What is Really Going On In There?

Autoimmunity is most easily defined as a complex immune disorder where your immune system stops recognizing parts of your body and begins to attack them.

If you have not read What is Autoimmunity – Please Do!

There are many stages to this process and many ways to make it better or worse in a hurry. The standard medical approach to an acute Autoimmune flare-up is immune suppression. That makes sense. If your immune system is behaving like an angry guard dog and your colon is the ‘shoe’ it is chewing on, you get diagnosed with Colitis. Drug the dog into submission and you have fewer symptoms and may even have decades of good health.

That decision makes sense if you are in a hurry.

Most people with Autoimmunity have erratic and gradually worsening health over time. Some choose to manage their symptoms with risky medications while others choose to focus on finding out what happened to their naturally adaptive and healthy immune system. And many people find themselves somewhere in the middle, not sure what else to do.

In Functional Medicine, we refer to this process as ‘Finding the Root Cause’.

It is easy to get focused on (or distracted by) your symptoms and your diagnosis. Your symptoms tell a story about what is happening deeper within the systems and tissues of your body. All too often, your diagnosis is often just a label for what you are going through and adds nothing to help you make some of the most important choices you may ever have to make. If you feel confused and unsure of what is happening and what to do, find the root cause. I always recommend finding a clinician who thinks like a detective.

It is usually cheaper and much more efficient in the long term to do some comprehensive and correlative lab testing. If both you and your clinician know why your immune system, stress hormones, and detox pathways are not working properly, you will both know what to do, why, and for how long.

This may sound like some tough love, but if you are not restoring and rebuilding your immune system, you are, consciously or not, waiting to see how bad things will get. My hope with this website is to give you the common sense and the inspiration to figure out your root cause, make some important choices about your diet, supplements, and lifestyle, and also give you a sense of how long this process will take.

The best place to start is with some awareness and understanding of what happens to your immune system when it turns into a ‘mad dog.’

Explaining how Autoimmunity works in a way that actually means something is not an easy task. What follows is a visual metaphor that seems to work for most patients and doctors. Let me know if it works for you in the comments.

Action Movies and Your Immune System

In this playful analogy, I am going to focus on the parts of your immune system that are involved in most front-line reactions to the dangers in the world. I will use the innocent imagery of a friendly small town and a series of made-up emergencies to demonstrate what is happening on a cellular level of your immune system.

I hope the imagery makes sense and the immunology gives you confidence that there is hope.

If you are a clinician – yes, I am oversimplifying this process a great deal.

Autoimmunity is a lot like an action movie and all too often it is like a Zombie movie. I will make up a movie script to help you understand this terrifying story.

Imagine you are on a road trip with a couple of friends and you find yourselves in a peaceful little town where most people know each other. There is very little traffic and even less crime. The police actually walk around helping old people carry their groceries.

Suddenly, a car crashes into you while you are driving on the main street. You are all OK and your vehicle is damaged, but the other vehicle is on fire.

The police show up to see who caused the accident, the firetruck hooks into the fire hydrant and the firemen go to work. The ambulance attendants are waiting for the fire to go out and see if they need to save a life or deal with any dead bodies. Also, there is a reporter running around taking pictures to let the town know about the dangers and heroes of life.

Inside your body, your immune system has a police force, firefighters, an ambulance with paramedics, and a journalist. The car that hit you represents an external injury or infection. The fact that their vehicle is on fire reminds us that the danger (so far) is coming at you from the outside.

In your bloodstream, T-Lymphocytes (the police), B-Lymphocytes (the press), Phagocytes (paramedics) and a combination of your innate and adaptive immune system, including Interleukins, Immunoglobulins and Cytokines that all determine your inflammatory status (the fire truck and firemen). 

In the next scene of our movie script, you are signing into and Bed and Breakfast with your friends while you wait for your car to get fixed. Then post office explodes!

Once again, the police, fire truck, ambulance and a journalist show up. They put out the fire, save some lives, get rid of a few unfortunate corpses, and take pictures of all of the evidence.

