If this raises your hackles, let me tell you a story. When I was a kid, one of the home remedy ways to treat my cacti for insects was to exhale cigarette smoke under an inverted jar with the cactus under it, and let it sit for some time (not that I actually did this, but I read about it). Now this is a perfectly sensible method - tobacco smoke contains nicotine, which is a very effective broad spectrum insecticide. Indeed, it is thought that tobaccos (and related plants) make nicotine to kill their insect pests. On a larger scale, nicotine was a major agricultural pesticide from about 1945 through 1980. Nicotine is all natural and totally "organic", but it has a problem - to mammals it is acutely poisonous. The only reason cigarette smokers don't drop dead after a few puffs is because tobacco smoke contains only small amounts of nicotine. Though it was never banned in the U.S., it is no longer in use as a pesticide because of its toxicity.
Here is a (very) partial list of other 100% all natural chemicals that are very hazardous in some way, with their broad class of toxicity and natural source in parentheses: aflatoxin (carcinogen, fungus), ergot alkaloids (neurotoxin, fungus), ricin (cytotoxin, plant), aconitine (neurotoxin, plant), arecholine (neurotoxin, plant), atropine (neurotoxin, plant), scopolamine (neurotoxin, plant), amanitin (cytotoxin, fungus), coniine (neurotoxin, plant), delsoline (neurotoxin, plant), colchicine (cytotoxin, plant), anabasine (neurotoxin, plant), ptaquiloside (carcinogen, plant), ouabain (cardiotoxin, plant), strychnine (neurotoxin, plant), morphine (neurotoxin, plant), and last but not least botulinum toxin (neurotoxin, bacterium), which is the most acutely lethal toxin known (in humans, about 100 nanograms is lethal when injected, a speck of the chemical too small to see by eye). And I am leaving entirely out of the list toxins produced by animals for hunting (snakes, cone snails, and many others) or defense (poison arrow frogs and many others), and irritants (urushiol from poison ivy being the most famous in the U.S.).
All of the above listed chemicals are most likely produced defensively, to prevent contact with or ingestion of the producing organism. They are the product of evolution, which has had notably outstanding success at producing toxins because they are so useful as defensive and offensive weapons. Most of the plant chemicals probably have insects as their main target, because they are the most damaging herbivores. However, in most cases all complex animals share with insects the target of the toxins, so they are often toxic to varying degrees to many or most animals.
This is not to say that man-made chemicals aren't dangerous - everyone is well aware that we have contributed our own ingenious toxins to the huge panoply of natural toxins, sometimes with more enthusiasm than wisdom. In short, each case has to be taken on its own merits (killing intended organisms) and demerits (killing other things). Rather than depending on the idea that natural products are safe, you should assess each chemical by using the amazing amount of information readily available on reputable sources like Wikipedia and government-sponsored toxicity pages.
For the most part, commercially available pesticides (natural or not) are relatively safe because they have been tested for their effects on fish, birds, mammals, etc., though both natural and synthetic pesticides should always be used with care, especially aerosols if they are sprayed. Pesticides allowed for home use are typically safer (it is easy to tell when they are not - if the smallest amount you can buy is huge and costs a bundle, it is NOT licensed for the home). Some are safer than others - again, look it up. You can make your own choice about what you consider acceptable risk for you, your pets, honeybees, fish, or whatever else you care about, but don't fall into the "natural is safe" trap.
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