Chapter 3: Handy Genes

Chapter 3 seems to me as if the scientists from the movie, Gattaca, decided to stop wringing out perfect individuals, but began playing with embryos just to see the outcomes and to harvest the mutants.
This chapter brought up a topic that intrigued me back then, the process of changing genes to change bodily features. It's too bad that my naive knowledge back then could not ameliorate the process of comprehending this complex series of explanations (Mr. Shubin, I appreciate your effort in explaining these interesting events). However, my interest was still ranging in the moderate-to-high levels. It started out moderately until i read the part when he stated that there are three dimensions in limbs and how altering the DNA could affect any of these three dimensions. Basically, the possibilities of the bone dimensions are endless!
Just like Gattaca and The Island, there are always morbid scenes, and apparently, there was an "era of slice and dice" (Shubin 49). Thinking about the occasional slicing and dicing that would occur every second in every other lab, I started wondering what my life would have been like if i were to be a chicken the next morning. (fml, right?) But these images made me also think, "With all these scientists illusioned into thinking that they're God, what would our future look like?"
Aside from my ranting, Shubin illuminated to me the fundamental fact that DNA really is behind everything. Genetics turns out to be way more perplexing as I originally thought it to be in 9th grade Biology when Mr. Shubin mentions that there appear mirror-duplicates of limbs. Gross. Any mishap, or wrong timing, or missing activation will lead to mutation. What the heck.
A mouse protein could be used to activate Sonic Hedgehog in Sharks. HUH?

So sonic hedgehog is behind the thumb-and-pinky anatomy?
How do embryos change genes to gain limbs 300 million years later if no scientists were alive to experiment with them? (I'm also assuming that the mutated ones become doomed by Social Darwinism's "survival of the fittest")