This dissertation is centered on problems within the history and philosophy of biology. The project identifies the philosophical roots of the current ecological movement and shows how a version of philosophical naturalism might be put to use within contemporary ethical issues in biology, and aid in the development of research programs. The approach is historically informed, but has application for current dilemmas. The traditions from which I primarily draw include classical American philosophy, particularly C.S. Peirce and John Dewey, as well as thinkers associated with the German Naturphilosophie movement, such as Goethe and Schopenhauer. There are deep, but often overlooked, resonances between these seemingly disparate traditions and contemporary biology that are located in the conflict between the developing organism and the ever-fluctuating environment. The dissertation makes the case for a shared description of nature among these traditions and proposes applications to burgeoning contemporary ecological interpretations of issues such as hybridization and epigenetics.