Awesome!
Rubiks Cube As Energy Source
Nice story, great read. I'm usually not a fan of such "long" stories on the internet but you grabbed my attention with a catchy conversation-style opening.
But still, I doubt this disproves the second law of thermodynamics ;)

I do need to fix that loophole about why no article on a counterexample to thermodynamics has appeared yet.
The picture in that article is remniscant of Escher's waterfall.
Since I too get easily bored of long stories, I decided I couldn't waste time with imagery. The first 3 lines were supposed to be between two colleagues, leading into a dialogue about how they could produce brainwash waves. Then it became scientist and child. :\

At the risk of being over-serious, the two things that stop this being a true reduction of entropy are the need to observe the cube and the need to turn the squares. Obviously with a real cube, the latter takes macroscopic energy, while the amount of entropy involved is tiny.
You could replace the cube by a "qube" which I define this as some sort of nanoscopic system with information that you define to represent the information in a Rubik's cube.
It doesn't really have to be that similar to demonstrate the point. Eg suppose you have 100 molecules in two boxes with a narrow pipe between them. Consider this qube to be "solved" if all the molecules are in the same box. Now one possibility is to just sit there and watch the molecules until random chance makes them all happen to be in the same box. Slam the door shut in the pipe in the middle and announce that you have both reversed entropy and produced a perpetual motion machine (because the gas in one box can be used as a source of energy). If the aeons of waiting is too much, you could put a small switchable door in the tube in the middle, and open it whenever a molecule is about to go left to right, but close it whenever a molecule is about to go right to left. (This latter one is rather closer to solving a macroscopic cube).
Where is the flaw? The answer is that when you look at this very carefully, it turns out the minimum amount of energy needed to observe the molecules is bigger than the amount of energy stored once all the molecules are on one side, and that the need for this energy also outweighs the apparent reduction in entropy.
I am confident that any experiment similar to this, where an apparent reduction of entropy is achieved will similarly require enough energy to cancel out any gains (regrettably including any Rubik's cube solvers).

I may have gotten a bit of terminology mixed up...
When I said entropy reversal, I meant generation of new energy. The energy needed to rotate the cube would still be around in the form of heat and sound. But in addition, electrical energy would be created. So although the act of changing information to energy doesnt reverse the entropy, I think that the act of just creating more information (adding disorder to the cube) would in a way, reverse it.
The cube in its original form would be chargeless, but it has potential potential potential energy. Then, when its mixed up, information is created and it has potential potential energy. When it gets solved, the information is converted into electricity so it becomes just potential energy (and new potential potential potential energy again) (imagine harvesting energy from a ball falling and being able to move it back up without using energy). Hook it up to a light bulb, it becomes light and heat energy.
About the qube -- I know that there are biological bilunar valves that allow our blood to flow in only one direction, that way its guaranteed oxygen gets to extremities and goes back to the lungs to recieve more oxygen. Though I'm not totally certain of how they work, I also know that they have mechanical pnumatic valves that allow air to flow in only one direction. So what prevents a quantum valve from being created to allow molecules to flow in only one direction?

In a prior life, I was that scientist, and me and my daughter, (now 7), took a space ship into deep space to visit a black hole. I had her throw the disordered cube into the black hole. As we left we could see it spiralling slowly down. We returned to our home and the next day she went to school. She mentioned our trip to the teacher who immediately sent her to the office, suggesting to the principal that someone notify the authorties of our adventure. I arrived at the office and as I was standing beside my daughter, our cube dropped out of the ceiling and hit the principal in the head. It was solved.

Well, if such a thing did exist, it would be possible to attach it between two vessels with gas in them and produce a source of energy (after a difference of pressure had been created. So the law of conservation of energy implies it cannot exist. A particular device that is meant to act as such a valve must therefore use energy of some sort (the same applies to any macroscopic valve that could be used to create a source of energy in a similar way). There are reasons why the US Patent Office no longer accepts submissions that claim to be perpetual motion machines.

