Just to save the trouble - I am not asking for general information on how DNA codes for proteins and definitely not how Hox genes work. I have a very good understanding of the evolutionary process and a better than average (for a layman) understanding of how DNA works.
I understand the process of Amino Acid being coded for by specific DNA nucleotides and the chains of Amino Acid forming specific proteins - however, I am unable to find information on the topic of how actual shape is determined / coded for by DNA (again, not Hox genes and body segments).
Here is a specific example of what I am asking about (but the answer can be generalized):
It's generally held that eyes evolved (in very basic terms) from a layer of photosensitive cells on the skin, which slowly formed into a cup that could detect direction, then the cup eventually closing in to form a smaller hole, and then a lens, and so on.
So my question, based on that example, is how does DNA (or a change in DNA) code for "create an indentation on the surface of the skin at this location". And then, "Deepen the indentation repeatedly until it is a cup". And so on.
Hopefully the question is clearly stated and not too long - I welcome any suggestions on how to clarify the question.