Creating An Autoimmune Paleo Health Plan

Auto Immune Paleo, Blog

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As science progresses, so should AIP.

What I did clinically two years ago with my AIP clients is vastly different that what I do now. As I see it, AIP will slowly fade away as a generalized diet and instead your individualized AIP diet will be the starting place based on your physiology. And the good news…you can do this right now! Right now you can implement the current Epigenetic trends to maximize your health outcomes if you get the right tests and listen to how stress affects your physiology. I am going to share with you my current AIP Complete Program recommendations. A basic guide to get started when you apply both the diet, functional nutrition and the most progressive mind-body approaches. But Note: If you bring this into your doctor and say “Hey, I want all these tests.” They may say no. There are different reasons for that. The top two reasons I notice doctors say “no” are they are not familiar with them or they don’t know what to do with them.  I am writing this post because A LOT of people ask me where to start.  Most of my clients are a year into AIP and still not feeling better, so I needed to figure out why. Diet is very, very important, and yet it holds the least amount of power as I see it. Your relationship to your disease is the most powerful tool you have.

These recommendations would be somewhat tailored for those who are knee-deep into AIP. What separates this kind of plan from other cookie-cutter plans you most likely see on other websites is that this kind of action and recommendation require a practitioner that knows physiology, biochemistry, blood chemistry, supplementation and immune system regulation. And those kinds of practitioners exist, but are harder to find. But, keep searching! Print this list out and take it to your doctor. I recommend this kind of workup before you start AIP so you can get your own personal baseline. Here is the other big news. Taking a heart-centered approach always comes first for me in my practice. That means that even though diet, physiology and supplements are incredibly helpful and important, they come second to love, appreciation and honoring the unfoldment of each person’s internal wisdom walking on the path of illness. Epigenetics through Quantum Loving and Quantum Mechanics come first in my practice now. I take the perspective that working on what you believe about your life will change your life and health the most quickly and profoundly.

Let me give you an example:

Shauna came to see me for AIP. She had Hashimoto’s, Celiac and Lichen Planus. Her ND had her on at least 20 supplements and she was super frustrated and not feeling any better. I got her down to 5 supplements that focused on calming her immune system and healing her gut. Then she did blood work and a saliva cortisol test and saw she has insulin resistance, her circadian rhythm was off and she had iron overload. She started meditating daily and gave herself permission to carve time to read a book every day (her most favorite activity). She worked on clearing her held beliefs that she did not deserve to have “time off” because she was a stay at home mother, and she translated that to not working hard enough. She went full-bore AIP, but still had lingering fatigue and bloating even though she was on digestive enzymes and SIBO probiotics. So she started calming her elevated cortisol at night with topical phosphatidylserine and taking her HRV (heart rate variability) each morning. On the days she scored green she would work out and on the days she scored orange or red she knew she should skip exercise and just be as restful as she could. She also did Array 10 from Cyrex. Turns out she is having an immune reaction to quite a few AIP foods. Kale, zucchini, ginger and coconut just to name a few. The Cyrex Array 10 also told her what non-AIP Paleo foods she was sensitive to..namely almonds, eggs, vanilla and dairy. She also found out she had elevated Epstein Barr antibodies, so she went on a protocol for that. In doing this whole protocol, Shauna had an outbreak of Lichen Planus. She took it pretty hard because she was working SO hard and doing so much work to ‘get healthy’ and this felt like a failure. But I encouraged her to take a different perspective. To consider the idea that the Lichen Planus was ready to tell her something it had not been ready to tell her before simply because she wasn’t ready to hear it. Skin eruptions can be linked to anger issues and I wondered if her body was erupting some untold anger that was ready to be dealt with. We talked about big events in her life and it turned out that the Lichen Planus first showed up 10 years prior when her very special aunt died suddenly. Heartbroken and grief-stricken, life seemed unfair and cruel. Shauna was very angry at God for taking away her beloved aunt. But her religious upbringing made her feel ashamed at being angry at God and so she silently suffered and stuffed her anger down with exercise, distraction and working on finishing her Masters Degree (in guess what..psychology!). Shauna was resistant at first about considering this was linked to her health. She had been in therapy for the last 5 years constantly working on herself and thought that her grief was already resolved.  But I asked her to consider it to be another layer of humility and compassion training that would ultimately be useful for her psychology practice and actually add to her life by resolving. Now it was time to come to peace with another layer of anger and let herself feel sad and upset. She started doing this first by just admiring her anger and being open to it. We developed a plan  to help her cooperate with her anger in ways she felt was manageable and not overwhelming. She also had fears that tapping into her anger would overwhelm and take over her life. So we worked on those too. She went to a homeopath and who recommended a remedy for unresolved grief. She also dedicated herself to re-frame her life from a place of wholeness. We created tailored affirmations just for her and she created post-it notes for her car and inside kitchen cabinets so she could be constantly reminded of the value of her journey. When she decided to cooperate and trust the anger and give herself permission to feel the heartbreak, the Lichen Planus got better. With the blood chemistry, Cyrex Array 10, new supplement regime, modified AIP diet and new outlook on life, Shauna reported she felt 95% better.

