If the universe started out isotropic and homogenous and of all fundamental particles then how could there now be any concentration of energy anywhere? If you say that nothing is really homogenous because of the grainy quantum nature then what about when it was all compressed in one Planck volume? Is the universe allowed to do this because it emerged hot, essentially getting all its heat from nowhere? All that heat dissipated into the CBR. But nonetheless some things are hotter than others and we can do meaningful work now while in the beginning everything was the same state, temperature and particles.
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3Related: http://physics.stackexchange.com/q/14004/2451 , http://physics.stackexchange.com/q/21096/2451 , http://physics.stackexchange.com/q/18702/2451 and links therein. – Qmechanic Oct 16 '15 at 05:48
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1Lack of thermal equilibrium in the early universe is one of the Sakharaov conditions for baryogenesis. – rob Oct 16 '15 at 07:36
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1In a word, gravity. Penrose has nice discussions of this. – innisfree Oct 16 '15 at 08:38