Medicine is any substance that has a demonstrable healthcare effect (demonstrated through double blind tests and not some rando's anecdote). That includes natural substances.
To put it another way, medicine and natural substances are not two mutually exclusive (i.e. disjoint) sets, as you and/or your doctor friend appear to be implying.
Thanks for clarifying. Although I don't agree with your doctor friend from an ethical standpoint, the point about natural products not being patentable is an interesting one and hadn't occurred to me before.