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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."
Does Unisys have a patent on this?
If tits were wings it'd be flying around.
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
I'm starting to think more and more than life is a computer system. Perhaps we are all running in some ultimate program... Or even worse, what if we are just "running" in a crazy program thats not finished yet.. and some programmer is just getting his jollies seeing how far along his project is with an incomplete test-build... but that's another story :-P
Bottom line.. DNA error-checks.. we are in the Matrix.
"I think all foreigners should stop interfering in the internal affairs of Iraq"
-- Paul Wolfowitz, 7/21/2003
Does anyone know any way see this in a readable font?
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.
This Story is not on slashdot front page!!! I got to it through the sidebar !! in the story it says previous story is gene map and next is KODAK, but on the front page there is no sotry between these 2 stories!! TAco theres a bug in slashdot!!
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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".)
By default Slashdot doesn't automatically show every single story on your front page unless you tell it to do so in your preferences!
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...
How can there be selection when the descendents have little chance of being the same as their parents? Selection is only a possible mechanism when mutations are rare, otherwise a spiral into chaos is the only outcome.
The article reads:
"Malfunctioning genes can cause diseases and defects. Errors can occasionally have beneficial effects - they create the mutations that drive the evolutionary process..."
I think the word "Error" should rather read "deviation". Many scientists, including some Nobel Laureates; believe that the evolution may be occuring due to gene deviation but such deviation may not be simple errors, but may be a deliberate deviation by an intelligence universe.
I forwarded this to my wife, who is an Expert in All Things (other husbands will understand...) Her reply:
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.
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...
...(drumroll)... RNA! This has led to the hypothesis that the first popular self-replicating, information-carrying biological polymer was RNA (which has bases A,U,G,C), and that this molecule also catalyzed its own replication.
I'm not an expert, either, but I think you're pretty close with the 'competing chemicals' concept. This is called 'chemical evolution,' which took place before the existence of RNA. The idea is that the first self-replicating molecule arose from the 'primordial soup' of organic molecules. Most enzymes today are encoded by DNA, but there are some very old and essential enzymes that are coded by
nifty stuff.
- a.c.
Take a look at this, kids: "A parity code interpretation of nucleotide alphabet composition"
:)
It's the paper that the dumbed down Nature article is based upon... and probably more worthy of your criticism
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