The Gunn-Peterson effect, absorption of Ly alpha photons by a homogeneous component of the intergalactic medium (IGM), potentially provides a test of Big Bang Nucleosynthesis (BBN). With a lower limit on the UV radiation field estimated from the contribution due to QSOs, a measurement of the Ly alpha opacity of the intergalactic medium would permit the derivation of a lower bound to the baryonic density of the universe. The effect, however, has continually eluded a convincing detection, both in H I and He II, despite extensive searches. Recent cosmological hydrodynamical simulations of structure formation in the intergalactic medium suggest an explanation for its absence. In a Cold Dark Matter dominated cosmology, the fragmentation of the baryons is nearly complete, leaving a negligible remnant to comprise a smoothly distributed component. The fragmentation extends even into regions that are underdense, where it gives rise to most of the optically thin H I systems and nearly all of the He II systems, both thin and saturated. The result is a Ly alpha opacity from a smooth IGM that is suppressed by over two orders of magnitude from the BBN value.