Top 3 weight management strategies on the Autoimmune Protocol

JFC Petra WW and AIP1This is the 4th in a series of posts about Women, Weight and the Autoimmune Protocol (AIP).

Find the first on Joanna Frankham’s blog.

This post focuses on the top-three strategies for weight management identified through research that Joanna and I conducted with 20 long-term AIPers, 90% of whom indicated that weight management still causes them stress.

Our Method

Through a confidential survey, one question we asked respondents was about weight management strategies that worked for them while on the AIP. The question wasn’t multiple choice: people had to come up with their own ideas.

11 of the 20 women who participated in the survey had not yet identified things that worked. Nine of the 20 women had. From these responses, three strategies emerged. Continue reading

Autoimmune Citizen Science


Vivek Mandan

Many people who improve their autoimmune symptoms want to share what they have learned, so others can benefit too.

Most people just start a blog.

Vivek Mandan is creating Autoimmune Citizen Science, a free site that will enable anyone with an autoimmune condition to track personalized data to support their healing process.

Vivek and his team are looking for testers for the beta launch of their site this Spring. I’ve already signed up. Anyone else who is interested in the potential of measurement as part of their recovery will want to scoot over to Autoimmune Citizen Science to sign up as a beta user, too.

Consider this post to be your personal invitation from Vivek!

This month, I interviewed Vivek, who is 24 and lives in Ohio, USA, to find out more about his experience with autoimmune disease and about his vision for how Autoimmune Citizen Science could change the way we research and treat complex chronic health conditions. Continue reading

When Genitals are Involved (& not in a good way!)

SexualityA lot of people have a secret.

I know because they’ve told me.

Their autoimmune disease affects their reproductive organs, but they keep that painful fact to themselves.

Autoimmune diseases that affect the genitals include Psoriasis, Lichen Sclerosis, and Hidradenitis Suppurativa, among others.

Then there are the conditions that affect the reproductive system internally, like Endometriosis.

Still others occur in the pelvic region, like Interstitial Cystitis.

Any of these conditions can have a profound affect on a person’s sexuality.

Why the Silence?

Secrecy about the impacts of these autoimmune conditions is a by-product of our repressive attitude toward sexuality generally (a subject I explore in 3 Steps for Hacking Sexuality).

Today I shed more light on autoimmune conditions that affect the reproductive organs by sharing a case study of a person who lives with genital psoriasis, a form that affects up to 50% of people with psoriasis according to the National Psoriasis Foundation, but is rarely mentioned.

Genital Psoriasis

Websites that address genital psoriasis are brisk and cheerful.

They suggest that with the right ointment and the right attitude, a raw and weeping genital area could be almost invigorating. Or at least no more than an inconvenience. Continue reading

Stress, the Brain and Blood Sugar

Stress, the Brain and Blood SugarStress.

We had a really big, bad financial surprise last week.

It caused a huge amount of stress.

Even as we’ve been experiencing this stress, I’ve been observing how we’ve been reacting to it.

Matthew and I have responded differently:

  • He’s had a major flare of autoimmune symptoms as well as a significant increase in nausea. All the progress he made through his recent biofilm & yeast-busting protocol evaporated almost overnight. Not necessarily permanently. But for the time being, he’s back to where he was at this time last year. Hardly able to eat. Not able to do much.
  • I have been experiencing increased anxiety, but I have also been noticing a decrease in my brain’s ability to function and I’ve been feeling spaced out and irritable between meals. Which I know from experience is related to a blood sugar imbalance.

We already know that Matthew is acutely susceptible to stress. So we aren’t learning too much from the reaction that he’s having.

But I am learning a lot about my own physiological responses to stress, and how it affects my blood sugar and my brain.

Stress, the Brain and Blood Sugar

Continue reading

Personalize Your Diet for Weight Loss

Personalize Your Diet for Weight LossWe each respond differently to the same food.

Specifically, our blood sugar responses differ.

And elevated blood sugar leads to all kinds of health issues, including obesity.

A New Scientific Understanding about Obesity

Like most people who have struggled with being overweight for most of their lives, I’ve suspected for decades that our response to food is individualized.

Because I’ve spent those decades watching my effortlessly-slim sister scarf down all the food she wants.

If I ate like she does, I’d be obese.

I know. Because I used to be.


