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

//Phase Two of the Ancestral Autoimmune Protocol (A-AIP)

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


Reset Your Metabolism, Rebuild Your Membranes and Connective Tissues 

Your Metabolism has momentum and your body has bank accounts!

Before beginning Phase Two, I usually recommend one to two weeks of the Anti-inflammatory Phase One Diet and Protocol.

Tap HERE to go to Phase One

After Phase One, your immune system has had a chance to rest, settle down, and begin the recovery process.

In Phase Two, it is time to reset your metabolism and rebuild all of your membranes, connective tissues, muscles, brain and bones. Your body needs several nutrients and tissue surpluses to heal in this way.

Phase Two also focuses on repairing a leaky gut. A leaky gut happens when the mucosal membrane of your intestines breaks down and becomes porous. A porous or permeable bowel has been associated with the intensity and rate of progression of many Autoimmune diseases.1The intestinal epithelial lining, together with factors secreted from it, forms a barrier that separates the host from the environment. In pathologic conditions, the permeability of the epithelial lining may be compromised allowing the passage of toxins, antigens, and bacteria in the lumen to enter the bloodstream creating a “leaky gut.”

When you are ready, your muscles will need to be active and toned to help keep your Human Growth Hormone (HGH) high for a few months at least. HGH can help your body maintain an Anabolic (growth and repair) state while your whole body heals. After 40 years of age, most people need to exercise regularly to maintain healthy HGH levels.

Phase Two includes a careful but necessary approach to getting fit, especially if you are new to resistance training.

In this article, I will discuss:

      • The importance of momentum and patience
      • Solving the Modern Metabolic Syndrome Crisis
      • How reducing inflammation is necessary for tissue repair
      • The right way to do Collagin Loading
      • How Resistant Starch can repair your Microbiome
      • The Phase Two ‘Scavenger’ Diet
      • The Reason Braising is the BEST WAY to cook Meat
      • Mindfulness Opportunities and Fitness Challenges for Phase Two
      • Supplement Guidelines for Phase Two
      • Spiritual Practices and Personal Support

The Barge Analogy

I often share a story with my patients to help them develop a conscious relationship with the process of recovering from any diagnosis. As a young man I once had the job of driving a barge. Basically, a barge is a giant boat that weighs many tons and delivers a massive amount of cargo. The most frustrating part of driving a barge is when you suddenly have to turn around. Spinning the barge to face the other direction takes a while and you have to be careful depending on the cargo you are hauling.

Once you are facing the other direction, the hard part is actually gaining any momentum in the other direction. I remember once being about two miles along an eight mile trip when my employer called me on the radio and said “you have to come back as fast as you can”.  So I turned the engine down and gradually turned the barge around. I actually went just over another mile in the wrong direction beforebegan to gain any speed in the other direction.

I share this with people because it mirrors exactly the process of going from illness to disease, as well as going from disease to back to health.

Once you get the message that you need to turn things around, your symptoms may keep going towards disease. Depending on your particular barge (body/age/momentum) and cargo (stress/trauma/genetics), the time it will take to actually build up enough momentum to feel you sysmptoms start going the other way.

It doesn’t usually take very long.

It depends of how far out of balance your metabolism is, how aggressive your immune system is, and how long you have been drawing from your body’s deepest tissue resources.

Metabolic Syndrome

If there has ever been a world champion of underlying causes for the modern epidemic of chronic disease, it is clearly Metabolic Syndrome. Also known as Syndrome X, this overall metabolic imbalance is caused by the perfect storm of stress, malnutrition, overeating, poor sleep and an over-reliance on stimulants, sedatives, and intoxicants to get through our day-to-day lives.

Metabolic Syndrome has become a catch-phrase for a chronic excess of Insulin, Cortisol, deficiencies of other regulatory hormones, as well as Neurotransmitter imbalances. The scary part of this, in the long-term, is your body eventually loses its adaptability and begins the slow grind towards exhaustion.

Metabolic Syndrome is a perfect example of a vicious cycle. The stress, insomnia, or chronic pain will convince anyone to seek comfort in anything that makes you feel numb. Those choices change your body chemistry, your mood, and often your self-respect – making numbness sound a lot better.

