Autism treatment protocol
Autism spectrum conditions are increasingly understood as systemic disorders rooted in early immune dysfunction, mitochondrial stress, and microbial imbalance—particularly in the gut. It seems NAD+, niacinamide, magnesium, calcium, vitamin D, and the rest of the B vitamins are all crucial for regulating immune function—not just in “boosting” it, but in modulating it appropriately. These nutrients help the immune system respond effectively without tipping into chronic inflammation or autoimmunity. They support mitochondrial function, energy metabolism, and the body's ability to repair tissue and neutralize oxidative stress—key factors in managing microbial overgrowth and damage.
Choline, in particular, plays a long-term role in neurological health. Sustained choline supplementation—over a year or more—can significantly improve sensory processing issues. This makes sense given that choline is essential for synthesizing acetylcholine (a key neurotransmitter) and for metabolizing cholesterol, which is vital since the brain is composed primarily of cholesterol-based structures like myelin and cell membranes.
1. Key Nutritional Foundations:
Restoring cellular energy and immune modulation begins with essential micronutrients:
NAD+ & Niacinamide (Vitamin B3) – Crucial for mitochondrial function and cellular energy. A deficiency in B3 impairs immune regulation, gut microbial diversity, and bioenergetic pathways—leading to long-term dysbiosis.
Magnesium, Calcium, Vitamin D, and B Vitamins – Together support immune balance, nervous system repair, tissue regeneration, and oxidative stress reduction.
Choline (especially Alpha-GPC) – Vital for acetylcholine synthesis, cholesterol metabolism, and neurodevelopment. Long-term choline supplementation can significantly improve sensory integration and cognitive regulation.
The lack of B3 I believe that prevents the bacteria from forming the necessary diversity to get back to the healthy gut stasis, which explains why the autistics never recover — they experience early childhood gut trauma (usually from bacteria and viral coinfections before or after birth) and digestive disorders, only schizophrenics have worse disruptions to their gut diversity and digestive dysfunction. At least after reading that NIH research summary, it seems to come together directly tied to the B3 and energy chain from there to the mitochondria and their support enzymes not working, especially with how the bacteria diversity never gets back to normal once the immune system goes haywire without the B3.
Alzheimer’s and Parkinson’s and autism and other dementia have similar symptoms in that cells or immune cells seem to be “tired or exhausted” to realize that one of the energy pathways is disrupted… and it isn’t easy to disrupt an energy pathway. And almost all the old centenarians have their gut bacteria become disrupted before they start to die. The older you are, the more susceptible you are to these energy pathway disruptions.
2. Gut-Immune-Mitochondrial Axis:
Children on the autism spectrum often show:
Early-life gut trauma (from infections, antibiotics, or environmental insults)
Low microbial diversity
Mitochondrial inefficiency and energy "exhaustion" in immune and neural cells
This mirrors patterns seen in Alzheimer’s, Parkinson’s, and even schizophrenia—where energy metabolism breaks down before full neurological symptoms appear.
However, while nutritional sufficiency sets the stage for recovery, the body often can't heal fully until the root microbial imbalance is addressed. Pathogenic bacteria and fungi must be reduced or eliminated—otherwise, they continue generating bioactive toxins, disrupting barrier integrity (gut, brain, skin), and hijacking host resources. In other words, the body doesn’t enter this dysregulated state spontaneously; it’s reacting to persistent biological stressors that must be resolved.
3. Addressing the Root Cause:
While nutrients set the foundation, healing requires microbial reset:
Pathogenic bacteria and fungi must be suppressed or eliminated
Persistent biofilms must be disrupted
Barrier tissues (gut lining, blood-brain barrier) must be repaired
Without addressing the underlying microbial burden, the body remains in a reactive, dysregulated state—producing inflammation, neurotoxins, and immune chaos.
Shawn Blake
Los Altos, Ca
Cognitive Identity Shift Driven by Neuroimmune Rewiring
The subject, David, reported a notable shift in cognitive identity following neurological and immune system changes from ATP (Autism treatment protocol). These changes appear to rewire how memory, emotion, and perception interact, resulting in a cascade of functional shifts:
1. Loss of Photographic Encoding Memory
This likely reflects changes in hippocampal plasticity, PKR activation, and limbic-sensory integration. Individuals with strong sensory-based encoding—especially visual and emotional—tend to be more vulnerable to PTSD. The trauma loop is often reactivated through high-fidelity memory recall, a mechanism still underexplored in mainstream PTSD research. David’s observation that roughly 20% of people experience this type of encoding aligns with clinical estimates of enhanced autobiographical memory prevalence.
2. PKR Pathway as Viral Defense Mechanism
PKR (Protein Kinase R) is a critical part of the innate immune response. It detects double-stranded RNA—a signature of viral activity—and shuts down protein synthesis to halt viral replication. In neurons, however, this defensive action can impair synaptic function, memory formation, and neuroplasticity.
When chronically but moderately active, PKR may:
Suppress viral reactivation (a protective effect)
Simultaneously downregulate plasticity, glutamatergic signaling, and memory encoding
This could explain the “cognitive dulling” David experiences—less intense memory and emotion, but also less vulnerability to trauma loops.
3. Biofilm Burden & PTSD Susceptibility
Chronic, subclinical infections—especially those involving microbial biofilms or latent viruses—create persistent “immune noise” (e.g., LPS, cytokines). This background inflammation:
Sensitizes the nervous system
Destabilizes limbic-vagal regulation of memory and emotion
If only 15–20% of people are predisposed to high-fidelity, PTSD-style encoding, biofilm-related neuroinflammation could serve as a tipping point—shifting the system into a chronic neuroimmune PTSD loop.
4. Shifts in Cognitive Identity
The most profound change isn’t just cognitive performance—it’s a shift in who David is cognitively. He reports changes in motivation, memory style, emotional responsiveness, and overall internal narrative. This likely involves:
Recalibration of the dopaminergic system
A transition from hyper-attentive, trauma-sensitive processing to a more emotionally buffered baseline
This may feel like a loss of self—especially if the prior identity was built around high-fidelity memory and emotional intensity—but it can also represent a release from overload. What follows may be slower, more reflective emotional processing, or new pathways for creative integration and resilience.
Shawn Blake
Los Altos, Ca
Case Summary: Subject – David
After 8 weeks on the outlined protocol—including NAD+ precursors (niacinamide), magnesium, calcium, vitamin D, full-spectrum B vitamins, and daily choline supplementation—subject David demonstrated significant improvements in both physical and neurological domains:
Cognitive Focus & Sensory Processing:
David’s hypersensitivity to noise and light noticeably decreased. He began sustaining attention during tasks for longer periods and was able to tolerate environments that previously caused distress.
Gut Function & Appetite:
His digestive symptoms, including bloating, inconsistent bowel movements, and food aversions, improved markedly. He began requesting a broader range of foods and tolerated fiber-rich meals better, suggesting rebalancing of gut flora.
Behavioral Regulation:
Emotional outbursts declined in frequency and severity. His baseline mood appeared more stable, with a stronger ability to self-soothe and communicate discomfort.
Energy & Physical Vitality:
Reduced fatigue and improved motor coordination were observed. Activities like walking, climbing stairs, and outdoor play were better tolerated without signs of muscular soreness or post-exertional crashes.