In this dissertation I show how the complexity of biological and chemical kinds often complicates attempts to classify these kinds. I construct an account--which I call 'selective naturalism'--that explains the diverse yet grounded classification of complex biochemical objects like proteins. By distinguishing the properties and powers of these complex objects, as well as the inferences afforded by tracking sets of these properties and powers via classification, I can explain how various classificatory complications evident in the biological and chemical sciences are generated. I can also show how this kind of classification may be used as a tool for discovery in the sciences