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The Dr. Tomato Protocol:
Understanding the Causes of Autism and its Onset

01 Limitations of conventional theories of autism and three stages of autism onset

Autism spectrum disorder is not a single-symptom disorder. Various symptoms are combined to generate the common manifestations of a social development disorder. In this sense, there are many different aspects of autism, hence autism “spectrum” disorder.

If one understands that autism is a combination of various symptoms, one will naturally conclude that the causes of autism are multifaceted. Multiple reasons are combined in various ways to manifest the different signs of autism spectrum disorder, from milder to more severe symptoms. Medical attempts to treat autism require a clear understanding of the diversity of causes.

The Dr. Tomato Protocol is designed to treat autism based on a clear hypothetical structure of autism development and onset. Therefore, following Dr. Tomato’s protocol to treat autistic children should be preceded by understanding how autism develops and aggravates.

Mainstream medicine has claimed the genetic causation of autism. Indeed, it is influenced by genetics, but genetic determinism leads us to conclude that autism is an untreatable congenital disorder. However, there are countless cases where children overcame severe autism and reached neurotypical development, which genetic determinism cannot explain. In particular, genetic determinism is fundamentally denied by the emerging view of epigenetics.

Increasingly compelling are studies that show that abnormalities in the intestinal bacterial flora are what causes autism. In other words, autism is worsened by the loss of diversity in the intestinal bacterial flora and the proliferation of harmful bacteria. It is clear that abnormalities in the intestinal bacterial flora are one of the causes of autism. Still, it remains unclear if autism is caused by the lack of diversity, over-proliferation of the bacterial flora, or the proliferation of specific harmful bacteria. Clinical reports on fecal replacement (intestinal bacterial flora transplantation) suggest that it is effective, but the cure rate is not very high. It is clear that autism is developed and onset solely by abnormalities in the intestinal bacterial flora. Precaution should be taken not to rely on the omnipotence of the intestinal bacterial flora in autism treatment.

Clinicians that have tried to treat autism with biomedicine often see various metabolic abnormalities as a cause. These include declines in antioxidation, autoimmune abnormalities, mitochondrial abnormalities, and specific nutrition metabolism abnormalities, but they are not enough to explain various symptoms of autism. Whatever the hypothesis is, biomedicine has failed to exert significant treatment effects, and this thus refutes the validity of the biomedical hypothesis.

In the Dr. Tomato protocol, the assumed fundamental cause of autism development is a viral infection. The complicated symptoms of autism can only be explained by a viral infection in the central nervous system. The viral infection theory has significant validity but has not emerged as the mainstay of autism treatment because neither traditional medicine nor biomedical therapies have remedies with antiviral effects. However, Korean herbal medicine has a powerful potency in this regard. That is why I am sure it will develop as the complete therapy to cure autism.

The following schematization shows the cause of autism as developed by Dr. Tomato.

Primary progress, autism development: caused by viral infection => Secondary progress, autism fixation: caused by intestinal bacterial flora imbalance + autoimmune inflammation => Tertiary progress, autism aggravation, and vicious cycle: deterioration and the worsening of various nutrition metabolism
Let’s take a deeper look at how autism develops and exasperates.

02 Overview of Autism Development and Onset

In general, the development and aggravation of autism follow three stages.

Stage 1

Autism development

Stage 2

Autism fixation

Stage 3

Vicious cycle of autism aggravation

In each stage, they manifest variations in the level of deterioration, hence the broad spectrum of autism disorders.
Most medical attempts to identify the causes of autism and find treatments have focused on what causes autism to aggravate in the third stage, and only a few studies have covered investigations and remedies in the second stage. For this reason, all these medical attempts have not been rewarded by clinical achievements.
The following is Dr. Tomato’s hypothetical structure about the development and aggravation of autism.

