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Parity Code And DNA

Posted by timothy on from the how-many-noses-sir dept.

jnana writes "There's an interesting article in Nature about error-correcting parity code in DNA. It seems that there are enzymes that check for even-parity nucleotides (according to a 0 and 1 assignment scheme in the article) and recognize odd-parity nucleotides as errors. The authors argue that this parity scheme is the reason that adenine, thymine, cytosine, and guanine became the building blocks of nucleotides instead of other types of purines and pyrimidines that must have coexisted with them."

4 of 43 comments (clear)

  1. And you thought checking parity on... by mhesseltine · · Score: 2, Interesting

    your serial port was a pain in the ass!

    <speaking from experience>Speaking as someone who builds measuring equipment for industrial manufacturers that communicates over RS-232. I can't tell you the number of times a customer calls complaining about getting their system to communicate with at PC, and it boils down to a stupid parity setting that's IN THE FSCKING MANUAL.</speaking from experience>

    --
    Overrated / Underrated : Moderation :: Anonymous Coward : Posting
  2. Epistemologically speaking... by Marijuana+al-Shehi · · Score: 2, Interesting

    ...we as a species have endured this digital age to be able to grok what transpires on the chemo-biological level in our cells.

    --
    "I think all foreigners should stop interfering in the internal affairs of Iraq"
    -- Paul Wolfowitz, 7/21/2003
  3. No parity, interesting complementarity by Ichoran · · Score: 5, Interesting

    As the previous poster pointed out, there isn't any parity to speak of in DNA. I have no idea why they're trying to make the comparison.

    Hydrogen bonding is a much higher-fidelity error correcting system than parity checking. With parity checking, you can catch any single error (the number of 1's changes), but not any pair. With hydrogen bond donors and acceptors, you have to have an exact match at all positions. Any number of errors ruins the complementarity.

    For what it's worth, the base pairing system is quite elegant: due to size constraints, purines (A,G) and pyrimidines (C,T) must pair with each other. Using the article's notation of 0=H-bond acceptor, 1=donor, the four nucleotides are
    A = 10_
    C = 100
    G = 011
    T = 101
    where _ is simply a hole. The best pairwise complementarity is (evidently) AT and CG.

    It's a chemically implemented RAID-1 system, not a parity check.

  4. Re:Parity schmarity by rpresser · · Score: 2, Interesting
    Your argument seems to be that parity checking is only parity checking if the parity bit is stored at the same level as the data. Since genes are stored in sequences of DNA codons, you reason, then the parity bit must be stored as a DNA codon.

    What you are overlooking is that the Nature paper is not talking about codon-level parity checking. It's talking about something different. It's asking the question, "What mechanisms might there be that ensure that DNA consists of only four bases, grouped always in the same two pairs?" It looks at the chemistry and finds evidence that the number of donors on each base seems to fulfill a parity checking relationship. They then imply that corrector enzymes, checking this parity relationship, can throw out chemicals other than A,C,G,T which might have mistakenly shown up in the nucleus.

    The parity checking, therefore, is not protecting the genes; it is protecting the bases. It is as if the electronics of your computer contained mechanisms which would make sure that every bit stored was a zero or a one - never a two, seven, 1.5, or something else.

    Guess what - there are such mechanisms. They ensure that the voltages found on any pathway are either low or high. They're an essential part of IC design, and are exactly analogous to corrector enzymes.