Autoimmunity is a lot like the Weather!

Autoimmunity is a VERY fluid and individually unique metabolic environment. Just like the weather.

No matter where you live you can expect a certain kind of climate. Also, no matter where you live, you have the most extreme forms of weather for that part of the world.

In modern life, a lot of the important stuff happens on your phone, computer, and TV set. Especially living in a Mid-Pandemic environment. Today, it is easy to take your body and your health for granted, like the climate. When an Autoimmune Disease gets triggered by a combination of many possible factors, the weather of symptoms can become chaotic or get very severe in one direction.

Every day is a unique combination of symptoms, depending on your overall health, your personal adaptability, and everything that can affect your immune system.

This naturally makes predicting what will happen tomorrow very challenging.

Over time, your immune system will get very specific and aggressive, or very tired and ineffective – or both.  This makes Autoimmune Diseases more predictable and easier to diagnose only when they are advanced and already life-changing.

If you feel that your immune system is challenged, please read this series of articles on the Autoimmune Spectrum.

This perspective on the progression and possible reversal of Autoimmunity may give you some guidance on where you need to start.

You do not want to wait and see how predictable and chaotic chronic inflammatory diseases can become.

As a clinician and as a patient who has lived with Crohn’s Disease and Colitis, as well as researched Autoimmunity for many years, I am comfortable saying that these conditions are much more easily diagnosable and reversible than most of us are aware.

Over my career of meeting many unique people, with their own unique medical histories and specific Autoimmune Condition, some patterns have started to emerge.

I am not the only clinician to notice these patterns. On an international level, there is a growing consensus that there are many warning signs of potential or Pre-Autoimmunity, and several stages of progression that are consistent among most, if not all Autoimmune patients.

If you have not taken the Autoimmune Warning Signs Questionnaire – TAP HERE!

The following Five Stages of Autoimmune Disease are not considered to be or meant to be specific medical conditions. This is meant to be a scale to help clinicians and patients make some important and difficult decisions. They also offer a sense of how long your immune system has been compromised and how long it is likely going to take to turn things around.

Perhaps the greatest benefit of being aware of these stages is the ability to observe your immune system overreact and settle down in predictable ways over time.

Most of my patients figure out what will and won’t work within a few months.

I sometimes describe the Autoimmune Spectrum in terms of a dysfunctional marriage. Partially, because that is the actual classic description of Autoimmunity in Traditional Chinese Medicine, and partially because it brings your relationship with your diagnosis into focus. This bad marriage metaphor is meant to guide us in two directions. First, your immune system is married to your body. There are many, many things that determine the quality of the relationship. Second, You are married to your diagnosis and/or your health. There are countless opportunities to be more conscious and improve that relationship.

In the classic text, it states, “Certain conditions are like a bad marriage between inner deficiencies and inner over-reactions, which will eventually use up all of the adaptive resources in the patient.”

Below is a general overview of the Five Stages and what they are like.

I will include some basic suggestions on what to focus on in the short term. As you progress through each of the Four Phases of Ancestral Autoimmune Protocols you will learn about many other tools, strategies and practices.

The Five Stages of Autoimmunity

Decide which stage your condition is at and make a plan. This is the perfect time to find an Integrative medicine clinician who understands Autoimmune Disease. Some deeper assessment and some correlative lab testing may save you a great amount of time and suffering.

Stage One – An Erratic and Reactive Immune System

“The first sign of an imbalanced immune system is allergies or other strange reactions.”

When I first started focusing my practice on Autoimmune Disease, I noticed how many of my patients had allergies or had an allergy as a child – or both.

Some allergies happen fast and it is easy to figure out the culprit. Other allergies are too slow to show a clear enough reaction to know what is causing your symptoms. Some people have both at the same time.

Many people are metabolically unstable (stress, stimulants, intoxicants) or malnourished, or just chronically inflamed. The more out of balance and/or out of shape your metabolism is, the more erratic your immune system becomes.

If you are an Autoimmune Disease patient and had allergies as a kid, and especially if you have allergies now, go to Stage Three.

If you have an allergy or are beginning to notice that you are getting strange symptoms like:

  • Sneezing
  • Itchy, runny or blocked nose
  • Itchy, red, watering eyes
  • Wheezing, chest tightness, shortness of breath
  • Cough
  • Itchy or tingling skin
  • Hives (a raised, red rash)
  • Swollen lips, tongue
  • Swollen eyes or face
  • Nausea
  • Bloating
  • Diarrhea
  • Constipation
  • Fatigue

Healing any Chronic illness is about Momentum

At first, you need to slow all of the erosive and expensive processes down. Only then can you start moving in another direction.

