Brain Fog (& what to do about it)

Brain FogHere’s a riddle:

Q: What do you do when your previously gentle and intelligent spouse starts to behave like a hostile toddler most of the time?

A: Do everything you can to reduce their brain fog!

When his brain fog was at its worst, Matthew reminded me a lot of a hostile toddler.

A hostile toddler with a driver’s license and credit cards.

It was not good!

The brain fog that accompanied the overall decline in his health was one of the scariest symptoms he experienced. And it is one of the many symptoms that has responded exceptionally well to the Autoimmune Protocol (AIP).

We first noticed marked improvement in Matthew’s cognitive function after seven months on the AIP.

And every month it has improved further.

After 27 months on the AIP, he’s almost all of the way back to his smart old self. Not completely. There’s still room for recovery, but his brain has mended remarkably well.

I am fascinated about brain fog, after having watched Matthew descend into its depths and come out the other side. Rory Linehan from the Paleo PI shares my interest, having been ‘there and back again’ with brain fog himself. So, he and and I conducted some research into the phenomenon.

In January 2016, we surveyed 18 people with first-hand experience with brain fog, all of whom were on a healing protocol diet, like the AIP.

This post contains the results of that research.

Our Brain Fog Research

We found it interesting that though they had no contact with each other while our research was being conducted, the way that people described their experience with brain fog was quite similar: Continue reading

The 5 ‘Rs’ of Gut Healing

Heal your gut, heal your life.Heal your gut, heal your life.

That’s the new mantra.

The new orthodoxy~.

And any orthodoxy deserves skepticism.



The ‘heal your gut, heal your life’ prescription needs to be thoroughly tested, to see if it holds up.

So, I’ve been testing it.


  • What does the science say?;
  • What experiences have my favorite healers & optimizers had?; and
  • How does all that fit with what Matthew and I have been learning through our own n=1 experiments, our attempts at biohacking autoimmune and biohacking peak experience~?

Between these three sources, I’m triangulating my exploration of these ideas. Which has resulted in the creation of a Microbiome Protocol.

Though I’m not suggesting we need yet another healing protocol (there’s already an abundance of those). Just a meta-protocol. That aligns the various healing and optimization protocols & provides a frame through which to contemplate them.

In that spirit, let’s consider the 5 ‘Rs’ of Gut Healing.

But first, a quick diagram of the Microbiome Protocol elements:

The Microbiome Protocol 2

Now let’s consider these elements alongside the 5 ‘Rs’:

The 5 'Rs' of Gut HealingThe 5 ‘Rs’ of Gut Healing

The 5 ‘Rs’ refers to the gut healing principles used in Functional Medicine.

Those principles are: Remove, Replace, Reinoculuate, Repair & Rebalance.


We need to remove everything that negatively affects the gastrointestinal tract.


  • Things we voluntarily consume, like foods that upset the microbiome and cause intestinal permeability;
  • Things we involuntarily introduce, like chemicals that harm friendly microbes; and
  • Any pathogenic microflora lurking in the GI tract, like yeast, parasites or unfriendly (or unbalanced) bacteria.

The removing phase involves a healing diet, like the Autoimmune Protocol, in which all potentially problematic foods are removed.

It also involves removal of chemicals that are harmful to the gut, both external chemicals, like artificial sweeteners, and harmful internal chemicals like excessive cortisol from chronic stress.

It may also involve taking drugs or herbs to eradicate unfriendly bacteria, yeast or parasites. In the event that pathogenic microflora has armored itself inside biofilms, removal also needs to involve eradicating those biofilms, so the microbes inside become vulnerable.

Elements of the Microbiome Protocol covered by the principle of ‘removal’ include an anti-inflammatory diet, stress management, reduced chemical exposure, mindful drug use & mindful caffeine use.


Replacing restores naturally occurring digestive aids, including enzymes, hydrochloric acid, and bile acids that support proper digestion.

These can be taken in supplement form before eating (& aren’t explicitly included in the Microbiome Protocol).


Reinoculation supports and reintroduces beneficial bacteria. Reinoculation includes dietary approaches, like fermented foods, probiotic supplements and resistant starches, as well as medical interventions, like Fecal Microbiota Transplants.

