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I have seen many patents related to use of herbs in medicines, like some homemade remedy for cough syrup etc. A large number of such remedies are already listed in many ancient medical books, one being Ayurveda in India, dating back to 300 BC.

Clearly, the book and the remedies are the part of archaeological heritage of a country and comes under public domain. So, shouldn't the patent for such remedy be invalidated? If yes, then how one can challenge such issued patent?

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In theory anything "published" anywhere at anytime in the past is fair game as prior art. The particular issue you bring up is called "Traditional Knowledge and Intellectual Property" and is a current, important topic in the IP community. This is a link to a discussion at WIPO on it here

Patents that might fall under this category may be very deserved due to a specific active ingredient being identified and purified. If you think a particular patent is not properly granted, patents are subject to reexamination and other USPTO procedures that a third party can initiate. This can be expensive and might be done defensively if and when a particular patent was asserted.

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