Biochemical pathways are sequences of chemicals that constitute successive stages in some useful process, like the release of energy or the synthesis of an important substance. Each step in the pathway needs an enzyme - one of those large molecules that is shaped to act like a machine in a chemical factory. Different enzymes are needed for different steps in the chemical pathway. Sometimes there are two, or more, alternative chemical pathways to the same useful end. Although both pathways culminate in the identical useful result, they have different intermediate stages leading up to that end, and they normally have different starting points. Either of the two alternative pathways will do the job, and it doesn't matter which one is used. The important thing for any particular animal is to avoid trying to do both at once, for chemical confusion and inefficiency would result.
Now suppose that Pathway 1 needs the succession of enzymes A1, B1 and C1, in order to synthesize a desired chemical D, while Pathway 2 needs enzymes A2, B2 and C2 in order to arrive at the same desirable end-product. Each enzyme is made by a particular gene. So, in order to evolve the assembly line for Pathway 1, a species needs the genes coding for A1, B1 and C1 all to coevolve together. In order to evolve the alternative assembly line for Pathway 2, a species would need the genes coding for A2, B2 and C2 to coevolve with one another. The choice between these two coevolutions doesn't come about through advance planning. It comes about simply through each gene being selected by virtue of its compatibility with the other genes that already happen to dominate the population. If the population happens to be already rich in genes for B1 and C1, this will set up a climate favouring the A1 gene rather than the A2 gene. Conversely, if the population is already rich in genes for B2 and C2 this will set up a climate in which the A2 gene is favoured by selection rather than the A1 gene.
