Being a geneticist I feel compelled to add a few comments, not as an expression of personal opinion, just as food for thought:
1. The vast majority of agricultural produce (organic or not) has in fact been genetically modified at some point in the past to satisfy the growing demand for quality and quantity and there is nothing wrong with that.
2. There are many ways to genetically modify an organism. In the old days they could only use "genetic selection", just by crossing individuals with desired traits and selecting the "best" offspring over several generations. Then, with the discovery of "targeted mutagenesis", it became possible to influence a specific gene of interest, causing it to mutate towards a more favourable trait. Of course they had to use mutagenic (potentially carcinogenic) factors to cause these mutations in the first place, however once the mutation has occurred it's passed-on to following generations with no need to apply mutagens, so no worries about the end product here.
Another way to get GMOs is by genome manipulation: they "cut" a piece of foreign DNA (possibly from other species) and insert it into the genome of the subject to give it new properties. The concerns in this case are related to possible allergies (if the foreign DNA happens to code a protein you are allergic to) and to the behaviour of this foreign DNA within the "host". The good news are that nowadays scientists are able to take measures to prevent any "extra-curricular" activity of the foreign DNA, so it is unlikely to cause any further modification to the host and certainly not to the consumer (whatever the case, there is never any direct genetic interaction between us and the plants we eat, we can only react to the substances that their genes have already generated during their lifetime).
3. Even though pesticides are not used in organic farming, it's very difficult (if not impossible) to shelter this kind of produce from environmental toxins, as our soil, air and water are polluted anyway. We also have to keep in mind that, having no protection from microorganisms, they are more likely to carry dangerous infections, so extra care is needed especially with raw organic fruit and vegetables. Now looking at non-organic crops, we do take in some nitrates, but we can probably feel a bit better knowing that our body is very good at getting rid of (or inactivate) those chemicals and there are many ways to minimize their content in our vegs by the time they reach our table. Whatever the choice, don't take safety for granted and proceed with caution.
4. There is a controversy about soy since I can remember and the truth is, it can be both harmful or beneficial depending on the hormonal background (including thyroid function), the immune system status and digestive health. It is indeed a common allergen and hard to digest for some people, but for the most part this has nothing to do with its genetic modification. The estrogenic effect of soy is actually extremely weak, despite the fact that it is high in phyto-estrogens, as these molecules are hundreds of times weaker than our own estrogen. When they "compete" with estrogen for the receptors and take their place, the "full-strength" hormone is replaced by a much weaker one, so the result for the body can in fact be "anti-estrogenic", which is beneficial for women with too high estrogen and low progesterone (usually right before menopause) and may prevent breast cancer. On the other hand, if someone has an estrogen deficiency, then not all receptors are taken and the phytoestrogens will bind to the free receptors giving a very weak estrogenic kick. This is hardly the whole story, just an example of how the effect from food can be different for different people.
5. The increase in food allergies over the last decades is a complex phenomenon and there are countless reasons for that, with GMO hardly being within the top 10. Food habits are key though, especially the almost epidemic obsession with simple carbs/sugars and hydrogenated fats. Enviromnent, medication over-use, immobility and stress come next... These can cause imbalances that in turn affect our offspring and the generations to come, so more and more babies are born with immune or metabolic defects.
Oh no, this post is so log, I guess I got carried away...
Oooops
Take care everyone!