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Biotech Science

RNA May 'Run' Genetic Coding 168

Posted by Zonk from the new-boss-same-as-the-old-boss dept.
leonbrooks writes "First a Stanford Medicine Magazine article speaks about RNA 'produced by plants that turn genes on and off', and now a Science Magazine issue says 'For a long time, RNA has lived in the shadow of its more famous chemical cousin DNA and of the proteins that supposedly took over RNA's functions in the transition from the 'RNA world' to the modern one. The shadow cast has been so deep that a whole universe [of RNA] has remained hidden from view, until recently' and speaks of 'an order of magnitude more transcripts than genes', suggesting that more actual coding is done through RNA than DNA. Is everything we know about genetics off-base? (no pun intended)"
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RNA May 'Run' Genetic Coding More

RNA May 'Run' Genetic Coding

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  • Of course it's off base... I mean... first of all you've got that stuff about ribosomes... they're not even really called that... I was talking to God... and when He made them He actually called them, "those thingies" apparently we didn't realized that and started calling em something else... silly humans...

  • Science (Score:5, Insightful)

    by Mozk ( 844858 ) on Sunday September 11, 2005 @01:33AM (#13529961)
    This is how science evolves. One theory revises another. At least they're willing to say they they were wrong, unlike hundreds of years ago.

    • Re:Science (Score:4, Insightful)

      by QuantumG ( 50515 ) <qg@biodome.org> on Sunday September 11, 2005 @01:36AM (#13529972) Homepage Journal
      There's nothing to be wrong about here. It's simply a question of focus. It took a long time to get to the point we are with genomics, now we can look at proteins and transcription control via RNA and actually discover what is going on.

      • Re:Science (Score:5, Informative)

        by Salis ( 52373 ) on Sunday September 11, 2005 @01:40AM (#13529981) Journal
        It'll more likely be translational control via RNA.

        RNA can quickly hybridize with regulatory regions of mRNA and change their translation rate.

        And these RNA transcripts can be very small, but still regulate the translation of many genes. It'll be a while until the function of all of these RNA's are understood.

        • Re:Science (Score:2, Funny)

          by M1000 ( 21853 )
          And these RNA transcripts can be very small, but still regulate the translation of many genes. It'll be a while until the function of all of these RNA's are understood.

          Its written in perl isn't it ?
          • Its written in perl isn't it ?
            Youth is always naive. :-)

            You can write unreadable code in any language, except maybe Cobol.

            There is one exception, something so terrible that assembler for an Intel processor looks nice.

            Google for TECO Emacs, consider programming with commands consisting of control characters -- and shudder. I am in awe of rms.

        • Re:Science (Score:5, Informative)

          by Anonymous Coward on Sunday September 11, 2005 @10:17AM (#13531271)
          There is much more to that already.

          It is widely known that small RNAs can regulate translation of mRNAs by binding to them in the context of specialized protein complexes (e.g. RISC) but they can also target these same mRNAs for degradation or impair their production in the first place by blocking transcription.

          I believe that you are refering to microRNAs (although there are many other types).
          MicroRNAs are commonly thought to control expression of cognate mRNAs only by inhibiting their translation but that is far from being the actual case. In fact, while this may be a common trend among the characterized microRNAs from animals, most plant microRNAs act by degrading the target mRNAs. In addition, a recent letter to Nature pointed that many microRNA targets in animals may be degraded in the process: http://www.nature.com/nature/journal/v433/n7027/ab s/nature03315.html [nature.com]
          (sorry, subscription only)

          Furthermore, there is clear evidence from plant and yeast species that small RNA molecules can regulate the structure of chromatin (the bundles of DNA and histone proteins which constitute the chromosomes themselves). By regulating the status of chromatin you can also regulate the expression of the underlying genes. It is still not clear if the same happens in animal cells...but it is possible (and many say likely).

          This adds to three different levels at which small RNA molecules can regulate the information flow from DNA->RNA->protein and we are just scratching the surface since most of these small RNAs and their targets are still being discovered (by the hundreds).

          The funny thing is that until 1998-99 these small molecules (20-40 nucleotide long) were simply dismissed as junk...
          • I was glossing over the differences (for the Slashdot crowd) between microRNA's, snRNAs, RNA interference, and other small RNA transcripts that bind to mRNA and perform X function.

