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Biotech Science

Scientists Measure How Quickly Plant Genes Mutate 67

Posted by Soulskill
from the starting-countdown-to-triffid-massacre dept.
eldavojohn writes "A recent study puts observed numbers on genome mutations in plants. This kind of research is becoming more popular in understanding evolution. The research 'followed all genetic changes in five lines of the mustard relative Arabidopsis thaliana that occurred during 30 generations. In the genome of the final generation they then searched for differences to the genome of the original ancestor.' A single generation has about a one in 140 million chance of mutating any letter of the genome (which has about 120 million base pairs). Sound like bad odds? From the article, 'if one starts to consider that they occur in the genomes of every member of a species, it becomes clear how fluid the genome is: In a collection of only 60 million Arabidopsis plants, each letter in the genome is changed, on average, once. For an organism that produces thousands of seeds in each generation, 60 million is not such a big number at all.' The academic paper is available in Science, though seeing more than the abstract requires a subscription."
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Scientists Measure How Quickly Plant Genes Mutate

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  • evolution ? (Score:5, Insightful)

    by polar red (215081) on Sunday January 03, 2010 @11:13AM (#30632082)

    Plants don't evolve, they get changed by the touch of his noodly appendages

    • Re: (Score:3, Interesting)

      by tomhath (637240)

      there are climate scientists trying to disprove global warming, but they fail,... what does THAT tell you?

      It tells me that you can't prove a negative.

      • I thought global warming was just observed fact, and the thing that is trying to be proven is the actual cause of it. Actually though, because of the strange climate we have here, global warming is only going to make my country colder at first. Hah.

      • Re: (Score:3, Insightful)

        by hey (83763)

        If you are having troubling proving negative hypothesis A ... try proving "not A".

      • Re: (Score:3, Insightful)

        by radtea (464814)

        It tells me that you can't prove a negative.

        You most certainly can prove a negative, and scientists do so all the time. The argument is generally of the form, "If X is true, the phenomenon Y must be observed under conditions Z. We have created conditions Z, proved by positive calibration that if Y occurred we would see it. Therefore X is false."

        Only people who are completely ignorant of exactly the kind of experimental science that has driven our understanding of the universe in the past century would cl

        • Re: (Score:1, Offtopic)

          by tomhath (637240)

          Yea, I took symbolic logic too. In your example you've proven that the conditions you believe represent Z did not produce Y. So either you didn't really produce condition Z (even though you thought you did), or your assumptions are wrong. But none of that matters, nor does it matter that some people cling to a supernatural explanation of what they observe in the real world.

          What's more important is whether transferring hundreds of billions of dollars from developed countries to less developed countries [newsdaily.com] is a

          • Re:evolution ? (Score:5, Insightful)

            by polar red (215081) on Sunday January 03, 2010 @01:34PM (#30633216)

            It's funny the people warning us about one world (elected)government don't issue warnings about our (unelected)corporate overlords.

            • by RockDoctor (15477)

              It's funny the people warning us about one world (elected)government don't issue warnings about our (unelected)corporate overlords.

              That's probably because they (the one-world-government-warning people) probably consider themselves to be likely members of the corporate overlord group, not of the boot-trampled masses. That's capitalism for you.

            • Because they are the same thing! Duh!

        • by Abcd1234 (188840)

          You most certainly can prove a negative, and scientists do so all the time.

          Um, no, they don't.

          Scientists never "prove" negative statements. They falsify (ie, provide counter-evidence for) positive statements.

          • by jjohnson (62583)

            Negating a positive statement yields another positive statement: "There are elephants in my office" becomes "There are no elephants in my office", which is an assertion susceptible to falsification (i.e., looking for and finding no elephants in my office). Thus, I've proved a negative.

            The slogan "you can't prove a negative" is meaningless outside a fairly narrow use in logic.

            • Proving a negative is more like, "There have never been elephants in my office" without a 100% accurate historical record.

              And "There will never be elephants in my office" could be proved only by destroying the office.

              • by jjohnson (62583)

                Your example is correct, but it doesn't have to do with negatives. It's as hard to prove the statement "there have always been elephants in my office" without the same 100% accurate historical record (more plausibly, and as difficult to prove, "All life on Earth is carbon-based").

