The study of biosynthesis is an important aspect of answering two questions that have preoccupied chemists. Where do natural products come from? Why are they produced? The development of ideas from molecules to genes has helped to answer these. Atomic theory from Plato to Democritus was a key pre-requisite. The study of whole, complex systems is challenging. Preformation was developed as a concept of how living systems are formed but it was succeeded by epigenesis. Macrovisualisation of the properties of individual plants is key to hybridisation and crop improvement. The development of the Signaturist approach to plants and disease suggested that remedies were best derived from plants that resembled target organs. The use of ‘affinities’ was later used to explain how atoms combine. The mechanics of biosynthesis and the involvement of genes can be explained using polyketides as an example of biosynthesis and biosynthetic gene clusters. Manipulation of biosynthesis leads to the development of directed evolution. The growth in synthetic biology for the production of valuable molecules can be studied using basic engineering principles.