The preceding discussion has been deliberately general insofar as very few constraints have been laid down as to how the genotype should encode for the system to be evolved. To some extent such an encoding is always domain-specific, but nevertheless there are some general rules that come into play as a system grows more complex.
With simple designs where there are no symmetries or repetitions to be expected, then the straightforward method is for the genotype to encode in sequence the type and parameters of each component part, together with the interconnections between such parts. However, as systems become more complex, then symmetries and repetitions can be expected to play a significant rôle in many circumstances. For instance, when designing a control system for a robot with bilateral symmetry, then there may well be good reason to expect this bilateral symmetry to be reflected to some extent in the controller. If designing an artificial retina, then repetitions of similar local structure across a 2-D array can be expected.
If the genotype constitutes in effect a linear description of each component of the system in turn, with for instance the left and right halves separately so described, then bilateral symmetry can only be achieved by separate independent evolution of each half of the genotype towards the same target. In a stochastic process such as evolution this is improbable and difficult; however it could be achieved relatively simply if the genotype described just one half, together with a routine which `called' the description twice with appropriate parameters, in the sense that a program can call a sub-routine. In the case of multiple repetitions as in a retinal array, such a process becomes even more efficient.
Earlier it was suggested that evolution was a method of avoiding the constraints of human design, which seems to require the decomposition of a system into semi-independent modules. The repetitions and symmetries now being discussed differ from such human decomposition in two critical ways. Firstly, any such decomposition can emerge from evolutionary choice, rather than being pre-determined by fallible human prejudice; and secondly, such repeated modules can be intimately connected with each other, as with neighbourhood relationships on a retina, and need not be semi-independent.
In the natural world the genotype does not constitute a description of the organism. Instead it acts as a constraint on the way in which a multi-cellular organism develops from a single cell, in such a fashion that symmetries and repetitions can naturally emerge. Attempts to replicate such emergence in artificial evolution are currently ad hoc and domain-specific.