My Experience with the Paleo Autoimmune Protocol

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a basket of eggs

“I wish for you a lifetime of eggs.”
~ Colleen Michaels

Where I Started

I shared part one of my story back in January when I started this blog. I talked about the onset of rheumatoid arthritis, my choice of the GAPS diet for dietary healing, and the results of that diet, which were profound. But after 5 months on GAPS, I plateaued in my progress, so I decided to try the Paleo Autoimmune Protocol (AIP). It’s now 9 months later, and here are the results:

Excruciating daily joint pain flares Moderate flares a few times per month No flares
Extremely stiff mornings & evenings Semi-stiff mornings Barely stiff mornings
Intense daily pain Mild daily pain No daily pain
Weather affects joints Weather affects joints Weather no longer affects joints
Pain interrupts sleep Sleep OK but get sore after 6 hours Sleep deeply and long most nights
Exhausted Normal energy High energy
Disabled in many ways Functional but weak Getting stronger every month
Couldn’t exercise at all 15 minutes on the exercise bike and gentle stretching Long daily walks, weekend hikes, gentle strength training
Road trips are painful Road trips cause stiffness Road trips are comfortable
High doses of painkillers daily 1 Aleve tablet morning and night 1 Aleve tablet morning and night


Food Reintroduction Results

The AIP is an elimination diet, where you avoid certain foods for a minimum of 30 days and then reintroduce them, one at a time, to test for food intolerance. Here’s what my body had to say:

  • Eggs: I reintroduced egg yolks first, and then whole eggs. I had no reaction to either one and happily included them back into my diet.
  • Chocolate: I reintroduced cocoa next because I missed it, and I believe we all need indulgences, even on restricted diets. Luckily, my body responded well. Note: I made homemade chocolates to be sure there were no hidden ingredients or cross-contamination issues.
  • Nightshades: In this category, I decided to reintroduce nightshade spices before the vegetables. I made some taco burgers and ended up having a huge reaction. My whole body became tender. I felt like I was 90 years old; all movement hurt. The pain made sleep difficult, and it took a couple of weeks before my body returned to baseline. I didn’t risk trying nightshade vegetables, since I reacted so strongly to the smallest amount of spice. They’re out of my diet long-term.
  • Dairy: First a confession: I never removed ghee from my diet. I felt like I was giving up so much already. However, I removed all other dairy, and chose to reintroduce grassfed butter first, fully expecting to eat it without a problem. Results? I got a huge stye on my eye, flared in two joints, got constipated and had PMS during my next menstrual cycle (something I hadn’t experienced since starting a healing diet.) A wise woman would have stopped there, but I had been told that: (1) goat’s milk is different from cow’s milk, (2) raw milk is better than pasteurized, and (3) fermentation makes it easier to digest. So, once I felt normal again, I made some raw goat’s milk kefir and had a smoothie. I flared in two joints again, felt stiffness bodywide, got 2 more styes (smaller ones), and my PMS that month was out of control. So, for my body, dairy is dairy, and it doesn’t like it! If any of you are surprised that dairy affected my hormones, I was, too. I knew that conventional dairy had hormones added, but I didn’t realize that raw milk naturally contains 28 different hormones. I was reminded that dairy is meant to be consumed by baby animals who need those hormones to grow. Their affect on me as an adult human was quite different. Dairy is out of my diet long-term. Update: Since writing this post, I have met a number of people who react negatively to ghee, so in 2014, I removed it from my diet to see if it was the key to my remaining inflammation. Result? I flared upon reintroduction. Unfortunately, its removal didn’t eliminate my need for Aleve, but I’m glad to have removed a source of hidden inflammation in my body. I now recommend anyone new to the AIP go ahead and eliminate it for at least 30 days and reintroduce, to see how your body responds. Interestingly, my polls in the autoimmune community show that most people who tolerate ghee tolerate butter as well, and those of us who react to butter also react to ghee. So even though it’s advertised to be allergen-free, there is something in it that can affect autoimmune expression. Read my complete research into ghee in my post: To Ghee or Not to Ghee.
  • Nuts: My reaction to nuts was more subtle. If you read my article on reintroducing foods on the AIP, I talk about 2 phases: (1) Reintroduce the food once, and monitor your body for the next 3 days. If you have no reaction, that food is potentially safe for you to eat. (2) To confirm this, eat a little bit of this food every day for a week, and monitor your body again. Food intolerance seems to come in two forms: either a strong reaction (like with the nightshade and dairy paragraphs above) or a cumulative inflammatory response (where you slowly feel worse the longer you eat the food). This was my experience with nuts. I took a couple of months to test them thoroughly, trying nut flours vs. nut butters vs. toasted nuts vs. soaked/dehydrated nuts vs. different varieties of nuts. I really like nuts, and was hoping I’d find a type that my body loved! What I discovered was that, to my body, a nut is a nut. If I just eat a small amount for one day, the reaction is so minor I wouldn’t notice. However, if I eat them daily, I develop insomnia within the first couple of days, digestive discomfort midweek, and increased joint pain by week’s end. So what does this mean for me? Whereas I’m acutely intolerant to dairy and nightshades and will avoid them altogether, I’m only moderately intolerant to nuts. As I continue to heal and my digestion improves, I expect to be able to eat nuts more comfortably. For now, though, I’m avoiding them.
  • Seeds: My reaction to seeds was very similar to my reaction to nuts, but milder. I had no digestive distress at all. With seed butters and soaked/dehydrated seeds, it took 4 days of daily consumption before I noticed my joints becoming more sore. With raw or toasted seeds, I noticed increased tenderness on day one. So, there’s more nuance here. I would say I am only mildly intolerant to seeds. For that reason, I include soaked/dehydrated seeds in my meals occasionally for some extra crunch and flavor, but I don’t make them a part of my daily diet. However, this will probably be the first group I’ll be able to eat again without trouble.

