Parity Code And DNA 43
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."
Someone please check (Score:1)
Not only does God play dice (Score:3, Funny)
Re:Not only does God play dice (Score:1)
And you thought checking parity on... (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>
Re:And you thought checking parity on... (Score:1)
In the Matrix... (Score:1, Offtopic)
Bottom line.. DNA error-checks.. we are in the Matrix [whatisthematrix.com].
Re:In the Matrix... (Score:2)
Re:In the Matrix... (Score:1)
Re:In the Matrix... 101010 (Score:3, Funny)
Well DUH, we're here to find the Question to the ultimate Awnser!
42!
Epistemologically speaking... (Score:2, Interesting)
Re:I can't read it (Score:2)
Give evolution a few dozen generations to improve your eyes, and that should do the trick. Or maybe someone will have fixed the font size fluke by then.
Re:I can't read it (Score:2)
In other news... (satire) (Score:5, Funny)
In the meantime, I'm still searching my newly aquired Gene Map for a copy of DeCSS...
Parity schmarity (Score:5, Insightful)
Parity checking (in computers) involves adding up the number of 1's in a byte, and putting another bit on the end purely as a form of error control. In even parity there are always an even number of 1's in the (byte + paritybit).
In the article they've figured out that cytosine has 1 donor, and guanine has 2 donors. Then they invent the whole parity thing by letting cytosine equal 1 and guanine equal 0, and when you add all the numbers together you get an even number of 1's. Sounds like circular reasoning to me.
If there was a regular parity bit in the DNA to make sure that an even number of G's or A's occur every 8 or so pairs, then fair enough! But what the article is describing isn't the same parity as you get on your serial port.
It's like saying "Let all starfish with 5 arms equal 1, and all starfish with 6 arms equal 0. Add the numbers up and bingo we've got even parity! Nature is a computer!"
Stinks of looking for more funding to me.
Re:Parity schmarity (Score:2)
Give 5 legged starfishes the number one. Give 6 legged starfishes the number zero. Now grab any 5 or 6 legged starfish. Add the starfish number to the number of legs you get. When you convert to binary the last digit of this number is always zero. This is very similar to what is going on in the paper and it says nothing whatsoever about starfish.
Re:Parity schmarity (Score:2, Interesting)
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.
Re:Parity schmarity (Score:1)
Stinks of acute criticitis to me.
Like another poster said, this is chemical-, not codon-level parity. Sure their interpretation of purines as 0 and pyrimidines as 1 is arbitrary. If they'd done it the other way, it'd still be parity, just odd parity. The point is, if a proofreading enzyme had to match specific H-bond donor/accepter patterns with nucleoside type, or if there had to be a separate proofreader for each invalid combination, proofreading would be extremely expensive (either too complex to reliably implement or require too much overhead for all those proofreaders). If the proofreading enzyme can check for validity with simple rules based on "purines have an even number of proton donors, pyrimidines have an odd number" it has more of a chance of succeeding. In biology as most everywhere else, simpler is better.
?? pulled (Score:1, Offtopic)
No, you fool! (Score:1, Informative)
natural selection? (Score:2, Insightful)
Natural selection picked out the chemical basis of genetic information transfer probably because it was the best of the available options for ensuring fidelity in reading and copying information.
Assuming that they mean "selection" as in an evolutionary sense, I fail to see how this can be true. Isn't the whole genetic chemistry (ATCG, DNA, etc.) necessary before any selection can take place at all? In other words, isn't this a chicken-and-egg problem? You need a self-replicating structure before you can have reproduction, which is necessary for selection (right?). Or are we to believe that there was once a whole slew of competing chemicals, and our good friends A,T, C, and G won the grand prize because they had a 'parity check'? But even if you buy into that, where did the repairing enzymes come from? Aren't enzymes encoded by... (drumroll...) DNA? I'm a bit out of my area of expertise here (I ain't no biochemist), but it does seem a bit strange to me...
not necessarily (Score:2, Informative)
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
No parity, interesting complementarity (Score:5, Interesting)
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.
Oops, T = 010 (Score:3, Informative)
Re:Oops, T = 010 (Score:2)
Re:No parity, interesting complementarity (Score:1, Informative)
Re:No parity, interesting complementarity (Score:2)
Karma: SSW, force 2, good.
There IS parity checking...in a sense (Score:2, Informative)
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.
Re:There IS parity checking...in a sense (Score:1)
From the original paper, referred to in the article:
'Error-coding analysis however suggests that mixed parity alphabets with interpurine or interpyrimidine distances of one have an inherently low fidelity.'
The point is that each purine differs from the other by at least 2 donor acceptor positions, as does each pyrimidine. The fact that there is even parity in all 'codewords' is a fancy way of saying that any two purines (or pyrimidine) in the system must differ by an even number of donor/acceptor positions.
Again, from the original paper:
'The role of D/A patterns is therefore twofold, serving to bind associating complementary pairs, while simultaneously opposing non-complementary associations. Any set of complementary nucleotides is approximately equivalent with respect to the former, however, a parity code alphabet is optimal with respect to the latter,
ensuring that the association of non-complementary pyrimidine-purine pairs will be opposed in two of three D/A positions.'
Bogus (Score:1)
This article fails to mention that Thymine and Adenine would have a code of 01,1 and 10,0, which breaks the "parity". Actually, I didn't like this argument even before I got to this problem. Assigning a 0 to purines is absolutely arbitrary, and is not needed to differentiate a C from a G. It is inherent in the first 3 numbers, that 100 is the mirror inverse of 011, and that pyrimidines only have two values, which are mirror inverses as well.
How could an enzyme "add" these together? DNA correction enzymes work by looking for parts of the DNA strands where the physical conformation is not normal. You could say that the error correction mechanism is encoded in their physical structure, but I don't see how the parity concept could be involved.
This sounds like someone who has learned the vocabulary without the information theory behind it. I'm suprised that Nature published it.
This thread is making my head bulge! (Score:1)
It's the paper that the dumbed down Nature article is based upon... and probably more worthy of your criticism