Explaining the world is a major activity of all pattern finders.  It helped us in the past to be better hunter-gathers. It helps us today to keep our technological-based civilization working.

Hunting, gathering and most day-to-day tasks are described by what might be called Theories of the Middle. This is the realm of engineering and mechanics. Theories of the Middle might be complex, but they can typically be explained by analogies and illustrations from everyday life.

Johnson concentrates on Theories of the Large and Theories of the Small.  

Theories of the Large, like Einstein's Special Theory of Relativity, or Newton's Laws of Gravity explain how our universe started, what it contains, where it is going.

Theories of the Small explain the largely hidden universe of molecules, atoms, electrons and sub-atomic particles  - plus the forces that control them.

These theories are at the extremes of scientific inquiry. They look to quantum theory (as yet in a cross-eyed manner) and tend toward the weird and inherently incomprehensible.

When Johnson wonders whether we are creating or finding order with our theories and if some theories have aspects of mythology, this is the science he is talking about.