These approaches are covered under ‘gut health therapies’ in the Microbiome Protocol.

In the case of significant gut dysbiosis, attempts at reinoculation through diet may exacerbate symptoms, for a variety of reasons outlined by Chris Kresser.

Chris notes that “the extent to which you react adversely to probiotics and fermented foods and prebiotics… is roughly proportionate to how screwed up your gut is. In other words, the more strongly you react to these things, the more likely it is that you need them over the long term”.


Repair restores of the healthy mucosal lining of the intestinal tract.

This includes supplying nutrients like zinc, antioxidants, and nutritional anti-inflammatories like curcumin and Omega-3 fatty acids, through food or in supplement form.

Bone broth is an excellent restorative for the GI mucosa. As is colostrum.

Repair relates to the ‘nutrient-dense diet’ element of the Microbiome Protocol.


Rebalance refers to the implementation of systemic restorative processes that will support gut health in the long-term.

These are the powerful lifestyle factors that can get neglected when we focus exclusively food and supplements, like sleep, physical activity and stress management practices (yoga, meditation & mindfulness) which are core elements of the Microbiome Protocol.

Putting the 5 ‘Rs’ into Action

Matthew started a new 3-month treatment this week to address the debilitating nausea that is not responding to dietary treatment.

The current hypothesis is that he has biofilm-protected yeast colonies in his gut.

Yeast can grow roots, called hypha, which puncture the intestinal wall and perpetuate intestinal permeability. Therefore, until these armoured yeast colonies are banished, all of his other efforts at removal, replacement, reinoculation, repair and rebalancing can’t fully heal his gut.


Here’s how his current treatment lines up with the 5 ‘Rs’:

Remove: This treatment targets removal of the biofilms with a plant chemical called Biocidin (in 3 forms: drops/advanced formula, capsules & throat spray) and removal of the yeast with Fluconazole, a pharmaceutical treatment available by prescription. Fluconazole needs to monitored with regular bloodwork due to its toxicity.

These removal strategies are in addition to the removal of every possible food, chemical and environmental influence that we know of (& have control over) for the past 20 months, including attempts to eradicate the yeast through diet~.

Replace: The treatment plan includes proteolytic enzymes with every meal. Which, for Matthew, has been all of one meal day for many months, due to severe nausea.

Repair: The final element of this new treatment includes a bovine colostrum product called GI Restore from NuMedica for gut healing.

Reinonculate: Matthew is unable to tolerate any fermented foods, probiotic supplements or resistant starches, but if the current treatment is effective and his gut heals, he should begin to tolerate dietary reinoculation. If not, his functional medicine doctor has suggested a trip to the Taymount Clinic in England for a Fecal Microbiota Transplant.

Rebalance: Matthew will continue with all his rebalancing practices, which are now his entire life~.

The Microbiome: The Protocol II

the microbiome protocolPart one of this post looked at stress management, diet, sleep and physical activity.

In this post we’ll survey the other elements of the microbiome protocol:

  • Drugs;
  • Caffeine;
  • Chemicals;
  • Environment; and
  • Gut health therapies.

Starting with a sneaky one:


Chris Kresser cites research about the benefits of coffee in this podcast and sums up that “it still might be harmful for an individual based on a number of different factors”.

Sarah Ballantyne considers the research in the Pros & Cons of Coffee including the health benefits and it’s effect on cortisol production. She summarizes: “if you are very healthy, have lost most of the weight you need to lose, have regulated your hormones and healed your gut, coffee (in moderation) is likely to provide you a health benefit.”

Coffee 2Dave Asprey, the originator of Bulletproof Coffee, is a advocate of daily low-toxin coffee.

He also suggests coffee naps.

Back in 2008, Mark Sisson cited research on the negative impacts of caffeine and echoes Chris when he asks: “Is it really just a pick-me-up, or is it a band-aid for a larger problem like sleep deprivation, hormonal imbalance, lack of physical activity, lack of adequate sunlight?”

Mickey Trescott writes about Kicking the Coffee Habit.

