How a healthy immune system works
A healthy immune system protects us in several ways. We have barriers that keep out dangerous substances. For those substances that get through, we have specialised cells that can tackle them in other ways.
Being able to recognise substances is an important part of this process. More importantly, being able to recognise the difference between self and non-self. In autoimmune disease, the immune system recognises self-tissues as foreign and destroys them.