The principles of bioengineering underpins the use of living systems as biological machines to effectively make desirable products. The concepts of vitalism and agency are important when considering biological systems. The quantum mechanical understanding of consciousness suggests that natural products may act at a quantum level. Collections of organisms allow for the concept of ultra-reductionism (Descartes) to be explored. The example of polyketides can be used to explain bioengineering and the manipulation of systems to create new products. The concept of silenced genes, metagenomics and their incorporation and expression in suitable hosts, increases the numbers of possible natural products. The BioInternet of Things (BioIoT) has significant bioengineering potential. Communication within and between biological systems is important if this potential is to be realised. Homologous and heterologous gene expression are possible and are a valuable source of specific natural products. The development of systems biology is essential to support the concept of bioengineering.