I'll admit - when I set out to do research for this article, I already had an idea of how (I thought) the article was going to go.
Based on what I knew about genetics technologies, my take was that fundamental technologies behind genetically modified organisms (GMO) are fairly harmless from a health and nutrition perspective. The problems with GMO's come from how the technology is used practically in the world, specifically the troubling levels of herbicides and pesticides sprayed on GM crops.
Yet, as I delved into the body of research on the safety and health implications of GMO's in our food system, I learned that I was only partly correct, at best. Yes, the excessive levels of pesticides used on many GM crops are probably the most problematic issue from a health and nutrition perspective, but this is far from the only issue.
GMO's: The Fundamentals
A gene is a specific section of DNA that contains the information a cell needs to produce one specific protein. In most cases, when genetic engineers modify a food crop, they are insert a gene from another organism into the genome of that plant. Occasionally, the desired modification is achieved by removing or altering an existing gene in the plant's genome, but this is far less common.
It's important to note that the new genes inserted into the plants aren't constructed from scratch - our understanding of protein formation (aka "protein folding") is not nearly advanced enough to engineer a gene from scratch. Rather, genes are sourced from other plants, bacteria, fungi, even animals.
For example - the "roundup ready" gene that is now found in the vast majority of US corn, wheat and soy crops comes from the bacteria Agrobacterium tumefaciens.
So while these new genes and proteins are "foreign" to the genetically modified plant, these genes have existed safely in biological systems for, at minimum, hundreds of thousands of years. While there's plenty of proteins in nature that are quite toxic to humans and other animals (i.e. botulism, ricin), my assumption was that surely a biotech company spending hundreds of millions in developing a GM crop would extensively test the imported genes and proteins to ensure they are not toxic or inflammatory in animal systems.
To find out that I was incorrect in this assumption came as quite a surprise.
GMO Toxicity and Inflammation: The Evidence
What we've learned over the past 15 years is that the health implications of a GM product often take years to come to the surface, well after the product is on the market and in cultivation.
The initial testing on GM product is often financed by the manufacturer, or even done in-house by manufacturer itself. Unsurprisingly, much this initial manufacturer-supported research is designed such that it is highly likely to produce data supporting the safety of the product.
In the years after a GM product comes to market and enters into commercial cultivation, data from independent research accumulates such that we get a more honest picture of the health implications. Troublingly, this process is often impeded by the manufacturers, who are notorious for making it very difficult for independent researchers to even access their products for testing. 
When we do get good data from independent studies, foods from GM crops no longer look like as benign as they were initially proclaimed to be.
Here's some of what we've learned:
- Rats fed a diet of a specific GM corn (MON863 Bt) grew more slowly and showed higher levels of triglycerides in their blood. They also showed problems with liver and kidney function. 
- Mice fed GM Soy showed disturbed liver, pancreas and testes function. Researchers also found abnormally formed nuclei in liver cells, possibly indicative of altered gene expression. 
- Female rats fed GM soy showed changes in the uterus and ovaries when compared to control rats fed organic soy and a non-soy diet. (Interestingly, both soy groups showed ill effects on the uterus, highlighting the problems with phytoestrogen-rich soy diets). 
- A meta-review of 19 studies (including some conducted by the GM manufacturers) on mammals fed with commercialized versions of GM soy and corn crops showed consistent toxic effects on the kidneys and liver. It should be noted that this meta-review looked exclusively at studies done on GM varietals currently in widespread use globally. 
- Rats fed GM rice showed significantly altered weight of several organs and increased immune response compared to control mice fed non-GM rice. Gut flora was also significantly altered in the GM-fed mice. 
Problems With "The Evidence"
There's no shortage of studies like the ones listed above. In my far-from-complete searches on the subject, I found no fewer than 30 studies that suggest some degree of toxicity from GM crops currently available on the market.
While this body of research certainly justifies a degree of concern and caution around GM crops, there are fundamental problems with the studies that keep me from making a definitive judgement on the issue.
The studies are all done on small animals, which can be sometimes be misleading if the conclusions are assumed to apply directly to humans. In this case, however, the organs studied (kidneys, livers etc) are structurally and functionally so similar between humans and rodents, it's not a stretch to assume any effects observed in mice would also be observed in humans at comparable dosages. If the studies were looking at digestive function, for example, this would no longer be the case as the digestive systems of rodents are too different from our own.
This brings me to my main issue with these studies: the dosages. The animals in these studies are generally fed diets consisting exclusively of the GM food. If you were to feed mice a diet of exclusively organic heirloom corn or soy, I would expect to see some degree of negative consequences in the mice - it's simply problematic to eat such an unbalanced diet.
This means the data we're getting from these studies is gathered from animals who would likely be showing signs of adverse health consequences anyways. Not exactly high quality data in my opinion.
