time now. In mammals, RNA modifying enzymes will act on specific mRNAs to alter their base structures, thereby changing their amino acid encoding. (too tired right now to provide a link, but this happens for mRNAs coding for AMPA-class glutamate-gated ion channels). It's not so much that it happens per se that is amazing; its that it happens at this large scale.

    Much of this stuff is based on nex-gen high throughput sequencing technology, w

  • The blerb is intentionally misleading etc. We have known for a long long long long long while that there are indeed mutations in cells so not ever fricking set of DNA within your own body is exactly identical. ffs does cancer not ring a bell to anyone?
  • The article says that the same ''mis-spellings'' seem to happen all of the time. This suggest that that this is a ''standard'' transformation in the path gene to phenotype. What the article is saying is that this path is more complicated than we thought it was, we have discovered similar things before and I expect more in the future.

    I thought that I would say that before some religious nutter makes the claim that ''this shows that Darwin was wrong''.

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