This research investigates biopigments and other biomolecules in complex keratinous systems, such as bird feathers and human hair for interdisciplinary research at the interface between materials science, humanities, and computational modeling. Specific target areas include: visualizations of color-producing micro and nanoarchitectonics in hummingbird feathers and finite-difference time-domain (FDTD) modelling of the nanophotonic structures, inspired by pre-Hispanic feather artworks in Mesoamerica; advances in surface-enhanced Raman scattering (SERS) methodologies for non-invasive detection of trace amounts of biopigments in bird feathers; label-free detections and structural characterization of psychoactive compounds in ancient hair, and conformational studies complemented by density functional theory (DFT) of bufotenine biomolecules. The thesis offers novel transdisciplinary multiscale and multimodal methodologies integrating experimental and computational analyses providing new insight into natural and cultural processes.