It's not just "muddy", it's thoroughly inconsistent and impenetrable (which probably has a lot to do with why there is so little engagement here). You say "TL;DR I claim that modern science is synonymous with open source software" which is radically different from your "slightly more precise" statement.

I won't put any more time into this ... good luck in figuring out what it is you really want to claim and presenting a coherent and cogent argument for it.