Cells in Petri Dish have two control systems that enable them to regulate their own internal environments (homeostasis), respond to stimuli from the external environment, and take on specialized roles as part of a colony of cells (differentiation). Without these control systems, a cell would not be considered a living organism.
The first control system involves gene expression. A cell’s genome contains templates for every type of protein that the cell can build. When a gene is activated, a copy of its template is made and transported to a ribosome enzyme, which then uses the template to assemble the protein out of amino acid molecules.
This process takes many steps, but in our cell model, we are abstracting it down to two: a gene is activated and a ribosome enzyme assembles the protein out of amino acid molecules.
At the start of the game, gene expression occurs when the player manually activates a gene. Later in the game, in order for cells to become autonomous and begin forming multicellular colonies, the player will program the cell to activate its own genes.
Once a protein has been assembled, it runs on autopilot and the player no longer has any control over it. This means that an unregulated O2 transport protein will continue transporting O2 into the cell as long it has O2 molecules and energy available, even if the cell has more O2 than it needs. This is wasteful (transport proteins use up energy) and can lead to chemical imbalances that can damage the cell.
To prevent this, cells implement a second control system to regulate individual proteins. Proteins can be programmed with a closed-loop control system that acts as a dimmer switch. A regulated O2 transport protein will turn itself down when there is plenty of O2 inside the cell and turn itself up when there is not enough.