Phase One of the Ancestral Autoimmune Protocol (A-AIP)

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Phase One of the Ancestral Autoimmune Protocol (A-AIP)


Rest Your Mind and Body, Allow Your Immune System to Recover

Phase One of the Ancestral Autoimmune Protocol focuses on resting your Body, Mind, and Spirit while giving your metabolism and immune system a chance to recover and return to a better baseline. This process is referred to as Down-Regulation, which is essential in actively and consistently lowering the inflammatory status of your whole body and brain.

As your Immune System becomes less hostile and inflammatory, your Metabolism will also Down-Regulate, reducing Stress Hormones, Insulin Levels, Triglycerides, and Oxidized Cholesterol in your bloodstream.

Chronic Inflammation is the driving force behind most chronic conditions and almost all Autoimmune Dysfunction.

Recently, increasing evidence has shown that the abnormal inflammatory response is closely associated with many chronic diseases, especially in autoimmune diseases, including Rheumatoid Arthritis (RA), Inflammatory Bowel Disease (IBD), Systemic Lupus Erythematosus (SLE), Gout, and Diabetes.

Restoring your metabolism and blood chemistry to normal is the fastest way to reverse the plague of the modern health crisis, Metabolic Syndrome.

Should You Start by Fasting?

Fasting is the most effective and efficient natural way to Down-Regulate and Reset the front line of your immune system.

One of your Six Pillars is Metabolic Adaptability, and for modern humans, fasting is a great way to give every system a break.

I recommend consulting your health care professional before beginning a fast to ensure that this ancient healing method is the best choice for you. This is especially true if you presently require any Pharmaceutical medication.

If you are feeling adaptable and strong enough for a fast, then 3 Days of Vegetable Stock or Bone Broth is ideal. If 3 days seems overwhelming, then try a 24-Hour broth fast. If you cannot fast for one day 24 hrs, then try Intermittent Fasting.

The best way to prepare for a fast is to eat only a warming Celery Soup and/or a cooling Avocado Puree the day before you begin. 

If you are always tired, your digestion doesn’t like raw vegetables (you seem them in your pop) or have a lot of digestive problems, then I recommend focusing on stews and chowders.

If the above is true and you need to settle your digestion down immediately and are/or are not ready to give up carbs all at once then recommend stating with a Nutrient-Dense congee.

An Anti-Inflammatory Diet

I often refer to the Phase One Diet as an ‘Ice Age Diet.’

One of my favorite subjects is Epigenetics, or the ways human genetics has changed over thousands of years as we have to adapted to changes in our environment. Throughout our long evolutionary history, our collective ancestors learned to thrive on many different diets. The more I  learn about Epigenetics I becoming aware of how many specific genetic pathways are completely vulnerable to one or many aspects of the modern diet and lifestyle.

During Ice Ages, there is no rain, so there is very little to eat and the competition is very high. For early humans, and even earlier primates, a lack of trees and plant life forced the survivors to the ocean. Anthropologists call this the ‘Aquatic Ape Theory.’

Imagine living at the beach, eating raw fish, shellfish, sea vegetables and any plant or animals you could find along moving freshwater. It is not a surprise that most people try and recreate this experience when they go away for a holiday.

Below is a list of the most anti-inflammatory and Nutrient-Dense foods that you can find in most grocery stores or specialty shops.

As specific and limited as this diet is, it is only going to be one to three weeks.

Remember that your ancestors thrived and evolved more rapidly on this kind of diet. Trust that your genes know exactly how to self regulate to this diet.

In my opinion, this diet is an Epigenetic Reset – a therapeutic benefit that occurs by stimulating ancient metabolic pathways and genes that tell your immune system and nervous system what to expect and how to behave.

People love to go to the beach because their genes are begging for a deep and familiar chance to return to something known to boost evolution.


Salmon, Oysters, Prawns, Scallops, Herring, and Sardines.

Sea Vegetables (Arame, Kelp, Kombu, Dulse)

Meat and Poultry

Turkey, Grass-Fed Beef, Lamb Shank.

Berries and Vegetables

Blueberries, Raspberries, Tart Cherries, Raspberries, and Strawberries.

Cucumbers, Avocados, Celery, Olives, Beets, Radishes, Broccoli, Cabbage, Kale, Collards, and Chard.

The Poop Rule:

If you see undigested vegetables or fruit in your bowel movements (poop) then cook, steam, stew your veggies and avoid raw fruit for a while.

