AFAIK the only output of DNA transcription are proteins but how are things like skeletal structure encoded? I mean things that are not functional specialization like the shape of my nose or the size of my forehead or the length of my legs.
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Have you ever played with a cellular automaton like Conway’s Game of Life? Each individual cell works on its own and doesn’t really know where it is. Rather they run on rules like “if you see this chemical and this chemical then you are now a bone cell so make this chemical.” During early fetal development cells figure out where they are and make an approximately human-shaped blob; then they basically grow according to their cell type and the cells directly touching them in the blob.
Getting this right is really hard which is why there are so few basic body plans for animals. They all have four limbs and a head and possibly a tail – because evolution figured that out and stuck to it. All the changes, like tail/no tail, or front legs/arms, are just minor variations on this. Instead of coming up with new signals to make arms instead of front legs, evolution found it easier to just convert the front legs into arms, or make the tail convert into something else or not grow.
Making the legs longer is relatively easy as you just make the chemical that makes legs grow last a little longer so they grow more, but adding another leg is difficult because it fundamentally changes how the legs figure out that they’re legs. It’s probably more likely that humans evolve a tail that works a little bit like a leg, than that they evolve a third actual leg.
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