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Plants May Be Able To Correct Mutated Genes

ddutt writes "NY Times is running a story that talks of an exciting new discovery, which, if confirmed, could represent an unprecedented exception to Mendel's laws of inheritance. The discovery involves.. 'plants that possess a corrected version of a defective gene inherited from both their parents, as if some handy backup copy with the right version had been made in the grandparents' generation or earlier.'"

363 comments

  1. Planet RAID. by caluml · · Score: 3, Funny

    It's just plants copying RAID or PAR files. This is nothing new - we've had those for years now.

    1. Re:Planet RAID. by caluml · · Score: 0

      Planet RAID, or plant RAID - you decide! :)

    2. Re:Planet RAID. by Savage-Rabbit · · Score: 4, Funny

      It's just plants copying RAID or PAR files. This is nothing new - we've had those for years now.


      Copying? If it bothers you so much you can always sue them for patent infringement. Of course the plants might lawyer up and come back at you claiming prior art....

      --
      Only to idiots, are orders laws.
      -- Henning von Tresckow
    3. Re:Planet RAID. by Krisbee · · Score: 0

      And they have had it for ....

    4. Re:Planet RAID. by bill_mcgonigle · · Score: 2, Interesting

      It sure does sound like a distributed parity scheme. I bet the RNA-backup theory is a red herring, or at least something like tRNA can read the parity and make corrections, but it needs multiple 'votes' to ensure a proper fix (e.g from unmutated grandparents' DNA).

      Of course I don't remember too much about sexual plant reproduction - for all I know plants don't have animal-type tRNA...somebody will correct me I'm sure.

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    5. Re:Planet RAID. by roman_mir · · Score: 2, Funny

      Of course the plants might lawyer up and come back at you - first Schiavo, now this? It has begun...

      I welcome our new plant overlords.

    6. Re:Planet RAID. by shellsiebell · · Score: 2, Informative

      Just to clear up any potential confusion, tRNA is not involved in sexual reproduction; that's just plain old DNA. tRNA is involved in protein synthesis. But for the record, plants use tRNA for protein synthesis in almost exactly the same way that animals do, and they do it using ribosomes closely analagous to animal ribosomes.

  2. How this impacts evolutionary theory by AKAImBatman · · Score: 5, Interesting

    FWIW, the paper this morning was pointing out how this discovery might leave a gaping hole in evolutionary theory. The crux of the problem is that "micro-evolution" as it were, is dependant on an organism's ability to mutate from generation to generation. If a mechanism exists that prevents or corrects mutations across generations, then the theorists may *again* have to go back to the drawing board.

    Isn't it amazing how the more we know, the less we know? :-)

    1. Re:How this impacts evolutionary theory by filmmaker · · Score: 3, Insightful

      Unfortunately, that will be the major headlines coming across the Fox News screen..."Evolution flawed: mutations don't occur. Jesus weighs in on Bill O'Reilly tonight!"

      But the reality is that they don't know what causes this, they don't claim that it stops mutations on the whole, and they don't know if it stops all mutations. As per the article, it may only stop harmful mutations.

    2. Re:How this impacts evolutionary theory by cot · · Score: 5, Insightful

      This would only be true for these specific plants and only if this mechanism ALWAYS prevented mutation.

      If these conditions applied to us, we wouldn't have cancer.

      --

    3. Re:How this impacts evolutionary theory by heauxmeaux · · Score: 1

      Perhaps there is a differentiation between a 'useful' mutation and a harmful/useless one.

      --
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    4. Re:How this impacts evolutionary theory by einstein · · Score: 2, Interesting

      from what I read, the backup only gets "restored" if the plant is stressed. this would allow for error correction, but allow "happy accidents" to advance the species.

    5. Re:How this impacts evolutionary theory by asoko · · Score: 1

      According to the article, it doesn't prevent all mutations, only the ones that put the plant under stress. Bad mutations stress the plant and trigger the restoration of the backup copy.

    6. Re:How this impacts evolutionary theory by mOoZik · · Score: 3, Interesting

      But couldn't it be that those who possess the backup gene - for example, against cancer - may not develop cancer, even if their parents did? Obviously, this is only in plants and has not yet been confirmed, but how is this any different from a gene that's turned on or off? If the backup gene is turned off, what good is it? If you can turn it off, why can't you turn off the bad one? I'm obviously not a biologist, but maybe someone can take a swing at my silly queries.

    7. Re:How this impacts evolutionary theory by Anonymous Coward · · Score: 0

      "Flamebait, but needed to be stated"

    8. Re:How this impacts evolutionary theory by AKAImBatman · · Score: 4, Interesting

      If these conditions applied to us, we wouldn't have cancer.

      Cancer is caused by a DNA mutation that your body failed to correct. Errors are extremely common. The only reason why we survive is our body's repair mechanism. In the case of these plants, neither parent had a correct gene. Without a backup copy, there should have been no way for the gene to revert. Yet it did, so we're left with an odd conundrum. :-)

      That's not to say that the theories behind mutations are all wrong, but we could be seeing something akin to problems with Newtonian physics.

    9. Re:How this impacts evolutionary theory by caluml · · Score: 1
      The paper this morning was pointing out how this discovery might leave a gaping hole in evolutionary theory.

      That's OK. Queue the religious zealots bringing their so-called "Gods" to fill that hole. :)

    10. Re:How this impacts evolutionary theory by jazman_777 · · Score: 2, Insightful
      But the reality is that they don't know what causes this, they don't claim that it stops mutations on the whole, and they don't know if it stops all mutations. As per the article, it may only stop harmful mutations.

      I expect a long series of posts detailing a lot of thought experiments and speculations on how exactly evolution uses this, many outright contradictory, none observed. Just more Evolution of the Gaps from the Crowd of Lawyer-Wannabes.

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    11. Re:How this impacts evolutionary theory by DogDude · · Score: 4, Interesting

      And just to add to your post, from what I understand from all of my doctor/veterinarian friends, cancer in the human body, at least, is quite common. We are simply able to, like with virus and bacteria based diseases, able to fight them off/correct them before they get out of hand. Full blown "Cancer" only happens when these problems get out of control, and the body can no longer contain/fix them.

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    12. Re:How this impacts evolutionary theory by MightyMartian · · Score: 1
      This doesn't pose any more of a problem for evolution than cockroaches with tough-as-nails chromosones. Why would a backup copy of genes demonstrate any flaw or hole in the theory? I realize that once the no-brain science journalists get their hands on it, the quacks and liars at the Discovery Institute will be blathering on, but perhaps you could demonstrate how this realistically is anything other than a pretty neat adaption.

      Of course, it could spell disaster for the plants in question if environmental conditions change substantially and they are too locked in to specific genetically-determined traits. Variation ain't necessarily a bad thing, even if it means the odd delerious mutation.

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    13. Re:How this impacts evolutionary theory by thefirelane · · Score: 3, Insightful

      it may only stop harmful mutations.

      Granted, I have just an armchair knowledge of evolutionary theory... but isn't that a little off point? I thought the point of evolution was the organism doesn't know which mutations are harmful, many are tried, and the ones that work survive.

    14. Re:How this impacts evolutionary theory by Phil246 · · Score: 1

      could just be another mutation, except back the way instead of forward. if its the one gene being changed, then its got a 1/3 chance in getting the gene it had before back in the next mutation, assuming its this gene mutating again

    15. Re:How this impacts evolutionary theory by ucblockhead · · Score: 1

      If this stopped all mutations, they'd have noticed about forty years ago.

      --
      The cake is a pie
    16. Re:How this impacts evolutionary theory by rob_squared · · Score: 4, Insightful

      Exactly, science doesn't work like that. If a part might be, or is, wrong, that doesn't invalidate the entire theory necessarily. Evolution is somewhat like gravity. We have all this obvious evidence, but the underlying stuff is kinda misty. Newton knew gravity existed and made some nice laws. Einstein said why those laws work. String theory is a more comprehensive way of explaining Einstein's theories. Science changes, because it needs to.

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    17. Re:How this impacts evolutionary theory by Kiryat+Malachi · · Score: 1

      Nope. That's the idea behind natural selection; actually, it's the combination of random mutation and natural selection, which is part of evolutionary theory, but by no means the entire parcel.

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    18. Re:How this impacts evolutionary theory by proteonic · · Score: 0

      I'd say it doesn't impact it in a very significant way. Basically this suggests certain genes are replicated (which is nothing new in an evolutionary sense), what's interesting is that the organism can detect mistakes in both loci of a gene, and correct them. What's not really clear is whether the oranism is actually altering those damaged genes, replacing the damaged copy with a functioning copy from nearby locus, or silencing the damaged copy in favor of an undamaged copy at a nearby locus. The latter seems the most plausable. Regardless of which it is, evolution continues as normal, there's just an extra error correcting mechanism to add to the model. Enzymes that replicate DNA have error correcting activity, too, since replication itself is inherently error prone. Remember, it's the mutations that are not detrimental to the organism's survival, those that provide a selective advantage, that are considered steps "forward" in an evolutionary sense.

    19. Re:How this impacts evolutionary theory by Anonymous Coward · · Score: 0

      No... This merely says that evolution has brakes in a sense. If things are getting out of control, some species have safeguards to put a bit of a halt to mutations. Perhaps very vital mechanisms in the DNA have this property of self-correction. It is logical that some genes are more dynamic than others in their ability to mutate. For instance height is more likely to mutate than say, thickness of the skin. Thus enters: meta-genetic DNA, which I'm sure these scientists will get to eventually.

      This only supports evolutionary theory, and show yet another complicated dimension.

    20. Re:How this impacts evolutionary theory by 14erCleaner · · Score: 1

      TFA does say that the self-correcting genes may only occur in non-sexual organisms, like arabadopsis (the plant everybody studies), or frequent slashdot posters.

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    21. Re:How this impacts evolutionary theory by Anonymous Coward · · Score: 0

      > Granted, I have just an armchair knowledge of evolutionary theory... but isn't that a little off point? I thought the point of evolution was the organism doesn't know which mutations are harmful, many are tried, and the ones that work survive.

      Now while they can not predetermine which genes are good and which ones are harmful, they certainly can tell during lifetime if they are suffering or doing great - and on those variables decide whenether the genes should be reverted back for the offsprings or not.

      this way you'd get a bit into the "inherits only good stuff" mechanics

    22. Re:How this impacts evolutionary theory by filmmaker · · Score: 3, Insightful

      Science changes, because it needs to.

      Right. But also, because is those changes. Science is not some dogma, it's a process. So, for anyone who wants to get snarky about "holes" in evolution, well, no pooh-pooh Sherlock. It's not about authority or control, science is, instead, a process by which we attempt to attain and refine knowledge.

    23. Re:How this impacts evolutionary theory by MightyMartian · · Score: 1

      There's nothing in basic evolutionary theory that says that the methods of inheritance we know of (DNA/RNA) are necessarily the only ones, nor that these molecules necessarily work solely in the currently observed ways. This may be a big opportunity to see some alternate forms of inheritance. The fact is that these plants are still imperfect replicators, just slightly less imperfect than most other observed replicators. Our understanding may be revolutionized as far as Mendelian inheritance, but nothing in this falsifies evolutionary theory, or the observed instances of evolution.

      --
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    24. Re:How this impacts evolutionary theory by null+etc. · · Score: 1
      FWIW, the paper this morning was pointing out how this discovery might leave a gaping hole in evolutionary theory.

      Probably not. We're still learning all about various aspects of genes, DNA, and evolution.

      For example, did you know that plants can activate certain genes in response to stressful conditions?

      Did you know that bacteria strains can hypermutate in response to conditions in which that bacteria might otherwise die out?

      Here are a few links I've just Googled. None of them are the original research papers that I read a few years ago, but they should provide any interested reader with a good starting point:

      Plants activate genes

      Plants and bacteria strains

    25. Re:How this impacts evolutionary theory by imploded_monkey · · Score: 0

      RTFA. "But up to 10 percent of the plants' offspring kept reverting to normal." The other 90% carry the mutation.

    26. Re:How this impacts evolutionary theory by FidelCatsro · · Score: 1

      Thats all we need , Creationalist plants that refuse to evolve just to prove a point.
      Seriously though , i left biolgy behind years ago as a possible avenue of study however this is extremly intresting , If we could isolate the gene that is used to check for equality (or genes which i would more suspect) it would be intresting in the field of cancer prevention , just imagine a hormone treatment that could scan your healthy genes and make a comparison against them and terminate any rouge cells. Ofcourse in a pure sci-fi writter vent what if people used these hormones already set to attack rouge cells for one person and inject them into another person ... its a new scary sci-fi plot.
      (c)me

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    27. Re:How this impacts evolutionary theory by shawb · · Score: 4, Informative

      Think of it this way: this ability stems from a mutation in and of itself. All that it does is checks for a flaw in a certain sequence and fixes it. Probably this particular sequence has a high probability of being detrimentally mutated, and so having the repair mechanism makes it more likely that when the mutation happens, it won't kill the whole organism.

      An organism repairing it's own DNA is not unheard of. There are certain somatic (IE: not passed down from generation to generation) mutations and other varieties of DNA damage that lead to cancer. There is a mechanism in place to replace these mutations with another copy. The body also has a way of detecting and removing some viruses and retroviruses that have embedded themselves in the DNA of the host organism, to a limited extent.

      --
      I'll never make that mistake again, reading the experts' opinions. - Feynman
    28. Re:How this impacts evolutionary theory by Anonymous Coward · · Score: 0

      Of course, there will be no such article coming from Fox News (not even an unsatirized counterpart to what you suggested) but, of course, on slashdot the important thing is to lump together all the groups we hate (conservatives, Christians, etc.) and post/mod up antagonizations of them at every opportunity.

      Honestly, where the heck does Fox News come in except that there was an opportunity to belittle them?

      I post anonymously because I've learned too well that people around here are quick to jump on the "-1 overrated" mod whenever someone steps outside the political orthodoxy.

    29. Re:How this impacts evolutionary theory by jdavidb · · Score: 1

      Ah, yes. All the mechanism has to do is make sure that it only reverses mutations that have the Evil Bit set.

    30. Re:How this impacts evolutionary theory by Koiu+Lpoi · · Score: 1

      The question becomes, how does a plant honestly know a harmful mutation from a benificiary one, in the span of one generation? Unless, the plants have some inborn performance monitoring system, and backup copies of genes. Very interesting, if true.

    31. Re: How this impacts evolutionary theory by Black+Parrot · · Score: 1


      > $SUBJECT

      Probably minimally.

      > If a mechanism exists that prevents or corrects mutations across generations, then the theorists may *again* have to go back to the drawing board.

      Except that we have overwhelming evidence that zillions of mutations have accumulated over the history of life on Earth.

      We're already aware of epigenetic effects that you inherit along with your DNA (i.e., you develop from a fertilized egg that is a working system rather than just a passive data repository), and this appears to fit in the same category. So while fascinating, and presumably even important, it isn't likely to rewrite any textbooks, let alone overthrow any well established theories.

      Also, it's going to take the scientific community some time to digest and evaluate this. As someone said on talk.origins a few hours ago (\me quoting from memory)

      The article wouldn't be in Nature if the title was "Back Mutation Found in Plant".
      --
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    32. Re:How this impacts evolutionary theory by shawb · · Score: 1

      I really don't see this blowing the lid off of evolutionary science in the way that relativistic/quantum physics did to Newtonian physics. This simply seems to be a repair mechanism which has been put in place to mitigate where a certain mutation (I'm guessing this mutation is harmful) occurs. The body is known to have several DNA repair mechanisms, although most of these seem to be for somatic (not passed down to offspring) mutations.

      --
      I'll never make that mistake again, reading the experts' opinions. - Feynman
    33. Re:How this impacts evolutionary theory by Chris+Burke · · Score: 2, Insightful

      Without a backup copy, there should have been no way for the gene to revert. Yet it did, so we're left with an odd conundrum. :-)

      There is a conundrum as to what the recovery mechanism is. There is no conundrum in evolutionary theory, because the parents both aquired a mutated gene and thus clearly the correction method isn't perfect.

      As you are obviously aware (re: cancer) most mutations are bad. An evolved mechanism for correcting certain kinds of harmful mutations is hardly a conundrum for evolutionary theory.

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    34. Re:How this impacts evolutionary theory by feepness · · Score: 5, Insightful

      Full blown "Cancer" only happens when these problems get out of control, and the body can no longer contain/fix them.

      Furthermore, if lethal cancer occurs once you are past child-bearing age (around 30 up until recently), it isn't such a "bad thing" for the species. Once you've reproduced, evolution is done with you.

    35. Re:How this impacts evolutionary theory by AKAImBatman · · Score: 1

      If we could isolate the gene that is used to check for equality (or genes which i would more suspect) it would be intresting in the field of cancer prevention

      Doubtful. We've known about Deinococcus radiodurans (aka "Conan the Bacterium") for quite some time now. The darn thing has an accelerated repair rate that makes it extremely difficult to kill via DNA damaging methods such as radiation. Unfortunately, the knowledge hasn't led to anything all that useful for humans.

      Still, it will be interesting to know what this plant will teach us. (More on DNA Repair)

    36. Re:How this impacts evolutionary theory by Anonymous Coward · · Score: 0

      The gaping hole alwayse exist. The finding neither increase nor decrease the hole a bit. The implied mechnism is not fault proof, thus, it is just one of the many mechanism exsit in the cell to correct an error. Error happen, mechenism to correct error exists, but does not work 100%. Genes still mutate, and evolution still go on.

      What is sad is seeing a scientific research being over or miss interpretated.

    37. Re:How this impacts evolutionary theory by FidelCatsro · · Score: 1

      We can but hope , this really reminds me why i so used to love genetics , cheers for the links .
      I really had intended on getting back into readding up on my Genetic theory and this seems like a good area

      --
      The only things certain in war are Propaganda and Death. You can never be sure which is which though
    38. Re:How this impacts evolutionary theory by AKAImBatman · · Score: 1

      We're left with a conundrum, because our understanding says one thing while the facts say another. So we learn from it, find our errors, and move on. :-)

    39. Re:How this impacts evolutionary theory by shawb · · Score: 1

      Why would a backup copy of genes demonstrate any flaw or hole in the theory?

      If anything, the backup genes would help support evolution theory. Why would there be a mechanism to fix the DNA if DNA never changed?

      --
      I'll never make that mistake again, reading the experts' opinions. - Feynman
    40. Re:How this impacts evolutionary theory by Anonymous Coward · · Score: 0

      RTFA yourself:

      The discovery also raises interesting biological questions - including whether it gets in the way of evolution, which depends on mutations changing an organism rather than being put right by a backup system.

    41. Re:How this impacts evolutionary theory by MagicDude · · Score: 2, Insightful

      If a mechanism exists that prevents or corrects mutations across generations, then the theorists may *again* have to go back to the drawing board.

      Just because there is a backup mechanism that can prevent mutations from being passed on doesn't mean it works 100% of the time.

      In DNA replication, there are enzymes that scan the replicated strands specifically to make sure base pair matching occured correctly, and when it hasn't it can fix the problem. Without it, the number of DNA errors would be several orders of magnitude higher than they are. However, this doesn't always work. For example, take a common replication error is when an incorrect base pair is matched. So where a G should have been matched with a C, an error takes place where a T is matched with a C. Now, ordinarily the error-checking enzyme would notice that error and change the T back to a G, but sometimes it goofs, and fixes the wrong half of the error, so in this case it would change the C (which is the correct base) to an A (to match with the incorrect T). Thus, a mutation has occured in spite of a backup mechanism to insure genetic reproduction. Who's to say that this mechanism of genetic protection in the article can't malfunction in a similar way?

    42. Re:How this impacts evolutionary theory by evought · · Score: 3, Informative

      It need not stall mutation, but merely reduce the impact of deleterious mutations by encouraging heterozygosity.

      Lets take a common human example: syckle-cell anemia.

      Syckle-Cell is a mutation in the blood cells which causes them to be deformed and clog capillaries (amoung other things). The condition is fatal without treatment. However, having sycle-cell anemia also makes one resistant to malaria. How is this helpful?

      If someone has only one gene for syckle-cell (they are heterozygous recessive), they are resistant to malaria but the anemia wont kill them. If they have both bad genes (they are homozygous recessive), they die of the anemia. If they are homozygous dominant (both functional genes), they die of malaria. In malaria hot-zones, you get a lot of heterozygous recessive individuals and a lot of children dying of one condition or the other.

