Guidedogsaint is correct. "Natura philosophy" was used to describe what we now call "science". The change in the language was happening during the time period in which Sherlock Holmes was written and set, and therefore it's possible to argue that Watson is using an old-fashioned term which fits with his character... I wonder if Holmes might use the modern term as his character is more progressive? I'm not sure about the answer but it's worth looking out for

I think it means delicate scientific equipment. In Holmes's time, science was also referred to a philosophy I think.