The certainty that natural phenomena and processes could be represented in a physical space ruled by Euclidean geometry was a fundamental epistemological assumption of theoretical creation in classical science. The possibility of a mathematical analysis of the continuum ensured an intuitive, pictorial description of mobile trajectories as studied in dynamics, as well as a precise determination of the effects generated within causal relations. These convictions and assumptions had to be reviewed when the Plank action quantum forced the development of a (...) new physics of atomic systems. Consequences, nevertheless, transcended the scope of Physics and extended to all regions of natural science, including Biology, which had to be built under the conceptual coverage of the nascent mechanics. The present work is a reflection on the philosophical problems posed by the encounter of physics of atoms and chemistry of molecules. (shrink)