Introduction to Root Causes of Illness

Last updated: April 30, 2024

Daniel Mališ
Daniel Mališ

Removing root causes of illness is the most important strategy for regaining health, along with introducing root causes of health.

The First RCM Principle is clear: To regain health, remove the root causes of illness and introduce the root causes of health. It’s worth repeating, because applying this core principle is still not common practice, especially not in Western Medicine.

In a nutshell, the most frequent root causes of illness are the following:

  • Unhealthy food
  • Chronic stress
  • Psychological trauma (typically in childhood)
  • Negative thoughts and beliefs
  • Heavy metals
  • Micronutrient deficiencies
  • Non-native electromagnetic fields (EMFs)
  • Synthetic chemicals
  • Pharmaceutical products.

What Do They Have in Common?

We’ll go over each category of the root causes of illness in separate articles, but from the list above, you can already see that the root causes of illness are either man-made or man-enhanced.

“Man-made” are causes that would not exist without modern human interventions, such as highly processed and other unhealthy food, non-native EMFs, synthetic chemicals and pharmaceuticals products.

By “man-enhanced” I mean root causes that could occur naturally in the past, but are now present in much higher quantities (chronic stress, heavy metals) or different qualities (psychological trauma) as a result of human activities, mainly during the last 70 – 100 years.

Negative thoughts and beliefs are also man-enhanced, particularly by the current environment of 24/7 media coverage and social media usage. Micronutrient deficiencies are mostly a result of modern agricultural methods, which strip the soil and plants of vital minerals and vitamins.

The point is that the man-made and man-enhanced causes were not naturally present during the evolution of the human species (we’re talking some 300 thousand years here). They either didn’t exist at all, or not in such excess.

As a result, the human body is not well designed to deal with such causes. Instead of being neutralized or eliminated from the body, the root causes of illness remain present in the body and keep disturbing it.

Our bodies are not evolutionally designed to deal with unnatural substances – it’s that simple. We just need to respect it.

This disturbance results from the fact that the body’s already low capacity to eliminate unnatural causes is exceeded. This is caused either by constant influx (e.g., in case of unhealthy food, chronic stress, EMFs or synthetic chemicals), or by sudden overwhelm (typical with psychological trauma or heavy metals in some instances).

Micronutrient deficiencies make things even worse, because minerals and vitamins are necessary for the proper functioning of the human body.

A Minor Detour: Immune System and Inflammation

Apart from the elimination system (liver, kidneys, etc.), which is not well suited for man-made or man-enhanced inputs, the human body has only one more system to deal with anything it considers dangerous or damaging: the immune system.

It’s primarily designed to fight against viruses, bacteria and other infections, as well as cancer cells. Last but not least, the immune system removes damaged and old cells from our bodies so that new cells can take their place.

A well-functioning immune system protects us against infections, cancer and aging.

The immune system is very powerful, so it needs to be kept under control, otherwise it can damage or even destroy the whole body. What calls the immune system into action is a process called inflammation.

The most important function of inflammation is to allow the armed forces of the immune system (the immune cells and various attack proteins) to enter the affected area and protect the body against the current danger or damage.

You’ve surely noticed the accompanying markers of inflammation before – the affected area becomes swollen and painful, as well as warmer and redder than usual. Typically, this also leads to an impairment in the function of the inflamed tissue – think how “well” you can walk with a sprained ankle or how cumbersome swallowing is when you have a sore throat.

Inflammation (calling the immune system into action) is quite literally vital for us, but it should be time-limited.

Once the immune system is finished with the threat, which is usually a matter of days or weeks, the inflammation subsides. There’s some collateral damage, but given the relatively short duration of the battle, the body repairs the damage soon after.

Chronic Inflammation

The inflammation process seems pretty straightforward and effective, except that it’s designed for natural threats. For more than 500 million years of its gradual development, the immune system of multicellular organisms knew nothing else than natural opponents – typically viruses, bacteria and one’s own defective cells (damaged, too old, or cancerous).

Junk food, synthetic chemicals, loads of heavy metals, and permanent stress came only less than 50 to 100 years ago, which is nothing compared to more than half a billion years of previous development of the immune system.

Our immune system still fights against those new opponents to protect us, but with less success. After all, how can an immune cell “kill” a synthetic chemical or a heavy metal? Or something intangible that we’re stressed about?

Our immune system is not well designed to deal with synthetic chemicals continuously developed in laboratories, among other modern “achievements.”

With the uneven battle being fought with little success, the inflammation becomes chronic. New and new armed forces (immune cells and attack proteins) are being called into the affected areas or the body’s weakest points, but the opponent is never defeated.

As a result, the collateral damage to body tissues and organs continues to grow, as does the impairment of their function. Do you know what the common denominator of almost all chronic diseases is? Yes, it’s chronic inflammation.

