Reset Your Metabolism

Rebuild Your Connective Tissues 

Your Metabolism has momentum and your body has bank accounts!

Before beginning Phase Two, I usually recommend 1 – 3 weeks of the Phase One Anti-inflammatory 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. [1]The 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 … Continue reading

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
      • How Resistant Starch can repair your Microbiome
      • The Phase Two high Collagen Tissue Repair 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 Four Phases of the Ancestral Autoimmune Protocol

If you have not read the articles on the other Phases, 

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

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 before The barge began 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 your symptoms start going the other way.

It doesn’t usually take very long.

It depends on 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 Why  People Have Carb Cravings at Night – 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, Ellagic Acid, 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 six weeks to three months depending on your situation.

The natural process of down-regulating your entire immense system, learning to de-stress and rest every day, repairing your gut, removing known triggers, and helping resolve any latent infections or epigenetic imbalances is as unique as each individual.

Leaky Guts and Chronic Dysbiosis

One of the most unforgettable facts that I share with people is that 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 of hundreds of trillions of mycobacteria and countless forms of yeast, parasites, and fungi. If you are stressed out, your immune system is low, or your diet is feeding the wrong ratio of microorganisms in your microbiome. I will introduce your microbiome in a moment.

If like most modern humans, you have had a parasite and or taken antibiotics, you will probably have a low-grade infection in your intestines. This creates chronic inflammation and slower tissue repair. Depending on your diet, stress level, and how your genes are adapting to the modern world, you may be prone to a chronic breakdown of the Mucous Membrane of your small intestine. This is usually referred to as a porous bowel or a leaky gut.

Leaky Gut Syndrome is often at the root of many immune system problems, from allergies to degenerative autoimmune diseases like MS and Parkinson’s Disease. The Phase Two protocol and diet will help your Mucous Membrane repair itself and help you feel the difference in your vitality when your immune system is not on red alert.

The Ancestral Autoimmune Protocol takes time. Keep in mind that you are accomplishing two things at once. You are repairing your body and immune system while you are learning what helps the most and which of the Four Phases makes the most difference in your health.

Your Heroic Microbiome

The Term Microbiome refers to an ecology of thousands of species of microorganisms that live in communities of trillions of miniature citizens that live on EVERY surface of your body. As unbelievable as that is, consider this. The genetic diversity and balance, as well as the overall activity of every specific region of your microbiome, tells your immune system what is going on in the world – and how to behave.

In Phase Two you are going to focus on starving the overfed starch and sugar-loving species while feeding the most stabilizing and protective species. Fermented foods will also start making a regular appearance on your weekly menu.

Collagen and Tissue Repair

The Four Phases of the Ancestral AIP are based on the natural process of healing, especially the process of tissue repair.

If you had a sprained ankle, the first step is to reduce the inflammation and swelling (Phase One). Then you would have to wait a few days for the soreness and stiffness to allow you to move your ankle around and give your repaired connective tissue a try. Those inflamed and stiff days are important. During this time, your body is doing some incredible things on a cellular tissue level.

Every tissue repair process in your body, from a sprained ankle to an ulcerated colon, begins with the formation of a collagen matrix. After your body has built a hammock-like structure, other kinds of collagen are used to build membranes, fascia, tendons and cartilage. As long as the inflammation stays under control (stress and environmental/food triggers), your metabolism is stable and your diet is high in the right proteins, vitamins, and co-factors to maintain consistent and generous support for tissue repair.

Trying to speed things up too much or taking the process for granted is the same as asking your body to keep complaining – especially as you age or when you have a flare-up. For the rest of your life. I can say from personal experience that giving your body a focused period of time to fully repair and restore itself is much wiser than getting back to work or the gym too soon.

There is a concept in Chinese Medicine called Jing – which describes your body’s adaptive resources and capacity on a cellular, nutritional and hormonal level.

I think of Jing as Mojo. 

As a patient who has recovered from a few Autoimmune flare-ups, I can attest that the difference between exhaustion and abundant energy is the most important resource to be aware of. Your body’s ability to self-regulate and self-repair is amazing and also very expensive. I mean expensive on a tissue level.  You only have so much of every vitamin, mineral, cofactor, enzyme on any given day.

I think of this as my tissue bank account.

It could be Vitamin B12, Vitamin C, Calcium or it could be Collagen. Your body has many different tissue bank accounts and the modern diet is very low in collagen. This is why the hospital used to give people gelatin made from animal skin collagen. Now, many hospitals give patients synthetic Jello, but not that long ago, we still remembered the common sense wisdom of increasing collagen while healing and for the time it takes to get back to physical fitness.

The Phase Two Diet and focus on metabolic stability, high collagen foods,  and whole-body fitness is designed specifically for the purpose of complete tissue repair – throughout your whole body.

Your Ancestral AIP Shopping List

Below is a list of common foods and recipe ideas to choose from.

If you want a more comprehensive list, Tap HERE – What Can You Eat?

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 Foods

Sauerkraut, Kimchi, Kvaas, Kombucha, Kefir, Ginger Bug

High Starch Vegetables

Yams, Sweet Potatoes, Turnips, Beets, Parsnips, Rutabagas, and Squash

Fruit, Berries and Vegetables

Apples, Pears, Bananas, Blueberries, Raspberries, Tart Cherries, Grapes, and Strawberries.

Greens, 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

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

A Few Recipe Ideas

Braised Oxtails and Root Smash

Beef Pho 

Chicken Wings and Sweet Potato Fries

Pork Ribs and Coleslaw

Braised Turkey Necks

Arctic Char Chowder

Braised Lamb Shanks

Liver Patee

Lamb Stew

Prawn Pesto and ‘Pasta’

Smoothies, Blender Salads and Pureed Meals.

