The discussion above suggests that the critical feature needed to allow the evolution of multi-cellularity is for a cell to be able to influence the expression of genes by its daughter cell. In the digital context, this means that a cell must be able to influence what code is executed by its daughter cell.
If we assume that in digital organisms, as in organic ones, all cells in an individual contain the same genetic material, then the desired regulatory mechanism can be achieved most simply by allowing the mother cell to affect the context of the CPU of the daughter cell at the time that the cell is ``born''. Most importantly, the mother cell needs to be able to set the address of the instruction pointer of the daughter cell at birth, which will determine where the daughter cell will begin executing its code. Beyond that, additional influence can be achieved by allowing the mother cell to place values in the registers of the daughter's CPU.
A large digital genome may contain several sections of code that are ``closed'' in the sense that one section of code will not pass control of execution to another. Thus if execution begins in one of these sections of code, the other sections will never be expressed. This type of genetic organization, coupled with the ability of the mother cell to determine where the daughter cell begins executing, could provide a mechanism of gene regulation suitable for causing the differentiation of cells in a multi-cellular digital organism.
Other schemes for the regulation of code expression are also possible. For example, digital computers commonly have three protection states available for the memory: read, write and execute. If the code of the genome were provided with execute protection, it would provide a means of suppression of the execution of code in the protected region of the genome.