How are immune responses to a pathogen distinguished from auto-immune disease?

Question

e.g. some types of arthritis compared to Lyme Disease, Thyroid Eye or an immune response to a virus, or psoriasis, asthma etc.

Answer 1

The immune system protects an organism from infection by identifying and then killing pathogens. This task is extremely difficult, since pathogens range from viruses to parasitic worms and these diverse threats must be detected with absolute specificity amongst the huge variety of normal cells and tissues. Pathogens are also constantly evolving new ways to avoid detection by the immune system and successfully infect their hosts.
Overactive immune responses comprise the other end of immune dysfunction, particularly the autoimmune disorders,. Here, the immune system fails to properly distinguish between self and non-self, and attacks part of the body. Under normal circumstances, many T cells and antibodies react with “self” peptides. One of the functions of specialized cells (located in the thymus and bone marrow) is to present young lymphocytes with self antigens produced throughout the body and to eliminate those cells that recognize self-antigens, preventing autoimmunity.
Please see the web pages for more details on Immune system.