It is very difficult to make sense of a world that is opaque. If a player does A and cannot see how the world responds, or a player does A and B happens but the player can’t see a connection between A and B, then it is going to take a long time for the player to build a mental model of how the world operates.

In Petri Dish, we attempt to enhance the transparency of our world by providing the player with tools to visualize what is occurring at all levels of the simulation. For example, when building a PO32- transport protein, the player is able to see the effect on the cell’s amino acid supply, the rate of PO32- transport into and out of the cell, the PO32- concentration inside of the cell, and reaction rates for chemical reactions in the metabolic network where PO32- is the rate-limiting factor.

If the player notices that the rate of PO32- diffusion out of the cell has increased, she can drill down to the molecular scale to see why that has happened. If she pulls back to the population scale and notices that her colony seems to be growing at a slightly slower rate, she can investigate by analyzing the metabolic pathways of those cells whose rate of reproduction has slowed. She may see that instructing her cells to build PO32- transport proteins has had the unintended effect of increasing the acetyl concentration inside of those cells, removing a bottleneck and diverting molecules from cellular respiration to phospholipid synthesis. The solution? Re-designing an enzyme to regulate the phospholipid synthesis pathway.

Transparency provides immediate feedback and makes the world feel more real. It also enables and encourages the player to debug unintended outcomes and emergent behaviors, building a more robust mental model of the world and cell biology along the way.