Whether it's Hashimoto's or any chronic condition, it's been determined that inflammation and the chronic fright or flight state are the reason behind almost all of them. Dysautonomia is not new; I learned about it over a decade ago and knew it made sense but was difficult to treat. Healing the brain is difficult as we have found out watching The Broken Brain series.
We've discussed stimulating the vagus nerve by throat exercises since the nerve runx behind both ears and the palate. There may be something more we can do. This explains what goes wrong.
Vagus nerve stimulation is a useful tool to reduce abnormally elevated levels of inflammation throughout the body, and is a critical tool for the reversal of traumatic and non-traumatic brain injury.
If the “fight or flight” Sympathetic brain commands are disrupted people may feel tired, crave salt or sugar, experience excessive hunger, or get anxious. People may get heart palpitations, tingling or numbness in their arms (hands or face), disrupted night vision, varicose veins, E.D., stiff necks and shoulders, severe (“migraine”) headaches, or insomnia.
If the “rest and digest” Parasympathetic brain commands are disrupted they may affect the intestinal tract (heartburn or constipation), immune system (autoimmune disorders), and produce chronic pain syndromes (fibromyalgia). People may get sleep apnea, “restless legs”, morning nausea, night sweats/hot flashes, power surge sensations when they should be at rest, or non-restorative sleep. But when the portion of the autonomic nervous that regulates blood pressure is not working well, the body is unable to keep proper blood flow and oxygen levels to the brain. This condition is referred to as autonomic (sympathetic) withdrawal.
Metabolic inflammation is the cumulative effect of a variety of problems. Excessive omega-6 fatty acids (vegetable oils) and deficient omega-3 fatty acids (DHA, ALA, EPA) in our foods are believed to be one of the major global triggers of obesity and diabetes. Compounding this is an imbalance of intestinal bacteria (SIBO) and the ingestion of chemicals referred to as AGE’s (advanced glycation end products).
A doctor I used to follow knew all about this and of course they took away his license. I guess it is dangerous for doctors to make people well.
There is bacteria that gets stuck in the intestinal tract which they call SIBO and it is hard to fix. Of course the one prescription antibiotic called Rimaxifin is very expensive. It stays within the gut and doesn't enter the bloodstream. Natural herbs they mentioned on the SIBO summit were berberine, Neem, Allicin, Schisandra to name a few. Eating foods that digest quickly keeps the food from fermenting and also eating infrequently.
And then there are stealth infections throughout the body. As you say, when things go haywire the body can't work as intended.
This doctor has developed a treatment in Arizona and I don't know if there are others but there are techniques to balance the nervous systems that can work as well which the doctor I first mentioned would encourage. There are binaural beat cds and other devices to help bring about the relaxation state but you have to dedicate yourself to doing it twice daily.
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Can we talk about diet and supplements please? 
Why we are not getting the treatment we deserve
I have had underactive thyroid for 35 years. Unfortunately I've also recently found out that my tpo is 450. So I guess that's hashi. 
Evidence showing why we can be ill with "normal" thyroid blood tests. 