And while we’re considering the elements of the microbiome protocol for gut health, what about reliance on coffee for gut motility?

Datis Kharrazian considers the need for coffee to provoke a bowel movement as a possible indicator of an issue with the gut-brain axis.

Reduce Chemical Exposure

Everyone agrees. Chemical exposure is a problem. And it’s insidious.

For example, Dave Asprey writes about chemicals in the air at Fitness Centres.

Mark’s Daily Apple considers chemicals in cosmetics and chemicals that harm baby boys (chemicals harm all babies, by the way, including baby girls and babies that don’t subscribe to the gender binary). He also covers 8 ways to reduce your chemical load and environmental toxins and gene expression.

And there’s chlorine in our water,  which indiscriminately kills bacteria, including many of the friendly microbes we’re trying to nurture inside the gut. Chlorine is flagged by David Perlmutter in Brain Maker (he recommends simple water filtration as a solution). It’s also addressed by Josh Harkinson in this Mother Jones article.

Chris Kresser explains how chemicals are making us fat and diabetic.

Datis Kharrazian explains how chemicals can trigger autoimmunity.  If you like a podcast, you can listen to his illuminating conversation with Eileen Laird about autoimmunity and chemicals.

Mindful Drug Use

Drugs aren’t necessarily different from chemicals. Except that they are ingested intentionally.

Over half of Americans are taking prescription drugs daily, according to Chris Kresser.

We all want to minimize pharmaceuticals, but sometimes drugs are appropriate. Eileen Laird considers where medication fits on a healing diet in a guest post on Autoimmune Paleo.

Chris Kresser points out that most drugs simply suppress symptoms and describes the ‘vicious cycle’ of using drugs to counteract the side effects of other drugs, and tells us exactly who makes money from that.

Mark Sisson has an entire ‘Big Pharma‘ category of posts on his blog. In some of these posts, Mark discusses the problems with antibiotics and some possible alternatives and considers harm reduction in We Like Drugs.

Mark also writes about The Pill: What You Need to Know about Oral Contraceptives (and Chris also covers how to recover from long term use of the pill in this podcast).

Attention to Environment

Epigenetics is the study of how the expression of our genes is affected by our environment.

My favorite Healers & Optimizers, from the top, left to right: Angie, Alt, Chris Kresser, Sarah Ballantyne, my husband Matthew~, Eileen Laird, Terry Wahls, Dave Asprey, Mickey Trescott, Mark Sisson

My favorite Healers & Optimizers, from the top, left to right: Angie, Alt, Chris Kresser, Sarah Ballantyne, my husband Matthew~, Eileen Laird, Terry Wahls, Dave Asprey, Mickey Trescott & Mark Sisson

We get issued our genes at conception, but our environment is more within our control.

The environment is exactly what this microbiome protocol is designed to address.

Terry Wahls reminds us that “diet is the most powerful epigenetic factor of all” and goes on to list toxic chemicals, physical activity level, stress, relationships, sleep, and the microbiome itself as other elements of our environment that turn our genes (for health & disease) on and off.

Dr Mercola adds emotions to the list.

Dave Asprey considers how we can optimize diet, behavior and environment to hack body and mind in How Your Environment Hacks Your Genes for You.

Mark Sisson refers to research  that indicates that where we live has significant impact on how our genes are expressed and considers Epigenetics and Depression.

This 2007 documentary on epigenetics is also excellent~.

Gut Health Therapies

All of the elements in this microbiome protocol are gut health therapies.

But additional interventions specifically target the health of the microbiome, including relatively simple approaches like inclusion of resistant starch, fermented foods & probiotics in the diet, and more radical interventions like Fecal Microbiota Transplants.

Let’s consider these therapies:

Resistant Starch

Mark Sisson has posted a definitive guide to resistant starch.

Eileen Laird has details the results of her n=1 resistant starch experiements in The Great Starch Experiment and recently also wrote about white rice as the paleo-non-paleo resistant starch of choice.

Sarah Ballantyne has written the the fiber manifesto, which explores all things fiber, including resistant starch, but she also warns that isolated resistant starch can be problematic.