I have gathered my new list of recommendations I tell my AIP clients to look at in addition to being on the AIP diet. Finding a practitioner usually is the hardest part. Someone who has a very good grasp on this kind of information can be a bit challenging. I say this because it is the number one complaint I hear from clients. When you look for a practitioner, consider what is important to you. Use your loving discernment and trust you can do this journey.

1. Cyrex Lab Array 10

I am seeing people wade through AIP and still feel not good enough. That is because they are complying perfectly with AIP and and yet they are reacting to things like pineapple, salmon, avocado or coconut for example. All foods allowed on AIP. There has been a lot of controversy about food sensitivity testing in the Paleo world, and while I agree to an extent with those conclusions, I think a closer look at how each lab handles testing rather than disregard testing should be considered. Instead of throwing the baby out with the bathwater, I consider it worthwhile to examine each lab and their practices to draw a conclusion about their validity. I consider it the most valuable starting point when going on an elimination diet to gather all the information and make a decision that feels best to you.  Cyrex Labs Array 10 is the only food sensitivity panel I recommend. They use 2 standards of deviation, have in-house quality standards, clean their ELISA plates regularly and use both cooked and uncooked foods/proteins in their panels. UNHEARD of in the testing world. Light years ahead of the pack. You can read a bit more about how they are different here. Btw..I don’t get a kickback from Cyrex Labs. I don’t even have an account with them. If you decide to go forward with a test like this, use it in conjunction with an entire plan. It is just one piece of the puzzle. Also, if you are IgG deficient, you won’t get reliable results and may have false negatives. Your doctor can and should take into account your IgG response. While not very common, I still see some folks with IgG deficiency and it will affect a test like Array 10.

I recommend this test because you may react to AIP foods and you should know which ones before you start AIP. Then you can modify AIP to you and your physiology. I prefer this OVER elimination and challenge diets because those diets take months to complete, are difficult and frustrating for most people. However, I only recommend Cyrex Labs Array 10 over elimination/challenge diets. If you are not going to do the Cyrex test, I recommend elimination/challenge diets. But here is the deal. Yes, it is expensive. But by the time you have reached AIP as an option, you are probably a bit sick and tired of being sick and tired. And because I personally would rather spend money to save myself time/grief/frustration/human error I choose lab work. Every single time.

2. Know your Blood Chemistry

If you are anemic (and there are 25 different kinds of anemia patterns) you will not heal even with the perfect AIP diet. Is your doctor looking for all of them? Or just iron deficiency anemia? Do you have slightly elevated blood sugars? Or pernicious anemia? What if you have an undiagnosed Iron Overload and you keep eating liver daily because it is nutrient dense? All of these questions happen daily with my crowd. Here is my favorite blood work to ask your doctor to run, or to run yourself. has this test called Apex 5 Panel for $350 in most states.

Comp Metabolic Panel w/eGFR
CBC w/ Diff
C-Reactive Protein
Hemoglobin A1C
TIBC (total iron binding capcity)
% iron Saturation
Serum Iron
Sed Rate
T-3 Uptake
T-4 Thyroxine  Total
T-4 Thyroxine Free
Reverse T-3
Free T3
Uric Acid
25 Hydroxy Vit D
Standard Urinalysis

If you have blood sugar issues that go unresolved, you will not heal even with the perfect AIP diet.