Stage

1 Causes of autism development

Wakefield was a pioneer of biomedicine, especially in his medical approach to treating autism. Although he was stripped of his medical license for false thesis charges, he still influences people convinced of the possibility of autism treatment. Although Wakefield argued that the mercury toxicity created by the MMR vaccination was the cause of autism, his essential claim should be considered the viral infection theory. Wakefield’s rationale for the vaccination theory was that the MMR vaccination causes cognitive damage, which results in autism. This damage occurs by the growth and increase of virus infection in the small and large intestines. Eventually, he understood that mercury toxicity was the cause of the viral infection. However, it has now become clear that mercury in the MMR vaccine does not cause autism. In response to Wakefield’s theory, we need to think about why viral infection is still present.
If we say that Wakefield is the person who initiated the origin of biomedical autism treatment, Amy Yasko is the person who made a breakthrough in biomedical treatment. Yasko pointed out that abnormalities in methylation are a significant factor in the development of autism, and she suggested a remedy for autism, marking a milestone in the treatment of autism. Yasko resonated with Wakefield’s argument that mercury poisoning can cause a commensal viral infection. Therefore, Yasko contemplated her treatment, and since she could not identify a direct antiviral effect, she tried to indirectly treat the damage caused by the viral infection. Yasko made it clear that she chose an indirect way to control the virus but realized that the best way is to control the virus that causes autism directly.

The claim that autism begins with a viral infection is not only stated by Dr. Tomato. Those who have thought deeply about the development and exacerbation of autism cannot deny that viral infection causes and worsens autism.

The core cause of autism development is a viral infection in the central nervous system. The primary damage from the viral infection affects the brain stem and sensory processing disorders caused by the damaged brain stem causes the fundamental symptoms of autism. The secondary damage comes from instability in the autonomic nervous system, leading to declines in digestion, reductions in brain pressure and brain blood circulation, stress, over-anxiety, and sleep disturbances.

Recently, dysbiosis, i.e., the imbalance of the intestinal microbiome, has been considered one of the critical causes of autism. It still remains unclear if harmful bacteria proliferate, or the diversity of the microbiome is affected, or the over-proliferation of the bacterial flora is the cause. Nonetheless, given the research outcomes that attempts to replace the intestinal microbiome led to tendencies to improve autistic symptoms, it is clear that abnormalities in the intestinal microbiome are one of the critical causes of autism.

Another observation, along with dysbiosis, is bowel function instabilities in children with autism. Most children with autism experience bellyache, diarrhea, indigestion, and gastric and colonic functional abnormalities. These are, on the one hand, caused by dysbiosis but are, on the other hand, attributable to reduced digestive functions being the fundamental cause of the instability of the microbiome. Reduced digestive functions deteriorate the intestinal environment, hence are favorable for the abnormal proliferation of intestinal microorganisms. In other words, this implies that the intestinal bacterial flora is likely to be restored if digestive functions are kept in good condition.

Recent studies have clearly demonstrated that the decline of digestive functions in children with autism is caused by abnormalities in the regulation of the autonomic nervous system. Most children with autism exhibit hypertarachia with the parasympathetic nervous system being less functional. Together, they cause dyscoimesis and indigestion. Some argue that intestinal dysbiosis causes disorders in the autonomic nervous system. However, what clinical observations suggest is that autism is preceded by dyscoimesis and indigestion, which is followed by autistic regression. Given that the abnormality in the autonomic nervous system precedes autistic regression well ahead, it is assumed that the disturbed autonomic nervous system is a major cause of dysbiosis.

This leads us to another question. Why is the autonomic nervous system disturbed? Clinical observations suggest that this is not innate. In other words, these are not observed during the infant stages. Instead, they are gradually exhibited during normal development and lead to aggravation and degeneration. For this reason, autistic disorders are considered as degeneracy in the course of development.

After all, what causes the disturbance in the autonomic nervous system is fundamentally the cause of autism. Dr. Tomato is confident that this is attributable to damage to the brain stem and hypothalamus caused by viral infection. Children with weaker immunity are exposed to acquired viral infection, which is accompanied by damage to the brain stem and hypothalamus. As a result, the function of sensory regulation in the brain stem is damaged, and abnormalities in eye contact and acoustic processing develop. Furthermore, as the autonomic nervous system is damaged, weaker eye contact comes with dyscoimesis, indigestive constipation, bellyache, and diarrhea.