      Now, imagine that you had a mechanism to correct a deleterous mutation, but *only* if the mutation is homozygous. A homozygous dominant individual dies of malaria. A heterozygous recessive individual is mildly affected by the anemia but is protected from malaria. A homozygous recessive individual is *corrected to heterozygous* and is thereby protected from malaria without dying of anemia! You have a fourth of affected children dying instead of half.

      Plants may use this to end up with a stable heterozygous population for deleterious mutations which have some benefit, say a root hair deformation which nevertheless protects from parasites. This can actually speed up genetic drift by preserving mutations which might otherwise die out. In the malaria example above, it is common for human populations to quickly lose the gene if the malaria threat is removed. In the case where a corrective mechanism exists, the anemia would not be as harmful and might stay in the population longer (for the next outbreak).

      Not only does this not invalidate current ideas of evolution, it is obvious how a critter with such a mechanism would quickly have an advantage.

    43. Re:How this impacts evolutionary theory by MightyMartian · · Score: 1

      What seems to count now is that science journalists will likely head off with idiotic bylines like "Evolutionary Theory Thrown Into Chaos", which cynical ID and Creationist advocates, knowing full well that the larger part of their supporters don't actually even know what evolutionary theory is, will grasp on to and declare that GODDIDIT. They'll also pepper it with things like "Hitler and Stalin were Darwinists", "Darwin recanted on his death bed" and "Have you ever seen an airplane get assembled out of spare parts in a junkyard" and the long and idiotic list of pseudo-arguments that get recycled.

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    44. Re:How this impacts evolutionary theory by aichpvee · · Score: 3, Insightful

      Should be noted, because a lot of the creationist kids around here don't seem to understand, that when someone says "know" or "they can tell" or "they decide" in these contexts, the poster is NOT talking about a conscious intelligence making a decision. They are making an anthropomorphization and only a moron would take it literally (as I have already seen several people do on this page.)

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    45. Re:How this impacts evolutionary theory by Chris+Burke · · Score: 2, Insightful

      It isn't clear to me how this contradicts anything we already know. It only presents a new behavior that we don't yet understand.

      The plant still mutates. These mutations can exist in the plants, and be passed on to children. That is what evolutionary theory predicts/requires. That there is a newly discovered and not yet understood mechanism for repairing some mutations is fascinating, but how does it represent an error in our previous understanding? Just because we weren't aware of all ways in which the negative effects of mutation could be mitigated?

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    46. Re:How this impacts evolutionary theory by Anonymous Coward · · Score: 1, Interesting

      There are theories about how the human life span is relatively long because grandparents played an active role in child-rearing, leaving the younger and healthier parents to hunt, farm, and fight off tygres.

    47. Re:How this impacts evolutionary theory by TrevorB · · Score: 1

      I've been reading Matt Ridley's The Red Queen: Sex and the Evolution of Human Nature. Jumping off Richard Dawkins ideas that it's not survival of the fittest species, or even the fittest individual, but the survival of the genes *themselves*, I'm not overly surprised that recessive genes can express themselves generations afterward. Genes in fact compete with *each other* in the same individual, struggling to force some genes out, other times co-existing. In fact, this fits right in with Dawkins ideas. These "repairing genes" want to survive to further generations, and if they happen to have to repair their host so that it can have sex and pass on the genes, then so be it.

      Genetics is an amazingly complex science. Genes sometimes actively kill off their competators. The concept of XX being female and XY being male applies to humans but not necessarily other animals, or even other mammals. (Some birds have XX and XY reversed for male and female, some mammals have a third "W" chromosome to determine gender. This just blew me away when I first read it.

      Think of genes as a computer program, perhaps like a computer virus. You can program a virus to rootkit other apps. Genetics provides more than enough complexity for genes to be able to perform a similar function.

      Mendel's work was very, very good, but seems ancient in the context of what we've learned from genetics in the past 25 years.

      Mendels laws of inheritance are like Newton's laws of Gravity. They hold in most everyday situations, but there are strange and unusual exceptions. Saying that this says there's a flaw in evolution is about the same as saying because of questions raised by Einstein's relativity, gravity might be false.

    48. Re:How this impacts evolutionary theory by Anonymous Coward · · Score: 0

      Why did this need to be stated? Is it illegal to hold a certain view of the Universe? Is it really that big of a stretch to think there is something more to life than random chance?

    49. Re:How this impacts evolutionary theory by DogDude · · Score: 0, Flamebait

      Unfortunately, the human species is already going downhill fast. We have the most intelligent people NOT breeding, and the idiots breeding like rabbits. Our hospitals (at least in the modern world) keep all kinds of unhealthy people alive, and stupid people are saved time and time again from their own stupidity by excellent health care. I'd love to see a real study of these issues, but I fear that any kind of study that tackles these issues will be shouted down by BOTH the Religious Righteous and the Politically inCorrect, just like the "Bell Curve" study was.

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    50. Re:How this impacts evolutionary theory by Anonymous Coward · · Score: 0

      So...you decided to have a little go at the people round here. And the way you decided to do that is to mock them for thinking.

      Well, you'll find that creativity and speculation are kinda seen as positive qualities round here: this isn't Sunday School, after all.

    51. Re:How this impacts evolutionary theory by thefirelane · · Score: 4, Insightful

      There are certain somatic (IE: not passed down from generation to generation) mutations and other varieties of DNA damage that lead to cancer. There is a mechanism in place to replace these mutations with another copy. The body also has a way of detecting and removing some viruses and retroviruses that have embedded themselves in the DNA of the host organism, to a limited extent.

      This is true, but everything you describe is where the organism detects genetic changes when it has a clear copy of the 'good' genes elsewhere. In the case of cancer... one cell mutates, but all the others still have the good DNA. The thing that makes this case so interesting, from what I understand, is that the entire organism had the new DNA so what would it compare against... (no I didn't read the article yet)

    52. Re:How this impacts evolutionary theory by Chris+Burke · · Score: 1

      Nice explanation. This kind of thing, while unexpected, seems perfectly natural to me. Evolution doesn't just occur on the traits expressed by DNA. Evolution also occurs on the mechanism for mutating/retaining DNA. It's not just about finding the ideal size/feature for an environment, but also the ideal mutation rate and bad mutation elimination mechanism.

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    53. Re:How this impacts evolutionary theory by stm2 · · Score: 1

      There are several mechanism for DNA repair. DNA polymerase has proof-reading function built-it. Nucleases are used to remove foreing DNA. All know mechanism till now used the other DNA strand as template for repair. What is new now, is that this new feature works EVEN when both sequences are mutated, because the missing info could be encoded in a RNA.

      DISCLAIMER: Didn read the original Nature article, just read a summary at new scientist, so this could be wrong :)

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    54. Re:How this impacts evolutionary theory by Zouden · · Score: 2, Informative

      ...but how is this any different from a gene that's turned on or off?

      From the article:
      A mutated gene can be put right by various mechanisms that are already known, but all require a correct copy of the gene to be available to serve as the template. The Purdue team scanned the DNA of the entire arabidopsis genome for a second, cryptic copy of the hothead gene but could find none.

      They then go on to say they suspect RNA of holding the backup copy somehow. But (as the article mentions) RNA is unstable and unsuitable for holding data for any decent amount of time.
      IANAB (I will be one soon), but I suspect there is something they overlooked. For instance, when they 'scanned the genome', they probably scanned the online version (database). If they sequenced the genome of their particular plant, they'll find a backup copy.

      --
      "A week in the lab saves an hour in the library"
    55. Re:How this impacts evolutionary theory by shawb · · Score: 1

      While there was not another copy in DNA, it is possible that there was a backup copy in RNA Maybe the mutation is very simple and repairing could be as simple as inserting a couple of base pairs in the right place, which really wouldn't even need a DNA template. A sophisticated enough protein could "recognise" the spot that repairs need to be made in, especially if it's a protein/RNA hybrid molecule (which is actually quite common.)

      I guess it all depends on the specifics of the individual mutations. The mutation may be as simple as one base pair being off.

      --
      I'll never make that mistake again, reading the experts' opinions. - Feynman
    56. Re:How this impacts evolutionary theory by MutantHamster · · Score: 1

      While the question is interesting, the objective statement reminds us that whatever impact it may have theoretically, must be empirically proven, and considering that right now the opposite has been empirically proven (there are documented cases of plants switching around their entire DNA sequence, as well as observed speciation) already. Despite what this discovery suggests, it doesn't change the fact that plants have clearly mutated before.

      --
      My Greatest Heist - Muisc partly inspired by the unbeatable Qwantz
    57. Re:How this impacts evolutionary theory by T'hain+Esh+Kelch · · Score: 0

      Ah, but a natural evolution would increase a plants fitness and make it a better survivor. Im pretty sure that this mechanism only works on certain alleles. (Spelling?)
      And second of all, you never know when this mechanism has 'mutated' into existence.. After all, the plants had to develop into, well, plants, at some point in history. :)

    58. Re:How this impacts evolutionary theory by rooBoy · · Score: 1

      An important thing to remember is that plant genomes undergo frequent duplication of the entire genome. Many important crops (eg cereals) are polyploid and have at least four copies of everything in their genome. If a plant has been polypoid at some point in history, some of these genes may have moved around in the genome and explain how the extra copies got there. Normally these extra copies would be deleterious to the plant as they would be out of balance with other genes, and silencing of them would evolve. All that would be required is that the silencing be removed, and if the plant is going to die there is strong selection for this to happen. I agree with other poster who suggested this is likely to be epigenetic ( a change in the way the DNA is packaged, rather than the DNA itself) to explain the high frequency. However a similar finding in bacteria turned out to be a greatly increased mutation rate in the dying bacteria as the cell systems stopped working correctly.
      For those of you in unis or with access to Nature journals the link below summarizes the debate on the previous apparently lamarkian results in bacteria.
      http://www.nature.com/cgi-taf/DynaPage.taf?file=/n rg/journal/v2/n7/full/nrg0701_504a_fs.html&filetyp e=pdf

    59. Re:How this impacts evolutionary theory by Zutroy+Of+Earth · · Score: 1

      > the theorists may *again* have to go back to the drawing board.

      I don't think we have to worry about that too much. At least we don't have to erase everything :)

      My thinking is, your "backup copy" will be damaged the same way that your DNA is damaged. How does the mutation detection mechanism work? By comparing the backup to the original? What if the backup is mutated? This hopefully can't be it. What if it detects "malfunctions" in the cell. Well, then it could copy the backup DNA on the new one, but which part do you copy? If you copy all of it you're still stuck with potential mutations. If you know which part to copy, there is still a chance (smaller, but still present) that your backup copy is damaged and that you'll also insert anoter (or the same) mutation back in the original.

      Like other posters said, we need a RAID (RAIDNA?) for these corrections to be right most of the time.

      I think I'll go RTFA :)

    60. Re:How this impacts evolutionary theory by filmmaker · · Score: 2, Insightful

      Well, I know what you're saying. However, I'd submit that the cultural climate right now is dangerous. I'd submit that those folks who subscribe to the Christian faith, a particular mythology, and a damn fine one if I may say so myself, have attained a position in America's mainstream consciousness, in its government and in its media that is dangerous. The average person is actually starting to believe his own hype, sort of like Bono did right around the time of Joshua Tree, hence all the subsequent sucky US albums. Fact is, just because media panders to the right for its own reasons (ad revenue, of course), that doesn't legitimize what are, let's face it, on the whole some pretty insane and downright dangersous beliefs and dogmatic belief systems.

    61. Re:How this impacts evolutionary theory by Anonymous Coward · · Score: 0

      Yes. It is illegal. Return to your suicide booth immediately.

      Seriously, there's no such thing as a "miracle" when you examine probabilities. With enough interactions going on, there's bound to be constant numerical "impossibilites" happening every second.

    62. Re:How this impacts evolutionary theory by AKAImBatman · · Score: 1

      Genetics is an amazingly complex science. [...] Think of genes as a computer program, perhaps like a computer virus. You can program a virus to rootkit other apps. Genetics provides more than enough complexity for genes to be able to perform a similar function.

      Indeed. With the discovery a few years ago that the human genome is shorter than it was supposed to be, it strikes me that the analogy can be taken even further to say that the organism is the "hardware" that the program runs on. :-)

      Mendels laws of inheritance are like Newton's laws of Gravity. They hold in most everyday situations, but there are strange and unusual exceptions. Saying that this says there's a flaw in evolution is about the same as saying because of questions raised by Einstein's relativity, gravity might be false.

      There is a problem with this statement. Newton started with the facts that objects are pulled to the ground. This was easily provable to a tolerance that is almost impossible to argue. Einstein's corrections then showed the mechanism behind that fact, and thus was able to correct various errors in the theory.

      Starting with Mendel's theories does not prove that a fish became a rodent to within any sort acceptable margin for error. All it shows is that genetics work in a specific fashion, and that we can extrapolate certain theories from that. These oddities that we've been finding may correct our understanding of provable genetic occurances by providing the precise mechanism behind them. :-)

      So to correct your analogy:

      An extrapolation of Newton's theories suggested that a spaceship should be able to visit another star system in less than a year Earth time. Einstein's corrections showed that to be impossible using Newtonian methods.

      Similarly, genetic theory provides a basis for how inheritance works. We can then extrapolate our currect hypothesis of single -> multi-celled life. Corrections to our genetic theory may make the hypothesis impossible.

      Honestly, I like the way the String Theorists phrase their theory: "It may be that the universe we live in is far stranger than anyone could have predicted!" ;-)

    63. Re:How this impacts evolutionary theory by Koiu+Lpoi · · Score: 1

      Excellent point. I didn't read the article, but perhaps, because the gene was mutated once, it had a 'predisposition' for mutation in that gene, and thus another mutation caused it to reverse? A fluke, but a possible fluke nonetheless.

    64. Re:How this impacts evolutionary theory by MightyMartian · · Score: 1
      Why did this need to be stated? Is it illegal to hold a certain view of the Universe? Is it really that big of a stretch to think there is something more to life than random chance?

      And it must be oft repeated that evolution is not blind chance. Individual mutations are random, but selection is not a random process. It isn't a law of the universe to hold incorrect views, but I'd hope most reasonable people, even if they were to decide to disagree with a major scientific theory, would actually bother to understand what that theory says.

      --
      The world's burning. Moped Jesus spotted on I50. Details at 11.
    65. Re:How this impacts evolutionary theory by harvardian · · Score: 5, Informative

      Your explanation is fairly on the mark, and I'd mod it up except that I want to participate in the discussion.

      The thing that's so remarkable about this case is as you said: BOTH alleles of the gene of the plant were defective as inherited from their parents, and yet they somehow reverted to an allele from the grandparents, across the entire organism. According to current theory, sexual replication causes a kid to inherit one allele of each gene from each parent (and by "theory", I mean you can watch this happen under a microscope). If both alleles received are "faulty" (which is a sticky term to use in many cases), there's no known way for a newly fertilized cell to know this. There's no information about what the correct gene should look like except the two copies of the gene it has. In cancer, as you point out to address the parent post, there is always a source of information used to correct the mutation.

      In the case of UV damage, information exists in the form of two fused thimidine molecules (two T's). If a cell sees two fused T's, it has a repair mechanism for correcting them. But, importantly, if this mistake is not corrected before DNA duplication occurs, then random bases are paired with the T's, because they're damaged. Once this happens, each daughter cell has lost the information required to correct the problem, and the mutation persists. If this happens in an unlucky spot, you can get melanoma.

      In the case of other more serious damage, like double-stranded breaks, your cell pulls in the other copy of your genes and edits against that. The information needed for repair is the "good" copy of the allele in the sister chromosome.

      So you can see why this is so confusing -- in the case in the article the daughter cells, with two bad alleles for the gene they studied, are supposed to have no information pointing them to the gene from the grandparents. And yet they did, since they were able to fix it. The article postulates that this could be because a THIRD copy of the gene exists as RNA that's passed down from the grandparents (third since there are two chromosomes, each with a copy of the gene). If this were true, then the RNA would be the source of information required to fix the problem. Alternatively, there could be a specific protein that hunts down mutations in this gene and somehow fixes it, since it somehow bonds only to the correct version of the gene. But that's just my wild speculation.

    66. Re:How this impacts evolutionary theory by harvardian · · Score: 1

      If these conditions applied to us, we wouldn't have cancer.

      We also wouldn't have the genetic variation required for evolution. So this obviously isn't something that can happen ALL the time.

    67. Re:How this impacts evolutionary theory by joak · · Score: 1

      I expect a long series of posts detailing a lot of thought experiments and speculations on how exactly evolution uses this, many outright contradictory, none observed. Just more Evolution of the Gaps from the Crowd of Lawyer-Wannabes.

      Typical. Talk about taking the fun out of cool stuff; a single interesting, but unconfirmed result in one species is used as "proof" that evolution is wrong by those creationists who claim to be such wonderfully cautious skeptics.

      And they didn't even need to RTFA to do so:

      But up to 10 percent of the plants' offspring kept reverting to normal.

      So 90%+ of mutations get through. Not exactly a huge stumbling block for any existing theory.

      Fascinating discovery, though, for those who actually care about science. It could have implications in any number of things.

    68. Re:How this impacts evolutionary theory by Artifakt · · Score: 1, Redundant

      That's not really ture for humans. Reproduction for humans involves getting your kids raised, not just born. As long as even grandparents and great grandparents may sometimes be healthy enough to contribute more to their offspring's survival than to diminish it, that is an evolutionary pressure for longer lifespans. In fact, that probably explains why we have the potential to live so much longer than any similar species.

      --
      Who is John Cabal?
    69. Re:How this impacts evolutionary theory by Mr.+Slippery · · Score: 2, Interesting
      They then go on to say they suspect RNA of holding the backup copy somehow. But (as the article mentions) RNA is unstable and unsuitable for holding data for any decent amount of time.

      It's been over 20 years since my last biology class (well, not counting some recent anatomy & physiology in massage school) so this might be a dumb idea; but I wonder if there could be some sort of "parity bits" in the "junk" DNA? Not a full backup copy, but enough extra information to be able to correct some mistakes.

      --
      Tom Swiss | the infamous tms | my blog
      You cannot wash away blood with blood
    70. Re:How this impacts evolutionary theory by logpoacher · · Score: 4, Insightful
      One counter-argument might run that although we might be going downhill fast in evolutionary terms, we're also going uphill very fast technologically.

      Doesn't matter how dumb the primordial organic neuroprocessor is when it's been augmented with a Cyberdyne Systems omni-intelligent prepare-to-be-assimilated super jewel. Or, translated into Earth-speak, in the time-frame that these problems might become manifest, we might be able to fix them, or make them irrelevant.

      Now, the above argument can be fired at all sorts of things where people might prefer to sit on their asses rather than fix something - the environment, for example! - but it raises an interesting point: if you don't like the Hope-We-Can-Fix-It answer, then just what alternative solution do you propose?

      We can't exactly just turn people away from hospitals; I don't think we want our government to start imposing sterilization orders on "stupid people". So the study that you propose isn't gonna result in any useful action - is it? Except that if it revealed what you suggest, it would just be used as ammunition by people who want to control everyone. And therefore, even if it's true, it isn't actually anything we want to have sanctioned!

      BTW, I'm not arguing against you here - it's pretty likely, in my view, that our capabilities and societies are acting pretty anti-evolutionarily, as you say. It's debatable about how strong such influences are - the nature vs nurture debate and so on - but even assuming that the influences are strong, I'm not sure what a decent humanitarian society can do about it.

      Apart from develop yet more remedial technology...

    71. Re:How this impacts evolutionary theory by extensis · · Score: 1

      DNA repair relies on that an organism can identify an error in it's DNA. DNA repair relies on the fact that DNA is a redundant double strand and that at least one copy will be correct, this is much much differnt. We have a species, Arabidopsis thaliana that has a homozygous mutaion in a gene called HOTHEAD. (For non geeks homozygous means that both parents donated the same mutant copy of the gene) This mutant was then crossed with itself (insert masturbation joke) and the off spring had a corrected, normal type gene. The normal version of the gene wasn't located in the parents! Random mutation was ruled out, recombination with other genes was ruled out, and there were no other copies of the gene in the DNA to act as spell checks. The closest source of a working gene copy was the grandparents, and this is incredible. And further more they're work suggested that this gene is not unique in it's mode of inheritance and may be genome wide. If anyone doubts the impact of these findings, you only need to see the cover of the next edition of the jounal NATURE, not a place that highlights insignifcant findings.

