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Science

Ancient DNA 39

Posted by michael from the deserted-island-needed dept.
PyroX_Pro writes "An interesting read over at the BBC says that 400,000 year old DNA has been found. The DNA has been broken into tiny pieces, so there is little chance of bringing any of the species back from the dead. "Soil frozen into the ice has also yielded fragments of DNA of large prehistoric animals, including the woolly mammoth, reindeer and musk ox" "Cloning is in our view impossible at this stage. You'd need the whole DNA and you would have to constuct a primitive cell to put the DNA in," added Mr Gilbert. " Sure he says that now, but they may find a way to splice it with other DNA, and then, well you all saw the movies..."
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Ancient DNA More

Ancient DNA

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  • That's how it always starts. (Score:5, Funny)

    by presearch ( 214913 ) on Friday April 18, 2003 @11:24AM (#5759882)
    Then later there's running and screaming.
  • Everyone knows that you can find some at the North Pole.

    On an interesting side note, reindeer is one of the few words that doesn't follow the "I before E except after C"
    • "I before E except after C"
      "What a weird rule." -- Albert Einstein

    • > On an interesting side note, reindeer is one of the few words that doesn't follow the "I before E except after C"

      From Usenet:

      There is, I believe, a simple mnemonic rule for getting the spelling of such words correct. It goes something like "I before E except after C or in absenteeism, Aeneid, agreeing, albeit, Alexei, Anaheim, Andrei, aniseikonic, atheism, atheist, atheistic, atheists, Bahrein, beige, Beijing, being, beings, Beirut, Bernstein, Blenheim, Bodenheim, Bodleian, bodyweight, Boeing, Bran

  • "Cloning is in our view impossible at this stage..."

    Anyone else notice the terrible lack of punctuation in this article?

  • I thought the way the Human Genome project worked was by breaking our DNA into lots of small bits and sequencing them in parallel, then putting those sequences together in a computer. How is the "broken" nature of this old DNA different from our intentional "breaking" of DNA for other sequencing projects? After it's sequenced, can the "broken" parts be re-connected in a computer? Once we know the sequence, can't we then make new copies in the lab? Sure, using that new DNA will be tough, but I thought someon

    • Re:Gene sequencing/splicing (Score:4, Informative)

      by !splut ( 512711 ) <sput AT alum DOT rpi DOT edu> on Friday April 18, 2003 @12:17PM (#5760276) Journal
      Excellent point; I was going to say something to that effect myself. Modern DNA sequencing techniques involve digesting or shredding massive genomic pieces of DNA into small fragments, in the neighborhood of 300 - 700 base pairs in length. The reason for this lies with the sequencers, which can only get a maximum of around 700 base pairs of reliable data per run.

      Sequences of the resulting fragments of DNA are used to reconstruct the entire genome based on the overlap between sequenced fragments. Overlap and a certain degree of redundency, in fact, is necessary as a form of error checking, as sequencing methods have an inherant error rate.

      So, if these prehistoric DNA fragments overlap sufficiently, it is theoretically possible for their sequences to be used to reconstruct an entire genome.

      However, a bigger concern might be damage to DNA. DNA, like all biological molecules, suffers a certain degree of degredation over time due to high energy radiation, exposure to free radicals, normal biochemical processes (such as nucleases present in the original cell, or secreted by microbes in the environment), etc. There are biochemical mechanisms in living cells that continually work to repair these damages, but in a dead, frozen cell those systems would not be present, and the DNA would just accumulate damage. Such damage can inhibit or introduce large error into sequencing attempts, so it is possible that the original sequence of the DNA can never be recovered.
      • However, a bigger concern might be damage to DNA. DNA, like all biological molecules, suffers a certain degree of degredation over time

        But in a chunk of tissue there would be billions or trillions of strands which were originally identical. They would not be damaged in the exact same way. It seems logical to me that if many different samples of these damaged strands were sequenced then statistics could be used to filter out the damaged portions from each individual sample and build a map of the original.

        • "But in a chunk of tissue there would be billions or trillions of strands which were originally identical. They would not be damaged in the exact same way. It seems logical to me that if many different samples of these damaged strands were sequenced then statistics could be used to filter out the damaged portions from each individual sample and build a map of the original."

          Add in a correction system in living cells and wham, a cure for cancer.
        • They would not be damaged in the exact same way. It seems logical to me that if many different samples of these damaged strands were sequenced then statistics could be used to filter out the damaged portions from each individual sample and build a map of the original.

          The problem with this is that the estimated rate of damage leaves little to no trace of the original sequence after about 10k years. You'd basically be looking for a statistical link between millions of cells with completely random sequences(
          • But if they are all damaged that completely then I wouldn't think the researchers would even say that they found DNA, for example from a mammoth. It must retain much of the structure or it would be like saying they found a tree everytime they hit a layer of ash in the sediment.

            And yes it would be just like looking for a statistical link between millions of samples with partially damaged structures. But that is what computers are great at. The problem I think is in sequencing the millions of samples. Maybe

    • Re:Gene sequencing/splicing (Score:4, Informative)

      by nobody69 ( 116149 ) on Friday April 18, 2003 @12:27PM (#5760352)
      I thought the way the Human Genome project worked was by breaking our DNA into lots of small bits and sequencing them in parallel, then putting those sequences together in a computer.

