While thinking about how the universe works and questioning it I have come to the conclusion that it might not actually sense and cannot ever make sense. It all starts with the question "Why?", you can tell me how but then there is also a why for that how answer. "The apple falls because of gravity." makes sense... but what is gravity "Gravity is caused by the curvature of space, curved by matter/energy." but the further and further you go the more and more specific it becomes. Until you reach this question "Why not anything else?"... so now you could suggest a multiverse with every possible configuration and thats why its so specific... but then you have to ask "How does this multiverse work and why does it exist"... then "Why can't nothing exist everywhere and there not be a multiverse?" and finally a more abstract one "Why can't space be made of yarn and math not be able to exist in this universe?"... The only thing that would fundamentally make sense would be nothing at all, literally. If nothing existed it would make more sense. But then you have to ask "Why can't there be something"... Its a question with no answer that completely destroys the very goal of making sense of everything at a fundamental scale. So the only way out is to acknowledge that our universe isn't based on the question why and that asking for a sensible answer isn't the right question to ask in the first place. That everything in the biggest and smallest picture just doesn't make sense. Which is hard to grasp and I am unsure of it being the right conclusion to this simple question.
Here is a beautiful talk of Feynman about chains of why questions: https://www.youtube.com/watch?v=wMFPe-DwULM
In his case the chain ends in why magnetic and electric forces attract:
I can't explain that attraction in terms of anything else that's familiar to you. For example, if we said the magnets attract like rubber bands, I would be cheating you. Because they're not connected by rubber bands. I'd soon be in trouble. And secondly, if you were curious enough, you'd ask me why rubber bands tend to pull back together again, and I would end up explaining that in terms of electrical forces, which are the very things that I'm trying to use the rubber bands to explain. So I have cheated very badly, you see. So I am not going to be able to give you an answer to why magnets attract each other except to tell you that they do. And to tell you that that's one of the elements in the world – there are electrical forces, magnetic forces, gravitational forces, and others, and those are some of the parts. If you were a student, I could go further. I could tell you that the magnetic forces are related to the electrical forces very intimately, that the relationship between the gravity forces and electrical forces remains unknown, and so on. But I really can't do a good job, any job, of explaining magnetic force in terms of something else you're more familiar with, because I don't understand it in terms of anything else that you're more familiar with.
As for existence vs non-existence, according to eastern thought / religious philosophy, in particular buddhism and hinduism, the nature of nature (pun intended) transcends the human concepts of existence and non-existence.
For example in The Royal Seal of Mahamudra, an 18th century Tibetan manuscript:
The evident concept-free wisdom of mind essence does not fall into any extreme whatsoever, whether of existence or nonexistence, being or nonbeing, eternalism or nihilism. (p.263)
In shows up in western thought as well in the claim that the world is fundamentally unintelligible. For example as put by Chomsky:
Instead of trying to show that the world is intelligible to us, we recognized that it’s not intelligible to us. But we just say, ‘Well, you know, unfortunately that’s the way it works. I can’t understand it but that’s the way it works.’ And then the aim of science is reduced from trying to show that the world is intelligible to us, which it is not, to trying to show that there are theories of the world which are intelligible to us. That’s what science is: It’s the study of intelligible theories which give an explanation of some aspect of reality.
And by David Hume:
While Newton seemed to draw off the veil from some of the mysteries of nature, he shewed at the same time the imperfections of the mechanical philosophy; and thereby restored her ultimate secrets to that obscurity, in which they ever did and ever will remain.
So yeah, according to some, nature fundamentally transcends our capacity for making sense of it, and therefore you could say that it cannot make sense.
Basically what you're describing is the Munchhausen trilemma:
Knowledge is limited.