      --
      Mike Jones-{ Genetic Engineer, in Training }-
    72. Re:How this impacts evolutionary theory by Infinite+Entropy · · Score: 1

      You know, on Slashdot you can say shit. This isn't Fark! And I would really have to wonder what would happen if somehow someone found evidence that conclusively proved that evolution could not produce modern lifeforms. I already see a certian level of dogma in what Richard Dawkins says, like his response to spirit is broken Michael J. Behe's charge that some biomolecules would have been impossible to have evolved. Dawkins just said that they MUST have evolved and we just weren't smart enough to figure out how.

    73. Re:How this impacts evolutionary theory by Anonymous Coward · · Score: 0

      Science is a glorified screwdriver.

    74. Re:How this impacts evolutionary theory by unMasqre · · Score: 1

      Plants do have an inborn performance monitoring system: it's called the plant itself, its ability to produce seeds, grow tall, etc.

      "Harmful" genes impede the plant's fitness and "helpful" genes promote it.

      A plant with deleterious mutations "knows" it by not competing as well. What it doesn't know is a priori whether a gene will help or hurt. What it also (except somehow in the case in question) is what alternative configuration of an allele that's not present would be better than the one currently in use.

      Ftr, this doesn't change much in terms of evolutionary theory. Plants alreay do all sorts of whack things that we humans find incredible (because we couldn't do that). Evolution still happens and is still happening whether mutations are acquired rapidly or more slowly. 5 billion years is still a very long time, especially to things that operate in the millisecond world.

    75. Re:How this impacts evolutionary theory by glesga_kiss · · Score: 2, Insightful
      One counter-argument might run that although we might be going downhill fast in evolutionary terms, we're also going uphill very fast technologically.

      Which IS evolution true to the word. It ain't all roses though, I can see a world ahead where everyone needs corrective eye surgery as bad eyesight genes run rampant as their damage can be undone and there is no longer any natural gene filter. The weak are flourishing and breeding, where as one hundred years ago they wouldn't have made it to childbearing age. Our reliance on technology will only become greater the more we use it.

      It's a messed up issue. What can you do to prevent it? Nothing without breaking most moral and ethical taboos! We may actually be forced to start correcting genes in our children in the future should it start to get really bad. It's devolution of the species, but evolution of the society.

      Nature often has a solution. Plagues and such like, though not very nice, can actually serve as a strenghener for the population as a whole. It is reckoned by many that Europe has a lower HIV infection rate due to the bubonic plagues. I believe that the study found that 25% of the population were resistant to HIV entirely.

      So, we could be setting ourselves up for a big fall (and with our own bioengineering creating new viri...) but it'll likely all work out in the end.

    76. Re:How this impacts evolutionary theory by superyooser · · Score: 1
      Imagine science is not some dogma.
      It's not about authority or control,
      It's a process to attain and refine knowledge.

      Hey, finish the song!

      No need for greed or hunger,
      A brotherhood of man,
      Imagine all the people
      Sharing all the world.

    77. Re:How this impacts evolutionary theory by Artifakt · · Score: 1

      It's an EXTREMELY BASIC conundrum because, if there is an error correction mechanism, it must be at least roughly as good as the DNA it corrects to be of much use. If the error correction is something like RNA, well modern DNA makes copying errors with about 1/100,000th the frequency of RNA. There won't be much error correction out of a coding scheme that is that error filled iteself.
      Even without the multicelled organism's version of DNA polymerase and a follow on repair enzyme to help error correct, even what we call 'primitive' DNA based bacteria have at least several thousand times greater copying fidelity than with RNA.
      So, if the Error Correction Mechanism's copying system is much better than RNA, and at least close to as good as DNA, maybe even better, why isn't it being used as the main Genetic code? After all, RNA is still used by some viruses as their main genetic mechanism, and despite its flaws, hasn't been completely weeded out yet. RNA is used by more complex organisms only as a messenger. How could a much better coding system be weeded out for carrying the main code for actual heredity faster than a much worse one? And how come an apparently much better coding scheme than RNA exists, but isn't being used for short term transfer anywhere, just for this sort of error correction?

      --
      Who is John Cabal?
    78. Re:How this impacts evolutionary theory by Anonymous Coward · · Score: 0

      that doesn't legitimize what are, let's face it, on the whole some pretty insane and downright dangersous beliefs and dogmatic belief systems.

      You mean like Communism/Socialism? Don't be so blind as to believe one side has a monopoly on "dangerous" ideologies. It's all a matter of opinion.

    79. Re:How this impacts evolutionary theory by Anonymous Coward · · Score: 0
      Wrong.

      Humans have been outbreeding since around the time of the industrial revolution, from essentially inbred lines. This has dramatically increased worldwide genetic variation.

      Also you assume intelligence is inherited. No real evidence for this. Probably got more to do with opportunities than genetics.

    80. Re:How this impacts evolutionary theory by Queer+Boy · · Score: 1
      FWIW, the paper this morning was pointing out how this discovery might leave a gaping hole in evolutionary theory.

      Uh sure. All this explains is why plants don't get cancer.

      --
      Not since Marie-Antoinette played milkmaid has looking simple and honest been so fake and complicated.
    81. Re:How this impacts evolutionary theory by Artifakt · · Score: 1

      It poses a basic problem because most modern Evolutionists don't just claim that Natural Selection is responsible for Speciation, but that it is responsible for selecting the current Genetic code itself. By current theory DNA itself evolved from more primative hereditary mechanisms. Many Evolutionists try to extend this even farther, talking about cosmic and stellar evolution.
      Just like RNA was a more primitive precursor to DNA (by the standard theory), this Error Correcting Code would have to fall somewhere in that model of mechanism evolution. It also has to be pretty good at copying fidelity, because DNA is pretty damned good (as in one error per billion passes good), and if this code is thousands of times worse, it won't survive unchanged long enough to be useful as an error corrector. That means this is a coding that could be used for the basic mechanism of heredity, just as DNA and RNA are, and it has much better copying fidelity than RNA. In copy quality, it has to be close to, or even better than DNA. (From basic chemestry, it seems very, very doubtful any other chemical combination could be exactly as good as DNA but no worse or better).
      OK, so where is it? Some primative life forms still exist that use RNA for a genetic code, but this code, tens of thousands of times better, isn't still used in any living organism for actual heredity? What, the better code got weeded out of one application faster than the worse one? Advanced organisms still use RNA for short term information transfer, but this code, tens of thousands of times better on at least one count, isn't used anywhere for short term transfer either? How can a code be good enough to survive multiple generations of tranfer until it is needed, but simultaneously not good enough to use short term?
      Handwave over all that, and the theory stands as elaborated. Admit that it is a very major example of 'survival of the less fit code" and the theory of Evolution explains only how species diversify and otherwise change. It becomes impossible to claim that Evolution reveals how life gets started and advances to near flawless replicators like DNA. Of course, that was why Darwin called his best book "The Origin of Species", and not "The origin of Life". He had the sense to limit his theory to what he had enough evidence to support. There are at least five apparently sound arguements against extending natural selection to 'explain' the origin of life. This was just one more. You won't hear any of them from the current establishment.
      I like the quacks, no brains, and liars remarks in your post. Sure, many of those people have a bias from their religion. They also include people who have noticed many other flaws like this one. Those flaws aren't going to go away faster by you resorting to name calling. They are real, they cry out for an explanation, and sooner or later, that explanation will be part of the theory that is to come.

      --
      Who is John Cabal?
    82. Re:How this impacts evolutionary theory by Anonymous Coward · · Score: 0

      IE: . . . mutations . . . that lead to cancer.

      IE causes cancer. I knew it!! You read it here first, folks. Switch browsers while you still have a chance!

    83. Re:How this impacts evolutionary theory by Anonymous Coward · · Score: 0

      That's right, there's no such thing as mutation. So how shall we describe you? retard.

    84. Re:How this impacts evolutionary theory by Mr.+Slippery · · Score: 1
      We have the most intelligent people NOT breeding, and the idiots breeding like rabbits.

      You're assuming that intelligence is highly inheritable, a very debatable premise. Indeed if the most intelligent people were to start having more children, they'd be less able to care for them all, degrading the development environment and probably leading to less intellectual development in the kids.

      The concern that the "feebleminded" are outbreeding the able dates back at least to the dawn of the 20th century; despite the rising tide of idiocy that century saw the development of powered flight, space travel, and solid state electronics. (And eugenics programs in the U.S. and Europe that attempted to weed out the "feebleminded".)

      --
      Tom Swiss | the infamous tms | my blog
      You cannot wash away blood with blood
    85. Re:How this impacts evolutionary theory by espressojim · · Score: 1

      Since central dogma states that info flows DNA->RNA (except in odd cases with viruses), how does the RNA exist in the organism to correct the DNA? RNA degrades pretty quickly (otherwise, regulation of protien levels would be difficult), so it's not going to be around.

      Hm, unless this happens at meiosis, and the parent's plant corrects it - but how would *it* know, since it has one copy of each allele?

      There isn't by chance a pseudogene that is encoding almost the same info as this gene, and it's correcting off that?

      I'm very interested in reading the actual paper, and starting to get to the bottom of this. Maybe my group at the Broad will talk about this in the next week or two (even though we do human genetics, it would be pretty cool to talk about.)

    86. Re:How this impacts evolutionary theory by Anonymous Coward · · Score: 0

      >>>>>That's not to say that the theories behind mutations are all wrong, but we could be seeing something akin to problems with Newtonian physics.

      Hardly. This fits perfectly well within evolutionary theory as an extraordinary adaptation. The very fact that this is considered remarkable should be a hint that the mechanisms that fall under the rubrik of "evolution by natural selection of genetic variation" are still generally prevalent.

      If this could not be explained in evolutionary terms then you might see something like the overturning of Newtownian mechanics. But this CAN be explained in evolutionary terms. The species that can do this have developed a remarkable physiological system for repairing particular parts of their genetic material. It doesn't always work but obviously it confers some advantage on the plants.

    87. Re:How this impacts evolutionary theory by MightyMartian · · Score: 1

      This whole post simply attempts to confuse abiogenesis and evolutionary theory. Abiogenesis is a seperate (though related) field of inquiry. Evolutionary theory requires only that there be imperfect replicators. The question of how the original replicators came about is a trickier one, but if one simply invokes God as the answer, then one does nothing more than deny that the beginning of life is really explainable. In other words, it's a God-of-the-gaps argument. We have a hole in our knowledge, and your answer is to shove a magical explanation in the middle. That may be fine for now, but gap-gods can only get smaller as knowledge grows. I for one find some of the current theories of abiogenesis fairly compelling, though obviously we may never be able to know the full history, as it is hidden by nearly 4 billion years of geological and biological evolution.

      --
      The world's burning. Moped Jesus spotted on I50. Details at 11.
    88. Re:How this impacts evolutionary theory by shawb · · Score: 1

      how does the RNA exist in the organism to correct the DNA? RNA degrades pretty quickly

      While pure RNA might not stick around very long, RNA associated with a protein and/or lipids could be fairly robust. The central dogma, while generally correct, does have some exceptions, namely retroviruses and retrotransposons. If you are of the school of thought that viruses originated as a flaw in the DNA reproduction/repair process (as they can not reproduce without a host) then it is trivial to see that reverse transcriptase could have at one point been created in an organism, allowing for RNA->DNA.

      I'm not saying that this is the way it is, I'm just saying that this is one possible explanation. Basically this does not have to be the hand of god coming down and putting the genes back into the plant.

      --
      I'll never make that mistake again, reading the experts' opinions. - Feynman
    89. Re:How this impacts evolutionary theory by bodrell · · Score: 1
      An organism's cells can certainly identify and discard misfolded proteins. And although DNA is supposed to be just the "template," certain patterns result in less stable DNA. Here's an interesting article about other selective pressures on DNA, such as stem-loop formation.

      But much of the time, the mutation is harmless. Part of this is built into the genetic code. Amino acids with similar properties (acidic, basic, polar, nonpolar) have similar codons, meaning that the result of any mutation is more likely to yield a functional protein. From the wikipedia article, notice that all the nonpolar amino acids have a U (T for DNA) in the middle of the codon? Additionally, DNA sequences yielding malformed proteins often just don't get expressed. And most of the time there's enough redundancy so that single protein doesn't matter. We know that from gene-knockdown studies with mice.

      --
      Si la vida me da palo, yo la voy a soportar Si la vida me da palo, yo la voy a espabilar
    90. Re:How this impacts evolutionary theory by bodrell · · Score: 1
      Maybe the mutation is very simple and repairing could be as simple as inserting a couple of base pairs in the right place, which really wouldn't even need a DNA template.
      Exactly. And I looked it up--it really is only a single base mutation.
      --
      Si la vida me da palo, yo la voy a soportar Si la vida me da palo, yo la voy a espabilar
    91. Re:How this impacts evolutionary theory by DrKyle · · Score: 1

      After reading the actual Nature paper, it looks like they have tried to address any possible explanations I could come up with as a geneticist. I am however reminded of cases of papers which get withdrawn when another lab can not replicate their results or even withdrawn when the primary researcher finds out his grad student falsified data. I am not saying that either of these may be the case, but I think the thousands or more similar crosses done each year by researchers on arabidopsis alone would have turned this phenomenon up earlier if it were in any way general to this weed, and if it were applicable in any but the most rare of circumstances to animals it would have definitely been found earlier.

      Mendel, Darwin, stop spinning in your graves, the majority of the genetics community still thinks you were right.

      An older article on the prevalence of scientific fraud.

    92. Re:How this impacts evolutionary theory by bodrell · · Score: 1
      So you can see why this is so confusing -- in the case in the article the daughter cells, with two bad alleles for the gene they studied, are supposed to have no information pointing them to the gene from the grandparents. And yet they did, since they were able to fix it. The article postulates that this could be because a THIRD copy of the gene exists as RNA that's passed down from the grandparents (third since there are two chromosomes, each with a copy of the gene). If this were true, then the RNA would be the source of information required to fix the problem. Alternatively, there could be a specific protein that hunts down mutations in this gene and somehow fixes it, since it somehow bonds only to the correct version of the gene. But that's just my wild speculation.
      I would definitely like to know the mechanism the plants are using to fix the DNA, and I think your suggestion of a specific fixer protein for this gene is a perfectly reasonable guess, but the hothouse gene is only a single base mutation away from the wildtype. There could have been many ways it was repaired. See my other comments on this article for more. I don't feel like being redundant, but I do like discussing molecular biology.
      --
      Si la vida me da palo, yo la voy a soportar Si la vida me da palo, yo la voy a espabilar
    93. Re:How this impacts evolutionary theory by jafac · · Score: 1

      PS. It also leaves a gaping hole in theory about how plants inherit genetics - and frankly, the way Monsanto's spewing engineered plant genes in to the biosphere, this kind of scares me a little bit.

      --

      These are my friends, See how they glisten. See this one shine, how he smiles in the light.
    94. Re:How this impacts evolutionary theory by jafac · · Score: 1

      maybe some genes are "backed up" by partial copies or hashes or something, stored elsewhere on the chromosome? Or maybe there's a "backup" function in mitochondrial DNA that we don't yet know about? (just wildly speculating)

      --

      These are my friends, See how they glisten. See this one shine, how he smiles in the light.
    95. Re:How this impacts evolutionary theory by Junior+J.+Junior+III · · Score: 1

      It's not the backup gene, it's the write verifcation gene. Organisms keep thinking they can reproduce faster without verifying, but they have less assurance of data integrity. Hum.

      --
      You see? You see? Your stupid minds! Stupid! Stupid!
    96. Re:How this impacts evolutionary theory by bodrell · · Score: 1
      Since you're a "Genetic Engineer, in Training" you should also appreciate that the mutation is only a single base, and that certain genes are important enough that proteins are dedicated to their repair. Not that those facts make this finding insignificant, but it would be much more significant if the mutant gene were even two bases different from wildtype. A single base, though . . . I'm not convinced the repair was due to genes from the grandparent plants.

      I just spent a few minutes trying to find (without paying Nature) what the exact mutation was, but no luck.

      --
      Si la vida me da palo, yo la voy a soportar Si la vida me da palo, yo la voy a espabilar
    97. Re:How this impacts evolutionary theory by bikerguy99 · · Score: 1

      Note that this observation was made in a laboratory-kept strain of plant. These type of event has little chance in the wild. So, evolution is not an issue here whatsoever. Instead, a more important point here is that such permissive lab conditions allow us to uncover events that are rare or invisible in large or wild life populations. Hopefully this is not an example of missing a related gene in the genome due to incomplete sequencing of very complicated plant genomes (this is issue is mentioned elsewhere in this discussion) but a record of a true fact that has real biological mechanism behind it. Most revolutionary finding in biology since the discovery of DNA as the hereditary substance, namely RNA interference, started with a similar puzzle and also in plants - and it took quite sometime to figure out that it is a general phenomenon throughout the living matter.

    98. Re:How this impacts evolutionary theory by Artifakt · · Score: 1

      1. I am most certainly not attempting to confuse anything, including you. That by the way is an ad hominem. You seem prone to them.
      2. I didn't mention God as an explanation in my post. You did. That's an error of attribution to imply otherwise. On the other hand, if you're conflating God and the Necessary Complexity arguement, I'll plead guilty to offering an arguement that at least tangentially relates to the latter. That means you just made an error of the excluded middle instead, although granted it's not as obvious as the other possibility.
      3. Any good standard textbook will tell you that for Evolution to be true, more is required than imperfect replicators, and your statement there is simply wrong. In fact it's a classic wrong assmption a first year college Biology student often leaps to, and is, in the better courses, soon corrected. Darwin himself said "If it could be shown that unlimited blending of the mechanisms of heredity could occur, my theory would be fundamentally in error.". The modern version of this is sometimes phrased as "Quantization of the genetic code is absolutely fundamental to the theory of Evolution, and is why Mendelian Genetics is necessary to validate Darwin's work.". Incidentally, you might read the papaers accompanying Crick and Watson's Nobel award. They got it in part for demonstrating the particulate nature of the genetic code and thereby removing one of the then still extant objections to classical Darwinism.
      What is this Geological Evolution of which you speak? What mechanism of "heredity" prohibits blending of the genes for being "Basalt" or "Granite"? What process kills living geological features selectively, sometimes before they can reproduce? What evidence do you have for Geological features being quantized into species? You're spouting mystical assertions there.
      Oh my God, I'm argueing Evolutionary theory with someone who obviously hasn't even read Dawkins! I give up!

      --
      Who is John Cabal?
    99. Re:How this impacts evolutionary theory by bodrell · · Score: 1
      Just like RNA was a more primitive precursor to DNA (by the standard theory), this Error Correcting Code would have to fall somewhere in that model of mechanism evolution. It also has to be pretty good at copying fidelity, because DNA is pretty damned good (as in one error per billion passes good), and if this code is thousands of times worse, it won't survive unchanged long enough to be useful as an error corrector.
      You're making some pretty big assumptions. Haven't you heard of recursion? Why is it not possible for DNA to repair itself? We have kinases that act on other kinases, proteins that help fold other proteins, so why not? Imagine that the hothead gene (the single base mutant in this case), normally produces an enzyme with multiple functions, and one of those functions is to turn OFF gene foo. But when the hothouse gene is mutated so badly that the proteins it produces can't turn off gene foo, foo expresses a protein that binds to the segment of hothead that encodes the enzyme's active site, and makes sure the active site contains, say, an aspartic acid codon. I couldn't find out what the actual mutation is, but there are only a few amino acids in enzyme active sites.
      Admit that it is a very major example of 'survival of the less fit code" and the theory of Evolution explains only how species diversify and otherwise change. It becomes impossible to claim that Evolution reveals how life gets started and advances to near flawless replicators like DNA.
      Actually, this is an example of how "less fit code" was detected and eliminated. Though the mechanism is unclear, the gene was obviously detrimental.
      There are at least five apparently sound arguements against extending natural selection to 'explain' the origin of life. This was just one more. You won't hear any of them from the current establishment.
      I certainly hope the other apparently sound arguements [sic] are more sound than the one you just described, because I'm not convinced at all.
      --
      Si la vida me da palo, yo la voy a soportar Si la vida me da palo, yo la voy a espabilar
    100. Re:How this impacts evolutionary theory by extensis · · Score: 1
      I'm lucky in that i get full access to Nature through my university library. Though I have never heard of a gene specific protein-mediated repair mechanism, it may exisist.

      As for the exact mutation, there were 3 single base point missense mutations that were seperatly looked, and all three seperatly reverted back to a sequence that was homologus to previous generations, even tho that particular sequence was not found anywhere else in the genome. So where was this hidden information genome?