            I hadn't heard about RNA's regulating chromatin compaction. In yeast, is the mechanism known? Does it help catalyze acetylation? Does it inhibit histone binding to DNA?

    • Science still said it was wrong hundreds of years ago. It's the basis of scientific thought, after all. Theories from evidence, rather than immutable certitude. Or were you talking about things like Galileo recanting [wikipedia.org]?
    • Indeed this is how science works: through incremental and (sometimes) casual findings.

      I hope this new capability of comprehension of how living matter works, could open the path to further discoveries with big impacts on the treatment of genetic diseases.

    • Re:Science (Score:4, Funny)

      by rve ( 4436 ) on Sunday September 11, 2005 @02:48AM (#13530162)
      On the contrary, whenever a scientific theory is proven wrong or incomplete, that just proves that all of science is wrong and the earth was created in 6 days, 6000 years ago.

    • Re:Science (Score:4, Insightful)

      by Tim C ( 15259 ) on Sunday September 11, 2005 @04:24AM (#13530395)
      Thats not entirely true - scientists have held their hands up and said "we got it wrong" since people started doing science. Likewise, there have always been people who - for whatever reason - have not done so, even when presented with evidence proving it.

      Often it's because it's incredibly hard to admit even to yourself that the thing you've spent most of your working life on so far is wrong, that you've "wasted" all that time. Also, don't forget that there have been times when theory Y has replaced theory X, only for it to turn out that theory X is *also* right (I'm thinking especially of wave/particle duality - for a long time we "knew" that light was made of particles, then we "knew" that it was actually made of waves, now we "know" better)
      • The next generation of wave/particle duality theory is the Wave Structure of Matter (WSM) [wikipedia.org].

        This is currently my favorite physics theory, makes for some great reading and conjecture.

    • Re:Science (Score:1, Funny)

      by Anonymous Coward
      That's what we like about the Bible story, it doesn't keep changing around every few years. God said it, I believe it, end of discussion, question answered and I can happily go about my business in small town USA. If you try to understand the scientific viewpoint you have to 'keep up' with 'current thinking' and relearn everything several times.

    • This DNA/RNA combination sounds familiar if you're in Canada and caught the first couple of episodes of ReGenesis [themovienetwork.ca].

      One of the plotlines of the show deals with a genetically engineered combination of Camel Pox (bacteria/DNA) and Ebola (virus/RNA). Trust the brilliant researchers to claim it as their own "new" idea instead of crediting science fiction...

    • At least they're willing to say they they were wrong, unlike hundreds of years ago.

      They are... as long as profits are not at stake.

      While the scientific research community is willing to acknowledge the limits of their understanding, the corporations developing genetically engineered foodcrops maintain that their products are proven perfectly safe (implying that they have a perfect understanding of the effects of the changes they have made). This claim flies in the face of significant research [actionbioscience.org]. And they hav

  • no pun intended (Score:4, Funny)

    by Anonymous Coward on Sunday September 11, 2005 @01:36AM (#13529968)
    All your base are belong to RNA.

  • Too Bad... (Score:5, Funny)

    by xski ( 113281 ) on Sunday September 11, 2005 @01:44AM (#13529993)
    Is everything we know about genetics off-base? (no pun intended)

    I thought it was a great pun.
    • Yeah, seriously, why does everyone always say "no pun intended" what it obviously was intended.
    • Is everything we know about genetics off-base? (no pun intended)

      I thought it was a great pun.

      Yep... A friend of mine has the last name Sohm, and does color photography... his company name is Chromosohm. [visionsofamerica.com]

      Tell a mere pun, get modded up allele. ;-)

  • I-4-1 (Score:1, Interesting)

    by Anonymous Coward
    I 4 1 welcome our new ribo-nuclaic-acid overlords.
    In some respects this seems kinda like a Duh.
    There are obviously undiscovered genetic mechanisms that contribute to the "directedness" of evolution. I feel that random mutation really doesn't explain the the effectiveness of genetics that we observe. And NO i dont think it has anything to do with religion. It is some kind of smarty feedback loop mechanism built in on a low level, somewhat like how neurons learn, but for genes. I suspect there is a mechanism

    • Re:I-4-1 (Score:2, Insightful)

      by amiable1 ( 770808 )
      This is off topic but...

