Imagine that your immune system has just been assaulted by a nasty virus or bacterium such as cholera, norovirus or e-coli amongst others. The first line of defence is to fight the invader; white blood cells are mobilised to eat the unwanted guests and zonulin is released to open up the gaps between cells in the gut wall. Opening up these gaps allows water to flow through from the blood, flushing the virus or bacteria through with it. The resulting diarrhoea is a protection mechanism designed to purge the body as fast as possible and is something which developed in humans after we diverged from other primates. As a result, only humans have autoimmune diseases.
Zonulin was identified as the trigger for opening up gut gaps in 2000 and its production is increased by the presence of gluten. The problem is that opening up these gaps allows particles to pass in both directions and if they are opening in response to gluten rather than bugs partially digested food is getting through into the bloodstream.
Normally, when food is digested it is broken down into very small nutrient particles which pass through the cells lining the intestine, into the bloodstream.
They are then transported through the bloodstream to the cells where the micronutrient particles are rebuilt into larger proteins and fats.
The problem is that some of the larger particles which get through the gaps between the cells in a leaky gut are the same as the proteins being reassembled in cells. Their presence in the bloodstream triggers white blood cells to remove them and once they are recognised as being an invading species the white blood cells will also start attacking the cells in which they are being manufactured. This is the origin of autoimmune disease.