Simple Answers Can Feel Very Difficult!

The Evolution of the Autoimmune Protocol

I was first diagnosed in the 1990s, and back then there was very little information on natural treatments for autoimmunity. Elaine Gottschall’s classic Breaking the Vicious Cycle -The SCD Diet,[1] was the only mainstream book available.

Fortunately, that book and many others have instigated one of the most exciting and important questions and discussions in modern nutritional medicine.

Is it true that eating more like our ancestors can help resolve many modern chronic diseases?

In my experience, yes!

In 2004, many people started eating more like Palaeolithic Hunter-Gatherers for almost every health condition and fitness goal. The people with autoimmunity that shifted to the Paleo Diet were thrilled.  Their overall health and lab results improved even more rapidly. Over the last two decades, the amount of scientific research that has proven exactly why these dietary changes are so effective has changed our understanding of exactly how chronic inflammatory diseases work.

It is worth saying that therapeutic diets have been around since humans had a choice of what to eat. Over thousands of years, Folk Healers and Grandmothers have learned through trial and error. It is fascinating and inspiring to me that most of the intuitive wisdom passed on by our Ancestors is now provable by modern science to be valid, especially with food.

This combination of ancient tradition, modern research and literally millions of people experimenting on themselves has proven to be a much-needed opportunity for the ever-increasing number of chronically ill people walking through their lives wounded, tired and hoping for a cure.

Over the next few years, the research on why an Ancestral diet was working started to become clear. The modern diet is chemically hostile to your body in many specific ways. By removing the foods that are the most directly hostile to your immune system, many people with Autoimmune Dysfunction notice results within a few weeks, if not days. People who stay on these restrictive but very healthy diets for a few months often reverse the progress of their condition or stop it in its track.

If you are ready to dive in and get started, this is where you begin. It is best to commit to all of these recommendations completely. If you negotiate with some triggers, hoping it will be enough, and you do not get great results you may give up on one of the best opportunities there is.

Remove All Triggers

This is going to be hard!

If you are stressed out and in pain, and/or have a diagnosis that is taking control of your life in some way, taking away convenience and comfort foods probably seems crazy.

The only thing that would be crazier would be to continue making the situation worse.

Below, I am going to list the list of trigger foods to remove immediately, or as soon as possible. In the next post, I will share What you can eat on the AIP

Please, please, DO NOT wait to find out how bad your condition can actually get.


As yummy as sugar may be, it is not food.

There is no natural source of sugar in the way we eat or drink it today. Usually, in nature, the more sugar a fruit, or a tuber, like sugar cane, the more fibre the sugar is bound up in. In order to digest the sugar, humans have always had to digest the fibre first.

This means we have evolved to assimilate high sugar/glucose and fructose foods very slowly.

When you eat a rapid source of glucose like table sugar, or candy, or soft drinks, the faster your insulin spikes. This activates your immune system in a way that generates an inflammatory response. If you do this too often, you will store the glucose as fat. Human adipose tissue (fat), can also produce inflammatory cytokines as well as other challenging hormones like Estrodial – the ‘bad’ estrogen.

Coming off of a high sugar (glucose/fructose) lifestyle is VERY HARD to do because sugar is almost as addictive as heroin.


Coffee and green tea have many health benefits and are enjoyed daily by most adults on earth every day.

Caffeine may be an ingredient in these beverages, but by itself, caffeine is a significant metabolic disruptor. The reason we all love caffeine is it makes us feel more alert and become more productive. This happens because caffeine blocks the neurotransmitter that induces rest. I will explain the chemistry in a later post.

If you have ever used caffeine as a source of ‘energy’ and then tried to use less or stop, you probably felt tired and grumpy and get headaches for a few days. This happens because caffeine doesn’t give you energy. It just makes your metabolism out of balance in a way that releases more stress hormones.

If you have any form of chronic illness, the last thing you need is more stress hormones. When you are ready to get off of the caffeine train, reduce your dose in half every few days until you are down to half a cup a day. If you feel you cannot function without any caffeine, use Matcha. The caffeine releases slower over a few hours and will produce a crash.


There are many reasons why the overuse of alcohol is a negative influence on people’s lives and on human health. There is also some evidence that mild to moderate use may have some long term health benefits.