      • Re:evolution ? (Score:5, Informative)

        by polar red (215081) on Sunday January 03, 2010 @01:38PM (#30633254)

        Scientists are always trying to disprove. 'proving' a new theory is much harder than disproving the most widely adopted theories. see 'falsifiability' http://en.wikipedia.org/wiki/Falsifiability [wikipedia.org]

  • Enough Already ! (Score:5, Insightful)

    by daveime (1253762) on Sunday January 03, 2010 @11:25AM (#30632154)

    The academic paper is available in Science, though seeing more than the abstract requires a subscription

    I thought this was "news for nerds, stuff that matters", not "Science magazine touting for subscriptions".

    If we can't even RTFA without paying first, then it has no place on this site IMHO, as we have all come to realize that TFS is at best "a summary", and at worst, complete BS.

    • by RDW (41497) on Sunday January 03, 2010 @11:51AM (#30632306)

      Sounds like you might be interested in this exciting new media access concept!:

      http://en.wikipedia.org/wiki/Library [wikipedia.org]

      • by daveime (1253762) on Sunday January 03, 2010 @12:02PM (#30632386)

        Morpheus

        This is the construct. It's our loading program. We can load anything from clothing, to equipment, weapons, training simulations, anything we need. But if you want to read a Science article linked from Slashdot, you'll have to get on the bus and nip down to the local library.

        • Morpheus: This is the construct. It's our loading program. We can load anything from clothing, to equipment, weapons, training simulations, anything we need. But if you want to read a Science article linked from Slashdot, you'll have to get on the bus and nip down to the local library

          Oh, come on, you can't expect us to be able to computerize everything! Accessing magazine articles online has been a very tough problem to solve, due to the inherent difficulties in the process. Enjoy the advances we have made

        • by mkarcher (136108)

          Morpheus

          This is the construct. It's our loading program. We can load anything from clothing, to equipment, weapons, training simulations, anything we need. But if you want to read a Science article linked from Slashdot, you'll have to get on the bus and nip down to the local library.

          Wasn't that the entire plot of the movie? They couldn't jack in from their comfy cave complex.

    • by Daniel Dvorkin (106857) * on Sunday January 03, 2010 @11:58AM (#30632364) Homepage Journal

      Slashdot regularly reports on new products costing hundreds or thousands of dollars, sometimes tens of thousands. You don't get to use the product (particularly if it's hardware) without paying for it, yet many more people will talk about it than will pony up the cash.

      If you want to read the article without a subscription, you can do so for fifteen bucks. If you're in school, or know anyone who is, there's a good chance you can do so for free.

      For those of us in bioinformatics, this kind of thing is our bread and butter. Don't dismiss this as "not news for nerds" just because it doesn't happen to relate to one of the particular kinds of nerdiness about which you care enough to pay a small amount of money.

      • Re: (Score:1, Insightful)

        by daveime (1253762)

        I don't care to pay *any* amount of money for nerd news, that's why I'm here in the first place.

        Having essentially a "free" news for nerds site, then linking it to paid-only subscription articles kind of defeats the purpose, wouldn't you agree ?

        Which was my original point and seems to have got lost. It's not about whether or not I'm prepared to pay X amount to get Y information, it's about the fact that this is supposedly a "free" site.

        It's the same kind of scam which means when I search for "free software"

        • Slashdot calls itself "news for nerds," not "free stuff for nerds." There is no requirement that linked information be free. It's nice when it is, of course, but that's a bonus.

          Again, do you have a problem with articles that discuss proprietary hardware or software? You can't, I hope you'll agree, get complete information on the latest offering from, say, Apple or Oracle, without buying and using it.

        • I don't care to pay *any* amount of money for nerd news, that's why I'm here in the first place.

          You got the news - "Scientists Measure How Quickly Plant Genes Mutate". Even more so, you got some numbers - 1:1,4*10^8 per gen. This is news.

          What you are asking is "Science papers for nerds", or maybe you want a free book with book review.