Exploding post offices are new for the town and for the Mayor. After a dramatic meeting that reviewed the entire history of the town, the Mayor, Police Cheif, and Fire Chief decide to go through the town looking for the bad people who are blowing up buildings. A police officer comes to your hotel and asks to check your identity, the fireman shows up to test your fire alarm and install an upgraded one if you need it. A paramedic drops by to remind of the importance of having a good first-aid kit and the now investigative journalist wants to take your picture and see pictures of any of your relatives. , however, strangely sends photos of your house on a good day and then a made-up picture of your house as if it was sketchy or broken down.

Inside your immune system, this part of the movie represents a process called self-sensing.

Your immune system does this regularly.

If you damage some tissue, get a small infection, or eat some food that is ‘off’, the commander of your immune system, the Mayor or your Thymus Gland sends out a request for more information. If the problem goes on for long, your Thymus Gland will activate your entire Immune System. Each of us has both an Innate and an Adaptive immune system.

Your Innate Immune System is always in the background physically (skin, mucous membranes) and chemically fighting off bacteria, managing tissue repair and cleaning up the mess.

Your Adaptive Immune System is on call 24/7 and shows up to deal with new and unique pathogens. These two aspects of your immune system work together to keep your body healthy and up to date on the season, your environment, and any recent car accidents.

Now your T-Cells (police) have to physically ‘pat-down’ each of your cells to make sure that they belong in your body. All of your cells have chemical passports that tell your immune system where they were born. Your B-Cells are sending back pictures of what they see, but they also start creating images of possible antigens that look similar to what they find. This is a very smart move for your immune system.

Why just go after one gang member when you can go after anyone wearing a leather jacket with patches on it. 

This is a critical component in the onset of the Autoimmune process.

Your immune system creates images of your tissues that are not normal, just in case not normal things are happening anywhere. As long as your Thymus is working properly, it will throw out the paranoid pictures. If not, your immune system becomes more aggressive, sensitive, and reactive.

Your Phagocytes call in some Macrophages and start looking for tissue problems and ‘bad guys’ through your Dendritic cells. Your inflammatory cells start looking for any tissue that needs repair and goes to every construction site (membrane in repair) and gas station (overworking gland) to make sure they are not going to explode like the post office. This situation is what I describe as Stage Two of the Autoimmune Spectrum. At this point, most people are having allergy or injury like symptoms that are becoming chronic – even if they keep moving all around your body. 

Now back to the movie script.

You guessed it, more explosions. No one knows why, but random construction sites (normal tissue repair), gas stations (glands), and car repair garages are being vandalized and/or set on fire. The usual heroes are getting burned out and frustrated. The Mayor decides to call in the SWAT team and an FBI investigator.

Now there are highly armed police and some national guard infantry running around this once friendly town. There are snipers on buildings, roadblocks everywhere and the grocery store is empty. School gymnasiums look like refugee camps and everyone is hiding in their basement waiting for someone to get the bad guys.

The Mayor announces martial law.

That never goes well…, but it makes for great action movies.

The police are now going door to door. They are not sure who belongs in the city and who doesn’t.  The Fire Chief has begun checking every home with the bomb squad. The ambulance people are training anyone and everyone to help with triage care.

Although you and your friends are from out of town, you were all accepted and taken to a shelter. Unfortunately, the police kicked down the door and are demanding your identity. Somehow, in all of the chaos, fires, and running away from explosions, you have lost your passport.

Inside your immune system, things are getting impatient and aggressive.

Your activated Memory B-Cells (now FBI investigators with a passion for wanted posters) are checking the pictures of normal cellular membranes and making antibodies for everything that doesn’t have a cellular passport.

Your T-Cells are getting more aggressive and are now producing NK – Natural Killer Cells  (SWAT teams with snipers). Your immune system no longer trusts any identification that is not recent and validated.

