I'm a junior physics major at a small college and I've read about the importance of CMB anisotropies in popular literature. One thing has bugged me: as its wavelength stretched, at some point the CMB must have been at the right temperature for a measurable portion to be absorbed by interstellar hydrogen. I know there isn't much interstellar hydrogen, but then the anisotropies are extemely small. Is the absorption by interstellar matter negligible? If not, how would an astronomer separate the anisotropies caused by fluctuations in primordial universe from anisotropies caused (much later) by interstellar matter?
You are right that there will be appreciable absorption from interstellar hydrogen at certain wavelengths. However, these wavelengths do not correspond to those used for studying the CMB. As you know, the peak of the CMB is at a wavelength a little less than a millimeter, while interstellar absorption from neutral hydrogen in our galaxy occurs at 21 cm (and longer wavelengths for redshifted hydrogen). Most studies of the CMB are at low wavelengths where there is no absorption from neutral hydrogen.
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