    • Slashdot posts news stories about hardware that you can't get your hands on without paying for it. It posts reviews of books that you can't read without paying for them (short of going to a library). Why should it be any different for a scientific journal that happens to have an online edition? The news is the discovery. The article happens to contain more information about the methods, data, and the findings. So what if it costs money to read it? Isn't supporting the scientific community worth someth

      • by daveime (1253762)

        You wouldn't buy a house without seeing inside first and having a full structural survey done.

        You wouldn't buy a car without test driving it first, and having the engine checked over thoroughly by a mechanic.

        But you say to me, "Here's an article on Science, it's really interesting, honest. But if you want to know the nitty-gritty, you'll have to pony up 15 bucks first" ?

        The Honest Indian Business Model is a bit outdated, don't you think ?

        • You wouldn't buy the article AFTER reading the whole thing and knowing what it already says, either, would you? Ah!

          I guess scientists should spend years studying and researching and publish their findings for free, and for dinner they can eat the rainbows that shoot out of your butt.

          If you're casually interested in the topic, probably you don't want to bother paying money for it. Bitch about it if you want to; the unfair world doesn't publish scientific findings for free and hand deliver them to your do

          • by jbengt (874751)

            I guess scientists should spend years studying and researching and publish their findings for free, and for dinner they can eat the rainbows that shoot out of your butt.

            Well, that might be better than the current situation, where in order to get published by a reputable journal they must give up their copyrights for free and agree to not publish their own works elsewhere, and for dinner they eat the funding that they begged for in order to do the research, which funding they will probably not get without the prestige of having articles published in a reputable journal that charges you money for reading but pays no money to the scientist for writing, depending on how good t

    • Re: (Score:2, Insightful)

      "If we can't even RTFA without paying first, then it has no place on this site IMHO"

      WTF!? IANAL but AFAIK on Slashdot, RTFA-ing is BS! LMAO!

      I'm sorry,,, I'll leave now....
    • Wait a minute, you're complaining that you can't RTFA? You must be new here.
      • by daveime (1253762)

        Not reading TFA and not being *able* to read the TFA without paying first, are two different things ;-)

        I'm really just trying to shame them into not linking to paid articles, so then I can safely ignore TFA, and in principle, save myself 15 bucks in the process ;-)

        (For those with sleepy neuron deficiency, the above *IS* sarcasm).

  • by jbengt (874751)

    With four different DNA letters, there are six possible changes . . .

    Can anyone explain this? Are they saying that a change from, say, for example, T to A is the same as a change from A to T? Are they just wrong? Or is there some good explanation that eludes me?

    • by mikael (484)

      Wikipedia has a better explanation of the genetic code [wikipedia.org]. It's probably better to understand that
      in just about every species, groups of three letters form a codon [bioephemera.com], which defines a particular amino acid, of which there are 30 or so, but most species only seem to use around 24, along with a STOP command.

      Some funky stuff goes on, with some DNA being used in reverse, or offset by one or two letters, so that you get six possible sequences from the same set of letters.

      • by jbengt (874751)
        Still looks like there would be a lot more than 6 possible mutations, even if they're only counting the mutations that make actual functional changes to the codons. I have a feeling that TFA got something confused or left something out.
    • by kmcarr (1185785)

      First the "six possible changes" is only referring to single nucleotide polymorphisms (SNPs), which is the substitution of on one base for another. There are more complex alteration, insertions, deletions, inversions, etc. are not counted among these six. For a SNP to become "fixed", that is stably maintained through subsequent replication cycles you have the initial mutation event (altering a base) but then you must also have the complementary substitution on the other strand of the double helix. If an

  • Great piece of work! (Score:5, Informative)

    by elyons (934748) on Sunday January 03, 2010 @02:55PM (#30633714) Homepage
    For those that don't know much about either the significance of the science or the technology involved with generating the data, this might be useful. One big gray area in our understanding of evolution is how quickly genomes are changing, where they change, and the types of changes that are occurring. Yes, a genome is usually made up from DNA (RNA viruses being the major exception), and encoded in the DNA are genes, many of which get translated into proteins that do much of the "work" in an organism. However, depending on the organism, much of the DNA does not code for genes. The human genome for example is ~3,100,000,000 nucleotides (DNA's building blocks) long. Of that, ~1.5 percent codes for protein. Of the rest, the vast majority are ancient, dead, "selfish" chunks of DNA such as retroviruses (RNA viruses that convert to DNA and integrate into a genome. HIV is an example of one of these guys) and transposons (a major class of which are just like retroviruses but lack the genes for cell-to-cell transfer). Periodically in the evolution of many multicellular organisms (e.g. plants and animals), there are explosions or blooms of these types of elements that suddenly take off and integrate around a genome. This is one type of mutation (or genome evolution), and there are many others. Single nucleotides can change (e.g. C->T, as discussed in the paper), individual genes can get duplicated through a process known as unequal crossing-over or nonhomologous recombination, and the entire genome can be duplicated (known as polyploidy and is a dominant feature in flowering plant genome evolution.)

