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.
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From virtual to real

I must admit, there was a time when I would play computer/video games late into the night. I was a wee-lad back then, so impressionable and curious about the whole plethora of things of this universe. And the allure of the virtual worlds to such mind was just too sweet to resist. I gave a lot of thought to my then-current condition during the phase of my life. Why would I be captivated by certain types of virtual reality? Is there something shared in common between the hundreds of different worlds constructed using a number of different mediums-writing, visual, and aural-that composes the fundamental idea of what an enjoyable world should be? Would the impression of such an ‘idea’ of the mysteriously attractive world be common to all human beings? Or only human beings of certain memories and experiences? I would spend many days just thinking about the nature of all possible virtual worlds imaginable by human mind and their possible implications while my hands played the mechanical play of controlling my representation within the display.

Deus Ex was a computer game created by the now-defunct ION storm that came out during the aforementioned impressionable period of my life. This game isn’t aesthetically pleasing by any stretch of imagination. It’s gritty, ugly, in a very superficial and unintended kind of way. It is based in imaginary near-future where nanotechnology and artificial intelligence are just coming into full gear among the financial and political turmoils of a new human age. Conspiracy theories based on some real-world conspiracy fads play an important role in the setting and the plot, and there are lot of techno-jargon thrown around in one of the numerous conversations within the game world which might add to its depth. Any way you look at it, Deus Ex is not a work of art, and it was never meant to be. Deus Ex as a game was designed to be immersive. Immersive as in realistic within the confines of the plot and available technological means to execute that plot. Whatever the Deus Ex was meant to be, it did its job and it did its job fantastically. Deus Ex took itself just serious enough to be immersive.

I played and finished Deus Ex numerous times since the day it came out. The game had the semblance of a virtual world, just enough to be a better game, not enough to be a real virtual world, which was actually a good thing. I’d figure out a number of different ways to achieve the objective of the specific stages and the game as a whole, each of those paths gradually beginning to encompass different processes that the designer of the game probably never intended in the first place-a first form of truly emergent game play on digital medium. I can still remember a number of quotes and conversations from the game by heart, not through any diligent study, but simply through repeated exposure stemming from the interest in the world itself. And to be perfectly honest, while I was aware of nanotechnology and its growing prominence before playing the game (I was a little precocious for my age), I began to truly comprehend what such technology could mean to the world and the people in the far future by seeing it applied within the virtual world built and maintained by fictional premises. It would not be far from to truth to say that my interest in ‘industries’ of biology and other fields of science (with my current ‘official’ pursuit being plasma physics, which is an entirely different field altogether) began with my introduction to this game… I place much emphasis on the term ‘industry’ because it was through the application of the idea of technology within a virtual (no matter how absurd it might be compared to the real) world that I began to grasp the requirements of science and its true impacts in the modern human civilization of rapid prototyping and mass production. Yes, I’ve come to learn that science effects the human world as a whole, just as the hand of economy reaches into the deepest pockets of the remotest corners of the globe, and such permutation of ideas and information might have a reasonable pattern of causality behind it, forming a system of sorts. All this at the first year of high school, all this because I’ve seen it applied in a limited virtual world whose goal was to entertain, perhaps mindlessly.

People talk of the web 2.0, the web based virtual reality (like the second life) all the time, perhaps without grasping what it truly means. To me, the change on the web and its technical and semantic updates are merely superficial effects of the real change that is taking place right now. The real change we are about to face at this moment, is the change to the nature of the human network. I find that I’m using the term human network more often these days. The human network had been present since the very first moment of human civilization (perhaps even before, going back to the start of the human species) and has the same mathematical and sociological properties of networks that more or less remains the same on some compartmentalized level. The changes we are seeing in the emergence of the web 2.0 ideas and virtual realities merely reflect the technological advances applied to the same ever present human network that had been in place for as long as anyone can remember. At the core of the web 2.0 is the idea of user interactivity. What happens when there is a freedom of interactivity between millions and billions of people? The medium providing the room for interactions itself begins to take on closer resemblance to the concept we call ‘the world.’ Forget reality. What is a ‘world?’ What satisfies the definition of a ‘world?’ The core of a ‘world’ as it stands happen to be a place where people can interact with the very components of the world itself and with each other. In that sense, if our reality somehow forbid certain type of interaction between us and the ‘world’, it would cease to be real.  The world as seen from information perspective, is a massive space/concept/thing for interactivity, and interaction between the ‘things’ within the world builds and evolves the form of the world itself.

