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The immunesystem protects the body from potentally harmful substances.
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Food itself is different than a bacteria or virus.
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When the allergen is eaten, a IgE antibody is formed and attaches itself to cells found in the tissues of cells all over the body.
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When the food enters the body again, the allergen binds to IgE antibodies and sends out signals for the body to release large amounts of histamine.
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There are certain circumstances that present issues when digesting food
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Genetics, Circumstances under what the food was first encountered, Microorganisms that live within the digesive tract, and other diseases.