      As someone who has thought about this seriously, I basically agree with much of what you said, but it needs clarification. A basic reference is "Darwin's Dangerous Idea", by Daniel Dennett, and his basic slogan is "Cranes but no skyhooks".

      One basic idea is that hereditary variation occurs on many different time scales simultaneously, e.g. cutlural (mimetic), epigenetic (DNA methylation), as well as regular DNA mutations which themselves fall into several classes each with a di

  • mRNA is fascinating stuff... (Score:3, Informative)

    by RyanFenton ( 230700 ) on Sunday September 11, 2005 @01:58AM (#13530033)
    Speaking just as a layman, mRNA is truly a fascinating subject [wikipedia.org]

    Using it, many, many parts of DNA can be turned off, and countless experiments can be done to find out exactly how we work. mRNA seems to be the scientific advancement we needed to spark the next revolution in the understanding of our most basic mechanisms. It is by turning things off that we can see most of what was hidden to us this far.

    Already, it has some medical use, in reducing the further damage of macular degeneration caused by excessive production of blood vessels in the eye. And it's only just begun.

    There's a lot of justified hype here. But so long as it can allow for real progress of science, I'll be happy - research in general needs some general PR on the public stage. Hopefully private and public interest in general research could at least be put in a positive trend for a while at least.

    In the words of the fictional "MC Hawking", what we need more of is science.

    • I think you might be thinking of RNAi [wikipedia.org]....

      • Re:mRNA is fascinating stuff... (Score:5, Interesting)

        by RyanFenton ( 230700 ) on Sunday September 11, 2005 @04:35AM (#13530419)
        Nah - iRNA is a subset of mRNA (see your link), which is all a subset of RNA. mRNA is so fascinating to me because of the ranges of messages that can be sent, and what all those interactions really mean. So far it seems that various kinds of mRNA, not just iRNA can be used ultimately to manipulate DNA on and off to help us see what the whole of DNA ultimately can functionally mean.

        Again, I'm just a layman on the issues - and find it deeply fascinating in terms of the pure science of it.

        Ryan Fenton
        • OK, I think I see where this is going and where the confusion might lie.

          The grandparent (and myself) wanted to point out that mRNA (messenger RNA) is a very old discovery. It was found back in the 1950s. Back then, no one knew how the information got from DNA to protein. Elliot Volkin, among others, found that there was a rapidly renewing (degraded/resynthesized) DNA-like RNA product in the cells. Meanwhile, at the Pasteur Labratories, Jacob and Monod were building a model of the lactose operon that was per
    • In the words of the fictional "MC Hawking", what we need more of is science.

      MC Hawking is my homie, you insensitive clod!

  • I suspect so but didnt know for sure (Score:5, Interesting)

    by taj ( 32429 ) on Sunday September 11, 2005 @01:59AM (#13530035) Homepage


    RNA is the hardest to work with in the laboratory. It just fall to pieces. When I was working with DNA/RNA/protien it was just really hard to work with RNA.

    so DNA->RNA->Protein

    We could work with DNA we could work with most protiens. RNA? no way. well sortof but.. no way.

    So DNA and Protein do play major rolls no doubt. but we could not get an angle on the RNA. 1990's tech.

    • Re:I suspect so but didnt know for sure (Score:5, Informative)

      by mlush ( 620447 ) on Sunday September 11, 2005 @04:25AM (#13530397)

      RNA is the hardest to work with in the laboratory. It just fall to pieces. When I was working with DNA/RNA/protien it was just really hard to work with RNA.

      I'd disagree, sure RNA is fragile and falls apart at the drop of an RNAse (1), but its chemically uniform, one batch is pretty much like the next and there are plenty of commercial protocols and reagents for manipulating it.

      Working with RNA really a matter of good technique (paranoid levels of cleanness and make sure all reagents are free of RNAse). If I had a sample of RNA that coded myosin, a sample that coded for pepsin and a sample of total RNA (all the different RNA molecules in a cell). I can use exactly the same methods to purify and study them.

