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tetsuo55 comments on Fix My Head - Less Wrong
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If this is your real diet then I am shocked at it, and and not surprised that it might make you sick in one or more ways.
As others have said headaches can have many causes, and even this diet might be unrelated.
As for the most likely cause, i would point to the milk. According to studies i don't have links to up to 76% of adults are allergic to cow milk. It takes a while and sometime high amounts for symptoms to start showing, it also takes a while to make them go away again. You could try not drinking milk at all for about a month and see what for effect that has on your headaches. In my own research into my chronic diarrhea i found that some foods take a long time to cause symptoms while others are immediate.
As for a better diet, i suggest reading this sequence: http://chronopause.com/index.php/2011/08/12/interventive-gerontology-101-01-the-basics/
You are thinking of lactose intolerance, which is a digestive problem (enzyme deficiency), not an allergy (immune reaction, typically to a protein). Actual milk allergies do exist, but they are much rarer among adults. Headaches are not known to be a symptom of lactose intolerance.
I am specifically talking about allergy, which is indeed completely unrelated to lactose intolerance, and are said to be very common, but that generally symptoms of the allergy are so weak that you can ignore them.
"A group of phosphoproteins in milk are commonly referred to as “casein”. Casein, which comprises 78.7% of all the protein in milk, is a major trigger of migraines and other types of headaches." http://www.metabolism.com/2008/08/23/stress-foods-food-additives-hormones-initiate-headaches
I have seen numbers showing ~75% of adults have some degree of lactose intolerance. I have not seen such numbers for milk allergies.
75% of adults worldwide are lactose intolerant, but it's strongly bound to ethnicity and North European backgrounds are outliers on the low side. Lactose intolerance rates for adult Americans of European ancestry are between 8% and 15% depending on what numbers you trust (self-reporting appears to give lower prevalence than other approaches), with the rates for Americans generally being about twice that.
I don't know anything about the allergy, but I am lactose intolerant and my symptoms do not include headaches. Nor have I ever heard of that showing up for others with the problem.