No, it's not literally what the entire article is about. The article is about how some modern medicine has its origins in supersition, but "has its origins in"

No, it's not literally what the entire article is about. The article is about how some modern medicine has its origins in supersition, but "has its origins in" and "is based on" are completely different things. Compare: "Modern chemistry has its origins in alchemy" (true); "Modern chemistry is based on alchemy" (false).