Have We Detected Patchy Reionization in Quasar Spectra?

The Lyman-alpha forest at z >~ 5.5 shows strong scatter in the mean transmission even when smoothed over very large spatial scales, >~ 50 Mpc/h. 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, with a uniform ionizing background, using analytic arguments and simulations. This scatter alone is comparable to that observed. It rises steeply with redshift and is of order unity by z ~ 6, even on ~ 50 Mpc/h scales. This arises because: i) at z ~ 6, transmission spectra, which are sensitive mainly to rare voids, are highly biased (with a linear bias factor b >~ 4-5) tracers of underlying density fluctuations, and ii) projected power from small-scale transverse modes is aliased to long wavelength line-of-sight modes. Inferring patchy reionization from quasar spectra is therefore subtle and requires much more detailed modeling. Similarly, we expect order unity transmission fluctuations in the z ~ 3 HeII Lyman-alpha forest from density fluctuations alone, on the scales over which these measurements are typically made.