Paleo AIP Reintroduction Guide | Phoenix Helix

Emotional Experience

When I started AIP, it was hard. During the elimination phase, I felt deprived, and a little pissed off that I had to do it. However, I really wanted to feel better, and within a few weeks, I started to notice improvements. So, obviously at least one of these foods was problematic for me. My hope was that it would only be one food, so I was looking forward to the reintroductions with optimism. My original intention was to do the elimination protocol for 2 months before reintroducing foods, but at the 6 week mark, I found myself getting angrier at my food limits, bored with my food choices, and resentful that the joy seemed to have been sucked out of my kitchen. I even started craving standard American junk food, something I hadn’t craved since starting a healing diet. I was afraid that I might binge and set myself back. I was also afraid that my emotions themselves would cause my joints to flare. I had experienced that in the past, and I didn’t want to create a situation where it would happen again. Elimination diets are usually done for 30 days, and I had set my own 2-month goal randomly. So, I started reintroductions after 6 weeks.

The reintroduction phase ended up being an emotional rollercoaster. With each reintroduced food, I had high hope that I would be able to eat it without trouble. Every time my body reacted negatively, I grieved the loss of that food, and I also had to deal with the symptoms of the reaction itself. Meditation was an important part of my daily routine. I discovered that you need a lot of patience for the reintroduction process; it usually takes many months to complete the reintroductions, and if you rush things, you blow the whole experiment by introducing too many variables at once.

The other aspect of the rollercoaster were the positive emotions I experienced: a deep gratitude to have such clear communication with my body, and the joy of feeling better and better the longer I was on the autoimmune protocol. By the last reintroduction (which for me happened to be dairy), I wasn’t grieving at all any more. I just wanted to be done and know which foods I could eat and which I needed to avoid. During the elimination phase, I gave up all these foods based on a theory. By the end of the reintroductions, it was no longer theoretical. It was very practical. I had reintroduced some foods successfully and happily, and the ones I could no longer eat gave me very clear reasons for avoiding them.