When it comes to Autoimmune Disease and any attempt to restore normal function to any and every system in your body, alcohol is rarely going to be helpful in any way. Alcohol is inflammatory to your gut, vascular system and brain. It acts as an antibiotic in your gut and can create an imbalance in your microbiome, which we are all learning is a significant limiting factor in almost all chronic diseases.

If you feel that the calming effects of alcohol are worth the risks, please look into medical Cannabis, especially CBD.

Here is an article on CBD and Autoimmune Disease.


Although grains have been a staple around the world since the advent of agriculture, they come with a host of Anti-nutrients like Lectins, Prolamins, Phytates, and Enzyme Blocking Compounds. All of which can trigger a host of irritations and insufficiencies to normal health.

After a few months of going grain-free, most of my patients can tolerate a small amount occasionally.


Beans and Legumes also contain the same anti-nutrients that grains have. Legumes also contain certain starches that feed bacteria that can either support your gut or cause a serious imbalance in your Gut. This is why they cause so much gas!

After your gut and microbiome have had a chance to come back into balance, most people tolerate beans very well. Some people need the specific ratio of fibre in beans to have regular bowel movements. If that is you, eat a lot of boiled and cooled roots for the Resistant Starch. I will be writing an extensive article on this soon.


Nuts are also on the ‘bad’ list because they are highest in Phytates, or acids that bind with minerals. This can potentially create long-term nutrient deficiencies.

It can take a long time for nuts to get from the grower to your local grocery store. Most nuts are also high in Omega-6 fatty acids, which can promote an inflammatory response – especially if the oil (fatty acid) is rancid.


Although full of useful nutrients, seeds are typically highest in the chemicals that block your digestive enzymes. They are also highest in Tannins, reactive compounds that can trigger inflammation. Both Enzyme Blockers and Tannins can interfere with the proper absorption of nutrients.


Vegetables like Potatoes, Tomatoes, Peppers, and Eggplant, all belong to a genetic family of plants called Nightshades. This class of plants contains neurotoxic triggers called Glycoalkaloids. These triggers can increase anxiety, inflammation, and aggravate chronic pain.

Give Dairy and Eggs a Break Too!

One of the hardest truths to bear when learning about Autoimmunity is that we all become more sensitive to the foods we eat the most often. Two of the most common staples in the modern Western diet are Eggs and Dairy Products. These common foods also contain proteins and other chemicals that can aggravate an already aggressive or tired immune system.

I am just going to scratch the surface with the research because it can get very deep. Most people who follow the Standard AIP for a few months find that they can tolerate small amounts of hard cheese, organic full fat yogurt and eggs once or twice a week. If you are unsure if you are willing to take this step just yet, then focus on unpasteurized, full fat, organic dairy products and local farm fresh organic eggs. Always prepare your eggs with soft yolks.

So, what could be wrong with these foods you ask?

Some Eggs are Better Than Others

Eggs are one of the most Nutrient-Dense foods available.

Unfortunately, eggs contain a protein called Lysozyme that can trigger an inflammatory response as well as carry other offending proteins across your protective Gut membrane. This can make an already Leaky Gut more of an issue.

If you are going to eat eggs, try and make sure that they are from a local farmer. If you can, ask the farmer NOT to wash your eggs. This ensures they are as fresh as possible when you use them at home. Remember to wash them just before you use them.

Most people on the Ancestral AIP only have to restrict eggs for the first two months. If you feel like your immune system is adaptable and you enjoy eggs a lot, only have them three days a week.

The Devil in the Milk

If you want to learn ALL there is to know about cow dairy and how it can irritate your immune system, check out Keith Woodford’s ground-breaking book, ‘The Devil in the Milk.’ There are many ways that modern commercialized and over-processed dairy products can make a confused immune system more aggressive, but I will stick with two for now.

Your immune system is like a village. You have an ambulance, a fire truck and some hopefully friendly police officers there just in case. If there is an accident (injury or illness) in your village, your inner heroes should save the day just like they always do. If you keep having repetitive accidents in the same place (chronic illness), then your body may call on deeper and more complex resources to find the bad guys.

Your immune system has a memory. Some of your immune cells, specifically your Memory B-Cells are like bounty hunters. They travel around your body with a wanted poster and a gun, on a search and destroy mission looking for the bad guy. Not only is Cow Dairy full of potential proteins that may irritate your immune system, but some of the proteins in dairy look a lot like other high reactive proteins in other foods. This is called Molecular Mimicry and this process is most dangerous when the proteins in your food look like the proteins in your body. For example, there is a protein in milk called Casein that looks like a protein in Gluten called Gliadin which happens to look like your Thyroid Gland. Crazy, but absolutely true!