      Protein on the other hand is a pit of horrors, the thing is that every protein is different, what works with one protein will completly degrade another, some proteins are so unstable that they degrade with time even under perfect conditions, some are so rare that there may only be 2-3 molecules in a cell. With RNA there are thousands of labs and really BIG money working on essentially the same molecule, with protein you may be the only person ever to study it

      (1) RNAse is the bugbear of RNA work, its a normal part of every cell and its job it to break up RNA (which it does very well). When its in the cell its kept under close control, however if the cell is broken up (to extract RNA for example) the control is broken and it eats any RNA it can find. When prepareing RNA the first step it to break up the cells/tissue and inactivate the RNAse without damaging the RNA (not too hard there a strong solution of salts it used). The trouble is that RNAse is really really stable, you can spit in a testtube boil it for 10 minutes and the only enzyme still active is RNAse. When the salts are removed and RNA extracted, any RNAse contaminant will reassemble and eat the RNA.

      • RNAse is the bugbear of RNA work, its a normal part of every cell and its job it to break up RNA (which it does very well). When its in the cell its kept under close control, however if the cell is broken up (to extract RNA for example) the control is broken and it eats any RNA it can find.
        Darned DRM. You'd think I would at least have fair use rights over my own body!

        • >> RNAse is the bugbear of RNA work, its a normal part of every cell and its job
          >> it to break up RNA (which it does very well). When its in the cell its kept under
          >> close control, however if the cell is broken up (to extract RNA for example) the
          >>control is broken and it eats any RNA it can find.
          >Darned DRM. You'd think I would at least have fair use rights over my own body!

          Don't sweat it, the binarys have DRM but the source code [ensembl.org] is freely avalable

      • RNAse is the bugbear of RNA work, its a normal part of every cell and its job it to break up RNA (which it does very well). When its in the cell its kept under close control, however if the cell is broken up (to extract RNA for example) the control is broken and it eats any RNA it can find

        You're telling me God exists, and he put in protection against reverse engineering?

        Eivind.
  • It has been known for some time that transcription factors can help determine what other genes can be transcribed. For example, in maintaining circadian rhythms in fruitflies there is the PER and TIM (timeless genes). These bind to the gene promotors, creating a negative feedback system, such that both are inversely proportionate to each other, and are antiphase with CLK/CYC transcription factors:

    (first link I found on the subject)
    http://users.rcn.com/jkimball.ma.ultranet/BiologyP ages/C/Circadian.html [rcn.com]
    http: [scienceden.com]

    • Re:some related genetics.. (Score:2, Informative)

      by Anonymous Coward
      Wow, and I thought my background in circadian research would never be useful!

      A proposed schematic of the Drosophila's circadian system is illustrated here [biophysj.org]. In the associated paper [biophysj.org], we basically created a mathematical model of the schematic using standard biochemical equations and harnessed the power of computers to test the model against results from actual "wet-lab" experiments.

  • oh good lord (Score:5, Insightful)

    by CupBeEmpty ( 720791 ) on Sunday September 11, 2005 @02:01AM (#13530039)
    ok as someone that works in this field let me say this:

    RNAi is a very useful tool, but this is definitely several years behind the curve. RNA has been shown to regulate much more than previously thought. However talk about "the secret world of RNA" is pretty much like claiming that there is a "secret world of open source software." Neither one is very secret or very new.

    The biggest contention I have is this quote from the article: "This knack of completely eliminating a protein makes RNAi a valuable research tool." This is wrong, because RNAi does not work like this at all. This is actually one of the drawbacks to using RNAi to eliminate proteins. It does not eliminate, it reduces. To get rid of a certain protein, the classic method is to completely remove the DNA that codes that protein from the organism studied. This is referred to as a "knock out" because the organism has no ability to make that proteind from the removed DNA. RNAi however, provides only a "knock down" because the DNA is still there and no matter how much RNAi is used there is still some expression of the protein. Also, many RNAi protocols are transient supressors not permanent knock outs of protein.

    So basically this is an exciting new field but don't necessarily believe all the hype because this is no miracle answer. The article is good, but oversimplified.
    • Wow, that's interesting. How is RNAi related to the natural processes for "turning on" and "turning off" genes? Do our cells naturally produce a "low line" amount of every protein? (Since you said that there's no way to completely turn off a gene with RNAi, I assume that the cell's regular RNA mechanisms have a similar effect.) Would an RNA "regulation malfunction" explain some biological oddities that just can't be explained with genetics? (For example, I have a friend with one attached and one free e
      • RNAi signals the destruction of messenger RNA. However, it is not a 100% efficient so any protein being expressed is severely reduced. but since the DNA is still there in the genome there is always some expression.