      --
      Mike Jones-{ Genetic Engineer, in Training }-
    101. Re:How this impacts evolutionary theory by bodrell · · Score: 1
      I came across this line in the abstract:
      This previously undescribed process is shown to occur at all DNA sequence polymorphisms examined and therefore seems to be a general mechanism for extragenomic inheritance of DNA sequence information.
      I was wondering how many polymorphisms they examined, so thanks for the info. I have full access to Nature at work, but I guess I'll have to wait until tomorrow to read the complete article.
      Though I have never heard of a gene specific protein-mediated repair mechanism, it may exisist.
      In biology, nothing surprises me much anymore. Did you know a stop codon is used to encode the 22nd amino acid? Nature is amazing. And I'm not talking about the magazine (though it ain't shabby).
      --
      Si la vida me da palo, yo la voy a soportar Si la vida me da palo, yo la voy a espabilar
    102. Re:How this impacts evolutionary theory by cot · · Score: 1

      "We also wouldn't have the genetic variation required for evolution. So this obviously isn't something that can happen ALL the time."

      This is exactly my point, I was trying to head off the creationists trying to use this as a wedge to "prove" evolution is false.

      --

    103. Re:How this impacts evolutionary theory by andreyw · · Score: 1

      DogDude may espouse a message that is politically incorrect and offensive to the irrational and the mentally unstable, yet has a valid point. Why mod something flaimbait simply because you disagree?

    104. Re:How this impacts evolutionary theory by Anonymous Coward · · Score: 0

      "I don't think we want our government to start imposing sterilization orders on "stupid people"."

      No, we want sterilization imposed on EVERYBODY. Only when you prove that you are capable of taking care of a child will the sterilization be reversed.

    105. Re:How this impacts evolutionary theory by ketamine-bp · · Score: 1

      I've got karma to burn, so:

      nobody knows how intelligence is inherited, nor would there be any significant experiment be done in the future, assuming that the ethical committee (tm) does not change their crappy mind. (on that, i suppose if there is such thing as an ethical committee in the past years there won't be vaccinia vaccine (pardon for redundancy) at all.) -- (1) you will not be able to carry out human experiment, (2) you will be able to carry out animal experiment, but nobody cares the result, and (3) as all of us know, the sample size for identical twins studies are way too small for any significance citation.

      but then while intelligence may or may not be highly inheritable, what gives rise to a human is highly inheritable, and identical twins tends to have similar intelligence despite being raised in different background.

      and the problem isn't that the 'feebleminded' are outbreeding the able ones, but the fact that the community is trying hard to work against natural selection (reads: social security)...

      ketamine

    106. Re:How this impacts evolutionary theory by BioCS.Nerd · · Score: 1

      The thing I didn't understand from the article was if this was a phenotypic reversal or genetical reversal (i.e. the gene of interest mutated back to the exact sequence as the wild type sequence). If it's just a phenotypic reversal couldn't that just be attributed to a mutation in and of itself that mirrors the wild type phenotype?

      That aside, does anyone have a reference so I can read the actual Nature article?

    107. Re:How this impacts evolutionary theory by BioCS.Nerd · · Score: 1

      My apologies, the article does in fact say that the change was on the genetic level, albeit in a very guttural way:

      Various rare events can make this happen, but none involve altering the actual sequence of DNA units in the gene. Yet when the researchers analyzed the mutated gene, known as hothead, they found it had changed, with the mutated DNA units being changed back to normal form.

      Does anyone else by their hypothesis of an RNA backup to the genome? If this existed, where could it be stored, or how could it be stored in a manner that prevented the rapid degradation that plagues RNA?

    108. Re:How this impacts evolutionary theory by Conanymous+Award · · Score: 1

      RTFA still.

      This gets in the way of evolution as much as a small stone gets in the way of a car.

      Besides, we now have observeed this in one plant, Arabidopsis. Now we have to find out, whether this applies to
      a) Other plant species b) Animals, say, insects and vertebrates.

      And still, 90% of the occurred mutations went on unreversed. Not a big deal. Those, who actually are interested in science and its revelations about this world know that this is fantastic news. Creationists, on the other hand, hang onto this as a new "Evolution Killer". Despisable people.

    109. Re:How this impacts evolutionary theory by Anonymous Coward · · Score: 0

      We're making our genes complacent

    110. Re:How this impacts evolutionary theory by RoLi · · Score: 1
      Furthermore, if lethal cancer occurs once you are past child-bearing age (around 30 up until recently), it isn't such a "bad thing" for the species.

      Wrong, only if it occurs after your children can take care for themselves. If the parents of a 5-year olds die, the 5-year old will have worse chances of becoming successful in life.

    111. Re:How this impacts evolutionary theory by mcrbids · · Score: 1

      Mod or reply, mod or reply... GRRRR... REPLY!

      science is, instead, a process by which we attempt to attain and refine knowledge.

      This is perhaps the shortest, most succinct expression of an idea I've espoused for years. Well done!

      When I hear "but it's only a theory..." as though that proved that Yahweh did it, I've learned to respond by having the person explain what a theory is.

      And, once I get a definition, something like "a shadowy, unproven idea", I re-iterate, and make sure that the definition they have is very, very clear.

      Then, I ask them about the theory of gravity, and if, because it's just a 'theory', would they be willing to jump off a bridge?

      Well, it's a theory isn't it?!?! What about the theory of electro-magnetism? Would you turn on your radio, trusting that this theory upon which almost all of modern society is based on, is true? Why?

      Why would you trust these theories any more than evolution?

      That's when I discuss what science is, that it's not a bunch of facts, but instead a process for discovering the truth about how the world works.

      Sad, but in today's world, you have to have a prepared plan for dealing with bigoted, dogmatic idiots, and the best way to do that is to give them enough rope to hang themselves before you say much of anything at all.

      --
      I have no problem with your religion until you decide it's reason to deprive others of the truth.
    112. Re:How this impacts evolutionary theory by RoLi · · Score: 1
      One counter-argument might run that although we might be going downhill fast in evolutionary terms, we're also going uphill very fast technologically.

      Doesn't matter how dumb the primordial organic neuroprocessor is when it's been augmented with a Cyberdyne Systems omni-intelligent prepare-to-be-assimilated super jewel. Or, translated into Earth-speak, in the time-frame that these problems might become manifest, we might be able to fix them, or make them irrelevant.

      All that is only true in the very short time of plenty aka the Oil age which extends from about 1900 to 2050 (with the real golden age of luxury being 1950-2000), which is a very, very short period in human evolution. Even in that time, most parts of the planet don't experience that plentiness.

      The real golden age is already over, what we call "economic downturn" will become a real crisis in a couple of years.

    113. Re:How this impacts evolutionary theory by CactusCritter · · Score: 1

      To expand a bit on evought's reference to the genetic cause of sickle-cell anemia, I refer to "The Misunderstood Gene" by Michel Morange. On page 51, he states, regarding the genetic defect which causes sickle-cell anemia, "It should be added that, in men, this mutation can sometimes lead to sterility; indeed, in some cases, this is the only sympton."

      It just goes to show how complex molecular genetics is.

    114. Re:How this impacts evolutionary theory by TummyX · · Score: 1

      Perhaps it doesn't have a third and "correct" copy of the gene but maybe both copies have sequences of dna that work like ECC (error correcting codes/hamming codes) and allow the error in the gene to be corrected.

      Not all errors can be corrected but maybe 5% is enough to allow the survival of the species in the event of a catastrophic and widespread gene mutation.

    115. Re:How this impacts evolutionary theory by Anonymous Coward · · Score: 0

      Evolution is nothing like science. Science, true science, does change almost daily as we learn more about our world and as we discover our previous concepts were incorrect, or incomplete. But Evolution is not, and never has been, based upon science. It is, and always has been, based upon just so stories to support a 'theory' about the origin of life that does not agree with the Bible. That was and is its sole purpose in being: to try to refute the Bible.

    116. Re:How this impacts evolutionary theory by andreyw · · Score: 1

      (about turning away people from hospitals) No, we simply turn away paying *citizens* who don't have enough insurance, while somehow managing to provide free healthcare to illegal 'immigrants' (what a joke).

    117. Re:How this impacts evolutionary theory by Mr.+Slippery · · Score: 1
      and the problem isn't that the 'feebleminded' are outbreeding the able ones, but the fact that the community is trying hard to work against natural selection (reads: social security)...

      Under pure "natural" selection, those who thrived would not be the most intelligent. Social darwinists forget that we've created an "unnatural" environment.

      It can be argued that having taken action to create such an environment, it is ethically incumbent on us to give some protection to those screwed over by it. ("You would have made a hell of a hunter-gatherer, kid, but you're a lousy city dweller"). And that it's wise to preserve those attributes within the species, because that environment will change and we need to stay diverse. ("Now that industrial civilization has collapsed, we need those excellent hunter-gatherer types!" Or, if you want to be optimistic, "Turns out those excellent hunter-gatherer types are just who we need to crew our starships!")

      --
      Tom Swiss | the infamous tms | my blog
      You cannot wash away blood with blood
    118. Re:How this impacts evolutionary theory by Artifakt · · Score: 1

      Though the mechanism is unclear, the gene was obviously detrimental.

      When I wrote code, I didn't mean "block of DNA based code". I meant an entire code, seperate from DNA. (This is what the article meant, too).
      We're not talking about a single gene, but an entire seperate encoding mechanism being detrimental. The original article suggests it might be an RNA based scheme. I've pointed out that this is extremely unlikely, because RNA's copying error rate is so many times greater than DNA, that using RNA to correct DNA would be about as useful as using third generation photocopies of had written notes that had been passed through an old fashioned purple ink - handcranked drum offset lithograpy machine, to correct current generation optically scanned text. The Researcher's don't think the information is in the DNA itself. If its not in either of those two, it has to be in some third encoding method. That 5% rate for correction some people are discussing sets some upper and lower bounds for how good such an encoding scheme could be. It's roughly an order of magnetude less fidelity than is DNA with additional error corrction from DNA transcriptase and other enzyme based correctors, roughly two orders of magnetude better than basic DNA as found in primative bacteria (without all the correcting mechanisms we multi-celled organisms share), and six or so orders of magnetude above RNA.

      So how could this other encoding scheme be obviously detremental? What flaw could it have to make it universally unused for heredity (as a replacement for either basic DNA in bacteria and some viruses, or DNA plus its additional error correcting mechanisms in advanced organisms) or short term data transfer (as a replacement for tRNA)? What you're saying amounts to, "I can't think of a problem big enough to make this detremental, the researchers can't think of one, nobody has the remotest clue as to what a negative big enough to offset the positive of having a million fold better error correction is, but it has to be there, because the theory can't be flawed".

      --
      Who is John Cabal?
    119. Re:How this impacts evolutionary theory by Anonymous Coward · · Score: 0

      A good effort! ...but you might want to check out :
      "scansion" http://www.stedwards.edu/hum/klawitter/poetics/sca nsion.html
      if you want to write Filk-song lyrics http://www.electricpenguin.com/filking/columns/fil kfaq/archives/001781.html

    120. Re:How this impacts evolutionary theory by Anonymous Coward · · Score: 0

      IANAP (I am not a philosopher) but:

      The "theory" of evolution or of releativity are theoretical in the sense of "music theory": they are formal systems for the organization of thought or knowledge. One of the things that distinguish Scientific theories, as such, is that they are, in principal, capable of being tested (one meaning of the word "prove" is "test" (think of "white sands missile proving grounds" in New Mexico)).
      A RELIGIOUS theory, as a formal organisation of thought, can certainly be constucted. Since it cannot be meaningfully tested*, however, a religious theory is NOT a scientific theory!

      *Indeed, religious theories are often forbidden from question or test!

    121. Re:How this impacts evolutionary theory by ketamine-bp · · Score: 1

      there is nothing unnatural about anything created by human beings. we are a part of this world, and anything we do is just like what a herd, or thousands of herds of leopard, panda (as if they can do anything), cows, sheeps or tiny little mice do.

      just to say a 'for-example'. those who do not even consider to benefit from the environment (reads: going to hospital when they have rectal bleeding) are doomed to extinction of their own genes.

    122. Re:How this impacts evolutionary theory by daddymac · · Score: 1
      Science changes, because it needs to.
      It's almost like there's some sort of back-up "Science RNA". If Science changes incorrectly (The earth is flat and the Sun rotates around it!) The back-up RNA (aka Scientists) automagically re-mutate the incorrect change into the "correct" version.
      --
      If something I said can be interpreted two ways, and one of the ways makes you sad or angry, I meant the other one.
    123. Re:How this impacts evolutionary theory by cookie_cutter · · Score: 1
      You don't go far enough. There isn't ANY isolated behaviour which could completely contradict evolutionary theory. This is because we know, from the theory of molecular evolution, that their is always some small possibility that some otherwise unlikely trait could not only evolve but become common. Even if it is harmful.

      For more background, look up Neutral theory of molecular evolution.

    124. Re:How this impacts evolutionary theory by Mr.+Slippery · · Score: 1
      there is nothing unnatural about anything created by human beings.

      Fine. Then under that defintion don't you have to retract you assertation that "the community is trying hard to work against natural selection"? If the community's actions are natural, they're part of natural selection.

      --
      Tom Swiss | the infamous tms | my blog
      You cannot wash away blood with blood
    125. Re:How this impacts evolutionary theory by Chris+Burke · · Score: 1

      So, if the Error Correction Mechanism's copying system is much better than RNA, and at least close to as good as DNA, maybe even better, why isn't it being used as the main Genetic code?

      Because evolutionary pressure hasn't forced this to be the case? We don't know what the mechanism is; it might just be redundant backups of certain genes, in which case it would be better than a single gene, but require a multiplicative increase in the total amount of genetic code to use in every case. Perhaps it was this one gene that was subject to negative mutations that caused this correction mechanism to arise. Certainly not all mutations are bad, and thus it doesn't make sense to try to entirely eliminate them in the entire genetic code -- in fact, species which lacked the ability to propagate mutations would be at a disadvantage.

      There is still no fundamental conundrum. it's just a correction method we don't yet understand. "Why aren't all genes like this?" is a red herring.

      --

      The enemies of Democracy are
    126. Re:How this impacts evolutionary theory by espressojim · · Score: 1

      As someone with a reasonably strong backround in molecular biology and population genetics (I do informatics analysis work at the Broad institute of harvard and mit on population genetics issues), I don't think this has anything to do with the "hand of god" :)

      If RNA is associated with protiens or lipids, those have to still be present at the time the progeny is created, and passed into that. I'm not exactly sure that even if that is an explanation, that it would be universally true - I'm no plant biologist, but I wouldn't expect to see every protien expressed in the progeny immediately so that RNA could stick around. And, this RNA has to stick around from the grandparents to the grandchildren - that's a LONG time.

      I still haven't read the 'real' paper yet (waiting to get my hands on the paper copy of nature), but it seems pretty unlikely that RNA is staying around that long. I'm not sure if they did the more obvious things (I would guess so) like checking for pseudogenes, etc. But those seem more likely.

      I await with interest new data to see how this goes forward, but I'm not sure that they have any reasonable evidence for their current hypothesis. Again, the nature paper may shed some light on the topic of 'RNA stores', but that's the sort of thing (given how much expression work is being done) that I would have thought people would notice an extra stockpile of RNA lying around - and that it's levels would stay constant regardless of changing backround conditions.

      Of course, I'm not sure if anyone's even done expression profiling on this model organism yet...

    127. Re:How this impacts evolutionary theory by shawb · · Score: 1

      I don't remember who posted it, but someone got a hold of a much more detailed article. That article said that this is just a single base mutation. Hmm... maybe I'll try to find that post. Here it is.

      So a single base mutation could easilly (well, maybe not easilly so much as feasibly) be repaired by a protein encoded for somewhere else in the DNA. That kinda moves this from the realm of "Wow, how does that work?" to "That's kinda neat."

      --
      I'll never make that mistake again, reading the experts' opinions. - Feynman
    128. Re:How this impacts evolutionary theory by yet+another+coward · · Score: 1

      Errors are extremely common. The only reason why we survive is our body's repair mechanism.

      It is not the only reason. Many errors have no big consequences. Other errors cause a cell to die, and a few dead cells are unlikely to matter.

  3. Yous a vine muthafucka! by heauxmeaux · · Score: 4, Funny

    Back that gene up!

    --
    Beat 'Em and Eat 'Em
    1. Re:Yous a vine muthafucka! by wankledot · · Score: 1

      The pun in your title alone is worth serious +Funny mod points. I would have you given some, but I'd rather comment and give you mad props directly.

      --
      My sig is blank, I typed this by hand.
  4. Parity bits? by aristus · · Score: 4, Funny

    ECC DNA? That's pretty damned cool. hard to believe we hadn't suspected that before.

    --
    Sometimes seventeen/Syllables aren't enough to/Express a complete
  5. Maybe... by Anonymous Coward · · Score: 0

    Maybe it was a defective defective gene, so it then wasn't not non-defective.

  6. Finally. by Anonymous Coward · · Score: 0, Offtopic

    Finally some INTERESTING news on Slashdot. Fuck was today ever boring.

  7. Plant Superheroes! by The+Amazing+Fish+Boy · · Score: 5, Funny

    I'm gonna start putting my cactus near my spider plant and praying for some of that mutated gene action.

    OK, OK... and some hot plant-on-plant action.

    OK, OK... and some hot plant-on-plant-on-me action.

    1. Re:Plant Superheroes! by gammygator · · Score: 1

      With a cactus?! That just ain't right.

      --

      No Nyarlathotep, No Chaos
      Know Nyarlathotep, Know Chaos
    2. Re:Plant Superheroes! by The+Amazing+Fish+Boy · · Score: 0

      If lovin' a cactus is wrong, baby I don't wanna be right.

    3. Re:Plant Superheroes! by Anonymous Coward · · Score: 0

      OK, OK... and some hot plant-on-plant-on-me action.

      Why do I never have mod points when I really need them? That's some plus-five-funny shit.

    4. Re:Plant Superheroes! by BearJ · · Score: 1

      And this is why we need a +1 Ew and a +1 Painful tag.

      --
      Stand clear of the doors. The doors are now closing.
    5. Re:Plant Superheroes! by The+Amazing+Fish+Boy · · Score: 1

      PLUS one? Please, folks, don't encourage me.

    6. Re:Plant Superheroes! by dzym · · Score: 1

      I have 2 (two) words for you:

      Poison Ivy.

    7. Re:Plant Superheroes! by Xyrus · · Score: 1

      At least we'll know those moans and screams aren't from pleasure.

      ~X~

      --
      ~X~
  8. Hmmmm, like RAID for plant genes.. by the_rajah · · Score: 0, Redundant

    Now is that RAID 1? I never can keep those straight.

    Seriously this is a very interesting development with important implications.

    --


    "Do the Right Thing. It will gratify some people and astound the rest." - Mark Twain
    1. Re:Hmmmm, like RAID for plant genes.. by Anonymous Coward · · Score: 0

      Its iroic that a post about raid got modded "Redundant".

    2. Re:Hmmmm, like RAID for plant genes.. by Duhavid · · Score: 1

      No, RAID -1

      ( get it? )

      --
      emt 377 emt 4
    3. Re:Hmmmm, like RAID for plant genes.. by Anonymous Coward · · Score: 0

      Does anyone else appreciate the humor in a post about RAID 1 being modded as redundant?

    4. Re:Hmmmm, like RAID for plant genes.. by The_DOD_player · · Score: 1

      ROTFL... I found it pretty funny. Though it was a bit tough to explain the humor to my wife.. :)

    5. Re:Hmmmm, like RAID for plant genes.. by Anonymous Coward · · Score: 0

      no.

      you're a faggot. shut up.

  9. Plants May Be Able To Correct Mutated Genes by Anonymous Coward · · Score: 0

    Or maybe not.

    Nobody really has a clue yet.

  10. Er... by mog007 · · Score: 0

    Too lazy to RTFA, but I assume this may hold a place for curing cancer?

    1. Re:Er... by uberdave · · Score: 1

      It may not be a cure for cancer, but it will allow for secure transmission of credit card data over the internet.

    2. Re:Er... by Anonymous Coward · · Score: 0

      No

    3. Re:Er... by Rob+Carr · · Score: 1
      No

      Incorrect. Try "Maybe, but probably not."

      The first question is whether this happens in human DNA. Then the second question would be, if the first answer is positive, is there any way to ensure that it occurs? It occurred very rarely in the plants, which ain't a good sign. Third, is there a way to take advantage of it even if it could be made reliable?