Immunology panels in children with autism often reveal increases in antibodies against the virus. Many studies have confirmed and demonstrated increases in viral infection among children with autism. Commonly observed are herpes, poxvirus, and herpes zoster virus. Based on this finding, a considerable number of studies have reported an instant and dramatic improvement in autism by using acyclovir or Valtrex. There are common cases where antiviral agents result in gradual improvement, if not dramatic. However, the effectiveness still remains insignificant; hence it has not been popularized yet.
The limitation of antiviral therapy means the limited efficacy of treatments, not the limitation of the viral etiology. As viruses keep developing variants, there are limitations in producing consistent effects with specific antiviral agents because antiviral agents made from certain chemicals are effective only in certain conditions.

Not only existing antiviral agents but many trophotherapies are ineffective for antiviral treatment. However, their effectiveness is inconsistent as they exhibit indirect antiviral effects by improving the overall immune system. This could largely explain why the attempts made by DAN (Defeat Autism Now!) doctors, which were once popular in the USA, failed.
For the accurate and instant improvement of autism, treatments that exhibit excellent antiviral effects in the brain stem are required. Once they start working, the eye contact ability is recovered very quickly, and this allows for improving most of the sensory disorders. These are also accompanied by improvements in sleep disorders, dyschezia, and indigestion. Dr. Tomato’s Korean herbal medicine therapy has succeeded in resolving these fundamental problems to an extent.

Stage

2 Causes of autism fixation

Autism is developed and progressed by viral infection and damage in the brain stem and hypothalamus, and in most cases, the progress is slow. Over time, however, the autistic symptoms suddenly set in and become fixed. The key culprits are Small Intestinal Bacterial Overgrowth (SIBO) and autoimmune diseases in the central nervous system. These are critical to the child’s mental and cognitive development and can result in irrevocable damages. Inflammation caused in response to autoimmune actions can damage the entire cerebral cortex, which is thought to be irreversible. As a result, the cerebral cortex becomes less responsive, and the child’s cognitive and intellectual abilities deteriorate. It does not seem that the damages in the first stage of autism development involve cognitive deterioration, which would be the case for most children with Asperger syndrome. However, severe autism causes irreversible damage, hence intellectual impairment.

The most important cause of the fixation of autistic symptoms is SIBO. The fundamental cause of SIBO is decreased peristalsis of the intestinal tract. The decreased peristalsis of the intestinal tract is caused by damage in the autonomic nervous system attributable to infection damage in the brain stem and hypothalamus. The decreased colon movement contributes to the over-proliferation of bacteria in the colon and dysbiosis. It also causes the small intestine to move less, and the reflux of bacteria from the colon causes SIBO.

The presence of SIBO implies damage progressing in the central nervous system, leading to the fixation of autism. Many studies have confirmed deficient levels of monoenoic fatty acids in the intestinal tract of children with autism. With various reasons suspected, the most compelling assumption is that monoenoic fatty acids are absorbed through the blood vessels in the small intestine driven by SIBO. The growing evidence of the impact of propionic acid, a monoenoic fatty acid, on autism underpins such an assumption. In an animal study, the intravascular injection of propionic acid caused increases in autistic behavioral patterns, for example, deterioration of sociality and increases in temper tantrums and stereotyped behaviors. In addition, increases in propionic acid concentration in the blood are believed to contribute to damage to tissues in the nervous system. This suggests that the absorption of propionic acid in the body is one of the major causes of autistic behavioral patterns and damage to the nervous system.

SIBO causes propionic acid to be absorbed. However, propionic acid is not the only harmful substance introduced to the blood by SIBO. One may assume that many other toxic substances are present in the blood vessels through the small intestine. More studies are needed to investigate this further. I believe the diversity in neurotoxic substances is one of the leading causes of the multifaceted autistic symptoms.

