Citizen science: Phylo the sequence alignment game

Citizen science in the form of computer games are coming think and fast. Phylo is the latest offering and I've got to say its pretty additive.

Phylo, match up the coloured blocks, score points, help scientist fight diseases!

This time the aim is to help scientist who study genomes match up the DNA in the genes from one species with those of another species. The is important because if a gene is more or less the same in many different species then it probably means that its particularly important.

So how come scientist don't just let computers work it all out? Well it turns out that computer programs are pretty rubbish at this sort of problem because they painstakingly work through all possible ways to align the bits of DNA and that takes ages. But the human brain is really good at spotting patterns, so we get the job done much more efficiently. Have a go at the game and you'll soon find you are scoring better than the computer.

The game is really quite simple, each building block of the DNA (remember those A,T,G & Cs) are represented by a different colour block. All you have to do is slide the blocks around and get the colours on one line to match up with colours on another line. You get points for every match and points taken away for incorrect matches or gaps.

The other really nice thing about Phylo is that you can enjoy it for its own sake. You don't have to know a thing about DNA, genes or genomes to be able to play it. So literately anyone can have a go.

If you'd like to read more you can find the original journal article here.

Citizen science: The protein folding problem

The fold.it and fold@home projects are a fab way to get involved in some really BIG science. And the best thing about it is that all you have to do is play a computer game or just install a bit of software on your PC!

http://fold.it/portal/
http://folding.stanford.edu/

Basically both these projects are working on something called the protein folding problem. Proteins are the molecular machines that are involved in just about every conceivable job in your body. They replicate  DNA, hold your joints together, fight infect, you name it they do it.

Not only are proteins amazingly useful but they are also fabulously beautiful structures. These two images show the structure of two very different proteins. The first one is called catalase and it mops up harmful hydrogen peroxide that your cells make as a waste product of metabolism. The one below is called rhodopsin and it is produced in the cells on the retinal at the back of your eyes, its sensitive to light and acts like the film in a camera.

The thing is that proteins are all made up of just 20 different building blocks called amino acids. These amino acids fit together to form a long chain, just like beads on a string. For a protein to do its job this string of amino acids needs to fold up in exactly the right way. The astonishing thing is that there are more ways that a protein can fold than there are atoms in the Universe. But somehow proteins 'know' which 'fold' is correct and how to get there in fractions of a second. Its sort of like throwing all the pieces of a complex robot into the air and expecting them to land as a fully functioning machine.

So how do proteins do it? Well the short answer is we really don't know. Despite a massive amount of computer power we still aren't very good at predicting how proteins fold. And thats were you come in. Because the fold@home project lets you run protein folding simulations on your desktop PC or  Playstation. You might think that this won't make much of a difference, but over 5 million home computers all round the world are running fold@home and  together they make up the second most powerful computer on the planet.

The fold.it game takes another tack. The idea here is to get people to play with proteins and get them to fold. Then scientists look at the strategies that gamers used. They then take this information and input it into computer algorithms. Nice idea and really quite successful, they and their gamers have published their findings in the most prodigious scientific journals (http://www.cs.washington.edu/homes/zoran/NSMBfoldit-2011.pdf).