Is it game night yet?

It’s Thursday night. Just one more day to plow through until you reach Friday night with all its movies and drinks. Well, we can’t tell you how to speed up time but we can tell you how to feel like it’s going faster. Play computer games. 

Now, we are talking about Genspace, and we do have a bit of reputation to maintain. So as much as I would like to recommend everyone to get cracking on the battle.net with Starcraft 2 we’ll have to make do with something different; a computer game with science in it.

It’s called Phylo, and you can find it here. Phylo is an entirely browser based (flash based, to be specific. Sorry to disappoint all my iPad toting readers) and doesn’t require any serious computing muscle on the player’s end. I’ve been playing it for the last hour or so, and it’s an odd piece of work. On the surface the game follows some basic rules of pattern matching casual games you might be familiar with like Bejeweled. Yet the experience of playing the game feels far more complex than that, and I don’t necessarily mean that in a bad way. Also, there’s a real benefit to playing this game on your spare time, other than gaining the l33t skills to pwn the n00bs with.

You see, Phylo is ‘a human computing framework for comparative genomics.’ Basically it gives you real multiple sequence alignment problems represented by 4 color blocks scattered on a grid. And of course, budding bio-enthusiasts like us know what’s up when a science programs give us 4 of anything- they represent nucleotide sequences. As you match same colored blocks with each other, you contribute some of your brain power to finding aligned sequences between different genes. If you misalign the blocks you lose a point, and if you create gaps between the blocks (which represent mutation) you lose lots of points. You can gain points by aligning same color blocks on vertical row and you need to gain certain amount of points to pass a level or get another gene to align with your existing sequence. This is a very abstract process of optimization that is usually done with complex computer algorithms and lots of processing power, which would be prohibitively expensive when brute-forced. The authors of the program hope to use the human-computer interaction on a large scale to come up with optimized heuristic pattern.

 

This is how Phylo looks
The logic is sound. After all, usefulness of human ability to find patterns in complex biological simulations have already been proven worthwhile with the fold.it protein folding puzzle game and the Nature paper that came out of it. Guess who’s a co-author of a nature paper.  😉
 

This is how it might look on a scientists’ computer
I’ve played around with the DNA code responsible for idiopathic generalized epilepsy and already 160 other people attempted to solve the puzzle… And 146 people failed. And there lies the problem of biology-turned games. You see, unlike regular puzzle games like Bejeweled or Tetris, not everything will fit together with perfect logical coherency. Granted, there are a few techniques you can use to treat this like any other game (for example, don’t waste your time moving around single blocks in the beginning stages. Crush them together into single group for maximum points in shortest amount of time), but the fact is not everything will fit together and it can be rather jarring for a beginner to figure out what he/she’s doing right, since there isn’t any satisfying feedback to a ‘correct’ sequence formation. It can’t be helped though. This is science, and no one knows the correct answer to detect and give you feedback with. Maybe that’s the whole reason why you should play this game. After all, would you play a match in starcraft with predetermined outcome?
I for one, am looking forward to the future where all games contribute to the discovery of science in some shape or form.

Sketch-Creativity and origin of creativity

I’ve been listening to Amy Tan’s talk on TED titled ‘Where does Creativity Hide?’

Interesting stuff. I didn’t have enough time to mull over it properly yet, but listening to her gave me a few thoughts on the issue of the origin of creativity, an issue I am very passionate about.

It is relatively simple matter to simulate the process of creativity, I think. Plenty of mathematical constructs and randomly generated ‘events’ linked together has the resemblance of pure creative output, and despite some number of conflicts and arguments for and against such ‘engines of creation’, I do believe that what we do might in essence be not so much different from the simulated behaviors of such random patterns and mechanization.

However, the real problem, at least for me, lies in the issue of the origin of creativity rather than the process of it. Human beings are not machines or algorithms specifically designed to be creative. In fact, human beings as molecular machines might not have been built for anything (and everything, in that sense), for evolution tend to be quite blind in such matters of directionality in nature (there are theories and viewpoints arguing otherwise). I will not even look at the possibility that the wellspring of creativity emerges from some spiritual source, instead approaching the problem from purely materialistic and reproducible viewpoint.

As physio-chemical complex dissipative systems, what drives human beings to create and innovate throughout their duration of activity, i.e. life? What kind of mechanism underlies this strange anomaly emerging from entangled soups contained within chunks of chemicals? Even more, how would we be able to replicate such behavior using less than usual components? This, ladies and gentlemen, is the question of the ages, the true question toward the question of creativity.

This, I believe, is the true crossroad between the arts and the sceinces, the significance of artificial life in science, society, industries, and the zenith where the artificial intelligence becomes simple intelligence.

More to follow.

Brain Simulacrum

There is a semi-community project to simulate human brain using spare computing cycle in the works.

The members of the projects seem to be looking at eventual commercialization of what they achieve using this project. I assume that it might turn off some of the more devoted advocates of GNU philosophy among us, but I still think this is project is interesting enough to devote some of my unused cpu cycles to the cause… Since, well, what’s the point of letting the spare computer time go to waste? Right?

Science is fundamentally specialist and will never be able to achieve the kind of 2.0-everyone pitch in- status afforded by larger community web services today. However, the systems such as BOINC (the system used for the simulation project as well as a number of other worthy, non-commercial projects) gives us a glimpse of what ‘open-science’ in the future might be like, in that it allows concentration of necessary energy and resources to make the research come to fruition, not through any large scale departmental bureaucracy but through a sort of grassroots recycle programs of the commonly wasted byproducts of our civilization. Indeed, I’d refer to it as making full use of the machinery of the human civilization itself.
I’d like to urge anyone even passively interested to visit the BOINC website and participate in a project of your choosing. They have a number of projects in progress and the list is likely to grow in the future. Who knows, our little contribution might make the future a bit more interesting place to live.