      When scientists do sequencing on DNA, they use enzymes that cut the strands at specific sequences (frex: an enzyme will 'look' for the sequence ATGCCGTAATCGA and cut the strand so you get a segment that ends ATGCCGTA and one that begins ATCGA) so you you get known beginning and ending points. Also since the DNA strands are complementary you know that if one side of the double helix has the ATGCCGTAATCGA sequence, you also know that the other has TACGGCATTAGCT. Which helps with making sure that you are connecting your cut strands in the right order. If your strands are broken into too many small pieces in a random pattern it's much harder to put them back together again. It's the difference between re-assembling an Encyclopedia Brittanica that has been cut between each article and one that has been run through a cross-cut shredder.

      The one thing Jurassic Park never explained was how they made the dinosaur eggs.

      They called the FX department. ;)
    • DNA can be made from scratch, but the longer the sequence the more errors will be in it. Thus you can make a polio virus but not an elephant. IT is much better to start with whole segments of DNA.

  • Haven't you heard the song? (Score:3, Funny)

    by Eye of the Frog ( 152749 ) on Friday April 18, 2003 @11:53AM (#5760074)
    "Sure he says that now, but they may find a way to splice it with other DNA..."

    Haven't you ever heard that song by Loverboy? Pig and elephant DNA just won't splice.

    --no sig is good sig

  • The fossil from Hell [cmnh.org]... er, Creek, Montana. Big silence on this one ever since, which is possibly significant in itself because definite indications of contamination would have to have been published somewhere.

    Preserving something as frail as an organic macrostructure over as much as 1% of that timespan is of course well beyond impossible, so the fact that it appears to have happened should be telling us something important about our leading assumptions.
    • "Preserving something as frail as an organic macrostructure over as much as 1% of that timespan is of course well beyond impossible..."

      Says who? Remarkable preservation of fossils...even soft bodied organisms (Burgess Shale for one...and that is in *much* older rocks), does occur. I don't find it so hard of a stretch that the conditions for burial and preservation were such that the entire bone did not become mineralized and left some traces of blood cells.

      "...so the fact that it appears to have happene
      • Says who? Remarkable preservation of fossils...even soft bodied organisms (Burgess Shale for one...and that is in *much* older rocks), does occur. I don't find it so hard of a stretch that the conditions for burial and preservation were such that the entire bone did not become mineralized and left some traces of blood cells.

        Says the majority of the scientific community. There is a huge difference between fossil preservation of basic structures and preservation of actual organic matter. Laboratory observat
        • "Says the majority of the scientific community. There is a huge difference between fossil preservation of basic structures and preservation of actual organic matter. Laboratory observation of DNA break down suggests 10k years as the upper limit beyond which it will have completely broken down. Even under extra-ordinary preservation circumstances the longest survivability I've seen suggested is 100k years. Preservation over a million years is simply not expected."

          I completely agree actually. All I was tryi

      • You mean that the entirety of geology is completely wrong because we "assume" the Earth has been around for 4.6GA?

        Surprisingly little geology is entirely reliant on a precise (or even vague) age for the Earth. All that matters for a great many things is the order in which things happened, not the time they took to get that way.

        For the remaining few, circumstances there are some substantial hints in the field (e.g. paraconformities, massive undisturbed polystratic fossils, rapid paleomagnetic reversals,

        • "Surprisingly little geology is entirely reliant on a precise (or even vague) age for the Earth. All that matters for a great many things is the order in which things happened, not the time they took to get that way."

          Oh how wrong you are. The basic concepts of geology (rock types, relationships, etc) do not necessarily depend on the age of the earth. However, in most research done on real world applications, the exact date of an event is very important. As they say, timing is everything. This is why mo

          • Surprisingly little geology is entirely reliant on a precise (or even vague) age for the Earth. All that matters for a great many things is the order in which things happened, not the time they took to get that way.

            The reason this is important is so that correlation to events of a known age is possible. For example, say I have a lead-zinc mineralization event that I'm trying to find a cause for. Well ok...one of the most important things to do is get an estimate on the date of mineralization, and then se

      • Remarkable preservation of fossils... even soft bodied organisms (Burgess Shale for one...and that is in *much* older rocks), does occur.

        This unfortunate stream of reasoning goes as follows:

        1. I believe that this piece of rock is X years old; and
        2. This rock contains remarkably preserved fossils including organic matter; therefore
        3. I believe that organic matter can survive intact for X years.

        4. All that you really know is that a certain stratum contains well-preserved organic material. Nobody was there scrat

        • Actually, I wasn't referring to the actual preservation of the original organic material, but to the preservation of the appearance of the material (in other words, is it a fossilized red blood cell?)

          • AFAICT, they're actual platelets, with genuine organic material in them, not fossil (ie not mineral-replaced objects or outlines). The dude in charge of the lab that discovered them (a student saw them under a microscope) has bent over backwards to find a suitable reptilian source of contamination, without success. Truth is sometimes stranger than fiction. (-:

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