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The second law of thermodynamics states that the change in entropy of an isolated system can never be negative (`Delta S geq 0` ). In the given scenario, the system would be the room, including the person inside the room (and other factors..but let's focus on this, at the very least). The room became organized because the person organized it. Obviously, the entropy of the room decreased (since it became less chaotic). However, the room is NOT the entire system. Somewhere within the system, there must have been an increase in entropy -- and that part of the system would be the person who organized the room. The person will have a positive entropy, with magnitude higher than the organization of the room, to make the cleaning of the room possible. Where does this increase in entropy come from? When the person cleaned the room, he used up energy -- he produced sweat and heat (heat is the most disordered form of energy!!). Aside from this, the energy came from food that has been digested. Digestion of food is breaking down of food to its smaller, more useful components -- this is an increase in entropy. (Of course, there's a complicated machinery behind digestion, but the sum of all process would be favored by either a decrease in enthalpy or an increase in entropy). What violates the 2nd Law is if the room became organized WITHOUT anyone organizing it! This would be a negative total entropy -- which is not possible; and indeed, we don't see rooms becoming clean spontaneously!
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