        • Re:oh good lord (Score:2, Interesting)

          by Maset ( 190867 )
          WHAT?

          silencing RNAs work by binding to mRNA (creating double stranded RNA) so that normal translation (mRNA -> protein) cannot happen.

          The destruction of RNA from siRNA (or RNAi as is being touted) is due to the cell's normal defenses to fight viriii and creating essentially an immune response.
    • But this may be one of the reasons it's getting a lot of attention. Drug companies are rarely excited about a cure, but pay close attention to long-term treatments. One suggested use for this is reducing the viral load of hepatitis C. While some have suggested that the immune system may be able to knock it out if the viral load is reduced by a factor of ten, the likely outcome is that people take this RNAi treatment for life in order to avoid liver damage.
      • Its interesting that you mention HCV because that is exactly what my lab is working on. The problem with RNAi is that there no effective delivery method for humans.

  • Short Interfering RNAs (Score:3, Informative)

    by Anonymous Coward on Sunday September 11, 2005 @02:03AM (#13530043)
    The article is referring to short interfering RNAs (aka micro RNAs), which exert their effect post-transcriptionally (i.e., they are not involved in 'coding' as the summary suggests, but rather in suppressing the expression of 'coding' mRNAs that have already been produced via transcription).

    It is not that what was previously known was 'wrong'; RNAi is just an additional (and important) layer in the regulation of gene expression beyond what was previously recognized.

  • no pun? (Score:2, Funny)

    by Anonymous Coward
    I hate when ppl say, "no pun intended" when they obviously intended to pun.

    • Re:no pun? (Score:4, Informative)

      by djupedal ( 584558 ) on Sunday September 11, 2005 @02:32AM (#13530114)
      Puns, as anyone who understands the concept of this particular type of humor knows, generally fall into two categories: obvious and subtle.

      In the case of an obvious pun, the tag line has come to be expected, and functions as a means of self-effacement, which is a respected attribute in many cultures. "Oh, wow...look...I just made a funny! I hope everyone appreciates the serendipitous nature and doesn't think I wrote the entire paragraph just for that purpose...? Honestly, it was just luck!"

      Then of course, you have the punster who, fearing that their efforts at humor will go unappreciated, use such a tag to help focus/force attention on their autoring prowess, and thereby increase the overall audience. Leave no laughter behind...

      In the case of 'i hate when ppl say...', most agree that this is simply an act of jealousy, where the childish hope is a dig will get them part of the (positive) attention as well, when, in fact, it usually warrants little more than pity.

      In those cultures where punning is a part of daily life, intended or not, such gestures should be encouraged, not derided, since they help us to identify with others, while allowing us to show our individual ability to give and take - aka share.

      Try living in a culture where the pun is non-existent. Conversations become boring rather quickly, and you have to find less elegant means of making a point. Some learn alternate means of expression, and some find it just too much work, and then become nothing but spectators. Personally, I find being able to use a pun means being able to craft better conversations, and I hate it when people don't 'get it'...

    • Re:no pun? (Score:3, Funny)

      by ShieldW0lf ( 601553 )
      I'm with this guy. That sort of shit just isn't punny at all. Something should be pun. These punks need to be punished. As Jar-Jar would say, "As you be sowin, so you be reapun."

  • C'mon (Score:5, Insightful)

    by Otter ( 3800 ) on Sunday September 11, 2005 @02:08AM (#13530053) Journal
    Is everything we know about genetics off-base?

    It's worth noting that the field of "genetics" precedes even the identification of DNA and RNA. It may be that what we now know about gene regulation is wildly incomplete (although even that is unlikely, although possible) but Mendelian genetics is completely agnostic as to whether "genes" are protein-coding or not.

  • In Soviet Russia... (Score:3, Funny)

    by FlyByPC ( 841016 ) on Sunday September 11, 2005 @02:16AM (#13530072) Homepage
    ...DNA and RNA code *you*!

    No, wait. That can't be right...
  • There may not be that many single genes, but apparently, genes also code in combination. So combinations of two genes would give you the square of the number of currently identified genes, being 30.000 ^ 2 = 900.000.000. Think what triple combinations would do.

    • Re:Combinations... (Score:1, Interesting)

      by Anonymous Coward
      I'm not sure who told you this, but it's wrong. I assume what they meant to tell you is that one gene can code for multiple proteins. This is actually very common and we call these splice variants. Take the mass1 gene. It has something on the order of 90 exons. Now, not all of those are used for any one protein but they're all the same gene. You can combine different exons and get a lot of different proteins (though, to confuse things, we usually call all of the resulting proteins by the same name).

