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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."
but he uses a d2, apparently
.cig - what you do after winning a good flame war
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
dude, when this thing compiles, we're screwed.
.cig - what you do after winning a good flame war
"I think all foreigners should stop interfering in the internal affairs of Iraq"
-- Paul Wolfowitz, 7/21/2003
Several bio-tech and software companies, the names of whom are undisclosed, today filed a joint patent infringement lawsuit against Universe Creator, Inc. [GOD, 12777.12, +65-1/8] for allegedly violating a patent on the use of parity checking algorithms in DNA genetic sequencing. "We don't see any evidence of prior art.." a legal representative commented, "Much like Corn(tm)--we invented that too. That stuff the Native Americans used to grow was some other crop they called 'maize.' We've been gyped for all these years." If they win the lawsuit, the parties involved will release an army of Red Robots to extract royalty fees from all Hu-mans.
In the meantime, I'm still searching my newly aquired Gene Map for a copy of DeCSS...
This sounds to me of another case of "If you look for something hard enough, then you'll find it". In actual fact there is no parity checking there at all.
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.
I am artificially intelligent.
Does anyone know any way see this in a readable font?
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.
Donate background CPU time to fight cancer.
From the article:
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...
MSN 8: Now Microsoft even has bugs in their ad campaigns.
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.
(That'll teach me to hit "submit" before "preview".)
In Mozilla or Netscape, a simple CTRL-KP+ does the trick.
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 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.
Perhaps we are all running in some ultimate program...
Well DUH, we're here to find the Question to the ultimate Awnser!
42!
You can't take the sky from me...