The web 2.0 in that sense, is the beginning of a virtual world that builds upon human interactivity rather than superficial (though still quite important) reliance on resembling the physical characteristics of the real. And the real change being brought on by the advent of the web 2.0 thought to the general population is the enlargement of the perspectives of the real world brought on by interactions with other human nodes within the virtual world. I am not suggesting that people are somehow becoming more conscious. Just as I have demonstrated with my old experience with the computer game Deus Ex where seeing certain kind of ideas applied to a virtual world left an impression of impact of such ideas on a rapidly prototyping, global world, the population of this world is becoming increasingly aware of the true global consequences of their and others actions and thought. It is the awareness that in this highly networked world, science, industry, economics and politics all walk hand-in-hand as ‘ideas’ and its currencies, a single change in one sector of one corner of the world giving birth to certain other events on the opposite corner of the globe in entirely different field of ideas. It is the beginning of the understanding of the malleability of the human world and its thought.

I’ve started with remembering my experience with an old computer game, and came to the talks of virtual reality, the human network and the changes of the world. I hope I didn’t confuse you too much. This is what I call ‘taking a walk’, where I begin with one thought and its conclusions and apply them to different yet related thoughts to arrive at interesting ideas. In case you are wondering about the game itself, it seem that they are giving it away for free now. Go grab it and spend some time with it. It’s still fun after all these years.

The videogame art

Today’s my day off, so I have a bit of time for some contemplative rambling about nothing.

Does anyone remember the game Vagrant Story? It was a game for the PSX that came out at the end of lifecycle of the system. I happened upon it by chance and was completely captivated by its unique brand of aesthetics and gameplay. I’ve always been curious as to what kind of real world inspiration was drawn for the Vagrant Story universe, so I did a little bit of researching while on one of my excursion to the Met.

Overall, the general aesthetics prominent during the gameplay is definitely 15th~16th century Italian, the period of high Renaissance on verge of crossover to the Baroque, another primarily Italian movement. However, being an artificial construct designed to represent a thematic world, the Vagrant Story and its version of Ivalice show certain interesting qualities while depicting the chronological changes within its own world using the subtle hints in architecture. The 15th~16th century Italian flair of the Vagrant Story universe is used in depiction of the ‘present time’ of the world from the player’s perspectives, against which the story of the forgotten city of Lea Monde and subsequent search for the Gran Grimoire are set. However, as apparent from quite a number of architectural stylings of the older part of the city of Lea Monde, like the Kildean Temple at the center of the city (which is told to have been built at the height of the city and the cult of Mullenkamp’s power, which in terms of the Vagrant Story timeline would possibly be ancient) shows distinct and unmistakable influence of the Byzantium art and architecture. The structure of the deities of the more ancient part of the city, the tiled backgrounds of the inner Kildean Temple, the majestic yet definitely not European or Middle Eastern arches of the walls, towers and ceilings, and the exquisite structure of the central dome of the Kildean Temple where the climatic battle between Ashley Riot and Guildenstern Rosencratz took place shows distinct Byzantine milieu, most likely taken from the real world example of the Hagia Sophia in the city of Constantinople, present day Istanbul. Indeed, the vast underground network of crypts and libraries beneath Lea Monde shows certain unusual Roman influences, putting it squarely within the timeline of the real world Byzantium.

