Root Cause | 1. Heartburn, Reflux, & GERD.
Everything you need to know - most of which your doctor either doesn't know or won't tell you.
Background
Heartburn is one of the most common health problems in the western developed world. It is estimated that approximately 18-25% of Americans experience heartburn.
Unfortunately, when most people go to their doctors they will be provided with:
An inappropriate understanding of how heartburn develops
“Your stomach is making too much acid and your esophageal sphincter isn’t working properly”
A perpetual cycle of ineffective treatments and testing
“Let’s try these proton pump inhibitors +/- antibiotics and scope your esophagus and stomach to see if there are ulcers”
The mainstream medical perspective is not only inaccurate, it is blatantly misleading.
For example, how does this make sense?

In this article, you will learn:
Anatomy, function and physiology of the stomach and relevant structures
Distinctions between heartburn, reflux and GERD
How reflux and its symptoms arise
Most effective ways to treat heartburn and GERD
You may be surprised to know that it isn’t with prescription drugs or surgery
But, before we get into all that - we first need to understand basic anatomy and physiology of the stomach…
The Basics
Above is an illustration of the stomach. The stomach has many layers and compartments with different functions.
Near the top of the stomach is a band of muscle called the lower esophageal sphincter (LES), which regulates passage of food between the esophagus and stomach. At the other end is the pyloric sphincter, which serves the same function between the stomach and duodenum. These sphincters are regulated by a combination of neural, hormonal and mechanical signals.
The Stomach
The stomach is the first major hollow organ of the gastrointestinal tract. Its proximity to the external environment (via the mouth) accounts for some of its functions. First, it is one of the most caustic cavities in the human body - with a pH ranging from 1.5 to 3.0.
For comparison, pH of battery acid is < 1.0, pure water is around 7.0, and normal human blood is around 7.3.
The highly acidic environment of the stomach helps break down the large and complex macromolecules that you swallow. Additionally, this environment makes it nearly impossible for most bacterial life to survive. The high acidity is both digestive and protective.
With respect to digestion, low pH is ideal for activation & function of the digestive enzyme pepsin. Some believe that reflux of stomach acid into the esophagus causes damage not on its own, but by activation of pepsin. The pepsin then proceeds to digest the lining of the esophagus.
Key Points
A part of the normal function of the stomach is to release acids and digestive enzymes when you eat. High acidity (or low pH) is a component of a normally functioning stomach.
When your stomach is actively digesting, the low pH signals to keep the LES (esophageal sphincter) closed.
Yes - highly acidic content in the esophagus is bad. But, that does not mean that high acidity is the cause of reflux. This is a critical distinction.
Surrounding Anatomy
It is important to note that the stomach does not exist and function in isolation. By way of hormones and the nervous system, the stomach is in constant communication with organs near and far.
The stomach is surrounded by other organs - as depicted in the illustration above. One which is seldom discussed in the context of our current conversation is the diaphragm.
Most know about this structure as it relates to breathing. But, this large muscle separating the chest from the abdomen has holes through which certain structures pass. One of them is the esophagus, which passes through the esophageal hiatus.
To further our understanding, we now turn to the nervous system and the innervation of these structures.
Innervation
The important thing to keep in mind is that digestion is not under conscious control - which means it is innervated by the autonomic nervous system - which is subdivided into parasympathetic (rest and digest) and sympathetic (alert & active) systems.
With one caveat: you can consciously control your rate of breathing, and in doing so can modulate the tonal balance of major autonomic nerves, like the cranial nerve 10 (aka the vagus nerve).
Each organ is balanced by complementary activation/inhibition by these nervous systems.
Lower Esophageal Sphincter - parasympathetic by vagus nerve, and sympathetic by the greater splanchnic nerve (which is composed of spinal nerve roots T5-T9)
Esophageal Hiatus (diaphragm) - phrenic nerve (spinal nerve roots C3-C5) with element of activity modulated by the vagus nerve
Stomach - parasympathetic by vagus nerve, and sympathetic by the greater splanchnic nerve (which is composed of spinal nerve roots T5-T9)
Key Points
Things which impact the overall tone and balance of the nervous system will impact digestion - including diet, environmental stress, and breathing.
even something as commonplace as caffeine, can impact reflux by increasing net sympathetic tone - which reduces gastric function and impacts sphincter tone.
Lesions in specific anatomic regions will impact function of the esophagus, stomach and relevant sphincters
For example: a lesion between spinal segments T5-T9 may impact the nerves which innervate the stomach and LES
This lesion can be benign (disc herniation) or concerning (paraspinal tumor)
Heartburn, Reflux and GERD
Heartburn is the sensation of a nagging burning pain, usually in the middle of the chest and extending to the neck. We believe that these sensations occur as a result of gastric reflux, which is when stomach content moves backwards into the esophagus.
Both heartburn and reflux can occur sporadically in humans, often in the setting of indigestion or untimely activity. As isolated incidents, these are not very concerning. Just don’t go playing basketball 15 minutes after eating a meal.
Gastroesophageal Reflux Disease (GERD) manifests when this reflux persists across time, and can irritate or damage the esophagus.
Usually, when people have a random occurrence of heartburn they will self-medicate with Tums or Pepto-bismol. They typically seek medical attention when it becomes a persistent problem - aka GERD.
Causes & Contributing Factors
If you were to check a resource like the National Institute of Health, you would find the following information:
GERD may develop if your lower esophageal sphincter becomes weak or relaxes when it shouldn’t. Factors that may affect the lower esophageal sphincter and lead to GERD include
being overweight or having obesity
being pregnant
smoking or inhaling secondhand smoke
Although the above ‘risk factors’ are relevant…it is not even close to the entire story.
As is common in modern medicine, there is rarely a look at the entire causal chain of events which lead to disease.
Inflammation
The first important contributing factor is inflammation. In my estimation, this is probably one of the most common factors causing GERD. Not surprising, because inflammation is one of the most common factors causing virtually all chronic disease.
Generally speaking, the tissue changes that accompany ‘inflammation’ cause organ dysfunction. The severity of the organ dysfunction will depend on the severity and duration of inflammation.
Inflammation causes swelling, poor perfusion, poor drainage of waste, and otherwise preoccupies the organ with the stressor that is causing injury.