But now, we have scientific proof to back up what most overweight people have always known…

Breaking News: Maybe Overweight People Haven’t Been Secretly Binging & Lying About It All This Time

Continue reading

Biohacking Update (& a New Hypothesis)

Biohacking updateMatthew has been on the Autoimmune Protocol (AIP) for 18 months.

17 of those have been low-FODMAP.

For the last 2 months, he’s been doing the most extreme low-FODMAP AIP variation yet: a gut-healing protocol outlined by Aglaée Jacob in her book Digestive health with Real Food.

The only carbohydrates he’s been eating for the past 9 weeks are carrots and spinach. And he drinks gallons of bone broth~.

The Results

This is the reporting part of the Scientific Method.

  • Nausea: As I mentioned in my post Dietary Treatment for SIBO, after 9 days on this new Protocol, Matthew’s unexplained and debilitating nausea went from a 7-10 on a scale of 0-10 to a 4-6. And stayed there. Two months later, his nausea is still in the 4-6 range. This reduction has enabled him to participate in life, including cooking for himself (and me), engaging in moderate exercise, and doing things around the house. But the nausea has plateaued at the 4-6 level and that is barely tolerable much of the time.
  • Brain Fog: Over the past 2 months his brain fog lifted further. He’s winning at scrabble again. For the first time in years.

A New Hypothesis

Our Functional Medicine Doctor, Dr Cline, was as perplexed as everyone else about Matthew but (unlike everyone else) he didn’t give up.

Dr Kline talked to several colleagues and has a new hypothesis: yeast colonies protected by biofilms in the gut.


Biofilms are communities of microscopic organisms, such as bacteria and yeast, that produce their own protective matrix.

Organisms inside a biofilm are highly resistant to eradication attempts and, it seems, are also capable of complex, coordinated behaviour like quorum sensing.

The hypothesis that Matthew is colonized by biofilm-protected yeast colonies in his gut comes from a re-analysis of the results of a comprehensive stool analysis that Dr Kline ordered last year.

As Matthew had been on a low-FODMAP AIP for quite some time when that test was conducted, his results were better than any Dr Kline had ever seen.

Apparently, he should have been feeling great!

But he wasn’t.

The trace amounts of yeast in each of the three tests didn’t seem consequential at the time. But the specialist Dr Kline consulted with, Dr Tom O’Bryan, thought they were. Quite.

Vratislav Šťovíček, Libuše Váchová and Zdena Palková explain: “Pathogenic yeasts can colonise various surfaces within the human body, including host tissues… and form biofilms that resist otherwise effective drug therapy. Biofilms are thus very difficult to eliminate and serve as a source of serious systemic infections.”

Apparently yeast can grow roots, called hypha, which can puncture the intestinal wall and thereby create intestinal permeability (leaky gut). So even though Matthew has been on increasingly restrictive gut healing protocol for a year & a half, if the yeast is armored inside biofilms and putting down roots, his gut is still leaky.

It makes sense~.

A New Protocol

Dr O’Bryan has recommended a 3-month protocol designed to attack the biofilms and eradicate yeast colonization, with supplemental colostrum for gut-healing.

Biohacking modes: Reporting, Current biohacking modes: Reporting, hypothesizing & designing a new experiment~

Current biohacking modes: reporting, hypothesizing & designing a new experiment~

He has also recommended an ‘Intestinal Antigenic Permeability Screen’ from Cyrex Laboratories to measure Matthew’s gut permeability before and after the protocol. That will enable us to get a baseline and then measure any improvement.

Dr Kline has suggested that we may want to consider a fecal microbiota transplant at the Taymount Clinic in England after that, to repopulate Matthew’s micobiome. Maybe even as soon as this winter.

We might have sell our house to finance that, but hey~.

If I want to go on losing at scrabble for the rest of my life, that might just be what we have to do…

Depression as a Food Reaction

Matthew & Petra

Recently I tried reintroducing Macadamia Nuts into my Autoimmune Protocol (AIP) and I learned something about my mental health.

Organic raw dehydrated Macadamias were a go: I noticed no untoward effects.

But the supermarket non-organic kind in a tin were not. My stomach felt mildly inflamed, my energy plummeted and most interestingly, I felt quite depressed for several hours.

I could easily have ignored the stomach thing, but the depression was untenable.

