The distinction between organism and mechanism is often subtle or unclear and yet can prove to be fundamental to our understanding of the world. It has been tempting for many thinkers to seek to ‘understand’ all of reality through the lens of either the one or the other of these concepts rather than by giving both a place. This article sets out to argue that there is a substantial loss of understanding when either of these metaphors is absolutised to explain all causal processes and patterns in reality. Clarifying the distinction between the two may provide one more tool to grasp what is reductionist in many of the perspectives that have come to dominate public life and science today. This contention is tested on the quest for the design of self-replicating systems (i.e. synthetic organisms) in the nanotech industry. It is common that the concepts of organic functioning and mechanism are used imprecisely and in an overlapping way. This is also true of much scientific debate, especially in the fields of biology, micro-biology and nano-science. This imprecise use signals a reductionist tendency both in the way that the organic is perceived and in terms of the distinctive nature of mechanisms.