      That's a lot of ifs. People get Nobel Prizes for such ifs. People also spend their entire lives doing such research and come up with crapola.

      --
      This sig seemed like a good idea at the time....
  11. Oh, that's going to be a problem by Dark+Paladin · · Score: 4, Funny

    Odds are, now the grandparent plants are going to have to sue the grandchildren plants for having "stolen" their copyrighted and patented genetic code. As we've learned from Beatallica and Dangermouse, mixing older generations of information to recreate it anew is against the Laws of Copyright Nature.

    Who gave these plants permission to make backups of their grandparents material? I mean - really!

    OK - seriously, this is a fascinating idea, one that hopefully is indeed correct and can be explored. With this information, perhaps 20 years from now we can correct genetic abnormalities by having fetuses fix themselves. Kudos to the researchers for their hard work.

  12. They said it might be from RNA by Anonymous Coward · · Score: 0

    but it could be a huffman code in the DNA.

  13. Here's a hint: by ironflippy · · Score: 0, Redundant

    Always back your genes up before you reproduce.

  14. Perhaps it's a result of evolution by PornMaster · · Score: 2, Insightful

    DNA containing redundancy certainly isn't efficient, so perhaps it's something that happened *because of* evolution, and doesn't negatively impact evolutionary theory, just requires that we modify our understanding of it.

    1. Re:Perhaps it's a result of evolution by shawb · · Score: 1

      It may not seem efficient, but there is actually a lot of redundancy in DNA. One place that redundancy often occurs is with proteins that are produced in large quantities over a short period of time. Multiple RNA transcriptions can be made simultaneously which then go and get transcribed into proteins. I don't think that efficiency is much of a concern, anyways. If I recall more than half the DNA in most advanced organism does not actually code for proteins, it's just tagging along. Although some of this is related to timing of transcription, reproduction, and other events.

      --
      I'll never make that mistake again, reading the experts' opinions. - Feynman
  15. Yeah... by bigtallmofo · · Score: 0, Offtopic

    But what if your name's not Gene?

    --
    I'm a big tall mofo.
  16. could this.. by Turn-X+Alphonse · · Score: 1

    Could this some how be manipulated to work with humans as well? We could stop cancer right off, sure several disabilities in a family bloodline and so much more..

    Obviously they would make a law against this though because no one wants "super humans" let alone humans without defects.

    --
    I like muppets.
    1. Re:could this.. by John+Seminal · · Score: 1
      We could stop cancer right off, sure several disabilities in a family bloodline and so much more..

      Better place to look is with viruses. They are the perfect vessel to carry DNA to specific cells. They can pass all the millions of cells until they find the exact right mix of sugars and protiens sticking out the cell. Yess, this is where the Johnsons live, the house with the window air conditioner sticking out of the left window, and the rusty plymoth dodge in the driveway.

      TuPac said you have to operate the easy way. I say nuke the inside of a virus known to attack cell "A", where cell "A" is also the type of cell that gets disease "B". Insert DNA "C" into virus "A" and kill disease "B". It is so simple...

      TuPac also rapped about the war in the middle east. But that is another story. Time for some changes. ;)

      --

      Rosco: "If brains were gunpowder, Enos couldn't blow his nose."

  17. the 'correction' is rare, thus no impact on theory by Anonymous Coward · · Score: 0

    The corresion only happened in 1/10 cases -- so for the most part, it doesn't affect evolutionary theory; if the 'corrected' gene is bad, then it only gets 'fixed' in a minority of cases; it's not like this correction always happens.

  18. Makes Sense by latent_biologist · · Score: 5, Insightful

    Most Plant genomes are crazy complex. Besides that, polyploidy is often the norm in plant chromosomes. With that much genetic material to work with, i guess you'd be bound to find a 'do-over' someplace.

    1. Re:Makes Sense by GAATTC · · Score: 3, Insightful

      If you read the actual article, you will find that: - The research was performed in Arabidopsis, which behaves as a diploid - There are no other copies of the hothead gene which could have corrected the mutant copies There is something more complicated going on here

    2. Re:Makes Sense by D3 · · Score: 2, Insightful

      Yes, but this was seen in Arabidopsis (Mustard plant) which is not a polyploid plant. The article states that when they checked the genome there were no other "good" copies of the gene available to revert to. Both copies of the gene (one from each parent plant) were mutated copies. Yet somehow the DNA got reverted back to the non-mutated "grand-parent" copy in about 10% of the plants.

      --
      Do really dense people warp space more than others?
    3. Re:Makes Sense by fsmunoz · · Score: 1

      With that nick I must confess I was expecting the solution to this when I clicked it :)

    4. Re:Makes Sense by espressojim · · Score: 1

      There were no extra functional copies of the gene, but were there pseudo genes available with a large amount of sequence similarity? They probably already checked that by blasting their gene against the genome, but it would be worth checking that out at fairly low stringency to see if there were portions of the gene somewhere else, and that was being used Beats me to how it would be used, though - I can't imagine a molecular mechanism for my story that is even remotely plausable...

  19. Sex bias in reporting? by GAATTC · · Score: 3, Interesting

    Funny how this story only quotes Dr. (Bob) Pruitt. Most of this work was done by the first author Dr. (Susan) Lolle. The other two authors apart from Bob are both female. In the actual Nature article, this is reflected in the authorship credits. All of the comments in the NYT writeup are from male scientists. Why does the male scientist get nearly all the credit here? On the heels of Dr. Summers' (Harvard) comments that women are inherently less able to succeed as scientists, you would think the NYT would report this big story more carefully and give credit where credit is due.

    1. Re:Sex bias in reporting? by mveloso · · Score: 1

      Maybe it's because the reporter didn't have phone numbers for the female scientists, so was unable to call them?

      It could be bias, it could be the women were too busy to take the call, it could be that old Bob is a glory hound.

    2. Re:Sex bias in reporting? by Anonymous Coward · · Score: 0

      Why does the male scientist get nearly all the credit here?

      Because he's the one with the penis, silly!

    3. Re:Sex bias in reporting? by Anonymous Coward · · Score: 1, Informative

      Um, I'm sitting here with a copy of the paper in my hand, and Lolle and Pruitt are explicitly marked as having "contributed equally to this work". Furthermore, looking at the departmental web page, Pruitt appears to be the most senior author: he's an associate professor (faculty), whereas Lolle is a research associate (staff). I don't think it's unnatural that they're interviewing the most senior person.

    4. Re:Sex bias in reporting? by Anonymous Coward · · Score: 1, Insightful

      It's always possible that the other scientists involved had no comments to offer.

      Don't look for conspiracy where stupidity or simplicity can solve the mystery.

      Also, are you REALLY shocked that the New York Times has failed to completely and accurately reflect all of the facts in their journalism?

    5. Re:Sex bias in reporting? by GAATTC · · Score: 1

      Yah - Like the PI (Principal Investigator) in a lab ever actually does any of the work. They are much too busy going to meetings and writing grants and papers.

    6. Re:Sex bias in reporting? by Anonymous Coward · · Score: 1, Insightful

      Come on people. Why is it that every time there is a woman involved it automatically becomes an issue of gender discrimination????

      Most scientific articles have a single author that deals with inquiries and correspondences. Look at the actual paper (Nature, 24 March 2005). The author to which correspondences should be directed is Dr. Pruitt.

    7. Re:Sex bias in reporting? by Xylantiel · · Score: 2, Insightful

      Right - going to meetings, writing grants and papers... i.e. commenting on the work. That's what the reporter wants. PIs generally are quick to answer questions of what's going on in their lab and why it's interesting.

    8. Re:Sex bias in reporting? by Anonymous Coward · · Score: 0

      On the heels of Dr. Summers' (Harvard) comments that women are inherently less able to succeed as scientists

      He said no such thing and I challenge you to show otherwise.

    9. Re:Sex bias in reporting? by GAATTC · · Score: 1

      How about this quote http://www.president.harvard.edu/speeches/2005/nbe r.html from what he said: "So my best guess, to provoke you, of what's behind all of this is that the largest phenomenon, by far, is the general clash between people's legitimate family desires and employers' current desire for high power and high intensity, that in the special case of science and engineering, there are issues of intrinsic aptitude, and particularly of the variability of aptitude, and that those considerations are reinforced by what are in fact lesser factors involving socialization and continuing discrimination."

    10. Re:Sex bias in reporting? by Anonymous Coward · · Score: 3, Informative

      Funny how this story only quotes Dr. (Bob) Pruitt. Most of this work was done by the first author Dr. (Susan) Lolle.

      Sigh. Pruitt is last author. In the bio-sciences, this means that he's the principle investigator - the guy with the lab, the guy with the money, the boss, the big cheese. More to the point, he's listed on the Nature paper as the contact person. You know, the person to talk to if you're wrighting a story? There are *plenty* of PI's who are female - if something happens in their lab, they're the ones who get to talk to the press.

      All of the comments in the NYT writeup are from male scientists.

      That's because you get quotes from the authorities in the field - those people who have the most experience. The ones with 20-30 years of experience. The ones who got their Ph.D. in the 70's or before. When there wasn't a lot of female graduate students.

      Your complaints are like saying that the CEO of a company shouldn't be quoted in news stories because all of the work to make the company sucessful is performed by others.

    11. Re:Sex bias in reporting? by Oligonicella · · Score: 1

      If by work, you mean the grunt crap, like taking endless measurements, you're probably right. If, however, you mean doing the primary conceptualizing, design and analysis, you're probably wrong.

    12. Re:Sex bias in reporting? by Oligonicella · · Score: 1

      Interesting thing. People make a big deal out of what he said, yet ever fail to acknowledge that the stats on which he based that part of his talk are emperical.

      By the way. Men can move heavier objects than women, women are superior to men linguistically, etc. Get a grip and view differences as that, differences.

      None of the above infers in any way the superiority of one sex to the other overall.

    13. Re:Sex bias in reporting? by Anonymous Coward · · Score: 0

      there are issues of intrinsic aptitude

      I assume you take this to mean "women are inherently less able to succeed"? You are wrong, and jumping to conclusions, presumably because you want to see a bigot where there isn't one.

    14. Re:Sex bias in reporting? by Anonymous Coward · · Score: 0
      You forgot the next line...

      I would like nothing better than to be proved wrong, because I would like nothing better than for these problems to be addressable simply by everybody understanding what they are, and working very hard to address them.

      Furthurmore, I do not see anything in what he has said that would justify him being hounded out of academia.

    15. Re:Sex bias in reporting? by extensis · · Score: 1

      Lolle is listed in NATURE as the primary author, I think that's more important than an NYT interview

      --
      Mike Jones-{ Genetic Engineer, in Training }-
    16. Re:Sex bias in reporting? by joak · · Score: 1

      Interesting thing. People make a big deal out of what he said, yet ever fail to acknowledge that the stats on which he based that part of his talk are emperical.

      And yet more applicable empirical facts go against his proposal (for example: otherwise identical scientific articles are rated lower by reviewers if they are given a woman's name; in other ccultures, women test out better in the sciences). Summers himself later admitted unfamiliarity with the overall literature on the study.

      I agree the thing's been overdone a bit, but when you collect only a small sub-set of facts which happen to support a pet theory, ignore all the rest, and then pat yourself on the back for being "open-minded", you deserve a good bit of derision.

    17. Re:Sex bias in reporting? by cpeikert · · Score: 1

      Dr. Summers' (Harvard) comments that women are inherently less able to succeed as scientists

      He didn't say that, or imply it. He said that one reason (among 3 he listed) for women's under-representation in science may be inherently genetic.

      Think what you will of that hypothesis -- but don't blatantly misattribute.

    18. Re:Sex bias in reporting? by jezmund · · Score: 3, Informative

      The explanation for this is pretty simple, and is pretty much standard practice whether you are male, female, or other. The order in which the authors are listed (in most scientific journals, at least) is a standard heirarchy. The author listed first contributed "the most" to the paper in terms of the research. To my knowledge, this generally also means this person wrote the paper. Authors listed after the primary author are understood to have contributed less to the paper. The final author listed is special, however. By convention, this author is the "owner" of the lab the research was performed in. In other words, Robert Pruitt is Susan Lolle's boss. So he gets asked all the questions because he's the most important person in the lab. Also (as noted in another comment) he likely doesn't do much research and spends much of his time shmoozing with reporters, writing grants, reviewing papers, and supervising the various different projects which may be running in his lab at any one time.

      --

      "fist in the air in the land of hypocrisy"
    19. Re:Sex bias in reporting? by Anonymous Coward · · Score: 0

      And yet more applicable empirical facts go against his proposal (for example: otherwise identical scientific articles are rated lower by reviewers if they are given a woman's name

      I can't believe that you are so keen to label him a bigot that you failed to notice this actually agrees what what he said.

      He never claimed there was no sexism, and the quote from him posted above explicitly acknowledges that sexism exists.

      Why don't you stop, take a deep breath, and read what he said before deciding he's scum?

    20. Re:Sex bias in reporting? by joak · · Score: 1

      I read what he said. He said there were various problems, and based on an incomplete view of the data announced sexism was the least important of them.

      Now take a deep breath read what I said. I never labelled him a bigot, or scum; in fact, I agree the response was overboard. Did you miss that?

      My personal opinion is that he's probably a succesful man whose become over-confident of his opinions, even when it's on subjects outside his field like biology or female scientists. So he went off half-cocked, unfamiliar with research on the subjects, figuring he was the smartest guy in the room, and blabbing to a room full of equally opionated Harvard professors, and got called on it. Go figure.

    21. Re:Sex bias in reporting? by Anonymous Coward · · Score: 0

      He said there were various problems, and based on an incomplete view of the data announced sexism was the least important of them.

      No. He didn't. Read it again:

      those considerations are reinforced by what are in fact lesser factors involving socialization and continuing discrimination.

      Firstly, there is a world of difference between "lesser" and "least". He said lesser. He didn't say least.

      But, more importantly, you started off by saying that he was completely denying the existence of sexism as a contributing factor. You said:

      And yet more applicable empirical facts go against his proposal (for example: otherwise identical scientific articles are rated lower by reviewers if they are given a woman's name

      Now how does the existence of discrimination contradict what he says? It doesn't. In fact, since he acknowledges sexism as a contributing factor, however slightly, it actually agrees with him.

      So if you aren't keen on labelling him a bigot, why have you continued to misrepresent what he is saying?

    22. Re:Sex bias in reporting? by joak · · Score: 1

      (sigh)

      Firstly, there is a world of difference between "lesser" and "least". He said lesser. He didn't say least.

      Two houses on a street are smaller than the other ones, they are the smallest on the street.

      Discrimination makes a lesser contributions than the other factors discussed, it is the least important one discussed.

      But, more importantly, you started off by saying that he was completely denying the existence of sexism as a contributing factor

      No, I didn't.

      Now how does the existence of discrimination contradict what he says? It doesn't. In fact, since he acknowledges sexism as a contributing factor, however slightly, it actually agrees with him.

      I'll let you try and figure out whether there's any way at all those two points I raised might be relevant to a discussion of the relative importance of discrimination and innate effects. (Look at both points, including the one you edited out; it'll be easier for you.) I'll get you started: see if they're relevant to a defense of the antithetical idea ("Active and passive discrimination are factors, with lesser contributions from innate male/female differences.")

      So if you aren't keen on labelling him a bigot, why have you continued to misrepresent what he is saying?

      Huh? I do know insulting words besides "bigot", you know. It should be obvious the label I want to attach to him is "arrogant".

  20. Yous a vine muthafucka! by darth_MALL · · Score: 1

    back that grass up!

    That's comedy GOLD!

  21. If we port this technology to humans by Ulrich+Hobelmann · · Score: 3, Funny

    Does that mean that the kids of two geeks will not read /. ?

    1. Re:If we port this technology to humans by mobby_6kl · · Score: 1

      That's right. They'll only post comments, without reading anything. Hmmm, maybe we already have something to back up the theory with...

  22. Restore point? by caryw · · Score: 3, Funny

    Stupid NY Times. The LA Times has an article on it too available here.

    So plants create restore points they can roll back to? I predict Microsoft filing suit against the plant kingdom. They've been fighting the proliferation of tree based products for years!
    --
    Fairfax Underground: Where Fairfax County comes out to play

  23. no, RNA backup by Anonymous Coward · · Score: 0

    the article didn't suggest parity bits, it suggested RNA backup

  24. Also on New Scientist by jwgoerlich · · Score: 5, Informative

    New Scientist has coverage. No registration required.

    http://www.newscientist.com/article.ns?id=dn7185

    J. Wolfgang Goerlich

    1. Re:Also on New Scientist by WillAffleckUW · · Score: 1

      New Scientist has coverage. No registration required.

      I should point out that link will only work for a couple of days, even if you are registered.

      --
      -- Tigger warning: This post may contain tiggers! --
    2. Re:Also on New Scientist by WillAffleckUW · · Score: 2, Informative

      The prior article on the research they did on this is at PubMed Article, or you can look up the current article at PubMed yourself.

      --
      -- Tigger warning: This post may contain tiggers! --
  25. How this impacts ME by ari_j · · Score: 3, Funny

    This behavior can be observed in humans, too. For instance, my parents were both uncool, unintelligent jerks with no sense of humor whatsoever, and I'm an extremely hip, brilliant jerk with a great sense of humor.

    1. Re:How this impacts ME by manifoldronin · · Score: 1

      You got any kids yet?

      --
      Tyranny isn't the worst enemy of a democracy. Cynicism is.
    2. Re: How this impacts ME by dapyx · · Score: 1
      I'm an extremely hip, brilliant jerk with a great sense of humor.

      ... and modest too!

      --
      I'm sorry, the number you have dialed is an imaginary number. Please rotate your phone 90 degrees and dial again.
    3. Re: How this impacts ME by ari_j · · Score: 1

      I truly am the most modest person ever to live.

    4. Re:How this impacts ME by ari_j · · Score: 1

      Not that I admit to their mothers' husbands. ;)

  26. So what happens to gentically modified plants? by buro9 · · Score: 1

    Will they mutate over several seasons back towards their original form?

    1. Re:So what happens to gentically modified plants? by buro9 · · Score: 1, Funny

      clearly i cannot type... ignore the spelling mistakes you grammar/spelling nazis... instead think of better input devices to prevent so many silly typos ;)

      keyboards, how antiquated

    2. Re:So what happens to gentically modified plants? by MutantHamster · · Score: 0

      Seriously, ewe knead two get won of those "Type-and-Speak" programs. Yule never half two worry about making errors again.

      --
      My Greatest Heist - Muisc partly inspired by the unbeatable Qwantz
    3. Re:So what happens to gentically modified plants? by Artifakt · · Score: 5, Informative

      A lot of genetically modified plants will be selected against where they escape into the wild. Golden Rice, for example, uses a lot of energy making Beta Carotine, that is, (from the plant's view), wasted. When its seeds get cross fertilized by wild rices the genes tend to be weeded out in the wild areas quite rapidly. Rice has generations lasting a year or less, and it's been estimated that the genes are 99% gone within 10 years. Even in cultivation, farmers have to suplement their seed stock saved from the last harvest with new purchases of fresh Golden Rice every few years to keep the yields up.
      That's not mutation as you've described, it's natural and artificial selection, but so long as there are unmodifed plants in the same areas as the GE ones, it tends to work that way, as the vast majority of GE features are disadvantagious under natural selection, and a lot of them are so disadvantagious they require real rigor to preserve via artificial selection. They're like Pekinese dogs in the wild.

      --
      Who is John Cabal?
    4. Re:So what happens to gentically modified plants? by vsprintf · · Score: 1

      I think I followed most of that, but what about genetically engineered plants where the modification may include a survival trait, e.g., the "Roundup" resistant crops? The companies that produce the seeds forbid growers to use the resulting crops for seed. If the crops were used for seed, would the modification stick or eventually (after some generations) revert to the original, unmodified plant? If this is the case, most of the arguments against genetically engineered crops go out the window.

    5. Re:So what happens to gentically modified plants? by Artifakt · · Score: 1

      You've just asked a hard question. (A lot of experts disagree on the answer). Some geneticists argue that an advantageous trait like that must have some big hidden costs to offset it or it would have already developed naturally. By them, our "improvements" are all short term only. Others argue that we don't have to be perfectly insightful or understand all the consequences of our actions to do better than nature. Nature, by this arguement tries for workable, not perfect, and we can sometimes beat her.
      Then too, what's short term for an apple tree? Ten generations there may be a thousand years. A subtle flaw in a GE apple tree, might be a net negative, but might take 50,000 years or more to be selected out.