I’d been upbeat & happy, then suddenly, about an hour after cracking the mac nut tin, all the joy and potential bled out of the world. I was no longer able to do my day. All I could do was steep in gloom, deep under the covers, with the woe of the world crashing down on me.

The first time it happened, the experience was so real and consuming it took awhile before I realized I was having a food reaction. That put things in perspective, and I made myself go outside for a walk, where I could begin analyzing my reaction rather than just getting lost in it.

Testing, Testing…

Over the next few weeks I tested my reaction several times, using an ABAB time series:

  • Organic raw dehydrated Macadamias: fine!;
  • Non-organic supermarket Macadamias in a tin: feeling of mild inflammation in my digestive system, low energy and depression;
  • Recovery time;
  • Repeat~.

The more un-organic mac nuts I had, the worse the reactions was.

Depression as a Food Reaction

Depression is a primary food reaction Matthew experiences when he tries to reintroduce foods, only his effects last longer (24-48 hours compared to my 4-6) and are more severe.

Even now that we know that this is a reaction he is likely to have, we still get bowled over by his feelings of absolute futility.

ABABWhen he’s in it, the reaction is so strong and deep, he loses the ability to remember that the reaction is caused by food.

That is a dangerous time.

The last time it happened, his feelings led him to question whether he even wanted to be here anymore.

It reminds me of the scene in Harry Potter & the Half-Blood Prince, when Professor Dumbledore consumes the Drink of Despair, a potion that causes him to re-live all his worst memories and fears. Matthew gets like that.

His despair results in very negative (short-term) attitudes about the severity of the restrictions he lives with on a low-FODMAP version of the AIP and a sense of hopelessness about the slow progress he is making, among other things.

This often results in a impulsive decision to reintroduce a bunch of other non-compliant comfort foods, because nothing matters anyway.

This unintended cascading reintroduction of non-AIP foods occurred for Matthew a year ago, after 3 months on the AIP, though we didn’t fully understand the phenomenon at the time. Once he recovered his ability to think clearly and got back on track, it took months to recover the progress he had made before that first derailed reintroduction experiment.

During an attempt at reintroduction, we now know that I have to be present and available to remind Matthew that he is having a food reaction, and that it is not a good time to make the decision to abandon his 15-month commitment to the AIP.

When he’s deep in despair, he’s not appreciative of my ministrations. But after, when he is able to look back and comprehend what just happened, he is.

So, We’re Careful With Reintroductions

We don’t do a lot of reintroduction experiments.

So far, Matthew has successfully reintroduced coffee and organic full-fat yogurt. They don’t cause a depression reaction, but he is only 70% confident that he actually tolerates them, so he’s still experimenting (ABAB~).



Chocolate & Mac Nuts? Not good. No matter how organic.

These observations have led me to reflect on the potential relationship between food and mental health issues in the general population.

People who are on a strict, clean dietary protocol are able to directly track the effects of reintroduced foods, but those who are consuming potentially problematic foods (or food additives or chemicals) all the time aren’t able to tease out the impacts of particular triggers on their well-being, including on their mental health.

Food & Mental Health

It is now widely accepted that gut health=mental health.

I experienced an alleviation of my decades-long battle with depression and anxiety after 6 months of paleo eating. Since then, I’ve surmised that perhaps gut health=psyche health, too.

What if certain foods (or fungicides, pesticides, or other chemicals) are also directly contributing to mental health problems? How would people know?

Only by adhering to a strict, clean dietary protocol for a significant period of time and then reintroducing foods (or additives or chemicals) to test their reactions.

Use of antidepressants are increasing all the time. More than 10% of Americans are now using them in an attempt to manage their depression. This number increases to 23% for women in their 40s & 50s (also the age group with the highest prevalence of autoimmune).

More research into the phenomenon of depression as a food (or chemical) reaction is warranted.

The New Astronomy of the Human Gut: Mapping the signature constellations of our microbiome


Constellations: inside & outside~

The Autoimmune Protocol is founded on evidence that gut health is the key to reversing systemic inflammation and autoimmune symptoms.

According to recent research, it turns out that particular microbiome ‘signatures’ in the human gut can be linked to specific autoimmune conditions.

Stick with me: this stuff is important. And medically, it’s paradigm-altering.

