Since the dolphin has evolved flippers would you therefore say that “natural selection operates on flippers?”

Yes - provided we were talking about a process that included dolphin evolution. The process of natural selection in general does not necessarily involve prediction - but from the beginning I have been discussing natural selection in evolution - which does involve prediction.

Regarding Popper, I won't say much - since I would be preaching to the choir on this blog. I recommend you start by going and reading the bit beginning: "Previously, the most popular philosophy of science was probably Karl Popper's falsificationism - this is the old philosophy that the Bayesian revolution is currently dethroning." on this page.