@Landy then why bring up hypotheses? Evolution is a theory.
I don't know - you brought hypothesis up. You just called it 'building a theory'.
The upshot is that yes, there are things science doesn't yet know. Whether we're talking about this particular bee in your bonnet or one of the many other areas of research. There will be things science doesn't fully understand for a long long time yet.
What you can't do. What is totally outside the realms of scientifc endeavour is attribute anything you don't understand to a God. So yes, scientists can and must close their minds to the existence of a god.
Whether God exists or not is (and you have alluded to this in that Berkeley snippit but I don't think you grasped its meaning) totally and absolutely irrelevant when it comes to science. Scientific explanation always has to stand on its own two feet and not accept that tinkering from God had any influence on natural phenonenom.
And so far they're doing a pretty good job.