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But this came at a cost: some of these genetic variants are risk factors for the autoimmune diseases rheumatoid arthritis, lupus and Crohn’s disease. In the same way that the military culture of a society is inherited from generation to generation – ranging from open and tolerant to hostile and defensive – the culture of our defence system is passed down to us through DNA. One positive consequence for our ancestors living in filth was that, from an early age, their immune systems were vigorously trained to differentiate friends (food and ‘good bacteria’) from pathogenic foes. In today’s sanitized, antibiotic society we are less likely to have this opportunity to help our immune system develop tolerance, refining its predictions about what is ‘self’ and what is ‘non-self’, what is safe and what is a threat. This is the core of the ‘hygiene hypothesis’, which is a widely accepted theory to explain the staggering increase in rates of allergy and autoimmunity in the modern world.
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Monty Lyman (The Immune Mind: The Hidden Dialogue Between Your Brain and Immune System)