DNA's Error Detecting Code

MagnetarJones writes "Science News Online and Nature.com - Genetic information stored in DNA is read out - transcribed - every time living cells make a new protein molecule to perform some cell function. And this information is copied onto a new strand of DNA when a cell divides. The consequences of wrongly read or copied information can be disastrous. Malfunctioning genes can cause diseases and defects. Errors can occasionally have beneficial effects - they create the mutations that drive the evolutionary process - but they are usually detrimental. Strands of DNA carry information--of the genetic sort--encoded in their chemical structure. Chemist Dónall A. Mac Dónaill of Trinity College in Dublin, Ireland, has now shown that patterns inherent in the chemical makeup of DNA correspond to a digital error-detecting code. His report appears in the Sept. 12 Chemical Communications."

REPEAT

[Viadd]

This is a duplicate of Monday's /. [slashdot.org]

Re:REPEAT

[singularity]

One thing that people never think about (they always blame Taco and others) is that someone had to submit the duplicate story.

Some Slashdot reader sees an interesting article, did not see it earlier that week/month/year on Slashdot, thinks "Wow, Slashdot readers would like this", does not take two minutes to search the search-able Slashdot archives, and posts it.

I have submitted about three or four stories since first reading Slashdot. Everytime I do so, I search and make sure they story has not been submitted already.

Can we not move some of the responsibilities to the people submitting?

Re:REPEAT

[alonsoac]

maybe some responsibility but in the end the editor's job is to pick the good submissions and leave out the bad ones, so if he picks a dupe then it's his failure. I figure he's getting paid for htat job so we expect better from him thatn from any person who simply happens to submit a story.

Re: REPEAT

[Black Parrot]

> This is a duplicate of Monday's /. [slashdot.org]

d00d! Didn't you know that redundancy is the key to error detection?

I don't like that term 'read out'

[Anonymous Coward]

There's nothing doing the reading, it's inherent.
'Read out' somehow implies computer terms. A piece of tape with magnetic pulses is 'read out' by a complex machine.
OK. But with DNA, the data IS the machine! I don't think DNA can 'read out' anything, like keeping things in memory and calculating a checksum.
I think the very combinations of chemicals imply certain reactions. Each DNA 'data bit' will react a ceratin way.
It's not like computer data where you can have GBs of data that is essentially random and mute. DNA is self-selfing, you know? Two bits of DNA information is worth a lot more than two bits of binary data. The binary data needs a big big machine to mean anything. The DNA bits are inherently meaningful.
The data IS the CPU.
Chemistry is the OS.
Physics is the BIOS.
And I am incoherent.
It's hard to express my idea which is pretty much just a feeling I have.

Sigh, again

[ljhiller]

Not only a repeat [slashdot.org], but we pretty much decided that he's not telling us anything new. Suprise! DNA is more reliable if you require 3 valid hydrogen bonds, than if you only require two, or one. Only two interesting points to the article: They showed that the full alphabet of the even parity (4,3) code isn't used because those nucleotides would be unstable. Another Suprise! An alphabet of 4 yields 2 bits of information per nucleotide. The other interesting thing I found in the paper is that the normal polymerase will replicate a strand of odd-parity nucleotides just as well as even. Except that wasn't even part of this research, it was in a reference!

Not every time...

[Raskolnk]

Genetic information stored in DNA is read out - transcribed - every time living cells make a new protein...

IIRC, some mRNA transcripts stay in the cytoplasm and are translated multiple times. In addition multiple ribosomes can "read" a single mRNA strand at once. So, it isn't a one transcription to one protein relationship.

If I'm wrong on this, please call bullshit.

transcription vs translation

[spineboy]

Ribosomes, when reading mRNA, are TRANSLATING the messge into protein. When DNA is copied into mRNA that's called transcription and it's done by polymerases..

It wasn't clear to me, but I think you got it right. This is just to clarify the issue for the uninformed of translation vs transcription.

Old Tale

[ivanandre]

This information is old. Is well know since years (decades?), cells read DNA in their protein making process.
And allways a somatic cell reproduces (or divides?) the DNA is duplicated, and many errors can arise in this process.

This is responsable, among others thing, for age decay, and cancer...

Re:Old Tale

[Sgt York]

But this is a new error checking mechanism. I don't really see the point in it, though.... It seems to me that the only way you'd get odd parity is by getting 2 purines or 2 pyrimidines to pair with each other. Because pyrimidines are smaller than purines, you'd get a physical defect anyway. A pur/pyr pair gives you a base pairing of a certain distance. Pyr/pyr would be significantly smaller, leaving a "dip" in the strand; Pur/pur leaves a kink because the 2 purines are too big to fit.

Mutations do not have to occur with division. They can occur as a resut of DNA damage that is incorrectly repaired, or not repaired at all (Damage from radiation, chemicals, etc). This is certainly responsible for cancer. Probably responsible for aging, too, but there are people who disagree with that and have good points.

Umm..

[Fweeky]

If you're going to use windows-1252 characters in stories, the least you can do is actually *mention* it in the Content-type or meta tags.

Well, no, the least you can do is not provide any charset data at all, which is exactly what /. does. Well done. We all really enjoy those ?'s and squares in place of em-dashes and co :)

Twisty little passages.

[rossy]

A little pirate chuckles... taking your bag of gold. 20 gold pieces missing.

Port this

[Sanga]

Port this to and we can go sleep :-)

Yeah, I did not RFTA.

Upon conversion to ASCII...

[Guppy]

And upon conversion to ASCII, the following pops up in the Human genetic code:

"!!!seineew era stsinoitaerC"

NSA Reaction

[rossy]

Upon discovery, the NSA has sent federal agents to people in the act of procreation to arrest them for violation of the national securities act. When queried a spokesman responded: "We can't allow these codes to fall into enemy hands, and also need time and additional funding to be able to decipher these codes for national security reasons"

Can YOU predict the next DNA/computation analogy?

[Tsar]

Lessee, if you represent each base with an odd-parity number, then DNA seems to be doing parity checking? Perhaps another researcher will interpret each nucleotide as a physical representation of a large prime, and claim that DNA is actually RSA-encrypted.

Honestly, does anyone really think that the the "Publish or Perish" academic survival constraint has encouraged the evolution of better academics? Perhaps Slashdot's karma model should be extended to all of academia, with some large percentage of all available funding distributed accordingly.

"How's your ZPE-generator work coming, Roy?"

"It's been cancelled, Sigfried. The whole project got modded Offtopic! But everyone says your 10^1024-qubit computer is quite Insightful. What do you think your chances are of getting the Nobel for this one?"

"Excellent--mostly affected by moderation done to my papers."

Unfortunately...

[quintessent]

While DNA has error correction working well, it has not yet developed a reliable way to avoid redundant information.

Re:Unfortunately...

[Sanga]

Isn't redundance key to fault tolerance. Even if parts of the DNA were broken and reinserted, you increase chances of it being the good stuff instead of random junk