There really isn't much out there on this important subject, but its the basis for many of the organic movement and food industry arguments alike. One side claims that natural, wholesome food is healthier than processed food laced with additives, preservatives, and artificial colors. Indeed, processed food made in factories are more a product of the lavatory than of the kitchen. But that doesn't meant their safer or superior to organic natural foods. And organic natural foods aren't always safer than factory-made food. At the root of this conflict is are society's distrust of nature and all things natural. The pharmaceutical, food, and agriculture industries are a dark example of this distrust and fear. Of course, other factors such as "convenience", cost, and time are in the picture as well. So our obsession with chemically-processed food has to do with economical constrains almost as much as our general attitude towards natural food.
But what is the difference between between the synthetic toxins found in processed food and the difference between natural toxins found in natural foods? First, I'd like to make the distinction between the two. Usually processed food is the name for food you typically buy at a large commercial or chain grocery store in a pre-packaged container that has a long list of ingredients on the back while natural foods are not processed at all and come in the form of fruits, vegetables, nuts, herbs, and meat/dairy products. I've written a previous post on the toxins commonly found in processed food: excitotoxins, azodicarbonamide, petroleum-based artificial colors, preservatives, pesticide residue, and nutrient-stripping processes such as pastuerization. Natural foods contain their own toxins as well such as mycotoxins (toxins from mold), goitrogens (cause enlargement of thyroid gland), phytoestrogen (estrogen-mimickers), anti-nutrients, oxalate (can inhibit calcium intake), and glycosides that can be poisonous in large amounts.
Its important to point out that humans evolved with the natural toxins found in plants for millions of years. While our hunter-gatherer ancestors mostly hunted wild game meat they still consumed seasonal vegetables and fruits. However, they never picked any packaged cookies or cakes off a stem when out hunting for game. They never had to deal with synthetic additives. I think that evolution holds the best answer to the question of whether synthetic or natural toxins are better for you (or the lesser of two evils). Of course, there are some deadly poisons found in nature such as the Poison Hemlock and raw potatoes, which you should never consume. Usually its safer to cook food though this doesn't always disarm potential plant toxins. Generally, our bodies can handle natural toxins better than synthetic as synthetic introduces foreign chemicals only invented in the last hundred years. And most of these chemicals are unnecessary anyways. Its perfectly safe and possible to prepare real wholesome food from real ingredients instead of toxic synthetic foods so I think I'll stick with my veggies and herb soup for dinner!
(Links to sources are in orange text. Please click on them.)