The CPA System is the fundamental system behind the gameplay of the first half of the game. It has three components, the compound system, population dynamics, and auto-evolution. Together, these three sub-systems will create an overarching system that will account for the evolution of species from when you are a cell to when you are an organism.
A prototype is in the works by tjwhale here.
Main Article: Compound System
Compounds are the materials that the world and organisms are made of. So, stuff like elemental compounds (like carbon), natural resources (salt, water), organic compounds (amino acids) and organic polymers (proteins). The compound system deals with the transfer of compounds between organisms (microorganisms, aka cells, and macroorganisms) and the environment. Many natural processes will exist that will cycle these compounds from one form to another, while some processes will only be possible via the internal functioning of an organism, such as photosynthesis.
Main Article: Population Dynamics
Population dynamics handles the growth and decay of populations of organisms across your world. It is primarily a behind-the-scenes subsystem. It operates every time the player reproduces to calculate the change in populations of the player's species and the NPC species around them. Population dynamics is critical to determining the fluctuations in populations of species after evolution in a generation.
Main Article: Procedural Evolution
Auto-Evo handles the evolution of NPC species around the player. While the player will be directly making the changes to their organism every generation, Auto-Evo will have to use algorithms to calculate randomly mutate the NPCs.