In my experience, the momentum is always determined by the first signs and frequency of immune system dysfunction. Approximately 85% of my Autoimmune patients have medical histories that go back to early childhood. From Seasonal Allergies to Earaches, and from Strep Throat to Asthma, most of the people I have worked with also had reactive and erratic immune systems as children.

If your immune system has been haunting you and taunting you for many years, or perhaps even since you were born, then the probability of your Autoimmune Disease to progress more rapidly is higher. It is also more likely that you will express, or ‘turn on’ other genes you may have for other metabolic problems or actual diagnosable conditions.

But it all starts with the haunting and taunting.

 At present, Thirty percent of children and approximately ten percent of adults have allergies – which are over-reactions to your environment. Any immune overreaction can be an important warning sign for people who may be prone to Autoimmune Disease. Some allergies only happen because of the seasons. If there is pollen in the air all year, people with hay fever would be really upset.

The rest of the world does not over-react to pollen.

Some allergies seem to happen erratically. They only over-react with a perfect storm of environmental and internal triggers and imbalances.

Have you discovered your trigger(s)?

Are you avoiding your triggers or are you waiting to see where the chronic, erratic, and irresolvable conflict will take your health? Remember that the quality of this marriage is determined by how much you are focusing on all aspects of your well-being.

Imagine being married, and your spouse started acting very differently on the full moon? Immune system triggers can seem random and they can come from many directions at once.

Figure out what the reaction is about. Connect the behaviour of your immune system to the rest of your life – it matters!

Find out what part of your immune system is the most unstable or overwhelmed.

Try an Elimination Diet (Phase one to Phase Three of the Ancestral-AIP). If you can, get some lab testing done and find out exactly what your immune system is reacting to. Just as important, get a sense of the adaptability of your body and your immune system and the momentum of your present condition.

Fall back in love with your immune system and take care of each other for a while.

I encourage everyone to take a Stage One immune flare-up as an inspiration to get healthy, reduce stress, look into your family medical history, and take advantage of any modern tools that help you track your metabolism.

Make your relationship with your immune system a life long commitment to better days.

Reset Your Immune System

In Traditional Chinese Medicine, health is all about the balance of your Adaptability, your age, and the erosive parts of your life.

In Stage One of the Autoimmune Spectrum, it usually takes four weeks to reset a reactive immune system.  Below are the recommendations I often suggest to my patients who are at risk of developing an actual Autoimmune condition in the future.

These are just general suggestions. This is not my medical advice to you as we have not met.

In order to make these protocols safe, relevant, and specific to your individual health, you will need to work with a clinician who is very up to date with Autoimmunity.

I will suggest some directions for lab testing when appropriate, but these decisions and making sense of the results should be up to a clinician who you feel you can trust to guide you through this process.

Stage One ~ 28 Days

If your immune system seems to be over-reacting to little things or can’t seem to make up its mind, then you may want to give the front line a few weeks off.

The best way to enter into allergy season, or to just down-regulate your immune system is with a three day fast.

For one month, do your best to eat a Nutrient Dense and very low antigen diet.

The Phase Three Protocol would be sufficient for most people, but if you feel you are dealing with something more complex, then a week on the Phase One Protocol and three weeks of the Phase Two Protocol would be better.

You want your immune system to have a very gentle and predictable four weeks.

There are many supplements that can settle an over-active immune system and many Adaptogens that can support a more balanced immune response to pathogens. Working with a knowledgeable clinician will save you a lot of time and money.

If your situation persists after one month, look into Stage Two of the Autoimmune Spectrum and talk to a clinician about some appropriate lab testing.

Drink two litres of water a day and try and get the first litre in the first two hours in the morning.

You may need to do a Stage One reset every year or after a flare-up, so dig in and make sure you are going to get the best results possible.

I would also encourage you to take a step back and look more deeply into your medical history, your family history, and your relationship with your health in general. You may be having an annoying allergic reaction, or your immune system may be telling you something about its long-term tendencies. Take this chance to learn as much as you can.

Another source of information and accountability is to get a self-quantification device or basic health APP. In the modern world, there are many easy ways to track your health and get into the habit of noticing patterns.

Learn about Stage Two of the Autoimmune Spectrum? – TAP HERE

Ancestral Autoimmune Protocol


If you have not read these articles,

they may have some important answers, perspective, and guidance.


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    Michael Smith is an internationally respected Clinician, Author, and Speaker.

    Michael practices Functional Medicine, Acupuncture, and Traditional Chinese Medicine, and encourages his patients to follow an Ancestral approach to lifestyle and diet. Dr. Smith has dedicated the last 25 years to the research and treatment of Chronic Illness and Autoimmune Disease. As an Autoimmune patient, Michael is intimately aware of the devastating impact these conditions can have on your quality of life.