Dr. Grace Liu has a podcast on Bulletproof titled resistant starch & probiotics.


Almost everyone agrees: fermented foods (and probiotics) are important elements of a gut healing protocol.

Chris Kresser gives an overview of gut heath and recommends both.

Sarah Ballantyne offers a post on the benefits of probiotics.

Mark Sisson covered the health benefits of fermented foods back in 2009.

Eileen Laird offers a podcast with Sarah Ramsden, fermented food expert.

Mickey Trescott, who co-blogs with Angie Alt at Autoimmune Paleo, has a post about how to evaluate supplements, including probiotics, when on a healing protocol.

Other bloggers have some caveats. Dave Asprey has written about Why Yogurt and Probiotics Make You Fat and Foggy. Chris Kresser considers 4 reasons why probiotics or fermented foods may not be tolerated.

Fecal Microbiota Transplants

Jaime Hartman shares a 1st-person account of a successful fecal microbiota transplant on her blog Gutsy By Nature.

Eileen Laird offers a podcast on the subject.

The ever prescient Mark Sisson wrote briefly about Fecal Transplants back in 2010. In 2011 he also referred to research for Do-It-Yourself fecal transplants.

In Conclusion

At the beginning, a protocol like this can seem overwhelming.

Like a whole-life overhaul.

Because that’s what it is~.

But there are ways to make it manageable (and fun). Soon I’ll address how to break it down to by assessing leverage, so it’s easy to create a plan of action.

We got to this point by building a system map. Then we deconstructed that map to determine which elements are actionable.

By understanding the system, we can each develop a strategy to improve our microbial communities~.

Actionable Microbiome 2

The Microbiome: the Protocol

My favorite Healers & Optimizers, from the top, left to right: Angie, Alt, Chris Kresser, Sarah Ballantyne, my husband Matthew~, Eileen Laird, Terry Wahls, Dave Asprey, Mickey Trescott, Mark Sisson

Some of my favorite Healers & Optimizers, from the top, left to right: Angie Alt, Chris Kresser, Sarah Ballantyne, my husband Matthew~, Eileen Laird, Terry Wahls, Dave Asprey, Mickey Trescott & Mark Sisson

Health and disease begin in the gut. Hippocrates said it and these people agree:

So, I mapped the systems that are impacted by intestinal microflora in the Origin of Illness.

Then I used that map to determine what parts of the system are actionable, to create a list of things we can do to support microbiome health.

Thereby creating a microbiome protocol~.

In this post, let’s look at what some of my favorite healers and optimizers have to say about each of the elements in this protocol:

Actionable Microbiome 3

We’ll find out what they think, classic web-log style~.

In part one we’ll cover stress management, diet, sleep and physical activity. In part 2 we’ll review caffeine, chemicals, mindful drug use, environment and gut health therapies.

Stress Management

Sarah Ballantyne, the Paleo Mom, explains how stress undermines health & how it can lead to hormone imbalance. She also writes about her personal battles with stress.

Mark Sisson, originator of the The Primal Blueprint, offers the definitive guide to stress, cortisol and the adrenals and covers how stress can make you fat.

Eileen Laird, of Phoenix Helix, interviews Datis Kharrazian in this podcast, in which Dr Kharrazian refers to stress as “the single most impactful factor on the expression of autoimmune disease”.

Dave Asprey, the Bulletproof Executive, shares 6 ways to hack stress  and covers meditation for stress relief and anxiety.

Mark Sisson also offers 15 stress hacks and 10 forgotten stress relief tips.

Susan Vennerholm, of Backcountry Paleo, considers restorative yoga and  how optimism helps manage stress in her guest posts on the Autoimmune Paleo blog.


An anti-inflammatory & nutrient-dense diet is the core of all the healing and optimizing protocols, including:

As well as customized variations, such as a low-FODMAP AIP.

All of these protocols are based on the same science and are fundamentally aligned. They are all gut-healing, anti-inflammatory, ancestral eating systems.

This is a big subject, but in short, healing protocols (like the AIP & Wahls) tend to be be more restrictive than the optimization protocols (like Primal & Bulletproof), but then they are elimination diets, with the assumption that some off-limits foods may be reintroduced in time. Whereas, though both Primal & Bulletproof make allowances for more dietary flexibility, optimizers recommend this pattern of eating as a lifelong commitment to peak performance.