The obvious issue with the dosages in these studies is that a human is (hopefully) never going to eat 1/10th their body weight in GM corn in a single day as a mouse or rat can. The dosages we'd expect for humans are likely several orders of magnitude less, and there's no way to know if we'll see the same health abnormalities show up at these lower dosages.
Finally, most of these studies are designed to produce statistically significant data over the course of a few weeks. The consequences of eating small amounts of GM foods over the course of years remains largely unknown.
This is the elephant in the room in any conversation about the toxicity of GM foods - we have no idea what the effects are of consistent low-level consumption of GM foods over the course of years and decades.
The Real Issue With GM Foods: Glyphosate
If the problems with the studies done thus far on GM foods have you unconvinced about the dangers of the technology, don't worry - there's an even more convincing reason to keep these foods out of your diet, and one much better supported by research.
By far the most common GM products in cultivation today are crops (primarily wheat, corn and soy) engineered to be resistant to the herbicide glyphosate (aka "Roundup").
In the US, 88% of the annual corn crop and 94% of the soy crop comes from plants grown with GM seeds.  While the exact percentage of these crops that are specifically from "roundup ready" seed is harder to find, everything I've seen seems to point to the vast majority of these crops being "roundup ready". My approach is that unless a product containing one of these three grains (wheat, corn, soy) is explicitly organic or non-GMO, you should assume it contains roundup-ready genetics.
While the genetics themselves may be reason for concern, it's the way these genetics allow farmers to change cultivation practices that is the most troubling.
Because roundup-ready crops can continue to grow in the presence of glyphosate (which is toxic for almost all other plants), farmers can dump huge amounts of the herbicide on the soil around their crops (to discourage the growth of "weeds" that compete with the crops for nutrients in the soil). Although glyphosate isn't toxic to the GM crops, it is still absorbed readily by these plants and shows up in the foods they produce in significant levels. 
Since the statistics require us to assume that any corn, soy or wheat product not explicitly labeled "organic" or "non-GMO" is from a plant with roundup-ready genetics - we also have to assume that these products almost always contain residues of glyphosate.
Is Glyphosate Toxic To Humans?
While initial studies showed that glyphosate was not toxic in humans, more recent studies have shown this to be far from the case (If it seems like this is a recurring pattern in agricultural products, you're right). Here's some of what we now know about the effects of glyphosate in the body:
- Glyphosate and its breakdown products have been shown to exhibit cytotoxicity, oxidative effects and apoptosis (cell death) in human cells in concentrations as low as 3 parts-per-million, levels commonly found in foods produced by GM crops. 
- Glyphosate is toxic to the kidneys and may be the cause behind the recent kidney disease epidemic in developing countries among farmers harvesting roundup-ready crops. 
- Glyphosate induces human breast cells cancer growth by stimulation of estrogen receptors in breast tissue. 
- Glyphosate in feed has been shown to disrupt the gut microbiome in cattle, leading to proliferation of of pathogenic bacteria in the digestive tracts of these animals.  It is safe to assume that the human gut microbiome would also be disrupted by trace amounts of glyphosate found in GM foods.
Looking at the data from the research cited above, there's clearly plenty of reason for concern about the effects of both GM crops and glyphosate residues in our foods. That being said, when I look at the data, my impression is that prolonged exposure over time is where the greatest cause for concern lies.
The cytotoxicity of glyphosate or the nephrotoxicity of GM corn, for example, are not characteristics we want from our foods - but realistically the consequences of an isolated meal containing GM foods is not likely to be that significant. At most, you may experience slightly more inflammation in the hours and days after the meal.
Not ideal, but also not worth freaking out about.
This all changes if you're eating these foods on a regular basis, which is why I treat GM foods according to my "staple principle". This principle says that it's the foods you eat every day (i.e. your "staples") that are the greatest determinant of how well your body and brain feel and perform.
If you eat low-toxin, nutrient-rich, anti-inflammatory foods every day, you should have a high-functioning, resilient body - and occasionally eating a meal containing GM foods or other "marginal toxins" is not going to have a huge impact on your health and performance.
If your diet is not of this high quality and GM foods and other marginal toxins are making it into your meals a few times a week (or more), now you're looking at the possibility of measurable adverse health consequences.
I should clarify that food allergens and moderate-to-highly inflammatory foods (i.e. wheat, A1 casein) are not covered by the staple principle. These foods have immediate and significant effects on the way you feel and perform that can last days after your meal and are simply not worth eating.
"Marginal toxins" like plant anti-nutrients, oxidized cooking oils, mycotoxins and GM foods are what I apply the staple principle to. As long as the rest of your diet is awesome, eating these foods once a week or less is not likely to have a huge impact on the way you feel and perform.