Much of the ``physics and chemistry'' of the digital universe is determined by the specifications of the operations performed by the instruction set of the CPU. However, the operating system also determines a significant part of the physical context. The operating system manages the allocation of critical resources such as memory space and CPU cycles.
Digital organisms are processes that spawn processes. As processes are born, the operating system will allocate memory and CPU cycles to them, and when they die, the operating system will return the resources they had utilized to the pool of free resources. In synthetic life systems, the operating system may also play a role in managing death, mutations and flaws.
The management of resources by the operating system is controlled by algorithms. From the point of view of the digital organisms these take the form of a set of logical rules like those embodied in the logic of the instruction set. In this way, the operating system is a defining part of the physics and chemistry of the digital universe. Evolution will explore the possibilities inherent in these rules, finding ways to more efficiently gain access to and exploit the resources managed by the operating system.