I still don't like how we just assume that the laws of Thermodynamics are true. Same for the 5 postulates of geometry although those are a bit more intuitive. I guess the 3 laws are also intuitive, but since quantum physics, nothing has really been certain (pun sort of intended). We'd never have believed harnessing lightning and fire were possible a few hundred years ago, but now we do. And flying. And space travel. So, maybe energy creation is coming in the next few years based on some whack property of quantum mechanics. Is it not written, "The only reason there are laws is so we think before we break them"? (Thanks Elroch, T. Pratchett is now one of my favorite authors!)
17000mph: Black holes are much smarter than we give them credit for. I just wish they would let us see them, but they always pull back any light holding a shred of their image. They're shy like that. But they can always be relied upon to return lost items to the proper owner.

I don't think we just assume the laws of thermodynamics are true. They have been empirically shown to be true by evidence. They are consistent with observations.
A note about the term law as used in this case: it is merely a description of statistical averages, not an absolute rule existing over and above nature.
I could imagine that there could be localized non causal quantum fluctuations that taken by themselves seem to violate the law of conservation of matter and energy. But over a sufficient amount of space/nothingness/vacuum, these random fluctuations tend to average out and the averages are what the laws describe.
I think that many words seem to be saying more than they are because of the vestiges of Platonic philosophy still lurking in our common use of language.

Yes, Timotheous has put it very well. All of the laws of quantum mechanics and thermodynamics are essentially statistical statements about observations, and are very well verified by experiments.
With any specific experimental setup, it can be possible to show that the general laws of thermodynamics are not broken. One example is the Maxwell's demon thought experiment, where you can do a detailed analysis using quantum mechanics. From this you can show that it is necessary to use more energy observing the molecules (in order to shut the door at the right time) than you get once you have waited for the molecules to all move to one side. And I am sure similar detailed analysis can be done in many hypothetical machines to reverse the arrow of entropy, produce an infinite source of energy, etc.
However, it is certainly true that a radical change in knowledge could make huge differences to technology, but I don't think things like the laws of thermodynamics are going to be among the things that are going to be usurped. These days it has become clear that thermodynamics is largely about information, and the mathematics of information is general enough to withstand even a refinement to the laws of physics.
I remember when I was at school I thought of a perpetual motion machine and for a while couldn't see what was wrong with it, and even believed it might work! Rather than tell you what I realised eventually, here's the machine for someone else to disprove: You have a completely isolated vessel with some water in the bottom and some air at the top. In the vessel is a capilliary tube which is short enough to draw water up its entire height. At the top it is bent over and the water drips from the open end back into the water below. There is a little paddle wheel driven by the drips.
Seems pretty obvious now why this doesn't work. Is it as obvious to everyone else?

I think its because a capillary tube needs a vacuum on one side to siphon water up and that means that that end must be closed so water cant drip back out?
Although in practice there probably won't ever exist a perpetual motion device, or at least for a long time, there still exist a few on paper. For example, 9 is heavier than 6, so the wheel will turn counterclockwise with accelerating pace.
We could also always just make a new universe with different physics (enjoy the apple pie) and have a continual nuclear reactor (Source: The Gods Themselves - Issac Asimov). In that universe, some isotope of tungsten is radioactive and decays into plutonium, so we can constantly trade plutonium for tungsten and have each decay into the other giving (theoretically) infinite energy.
Afterthought: Is there a way to affect particles without observing them? Even if we don't observe photons, if we put a mirror before a pair of slits, the interference pattern should still appear. So maybe if we didn't have to waste our energy observing particles, we could somehow... do something to them to... I didn't think it through much. Something related to the Elitzur-Vaidman Bomb tester. I think it showed its possible to affect photons without directly observing them, or test bombs without directly testing them?
I never really trusted statistics... another idea at a perpetual energy source is have someone like Edward Thorp bet on the percent change of energy in a system within the next minute. If he bets on a percent increase, heat up the system to add energy, increasing the flat increase, and if not, coll it down. Overall, energy will be gained. I know that thermodynamics isn't that simple, but that's sort of why I don't trust statistical averages. Everything should be explainable by some equation no matter how complicated (coin toss in terms of air friction, angular release, velocity, pint of release, etc.), and quantum thermo violates all of it. Unless deep down in the multidimensional quantum fabric of space time, down to strings and further, this universe really is just a multidimensional Conway game of life.

