Have we detected patchy reionization in quasar spectra?

The Ly alpha forest at z greater than or similar to 5.5 shows strong scatter in the mean transmission even when smoothed over extremely large spatial scales, greater than or similar to 50 Mpc h(-1). This has been interpreted as a signature of strongly fluctuating radiation fields or patchy reionization. To test this claim, we calculate the scatter arising solely from density fluctuations, assuming a uniform ionizing background, via analytic arguments and simulations. This scatter alone is comparable to that observed. It rises steeply with redshift and is of order unity by, even on similar to 50 Mpc h(-1) scales. This arises z similar to 6 because (1) at, transmission spectra, which are sensitive mainly to rare voids, are highly biased ( with a linear z similar to 6 bias factor) tracers of underlying density fluctuations and (2) small-scale transverse modes are aliased to long- b >= 4 wavelength line-of-sight modes. Inferring patchy reionization from quasar spectra is therefore subtle and requires much more detailed modeling. Similarly, we expect density fluctuations alone to produce order unity transmission fluctuations in the He II Lya forest on the scales over which these measurements are typically made.