I read an interview with Michael J. Fox, where he talked about his Parkinson’s disease. This quote reflects how I felt at the end of my AIP experience:

“There’s an idea I came across a few years ago that I love. My happiness grows in direct proportion to my acceptance and in inverse proportion to my expectations. That’s the key for me. If I can accept the truth of ‘This is what I’m facing – not what can I expect but what I am experiencing now’ – then I have all this freedom to do other things.”

What Symptoms Remain?

I’ve come a long way, baby. In the summer of 2012, I didn’t know how I could make it through each day. When I re-read part one of my story, my eyes filled with tears. It was such a painful and terrifying time in my life, and I’m so glad it’s in my past. In contrast, I feel good now on a daily basis, and every month I regain an ability I had lost. But I’m not yet symptom-free:

  • When I walk and hike, there is occasional tenderness in the balls of my feet. It’s not to the level of pain, but it’s no longer that glorious “taking my feet for granted” that I felt before developing RA.
  • While my hands no longer hurt, and I’ve regained grip strength, I have two fingers that have restricted range of motion. As I’ve healed and my inflammation has lessened, other joints in my body have returned to full range of motion. Will that happen to these joints, too? I don’t know; time will tell.
  • My joints aren’t as strong as they were pre-rheumatoid. The heavy lifting, crossfit phenomenon that’s so popular in the paleo community, is beyond me. However, I can do gentle strength training, and that suits my personality better anyway. I can get up and down from the floor easily now, when prior to AIP, that was painful. But when I do yoga, certain poses like plank and downward dog put too much pressure on my joints to be comfortable.
  • I tried recently to go off the small dose of Aleve I’m taking. Unfortunately, within 2 days, the inflammation ramped up to an uncomfortable level, so apparently I still need this medication. The good news is that I don’t need any steroid or immunosuppressant medication, and my NSAID dose is less than any prescription. Some day, I hope to no longer need it, but I haven’t yet reached that day. (Read this article for my perspective on NSAIDs and the autoimmune protocol.)

Need Help With Your Own Reintroduction Process?

I’ve written a detailed guide to help you do it correctly. Learning to communicate with your body like this is a powerful gift. And if you’d like to read other people’s experiences with reintroductions, check out this series of interviews.

What’s Next for Me?

The holy grail for me is full remission – turning my rheumatoid genes back off again. I’m not there yet, but I am managing my symptoms very well, and it feels like deep healing is happening inside my body. I’m very grateful to feel this good.

My plan going forward is to keep doing what I’m doing. On GAPS, I plateaued in my healing. On the AIP, I haven’t. Every month, I improve. And that’s in spite of the fact that during the autoimmune protocol experiment, my body kept getting spiked with inflammation as I reintroduced foods to test for tolerance. This is a necessary part of the process, because it’s how you communicate with your body and really understand why certain foods need to be avoided. However, Dr. Sarah Ballantyne says, “If you continue to eat something that you have an allergy or sensitivity to, it is very difficult for your gut to heal and for your immune system to deactivate.” Now, that I know what foods to avoid, I’m looking forward to my healing progressing without interruption.

I also have options for future experiments if I plateau again, which are listed on the Autoimmune Protocol page. There are also more supplements I can try. But I think healing through diet mostly requires time and patience. Dr. Terry Wahls (who is in the process of reversing her MS) says that autoimmune disease takes years to develop in the body, and  therefore takes many years to heal. As long as you’re improving, you’re on the right track.

This is me, hiking again, after a year of healing. That’s bliss in my smile:

Eileen at the top of a mountain with her hands in the air, celebrating hiking again

Updates to My Healing Journey

It’s been a few years since I wrote this post. The paleo autoimmune protocol made major improvements in my health and remains an important part of my health protocol. It just wasn’t enough to control my disease altogether. I now combine diet, lifestyle, and medication to feel my best. Here’s the journey of where I started, my decision to take medication, and what I’ve learned in 5 years of healing:

Special thanks to Nicole of Eat This Poem, for the opening quote that starts this post. I read the poem on her website the very week I was reintroducing eggs, and as it was the food I missed the most, the timing was perfect.

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