Intelligent design (ID) is a scientific theory that uses the methods of historical sciences to infer that many features of nature are best explained by an intelligent cause because they exhibit forms of information and complexity that in our experience only come from intelligence. ID is fundamentally a theory of design detection, but it has also been applied as an experimental science to guide research into how the natural world operates in the present day. ID uses a positive argument, beginning its investigations by studying known-designed objects and the actions of intelligent agents to identify properties that indicate design, such as complex and specified information, irreducible complexity, purposeful coordination of parts, common design patterns, and functionality. Natural features can then be studied to determine whether they meet the criteria for detecting design. These hallmarks of design can then be further applied to model or predict how designed natural systems function. Discoveries made through such studies of natural systems can then lead to improvements in human technology through biomimetics. This paper will review how ID has been applied within a variety of fields, including protein science, genetics, and systematics. It will also detail how engineering-based methodologies grounded in ID principles, such as systems biology and systems engineering, have advanced the study of multiple biological systems, including the flagellum-chemotaxis system, glycolysis, vertebrate limbs and joints, feathers, and brain blood flow.