Another challenge with cow dairy is about genetics. Some cows produce milk with a Casein protein called A-1 and other cows produce a protein referred to as A-2. People who are prone to hyper-immune overreactions are more likely to have a problem with A-1 milk products. The reason that this matters is almost all of the cows that are farmed in North America are A-1 cows.

If you love dairy and can eat it with respect to your immune system’s present state of health, goat milk has the A-2 protein.

Plant Embryos, Anti-Nutrients and Your Health

It is common for people to see undigested corn in the toilet. Have you ever wondered how corn, many seeds, some nuts, a few grains and beans can get through your entire digestive system intact or undigested? There are several reasons why and a few of them can hurt you.

Yes, whole grains, beans, most nuts and seeds are some of the least expensive, natural, and moderately nutrient-dense foods available. However, if you eat them too often, or if your immune system is in a state of war, these foods are actually bad for you in several ways. They can trigger inflammation, damage your mucous membrane, aggravate your immune system, cause malnutrition and basically weaken your whole body.

It is all about balance and some Grandmother Wisdom.

In most traditional cultures, these foods have not been eaten in their untreated whole form, until the 1960s. Until then, most cultures and their family traditions carried the wisdom to sprout these foods, soak them in an acid like vinegar or lemon juice with water for a day (24 hours), soak them in yogurt or milk at room temperature for a day or four, or to make sure that they were cooked after hours of being mixed with a sourdough starter. My indigenous ancestors used to soak tree nuts in Lye, something Indigenous people still do in Central and South America.

These traditions exist because they work. As you will learn below, these delicious and nutritious foods have some defence mechanisms that REQUIRE a chemical bath to be safe for modern Humans. It is this same chemistry that makes these foods unsafe for people with Autoimmune conditions.

Here is the Research

All seeds, nuts, grains and legumes are the embryos of plants. That may not sound very appetizing, but all plant embryos have actually evolved to get through the digestive tract of mammals in order to grow up in their manure.

Plant embryos actually have a surface membrane that is very high in Lectins, which are anti-nutrients. These are chemicals (glycoproteins) that irritate the mucous membrane of your digestive system in a way that weakens your ability to absorb your food. They also irritate your immune system and can make your blood cells and white blood cells stick together, making your blood weaker as vehicles for oxygen and nutrients, and your immune system full of tiny chemical bar fights. Flying bottles and all.

Most Lectins come from a structure called a Prolamin, which are common in grains, legumes and pseudo-grains. Prolamins are a flexible or elastic structure made of a specific protein and a kind of Lectin called an Agglutinin. Wheat, for example, has a Prolamin called Gluten. Gluten is actually made of a protein called Gliadin and a Lectin called Wheat Agglutinin. When Wheat flour is mixed with water, sugar and yeast or baking powder it produces carbon dioxide. As the carbohydrates in the sugar and flour turn into a gas, the bubbles get trapped in the Prolamin structure. In fact, if you extract enough pure Gluten you can use it to make a balloon. This is what makes bread rise and makes cakes so soft.

Over the last 100 years, the agriculture industry has bred new forms of wheat that have almost twice as much Prolamin (Gluten), in order to create many different kinds of flour. This explains one of the reasons that there is such an explosion in Celiac Disease and Gluten Sensitivity Syndrome. Recent research has shown that, when you digest a Prolamin like Gluten, you trigger the release of a peptide called Zonulin.  Zonulin has the unfortunate action of weakening the integrity of your mucosal membrane. The part of you that keeps your food and feces out of your bloodstream.

This leads to a medical problem called Intestinal Permeability, or Leaky Gut Syndrome. This is considered one of the fundamental triggers and drivers of most, if not all Autoimmune dysfunction.

Let’s say that you ate a slice of pizza. As the crust breaks down into carbohydrates, the Prolamin called Gluten breaks down into Gliadin and Wheat Agglutinin and triggers the release of Zonulin. As your mucosal membrane gets inflamed and the deep cellular connections that protect you start to fall apart, some of the Gliadin, some Agglutinin, some random food particles and some pernicious bacteria all get a free ride into your bloodstream. The Agglutinin sticks your red blood cells together while your immune system freaks out about the bacteria and the fact there is a complete protein inside your body.

