Our cognitive ability to interpret the world around us is largely based on metaphor and metonymy. Both of them let us see relations between unknown and known, remote and near, invisible and visible, based essentially on similarity and contiguity between concepts. The atomists created such a similarity or analogy between visible Greek alphabetic script and the invisible world of atoms. Contemporaneous biologists continue to use this model of thinking in molecular biology. By various examples – from biblical interpretation to the world of science and technology – the pervasiveness of such models of thinking (and partially their time-bound character) is shown. In the past, a big problem was European mainstream thinking, insisting on relations between words instead of concepts in the case of metaphor.