This describes what happens when your chronically inflamed and malnourished cells (risky areas) lose signalling through the Major Histocompatibility Complex One (MHC1) protein pathway. This is a major step in the loss of immune self-tolerance and the onset of measurable Autoimmune Dysfunction.

The metaphor of Martial Law inside your immune system is actually very accurate. When your cells are damaged enough or sick enough they can lose MHC1 signalling your immune system starts making wanted posters for your own cells, called auto-antibodies, or self-antibodies. This is still normal, but not ideal behaviour. Now Natural Killer cells (snipers) will start killing your own weak, defective, or infected cells.

If this continues for long, you get significantly malnourished, you get stressed out, your Epigenetic System can’t do its job, or you get an infection or are exposed to an environmental toxin, now your body looks like a zombie movie. Your Memory B-Cells will proliferate rapidly, redefining the landscape of your whole immune system and your symptoms.

Do not forget that your Thymus Mayor is a big fan of profiling – attacking anything that looks ‘close enough’ to the actual problem. This is not normal immunity – it is reactive and complex immune system dysfunction.

Back to the movie.

After all of the damage that has happened to this once friendly town, they have lost tolerance for strangers and people who cannot prove who they are. You and your friends were eventually hunted down and killed. Sorry, I didn’t write this script. The special effects should get an Oscar Award, though. They found your passport in your damaged and blown-up car. They assumed you were at the scene of some crime and that is a bad thing in some towns.

Don’t Become a Zombie!

If you have an Autoimmune condition, you are in the audience watching this story play out every day inside your body.

If you do everything you can to get your town to be as peaceful and friendly as possible, you will have much better health and need a lot less medication.

If your immune system does not repair itself, the chronic inflammation, malnutrition, reactive and aggressive immune biochemistry will keep telling your genes that action movies and martial law are the way to go.

When I first started studying Functional medicine 20 years ago, we used the term ‘Walking Wounded’ to describe chronic illness and Autoimmune patients. Not out of disrespect, but to remind ourselves that we are working with people who are living through an internal unseen war. I have been there as a patient. No one wants to feel weak, sick, tired, and in pain all of the time. No one who lives that way every day is going to feel good or normal. At a certain point, we all start to shuffle around feeling un-dead like a zombie.

Loss of self-tolerance and having your immune system convinced that your Pancreas, Thyroid Gland or 100 other possible tissues are potential enemies is the essence of Autoimmunity. It is complicated, but it is also fairly intuitive.

Here is a very common and straight forward example.

The most common trigger for Autoimmune Thyroid Disease (Grave’s Disease or Hashimoto’s Thyroiditis) is a constant load of immune distress and constant exposure to Gliadin.

Gliadin is a protein that is found in foods that contain Gluten. If your Memory B-Cells develop a wanted poster for Gliadin from eating a diet high in Gluten AND have an overly reactive or overwhelmed immune system, your T-Cell snipers may attack your Thyroid gland because its surface membrane looks enough like Gliadin to deserve getting shot at. It is that simple.

The accumulative damage weakens and disrupts normal thyroid function, turning you into a very tired and slow or a hyper and manic zombie.

Take all Gluten out of your diet for three months and most of us feel a lot better.

Although this example is about your Thyroid, it is also about any constant load of highly triggering molecules. See The Standard AIP to learn about the challenges with several popular foods.

There are many ways to look at the Autoimmune epidemic. It is helpful to have a personal, meaningful, and motivating understanding of what is happening to your body. Being told you are allergic to yourself and need to suppress your immune system is not very helpful in the long run. In the short term, that may give you the time, energy and focus to begin figuring out the root cause.

Functional medicine practitioners use some of the most precise and leading-edge lab testing available. Find a good detective and write a different movie script – one where science and personal commitment lead to saving the world from a Zombie apocalypse.

More Functional Medicine Resources

Autoimmunity – Early Warning Signs
Phase One of the Ancestral AIP
Start Here – What Can You Eat?