3. Know how your Vagus Nerve is doing by measuring your HRV (AKA: The H-P Axis riddle?)

The gut-brain axis terminology is everywhere. The Gut-Brain Axis is the map of the route the Vagus Nerve takes from the hypothalamus around the heart down into the gut. The Vagus nerve is the gut-brain superhighway. But how do we measure the vagus nerve and how well it is functioning? Unfortunately, we can’t directly measure the vagus nerve. But you can indirectly measure it by measuring Heart Rate Variability. HRV is the measure of the variation in time between heart beats. Turns out that measurement can tell us a lot about the autonomic nervous system and how well we as individuals respond to stress. And how you respond to stress is now considered the biggest variable in turning off and on genes of disease. Ground zero for monitoring the autonomic nervous system is the Vagus Nerve. When the vagus nerve is sluggish from disease, pollution, thoughts, stress and bad diet it is known to affect vagal tone. Low Vagal Tone may be implicated with: depression, constipation, low gut bacterial diversity, slow transit gut times, digestive secretions, anxiety, inflammation, co-infections, neurotransmitter issues, adrenal fatigue. I know I left some out..but that was just off the top of my head. The vagus nerve is ground zero for communication between the GUT – BRAIN – HEART. That is pretty profound. And while vagal nerve exercises are helpful and I have been recommending them to my clients the past year (gargling, singing, deep belly breathing) implementing them is just sort of a stab in the dark because we cannot measure how well that is affecting you. Until now.

Heart Rate Variability is an indirect way to measure Vagal Tone. The higher your heart rate variability is, the better your vagal tone. Heart rate variability is the measurement of the heart between heartbeats. This essential for pulling together how well your parasympathic and sympathetic nervous system is working. When you implement strategies like meditation, love, acceptance, relaxation, mindfulness, exercise, sleep, diet and joy into your life, your vagus nerve will work more efficiently. When you vagus nerve works more efficiently, your gut and brain communicate better. I have recently started measuring my HRV (heart rate variability) daily to get a baseline of how well I am integrating diet, sleep, love, meditation, mindfulness, supplements and exercise. I use the Polar Heart Monitor with Bluetooth and the Elite HRV app. Every morning for 2 1/2 minutes I take my HRV and get a score the Elite HRV app on my iphone calculates for me. Then I know how well MY body will manage stress of all kinds. If my HRV for instance is not high enough (the Elite HRV codes your HRV measurement into green, yellow and red categories to make it simple to know how prepared for stress you are that day) then I can make decisions about exercise, how long I will meditate or being very diligent about having a super clean diet that day.

A few places to read up on Vagal Tone:

4. Examine The Beliefs About Your Life

This may be the most difficult but powerful path. What you believe about your life makes up the life you live.  When we bring conscious the limiting beliefs we made up at one time that may have served us for survival (ex: “I can’t trust life” when you were beaten as a child by a parent) they can be resolved.  As life unfolds, you no longer need certain beliefs that once served you.  But, because life promotes what we believe to be true, unless we change what we believe they will perpetuate and color how we live life. I suggest bringing  conscious the untrue beliefs we have about life and resolve them through forgiveness and love. Illness is a very useful opportunity to resolve those beliefs because it so clearly shows us what is working or not working in life. If for example you hold the belief that “life is hard,” it will color your life and reality. It will continue to promote a stress response in your autonomic nervous system. Doing yoga and deep breathing (while very, very wonderful and helpful) may not resolve that belief. That belief continues being promoted because you still believe it. I suggest a plan that will help uncover your beliefs so you can discern what may be contributing to your health. When we decide to look at what we believe about life, we can decide to engage those beliefs, forgive and release them, Then joy can come forward and wisdom is gained as we change the relationship to our circumstances from hostile to cooperative. I suggest the use of self-love, compassion for our path in life and forgiveness (one of my favorite techniques is Ho’oponopono).

A side note: Being positive is great. But I don’t buy into the whole “I have to be positive to heal” because that can trap you into the idea that if you are not positive you are failing at health and healing. The whole point of The Loving Diet™ is to come into cooperation with life and everything in it, which includes good and bad in our life. Life contains hard and difficult things along with beautiful and copious amounts of joy.

