But there is a benefit to holding a presumption in favor of natural substances. More often than not, they have been around longer, so the adverse reactions, to the extent there are any, should be known.

Not really. Unless the negative effects are very dramatic it is unlikely that tradition will have identified the danger. Prior to the 20th century, we simply did not have the statistical tools to uncover subtle effects nor the degree of communication to tie together data from tens of thousands of users. For example, a hundred years ago we would have never noticed that St. John’s Wort causes Parkinson’s disease.

The real danger in the modern use of “natural” remedies is that we ignore a lot of the traditional safeguards that traditional healers had learned through trial and error experimentation. For example, the concentration of medically active ingredients can vary from individual plant to individual plant depending on that plants particular history. Herbilst knew to harvest plants only at certain times of the year , to only harvest plants that grew in the shade or in certain ranges of soil moisture or to not use plants that showed signs of insect damage. All these factors cause the plant to alter the concentrations of chemicals inside them. In members of the nightshade family, for example, insect damage causes the plant to dramatically increase it’s levels of tropane alkaloids to the extent that a traditional preparation using the same amount of plant will turn from a medicine to a poison.

Today, we just harvest plants willy-nilly, grind them up and cram them into to everything from nutritional supplement to shampoos even though we have no clue as to how active the chemicals in the plants are. For example, it was found that “all-natural” phytoestrogens in the lilacs added to shampoos and body washes was giving teenage boys breast. Nobody even check the preparation for safety. They just tossed the lilacs in for the sake of marketing.

You also have the problem that plants that are safe for one genetic group may be fatal for another. Just because some natives in the Amazon have used a plant safely doesn’t mean someone from Poland can. Every known drug will react with some variant of a gene in somebody to cause a fatal reaction. Plant based drugs are no different. Once you have hundreds of millions of people gobbling down random chemicals from plants you start talking about a lot of hurt people.