Autoimmune disease is all around us. An autoimmune condition affects approximately 8% of the US population, 78% of whom are women. Autoimmune diseases happen when your immune system gets confused resulting in your immune system attacking your own body. The 3 most common autoimmune conditions are rheumatoid arthritis (immune system attacks your joints), Hashimoto’s thyroiditis (immune system attacks your thyroid), and celiac disease (immune system attacks the small intestine).
The cause of autoimmune disease is classically ascribed to some viral illness, which seems to be the thing that western medicine pins on most things that they don’t understand. I think this is one potential mechanism, but I think there are other things contributing that are much more common. Molecular mimicry and non-protein amino acids are two of the major mechanisms that make the most sense to me.

Molecular mimicry is when you are exposed to some foreign protein, your immune system reacts to it, and there is a protein in your system that looks similar. This sets the groundwork for your immune system to then attack yourself. This is most commonly believed to occur when someone has intestinal permeability leading your immune system to attack many proteins that look foreign in your gut. Some of these proteins may look molecularly similar to proteins in your body and this results in your body mistakenly attacking itself. The key to fixing this problem is to fix the intestinal permeability. The most common offender of causing this is gluten, but other lectins from plants can induce this as well.  A very interesting study found that antibodies that react with wheat germ agglutinin also have high reactivity to thyroid peroxidase. So if you have a leaky gut caused by lectin induced permeability and this results in your immune system reacting to wheat germ agglutinin in the bread products you eat, there is potential for you to develop an autoimmune response directed at your thyroid.

Non-protein amino acids are amino acids of plant origin that have no function in the human body other than messing things up. They can get accidentally incorporated into proteins, which can confuse our immune system into attacking these proteins, as they look foreign. Our immune system is designed to attack foreign things! If we have foreign looking amino acids being incorporated into our own proteins, then our immune system is just doing its job and accidentally hurting us in the process.

Viruses inducing inflammation and ultimately an autoimmune response isn’t really something within our control and I think if we are healthy a process like this should be short lived as our immune system will eventually figure it out.Ultimately, if we give our body what it needs and remove what it doesn’t, then our immune system will function at a high enough level and things like this will be a major contributor to autoimmune processes long term. Control what you can control. Unfortunately, viruses you come into contact with isn’t something you can control.

Now that we have learned the major mechanisms of autoimmune disease, how do we treat it? The most obvious way is to avoid the plant parts that are high in plant defense chemicals (roots, stems, nuts, seeds, and leaves) or at the very least, process them so these compounds are mostly broken down. I personally feel better without those parts of the plant in my diet, so I avoid them. However, some will not be able to make that transition right away and finding ways to process them like fermenting, pressure cooking, soaking, sprouting, etc. can decrease their toxic burden and likely improve symptoms. The most efficient way to reverse an autoimmune disease that I have seen is a carnivore diet. It’s pretty simple: eat meat, salt, and water. The next step up from this is an animal based diet where you combine Weston A. Price, GAPS, carnivore, and Terry Whals’ diet principles and hope that you are limiting enough of these compounds that your system can handle it. Do one of these for 6 weeks and see where you end up. In my experience, it will be in a much better spot than when you started!
I will say something briefly about other treatment modalities. Of course you want to replace thyroid hormone with Hashimoto’s, but I also think that low dose naltrexone can be very beneficial for people with an autoimmune disease. Obviously this requires a functional medicine provider or an open minded rheumatologist, but this treatment is successful for many people to varying degrees. I think ultimately it comes down to nutrition, but treatments like this can make symptoms more bearable while we are treating the root cause.
If you have an autoimmune disease and are trying to resolve it, give the above a try and let me know how it goes!