Apr 21, 2010

Error-Correcting Bug

When you start to work with something, you soon begin to see that thing everywhere. In 2006 I started to work with statistical mechanics of error-correcting codes in the NCRG at Aston University and suddenly I noticed things I haven't before.

I always liked extremophiles. They are really interesting organisms. I guess that what fascinates me is how many extraordinary solutions to the survival problem they present. The guy in the picture above mix my interest in extremophiles with my present work. It is called Deinococcus radiodurans. It is probably the organism with the highest error-correcting ability in nature, and I believe that the exact mechanism is still unclear. Any biologist around please clarify if it is true.

This bacterium can stand radiation levels 500 times larger than a human being can survive to with no effort and even get to 3000 times sometimes. The way it does that is ingenuous. It blends hardware error-correction with software error-correction.

The first part is a pure hardware correction. Its DNA is arranged in a torus that is very tightly packed. As the main effect of radiation is to cut the DNA in parts, this configuration guarantees that most of the parts do not flow away in the cell, staying almost in the same place, which facilitate the correction by the relevant proteins. 

Now, if you look at the picture above, you will see that our star is formed by 4 compartments. In the Wikipedia article [1] I am linking below it is said that each part is a different bacterium, although in a second article [2] it is said that these compartments are of the same bacterium, and then of the same cell I suppose as, as far as I know, bacteria are unicellular organisms. In any case, I think that [2] is probably more correct as the next part of the correction uses DNA from all compartments.

It works actually as the simplest error-correction code of all, a repetition code. Repetition codes are simply codes where symbols are repeated a number of times so that if the number of errors are not that big, you can correct them by just following what the majority of the symbols in the neighborhood are. In the case of our guy, it has one copy in each compartment and (that's fantastic!) after the first hardware error-correction the DNA in one compartment unfolds, migrates to another and melds with the other one to correct its errors! Well, it is not exactly a conventional repetition code in the sense that there seems to be no global comparison between all four copies to decide on the correction based on the majority rule. However, it is still kind of.

I could not find the details of the process. For example, does it migrate and then come back to the original compartment? Does it do it in some specific order? Which is the first DNA to migrate? Again, if there is a biologist that can clarify those questions, please feel free.

Isn't that cool? I must confess that the first time I heard about it I was expecting some very smart kind of error-correcting code embedded in the DNA construction. I was a little disappointed when I learned that from the software point of view, it is as simple as it can get. However, the whole process is quite interesting and not less ingenious because of that.

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