Put simply, if the normal function of the stomach is to produce acid and digestive enzymes…and the normal function of the LES is to prevent reflux into the esophagus….
…then, in a state of dysfunction these will not occur. These functions will be sluggish or otherwise impaired.
Just as the stomach becomes dysfunctional with inflammation, so too will the LES.
Inflammation can also impact the diaphragm. Chronic inflammation leads to poor circulation, muscle weakness and dysfunction which can manifest with a hiatal hernia. These hernias tend to promote reflux.
Which means that one of the most important ways to improve digestion and reflux is to minimize exposure to inflammatory stressors. This concerns diet, environmental stress, and physical activity - amongst other factors. This is one reason why people have improved symptoms with simple dietary changes.
Not to mention the amplified benefit this change in lifestyle would have on the rest of your digestive tract and body.
Nutritional Support
One of the reasons I discussed the nervous system was to bring attention to the vital importance of its maintenance. Not only does our digestive tract maintain robust communication with our central nervous system, but it also has a brain of its own - the enteric nervous system.
Like all cells, neurons need several different conditions for optimal function. Everything from salts (like sodium and potassium) to vitamins (particularly B vitamins), to hormones (like melatonin).

Although this doesn’t receive as much attention, there are some studies which demonstrate near-complete resolution of all reflux symptoms with proper nutritional support, including:
Tryptophan or 5-HT, or high protein diets → promotes melatonin
L-Methionine
Betaine HCl (yes, the acid) - good alternative is apple cider vinegar
Vitamins B2, B6, B9, and B12
It would seem that optimal gastric functions is inextricably linked to optimal neurologic function. The melatonin is particularly interesting. Other than the pineal gland, the digestive tract is the only place that makes melatonin - and in much higher quantities. The reasons underpinning its efficacy are likely multi-factorial, and in my opinion overlap with melatonins anti-inflammatory properties.
But it is clearly quite effective. In one study, a patient was put on a vitamin stack to replace her proton pump inhibitor. The only time her symptoms recurred were after reducing the dose of melatonin from 6mg to 3mg. No other supplement or drug withdrawal caused heartburn symptoms.
Anatomic Anomalies
The other reason why we reviewed the nervous system, as well as the anatomy surrounding the stomach, was to account for anomalies and lesions which may be the underlying cause of reflux.
A great example is my father, who has had GERD for years.
In his case, we discontinued his proton pump inhibitor, changed his diet and put him on a few supplements - including betaine HCl.
His symptoms resolved.
But, it does not mean that this was the underlying cause. It simply means that we helped his stomach regain normal function by supporting it nutritionally.
I believe that degenerative disease and disc herniations in his thoracic spine may be contributing to his gastroesophageal dysfunction.
Remember we mentioned that the greater splanchnic nerve innervated the LES and the stomach? Well, this autonomic nerve is made of the T5 to T9 thoracic nerve roots. A lesion in this anatomic location can also lead to gastroesophageal dysfunction by disrupting these nerves.
Treatment Approach
From my perspective, the best initial treatment for reflux and gastric dysfunction should be simple. Hard, but simple.
Your stomach already has to deal with enough (as reflected by its highly caustic environment), and there is no need to place undue burden on it.
Keep It Simple:
Do not ingest things that are harmful to your stomach, including:
Alcohol and smoking
Highly processed and refined foods
Vegetable oils
Canola, Corn, Cottonseed, Soy, etc
Unnecessarily high quantity of ruffage
Eat at the same time, eat slowly and chew thoroughly.
Practice fasting - intermittent or time-restricted feeding.
Give your stomach time to rest.
Get good sleep (hint: melatonin)
Provide nutritional support - either through supplements or specific foods
this includes adequate salt and magnesium intake
animal protein is vital (again, melatonin)


Final Thoughts
You may have noticed that we haven’t discussed the typical medical management of reflux. The reasons are pretty straightforward, and perfectly encapsulated in the following study by Pereira (2006).
Two groups of participants (Group A = 176, Group B = 175) treated for 40 days
Group A received a supplement stack including B vitamins, Melatonin, & Betaine HCl
Group B received Omeprazole (PPI)
Within 7 days, 100% of Group A had markedly improved symptoms
After 40 days, >30% of Group B had persistent symptoms
This sub-group was then given Group A treatment
…and 100% of them had symptom resolution!
At best, medical management with proton pump inhibitors (PPI) and antacids masks symptoms. Despite the fact that this is one of the most prescribed drugs on the market… we continue to see complications of GERD.
PPIs do not meaningfully reduce the rate of erosions and ulcers
PPIs cause vitamin deficiencies (like B12)
PPIs cause increased release of gastrin (which signals acid release)
High gastrin continues to stimulate enterochromaffin cells of the stomach
…and in animal models, this leads to cancers of these cells
In humans however, if cancer were to arise…guess what they would blame?
The same thing they blame the reflux on!
They have a scapegoat.
Further Reading
If you think anyone would benefit from this information, please share.
Great text doc. Have been struggling with GERD for years now after being diagnosed with an ulcer. Could you please share the exact supplements that helped your father? Thanks.
Thanks Doc, my son has struggled with GERD for years.
Call me crazy but I believe it was caused by a week on a feeding tube from 2-8 days after birth
(Which of course proved entirely unnecessary)