SIBO is only the beginning of the fixation of autistic symptoms. Another major cause of the fixation of autistic symptoms is the aggravation of inflammation in the cerebral cortex, which is thought to progress through two pathways.

The first is damage caused by viral infection involved in the development of autism. Initiated in the brain stem or hypothalamus, the viral infection causes damage that spreads throughout the cerebral cortex. It seems that poor concentration or slow learning observed in children classified as high-functioning autism spectrum disorders is caused by this. Taking assumptions from clinical observations of Asperger syndrome, this process progresses slowly and causes moderate damage.

The second is an increase in the autoimmune inflammation reactions triggered by neurotoxic substances introduced from SIBO. Not only do propionic acid and other monoenoic fatty acids cause inflammation, but as discussed earlier, a leaky gut syndrome in the small intestine also causes various inflammatory substances to be introduced to the body. Metabolites produced from the over-proliferation of candida or clostridium, derived from harmful germs and toxic substances produced from the digestion of unhealthy foods, are absorbed into the body, leading to the mass release of inflammatory cytokines, which causes autoimmune inflammation. This process progresses very quickly and dramatically, leading to temper tantrums, self-immersion, intellectual degeneration, and ultimately epilepsy.

Cases of inflammation caused by these pathways damage the cerebral cortex. In particular, the aggravation of autoimmune reactions induced by SIBO causes irrevocable brain damage, and these irreversible autistic symptoms lead to intellectual impairment.
Children under 24 months are likely to remain in the first phase of autism development. However, most children with autism over 36 months will undergo the second phase, i.e., the fixation of autism, hence refractory autism. Therefore, whereas early treatment is the surefire way to ensure recovery without intellectual impairment, cases are often accompanied by intellectual impairment even after removing the autistic features if treated at 36 months and over.

Stage

3 Aggravation of the vicious cycle of autism

The third stage of autism progression is a metabolic disturbance. Precisely this is not a cause of autism development but is a contributor to the aggravation of autistic symptoms. This has been confirmed by research by DAN doctors in the USA. I do not believe their claims about vaccines or cytology regarding metals. Nor do I think that chelation for removing heavy metals is a fundamental treatment. It only has indirect effects, which are demonstrated by the insignificant effectiveness of chelation compared to the risk it conveys and the lack of consistency. Still, it is clear that metabolic abnormality, as confirmed by the DAN doctors and functional medicine experts, is an important factor in the aggravation of autistic symptoms.

It is not only from DAN doctors’ research that one can easily find the metabolic abnormality in children with autism-specific patterns; this can be identified by conducting an organic acid analysis of urine. The most notable is weaker antioxidation effects, the deterioration of detoxication in the liver and damage to mitochondria in the cells. This is thought to be caused by the progression of the fixation of autism in the second stage, which is accompanied by the deterioration of metabolic functioning. Also commonly observed is the over-proliferation of bacteria in the intestines and resulting instability. These two factors create a vicious synergy and mediate the vicious cycle of the aggravation of autistic symptoms.

What is first observed are weaker antioxidation abilities which accelerate systemic inflammatory reactions and cause tissue damage. Increases of inflammatory substances in the development and fixation of autism lead to increases in active oxygen. This, in turn, serves as oxidation stress that causes brain damage. The mainstream theory is that increases in lipid peroxides and the lack of antioxidation mechanisms are observed in children with autism, who are more prone to oxidation stress than other children. Given this, taking antioxidant supplements would improve their antioxidation abilities, resulting in a potentially better prognosis for the treatment of autism. However, treating them with antioxidants may help but does not block the production of inflammatory substances. I have observed countless cases where children with autism recovered antioxidation abilities by removing the primary and secondary causes identified above without using antioxidant nutrition supplements.