One of the most common triggers of autoimmunity is complete proteins entering your body.

As you digest the pizza, you will have the undigested protein called Gliadin floating around causing problems. This is because your digestive system and gut barrier are supposed to keep complete proteins inside your intestines, (which is outside of you) and break them down into tiny, useful amino acids.

When a complete protein enters your bloodstream, your immune system attacks it as if it was a virus. This creates antibodies so your immune system can hunt down and destroy the ‘bad-guy’ Gliadin. For many people this is a problem because they have an aggressive, reactive or tired immune system and every time they eat Gluten, their symptoms get worse. This can happen within minutes or can show up days later. For some people, especially women, Gliadin antibodies can potentially attack the membrane of their Thyroid Gland. This is because the protein structures of Gliadin and Thyroid tissue look similar to your immune system.

The relative Prolamin content of common grains is also a factor. Modern Hybridized Wheat is the world champion for the highest amount of the most irritating type of protein for those of us with Autoimmunity. Rye, Barley and Corn have approximately half the Prolamins of Hybridized Wheat. Oats have about half the Prolamins of Barley or one quarter that of Wheat. Rice has the least of all, containing only one-sixth, or about 16% as much as Wheat. I believe that this explains why most of Asia can eat rice every day for countless generations without a similar level of Autoimmune Disease.

Another anti-nutrient found in grains, beans, nuts and seeds is phytic acid. This chemical is in plant embryos to protect them from germinating too early and protects the active nutrients inside the embryo to ensure it grows rapidly. When we eat these foods without treating them, the phytic acid combines or chelates with important minerals such as zinc, iron, calcium and magnesium and makes them less absorbable in our digestive tract. Phytic acid may also interfere with protein absorption. Keep in mind that this acid not only binds to the minerals in the plant embryo but may also bind to the minerals in the rest of your meal.

In the long term, these mineral deficiencies can create the conditions for health challenges like osteoporosis, teeth decay, irritable bowel syndrome, anemia, allergies, skin conditions, hormonal imbalances, poor memory, neurological conditions, mood disorders, poor sleep, and immune system imbalances like autoimmune conditions.

Plant embryos also contain structures that interfere with the digestive juices or enzymes of insects. This strategy evolved to protect the “plant babies” from hungry insects. Unfortunately, these enzyme inhibitors also interfere with your digestive system, specifically in a way that weakens your ability to digest animal proteins. People who are particularly sensitive to these structures are more prone to an enlarged pancreas and the growth of cysts and benign tumours. They are also much more likely to trigger chronic inflammatory conditions, insulin resistance, digestive problems, poor immunity and allergies.

Which covers almost everything…

This is why most people in Asia eat white rice and split or shelled beans.

I find it funny that many people who respect the wisdom of Traditional Chinese Medicine, Daoism, Buddhism and Yoga, who believe that people from Asia must be foolish to eat white rice. One would think that thousands of years-old healing traditions would be pretty sure about how to eat one of their staple foods. I don’t mean to poke anyone in the eye, yet it is a bit funny. Sure, brown rice has more nutrients and fibre, and yes it is more nutrient-dense, but it is also going to be a more significant source of Lectins, Phytic Acid and Enzyme Inhibitors, making it more anti-nutrient dense as well.

If you only eat brown rice a couple of times a week and your immune system is stable you should be fine. If you were to eat brown rice at every meal almost every day, then consider the wisdom of thousands of years of experience and consider white rice instead. Grains and beans are not bad for most people as a seasonal food. If your ancestry comes from Northern or Eastern Europe, or if you have indigenous ancestry you are more likely to overwhelm your genetic adaptability if you eat them too often. Sometimes we all need to take a break, just out of respect for the seasons.

If your immune system is at war with the world, these foods will effectively start shooting back – proving your immune system right. If this goes on for a long time, your immune system will start attacking anything that is straining your body’s adaptability. Every old wound, every inflamed membrane, every over-worked gland and your very sensitive brain will potentially be labelled a wound sight.

In my clinical experience, the stress of these foods on your immune system is equal to the physiology of chronic pain or low grade chronic emotional distress.

Give them a break for a few months and see what happens!