One generally speaks of two sets of distinguishable molecules (say, rad and green ones) separated by a membrane. One removes the membrane, they get all mixed up, and the result is more disordered than when they were separated.
What about the case where the red molecules are oxygen and the green ones are hydrogen and taking away the membrane causes a spark? After the smoke clears away (and a lot of energy with it), the result is more ordered, it seems to me. In which case, the disorder idea does not work. Rather, one must speak in terms of diffusion of energy, which works very well.
One chemist, Frank Lambert, has taken on this subject on the Internet.
Any comments?