How to clear Brain Fog with Functional Medicine

By November 30, 2017Functional Medicine, Origins News

For many of us our mental acuity defines our personal and professional lives.  We strive to connect deeply in our relationships and push ourselves to new levels of professional creativity.  That is why it is so scary when we find ourselves fumbling for words, forgetting our train of thought, and unable to break through that next creative barrier.  Where once we were admired as the sharpest member of a professional team we now stumble to remember where we parked the car in the grocery store lot or fail to recall the name of an important business acquaintance at social function.  Our thinking feels mired in a thick soup of brain fog.  Many of us fear that this is perhaps the first sign of cognitive decline we have observed in our aging parents.  But, the truth is much more complicated.  The brain is an integrated part of our body and affected by all biological systems.  When brain fog can be caused by anything how do we begin to know what to do?  The answer is simple: test don’t guess!  This is where Functional Medicine steps in and shines!

What is Functional Medicine and how will it help you recover your sharp thinking and memory?  Functional medicine uses advanced lab testing to test the hormonal status, digestive tract, nutritional status, detox function, neurotransmitters,  chronic inflammation, and metabolic health of the entire body.  By measuring the health and performance of these critical systems we see exactly how they are affecting the brain and cognition.  Paired with a thorough health history this creates a personalized roadmap of how to restore health to the brain and body.  

This information is gathered through three main simple lab tests that are performed in the privacy and convenience of your own home.  Let’s take a brief look at each of these tests and how they provide the critical information needed to lift the brain fog.  

For the next three sections of this blog we will look at a case study… me (Duncan Macdonald)!  A few years after having my son I was not feeling right.  I had a wonderful happy toddler, but I felt so overwhelmed by brain fog I worried that the parenting experience was passing me by.  My sleep was poor, my mood depressed, and I felt as though I couldn’t even string words together.  Practicing medicine is dependent on logical and complex problem solving.  I was worried I’d need to find a new career!  Luckily for me I had the access to my mentor Dr. Dan Kalish and he ran the same three tests we use on every new patient.  Each test assesses a different aspect of physiology which, when combined, can give a clear diagnosis of the root cause of brain fog.  

Let’s see how my poor brain and body were faring after the wear and tear of new parenting.


BioHealth 201: How the stress hormones affect the brain, Lab cost $150


The first step in assessing any case of brain fog or cognitive problems is to examine the stress hormones.  Cortisol is a “Goldilocks” hormone, meaning it shouldn’t be too high or too low.  In proper amounts cortisol governs our alertness, mood, concentration, inflammation and sleep.  When cortisol is too high we feel intensely stressed and if that stress is not resolved the high cortisol dysregulates into a chronically low pattern.  This leaves us depressed and foggy headed and , yet, without the ability to properly rest.  Patients often describe this as “tired and wired.”  

Now, let’s take a look at a real life adrenal stress profile from BioHealth labs and see how my cortisol was looking after 3 years of parenting!

This test measures four separate saliva samples taken at intervals during the day.  The levels are measured of cortisol, our main stress hormone, and DHEA, our main anabolic hormone and the precursors of our sex hormones, such as testosterone.  We feel our best when we are at the high end of the references ranges for our samples.  We get a surge of cortisol in the morning, which wakes us up, then we should have a predictable drop until we go to sleep.  As you can see I was at the top end of the range when I woke up, which corresponded with the fact that I was waking at 4:30am everyday and unable to fall back to sleep.  Yet, my cortisol on all three afternoon and evening measurements were flat and on the low end of the spectrum.  This corresponds with the flat, foggy, and unengaged experience that were my days.  My poor little boy had to deal with a dad who was almost asleep the whole day!  Talk about brain fog!  My DHEA was also on the low end of the spectrum.  This is an excellent indicator of long term and grinding stress.  These levels would be robbing my body of testosterone, leaving me unmotivated and depressed.  Not a pretty picture, so what can we do with this information?  How did I get my hormones back in line?

Based on the labs we are able to create individualized therapeutic supplement programs to reset the body’s stress response.  These supplements include hormone precursors, adaptogenic herbs, and substances that can either lower or raise cortisol thereby correcting rhythm disruptions.  We are not looking to take control of the body’s hormones, but rather encourage the body to resume natural production by mimicking normal output.  This process can take 6 months or longer to stabilize, but patients usually notice an uptick in mood, mental clarity, and memory even within the first few weeks.  

For me it felt like someone turned the lights back on in my brain.  I felt as though I could think critically again and I didn’t stumble for words in conversation.  However, the story doesn’t end there.  In Functional Medicine we are always concerned with finding and correcting the root cause of the health issue.  Why were my stress hormones so out of whack?  For that we run our next test.


BioHealth 401H or Diagnostic Solutions GI MAP, Lab cost $350

When we think of stress we usually think of emotional stress, such as a fight with our spouse, work trouble, etc.  But, one of the biggest hidden stressors our bodies face are low grade infections of our gastrointestinal tract.  They cause a constant immune and inflammatory process.  This inflammation leads directly to brain and cognitive issues.  One of the hottest areas of medical research right now is around the gut biome and what is known as the Gut-Brain axis.  It is a fascinating topic that will get its own blog post in the future, but other common infections, such as H. Pylori are directly linked to anxiety and depression.  The brain fog you are experiencing may be due to a long standing and undiagnosed bacterial or parasitic infection.  In my case I was lucky enough to be hosting a significant H. Pylori infection.  

