Which chemical is responsible for making marker ink permanent?
The "permanence" is just a reference to it being waterproof. 


  In general, the ink comprises a main carrier solvent, a glyceride, a pyrrolidone, a resin and a colorant.


This is mostly the result of solubility. There are other markers sold on the market with labels such as "buff proof" (slang for removal proof), that are really just pens that use a different carrier solvent. With those, typically organic solvents would be the correct solvent for removal.