Couple this with the fact that you can not create an algorithm that can arbitrarily compress any given input string, and then for any given computer you can find input strings that requires more state to represent than said computer can contain. Even if you allow for output over time, for any given such computer you can find an input string that is sufficiently incompressible that finding the shortest possible representation requires more intermediate state than the computer can contain, and that can be true even if a sufficiently large computer will make it possible to find patterns that makes the data very compressible.
In fact, that is what the article is pointing out: The universe may be a lot more regular than it appears, but it is possible that we may never be able to determine what the patterns are because it may be impossible to hold or compute over enough state to be able to determine what the patterns are in a way that lets us identify the patterns.
It is also possible that it turns out to be possible to easily create such a minimal program, but the article also points out that the vast majority of possible universes are incompressible.
For us to be able to compute the most compact description of our universe we 1) need to be in a compressible universe (or the description will subsume the totality of the universe itself), 2) need to be in one where the shortest possible description can be computed with the intermediate states possible to contain within the observable universe.
As the article points out, without additional knowledge of what type of universe we are in, the odds are firmly against us in that respect.
That would be what the scientific method is about.
Likewise, our brains are engines, converting energy from one form to another, and hence governed by thermodynamics. Again, that fact may or may not be useful for investigating properties of the brain we care about.
Our brains are also matter, meat, networks, made of atoms, and squishy. These are all facts, they may or may not be useful.
We use metaphors to help understand things we lack a literal explanation for, or the full explanation is complex and ongoing (neuroscience, biology, chemistry).
(And that's probably a very difficult question, considering you had to acquire the concept of symbolism, numbers and relationships)
This seems wrong to me. There exists no general algorithm to find the shortest program to compute arbitrary data, but we can surely find specific shortest programs to compute arbitrary data.