These “primordial” density fluctuations were created in the very early universe when the universe went through a phase of accelerating expansion called inflation. This made the universe very uniform, but at the same time it stretched quantum fluctuations, which are usually only important on tiny length scales, and made them very large. We can calculate the statistical properties of these fluctuations, and they agree remarkably well with the way galaxies are distributed in the universe. In fact, this is the reason we believe that inflation happened.
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