      --
      Who is John Cabal?
    6. Re:So what happens to gentically modified plants? by dingfelder · · Score: 1
      Some geneticists argue that an advantageous trait like that must have some big hidden costs to offset it or it would have already developed naturally
      I dont follow that. It is almost like you saying that all "good" traits would already be present, via evolution. Maybe the trait is advantageous but the body has just not gotten around to advancing itself to have that trait. Maybe it might naturally occur in 10,000 more years but we just sped up the eventual process by introducing it earlier.

      or on a completely different tangent, maybe the trait (roundup resistance) just became advantageous because the plant has only been encountering the roundup spray for the last 20 generations or so... previously ( > 20 years ago) this trair would NOT have been advantageous (and so it would have gotten bred out) but now it IS advantageous, so it should be kept.

      Am I off track here?
    7. Re:So what happens to gentically modified plants? by cataclyst · · Score: 1

      Two words: seed sterility. Why would the major players in the GM food plant industry want to sell a seed to a farmer once and only once? Not to mention that he could share the resulting seeds with other farmers.
      Proof of that concept was published in 97 or 98, and was incorporated into BT soy by Monsanto a year or two later..

      --
      E = m * c^(Hammer)
    8. Re:So what happens to gentically modified plants? by Greg@UF · · Score: 2, Interesting

      I did microbiology and genetics at Uni.

      In bacterial cultures, it was fairly straightforward to select for resistance to a given antibiotic.
      You put a bit of antibiotic into the agar, and the colonies that survive got transferred to an agar with a higher concentration of the antibiotic. And so on, until either a level was reached where none of the strains would grow, or they were completely resitant. Pretty cool stuff :-)

      By this stage, we had usually got a strain totally resistant. Then came the interesting bit.
      We took the antibiotic out of the growth media, and grew several more generations. It took us quite a while, from memory, we spent a whole term working on this experiment.
      At the end, we took those colonies, and put them back on several different strengths of the antibiotic. The vast majority of the colonies had lost their resistance - without a force in the environment to select for it, it was lost from teh population.

      The same thing will happen for genetically engineered species, (eg roundup resistance) If there's no force in the environment to select for it, then the genes will disappear.

      --
      -- You can't give it, you can't even buy it, and you just don't get it!
    9. Re:So what happens to gentically modified plants? by term8or · · Score: 1

      Seed sterility is good in theory, but not completely effective at containment of plants in practice. Seed is just one of the ways that plants reproduce. There are many asexual ways that plants reproduce (e.g) Layering, root cuttings, rhizomes, leaf cuttings, stolons.

      --



      "As a writer / novelist you might want to spellcheck your sig. :) " - AC
    10. Re:So what happens to gentically modified plants? by defile39 · · Score: 1

      These comments are somewhat misleading. The bacteria loose this resistance because they have incorporated only plasmids into their cytoplasm. Plasmids are easily obtained and lost by bacteria. They are not part of the actual bacterial genome. In plants, artificially expressed genes that are passed on from generation to generation are typically obtained through a retroviral vector. The gene is physically fused into the plants original genome. This is much more difficult to loose (especially when you're talking about a multi-cellular organism).

    11. Re:So what happens to gentically modified plants? by Ayaress · · Score: 2, Interesting

      In a farm setting, it might. If it would "stick" though, it would be immediate in the first generation. The only "eventually" about it would be if the trait eventually bred out.

      If you keep constant pressure on them, you'll kill all non-resistant plants from the field. It's like with bacteria. As long as you keep ampicillian in the dish, they'll keep their resistance. If you stop challenging them, they'll start to lose their resistance.

      If that crop got out in the wild, though, it wouldn't last long at all. Most wild plants don't get sprayed with herbicides, so they'll be wasting energy. A pesticide producing crop very well could retain their special trait in the wild. Many plant already do produce pesticides.

      The reason that farmers are forbidden from using their own crop for seed isn't genetic, it's corporate. If they did use their own seed, they effectively become a competitor with the people they bought the seed from to begin with. If your customer can make the same thing you do, they'll always undersell it to themselves.

    12. Re:So what happens to gentically modified plants? by cataclyst · · Score: 1

      Yes, but those USUALLY require human intervention... and don't produce progeny on the kind of scale seeds are able to...

      --
      E = m * c^(Hammer)
    13. Re:So what happens to gentically modified plants? by Artifakt · · Score: 1

      I think you are very much on track there. I also tend to think that maybe most "good" traits are already there, but not all of them. Some pretty smart people do seem to disagree with both of us there, and say that if we watched long enough term (like a million years or so) it would turn out people's best edumakated guess would still always be worse than nature's methods. Since nature's methods are endless variations on the four horsemen of the apokalipse, that does not speak well for these people's opinion of the value of human intelligence.
      As long as roundup is being widely used, resistance should be advantagious, and the gene should spread. Neither back mutation/error correction, nor cross-fertilization with wild strains should weed (ouch!) the gene out with such a powerful net advantage.

      --
      Who is John Cabal?
    14. Re:So what happens to gentically modified plants? by vsprintf · · Score: 1

      If that crop got out in the wild, though, it wouldn't last long at all. Most wild plants don't get sprayed with herbicides, so they'll be wasting energy. A pesticide producing crop very well could retain their special trait in the wild. Many plant already do produce pesticides.

      That seems to be another reason why the internationally claimed fears of GE crops are misplaced.

      The reason that farmers are forbidden from using their own crop for seed isn't genetic, it's corporate. If they did use their own seed, they effectively become a competitor with the people they bought the seed from to begin with.

      Yes, that's the reason you'll get even from Monsanto, and I understand the monetary reason, being the cynic I am. :) My point was that because of the seed policies, there has been no (excuse the pun) field testing of the multi-generation trait inheritance of GE crops versus the RNA-based "memory" suggested in the article.

      In any case, thanks to you and the others who responded. This has been one of the more interesting topics on Slashdot recently.

  27. Maybe it's the result of mutation by manifoldronin · · Score: 2, Interesting

    Maybe it's just this generation of plant obtained the ability through mutation to make genetic self backups.

    --
    Tyranny isn't the worst enemy of a democracy. Cynicism is.
  28. I'm pretty close to this research... by Marx_Mrvelous · · Score: 4, Interesting

    My wife was second author on this paper, and did quite a lot of the research! I guess that blows my cover ;)

    This really is no joke, these results are really exciting! I suggest everyone read the article.

    --

    Moderation: Put your hand inside the puppet head!
    1. Re:I'm pretty close to this research... by MightyMartian · · Score: 2, Interesting
      It's pretty interesting. It could, from my limited understanding of things of this nature, suggest a secondary means of inheritance. Time from the microbiologists to start digging around.

      Never the less, this is not the death-knell of evolution, or in any way contradictory to it, though I know kook organizations like Answers in Genesis and the Discovery Institute will lie their heads off to make it look that way.

      --
      The world's burning. Moped Jesus spotted on I50. Details at 11.
    2. Re: I'm pretty close to this research... by Black+Parrot · · Score: 2, Funny


      > This really is no joke, these results are really exciting! I suggest everyone read the article.

      Sorry; that's not customary on Slashdot.

      --
      Sheesh, evil *and* a jerk. -- Jade
    3. Re:I'm pretty close to this research... by stm2 · · Score: 1

      Congrats her!. Could you please send me a reprint? (or the PDF).
      My email is sbassi AT gmail
      thx!

      --
      DNA in your Linux: DNALinux
    4. Re:I'm pretty close to this research... by Anonymous Coward · · Score: 0

      Hey, congratulate her for such a great high-impact paper :)
      This is going to be doing the round in lunchtime seminars and journal clubs for a while ;)

  29. Wait a minute.... by the_rajah · · Score: 1

    I posted this when no replies were showing. It may be redundant, but certainly not intentionally so. Give a guy credit where it's due. I have mod points, too, and try to use them with some common sense.

    --


    "Do the Right Thing. It will gratify some people and astound the rest." - Mark Twain
  30. No, not really by Anonymous Coward · · Score: 5, Informative

    For the people who, ah, read the paper, if this particular gene (HTH) is mutated, then a whopping 5% of the second-generation genes manage to revert to the wild type. The other 95% are still mutant. So this mechanism (which is normally masked by the presence of a normal HTH gene) provides for a small number of mutant offspring to revert to wild type, so that a deleterious mutation won't completely destroy the population it occurs in. To disprove "micro-evolution", you'd have to show that this mechanism used to be turned on in every organism and operated at ~100% efficiency rather than 5%. Don't bet on it.

    Now, this is definitely a pretty cool discovery, and there's going to be a stampede of people hunting around looking for some sort of, say, RNA copy of the genome hiding somewhere in Arabidopsis, and there will be a lot of fun in epigenetics. But it isn't going to destroy evolutionary theory, although I expect creationists (excuse me, "intelligent design theorists") will be running around for decades insisting that because this phenomenon exists, it's impossible for mutations to happen.

    1. Re:No, not really by conan776 · · Score: 1

      > if this particular gene (HTH) is mutated

      This is all unconvincing, and seems to say little for natually occuring mutations versus ones forced in the laboratory.

      How are they doing the mutating? Virus? Gene slicing/splicing? Is there an unmmutated gene sitting out there in the pool after the process. Some little bugger that can undo some surgically malicious damage wouldn't be too surprising then.

      --
      "Reality is that which, when you stop believing in it, doesn't go away." -- Philip K. Dick
    2. Re:No, not really by hurfy · · Score: 2, Interesting

      Sounds more like some kind of check-sum than a backup copy.

      If the mutation is not too severe and/or there arent multiple mutations

      AND

      The plant is good at math (ok, the plant chromosonal equivalant)

      THEN it can generate a new copy of the old version when it reproduces.

      I am probably missing a second AND something to get it down to 5%.

      They didnt see an obvious Dup but we certainly don't know the plant chromosonal equivalent logarithems! ((or they hired the slashdot editors to look for the dup copy...))

    3. Re:No, not really by CactusCritter · · Score: 1

      The anonymous coward who started (IIRC) this topic wrote very knowlegeably. The work on araibidopsis (sp?) needs to be replicated and, if successful, fanned out to other plants.

      When the basis for epigenetics was discovered, it was in the the favorite animal genetic study species, C. elegans. The initial conclusion was that the results were so novel that they probably occurred in no other critter. Subsequent research revealed that epigenetics acts in every multicellular critter. It also resulted in recognition that the rather ignorant conclusion that non-coding DNA in genomes was junk resulted from the fact that genetic research had discoveries to make.

      The investigator(s?) who reported the recovery of ancient genes admitted that it might or might not be limited to araibidops. If it's really a fundamental discovery, it damned sure won't be limited to one plant species.

  31. All information not in yet by ucblockhead · · Score: 2, Interesting

    Before jumping to too many conclusions about this, remember that it is a report of a mutation one gene in one organism. It very well may be very specific to this particulary gene. Worthy of study. Not yet worthy of making broad conclusions.

    --
    The cake is a pie
    1. Re:All information not in yet by TheHornedOne · · Score: 1

      No, actually, they generalized it to lots of other genes.

    2. Re:All information not in yet by extensis · · Score: 1

      The title of the primary article is "Genome-wide", I guess RTF Title is in order. This work suggest that this gene might not be unique.

      --
      Mike Jones-{ Genetic Engineer, in Training }-
  32. Read the Proper FA by whitehatlurker · · Score: 2, Informative
    The original press release is at least visible without a subscription. It also has contact information for the author, Robert Pruitt, for those who have inquisitive natures.

    Beware, there are pictures of MUTANT plants here. Watch out for the triffids.

    --
    .. paranoid crackpot leftover from the days of Amiga.
  33. the plants don't actually "correct" mutations... by xlurker · · Score: 5, Informative
    just heard this report on NPR.

    What was reported is that although there were mutations in the DNA of the plant, its siblings didn't have them anymore. The researcher said that the best theory at the moment is that the non-mutated DNA was coming from the RNA of the plant. IANAB, but I think RNA usually is though to serve only a functional "middle man" role betweeen the genetic code and the cell machinery, and not actively involved in reproduction...

    He did not say that the plant was actively fixing its DNA for its offspring.

    The non-mutated RNA was itself directly inherted from the parents. In a way the RNA has become a bad backup copy of the DNA. That's the present theory... I guess this is what they'll start looking for... "Bad backup copy" since still 90% of the offspring of the plant still contained the mutated DNA.

    --
    ______________________________________________
    sigamajig...
  34. Finally... by azmeith · · Score: 1

    the invasion starts...

    <oblig>I for one welcome our new florine overlords..</oblig>

    -- Reality continues to ruin my life. - Calvin (Bill Watterson)

  35. Holy Hollywood Batman! by Anonymous Coward · · Score: 0

    Because each of the plant's two copies of the gene were in mutated form, they had virtually no chance of having normal offspring. But up to 10 percent of the plants' offspring kept reverting to normal.

    It's just like in "Jurassic Park"! What if these horrible "plant" creatures escape the lab and multiply to cover the entire planet?! Quick, let's burn them all, just to be safe.

  36. mod parent up by JeanBaptiste · · Score: 1

    I was gonna say that, but the parent beat me to it.

    how would a plant 'know' which mutations are harmful and which are beneficial?

    a: it wouldn't

  37. It is IBM by Imposter_of_myself · · Score: 1

    I knew IBM had been working on "self-healing" servers - this must be part of that research - self healing plants ;-) In the future, dual core processors will give birth to quad core processors. The ones that only give birth to three core processors will correct themselves when they breed and will have quad core offspring ;-)

    1. Re:It is IBM by Anonymous Coward · · Score: 0

      I like this ... just need more processing power for a slow routine? Send the "reproduce" command and sleep until the new processors are done ...

      Might make it a bit hard to manage the space and electrical supply inside the case, though.

  38. Plants have huge genomes by Anders+Andersson · · Score: 3, Interesting

    I haven't bothered to register to read the article, so maybe this is discussed already: I have been told that plants (or at least some of them) have a lot of DNA due to, among other things, spurious repetitions of partial sequences. I don't have any numbers for nucleic DNA, but I think I saw somewhere examples of plants having more than 100,000 base pairs of mitochondrial DNA, compared to some 16,500 for humans. I guess those repetitions might work as a backup, and help revert an earlier mutation.

    I'm not a geneticist by profession though, so what I'm telling here may be an urban legend...

    1. Re:Plants have huge genomes by Marx_Mrvelous · · Score: 1

      Actually, there is no "copy" of this gene anywhere in the genome of the plants the research was done on. This was intentional, both in selection of the plant (Arabidopsis), and the study group.

      So no, in this case, it's not another "backup" copy kicking in. This is why the research is such big news.

      --

      Moderation: Put your hand inside the puppet head!
  39. Intelligent Design by pablonhd · · Score: 0, Troll

    Why it so unacceptable to introduce the idea of "Intelligent Design" when everything about life is so structured and orderly?

    Why is chance so much more believable?

    1. Re:Intelligent Design by CuteAlien · · Score: 1

      Simply because it's not a scientific theory. Science is about finding out how thinks work and you don't find out anything if you just explain causes by a higher intelligence.

    2. Re:Intelligent Design by Anonymous Coward · · Score: 0, Interesting

      Because, with the latter, one doesn't have to face up to any sort of responsibility for ones actions. Admitting that a creation event might have been possible is the first step toward the slippery slope off the throne of godhood in one's own life.

    3. Re:Intelligent Design by MightyMartian · · Score: 4, Insightful
      Why it so unacceptable to introduce the idea of "Intelligent Design" when everything about life is so structured and orderly?

      Let's see:

      1. Things aren't so structured and orderly. Look at your own body. Anybody who designed such flawed systems as knee joints and eyes with blind spots ought to be fired, if not outright charged with criminal negligence. Living organisms demonstrate the slow march of blind evolution, with functions and organs being co-opted for other purposes, and not being calibrated for ultimate efficiency. As much as anything else, organisms tend to look like compromises, and not optimal designs. They certainly don't resemble entities that we observe to be designed.

      2. How could science ever pursue something like "Intelligent Design"? Who is this designer? Where did they design life? What forces did it/they bring to bear? How can a researcher hope to falsify any particular claim about the designer? These are the sorts of questions that must be answered, and in reference to evidence that can actually be gathered. That is how science functions.

      Why is chance so much more believable?

      This sentence betrays some substantial misunderstanding of evolutionary theory. Evolution is not pure chance. Mutations themselves are likely to be so, but the selective processes are not random.

      As well, what does "believability" have to do with it at all? Science follows the evidence, not the conceits and sensibilities of people. Imagine going back in time 5,000 years and telling some Mesopotomian that Earth is a sphere that orbits the sun, which itself orbits the central mass of a vast galaxy with billions of stars, which in turn is itself only a rather ordinary member of a vast cluster of galaxies. That you cannot imagine (or refuse to imagine) something to occur is not an argument against it, but merely fallacious thinking.

      --
      The world's burning. Moped Jesus spotted on I50. Details at 11.
    4. Re:Intelligent Design by Anonymous Coward · · Score: 0

      It's not chance, and an intelligent designer isn't required to explain observations.

    5. Re:Intelligent Design by pablonhd · · Score: 1

      So are you saying is science today is the search of an explanation that excludes the possibility that there may be something out there greater than us? My biggest question about our existence is what set all that we have now in to motion?

    6. Re:Intelligent Design by CuteAlien · · Score: 1

      No, i didn't say that :) I just said that this ain't the way science works. You're using occams razor and if you ever start speculation openly you usually do it in very small steps (like supposing in this case that RNA could be responsible for preserving the genetic information). Nothing stops a scientist from having a vision (like trying to prove god or something like that), but this does not make it a scientific theory.

    7. Re:Intelligent Design by pablonhd · · Score: 0, Troll

      If you came across a sand castle on a beach is your first reaction to say that the wind and waves created it. Or do you belive that something intelligent created it?

      The more macro and micro we look at things all we find is structure and order.

    8. Re:Intelligent Design by pablonhd · · Score: 1

      Understood.

    9. Re:Intelligent Design by frenchgates · · Score: 3, Interesting

      Wow, I have to say, your lack of an actual response to the very cogent parent is breathtaking.

      When you see Mt. Rushmore you think of a creator, I suppose, but when you see a rock outcropping ade to look like a face by weathering you also might think of a creator. In the second case you'd be wrong.

      --
      Syntax error: loose != lose, affect != effect, then!=than
    10. Re:Intelligent Design by MightyMartian · · Score: 2, Insightful
      If you came across a sand castle on a beach is your first reaction to say that the wind and waves created it. Or do you belive that something intelligent created it?

      Since I know from experience that sand castles are designed by people, when I see one on the beach, simple deductive reasoning allows me to say "That's very likely designed." In other words, your analogy is flawed, as all such watchmaker analogies are, at their very core. Beyond that, in the sciences that do deal with intelligence design (archaeology and forensics come to mind), a good deal of effort has to be put into showing that certain processes or artifacts are, in fact, the products of an intelligent designer. I personally could walk through a field strewn with Acheulian tools and not recognize them as being the product of an intelligent mind.

      The more macro and micro we look at things all we find is structure and order.

      I don't see this at all. The more we observe the world revealed by genetics, the more we observe the messiness of evolution, viral sequences in our genome, genes that are minimally active leading to primates like ourselves being unable to produce sufficient Vitamin C, thus requiring us to gain it in our foods. Simply waving your hands and saying "it's structured" doesn't really say anything at all, and is simply another demonstration of your fallacious thinking.

      --
      The world's burning. Moped Jesus spotted on I50. Details at 11.
    11. Re:Intelligent Design by blue+trane · · Score: 1

      Look up "Null Hypothesis" in your nearest statistics textbook.

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

      It's an argument from ignorance and a lack of imagination, and the structure is not the perfection that the Judeo-Christian IDers espouse.

    13. Re:Intelligent Design by Anonymous Coward · · Score: 1, Informative
      Look up "Null Hypothesis" in your nearest statistics textbook.
      Not to mention a quick lookup of Occam's Razor.
    14. Re:Intelligent Design by Anonymous Coward · · Score: 0
      It's an argument from ignorance and a lack of imagination, and the structure is not the perfection that the Judeo-Christian IDers espouse.

      Well, if you corner them on it, they usually respond with some claim that everything was fine until the Fall. I'm still waiting for some Fundie Creationist to explain what the shape of Eve's hips were prior to the Fall.

