This paper presents a real-time simulation involving “protozoan-like” cells that evolve by natural selection in a physical 2D ecosystem. Selection pressure is exerted via the requirements to collect mass and energy from the surroundings in order to reproduce by cell-division. Cells do not have fixed morphologies from birth; they can use their resources in construction projects that produce functional nodes on their surfaces such as photoreceptors for light sensitivity or flagella for motility. Importantly, these nodes act as modular components that connect to the cell’s control system via IO channels, meaning that the evolutionary process can replace one function with another while utilising pre-developed control pathways on the other side of the channel. A notable type of node function is the adhesion receptors that allow cells to bind together into multicellular structures in which individuals can share resource and signal to one another. The control system itself is modelled as an artificial neural network that doubles as a gene regulatory network, thereby permitting the co-evolution of form and function in a single data structure and allowing cell specialisation within multicellular groups.