What follows are selected quotes from a paper that was published in the January 2015 issue of Arthitis & Rheumatology, called Decreased Bacterial Diversity Characterizes the Altered Gut Microbiota in Patients with Psoriatic Arthritis, Resembling Dysbiosis in Inflammatory Bowel Disease by Dr Jose Scher and 13 other researchers.

This study adds additional scientific research to the mounting anecdotal evidence that Autoimmune Protocol pioneers have been amassing, regarding the connection between gut health and autoimmune. It begins to explore the unique constellations of intestinal bacteria that are associated with different forms of autoimmune disease.

This particular paper focuses on Psoriatic Arthritis (PsA) and Psoriasis, two of the interrelated autoimmune conditions that Matthew lives with.

In our ongoing quest to hack Matthew’s health, we constantly seek new information to inform, confirm or disconfirm our observations, hunches & hypotheses. This paper confirms everything we’ve learned through our biohacking to date. It has raised some new research questions for us & could potentially revolutionize standard medical practice for treating autoimmune.

The Findings

In summary:

  • People with Psoriatic Arthritis (PsA) have less diversity in the population of organisms in their gut than healthy people, and they lack particular types of of bacteria:  specifically, Akkermansia and Ruminococcus.
  • People with psoriasis also have reduced diversity in their intestinal microbiome, and the reduction follows a pattern, with maximum variety in healthy people, reduced flora in people with psoriasis alone, and even further reduced diversity in people who, like Matthew, have psoriasis and Psoriatic Arthritis.

In the words of Dr Scher et al:

“In this study…we have shown, for the first time, that patients with PsA and patients with psoriasis of the skin have decreased diversity in their gut microbiota, mainly due to the lower relative abundance of several taxa.”

Internal constellations~

Internal constellations~

In addition to less diverse intestinal flora, researchers have identified a “common gut microbiota signature in patients with psoriasis and patients with PsA.”

“Our studies constitute a novel and comprehensive approach to investigate the symbiotic relationship between gut microbiota and PsA. We have identified several organisms that are virtually absent from PsA patients (i.e., Akkermansia and Ruminococcus).”

“The gut microbiota profile in patients with psoriasis appears to be intermediate, between that of PsA patients and that of healthy subjects, suggesting that there exists a possible continuum in disappearing intestinal taxa through the natural history of the disease.”

A “key question left unanswered by our study is whether patients with current psoriasis of the skin alone will lose certain potentially protective taxa, such as Akkermansia and Ruminococcus, at the time of, or prior to, transition into PsA. This is crucial because, although it is established that 25-30% of patients with psoriasis will develop arthritis over time, there is currently no possible way to predict progression.”

Similar research has previously focused on the constellations of gut flora in people with rheumatoid arthritis. A comparable lack of diversity was found, but with a different signature. “We have previously utilized this same approach to examine the intestinal microbiome in treatment-naive patients with new-onset rheumatoid arthritis (RA) and found that expansion of Prevotella copri was associated with enhanced susceptibility  to as yet untreated human RA. This is contrast with our present findings in PsA patients and suggests that there is a distinctive pattern associated with each condition.”

Potential Treatment & Further Study

“These investigations may ultimately lead to novel diagnostic tests and interventions, in the form of probiotics, prebiotics, specific microbiome-derived metabolites or molecular targets, and even bacterial transplant techniques.”

“The role of the gut microbiome in the continuum of psoriasis-PsA parthenogenesis and the associated immune response merits further study.”

We agree~!

What if replacing the missing Akkermansia and Ruminococcus could assist in reversing Psoriatic Arthritis? This would likely not be as simple as repopulating the gut with these bacteria. Favorable gut conditions would probably need to be cultivated to allow these extinct organisms to thrive. And re-population might need to be done through ‘bacterial transplant techniques’ including, perhaps, fecal transplants.

We think these findings could revolutionize medical treatment for autoimmune arthritis (and autoimmune conditions generally).

Find the full Decreased Bacterial Diversity Characterizes the Altered Gut Microbiota in Patients with Psoriatic Arthritis paper here.


Biohacking Tip 4: Qualitative Methods

Qualitative Methods

Qualitative Tools

Qualitative methods enable deep and detailed exploration.

When you are aiming for lasting transformative change through your biohacking experiments, that might be just what you need.

Traditionally, qualitative research involved scribing zillions of pages of field notes. And then analyzing them, painstakingly, in the wee hours by candlelight while perched on a rickety, uncomfortable chair.

Who has time?