      Add to t
      • Yeah, I was trying to be short. But imagine the part where one gene produces an effect that triggers or changes the effect of another gene. That would count as a kind of combination. I think it has been shown such modifier genes exist, except I cannot remember the proper name.
  • NOVA's new, toned down, show recently did a piece on this. You can view it at http://www.pbs.org/wgbh/nova/sciencenow/3210/02.ht ml [pbs.org]

  • Slashdot science reporting (Score:3, Interesting)

    by dancingmad ( 128588 ) on Sunday September 11, 2005 @02:29AM (#13530104)
    For a long time, RNA has lived in the shadow of its more famous chemical cousin DNA

    What is this? Maybe during the OJ Simpson trial, but for anyone that's taken an intro bio course, that's bunk. RNA is a huge part of the entire thing...there are organisms that rely on RNA as their primary genetic material.

    Once again, Slashdot, if you're going to post science news, have someone as an editor that knows some basic science!

  • No subscription to Science mag online? No prob... (Score:3, Informative)

    by Veenix ( 613903 ) on Sunday September 11, 2005 @02:31AM (#13530112) Homepage
    For those of you without a subscription to Science magazine online, here's an amusing solution - Coral Cache, since NYU has basically a subscription to all academic publications :)

    http://www.sciencemag.org.nyud.net:8090/cgi/conten t/summary/309/5740/1507?rbfvrToken=bba41c737e9d32e 852952029f4e32998530ff0d1 [nyud.net]

  • RAM and disk drives (Score:3, Interesting)

    by idlake ( 850372 ) on Sunday September 11, 2005 @03:06AM (#13530197)
    until recently' and speaks of 'an order of magnitude more transcripts than genes', suggesting that more actual coding is done through RNA than DNA.

    No, that's not what it suggests. The coding is still done (almost) exclusively through DNA; we know that because we can synthesize DNA (and DNA only) from scratch and have it work.

    What they are talking about is that RNA isn't just a short-lived intermediate in the cell, but has many other functions. That's been known for several decades, although people are only now slowly waking up to how important and widespread those functions are.

    As a rough analogy, you can think of DNA as the disk drive of a cell and RNA as its RAM. The disk drive contains all the information you need to boot, but RAM is where most of the action happens, and a lot of stuff on disk is copied into RAM, often several times.

  • WTF? (Score:2, Redundant)

    by Randseed ( 132501 )
    RNA can't code for more than DNA, because the RNA is produced from the DNA. DNA -> RNA -> protein. Now, some RNA is catalytically active, and some of it kicks back and exercises regulatory functions, and that kind of thing, but the RNA doesn't code for anything itself.

    If the /. editor is trying to claim that RNA codes for things in and of itself, then that opens an interesting possibility: Mainly that RNA, in addition to DNA, must be transferred to produce a clone (for example) because some of the R

    • Re:WTF? (Score:2, Informative)

      by alicenextdoor ( 910558 )
      Of course RNA can code for more than DNA does: RNA editing, where the RNA sequence itself is modified after transcription; differential intron splicing, where different bits are cut out of the pre-mRNA to form different forms of mRNA. Then there's post-translational modifications to the proteins themselves... A single gene can produce dozens of different proteins (there's one expression in brain tissue which produces around 900 different proteins, but I don;t recall its name) many of which can be completel
      • Of course, as I mentioned. The miscommunication, I think, is from the definition of "coding." If a gene codes for a protein, and then that protein gets spliced to hell and back into a combination of products, there's still only one gene, and the DNA still coded for it. The RNA didn't code for anything. The RNA was merely transcribed from the DNA template. The same goes for post-translational modifications to proteins.

        • The information is in the machinery, too (Score:1, Insightful)

          by Anonymous Coward
          The machinery which is doing the splicing and dicing is effectively a form of coding, too, even if it doesn't have its official coding license from an appropriate scientific authority.

          DNA isn't the only thing inherited; in the case of mitosis, you get half a cell packed with stuff, and in the case of sexual reproduction the egg constitutes a whole cell packed with stuff. Complicated stuff, including RNA.
          • That depends on what definition of coding you use. If it means the root source, wouldn't that be DNA?

