We show that Bose-Einstein condensates in a honeycomb optical lattice are described by a nonlinear Dirac equation in the long wavelength, mean field limit. Unlike nonlinear Dirac equations posited by particle theorists, which are designed to preserve the principle of relativity, i.e., Poincaré covariance, the nonlinear Dirac equation for Bose-Einstein condensates breaks this symmetry. We present a rigorous derivation of the nonlinear Dirac equation from first principles. We provide a thorough discussion of all symmetries broken and maintained.