Besides, occasional heartburn I had no idea this infection was causing constant inflammation, anxiety, and increased cancer risk to me!  A pathogen screening is a simple test to do at home.  It is done with a single stool sample which is shipped directly to the lab.  The kit is hygienic and keeps the “ick” factor to a minimum.  The test checks for common bacterial infections, parasites,  biome imbalances, and the health of the immune barrier of the gut.  There is nothing more frustrating than to work with a patient for months restoring the balance to their stress hormones only to discover that they have had an underlying infection the whole time undoing our best efforts.

Different infections require different interventions.  Occasionally, we need to prescribe antibiotics for particularly nasty infections, but the vast majority of infections can be cleared using natural medicine antimicrobial and anti parasitic protocols.  Typically, infection clearing protocols take about two months, as many of these infections have a cystic phase where they will be dormant in the gut lining.  A recent study done at the Mayo Clinic using these exact protocols showed an over 90% clear rate.  For me the protocol worked almost immediately.  

My heartburn completely resolved and even more remarkable the background anxiety that I had come to associate with my brain fog cleared.  This may seem like a remarkably low bar for medicine, but I feel it’s not too much to ask that our patients be free of chronic burdensome infections!


Genova Organix – Comprehensive, Lab cost $410

Once we have checked the body for nasty parasites or infections we run our last major test, the Genova Organix.  An Organic Acids Test (OAT) measures the acids in the urine formed as byproducts from physiologic activity.  My measuring these acids we get a profound deep dive into the health status of the patient.  We get a direct look into how the body is utilizing fat, carbohydrate, and protein as energy, nutritional deficiencies, gut biome information, oxidative stress, insulin resistance, liver detox, and most importantly, for my poor brain, neurotransmitter activity.  

There are really two ways of measuring the neurotransmitters (serotonin, dopamine, etc.) in the brain.  One is to do a spinal tap (not recommended) and the other is to measure the byproducts of these neurotransmitters after they are broken down and recycled in the liver.  The cause of brain fog can often be found in the deficiency, imbalance, or inflammation of these brain chemicals.

In my case this test was done when I was a couple years into parenting and making the major transition of incorporating Functional Medicine into my practice.  My stress level was extremely high.  I felt as though I was coping, but still was plagued by brain fog and recall issues.  On top of that I had terrible insomnia, often awakening at 4am with an inability to get back to sleep.  My toddler was now sleeping fine through the night, but not Dad!  When I ran my Organix these were the brain related results.

Marker 22 and 23 (vanilmandelate and homovanilate) are breakdown products of dopamine.  Dopamine is the main excitatory and reward neurotransmitter.  The combination of high and low readings on these show a marked dopamine depletion in this brain.  This explains the low mood, lack of motivation, and fuzzy headedness I was experiencing.  Marker 24 (5-hydroxyindoleacetate) is a direct marker for serotonin.  Serotonin has many functions in relation to the brain, but it is commonly associated with mood.  This is the neurotransmitter that is targeted by most antidepressant drugs.  

Marker 28 (p-Hydroxyphenyllactate) indicates oxidative stress systemically affecting my body, including my brain.  We sometimes see this marker elevate in hardcore endurance athletes because of the oxygen turnover in their bodies.  That certainly wasn’t me at that time!  This elevation is likely due inflammation caused by the H. Pylori infection in my stomach at the time.

Treatment of neurotransmitter related brain issues is multifaceted, but straightforward.  It requires using specific amino acids that are the precursors for the neurotransmitters.  At the same time the body requires higher doses of B-vitamins and detox and methylation support.  These lab based protocols are quick to act, profound, and often we will see changes in mood, memory, and alertness in a few weeks.  

The information gathered by running these three labs and the subsequent lab based protocols I credit with giving me my life back.  Between the staging of the hormonal program, infection program, and neurotransmitter program I was on supplements for about 9 months.  During this time I felt like someone turned the lights back on in my brain!  My sleep returned, my thinking and memory sharpened, and my enthusiasm for life returned.  Many of us accept that being foggy headed, low energy and depressed is just a natural part of aging and parenting.  This is a sad lie we tell ourselves.  It’s not that we are getting older.  It’s that we’re getting more rundown.  With proper investigation and treatment we can do something about it!

In Health,
Duncan Macdonald, L.Ac.

One Comment

  • Marlon Price says:

    Hey Duncan!

    It has been a very long time! I glad to hear you are doing well. And you have a toddler? Congratulations!

    Great essay! Thank you for documenting your own progression and experience. I too have had what I feel is a decrease in cognitive “power”, if that is a way to say it. What is the process for looking into this? How do you start?

    I also need to return to doing acupuncture as well.

    Final question, you mention the cost of the tests. What was the cost for the supplements?

    — Marlon

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