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Computational Genomics

Posted by michael on from the throw-more-cpu-at-the-problem dept.

blamanj writes "Scientists at UC Santa Cruz have been using computational techniques to 'reverse engineer' the DNA of extinct species. David Haussler and colleagues created a hypothetical portion of ancestral mammalian DNA and let a computer model simulate the process of evolution. Then they made their algorithm work backward from these descendants, to see if it could recreate the original ancestor."

12 of 34 comments (clear)

  1. Reverse enginering by Ender_Stonebender · · Score: 2, Interesting

    Does this seem like "we'll get the original order of a list based on the sorted order and knowing how the sort algorithm took to run" (in otherwords, bound to be so wrong as to be useless)?

    Or is it just me?

    --Ender

    --
    Loose things are easy to lose. You're getting your hair cut. They're going there to see their aunt.
    1. Re:Reverse enginering by Lenale · · Score: 3, Insightful

      It does sound a bit fishy... I just attended a lecture on DNA-focused biophysics the other day, and they were all about "we won't be able to compute it for years, but..." And by the way, as the article said, we're quite a bit behind the rodents in losing bases... let's make babies :)

    2. Re:Reverse enginering by Anders+Andersson · · Score: 2, Interesting
      And by the way, as the article said, we're quite a bit behind the rodents in losing bases...

      The article explained the difference in mutation rates by referring to the shorter reproduction rates of rodents. However, as I understand the process of transferring DNA from one generation to the next, mutations may occur whenever a cell splits in two, not only when the animal reproduces. I seem to recall from Sykes' book The Seven Daughters of Eve that the average number of successive cell divisions in the reproductive organs from one human generation to the next is around 20 (or perhaps less). Do the corresponding cells in rodents really divide more often than in humans, just because they reproduce faster?

    3. Re:Reverse enginering by Anders+Andersson · · Score: 3, Insightful

      I would compare it to analyzing languages spoken today to determine how the language they descend from (such as proto-indoeuropean) may once have sounded. While many indoeuropean languages are mutually unintelligible today, they share certain fundamental elements that are best explained by them having been present from the start. It's not an exact science, of course.

    4. Re:Reverse enginering by fbjon · · Score: 3, Funny

      Fishy, you say? I immediately thought of hollywood science.

      "Detective, we have a new computer program that can predict the path of any bullet...."
      "Yeah, so?"
      "So we tried running it backwards, and we just found out where the suspect bought the ammo!"

      --
      True confidence comes not from realising you are as good as your peers, but that your peers are as bad as you are.
    5. Re:Reverse enginering by daymitch · · Score: 2, Interesting

      Think about this for a minute. Rat cells don't have to divide any faster than humans for them to have had more cell divisions since our divergence. They reproduce more often so they have more generations per unit time than we. The rats somatic cells are also probably just 20 divisions or so away from the original zygote. Just multiply it out and you have more cell divisions per unit time in the rats.

  2. 98 percent? by kureido · · Score: 3, Interesting

    From the article: "Then they made their algorithm work backward from these descendants, to see if it could recreate the original ancestor. The ancestor the algorithm came up with had a sequence that was 98% accurate..."

    Human and chimpanzee DNA are about 98% similar, too. In that context, 98% similarity doesn't seem that impressive. Maybe someone needs to invent a new benchmark for sequence comparison for species that are already similar?

    1. Re:98 percent? by Anders+Andersson · · Score: 2, Insightful

      Since the accuracy with which the artificial genome was recreated in the simulation isn't compared with that of other methods for doing the same thing, the 98% figure doesn't tell us much. For all I know, that could be the accuracy you would get using any method (but I suppose the scientists actually have more simulation data than was presented in the article).

      Likewise, comparing that number to the degree of genome similarity between humans and chimps isn't very meaningful either. Since the article doesn't mention chimpanzees but rather rats and pigs, I suppose the research is focused on longer periods of evolution than the few million years that have passed since the split between humans and chimps.

      By the way, is the 98% difference in relation to all human DNA, or merely to the part of the genome that is identical among all humans? I don't know how much of a difference that makes, but I believe there is a difference.

  3. Jurassic Park by Anders+Andersson · · Score: 2, Interesting

    I don't know how well understood the lineage from dinosaurs to modern birds are, but I suspect you would need the genomes from a few species that are not descended from dinosaurs (say, mammals) as well, for interpolation rather than extrapolation of the dinosaur genome.

    Even if we could recreate dinosaur DNA in this way, I doubt we have the technology to turn that DNA into a live animal, or even do a computer simulation of that process. Is anybody working on an open-source biochemical simulator?

  4. Algorithm testing. by Fortran+IV · · Score: 3, Interesting
    The process is interesting, but their description of how they tested their algorithm is less than confidence-inspiring.
      1. 1) Manually create a set of hypothetical data.
      1. 2) Run a mathematical algorithm to generate new data.
      1. 3) Run the converse of the algorithm on the generated data.
    If an algorithm is truly reversable then, without the necessary randomization, such a process is likely to generate the original data with 100% accuracy. I'd have felt much better if they'd run two independent algorithms against each other: create descendants with ForwardA() and extract ancestors with BackwardB(), then do the same thing with ForwardB() and BackwardA().
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    I figure by 2030 or so my 6-digit UID will be something to brag about.
    1. Re:Algorithm testing. by Anders+Andersson · · Score: 2

      I agree that the way this is expressed in the article leads to your interpretation:

      To assess their method, they created a hypothetical portion of ancestral mammalian DNA and let a computer model simulate the process of evolution, to generate sequences for its descendants.

      Then they made their algorithm work backward from these descendants, to see if it could recreate the original ancestor.

      However, I seriously doubt they actually reversed the simulation algoritm. Reading the entire article, it sounds more as if the algorithms for reverse engineering DNA have been under development for a long time, and that they wrote a separate simulation program to produce test data for evaluation of the newest version of the algorithm.

      A geneticist isn't necessarily a good computer scientist, and mistakes do happen in science, but somehow I doubt a mistake like that would slip by reviewers unnoticed. Maybe the algorithms are described in more detail in the associated papers (linked from the article).

  5. Planet seeding by Associate · · Score: 3, Interesting

    Once we get things like this under control along with teraforming, we can seed barren planets. We can walk the universe like gods. Probably have to kick the old one's out first.

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