This is a question that keeps coming back to me.

Was it encoded in them in the beginning and then the knowledge passed down and refined throughout the generations?

At one point in time this ability to “read” the environment would have been widely known and in everyday use.

When did we lose the knowledge? And, more importantly, HOW?

There are still people who live by the land and the sky today but not in the “developed” countries. We call them UNEDUCATED !