A Framework for Scientific Discovery through Video Games. Seth Cooper

are doing, and feedback from the player community is extremely useful in determining new features. However, in a scientific discovery game, as scientists post puzzles and player solutions are analyzed, this analysis must then be incorporated in the design of the game, progressing towards ever better results.

      Following this pattern, Foldit has evolved significantly since its initial release. A timeline of significant events in the evolution of the game are given in Figure 3.4.

      Figure 3.4 Selected events from the game’s evolution over time. The timeline is shown on the top. Screenshots are included from before release (bottom left) and the current version (bottom right). (Figure from Cooper et al. [2010b])

3.3.3 Categorization as a Game

      Although it relies heavily on simulation and visualization, Foldit can be classified as a game, as it possesses the qualities of a game set forth by Schell [Morgan Kaufmann]. Here we list the qualities and how Foldit embodies each.

      1.Games are entered willfully: We do not require players to play Foldit.

      2.Games have goals: Foldit’s goal is to find the best scoring structure.

      3.Games have conflict: Foldit has conflict with both the protein itself, trying to find a better score, and with other players, trying to outrank them.

      4.Games have rules: The rules of Foldit are given by the scoring function, available moves, global point structure, and so forth.

      5.Games can be won and lost: Each puzzle has a ranking, which could be broken down into “winners” and “losers”.

      6.Games are interactive: Foldit allows players to interactively reshape a protein and gives them immediate feedback.

      7.Games have challenge: Similar to conflict, Foldit’s challenge arises from achieving higher scores and competing with other players.

      8.Games create their own internal value: Foldit’s global points have value for ranking within the game.

      9.Games engage players: Foldit keeps players engaged in manipulating protein structures.

      10.Games are closed, formal systems: Foldit’s rules define the pieces of the system and how they work together.

3.4 Game Design Challenges

3.4.1 Visualizations

      While a user is playing Foldit, several visualizations are available. These help the player determine when they are or aren’t doing well, and show which areas of the protein they could improve and what is wrong with them, so the player can think about how to fix any problems. Figure 3.5 shows a screenshot of the game’s main screen. We intend for the game to look like a game and not necessarily a scientific illustration. While scientific illustration techniques are useful for scientists, they may not be for our purposes, and may in fact be intimidating for non-scientists. Many of the visualizations have options, or can be turned off and on by the player. They include the following.

      The protein. The protein itself is rendered in a cartoon-like style. This style is abstract and does not show the exact positions of all the atoms in the protein. The helices, sheets, and loops appear differently along the backbone, and sidechains are rendered very simply. The protein is colored by the score of each residue.

      Clashes. These are red flashing spiky balls. They appear where two atoms are too close together, which will severely reduce the score.

      Figure 3.5 Foldit’s main game screen. The puzzle Collagen is shown. The protein is in the center; some clashes are visible. The panel in the top right shows the player’s rank and score, leaderboards for groups and individuals in the current puzzle, and chat. Menus and information are in the other corners of the screen.

      Hydrogen bonds. These will appear as blue and white ladders where hydrogen bonds have been formed. These bonds improve the score and help hold the protein together.

      Hydrophobic sidechains. Hydrophobic and hydrophilic sidechains are shown in different colors. Burying hydrophobic sidechains in the core of the protein can improve the score.

      Voids. These yellow spheres will appear where there is empty space in the protein. Filling in the space can improve the score.

      The visualizations in a scientific discovery game must achieve several purposes in order to allow players to apply their problem-solving skills. They must reflect and illuminate the natural rules of the system, in a way that makes state of the system evident to the player and directs them to where their contribution will be most useful. At the same time, the visualizations need to manage and hide the complexity of the system, so that players are not immediately overwhelmed by information. They must be approachable by players who have no knowledge of the scientific problem at hand. Thus, they should look inviting and fun, and not bring back memories of high school textbooks. Ideally, they should be customizable, because as with other aspects of the game, it is not clear from the outset what the best visualization will be, and different players may have different preferences.

      In order to make the visualization of Foldit reflect and illuminate the fundamental properties of proteins, we worked with scientists to distill simple rules upon which to base them. The first rule is to avoid clashes. Clashes occur when atoms are unrealistically close to each other, causing a large repulsive force. These can be prevented by keeping the atoms from overlapping, and are represented by spiky, rotating spheres that float between the overlapping atoms. The second rule is to fill voids, or empty spaces in the protein. Packing the protein tightly will remove voids. Voids are represented as bubble-like objects that pop when they come in contact with the protein. Clashes and voids appear red, as natural proteins should not generally have any. The third rule is to bury exposed hydrophobics. Hydrophobics are sidechains whose chemical properties are such that it is favorable for them to be on the interior of the protein. Exposed hydrophobics are represented as small, pulsing spheres that move along their sidechain. These are drawn in yellow, rather than red, because natural proteins may have some exposed hydrophobics. The fourth rule is to maintain and create hydrogen bonds, which form between particular pairs of atoms and hold the protein together. Hydrogen bonds appear as undulating bars between the bonded atoms, and are drawn in blue, because they are good.

      Due to the spatial nature of the problem, the visualization of the protein closely matches the actual geometry of the protein. To make the overall structure stand out, sheets, helices, and loops are stylized, similar to many scientific visualization tools.¹ Sheets appear with a zig-zag pattern that will form hydrogen bonds when properly fit together. Color also plays a large role in the visualization of the protein. The backbone color reflects the score of the protein in a particular region—going from red in poor scoring regions to green in good scoring regions—so players can see where they can gain the most points. The sidechains are colored by hydrophobicity, so players can quickly see if they are extending them in the preferred direction. By coloring backbone and sidechain independently we can display more information while not introducing too much visual clutter.

      Foldit takes a number of approaches to manage and hide the complexity of huge networks of interconnected atoms that make up a protein. Many unimportant details are hidden. Hydrogen atoms, which are plentiful on the protein but do not add a lot of structural information, are hidden. However, hidden information will reappear if it becomes important to the player: sidechains can disappear entirely to make the overall structure of the protein’s backbone clearer, but will reappear if they are causing a problem, such as if they are involved in a clash. Many actual clashes themselves