  Recent observations of the transiting super-Earth GJ 1214b reveal that its
atmosphere may be hydrogen-rich or water-rich in nature, with clouds or hazes
potentially affecting its transmission spectrum in the optical and
very-near-IR. Here we further examine the possibility that GJ 1214b does indeed
possess a hydrogen-dominated atmosphere, which is the hypothesis that is
favored by models of the bulk composition of the planet. We study the effects
of non-equilibrium chemistry (photochemistry, thermal chemistry, and mixing) on
the planet's transmission spectrum. We furthermore examine the possibility that
clouds could play a significant role in attenuating GJ 1214b's transmission
spectrum at short wavelengths. We find that non-equilibrium chemistry can have
a large effect on the overall chemical composition of GJ 1214b's atmosphere,
however these changes mostly take place above the height in the atmosphere that
is probed by transmission spectroscopy. The effects of non-equilibrium
chemistry on GJ 1214b's transmission spectrum are therefore minimal, with the
largest effects taking place if the planet's atmosphere has super-solar
metallicity and a low rate of vertical mixing. Interestingly, we find that the
best fit to the observations of GJ 1214b's atmosphere in transmission occur if
the planet's atmosphere is deficient in CH4, and possesses a cloud layer at a
pressure of ~200 mbar. This is consistent with a picture of efficient methane
photolysis, accompanied by formation of organic haze that obscures the lower
atmosphere of GJ 1214b at optical wavelengths. However, for methane to be
absent from GJ 1214b's transmission spectrum, UV photolysis of this molecule
must be efficient at pressures of greater than ~1 mbar, whereas we find that
methane only photolyzes to pressures less than 0.1 mbar, even under the most
optimistic assumptions. (Abridged)