    Our current understanding of how dynamic a genome is, the types of changes that occur, and the factors that limit these changes is very limited. Much of this is because getting a genome of an organism can be expensive and laborious, depending on the size of the genome (RNA virus 15,000 nt, DNA virus: 150,000 nt, bacteria: 5,000,000 nt, yeast: 20,000,000 nt, multicellular organisms: 100,000,000-10,000,000,000). Since our understanding of how genomes evolve depend on getting genomes sequenced that are appropriately related to one another (e.g. populations of organisms versus diversity of organisms), we can only get answers for those genomes we currently have (current ~8000 for all viruses, bacteria, archaea, and eukaryotes). Fortunately, there is currently a major technological revolution happening in biology: generating DNA sequences fast and cheap. For example, the first human genome was approx a 10 year project and cost ~$1,000,000,000. Now, the record for a human genome takes less than a week and costs ~$15,000.

    This project is a major milestone as the authors sequenced 6 plant genomes (a mustard known as Arabidopsis thaliana) that are related to one another by 30 generations. Because of the close evolutionary relationships of these organisms, the authors can characterize the types of genomic change happening over very short time periods.

    The emerging picture is that genomes, the fundamental genetic blueprint for a lineage of organisms, are much more dynamic than we had previously thought.
    • Re: (Score:3, Insightful)

      by grikdog (697841)
      Mod this up to 10. This is important because plant genomes have been the source of some stupendously unexpected discoveries indicating that DNA is extremely plastic, and manages to squeeze into available ecosphere niches with ease -- resulting in closely related genomes that express forms as divergent as pineapples and plane trees. Linnaean classification schemes based on morphology therefore disconnect from reality and become first approximation maps. When the morphologies in question are fossils, the p
    • by Xest (935314)

      Can this data really be extrapolated beyond the genomes of the plants for which they have gathered data though?

      The summary suggests 1 in 60 million for a plant that produces thousands of seeds isn't such a big number, but in contrast, take a plant like Carnegia gigantea which produces around 60 million seeds a year, but which is lucky to have even one of those survive beyond a few weeks if it even germinates at all, for species like this, it's still a big number. For these sorts of species then, we have a 1

  • Has the DNA Sequencing been done on his E. Coli?

    If so, What was found?

    If not, when do we expect it?

    • Re: (Score:2, Informative)

      by elyons (934748)
      Yes. His group had a recent paper in Nature where they sequenced genomes from their Long Term E. coli Evolution experiment at generations: 0, 2000, 5000, 10000, 15000, 20000, and 40000.

      Absolutely stunning piece of work:
      http://www.nature.com/nature/journal/v461/n7268/full/nature08480.html [nature.com]
      • I thought I remembered that, but I couldn't find it. Don't know why. I don't have access to Nature, and $32 is too much money to me just to find out if the article talks about how the Cit+ E. Coli came about genetically.

        Did they discuss this mutation in this article? The abstract doesn't even mention the Cit+ E. Coli.

        I wonder if they found the answer to Lenski's question near the end of his 2008 paper: "What physiological mechanism has evolved that allows aerobic growth on citrate?"

        Is that discussed

        • by elyons (934748)
          I'll need to re-read the article for the specifics, but this was just measuring the background rate of mutations without any form of selection. They found an initial burst of change as the bacteria adapted to the experimental conditions, then not much for the first 20,000 generations, then a continuous burst of new mutations between 20,000 and 40,000 generations. They could attribute those mutations to a mutation that knocked out one of the DNA repair enzymes.

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