I am reading Mariam Thalos' book Without Hierarchy (Oxford, 2013). Patterns in nature are seen on large spatial and temporal scales and on small spatial and temporal scales. Life and intelligence are seen to be present at large scales. An electron is not alive or intelligent. Science (even physics) is not just about the smallest of things. PV=NkT is a useful description of behavior at a large scale. The shape of V doesn't matter. Many different experimental setups might yield exactly the same measurements.