    15. Re:Intelligent Design by fsmunoz · · Score: 1

      (archaeology and forensics come to mind), a good deal of effort has to be put into showing that certain processes or artifacts are, in fact, the products of an intelligent designer. I personally could walk through a field strewn with Acheulian tools and not recognize them as being the product of an intelligent mind.

      Big truth, in my first archaeology classes I was asked to pick several "artifacts" and select those that might be "interesting" (read, man made) and those that weren't.

      I - and everyone else - got it wrong, it's very, very hard many times (especially when we are talking about the very begining) to even consider a formless piece of rock as something carved by Man, and very tempting to see some kind of purpose in what is the result of erosion.

      The good news for ID people is that the Earth for them probably didn't exist at the time-frame we are talking, so no need to put a lot of work at making the distinction.

    16. Re:Intelligent Design by MightyMartian · · Score: 2, Insightful
      The lesson in all of this is that in the real world (and not in the demented heads of Intelligent Design "theorists") recognizing design is not a trivial matter for objects that we have not actually seen designed before. Of course one is going to know a sandcastle is constructed, because one's experience is that sandcastles are designed and built. If you have to actually deal with objects or processes where every day common experience cannot be used to compare to, then things get very tricky. Heck the first guys to spot pulsars thought the source might be LGMs, simply because of the extreme regularity of the signal. The lesson here is that regularity doesn't mean design, or, in other words, not every watch indicates a watchmaker.

      But Intelligent Design isn't really about that anyways. Its essence is nothing more than "somehow something somewhere is wrong with evolution". It's simply about disguising the obvious theological aspects of Creationism behind the guise of pseudo-science. The ID advocates change their tune depending upon the audience. To critics, the Intelligent Designer could be an alien race. To the Creationists, of course, they don't try to hide the fact that the Intelligent Designer is the Biblical God. It's the fundemental deceit of the movement that it's real interest isn't furthering knowledge, but trying to force science away from following lines of evidence that they believe questions their religious beliefs.

      --
      The world's burning. Moped Jesus spotted on I50. Details at 11.
    17. Re:Intelligent Design by Anonymous Coward · · Score: 0
      That you cannot imagine (or refuse to imagine) something to occur is not an argument against it, but merely fallacious thinking.

      No, not fallacious thinking, merely limited thinking. You really thing that humanity's understanding of the cosmos, of what matter is, or how biological systems work 5000 years from now could be understood by any of us now? Of course not. That doesn't make us "wrong", and neither was that Mesopotamian, it just points out that our understanding how the world functions will (likely) always be incomplete and fallible.

    18. Re:Intelligent Design by RoLi · · Score: 1
      Let's see:

      • Evolution is able to make forecasts. For example Mendel had differently colored flowers and could make forecasts about which colors the offspring had and at what ratios. If a theory can be used for forecasts, it's useful for many things (like creating better plants). ID doesn't make any forecasts, it's unscientific and useless. It's so useless that you would be worse off with no theory at all.
      • Life isn't structured and orderly at all. There are diseases and wars - that should have been created by an intelligent designer? Doesn't sound very intelligent for me.
      • Even the ID-crowd is following the rules of evolution deep down their hearts. For example I bet that you wouldn't want to mate and have a family with someone who is suffering from a genetic disease.
    19. Re:Intelligent Design by Anonymous Coward · · Score: 0

      Evolution is able to make forecasts. For example Mendel...

      This is nitpicking, I know, but forecasts from Mendelian genetics don't support evolutionary theory, except to the extent that a process of inheritance, that is replication, is a necessary precondition. A prediction based on evolutionary theory would be something like the development of antibiotic-resistant bacterium strains.

    20. Re:Intelligent Design by Anonymous Coward · · Score: 0

      Because the weakest, flimsiest, most tentative attempt at a scientific explanation is infinitely better than "We don't understand this, therefore it must be magic."

  40. Could it just be that the mutations by hsmith · · Score: 1

    mutate back to the original state? could this be a possibilty at all to explain it? my knowledge of biology is limited so i have no idea

    1. Re:Could it just be that the mutations by CuteAlien · · Score: 1

      It happens to often for that. It seems to happen in one of ten cases and you don't even have that much mutation usually.

    2. Re:Could it just be that the mutations by Anonymous Coward · · Score: 0

      It could be a very unstable mutation that does actually revert back to the normal state 10% of the time.

  41. Backup Copies Exist for Many Genes by jestill · · Score: 5, Interesting

    My lab does research on plant genomics, and we are involved in research concerning the duplication of genes in the plant discussed in the article.Many of the genes that a plant has exist in multiple copies and that is not a new idea. We can follow the evolutionary history of these duplicated copies and show that they often arise from duplication of the entire genome followed by selective genome loss. We also frequently find that single genes are duplicated by themselves, or that entire segments of a chromosome may be duplicated by the process of 'segmental duplication'. The interesting thing here is that the scientist believe that a second copy of the gene does not exist as a DNA copy, but as an RNA copy. That is an interesting hypothesis, that will need to be explored further.

    --
    "Asleep at the switch? I wasn't asleep, I was drunk!" -- Homer
    1. Re:Backup Copies Exist for Many Genes by WillAffleckUW · · Score: 2, Interesting

      I'm presuming you're referring to Plasmids, correct?

      We also frequently find that single genes are duplicated by themselves, or that entire segments of a chromosome may be duplicated by the process of 'segmental duplication'. The interesting thing here is that the scientist believe that a second copy of the gene does not exist as a DNA copy, but as an RNA copy.

      --
      -- Tigger warning: This post may contain tiggers! --
    2. Re:Backup Copies Exist for Many Genes by Dulimano · · Score: 1

      How do we KNOW that there is no DNA copy? Isn't it possible that the DNA copy is not word-for-word? Maybe some trivial bijective transformation is applied, and the repair mechanism decodes this transformation when it corrects the original. Could we find the DNA copy even if this is the case?

    3. Re:Backup Copies Exist for Many Genes by Dulimano · · Score: 1
      How do we KNOW that there is no DNA copy? Isn't it possible that the DNA copy is not word-for-word? Maybe some trivial bijective transformation is applied, and the repair mechanism decodes this transformation when it corrects the original. Could we find the DNA copy even if this is the case?

      ...I finally managed to RTFA, and my question is still very valid.

      "A mutated gene can be put right by various mechanisms that are already known, but all require a correct copy of the gene to be available to serve as the template. The Purdue team scanned the DNA of the entire arabidopsis genome for a second, cryptic copy of the hothead gene but could find none."

      So isn't it more plausible that they didn't search hard enough, or that the copy is more cryptic than they imagined? This second case would still make a quite interesting discovery, but it wouldn't involve RNA.

  42. This is new? by Dr.Zap · · Score: 1

    Doesn't this already happen in animals? e.g. Hair color in humans? Maybe it's just a recessive gene thing.

    1. Re:This is new? by dhope · · Score: 1

      No. These plants got the erroneous gene from _both_ parents. Yet 10% of the offspring still somehow managed to fix the problem. Fascinating!

  43. Therefore, what? by Delilah+Jones · · Score: 1

    It would be really cool if we could find out how to tap into similar genes in the animal kingdom--namely with humans.

    It seems that at this point the science (which hasn't even been confirmed yet) is mostly 'descriptive'.

    If it could get to the level of 'manipulative', that would be neat!

    Imagine how many genetic diseases could be overridden (and otherwise avoided) by finding the appropriate corrective RNA gene!

    --
    http://augustwestproducts.i8.com
  44. Redundancy and genes by Marko+DeBeeste · · Score: 1

    This is one of the core features of genes and gene pools. Back up, resistance to "shock" changes, etc. The fact that it happens on a mets-level is pretty much inevitable. Not that the mechanism isn't exciting, just re-inforces the basic model.

    --
    Faith: n. -- That human impulse that drives them to steal appliances when the power goes out
  45. Why plants have complex genomes by G4from128k · · Score: 2, Interesting

    Most Plant genomes are crazy complex. Besides that, polyploidy is often the norm in plant chromosomes. With that much genetic material to work with, i guess you'd be bound to find a 'do-over' someplace.

    Exactly, and there's a reason for that crazy complexity. The core challenge for a plant is that it cannot move. It has to handle all the processes of life whilst living where ever it happened to sprout. If the sunlight is intense or shaded; if the ground is wet or dry; if a caterpillar munches on the plant; if the soil is laced with silicon or deficient in phosphorus; or whatever, the plant can't do much about it but activate/deactivate genes. As a result, they have evolved a more complex genome with a greater number of IF-THEN or CASE statements built-in.

    In contrast, most animals are nicely mobile, if they don't like their environment, they move to a better location. As such animals don't need as complex a genome because they spend most of their lives in their chosen micro-climate.

    --
    Two wrongs don't make a right, but three lefts do.
  46. Plant Infringement? by Anonymous Coward · · Score: 0

    It's just plants copying RAID or PAR files. This is nothing new - we've had those for years now.

    Copying? If it bothers you so much you can always sue them for patent infringement. Of course the plants might lawyer up and come back at you claiming prior art....

    Please mod grandparent +1 .. and mod parent -1 defective.

  47. Little people with normal kids? by Humorously_Inept · · Score: 1

    When two "little people" have children, it's not unusual for that child to be of normal height. How does what is observed in the plants differ from the anecdotal observations of a similar nature in humans? Is this exciting because the plants have been modified or selected to specifically exclude any normal-plant characteristics wheras "little people" have not been?

    Can you tell that I elected to ignore all studies of biology starting at the eleventh grade?

    --

    ~Someday, I hope to be an aspiring author.
    1. Re:Little people with normal kids? by Anonymous Coward · · Score: 0

      When two "little people" have children, it's not unusual for that child to be of normal height.

      Galton called this inheritance effect "regression toward mediocrity". (incidently, this is why fitting a function to data is called 'regression') It can be explained fairly simply by supposing that the height of an individual is influenced both by chance and by inheritance.

  48. Where is the backup copy? Symbiosis? by Anonymous Coward · · Score: 0

    The article doesn't have much detail, but they seemed to be pointing at RNA, as the DNA sequence apparently doesn't seem a candidate and RNA is the only other option they can think of.

    I immediately thought of some kind of plant symbiotic relationship with nitrogen fixing bacteria. Kind of like mammalian cell's relation to mitochondria. Perhaps the plant scientists could speak as to the process used when growing plants for these experiments. I assume all the soils are free of bacteria or any environmental source of genetic material, but certain plants need bacteria to fix nitrogen, and could possible exchange genes with them. And all this no mutation vs evolution stuff might be moot because we aren't talking plant genome but the combined genome of the plant-bacteria symbiot.

  49. Double Mutation? by bryan8m · · Score: 2, Insightful

    Could this gene simply be more likely to mutate and it just mutates back to the normal state?

    1. Re:Double Mutation? by stm2 · · Score: 1

      That is called reversion (and bacteria who revert a mutated gene are called revertants). I guess researchers should have rule that out.

      --
      DNA in your Linux: DNALinux
    2. Re:Double Mutation? by Wabin · · Score: 2, Insightful

      That would be a possibility, but two things make it unlikely (from the actual Nature article, which I can read, being at a University with a subscription): One is that if it were just a region of high mutation, then you would expect to see other changes in the gene. They don't find them. The other thing is that they have this behavior at 11 sites in the gene. So it is not as if there is one site that is flipping around all the time. There is something strange going on. I don't really have a good sense of what it is, and the RNA backup hypothesis will be pretty easy to check. I expect there will be a lot of work on this in the next few years, and we should have some answers soon enough.

      --
      Most exciting phrase in science: not "Eureka!" but "Hmm... That's funny..." -Asimov (abridged for \. limits)
  50. Same story, no reg by statemachine · · Score: 2, Informative

    AP wire story via Yahoo. No registration required.

    Plants Challenge Genetic Inheritance Laws

  51. if both parent have the gene, who says it's bad... by xlurker · · Score: 1
    that's what a lot of the comments here seem to be missing.

    There is no such thing as inherently "good" or "bad", to say a mutation is good or bad is to imply someone is evaluating, we know were that idea leads off to... (If we didn't have mutations, we'd all still be one-celled *g*)

    No, if the offspring has a different gene than both of the parents, one must conclude that the source of the gene is not what one expected!

    A present theory is that the un-mutated DNA came from the RNA of the parents. The RNA of the parent s did not (yet) contain the mutation. (Since the parents got those from the their parents).

    It was also said that still 90% of the offspring contained the mutated genes. That means the parents RNA only sometimes had influence... (IANAB)

    So, the theory is testing the idea that the RNA could be serving an additional role as a bad backup copy of the DNA.

    In a way you could call this meddling of the grandparents in the parents lives, "telling" them how to raise their children, heh heh

    --
    ______________________________________________
    sigamajig...
  52. Or... by ACNiel · · Score: 1

    If the grandparents had a backup, why didn't the parents correct themselves?

    Are we sure it didn't just mutate back?

  53. Because pussy can't talk... by Anonymous Coward · · Score: 0

    Cause da bitches is for fuckin' and suckin' yo!

    Pussy can't answer science question! damn!

  54. evolution by nnet · · Score: 1

    What if the "mutation" is actually an environment-based evolutionary adaptation instead?

    1. Re:evolution by Artifakt · · Score: 1

      Then we have to give Lysenko a posthumous Nobel :-)

      --
      Who is John Cabal?
    2. Re:evolution by Artifakt · · Score: 1

      I really hate to reply to my own post, but this topic is heating up, and someone will probably ignore the smiley and everything, so just for the record, the above is an attempt at humor. Fellow slashdotters many be the judge it it's successful, but I am not seriously advocating Lysenkoism, Lamarkism, Marxist/Leninism, or anything else by it.

      --
      Who is John Cabal?
  55. Re:the plants don't actually "correct" mutations.. by fsmunoz · · Score: 1

    I'm also not a biologist (my official education is in History), but this article just shows to me how Wikipedia can be addictive. I went there the other day looking for something about the Battle of Covadonga and went on clicking... after 4 hours I was reading about reverse transcripase, RNA world theory, DNA unwiding and MRSA. This is related to your post in that I found that RNA is apparently not only a middle-man - as in mRNA - as I expected. There are living organisms that have RNA as their genetic foundation, and from several articles I was surprised with the suspected and known functions of RNA which I didn't knew about.

    This post isn't informative, insightful or informative in what relates to the topic, just an advise to fellow biology-ignorant slashdotters t browse Wikipedia on the subject... absolutly amazing topic for people like me with only a superficial understanding of it. Start here and you'll be addicted.

  56. "Junk" DNA isn't by GPS+Pilot · · Score: 1

    I've always thought it was presumptuous for biologists to declare that "95% of our DNA is junk that serves no purpose."

    No purpose that you know of, yet.

    I've always thought that "junk DNA" might just contain error-correcting algorithms, encoded backup copies, checksums, and stuff like that. Today I feel pretty vindicated.

    --
    That that is is that that that that is not is not.
    1. Re:"Junk" DNA isn't by MightyMartian · · Score: 1
      I've always thought that "junk DNA" might just contain error-correcting algorithms, encoded backup copies, checksums, and stuff like that. Today I feel pretty vindicated.

      Whatever comes of explorations of junk DNA, this article seems to indicate that the researchers looked into the genome of the plants, and did not find the "backup" buried within. I don't think you should start the victory dance quite yet, as this does not appear to vindicate your opinion at all.

      --
      The world's burning. Moped Jesus spotted on I50. Details at 11.
    2. Re:"Junk" DNA isn't by DigiShaman · · Score: 1

      I've always though "junk DNA" was obsolite data. For example, as live evolves newer genes turn on and the older ones are left alone but never deleted. Thus, it just gets carried over from replication over and over. I suspect this process has been going on for over millions (billions?) of years.

      I like to think of DNA like the Registry hive in Windows. After awhile, it gets bloated with useless junk and will eventually get corrupted.

      --
      Life is not for the lazy.
    3. Re:"Junk" DNA isn't by GPS+Pilot · · Score: 1

      I said *encoded* backup copies -- not straightforward backup copies. Of course they're not going to find the backup, if the way it's encoded is not yet understood.

      --
      That that is is that that that that is not is not.
  57. Could just be Plasmids by WillAffleckUW · · Score: 2, Informative

    Not all genes are in the chromosomes, sometimes they're in Plasmids, especially with plants - or in humans, some of your DNA isn't in your chromosomes, they're in your Mitochondrial structures, hence you inherit them from your mother.

    However, a good controlled experiment should be able to rule this out, and I'm sure we'll all be talking about this in Biochem labs here at the UW this week.

    --
    -- Tigger warning: This post may contain tiggers! --
  58. never seen "cruft" in designed code? by Anonymous Coward · · Score: 1, Insightful

    Dude - I'm not arguing for "Intelligent Design", but have you never seen so-called "cruft" in source code of years-old systems? Would you try to argue that such source code must have evolved itself through exposure to an invisible and external-to-the-source-code neural-net (i.e. dumb automaton that just keeps trying stuff until it finds things that work better than before even if sub-optimal) because any developer who wrote crap like that would have been fired after the first dozen sub-optimal changes?

    Something as bad as the Windows source code could only have happened by accident, right?

    Jeez ... wake up and learn to really (i.e. "critically") think instead of just parroting back what somebody told you to believe!

    1. Re:never seen "cruft" in designed code? by MightyMartian · · Score: 1

      Trying to compare a genome to source code is simply a bad analogy. I'll warrant you don't see too much source code that has incidental duplications, viral insertions and transcription errors. DNA/RNA are not simply some sort of computer code, they are intimately involved in the processes of producing proteins. I fault this computer codeDNA analogy as inadequate highschool biology education.

      --
      The world's burning. Moped Jesus spotted on I50. Details at 11.
    2. Re:never seen "cruft" in designed code? by hazah · · Score: 1

      It's not that bad an analogy. DNA simply is set in a different environment. The idea is the same, things happen that cause other things to happen. A computer is a very crude way to duplicate the same system. Instead of molecules, a pattern of electrical signals is used. What those signals mean is arbitrary to the underlying structure, but hey... we have a picture, don't we? To DNA the patterns are all molecular, and produce their own sets of reactions. To DNA, it's arbitrary, but hey, we have eyes, and ears, and all that good stuff. The main similarity is that it's all about layers, seemingly independant, but altimately interconnected.

  59. Re:the plants don't actually "correct" mutations.. by Anonymous Coward · · Score: 0

    You're correct that this is what the article claims. But, with what we know currently...it still doesn't make sense to me.

    First, they say that this can occur in introns as well, and mature message RNAs don't have introns - thus no template. They speculate that it can't be from a mature message.

    So what RNA is it coming from? Where is this RNA stored? And more importantly, what is replicating this "backup" RNA during cell division? (Remember, the plants start out as embryos and have to grow - so presumably they have replicate the RNA so that is is present in the next generation before the DNA can be repaired.)

    Why is this "backup" RNA so stable when other message RNAs are inherently not? (If it's a double stranded RNA, why isn't it degraded? dsRNAs are typically degraded by plants as a protection against viruses.)

    And, how does the RNA serve as a template to correct that specific gene (and not other similar genes which may share sequence homology)?

    They don't even look for an RNA containing the sequence that *must* be there. It seems a bit premature to publish a model for this when there is no evidence that it is even possible.

  60. You read it completely wrong... by hung_himself · · Score: 1

    The evolution of sexual reproduction is what is brought into question *not* evolution. A major impetus for the evolution of sexual reproduction is the advantage of getting a good copy of a gene to replace a damaged one when you exchange DNA by sex. The prospect of RNA backup copies makes this a bit more complicated since there would be less need for sex to repair the DNA. This is discussed a bit in the article - and they imply that the RNA backup system (if it exists) may be prevalent in organisms that primarily reproduce asexually and thus have a greater need for such a repair system.

    It doesn't invalidate anything and does not bring evolution into question. And, FYI, scientists are always at the drawing board - as working on theories as they "evolve" to reflect new data.

    Isn't it amazing how less we know, the less we know? :-)

  61. Nature by BarryNorton · · Score: 1

    The source on this article isn't the New York Times, nor as suggested the LA Times or New Scientist, but Nature (vol 434, p 505 - subscription only)

  62. Joy unbounding li li li by Swamii · · Score: 1

    the paper this morning was pointing out how this discovery might leave a gaping hole in evolutionary theory.

