Gene regulation and the epigenome 

Complex answer, but during development you get spacio-temporal expression cascades of proteins like wnt, nog, flag ect. that set up anterior-posterior and dorso-ventral gradients (french flag hypothesis of development) which alter expression of the genes so that the right gene is expressed at the right time and in the right place. These CG reading system help to accentuate the binary switch of feedback loops form positive to negative and vise versa. The egg itself already has gradients and pattern elements (cytoplasmic centers) to direct development

i can spot your evil ugly face tho Hitler

@@braintree7502 That's Guy Fawkes, dude.