Fats, Oils, and Spices

Olive Oil, Coconut Oil, Avocado Oil, Suet, Tallow, Turmeric, Ginger, Garlic, Cinnamon, Rosemary, and Thyme.

Recipe Ideas




Golden Mylk and Berry Chutney

Salmon Chowder

Turkey Stew

Lamb Tagine

Roast Beef and Roots

Prawn Stir-Fry

Sausages and Braised Cabbage

Avocado and Cucumber Salad

Smoothies, Blender Salads and Pureed Meals.

If you can rest and reset your health, you will almost certainly experience significant improvement.

After 10 days to 3 weeks it will be time to enter Phase Two!

Mindfulness and Fitness

The ideal approach to Phase One would be to stay at home or go to a retreat center. 

The Ancestral Autoimmune Protocol (A-AIP) is meant to bring you into a calm and nourishing environment, where you can feel supported enough to reflect and learn to hibernate inside and out. The following activities are very beneficial to resting and restoring all aspects of your physical, mental, and emotional health.

Meditation goes back as far as hunting and fishing, or the first person to have anxiety or insomnia. I cannot think of a more universally accepted skill and daily habit to help people wind down from modern life. Even if it is only 5 minutes a day.

Qi Gong, Yoga, and Deep Stretching are all excellent choices when you need to release tension and stress, improve circulation and restore optimal biomechanics. All you need is some music and a floor! And the music is optional…

Epsom Salt Baths have been shown to reduce muscle tension, stimulate capillary circulation, as well as improve your depth of sleep.

A Sensory Deprivation Tank or Float Tank Therapy can help you unwind your Central Nervous System and release old memories and traumas. Float Therapy is also a form of spiritual practice for those who are seeking visionary guidance.

Primal Swimming is the only exercise I  recommend during Phase One. This fun way of imitating our early Ancestors goes like this. Tread water for a while and then dive to the bottom, touch the bottom and return to the surface. If you are a strong swimmer go to a deeper part of the pool. If you are VERY fit and feel like you are going crazy without some exertion, throw a weight into the deep end. dive and pick it up until you are tired. *Only try this if you are an experienced swimmer.

Acupuncture and Massage Therapy also reduce pain, alleviate stress, and improve circulation. Hands-on therapies that immediately change your state of being are important if you tend to addictive behaviour. If you can predict some tangible stress relief, you are less likely to feel impatient or need compensate if you have a bad day.

Speaking of chilling out, avoid getting cold if you need to go outside to access any of the above opportunities while you are fasting. Once you are eating an Anti-inflammatory diet, you are good to go!


Anti-inflammatory Herbs and Nutraceuticals

Immune Modulators

Immune Adaptogens

Golden Mylk 

Trace Minerals

Natural Sleep Aids

Circulation Support

Support and Spiritual Practice

Healing is a Team Sport. We all need connection and allies on a healing journey. Find a friend and family member and ask them to be your ‘Reality Buddy’ for the next few weeks or months. Changing your life is hard and can bring up old wounds, insecurities, and traumas. Seeing a counsellor is an amazing opportunity to get to know your strengths, what really matters, and where you need some guidance. Seeking out the right professional support can save months of your life and a great deal of money.

Breathwork is becoming a household word. Finally! Deep, explorative and patient breathing is a proven method to reduce stress, blood pressure, and inflammation. 1Your breathing slows down naturally when you practice the “relaxation response,” a stress-busting technique developed by Dr. Herbert Benson, director emeritus of the Harvard-affiliated Benson-Henry Institute for Mind-Body Medicine. He recommends practicing the relaxation response twice a day, for 10 to 20 minutes. Here’s how to do it:

Inner Reflection and Journaling are two of the most undervalued healing opportunities – because they take time and are ‘unproductive.’ Listening to your internal dialogue can help you learn a lot about yourself, your situation, and your deepest needs. Writing down your thoughts, memories and dreams can help you understand your past and design your ideal future.

Phase One – Six Pillars at a Glance

Michael Smith is an internationally respected Clinician, Author, and Speaker. Michael practices Functional Medicine, Acupuncture, Traditional Chinese Medicine, and encourages his patients to follow an Ancestral approach to lifestyle and diet. Dr. Smith has dedicated 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.

Dr. Smith is also at the leading edge of the treatment strategies, dietary protocols, and the precise lab testing needed to resolve these complex conditions. 

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