It most often begins in young adults and lasts a lifetime.
Second sentence in the paper.
Second sentence in the paper.
For auto-immune diseases, the consensus (if we can call it that) mostly revolves around the hygiene hypothesis. Refrigeration is one aspect of this, but other things that fall in this category are the use of soap, rising cleanliness standards, disinfectants, aseptic methods, positive pressure toilets and good sewage systems, vaccines, antibiotics, not breastfeeding as much (not directly a hygiene issue, but breastfeeding transfers passive immunity to a child with a developing immune system, which has an effect not unlike being exposed to a different spectrum of microbes), caesarian births, always eating very fresh meats and vegetables, etc.
There is a grain of truth to "what doesn't kill you makes you stronger" (but don't take that idea too far, and please do wash your hands and do get vaccinated, for god's sake), and the essence of the hygiene hypothesis, in comp sci / ML terms, is that it's a training set problem.
Edit: it's unclear to me why people are downvoting this. This is my area of expertise, so I'd be curious to know what people find objectionable in this comment.
There is a critical period during infancy and early childhood when the immune system goes through a number of critical maturation processes. Afaik, once that's done there's no going back to a perfectly fresh slate.
After puberty, for example, your thymus (an important site for T cell maturation) begins shrinking and eventually all that remains of the organ is basically non-functional traces of scar tissue. That is not to say that T cell maturation doesn't occur afterwards, but it is a particularly striking example of the irreversible age-related change we can be talking about.
Another less-obvious example is that children born by cesarian have a different skin and gut flora through the rest of their lives than children who are born through the vaginal canal: the initial colonization of the skin with a different set of bacteria has some degree of permanence, though it is also somewhat plastic. Yet another example, children who are breastfed tend to have fewer food allergies or auto-immune diseases (atopy, generally) than children who are fed formula. Early conferral of passive immunity through maternal antibodies secreted in breast milk selects for different populations of gut microbes, and again there is some degree of permanence to this. In both cases, the differences are measurable throughout adulthood!
The hypothesis in the paper is that Crohn's isn't autoimmunity and that improving hygiene might prevent or treat it.
Edit: They do mention a training set factor, but at the level of population genetics instead of at the level of an individual developing immune system. Their evidence is that a history of the plague, rather than hygiene, promoted a genetic immune system weakness that made people more likely to survive the plague, but that Crohn's is a consequence of that today. A related example that comes to mind is the prevalence of sickle cell anemia in regions with malaria.