The metabolic abnormality in mitochondria was also considered a fundamental cause of autism among DAN doctors. There is evidence that autistic children have metabolic abnormalities due to the functional impairment of mitochondria. Pollutants and inflammatory substances introduced to the body hinder mitochondria’s functions, leading to DNA damage. Also, peroxidation in the course of fat metabolism in mitochondria contributes to tissue damage. Damages to mitochondria are not a primary cause of autism progression, but it seems clear that it is one of the causes of various metabolic abnormalities observed in children with autism. Nutrition supplements that are expectedly thought to have effects in improving the functions of mitochondria produce betterment in prognosis and the improvement of conditions partially, but they are not enough to bring out dramatic results to cure autism.

Other noteworthy metabolic abnormalities include the deterioration of the detoxication ability and metabolism of the liver. The organic acid analysis of urine has repeatedly confirmed this. Also, there have been reports that children with autism have reduced detoxication abilities of the liver, hence a tendency to exhibit higher AST and ALT levels. It is widely known that the anticonvulsant Valpolate causes autism. It is accompanied by the deterioration of the enzyme breakdown ability of the liver, which is believed to be a fundamental cause of autism development. Furthermore, animal studies have reported the restoration of the hippocampus by improving the enzyme metabolism in the liver. Reduced liver metabolism is not a cause of autism but seems to be a factor that hinders recovery.

In my assumption, the decisive cause of the aggravation of autism is the deterioration of carbohydrate metabolism. It is thought that children with autism have very unstable blood sugar control abilities and that there is a pathologic mechanism that hinders, during the carbohydrate metabolism process where excess carbohydrates are converted to and accumulate as fat, the stable conversion to an accumulation of fat as well as causes the over-production of inflammatory cytokines. For this reason, many severe autism cases cannot achieve betterment as long as they maintain overexposure to carbohydrates in their diet.

Also common are tendencies to exhibit increases in allergic sensitivity to food. It is not uncommon to encounter cases where sensitivity to all foods is eminent without the need to confirm with the delayed food sensitivity test (IgG). It is also clear that there is a tendency for the over-proliferation of intestinal bacteria. They include both malignant and beneficial bacteria, such as lactobacillus, and exhibit synergies to lead to mutual growth. For this reason, they are using lactobacillus supplements does harm rather than good in many cases. The fundamental causes of increases in allergic reactions and bacterial over-proliferation are the reduction of intestinal movement and the deterioration of digestion attributed to the primary reason discussed above. Therefore, it would be illogical to treat autism with supplements without making fundamental improvements in digestion.

The last but decisive factor for the aggravation of autism is the progression of epilepsy. Approximately 30% of children with autism exhibit epileptic brain waves or signs of chronic epilepsy accompanied by convulsions when they enter the adolescent period. This is a result of irrevocable damage to the nerve tissues due to prolonged inflammation in the brain. Convulsion is caused by abnormal electric activity in the brain cells. The development of epilepsy implies the last stage of the aggravation of autism, where significant betterment would not be expected. It is thought that at this point, autism is no longer recoverable and becomes a permanent impairment in the brain.

There are many metabolic abnormalities that further aggravate the symptoms of autism. DAN doctors have made reasonable endeavors to treat these abnormalities. However, it should be reiterated that their attempts may contribute to producing indirect treatment effects rather than directly treating it, only in rare cases. Cases where they may succeed in recovering patients from autism are for children of very young ages with extreme immune resilience or high-functioning autistic children with mild symptoms. In my opinion, they may be of little help to most children with autism and cannot change their fate.

The third stage of autism progression is a metabolic disturbance. Precisely this is not a cause of autism development but is a contributor to the aggravation of autistic symptoms. This has been confirmed by research by DAN doctors in the USA. I do not believe their claims about vaccines or cytology regarding metals. Nor do I think that chelation for removing heavy metals is a fundamental treatment. It only has indirect effects, which are demonstrated by the insignificant effectiveness of chelation in comparison to the risk it conveys and the lack of consistency. Still, it is clear that metabolic abnormality, as confirmed by the DAN doctors and functional medicine experts, is an important factor for the aggravation of autistic symptoms.

