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I have not proved that the universe is, in fact, a digital computer and that it's capable of performing universal computation, but it's plausible that it is.
All physical systems can be thought of as registering and processing information, and how one wishes to define computation will determine your view of what computation consists of.
One of the things that I've been doing recently in my scientific research is to ask this question: Is the universe actually capable of performing things like digital computations?
There are considerable advantages to using many degrees of freedom to store information, stability and controllability being perhaps the most important.
Of course, not everybody's willing to go out and do the experiments, but for the people who are willing to go out and do that, - if the experiments don't work, then it means it's not science.
Indeed, as the above calculation indicates, to take full advantage of the memory space available, the ultimate laptop must turn all its matter into energy.
It's also a reasonable scientific program to look at the dynamics of the standard model and to try to prove from that dynamics that it is computationally capable.
The amount of information that can be stored by the ultimate laptop, 10 to the 31st bits, is much higher than the 10 to the 10th bits stored on current laptops.
If you take a more Darwinian point of view the dynamics of the universe are such that as the universe evolved in time, complex systems arose out of the natural dynamics of the universe.
In order to figure out how to make atoms compute, you have to learn how to speak their language and to understand how they process information under normal circumstances.
Quantum mechanics is weird. I don't understand it. Just live with it. You don't have to understand the nature of things in order to build cool devices.
Every physical system registers information, and just by evolving in time, by doing its thing, it changes that information, transforms that information, or, if you like, processes that information.
If you wanted to build the most powerful computer you could, you can't do better than including everything in the universe that's potentially available.