Plant stress hypothesis
Latitudinal pest pressure gradients
Plant defense guilds
Apparency theory
Toxin/digestibilty reduction continuum
Optimal defense theory
Carbon/nutrient balance hypothesis
Resource availability hypothesis
Environmental constraint hypothesis
Plant vigor hypothesis
Growth-differentiation balance hypothesis
"Probability" hypothesis
To date none of these theories have been flat out rejected. By the same token, none of them have been found to be all encompasing. Each one of the theories fulfills the requirements of the model organism but fall apart as generalization start being made (Berenbaum 1995).
Most current research on alkaloids and phenolics, and other secondary metabolites, revolves around possible economic uses such medicinal and agricultural purposes. Generally in areas of biosynthesis, so that some of the active compounds with important effects can be synthesized for mass production for human use.