It is somewhat interesting to note that surrounding public quarters of the Lea Monde, unlike specialized constructs like the aforementioned Kildean Temple, displays consistent central and southern European themes, reflecting their real world counterparts where magnificent architectures of old are preserved while the ‘normal’ housings surrounding them change with the times.

The most unique characteristic of the composite civilization of the Vagrant Story, the one that made the study of the real world influence on the Lea Monde architecture so appealing to me in the first place, is the novel use of lighting through out the changes of scenery surrounding the architectural works themselves. No doubt a technical decision was made at the time to compensate for the aging hardware of the PSX, it nonetheless proved to be a genius decision that made the world come alive to the player (thought the music and sound effects also had great part in it).

Within the engine utilized by the Vagrant Story, each scene is placed within a world with its own lighting and default color cue, a sort of universal ambient lighting saturated into every single texture within the scene. It means that for the most part every single cityscape/building in the game was placed within an even greater box of light. This gave each physical locale within the Vagrant Story universe to possess incredible range of lighting effects, each area becoming living and breathing worlds unified by architectural themes. The undercity has the atmosphere of the Styx, and the perpetual sound of running water and shades of bluish darkness accentuated by light sources of different, yet suitable color and scale. The lower Kildean Temple is perpetually basked in burning glow of yellowish crimson sunset, looking out into the violently crashing oceans formed during the violent earthquake of the past, while the red sun hangs suspended in the sky. The upper Kildean Temple makes extensive use of the contrast between the opaque red permeating through the sky and the deep darkness between the falling columns and crumbling extremities, giving us the profound feeling of holiness intermingled with the unspeakable decadence. It clearly displays the theme of eternally dying cathedral for a forgotten deity.

The psychological impact of such brilliant yet low tech use of lighting, and design decisions made to accommodate such lighting condition made profound impression on my then young mind. I still can’t forget the bleak, opaque red sky seen from the upper edge of the Kildean Temple, perpetually bathed in ominous sunset without gradient, the sun itself nowhere to be found. Only the darkness leading to the depths below in stark yet harmonious contrast… It had the ominous qualities of the best of Clifford Still paintings, and it still retains certain nostalgic quality for me.

In terms of realism, Vagrant Story is lacking. Yet I still remember each memorable scenes vividly, enough to draw and write about it despite not having experienced the game in six or seven years. Quite clearly, physical replication of the real does not equate the mind’s perception of the real. There seem to be a few immutable essences of the world that makes an impact of the mind’s eye to perceive that specific information as real (in such light, I am beginning to feel that many of the works of ‘modern art’ to be severely anemic in terms of true contemplature of the real and the simulacra of the real). If true, human perception of ‘beauty’ should be intimately linked with the perception of the outside world by the human cognition. Human cognition, physiology, and the illusive ‘human psyche’ are all interlinked with each other when in light of the aesthetic fulfillment of the self. Mind and body are inseparable when in observance of the world it seems. Beauty might be the brain’s way of propagating through the material world.

Writing this post made me think about a few things of art I would love to see (or, provided that I have the time, do myself). Painting of cityscapes. Just as the artists of the Bohemian era wandered the world painting landscapes (Gustave Courbet comes to mind. Interesting person. I should do a post on him someday), people of today should wander the world and paint cities at its most unexpected and beautiful/hideous moments in time (being that both are aesthetically fulfilling). Or even, take a cue from the Eastern landscape painters. Draw beautiful pictures of imaginary cityscapes, the ones where the viewer can walk through and dwell, perhaps learn a thing or two through the mind’s eye. The artists of the Renaissance were truly genius in this regard, as they succeeded in formularizing geometrically sound yet surreal drawings of buildingscapes that have almost psychological impact upon its viewer, like the ones for the panel at chapel La Bastie D’Urfe. It is rather strange to see no one capitalizing on such style in this age of digital arts.