August 10, 2010

Tetris with Proteins

Life is messy.

An Example of Entropy
Very rarely in nature is there a straight line, or a single element. Life is messy, things mix, combine, bend and knot. The universe favors lower energy states, higher order systems require energy to be put in for them to work. As a result thingsare seldom ever neat and tidy. This is true of society, my bedroom, and of much smaller scale things, including DNA, RNA and proteins.

DNA, made famous for it's double helix formation, has even greater structure, going into tertiary and even quarternary structural units. The same is true of RNA and perhaps more importantly, proteins. Why is a protein important over DNA and RNA for it's form? DNA and RNA are, ultimately, blueprints for the body. Their structure is a result of what is easiest and lowest energy formation (caused because of negative charges, hydrophobicity etc...).

Proteins however can derive their function solely based on their shape, forming enzymes or otherwise. If a protein has an incorrect structure it will not react properly, and other biologic functions would not work, making the processes essential to life nealy impossible. As such outside of indentifying the constituent parts of the protein, another important aspect is determining it's structure. This is typically done using a Rosetta program via computer to determine the best possible arrangement of amino acids. The Rosetta program does well, except it does get stuck, as in getting to a lower energy state, sometimes you must cross through a higher energy one, causing the program to stop

So why am I going over protein structure and entropy? Much like the jellyfish article, I found another that was weird enough to catch my attention.

Protein folding is now a MMO game.

The use of the sorting algorthm is still invaluable, as the proteins can be several thousand amino acids long. However reaching the ending point of the program, researchers decided to make a game out of it, giving the virtual proteins to an online community to solve, getting points for making the protein have a lower and lower energy required. While algorthms and computer programs are extremely useful in science, human beings are definitely still needed... so screw you H.A.L.

The same tactic has begun to be used by astonomers and in other fields

I'm hoping in the future a biochem degree will boil down to a giant video game.

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