I agreed with your comment above, but this comment here has some problems with it.
Pythagoras' faith pretty much wields no influence on mathematicians or any other kind of scientist. I don't know why you think this. That might have been true in ancient Greece, but it is certainly not true now.
Now you make a mistake fundamentally in the claim that "I don't see any reason to believe that math is intrinsic in the universe though, the quantities it measures obviously are but the measurements themselves are not." Mathematics needs not measure any quantities. Nor does it have to even have quantities. Measurements are things in the world which scientists and engineers make to tell them about the world. Many mathematicians do not think that their work even corresponds with the world at all, and hence cannot be measured. Einstein is famous for saying:
"As far as the laws of mathematics refer to reality, they are not certain; and as far as they are certain, they do not refer to reality."
On the other hand, some mathematicians have postulated that the subject of the work exists in some other sense. This is the concept of Platonism. It holds that sets, functions, numbers, and other algebraic and topological objects actually do hold some external existence in some sense. Theorems are discovered, not invented, in this view. I would suggest perusing the SEP articles on this subject, as I'm sure there are several.
And lastly I just want to ask you what the heck you mean by having a "prime number equation." I don't know what that means, as there is no function which always yields prime numbers, and there is definitely no such equation in general. Just yesterday (I am a soon-to-be algebraist) I was working with a field in which there were numbers which were neither prime nor a product of irreducibles. In a Unique Factorization Domain, all irreducibles are primes, so colloquially, I was working with a ring which has numbers which are neither prime nor composite (but of course this ring is not a Unique Factorization Domain, I am just trying to put this into a context you will understand) . Such a field surely will never have such an equation - the notion doesn't even make sense.