The problem with the microwaves Penzias and Wilson discovered was that they were uniform in all directions. This implied that the distribution of matter and energy in the Big Bang was uniform. Since the universe today is definitely lumpy (there are loads of galaxies with vast gaps between them), something was up - the Big Bang should also have been lumpy! In 1992, the so-called Cosmic Microwave Background was studied in detail from a satellite called COBE. It finally found variation in the radiation, as shown below:
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