It seems like you’re thinking of entropy as a main driving force behind everything, where it’s not. Many processes create more complex things from less complex things, but ‘waste’ some energy in the process. It’s not a great analogy, but you could think of the universe as a block of marble. You can sculpt and carve it to form what you like, but every time you end up with less marble to work with.
The other thing is that there might be processes that can functionally “reverse entropy”. Our theories are limited to what we can observe, after all.
In the beginning there was nothing, not just any nothing, but every kind of nothing, infinite nothings. In this infinite nothing there was a perfect nothing. This perfect nothing was the holy ghost, ultimate perfection. In order for the holy ghost to be real, it needed to be percieved, so god came from this perfect nothing. Like two halves of a whole, together they gave birth to the universe. Perfect symmetry in the beginning that decays into perfect nothingness, but out of this perfect nothingness in the time in between the beginning and end, life creates god, god which arises out of chaos to seek perfection for the cycle to begin again.
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.
This is a great question and one part of the answer that is often overlooked is related to life on earth. First, let’s take a look at crystals. They form on their own some very well organized structures and in this way, form structures that have less entropy. Life has come about on earth in a very similar way. Life has found a way using DNA, amino acids, and other building blocks to _decrease_ entropy over time. This was very unlikely but it happened! It’s fun to think about this fortunate event.
Note that this answer just supplements the other great answers given.
Two things to explain:
1) Entropy is the measure of *usable* energy in a system. You can think of it like the energy contained in unspent fuel, or the heat difference that powers a thermocouple. It’s also irreversible–like you can put a hot brick and a cold brick against a cold brick, and the heat will flow from hot to cold until the heat balances out, but you can’t put two room-temperature bricks together and get one to steal all the heat from the other.
2) You can see structure in just about *any* flow of energy. Look at setting a pot of water on a stove: as the hotter water rises, cooler water sinks, and you end up with patterns of rising and falling currents. Patterns from chaos…but in the end, it’s just the water trying to balance hot and cold.
Now scale that up. As far as we can tell, the entire visible universe started off by expanding outward with so much heat and energy that even atoms didn’t exist. We’re in a universe-sized “pot of boiling water”: until all the energy balances out, we’re in for a *whole bunch* of patterns out of chaos.
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