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Parity Code And DNA
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."
(That'll teach me to hit "submit" before "preview".)
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well you could always have multiple parallel mechanisms to achieve the same end, if some of them didn't work as well (ie. in different species of organisms) they could very well have been weeded out by those who worked better (the organisms that "worked better" outcompeted those that could not keep up). This is just speaking in theory of course, i have no idea if there were parallel genetic systems competeting against one another in the past...
But even if you buy into that, where did the repairing enzymes come from? Aren't enzymes encoded by... (drumroll...) DNA?
yes, encoding enzymes and (theoretically everything) is encoded in the genetic material, but that doesn't mean that different means of storing genetic data could not have been "competing" at the same time...
all and all while this "parity" idea is kind of interesting it's not any kind of huge breakthrough (not to mention it's kind of a misnomer), traditionally it has been thought that repair enzymes sense steric strain caused to the DNA molecule when the base pairs don't properly align (ie: they look for a bulge in the strand width) as opposed to looking 'inside' the molecule at the hydrogen bonds (which if they don't line up properly cause the bulge). Repair enzymes certainly look at the H bonds later but these are excision & repair enzymes which don't check for errors, rather pull out the offending nucleotide and replace it with the correct one after the error has been discovered by other enzymes...
This is what i've been tought anyway, but what we know does change...
-tid242
With a few exceptions, secrecy is deeply incompatible with democracy and with science. --Carl Sagan
The point of the article was to point out that despit hydrogen bonding, other bindings can occur as errors in DNA. So what do you do when your nucleotides happen not to bond correctly? The chemical attachment is already made, what are your enzymes going to do about it? Obviously they have to have some way of ensuring that the paired values are indeed correctly paired. Whether you call this "parity checking" or not is beside the point.
The combination of the H-bond acceptor=0 / donor=1 (in each of 3 positions) AND purine=0 / pyrimidine=1 gives you a 4-bit number (nibble) for each base (example: C = 1001). Each of these bits represents one aspect of the molecule that should "fit" to make a good pair in a DNA double helix.
The point is NOT that some DNA repair gadget is coming along, adding the bits, and trying to fix nibbles with parity error.
The point is that the four nibbles for the four DNA bases (A, C, G, & U/T) are all different in at least TWO bits. This means that any screw-up in a double helix will be a mis-fix in at least two of the four aspects. In the analog world of chemical reactions in a cell, a two-way mis-fit is a far less probable accident than a one-way mis-fit.
It's easy to make up & spread cool- and credible-sounding stuff. Finding & checking hard facts is hard work.