The immune system is engaged in a process of somatic selection. It is constantly distinguishing foreign molecules or bacteria, viruses, and even another person's skin from the molecules of an individual body, or soma. The well-spring of immunologic defense is scattered through the body in the tissues and organs of the lymphatic system and is carried out by a set of proteins called antibodies. The ultimate target of all immune responses is an antigen, which is usually a foreign molecule from a bacterium or other invader.
Specialized antigen-presenting cells, such as macrophages, roam the body, ingesting the antigens they find and fragmenting them into antigenic peptides. Lymphocytes are white blood cells that destroy pathogenic microbes that enter the body. They can also attack cancer cells or act against foreign cells in transplants. If regulation of the immune system breaks down, lymphocytes can attack cells belonging to the very body they are meant to protect, leading to a potentially fatal auto-immune disease. There are two kinds of lymphocytes T-cells and B-cells. They are produced in the Thymus and Bone Marrow respectively. After leaving these primary lymphoid organs, they circulate in the blood until they reach one of the numerous secondary lymphoid organs, such as the lymph nodes, spleen, and tonsils. (Here they leave the bloodstream and enter the lymph system)Much of the activation of lymphocytes occurs in the lymph nodes. They then travel through the fluid in the lymphatic vessels until they reach the bloodstream and spread their protective influence around the body. Eventually the lymphocytes flow into other lymph nodes and the cycle begins again.
Traditional immunology is antigen driven, and the immune system is seen only as a defense against infectious challenge. For the new trends in immunology, what is needed is an organism-centered view, in which notions of immune networks are carriers of internal dynamics. In this view, the central self-recognition properties of the immune system are more fundamental (and certainly more unexplored) than the peripheral responses to infections. A question of particular interest in immunology today is how the immune system can react to so many different antigens without attacking the self. How can so many different antigen-specific lymphocytes develop and still not attack the myriad tissues and cell types that are part of the body?
The immune system is capable of learning. Once an antigen has been encountered and overcome, lymphocytes specific to that antigen remain in larger quantities than before in the immune system. This is the basis for aquired immunity to diseases such as chickenpox and the basis for vaccines that provide the immunity without the disease. Gerald Edelman calls this a "non-representational memory system."
For F. J Varela, "the molecular self should be conceived as an emergent property of both the immune network's global regulation and the history of the individual's somatic components."