Why do organisms make the types of chemicals that they do? Evolutionary theory tells us that individuals within populations will be subject to mutation and that some of those mutations will be enzyme variants that make new chemicals. A mutant making a novel chemical for that species will only survive in the population if the 'cost' of making the new chemical is outweighed by the benefits that result from making that molecule. The benefits, or adverse consequences, that a novel chemical X can confer to the individual organism are not a property of the simple existence of X in the cell but can be traced to one of the multiple properties that X will possess because of its molecular structure. By considering only three basic types of molecular property and by considering how selection pressures will differ for each kind of property, it is possible to account for much of the chemical diversity made by organisms. Such an evolutionary model can also explain why the properties of enzymes will differ depending on the molecular properties of the chemicals they make, and why the widely accepted terms 'primary metabolism' and 'secondary metabolism' have been so misleading and unsatisfactory.