You started out by saying that there is no scientific proof of, to pick one, beauty. I agree completely but this is because beauty is a projection of a human emotion onto an external object. There is a human emotion, the sense of beauty, which is some kind of chemical and electrical effect in the brain. What we are detecting is a property of the human brain, not a property of the object. If many people agree that a given thing is beautiful this indicates that their brains are wired up more or less the same way, not that there is something special about that object.
People complain that science takes the wonder or the mystery or even the fun out of things.
I say that science doesn't change the character of things, it merely changes what we know about them. If we once thought that something was spiritual and science says it really isn't, that doesn't make the thing any less spiritual than it was, it just means that we were in error before and now we know better. The spirit Boreas used to push the winds around. At least you are spared the futility of trying to placate the spirit. In my mind, the new knowledge which science has given us makes things seem even more wonderful than they were before.