Examples of chronic diseases linked to chronic inflammation include:

  • Cardiovascular diseases
  • Diabetes
  • Autoimmune diseases (Hashimoto’s thyroiditis, Crohn’s disease, multiple sclerosis, etc.)
  • Allergies
  • Joint diseases like rheumatoid arthritis and osteoarthritis
  • Neurodegenerative disorders (e.g. Alzheimer’s and Parkinson’s)
  • Neurodevelopmental disorders such as ADHD and autism
  • Pulmonary diseases such as asthma and chronic obstructive pulmonary disease
  • Chronic kidney disease
  • Non-alcoholic fatty liver disease
  • Cancer (last but certainly not least)
Chronic inflammation is behind the vast majority of chronic diseases. Remove the causes of chronic inflammation, and those diseases will start fading away.

Vicious Circle of Chronic Inflammation

The inflammation increases the permeability of natural barriers so that the immune cells can get to the affected area more easily. However, if the inflammation takes place in the gut, typically due to unhealthy food, it means that the intestine itself becomes more permeable (“leaky”) also for pathogens, toxic metabolites, peptides and other antigens.

If it weren’t for this “leaky gut”, these substances would normally never make it through the gut wall into the bloodstream. So the body naturally views them as opponents, which creates even more inflammation, worsening the situation further.

The difference between a normal gut and a “leaky gut.” Because of the leaks, a lot of irritating stuff makes it into the bloodstream.

Moreover, some of the antigens that made it unnaturally through the gut wall are similar to the antigens of your own tissues, which gives rise to autoimmunity – the antibodies against the similar antigens are killing your own cells, such as thyroid cells (Hashimoto’s thyroiditis) or the lining of your joints (rheumatoid arthritis).

A leaky gut, another link in the chain, is associated with many health conditions.

Particularly damaging are the effects of chronic inflammation on the blood-brain barrier, which results in a condition colloquially called a “leaky brain.”

The brain is a very sensitive tissue, and that’s why the blood-brain barrier is usually very tight. When it becomes more permeable, pathogens, toxic metabolites, and various antigens and antibodies enter the brain.

What results is neuroinflammation, which is associated with many chronic conditions such as brain fog, fatigue, memory impairment, concentration issues, headaches, anxiety, depression, dementia, ADHD and autism.

Neuroinflammation is yet another link in a chain that begins with the root causes of illness (the No. 1 root cause of illness being unhealthy food).

Last but not least, chronic inflammation impairs the ability of the immune system to do what it is primarily designed to do – protect you against pathogens and cancer, as well as to clean up damaged and old cells.

The result is detrimental but logical – chronic infections (which further add to chronic inflammation), increased susceptibility to acute infections (with a more severe course), increased risk of cancer, and faster aging.

It’s tough, but it all makes sense – if you have armed forces dragged through an ongoing war against an undefeatable or elusive opponent, they won’t be readily available to fight on yet another front. And when they arrive, they’d be tired, less effective and more likely to miss the opponent, causing even more collateral damage than usual.

Your immune system is no different.

Chronic inflammation makes your immune system weak and dysregulated. But you want your immunity to protect you properly again.

How To Break the Vicious Circle

How do we stop chronic inflammation? Western Medicine tries to suppress it with nonsteroidal anti-inflammatory drugs, such as aspirin or ibuprofen, or with corticosteroids. But that’s like trying to win a war by making your already ineffective armed forces even less able.

The inflammation is your body’s best attempt to fight the unnatural or intangible opponents, so we have to deal with them – in other words, we need to remove the root causes of illness. That usually comes in two steps:

The first step is gradually stopping the supply of the root causes of illness onto the battlefield (= your body).

That mainly means:

  • Not eating junk and otherwise unhealthy food
  • Limiting your exposure to heavy metals, synthetic chemicals and EMFs
  • Staying away from unnecessary stress
  • Working with your doctor on limiting or discontinuing the use of pharmaceutical products.
Step No. 1 is stopping the influx of unnatural substances (and unnecessary stress) to your body. Do it gradually, otherwise the changes will be too major for you to handle.

The second step is helping your body with the gradual removal of the root causes of illness from the body.

This is done mainly through the following procedures:

  • Various detox protocols (for removal of the “physical” root causes of illness)
  • Practices like mindfulness and cognitive restructuring (for changing negative thoughts and beliefs)
  • Deeper techniques like psychedelic-assisted psychotherapy or hypnotherapy (for discharging the emotional components of psychological traumas that affect your biology)
  • Supplementing vital micronutrients (such as magnesium, iodine, copper and vitamins A, B and C), preferably from natural (food-based) sources.
Step No. 2 is to remove anything toxic (such as toxic substances, thoughts, beliefs, and emotions) from your body. Do it gradually, but methodically.

This article is about the root causes of illness but I should certainly mention that there’s also a third step to be implemented on your journey – introducing the root causes of health.

I cover the root causes of health in other articles, so just as a quick reminder – they include things like proper (anti-inflammatory) food, meditation and other stress-coping techniques, good night’s sleep, physical exercise and proper breathing.

