Mathematical models are tools to examine existing theories, find gaps in knowledge and explain phenomena such as nutrient digestion and metabolism. Simulated data from a model can be used to examine model behavior, as in sensitivity analysis, and compared with experimental data to determine if the model makes biological ‘sense’. The objective of this session is to explore how concepts or theories of nutrient digestion, metabolism, and lactation physiology are translated into mechanistic mathematical equations and combined into a whole animal model using the Molly model as an example. Molly is a mechanistic model of a dairy cow composed of a digestive element and an animal element. The digestive element converts chemical composition of the diet to volatile fatty acids, microbial growth and absorbed nutrients using physical attributes of the diet such as proportions of large and small particles and water passage. The animal element converts products from the digestive element into tissues (protein), waste products, heat production or secreted products (e.g., milk, milk fat). Three processes that have been translated into equations in the Molly model will be examined in this session: (1) Passage of digesta through the rumen described in Baldwin et al. (1977; Agric. Syst. 2:255–288); (2) milk production by the mammary gland described in Neal and Thornley (1983; (J. Agric. Sci. Camb. 101:389–400); and (3) growth (protein synthesis) described in Oltjen et al. (1986; J. Anim. Sci. 62:86–97). In the lecture, representations of these processes will be examined using conceptual diagrams and differential equations. Then a full lactation simulation will be used to demonstrate how equations of passage, protein accretion, and milk synthesis fit into the model.