So, it’s kind of like this:

Healing & Optimizing Protocols


Chris Kresser considers sleep to be one of the 9 steps to perfect health.

Sarah Ballantyne writes about sleep requirements & sleep debt and the link between sleep & weight.

Eileen Laird considers skipping sleep as a cause of an autoimmune flare. Mickey Trescott has explored why sleep is important for people with autoimmune disease. Joanna Frankham describes her difficulty with sleep and what she’s doing about it.

Mark’s Daily Apple has over a dozen posts on sleep. Here’s one: How to Manufacture the Best Night’s Sleep in Your Life.

High Leverage Physical Activity

High leverage means you get maximum benefit for your effort.

In the case of exercise, it’s actually really easy (and pretty common) to be low-leverage: to put out a lot of energy in for a negligible (or even negative) result.

Chris Kresser explains this in his post Why You may Need to Exercise Less, and suggests that instead we move like our ancestors. He also advocates High Intensity Strength Training.

Exercising inappropriately can be problematic for people with an unbalanced microbiome. Sarah Ballantyne addresses this in two podcasts: Exercise Performance & Gut Health & The Too Much of Exercise. On her blog she also stresses the importance of exercise, explores the benefits of gentle movement, and tells us why she likes yoga.

Dr Terry Wahls explains how exercise to promotes brain health.

Susan Vennerholm, guest blogging again at Autoimmune Paleo, also cautions against over-exercise as a person with an autoimmune condition, and writes about cardio, high intensity interval training and resistance workouts.

Mark Sisson wins first prize for the highest number of exercise-related posts. His primal movement recommendations are summarized here. He has also written about  why exercise feels like a drag; why it’s the best medicine; the relationship between exercise and inflammation; and managing mitochondria through exercise. He also makes the case against cardio.

 Next up we’ll learn what these biohackers have to say about caffeine, chemicals, mindful drug use, environment, and gut health therapies~.

Find part 2 here.

Healing Optimization



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.


My ancestors came from candy-land

sweetsReally. They were candy makers.

They made candy in Northern England and when they came to Canada, they kept making candy.

There is still a Sweet Shop here in Victoria that was started my forebears.

As an aside, my grandfather wasn’t allowed into his candy-making grandparents’ house, because his mother, Bertha Bland (what a wonderfully unfortunate name), had been a factory-worker in the old country.

And they were lofty candy-makers.

So my grandfather, young Kenneth George, was only permitted on his grandparent’s front porch, whereas the other grandchildren could come & go into the house as they pleased.

My ancestors brought their classism & their candy with them.

That’s how I come to be from candy-land.

Or biscuit land.UK made from biscuits

Just ponder what all those biscuits are doing to people internally.

Another of my ancestors was a King of Scotland. Sort of a wimpy king, if you’ve ever watched Braveheart: Robert the Bruce.

I’ve already written a bit about my dismal experience as a vegetarian in Scotland.

But all this rambling about British stodge has a point.

The point is I’m descended from candy-making, biscuit-consuming, classist, wimpy colonists.

The health of their intestinal flora can’t have been great, even way back when they were colonizing this great land, and this thought has lead me to wonder about gut health & colonialism.

When all those biscuit eaters with their disorderly intestinal flora and associated nervous complaints arrived here, what did they find?

People eating a perfect paleo diet who were probably enjoying magnificent gut health. If all the research (and my own experience) about the correlation between mental health & gut health is to be believed, Indigenous people were probably also enjoying psychological well-being.

How galling.

All these happy people. How dare they?

Have another biscuit.

We really need to do something.

And that something was done.

The irony was not lost on me as I drove to work one morning last week, having had bison liver and an avocado and a smoothie made from dandelion greens for breakfast, and I saw three Indigenous kids walking to school with lollipops in their mouths.

The candy makers were thorough.

Just one more reason I am continuing my experiment in nutritional ethics on the Wahls Paleo Plus.

 I found the biscuit map here.