So, I am currently writing a story about an earth pony that dreams of creating artificial alicorns.

So, in my story, my main character would discover, via countless experiments, how different types of ponies are made. There is a magic protein that is not produced in earth ponies. However, unicorns and pegasi produce it in moderate amount. Alicorns have an abundance of this protein in their system.

*edit* (ran out of time to write the next part)

What causes a Unicorn or a Pegasus?
In the early embryonic stages, both wings and horn are present in the form of stubs. However, only one of these stubs actually form a limb, and the other recedes. The one that grows is the one that collects the magic protein, while starving the other limb.
Alicorns have an abundance of this protein, therefore they can have both organs form.

3269127

Seems reasonable to me. I'm not an expert, so am not in any way qualified to say what I'm about to say anyway, but I think that genes very often express proteins, and proteins do all kinds of work in the body. Some are structural, just holding stuff together, some direct cellular chemistry as enzymes, some function as hormones, etc.

It's semi-canon (Faust mentioned it, I think, but I don't think it shows up in the cartoon) that earth ponies do have magic, it just relates to growing things.

Which doesn't invalidate your idea at all -- whatever physical/chemical changes that make them different could still involve different proteins.

3269127 Have considered this?

Also, you could include cutting edge genetics in it:
http://www.extremetech.com/extreme/182119-first-living-thing-with-alien-dna-created-in-the-lab-we-are-now-officially-playing-god