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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."

6 of 34 comments (clear)

  1. 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?

  2. 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 :)

  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. 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().
    --
    I figure by 2030 or so my 6-digit UID will be something to brag about.
  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.

    --
    Someone hates these cans.
  6. 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.