All natural shopping skills which might steer you away from hormones in milk, pesticides on vegetables and mercury in fish might not include genetically altered (GM) seeds. Soy, which is now mostly genetically engineered (watch Dirt, The Movie) is found in many dishes these days. For example the oil in pizza dough comes from soy. Dextrose comes from corn which is also (in most cases) from a genetically altered seed. These genetically altered seeds are patented and made to include insecticides. Fish hasn't escaped either as AzuAdvantage Salmon combines salmon and another fish which is fast growing to produce a large salmon during a quicker time frame. These are currently being contested with the FDA and so far haven't been approved for consumption. Even eating meat that might otherwise be hormone free may not be totally "natural" as the livestock may have been fed on food grown from genetically altered seed. Corn that has been spliced with bacillus thuringiensis which kills bugs can also end up in your blood stream as shown in a study by Reproductive Toxicology. While we don't know for sure these genetically altered products/seeds are unsafe, we also don't know that they are.
How can you protect yourself? Look for blue/green stickers which are the result of the Non GMO Project that will approve a produce only if its ingredients have less than 0.9% GMO.