When you get to the point of asking how does DNA do things like encode instincts or morphological development things get really strange.

Example 1. A common thing for a 5 yr old is to be afraid of the "monster under his bed". Obviously it makes sense from an evolutionary perspective....however how do these collective memories pass down at the genetic level. Sure, I understand the explanation that "those that had this fear out-competed those that didn't"....but thats not exactly what I'm asking...I'm saying what is the mechanism that some amino acid patterns can then create thoughts about a monster under a childs bed.

Example 2. Even more puzzling is morphological development. How does an ear know to grow in an ear shape? Obviously at some point in the stem-cell reproduction of a nascent cell, they start to organize themselves somehow into "ear shape". How is this encoded in DNA? How does the arrangement of amino acids encode that these cells should organize themselves into an ear shape, and these others into nose shape.