Are there boundaries in modern science?

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People, let's get something straight here: I have absolutely nothing against speculation. In fact, I encourage it, and heartily take part it in it myself.

I also have no objection to science's speculative nature (if reality was obvious to us, we'd have no need of science).

However, while learning (=philosophy) may have no boundaries, science (which is just one of many branches of philosophy) does - otherwise, it wouldn't be a branch, but just another name for "philosophy". Science is limited that which is repeatable in experimentation, and science is limited to "how", "what", "which", "where", and "when" questions, it cannot ask "why" questions.

These are not just my opinion, they are what I've gathered from studying the Scientific Method (philosophy of science). I don't see why it should trouble people on the Philosophy Forum that science has boundaries. The real question is: does Philosophy have boundaries?