The root causes of health further reduce chronic inflammation, as well as boost your body’s self-protecting and self-healing abilities.

Root Causes of Illness vs. Triggers of a Disease

The onset of diseases is sometimes gradual, sometimes quite sudden. But it’s always the root causes of illness (or the lack of the root causes of health) that lay the foundation for the occurrence of the disease.

What you see (the signs or symptoms of a disease) is usually just the tip of an iceberg. The foundations of the disease have been many years in the making.

With the gradual onset of a disease, that foundation grows bigger and bigger until its signs and symptoms become apparent – you start feeling more tired or anxious, you can’t concentrate as well as before, your joints are somewhat painful, or your doctor tells you that your blood pressure, blood glucose or cholesterol levels are higher than they should be.

But a disease (or its relapse or new occurrence) can also present itself suddenly, seemingly out of nowhere, based on an event, substance or another cause that doesn’t seem to affect other people, or at least not all of them.

This final cause that immediately precedes the emergence (or reemergence) of a disease is called a trigger.

Triggers are not the root causes of illness. Therefore, let’s not make the mistake of focusing on triggers rather than the root causes of illness.

It’s the root causes of illness (or the lack of root causes of health) that make a person susceptible to a certain trigger; in other words, you need to load a gun for a trigger to have any effect.

A trigger quickly activates a condition that typically results from a years-long buildup of the root causes of illness.

For example, we shouldn’t just ask what triggered a panic attack, but instead focus on the root causes that led to the patient having panic attacks in the first place.

The same logic applies to asthmatic and migraine attacks, as well as allergies, food sensitivities, skin issues and any other diseases with episodic relapses, flare-ups or new acute onsets.

While we should pay attention to triggers, they will gradually lose importance as the susceptibility of a person to those triggers diminishes or vanishes completely. And that will only happen once the root causes of that susceptibility have been properly addressed.

What About Viruses and Bacteria?

You might wonder whether viruses, bacteria and other potentially pathogenic microorganisms also belong to the root causes of illness, or if they’re triggers, or something else.

Viruses and bacteria – friends or foes?

I’ll start with quoting the Eleventh RCM Principle (Microorganisms Are Essential): “There is no health without constant interaction with microorganisms inside, outside, and on our bodies.”

That itself rules out the possibility that microorganisms principally belong to the root causes of illness (although exceptions exist).

But of course, viruses, bacteria and other microorganisms do cause infectious diseases, as we all have experienced at certain points of our lives, at least in our childhood. When that happens, microorganisms can take two different roles in the process:

In their first role, they act as a trigger, causing the disease in a person whose immune system is not strong enough. How come some people got COVID, and some didn’t, despite the virus widely circulating in the population?

The only difference was the condition of their immune system, particularly their mucosal immunity, which serves as the first and most important barrier against all respiratory infections.

Therefore, along with removing the root causes of illness that lead to chronic inflammation, we all need to train, support and protect our immune system to prevent viruses, bacteria and other potential pathogens from triggering various infectious diseases in our bodies.

In their first role, viruses and bacteria act as a trigger, causing an infectious disease in a person with a weak or dysregulated immune system. But there’s also a second role.

The microorganisms’ second role relates to the immunity training I just mentioned. We are in constant interaction not only with “friendly” microorganisms like our gut microbiome, but also with potentially pathogenic agents like rhinoviruses, coronaviruses, enteroviruses, Staphylococcus aureus bacteria, and many others.

They act as trainers of our immune system, mostly without us even noticing it. You may feel a bit of an itch in your throat or experience mild diarrhea, but that’s mostly it.

But sometimes, the best training is the actual fight, not just casual training or sparring. That’s when you get a full-scale infectious disease.

Your immune system is very intelligent, so the immune cells and other members of your “armed forces” learn and remember a lot from those fights, including how to cooperate closely against a strong opponent. That allows for their future successful defense not only against the opponent that caused the disease, but also against its variants and even different opponents.

That’s why these fights are necessary – especially in childhood when the immune system is not yet fully developed, but occasionally also in adulthood.

You need your immune system to be ready to protect you at all times, so you must let it train, although the training can sometimes be tiring and exhausting.

If you don’t let the armed forces train, will they get better or worse? The same logic applies to your immune system.

If you avoid or artificially prevent the actual fights, you’ll deprive your immune system of the most valuable lessons, and it won’t be able to fully protect you when you need it most.

Sure, do support your immune system fully in those fights by taking vitamins, minerals and other supplements, but do not prevent the valuable training.

Martial artists often say that the best training is the actual fight.

It’s not a coincidence that immunity training is of the main root causes of health. As always, proceed in small incremental steps, slowly but steadily. Don’t be too adventurous, but be willing to lose a few battles to win the whole war for your long-term health.


And now, it’s your turn! Which part of the article did you find the most interesting? Or is there anything else you’d like to share with us?

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