The leading theory that I know of says that at the beginning of the expansion of the universe fluctuations in the fields that make up the universe were magnified. The expansion took those ripples and in effect moved what would become matter so that there were pockets of “empty” space and pockets of space with more densely packed particles.
As for objects that are complex that would seem to violate entropy, they don’t. In the case of living things, they invest energy to produce order. In some sense entropy is a measure of the available energy in a system. When livings things use energy to create complex things, the main source of increasing entropy is lost heat. That heat is in a form no longer usable to produce more complex things and entropy increases.
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