Actually capilliary tubes draw liquid up to a height which gets larger the narrow they are, and don't need a vacuum. Another explanation is needed.
I like the 9-6 perpetual motion machine! It makes me think of a rain powered device with little bowls on the arms, pointing upward at one side, so they fill up in the rain and turn the wheel. Or a light powered device where you have vanes that are reflective on one side, so the pressure of light turns the wheel (this one is a laboratory demo I have seen - the wheel is very light and in a vacuum. If you don't quite have a vacuum, it actually works better, but by the light heating the air above the vanes).
You don't like statistics? I sympathise, as I used to have an antipathy towards it. Einstein would surely sympathise as well, but the best he could do in his attempts to show physics was really deterministic was to show that "spooky action at a distance" exists rather than determinism. If you want to get away from statistics, you need to move to another universe. [CORRECTION: the universality of mathematics (including statistics) means that moving to another universe is not going to work]
There is a bit of a difference between the role of statistics in thermodynamics and in quantum mechanics. In quantum mechanics the statistical part is absolutely fundamental - there is a point where you can only give probabilities of things happening rather than being certain about them. In classical thermodynamics (say dealing with a gas that is made up of idealised snooker balls bouncing around) you get a high level statistical theory as a result of low level deterministic things. So if you put a load of idealised snooker balls in an idealised box and let them bounce around you get the Maxwell–Boltzmann distribution of velocities. So you could say that the statistics here are not really fundamental. Of course in a real gas, the molecules are subject to quantum mechanics and have uncertain positions and momentum, so there is no deterministic view at the bottom. [It turns out you get the same distribution of velocities and many other things as if it was all classical].

If Penrose is correct that eventually as the universe finishes expanding, that black holes suck all of the entropy out of the universe, and then the universe collapses back towards a singularity in a highly ordered state to restart another BigBang, would that make the universe itself a perpetual motion machine?
I know ahead of time my understanding is so full of holes as to be a giant hole itself, but I had to ask.

It would appear so. Other people have pointed out the problem that this oscillatory model would require a period where entropy decreases, which is believed to be impossible. It is generally agreed now that Universe never will collapse. Penrose's (rather wacky) idea was that once the Universe died, any sense of scale would vanish and it would act as if it was very small without contracting, but this does seem like fantasy (and he is adamant that it is only an idea, not something he firmly believes). A problem I see with it is that the influence of massive particles never entirely goes away, as there is a sea of virtual particles in the vacuum. And regardless how dead the universe is, there is a probability of particles appearing if there is any energy left (a pile of photons near each other has a small probability of producing massive particles).
As some physicist said "the universe is the ultimate free lunch".
[EDIT: google tells me it was Alan Guth, inventor of the concept of inflation]
"Hey, check this out."
He nodded.
"A little over I think. Here, catch."
He decided that the metal cubes inside were too valuable to fall into the hands of the public. They would have to be supervised. Better to just sell plastic shells and host competitions for people to solve the cubes quickly with competition cubes having the metal part within them. Speedcubing. It had a nice ring to it. He removed the metal cube from the schematics and ran his computer to loop a hundred times. Machines stirred. Some created plastic. Others morphed plastic into pieces. Others were to put them together. Yet more labelled them with stickers. A very efficient assembly line. And the power for them was routed from the National Research Association building, a few miles away. Nobody seemed to notice a few mysterious wires taking energy from that building. In about an hour, 100 cubes, all exactly identical and already solved were deposited onto the metal slide and fell into a basket. He waited.
"The teacher looked at me strange after the principal told him to ignore everything I said about entropy."