Imagine it is winter 10,000 years ago. You would lucky to eat this way for three months.

After one to three months it will be time to enter Phase Three!

Braising Meat is Best

Braising is a method of cooking meat that is usually reserved for the tougher cuts, but can also be used to braise vegetables like cabbage. To braise some grass-fed beef, cut the meat into large and evenly sized chunks. Season with salt, pepper and other spices that will suit the meal you are preparing. Distribute the pieces evenly in a large metal or enamelled roasting pot. Add enough stock, wine, vinegar, healthy fats and oils and other flavourings to the pot until the fluid is about halfway to 2/3 of the way to covering the meat. I usually add some garlic, ginger, onions and fresh turmeric root if I can find it. Dried basil, oregano, rosemary or thyme would be nice too.

It all depends on your desired result.

Next, decide if you are going to braise the meat on top of the stove or in the oven. On top of the stove, you will want to keep it covered turning every hour at a medium temperature. Longer cooking at a lower temperature is ideal. When I make braised oxtails in a normal stew pot, it takes over six hours to completely cook, so that the meat literally falls off of the bone. I often use a pressure cooker for particularly stubborn cuts of meat and bone.

If you braise your meat in the oven, my recommendation is to preheat the oven to 310 F and cook the meat uncovered for anywhere between 3 – 4 hours. Turn the meat over and check the fluid volume every 45  minutes.

How Does Braising Work?

The connective tissue in the tougher cuts and joints of meat is made of myofascial tissue, tendons and ligaments. Although these tissues are made of proteins, they need to be broken down into simpler and softer proteins, especially collagen in order to be easily digested. Similar to making a good bone broth this takes heat, moisture, acid, and time.

Specifically, what we are looking to create is called a Maillard reaction. Pronounced may-Yar, this reaction refers to the remaining glucose in the meat causing an enzymatic process where larger and more complicated proteins are reduced to shorter and more easily absorbed proteins. This reaction not only changes the chemical structure of proteins, but it also changes the flavour in a way that is very palatable to our taste buds.

The Maillard reaction takes place more rapidly at higher temperatures without water but tends to produce carcinogenic compounds and Advanced Glycation Endproducts (AGE’s). The ideal environment for this reaction to occur is at 310 F with about half of the meat uncovered, turning over every 40 minutes. By adding onions and other easily broken down carbohydrates, the glucose, protein, heat and water combination is perfect.

Mindfulness and Fitness

The ideal approach to Phase Two would be to find a friend to go on this journey together. 

Phase Two can take from one to three months so it is a good idea to make a few other intentional lifestyle changes for the same amount of time or longer. This process always goes better if you keep your muscles active and your mind clear and relaxed.

A great place to start is a moving meditation practice. Many people with a chronic illness tend to lose connection and playful trust with their body, so a regular chance to reconnect and play sounds like good medicine. Skills like Qi Gong, Yoga, and Tai Chi, and very enjoyable choices. They have been practiced for thousands of years because they all so effective at helping people stay fit and feel relaxed.

Another great choice for Phase Two is the practice of Journaling. Some people prefer to journal in the morning and other people like to journal at night. The Ancestral-AIP Protocol can change your life and your health in some amazing ways. It can also be a powerful time for self-reflection.

You will get the most from Phase Two if you keep your muscles toned, flexible, and active.

If you are new to resistance training, the best place to start is Circuit Training. This form of exercise will reawaken the mitochondria in all of your muscles, improving your metabolic resistance and increasing your Human Growth Hormone (HGH), which will help all of your body heal.

Another good place to start in Phase Two is deep and slow stretching. Either along with resistance training or on its own, stretching can excite your muscles, nerves, tendons and fascia.

Healthy animals stretch every day. 


Vitamin B Complex
Hormonal Adaptogens
Immune System Adaptogens
Digestive Support
Vitamin C 
Ellagic Acid

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.

Phase Two is going to test your boundaries – especially with patience and discernment. We all get nervous, bored, lonely, angry, resentful, and seek out distraction or comfort. We all want to be able to control how we feel.

I believe that the ability to shift your state is your birthright.

Human beings have used experiential ceremonies for tens of thousands of years to connect with something deeper and feel transformed or healed in the process. The safest way to explore and altered state in the middle of a busy week is Breathwork.

Breathwork is a huge subject. There are many styles, systems, desired outcomes, and the amount of time or regularity of practice required. There are many resources online and free videos on Youtube.

If you are interested in learning Qi Gong and Breathwork, check out my other website:

On any kind of Healing Journey, it is assumed that you are going to be honest with yourself in some very new ways and that you are going to have to trust yourself on the way through that process. The best place to find that self-trust is through a Rite of Passage. Imagine how you will feel knowing that you can commit and show up every day. That is the best way that I know of to test and improve self-trust.

For most of my patients, Phase Two takes about two months. In many cultures, seven weeks or 49 days is a sacred period of time. Perhaps, after a week of preparation, you could commit to a morning walk or workout or meditation session, a Phase Two diet, Daily supplements and at least 2 litres of water a day.

You are going to be eating a lot of animal protein.

The last form of support and spiritual practice that I encourage in Phase Two is called Right Relationship. Humans are primates and all primates have an instinctual need for connection and collaboration. The term Right Relationship can sound like it comes with a list of rules, but it is much more invested in finding connections that feel right – on a primitive and instinctual level. If you want to learn more about your instinctual connection to other people, I encourage you to learn about the Poly Vagal System.

It may change your life and how you see your past.

Phase Two – Your Six Pillars at a Glance


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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.


    1 The 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.”