The integrated E region Pedersen conductivity can be an important parameter in determining whether the bottomside of the equatorial F layer will be stable against the Rayleigh-Taylor gravitational instability. The F layer is observed to become unstable when it rises to great heights after sunset. One effect of this height rise is to decrease the stabilizing influence of ion-neutral collisions at F region heights. It is shown here that the same eastward electric field that raises the F layer also decreases the Pedersen conductivity of the E region, which further destabilizes convective overturning. Because the conductivity of magnetic tubes that penetrate the main F layer is large compared to the E layer contribution, these effects are important only for the bottomside of the equatorial F layer.