    Wha??? Evolution...gaping hole...? Err uh bzztt *poof* Slashbot brain cannot compute result. You must be a Jeeeeeeezus person.. er bzztt *crash* boing bzzt must POST ANONYMOUSLY ...bzzt and INSULT your ... m.M.M.m.mother bzzt *boom*

    --
    Tech, life, family, faith: Give me a visit
  63. Order of credit by tlambert · · Score: 4, Interesting

    Credit order generally boils down to:

    (1) Who got the grant
    (2) Who has the most tenure
    (3) Who went to the meetings
    (4) Who wrote the paper
    (5) Whoever is politically in and most needs a paper credit to keep on tenure track
    (6) etc.

    Actually doing work tends to come dead last. Sometimes (as some recent scandals have shown), it doesn't come at all.

    Also, realize that to a scientist, it's not about the credit for getting something done, it's about the fact that it needed to be done, and someone did it.

    For every scientist popularized by the media, there are thousands of them of whom almost nobody has ever heard, but who were critically important for fundamental things we take for granted every day.

    For example, some of the first posts in this thread were going on about retrying the Scopes "Monkey Trial" vs. Darwinian evolution, when most biologists today know that the currently accepted evolutionary theory is Jerry Pounelle's "Punctuated Equilibria", and Darwin is generally only taught for having come up with, and written about, the idea of change in species over time.

    -- Terry

    1. Re:Order of credit by MightyMartian · · Score: 1
      Me'thinks you don't actually know what P.E. is. You certainly don't know who came up with it (hint: Jerry Pournelle is an SF author and sometimes strategic columnist/advisor). Stephen J. Gould would have been rather surprised to find out that P.E. somehow goes against Darwin's theory, as his last book went to great lengths to explain why P.E. nestles quite nicely into Darwinian evolution (if not into the mechanics as Darwin understood them in the middle of the 19th century).

      Here's a tip, head off to talkorigins.org and learn a little about evolutionary theory.

      --
      The world's burning. Moped Jesus spotted on I50. Details at 11.
    2. Re:Order of credit by espressojim · · Score: 2, Informative

      Hey yeah! That reminds me, I'll be submitting work to nature soon (in the next month), and since I'm not 1,2,4,5, I'm still somehow going to be first author.

      Oh wait, I wrote all the analysis code. Weeee. I guess I qualify for "going to the meetings."

      Seriously, I don't think all labs work that way. You'll have the PI get the last spot on the paper, and usually the person who did the most work get one of the first spots. Unless you work with a bunch of credit stealing a-holes, then it's time to work somewhere else.

    3. Re:Order of credit by CactusCritter · · Score: 1

      Jerry Pounelle's "Punctuated Equilibria"? Good grief! It was Steven Jay Gould and Miles Eldridge who formulated that theory based upon their interprestation of the fossil record.

      Shame on you, tlambert.

  64. Nature paper by scaryfish · · Score: 1
    At first I'm extremely sceptical about this. But apparently they managed to get on the cover on Nature (one of the most prestigious scientific journals) so maybe they're onto something here.

    Here's the issue of Nature. You can access the full article text if you've got a University connection or something.

  65. Why does it happen so seldom? by CuteAlien · · Score: 1

    I'm a little bit surprised that it seems to work only in 1 out of 10 cases. If there really is a backup and a way of transmitting genetic information without DNA i think it should be optimized by now to work in most cases and not that rarely. This sounds to me a little bit like finetuning the mutation rate at he positions after the decimal point.

    1. Re:Why does it happen so seldom? by joak · · Score: 2, Interesting

      The net effect may be "fine tuning the rate" as you say. What makes this so fascinating is the mechanism is completely new.

      Speculating wildly, I suspect it could be more an "accident" than correction mechanism--the correct sequence may be in some RNA reservoir which occasionally gets "mistakenly" inserted in the normal reproduction process. We never noticed before, because normally the RNA sequence would complement the DNA sequence completely. But even this would be amazing, since we don't know how or when that would happen.

      I can't quite figure out when this would be especially useful as a corrective mechanism; if it were actually triggered to come into play correct non-adaptive mutations a generation later, it would be mind-bogglingly huge as a discovery.

      A third possibility is, of course, a misleading experimental result. That would still be interesting, but only because it made the cover of Nature ;)

  66. No after market support from the manufacturer? by tlambert · · Score: 2, Insightful

    Why it so unacceptable to introduce the idea of "Intelligent Design" when everything about life is so structured and orderly?

    No after market support from the manufacturer?

    -- Terry

  67. So what? Consider your sand castle by Anonymous Coward · · Score: 1, Interesting

    The more macro or micro you look at it, the *less* structure and order you see. A sandcastle has no internal structure whatsoever. And a macro view of the entire beach would show far more chaotic disorder than structure.

    Until you got very micro--then you'd see crystal structure and atomic order *as described by science.* Or until you got very macro--then you'd see astronomical structure and order *as described by science.*

    Science goes beyond the mere recognition of structure and order, to read, understand, and predict, at a detailed level, what exactly the structure and order is.

    Not only is order and structure expected according to our most current scientific understanding of the world and universe, it conforms very closely to the scientific theories we have formulate to describe the structure and order.

    Besides, structure and order in and of themselves mean nothing to your argument. You're ASSUMING that structure and order can only arise from intelligence. To apply your way of thinking, what you would need to prove is that such structure and order could *only* arise through intelligent design. Good luck with that one.

  68. poof ... by btnheazy03 · · Score: 1

    there goes cowboy neals' excuse ...

  69. The ability to evolve had to evolve by couch_warrior · · Score: 1, Insightful

    While the religious side of me revels in the prospect that evolution may be proved impossible, the scientific side looks to the larger picture.
    The Darwinian view of evolution through slow mutation was proved wrong long ago by the fossil record. This knowledge has been closely held for fear the press would get ahold of it and have a field day. But based on the fossil record, it appears that evolution only happens when small populations are isolated and run short on resources.

    THERFORE - it is easy to theorize that genes have (at least) two maintenance modes programmed into them: ONE- we're thriving in a time of abundance - keep things from changing by repairng mistakes; TWO- We're dying off due to hostil conditions - quick, mutate and try to find a way to cope with this. This is why breeders can cause dogs, cats, birds, plants, to change into such bizarre forms in a few generations by breeding offspring back with parents - it simulates a dying population, and activates the evolve to escape mechanism.

    This evolutionary ability must itself have had to develop by the slow route, which is why life developed so little diversity for the first few hundred million years. But then, once the evolutionary mechanism was created - it kicked in and species began springing up all over the place.IMHO anyway

    --
    "Sic Semper Path of Least Resistance"
    1. Re:The ability to evolve had to evolve by TheHornedOne · · Score: 1

      Because I'm an idiot, "the religious side of me revels in the prospect that evolution may be proved impossible" because mah preacher done tol' me that "the Darwinian view of evolution through slow mutation was proved wrong long ago by the fossil record".

    2. Re:The ability to evolve had to evolve by scotsgit · · Score: 2, Interesting

      Evolution isn't caused by slow mutation. Darwin never said so. The main way evolution works is by reproduction and natural selection. Mutations only have a very small part to play and are in general not 'helpful'.
      The reason domestic dogs, cats etc. can be distorted rapidly is by replacing the natural selection by human intervention and selecting for another goal.
      Species form by separation of breeding populations when geographical boundaries are formed not by some weird slow/fast switch.

    3. Re:The ability to evolve had to evolve by Anonymous Coward · · Score: 0

      While the horned one, who went to school on the short bus, covers for his lack of understanding by mocking arguments he can not hope to comprehend...

  70. Hey by Anonymous Coward · · Score: 0

    you don't hear me bragging even though part of the DNA used in this research is mine, swabbed off the back of your wife's throat, do you?

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

      So you're a plant, capable of posting to slashdot - even after being swallowed by his wife

      Incredible ...

  71. What if it makes evolution work better? by JoeBuck · · Score: 1

    If there's a way to only turn on the backup if the organism isn't doing well, you could get a racheting effect, favoring positive mutations and limiting the damage from negative mutations. But it's too early to tell.

  72. MOD PARENT DOWN THAT'LL FIX HIS HOLY WAGON by Anonymous Coward · · Score: 0

    Don't want no 'vangelists 'round here. Except tech, science, and anime 'vangelists.

  73. I don't see this as anything amazing by scotsgit · · Score: 1

    DNA is full of all sorts of multiple copies of seemingly usless rubbish (tails in humans, the way flatfish bend into shape). It doesn't all get cleaned up in each duplication. What people don't always understand is that DNA is both the code and the copier. Mutations can change either the code controlling replication or the code for 'normal' purposes or both.
    All that's happend here is the code for copying has mutated to make two copies of a gene and another mutation in has made the plant use the non-stuffed up copy of the gene.

    1. Re:I don't see this as anything amazing by Anonymous Coward · · Score: 0

      Well this was in arabadopsis where the sequence is known. Because this is a Nature article, I'm sure the researchers would BLAST it to check the sequence strain and then also check the individual plants with the standard biochemical techniques to insure that two copies were not present in this strain.

      Then again, I don't have the PDF of the real paper in front of me (yet) so they may not have done the proper checks (though, as I said, I doubt this is the case).

    2. Re:I don't see this as anything amazing by scotsgit · · Score: 1

      I've read the PDF now and the second copy was in the RNA not the DNA. Which is the interesting but not against the principals of evolution.

  74. Re:Technology sucks... by Anonymous Coward · · Score: 0

    What's a "copywrite" moron? Are you perhaps thinking about a "copywriter" n. One who writes copy, especially for advertising.

    Perhaps you should just up when you obviously don't know anything on what you're talking about?

    But judging from your recent posts, you can't.

    Moron.

  75. obligatory comment about gene-fixing plants by djfray · · Score: 1

    yeah, but do they boot linux?

    --
    This sig is o Unfunny o Funny
  76. Big deal by greg_barton · · Score: 1

    In every one of you guys (and I do mean guys) is an nifty gene backup mechanism: the Y chromosome. Most of it is made up of gene palindromes.

  77. CRAP! You're right, Stephen J. Gould. by tlambert · · Score: 1

    I meant Gould. I am absolutely terrible with names.

    When I mentioned the references to Scopes, of course it was with regard to the mechanics as they were understood directly from Darwin's writings, which meant his understanding of them.

    Pushing a non-scientific position is always all about intentionally picking an already discredited theory as a whipping boy, and then citing the evidence that was used to discredit it.

    -- Terry

  78. Not exactly suprising by cscoreo · · Score: 2, Informative

    It's been known for decades that baker's yeast have the ability to fix mutated sex determining genes via exchange with an intact "cryptic" copy. The mechanism has been worked out in extreme detail. I don't think anyone ever thought they were the only organism that could do this . . . I guess it's nice to have proof, though.

  79. Please, post a link to the paper! by Anonymous Coward · · Score: 0

    Thanks!

  80. Re:Technology sucks... by Anonymous Coward · · Score: 0
    This, coming from a homo who can't use HTML tags properly. As your homework assignment, fix the example code below:


    Fuck you
  81. Do they know the biochemistry? by argent · · Score: 1

    Do they know what protein the gene in question codes for?

    Is it possible that some similar protein is doing the same job, or some mechnism "patching" the defective protein? That is, are the "normalised" plants using the same mechanism to produce the same effect?

  82. An interesting fact by Marx_Mrvelous · · Score: 1

    An interesting fact that none of the news articles mention is the fact that Bob (Dr. Pruitt) was the one who first suggested using Arabidopsis as the model organism for plants. Now you Know! (tm)

    --

    Moderation: Put your hand inside the puppet head!
    1. Re:An interesting fact by Anonymous Coward · · Score: 0

      Goodness me! I have some queries about other facts that are highly relevant to this discovery:

      1) What is Bob's favourite colour?
      2) Who drives the fastest car in the lab?
      3) Is the tea urn old and rusty or new and fabulous?

  83. ROR! YUO ARE FUNNY! by Anonymous Coward · · Score: 0

    no

  84. Not quite... by zavyman · · Score: 1

    I've always thought it was presumptuous for biologists to declare that "95% of our DNA is junk that serves no purpose."

    It's actually 70% of the human genome which is junk DNA. And that 70% is actually really just junk. It's from retrotransposons (LINE (long-interspersed genetic element), if you want to look it up) that jump in and out of the genome at will throughout the genome. There are some bits of retrovirus in there as well, but it's predominantly retrotransposons.

    It's just junk. It's that simple.

  85. Intron data providing a checksum? by renuk007 · · Score: 1

    We've always wondered at the huge amount of apparently nonsense data in the intron segments, which also seems to contain portions of valid genes. Maybe it's a form of backup?

    1. Re:Intron data providing a checksum? by tongue · · Score: 1

      That's what I'm thinking... We're used to thinking of DNA as a linear data structure, but in reality its much more likely to have second- and third-order organizations that provide much greater depth to the genetic coding contained therein. For the layman, think of it kind of like steganography--read it straight through and it says one thing, read every word corresponding to the first hundred terms of the fibonacci series and it might say another. We KNOW there's more to the story than just looking at the linear sequences--there's far too many proteins in the body than could be coded for in the number of genes we've been able estimate are in the human genome. Also, when rna is being transcribed from DNA, there's an intermediate step in which a bunch of noise is culled out, which is what the parent is referring to. Depending on how you cull the noise, the same gene could code for a number of proteins, which may or may not be related. I think its entirely possible that important genes exist in multiple dimensions for just such a reason.

      its important to note that these results have so far only been seen in arabidopsis... it may be a mechanism unique to plant life or even to that branch of the family tree.

  86. DNA error correction / protein specificity by bodrell · · Score: 1
    FWIW, the paper this morning was pointing out how this discovery might leave a gaping hole in evolutionary theory. The crux of the problem is that "micro-evolution" as it were, is dependant on an organism's ability to mutate from generation to generation. If a mechanism exists that prevents or corrects mutations across generations, then the theorists may *again* have to go back to the drawing board.
    I think you might be talking about this (from the article):

    The finding poses a puzzle for evolutionary theory because it corrects mutations, which evolution depends on as generators of novelty. Dr. Meyerowitz said he did not see this posing any problem for evolution because it seems to happen only rarely. "What keeps Darwinian evolution intact is that this only happens when there is something wrong," Dr. Surridge said.

    I've read enough of your posts to guess you didn't mean to suggest this "gaping hole" in evolutionary theory implies that creationism is a better alternative, but do watch your rhetoric. This is a violation of Mendel's laws of inheritance, but Mendel was just a monk growing peas. Biology is mind-bogglingly complex. There are so many biological checks and balances, circular pathways, regulator proteins (and proteins that regulate the regulator proteins). If the article had a little more meat regarding the "hothead" gene in question, this would be more interesting. How much different was the mutated protein from the wildtype? If it was just a single base difference, there could have been ten different ways the mutation was repaired. If there were several amino acids difference in the final protein sequence, that would be much more exciting. Okay, after a bit of research I can answer my own question:

    "Yet in the Pruitt-Lolle lab, a small but steady percentage of hothead offspring had normal flowers, like their grandparents'. Somehow, the mutation -- a single misspelled "letter" of genetic code in a gene made of 1,782 molecular letters -- was being repaired."
    A plant repairing a single base mutation isn't that surprising at all, especially if the mutation made the DNA twist into some funky unstable form, while the wild-type DNA forms neat and thermodynamically stable loops. They may have already considered that.

    Incidentally, it is much easier than I once thought to create a functional protein from scratch, if you know what you're doing. This guy at Princeton, who gave a seminar at my workplace recently, created proteins made of four alpha helices just by varying the amino acids by polarity. And the most surprising part is that some of these de novo proteins have enzymatic activity! Some can bind to heme and then act as peroxidases. Some act as esterases. It was suggested that perhaps primordial proteins were highly non-specific, or multi-functional, and only later evolved specificity.

    --
    Si la vida me da palo, yo la voy a soportar Si la vida me da palo, yo la voy a espabilar
    1. Re:DNA error correction / protein specificity by shawb · · Score: 1

      Man, scientists are such dorks. From the article you quoted:

      The mutation was in a gene known as hothead, one of many related genes -- including fiddlehead, airhead, pothead and deadhead -- that when mutated cause abnormalities in stems and flowers.

      Gotta love it.

      --
      I'll never make that mistake again, reading the experts' opinions. - Feynman
  87. wrong by JeremyALogan · · Score: 2, Insightful

    "a corrected version of a defective gene inherited from both their parents"

    turns out that two wrongs DO make a right
    1. Re:wrong by gibson042 · · Score: 0

      You have my vote for funniest comment of the thread (and, incidentally, most underrated as well).

  88. hothead gene, not hothouse by bodrell · · Score: 1

    Probably a Freudian slip. I love hothouse vegetables.

    --
    Si la vida me da palo, yo la voy a soportar Si la vida me da palo, yo la voy a espabilar
  89. hedgehog by bodrell · · Score: 1

    When it comes to silly names, I'm a fan of the hedgehog genes: Desert, Indian and Sonic hedgehog.

    --
    Si la vida me da palo, yo la voy a soportar Si la vida me da palo, yo la voy a espabilar
  90. And the anonymous URL is... by Anonymous Coward · · Score: 1, Informative

    Grabbed this URL from the RSS feed which naturally bypasses the NYTimes requirement to devulge your personal information. Not sure why they keep posting links to NYTimes without finding the pain-free links that are in the RSS feeds.

    http://www.nytimes.com/2005/03/23/science/23gene .h tml?ex=1269234000&en=00306bf37c75a71b&ei=5088&part ner=rssnyt

  91. I honestly don't get Slashdot... by popo · · Score: 1


    After submitting this very same NY Times story myself ... (a good 12 hours before this story appeared on slashdot) it was rejected and the above story was posted by Timothy.

    This seems to happen every time I submit !?

    What gives? I give up. No more stories for you Slashdot. (Apparently Taco and Timothy would rather post themselves...)

    Pthpth & kiss my ass.

    --
    ------ The best brain training is now totally free : )
  92. Finally a solution by Lomithrandel · · Score: 1

    To the mutant threat, professor x will never see it coming! mwahahahhaha!!!

  93. Chernobyl by mikerm19 · · Score: 1

    I don't remember, but did the radiation from the disaster effect the plants at all? If so, does this mean that the future plants will be back to normal?

  94. :rolls eyes: by mcc · · Score: 1

    "Evolutionary theory" predates mendelian genetics and is not dependent on it. Mendelian genetics is simply the best available explanation for how evolution happens and the one best supported by evidence to have actually occurred.

    There is no such thing as "microevolution". It's a term invented by people trying to reconcile theology with science, has no definition which is either consistently applied or consistent with any sort of evidentially grounded theory, and has no place in a non-theological discussion. I'm sure there are better terms for whatever it was you were actually trying to express.

    The existence of a process which inhibits mutations does not "leave a gaping hole in" or even realistically impact the ability of mendelian genetics to explain even what you call "microevolution", as long as there is some process somewhere by which alleles may be accidentally altered, ever. Okay, so there's a mechanism which may in some species under some circumstances correct "errors"? What if the error corrector makes an error???

    Uncovering contradictions in the operation of a scientific theory is an indication of flawed theory existing somewhere. However uncovering facts which complicate how that theory applies to the real world is an indication of a strong theory, because they show the theory is robust enough to accommodate complicating factors without breaking down into contradictions or epicycles. Uncovering complications in a theory's applications, as this paper uncovers complications in the mechanics of genetics as we know them, is a good thing because it means our understanding of how "stuff" operates has been tested and expanded; a theory whose applicability to the real world is not constantly being tested is a theory which perhaps cannot be trusted. Unfortunately the press, aided by a rather decent-sized faction of persons who actively wish to attack the idea of science, seems to often interpret such events as if they were a problem. It becomes difficult to meaningfully explain science to the public in such an environment, where positive events for scientific understanding necessary to the operation of the scientific process itself are so frequently popularly interpreted as negative events which cast doubt on the results of the scientific process.

  95. Re:How this impacts phylogentics by big_bull_000 · · Score: 1

    How will this discovery impact phylogentics which reconstructs evolutionary TREE?
    We are having a cycle here!

  96. This is not a Scientific Paper by pancakegeels · · Score: 1

    This is just a journalist reporting for the New York times. I look forward to reading about this if it makes it to nature.

    1. Re:This is not a Scientific Paper by Marx_Mrvelous · · Score: 1

      Check out the next issue.. it's the cover story.

      --

      Moderation: Put your hand inside the puppet head!
  97. Plants are very good at sex by csoto · · Score: 1

    Sex was developed to maintain established genes, NOT to "mix genes up" as some people mistakenly assert. Sex is anti-mutational. Homologous recombination's magic is that it favors the reproduction of "known" sequences.

    --
    There exists no way of exchanging information without making judgments. --Bene Gesserit Axiom