  Following a self-contained review of the basics of the theory of cosmological
perturbations, we discuss why the conclusions reached in the recent paper by
Kaloper et al are too pessimistic estimates of the amplitude of possible
imprints of trans-Planckian (string) physics on the spectrum of cosmic
microwave anisotropies in an inflationary Universe. It is shown that the likely
origin of large trans-Planckian effects on late time cosmological fluctuations
comes from nonadiabatic evolution of the state of fluctuations while the
wavelength is smaller than the Planck (string) scale, resulting in an excited
state at the time that the wavelength crosses the Hubble radius during
inflation.