What is first observed are weaker antioxidation abilities which accelerate systemic inflammatory reactions and cause tissue damage. Increases of inflammatory substances in the development and fixation of autism lead to increases in active oxygen. This, in turn serves as oxidation stress that causes brain damage. It is the mainstream theory that increases in lipid peroxides and the lack of antioxidation mechanisms are observed in children with autism, who are more prone to oxidation stress than other children. Given this, taking antioxidant supplements would improve their antioxidation abilities, hence resulting in a potentially better prognosis for the treatment of autism. However, treating them with antioxidants may help but does not block the production of inflammatory substances. I have observed countless cases where children with autism recovered antioxidation abilities by removing the primary and secondary causes identified above without using antioxidant nutrition supplements.

The metabolic abnormality in mitochondria was also considered a fundamental cause of autism among DAN doctors. There is evidence that autistic children have metabolic abnormalities due to the functional impairment of mitochondria. Pollutants and inflammatory substances introduced to the body hinder the functions of mitochondria, leading to damage to DNA. Also, peroxidation in the course of fat metabolism in mitochondria contributes to tissue damage. Damages to mitochondria are not a primary cause of autism progression, but it seems clear that it is one of the causes of various metabolic abnormalities observed in children with autism. Nutrition supplements that are expectedly thought to have effects in improving the functions of mitochondria produce betterment in prognosis and the improvement of conditions partially, but they are not enough to bring out dramatic results to cure autism.

Also common are tendencies to exhibit increases in allergic sensitivity to food. It is not uncommon to encounter cases where sensitivity to all foods is eminent without the need to confirm with the delayed food sensitivity test (IgG). It is also clear that there is a tendency for the over-proliferation of intestinal bacteria. They include both malignant and beneficial bacteria, such as lactobacillus, and exhibit synergies to lead to mutual growth. For this reason, they are using lactobacillus supplements does harm, rather than good, in many cases. The fundamental causes of increases in allergic reactions and bacterial over-proliferation are the reduction of intestinal movement and the deterioration of digestion attributed to the primary reason discussed above. Therefore, it would be illogical to treat autism with supplements without making fundamental improvements in digestion.

There are many metabolic abnormalities that further aggravate the symptoms of autism. DAN doctors have made reasonable endeavors to treat these abnormalities. However, it should be reiterated that their attempts may contribute to producing indirect treatment effects rather than directly treating it, only in rare cases. Cases where they may succeed in recovering patients from autism, are for children of very young ages with very strong immune resilience or high-functioning autistic children with mild symptoms. In my opinion, they may be of little help to most children with autism and cannot change their fate.

Overview of the autism aggravation mechanism

Viral infection => Invasion of the brain stem and midbrain => Progression to sensory disorders => Aggravation of sensory disorders => Invasion of midbrain => Damage to autonomic nervous system => Deterioration of digestion + brain hypotension

Invasion of brain stem ==>> Invasion of the limbic system and cerebral cortex (damages to brain tissue branching) => Cognitive disorder, poor concentration and attention, intelligence impairment

Brain hypotension + expansion of infection ==> Reduction of overall brain immunity => Progression of autoimmune inflammation in the brain

Reduction of digestion functioning ==>> Aggravation of SIBO ==>> Propionic acid introduced to blood => Blank-out ==>>> Dead or harmful bacterial tissues absorbed in blood => Mass release of inflammatory cytokines => Inflammation worsening and brain tissue damage

Meaning of organic acid analysis indicators – Unable to identify primary and secondary causes, only able to check tertiary aggravation factors.

Increases in inflammatory substances => Increased oxidation damages: Heavier detoxication load in liver
Digestion and absorption disorder => Fat and carbohydrate metabolic disorder: vitamin B absorption disorder
Inflammation in the central nervous system => Deterioration of neurotransmitters
Instability of intestinal movement and weaker digestion => Over-proliferation of intestinal bacteria