Biohackers need a do-able system. One that is useful, convenient & enjoyable.

But let’s start with a brief introduction to:

Qualitative Methods

I introduced quantitative methods in my post: Biohacking Tip 1: Gather Data.

There I mention that data comes in 2 flavours: quantitative & qualitative. Quantitative data quantifies; qualitative data describes.

In Biohacking Tip 3: n=1 I touched on both qualitative and quantitative approaches.

A qualitative approach to biohacking will enable you to approach your experiments with open-mindedness and curiosity, whether or not you have a predetermined hypothesis.

According to Michael Quinn Patton, “qualitative inquiry documents the stuff that happens among real people in the real world in their own words, from their own perspectives, and within their own contexts.”

The most current and comprehensive resource on qualitative methods is Michael Quinn Patton’s 2015 book Qualitative Research & Evaluation Methods. It’s 806 pages of good times! (At least it is for me).

I have been a big fan of MQP for a long time. I have all his books and I owe pretty much everything I know about qualitative inquiry to him.

Including most what I offer in this post.


Anecdotes are the origin of hypotheses.

They elicit questions.

Exploring the questions inspired by anecdotes leads to new and deeper understanding.

Michael Quinn Patton notes that saying ‘that’s just anecdotal’ is an easy way to dismiss data that is generated qualitatively. And there are a lot of people who love to dismiss the qualitative.

However, as MQP points out, scientific knowledge starts with anecdotes. Like Isaac Newton’s apple, which fell, according to the anecdote, and thereby provoked the theory of gravity.

Anecdotes also enable the identification of patterns. A series of anecdotes that support a theme become evidence. As Raymond Wolfinger notes: “the plural of anecdote is data.”

NietzcheSo don’t be shy about getting anecdotal:

  • Gather anecdotes: ask questions;
  • Ask questions: look for patterns;
  • Use patterns to create hypotheses;
  • Test your hypotheses.

That’s the anecdotal route to the scientific method.

Anecdotes are freely available. You can find them everywhere~!

All you need to do is construct a net to catch them.

Which leads us back to your do-able system. One that is useful, convenient & enjoyable.


Consider joy.

That might be a bit of a stretch. At first.

But when choosing research methods for your biohacking experiments, consider:

  • Which approaches you enjoy the most; or
  • Those you hate the least.

Do those~.

Above any other consideration, choose the methods that will bring you maximum joy. Because the more you enjoy the activities that support your biohacking, the more consistently you will do them.

If quantitative methods bring you joy: use them. If collecting anecdotes is what you hate less: do that instead.

Once your healing & optimization have progressed, you might find that your joy increases. That you have more joy. And enjoy more things, including other methods.

Useful & Convenient

I you have an autoimmune disease, you already know about inconvenience.

And documenting a bunch of dietary and lifestyle changes while living with an autoimmune disease raises the inconvenience quotient to a whole other level.

So a discussion of convenience in this context is relative.

What you are aiming for in selecting qualitative methods is something that is more convenient.

The written word is the traditional method for documentation: either pen to paper or typing on a computer (or mobile).

But video might be more convenient. Or audio recording.



Maybe you have someone who would be willing interview you, using open-ended questions you develop, at predetermined intervals. Or you could use the Experience-Sampling Method (I’ll write more on that soon), with your smartphone as interviewer, as in this study titled How Do You Feel?


As well as ease of documentation, consider how convenient it might be to return to your data later to divine themes and generate further research questions.

If you plan to take that step.

In an n=1, sometimes the qualitative documentation process is sufficient. You might find you can learn enough through the process of articulating (or otherwise expressing) your observations.

Unlike researchers who are working in an unfamiliar context, you don’t have to try to understand another worldview.

Even if you don’t plan to return to your field notes (or images) for a rigorous qualitative analysis process, keeping an archive will preserve your primary data so that you can return to it in the future, if you wish to.

To track themes during future experiments. Or triangulate with other biohackers.

Once you have one or more methods you like, all you need to do is consider what you want to document.


Document whatever will be useful for you based on the purposes of your biohacking experiment.

Eileen Laird, Autoimmune Protocol blogger at Phoenix Helix offers this list.

Decide whether you want to make your documentation public or private.

Do you want to place your observations in the bosom of blogosphere? Or keep them to yourself? Both are valid.

If you decide to blog, you are in good company.