5. Find and Treat Co-Infections

Any virus, parasite, yeast or bacteria can be a co-infection. They can be acute, chronic or sub-acute. They can swing from sub-acute to acute. Co-infections are somewhat of an epidemic in autoimmunity. I think autoimmune disease can make us more vulnerable to infections, and infections can make us more vulnerable to autoimmunity. Either way, if you have a co-infection and no one is finding and resolving yours, you won’t get better on AIP. It is like trying to bail out water on a sinking boat with a small cup. Yes AIP will lower inflammation (as long as your not eating AIP foods you are sensitive to!) but it will not lower inflammation enough to regulate the immune system when co-infections are involved. That is not to say that there is not cases where someone ate nutrient dense and their Epstein Barr finally stop re-flaring. But I don’t see it often. To find co-infections, you can look at white blood cells on blood work, check out bacteria in stool tests, examine old fillings and root canals, use organic acid or stool tests to find candida and parasites and/or do a viral panel like the one from Immuno-Science lab. The tricky part of this science is finding a practitioner who can can treat you while you have autoimmune disease and also resolve the infection. Part of your immune system is over-reacting and part of your immune system is under-reacting. I find co-infections to be the very hardest part of treating autoimmunity.

Some common co-infections that can be associated with autoimmune disease:

SIBO, candida, herpes, c-diff, EBV, giardia, pinworms, hepatitis, chlamydia, borrelia, babesia, mycoplasma, h-pylori

A link to a great podcast that talks about co-infections and autoimmunity:

Essential Reading about Co-infections:

Why Can’t I Get Better? Solving The Mystery of Lyme and Chronic Disease by Richard Horowitz

6. Other Helpful Tests:

Do you need all of these? No. But, these are the tests I find most useful. Almost all of them can be found online to purchase for yourself. Doctors usually don’t run these tests because 1. they don’t know how to interpret or understand them 2. they think it is an unnecessary cost for insurance.

23 and me

Stool Test (Genova, Doctors Data)

Saliva Cortisol Test (Bio Health)

Organic Acids (Genova)

Methylation Pathways (Doctors Data)

Gut Permeability Test (Cyrex Labs)

Immune Reactivity Panel (Cyrex Labs)

Viral Panel (ImmuneSciences)

UBiome (the ultimate test for learning the bacteria in your gut!)

7.Valuable Resources for Research:

Carrick Brain Center (if you have brain autoimmunity, this is your place)

Genetic Genie (will interpret your 23 and me results)

MTHFR-Support (will interpret your 23 and me results)

Dr. Lynch from

Dr. Grace Liu from Animal Pharm


8. Essential Reading!

The Biology Of Belief by Bruce Lipton

The Seekers Guide by Elizabeth Lesser

Why Can’t I Get Better? Solving The Mystery of Lyme and Chronic Disease by Richard Horowitz

Childhood Disrupted: How Your Biography Becomes Your Biology and How You Can Heal by Donna Nakazawa

Diet alone will not heal us. But your diet carries a large role in lowering inflammation. I consider diet to be the p.s. at the bottom of your life letter. The given. The part you just do. And now with Cyrex Array 10, you can create your own version of AIP that is applicable to you and your immune system. Brilliant. The more science progresses, the more we know exactly what and why your body needs what it does. Diet is merely a tool in your tool bag. But, what is your tool bag made of? Resentment? Fear? Isolation? Love? Tenderness? Gratitude? If you listen very carefully to all the leaders in this field and read all the literature, you will see that stress and how we manage stress is paramount. What you believe about your life is the nexus point for the stress you hold in your body and health.

If you pull the string called “stress”, you will gain very valuable information about why you think what you do. How you respond to stress is based on what you believe. Mindful practices like meditation, yoga, NLP, tapping and acupuncture are invaluable in assisting with this. They will help regulate your stress responses. However, I encourage you to go even deeper and consider there is tremendous value in examining the message your illness has for you by uncovering what you believe from a place of cooperation, trust and peace. Then you will get to the bottom of things. There you will  truly use your illness to springboard into wisdom.


  1. Cam

    Fantastic post Jessica! I love that you have covered more than just the usual suspects and have remembered that we are energy beings as much as physical beings.
    Thanks for sharing.

  2. Melanie

    Thank you for sharing this! I wonder what you might suggest in place of the Cyrex Lab Array 10? I live in Canada and unfortunately the test is not available here yet.

    • Jessica

      Hi Melanie! I don’t think Cyrex is in Canada yet….if I hear otherwise I will message you. You can also ask them on their fb page! warmly, jessica


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