            Looked at this way: I can take a novel and rearrange some of the words, take roots from others, and create a new novel or smaller story. Would that activity be the coding or would it be alteration?

            Your point about the butt-load of stuff that comes along with reproduction of any variety is point-on. We'll have to find RNA that has no basis in DNA to prove the point about it being a "root" code I
            • Think of it like a computer. The meaning of a program depends not only on the code of the program, but the semantics of the instruction set, the libraries it is linked with, and the I/O behavior of other devices. DNA, here, is the code, but other parts of hte cell are like linked libraries, their basic chemistry the underlying semantics, and other parts of the environment the I/O devices. You cannot determine cell development and behavior without at least a partial model of each of these aspects.
  • We got to know about DNA, no harm in that. Now we can get to know about RNA too. Isn't science marvelous.

  • TFA (Score:1, Informative)

    by Anonymous Coward
    Science, Vol 309, Issue 5740, 1507 , 2 September 2005
    [DOI: 10.1126/science.309.5740.1507]

    Introduction to special issue

    In the Forests of RNA Dark Matter

    Guy Riddihough

    For a long time, RNA has lived in the shadow of its more famous chemical cousin DNA and of the proteins that supposedly took over RNA's functions in the transition from the "RNA world" to the modern one. The shadow cast has been so deep that a whole universe (or so it seems) of RNA--predominantly of the noncoding variety--has remained hidden fro

  • Role of RNA in Early stages of Evolution of Life (Score:3, Informative)

    by Aeternal ( 876521 ) on Sunday September 11, 2005 @05:39AM (#13530524)
    Commentators in this thread seem to have missed one of the main implications of the quoted article (this implication is not a new one anyway): Early organisms were functionally organised, and genetically coded for, by RNAs. DNA and proteins, including the catalytic functions of enzymes, came later. See the following, for example: "1: Nature. 2002 Jul 11;418(6894):214-21. Related Articles, Links The antiquity of RNA-based evolution. Joyce GF. Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA. gjoyce@scripps.edu All life that is known to exist on Earth today and all life for which there is evidence in the geological record seems to be of the same form--one based on DNA genomes and protein enzymes. Yet there are strong reasons to conclude that DNA- and protein-based life was preceded by a simpler life form based primarily on RNA. This earlier era is referred to as the 'RNA world', during which the genetic information resided in the sequence of RNA molecules and the phenotype derived from the catalytic properties of RNA."
  • Um, no, you are not off base. ISTR my 9th grade bio teacher speaking of this back in 1983 or thereabouts.

  • Yes.

    It's pretty clear that there is a lot more to the story of biological regulation and inheritance than "DNA encodes proteins".

    Two facts:

    1) Far more proteins than genes

    2) Conserved "non-coding" DNA

    Biologists have known the first fact for a long time now--getting on for a decade. When the human genome was sequenced it was obvious that the 32,000 genes weren't sufficient account for the hundreds of thousands of proteins we know exist (I'm personally betting it's into the millions, depending on precisely ho

  • So much for intelligent design (Score:3, Interesting)

    by The Fun Guy ( 21791 ) on Monday September 12, 2005 @11:08AM (#13537961) Homepage Journal
    Not at all a well-designed, efficient and elegant system, it looks instead like the genetics is the most convoluted Rube Goldberg style mess you could imagine. To make a gene work you first express the DNA as mRNA, then edit the mRNA to remove to bits you didn't want in the first place, then reassmeble the parts you did. Except that some of that "non-coding" mRNA is used for spacing the "coding" mRNA.

    To turn a gene off, you don't just turn it off... you turn another gene on that makes a piece of interfering RNA that binds to some of the mRNA from the first gene. The second gene is controlled in the same way, maybe as a positive feedback from the first gene maybe as a negative feedback, maybe under the control of some other gene, which may or may not have the same promoter region. Layers on top of layers on top of layers of interlocking control systems.....

    Little bits and pieces of RNA, recycled and reused, adapted from their former functions to serve some new function, forming a hugely complex interlocking mess that somehow functions. This is like a typewriter constructed from a couple of staplers, a telephone and a box of paperclips.

    So, since inefficient, cumbersome and inelegant spaghetti code-type machinery is at the heart of every mammalian cell, that pretty much drives a stake in the heart of any thought that this was a product of rational design, right?

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