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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 an example of what I am asking about - please note that this is just an example and I'm not specifically asking about how eyes evolved. I'm asking how changes in shape/size/structure of any part of a body happens from changes in DNA.

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), would be, how does DNA (or a change in DNA) code for "create an indentation on the surface of the skin at this location". Or, "Deepen the indentation repeatedly until it is a cup". And so on.

More basic examples are "make the hind legs on a mammal slightly longer" or "make the cranium on an ape slightly larger". The question is not dependent on body part or animal type but is specifically about how DNA, in general, operates.

Hopefully the question is clearly stated and not too long - I welcome any suggestions on how to clarify the question.

Thank you!

--added-- canadianer's comment gave excellent information regarding some general principles that are involved, but I'm still hoping to find (if it's possible) a more precise and detailed answer to this.

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    $\begingroup$ Are you asking how eye morphogenesis evolved or how it occurs in extant organisms? Either question is interesting, but the answers may take the form of a text book. You might start with this review for the latter question. $\endgroup$
    – canadianer
    Nov 29, 2018 at 22:11
  • $\begingroup$ @canadianer The eye was just an example out of many possible examples - I'm not specifically looking for information on eye development. Rather, my question is how DNA codes for shape and shape changes (as opposed to how it codes for amino acids which form proteins). Other examples include how the shape of an ear is encoded in DNA and expressed, how DNA codes for the formation of fingerprints (place a ridge here, no ridge here, etc), and any other non-body segmant "shape" on an organism. $\endgroup$
    – jdfinch3
    Nov 29, 2018 at 23:33
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    $\begingroup$ Each example you listed would be different in the specifics, obviously, and incredibly complex. I understand you want a general answer, in which case you might be interested in and simultaneously disappointed by this post. This is just one example of tissue patterning in the developing embryo. Perhaps not as exciting as eyes or ears, but the underlying mechanism is the same: patterning is controlled by gene expression, expression is controlled by transcription factors, and transcription factors can be influenced by intercellular signalling. $\endgroup$
    – canadianer
    Nov 29, 2018 at 23:59
  • $\begingroup$ You can check out this post for my recommendation on a developmental biology text book. $\endgroup$
    – canadianer
    Nov 30, 2018 at 0:05
  • $\begingroup$ Thank you @canadianer ! What I'm interested is the underlying mechanism and not how any one part of the body is formed. Your links are a great start as well as the keywords "patterning", "gene expression", "transcription factors", and "intercellular signalling" which will give me a place to start searching and reading. :) I'm not afraid to do the work and take the time to actually learn the information, I just had no idea where to start and everything I tried was a dead end. $\endgroup$
    – jdfinch3
    Nov 30, 2018 at 0:44

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