This just sounds like one big confusion of the map for the territory. What you are describing are abstract concepts. The fact that concepts are not 'real' in

This just sounds like one big confusion of the map for the territory. What you are describing are abstract concepts. The fact that concepts are not 'real' in that they are not physical entities isn't much of an indictment of empiricism, nor does science claim to employ empiricism alone without any foundation of conceptual rationalism.