The Details Are Complicated, But The Symptoms Are The Same:
      • Abdominal obesity – (both visceral and subcutaneous fat)
      • High fasting blood glucose
      • High blood pressure
      • High blood triglycerides
      • Low HDL (the ‘good’ cholesterol)

At present, over half of adults are dealing with some aspect of Metabolic Syndrome.

In Phase Two, you are going to learn how to turn the barge of your metabolism around. By eating a low carb, high fibre, high connective tissue diet, and regular fasting, your metabolism will have to run on different fuels and use different pathways. It takes a few weeks, but with some exercise and meditation, you will feel a lot better and probably need some smaller pants.

NOTE:* If you haven’t read the article on Carb cravings at night yet – check it out here.

Inflammation and Tissue Repair

If your body and immune system have to heal any part of you, there are two conditions that need to be met.

First, the inflammatory response has to be down-regulated long enough for your body’s inner wisdom to say it is time to rebuild. This involves a lot of subtle hormonal communication. If you are not sleeping or stressed out, your body will not get the right chemical message to focus on repair

Second, you will need an abundance of collagen, Vitamin C, recovery time, and some other compounds to ensure proper healing and tissue repair.

The reason that most chronic illnesses are chronic is a dysregulation in the inflammatory process. This can due to stress, low-grade infections, environmental triggers, epi-genetics, a leaky gut, or an imbalance in your microbiome.

Phase Two of the Ancestral-AIP is meant to take one to three months depending on the situation.

Down-regulating your entire immense system, learning to de-stress and rest every day, repair your gut, remove known triggers, and help resolve any latent infections or epigenetic imbalances.

Leaky Guts and Chronic Dysbiosis

One of the most unforgettable facts that I share with people is your Small Intestine’s mucosal membrane is the size of a tennis court, or about 3,000 square feet. Another fact that makes this even more important is 75% of your immune system functions in your mucous membrane.

Hippocrates once said, ‘All Disease starts in the gut.’

The reason so much of your immune system is busy on the inside of you, is your intestines are the home hundreds of trillions of mycobacteria and countless yeast, parasites, and fungi.

ythe front line

mucosal immune 75%

mucosal membral (endo) approx size 3000

if body  is a city gut neighborhood – bad guys come from tells the rest of the city what proteins are fine and which proteins make your whole body dial 911

Your Heroic Microbiome

used to be candida

Collagen and Tissue Repair

The four Phases of the Ancestral AIP are based on the natural process of healing. sprained ankle

step two ROM as membranes heal perfect combo of nutrient density, collagen support, careful resistance training and deep strtetching.

you want your HGH to be higher so you can build the best connective tissue and membranes.

chronis stress and inflammation -continue with phase one

High Collagen foods

Foods that assist callagen

More Seafood and Sea vegetables

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

Sea Vegetables (Arame, Kelp, Kombu, Dulse)

Nose to Tail

Liver, Kidneys, Hearts, Necks, Tails, Hocks, Feet, Skins,and Tongues.

Broths, Shanks, Ribs, Steaks, Wings, Braised Meat.

Fermented Vegetables

High Starch Vegetables

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, Turmeric, Ginger, Garlic, Cinnomon, Rosemary, and Thyme.

A Few Recipe Ideas

Braised Oxtails and Root Smash



Salmon Chowder

Turkey Stew

Prawn Stir-Fry

Fresh Oysters 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 some, if not significant improvement.

After 10 days to 2 weeks it will be time to enter Phase Two!

Braising Meat is Best

context, content and cooking style.

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.

Tension and Relaxation Response


Recapitulation Practices

Circuit Training

Deep Stretching

Postural Alignment


Immune Adaptogens

Trace Minerals

Circulation Support

Neurotransmitter Support

Essential Fatty Acids

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 fw weeks or months. Changing your life is hard and can bring up old wounds, insecurities, and traumas. Seeing a counselor is an amazing opportunity to get to know your stregths, what really matters, and where you need some guidance. Seeking out the right professional support can save months of your life nad a great deal of money.


Rite of Passage/Right Relationship

Poly Vagal Awareness

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. 

YES! Please send me a FREE copy of the Autoimmune Protocol Ebook!

Begin your healing journey with this 65-page guide to understanding Autoimmune Disease and the Ancestral approach to restoring healthy immune function while repairing your body from the inside out.

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