Optical observations from sensors on satellites, moorings and autonomous underwater vehicles have emerged as some of the most useful sources of information on the variability of ecological processes in the upper ocean. In turn, models of optically driven biological processes — both estimates of primary production from ocean color and simulations of phytoplankton for biogeochemical ocean general circulation models — have become essential tools for describing the ecology and biogeochemistry of the sea. The roots of phytoplankton models run deep, and analyses have almost always relied on the quantification of chlorophyll a, an imprecise but easily measured proxy for the biomass of phytoplankton and its capacity to absorb light for photosynthesis. Following suggestions that have been made repeatedly for well over a decade but not yet implemented in a comprehensive framework, I describe a modeling system that simulates the dynamics of optical properties directly, that is, by replacing the concentration of chlorophyll with the more directly relevant absorption coefficient for photosynthetic pigments. Photosynthesis is estimated by constraining photosynthetic quantum yield vs. absorbed radiation as a function of temperature, nutrient status and acclimation to light as expressed in the chemical composition and optical properties of photosynthetic cells, all of which are included in the model framework. The resulting direct simulation of the dynamics of optical properties could have distinct advantages, especially for the application of data assimilation procedures that would use optical measurements to drive both hindcast and forecast models. Further, the new formulations are designed to implement developing knowledge of the mechanistic links between the optical properties of microbes and their physiology and ecology, guiding new research in the process.