It seems that in the 17th century the term philosophy encompassed the activities that we now call science, mainly physics, chemistry, geology, astronomy, biology and medicine. That is why the Philosophical Transactions, which has been in continuous publication since 1665, was not named the Scientific Transactions or something like that.
Here is another example along these lines. In the title of a letter that was published in the Philosophical Transactions in 1670, Robert Boyle was introduced as "That Indefatigable Benefactour to Philosophy, the Honourable Robert Boyle..."
Naturally, scientists of the 1600s were philosophers. Another title from 1670 reads: "An Experiment Concerning the Progress of Artificial Conglaciation, and the Remarkable Accidents, therein Observed by the Florentin Philosophers..."
The association of the term philosophy with the physical and biological sciences continued well into the 19th century. In last Friday's Science in an article about Joseph Hooker, Endersby* wrote:
..."philosophical" was a word with many complex meanings, starting with its derivation from the term "natural philosophy," which encompassed branches of science that sought to understand and explain the causes of natural phenomena. By contrast, natural history was merely descriptive: cataloging and naming, but not explaining. Natural philosophy was the forerunner of the elite sciences, especially physics, which provided the model for those naturalists who wished and worked to raise their disciplines to comparable status.I don't know when science displaced philosophy and became the preferred word to describe the study of nature in the general sense.
*Jim Endersby. 2009. Lumpers and Splitters: Darwin, Hooker, and the Search for Order. Science 326:1496-1499. Abstract