To carry out an enormous diversity of tasks, proteins can assume a variety of structures or disordered states, and years of work have made the connection between protein sequences, structures, and functions. Enhancers and other pieces of regulatory DNA regulate gene expression in highly disparate biological processes, but we still lack general principles that can help us connect enhancer sequence, transcription factor binding site arrangement (or architecture), and function. In my seminar, I will primarily describe two projects that seek to make connections between the way enhancers are built and the tasks they carry out in two biological settings: early development and the innate immune response in Drosophila. In the first part, I will describe a mechanism by which redundant (shadow) enhancers control expression noise, and in the second, I will describe the patterns of evolution that drive divergence in the expression response to bacterial infection.