An Interpretative Introduction to the Immune System

This chapter is intended as a gentle introduction to the immune system for researchers who do not have much background in immunology. It is not a comprehensive overview, and certainly does not stand in for a good immunology textbook. The interested reader should consult [14, 4, 13]. The goal of this chapter is to sketch an outline of how the immune system fits together, so that readers may then go and consult detailed research papers, knowing where to look. For this reason, the emphasis here is on interpretation, not details, with an interpretative bias towards viewing the immune system from the perspective of information processing, that is, in terms of the architecture, algorithms and principles embodied by the immune system. The basis of the interpretation is the teleological viewpoint that the immune system has evolved for a particular purpose. Fundamentally, such a viewpoint is wrong, but it is useful for expository purposes: it is easier to understand the immune system to a first approximation if the components and mechanisms are viewed with the assumption that they exist to solve a particular problem. It is thus assumed that the “purpose” of the immune system is to protect the body from threats posed by toxic substances and pathogens, and to do so in a way that minimizes harm to the body and ensures its continued functioning1. The term pathogen embraces a plethora of inimical micro-organisms, such as bacteria, parasites, viruses, and fungi, that constantly assault the body. These pathogens are the source of many diseases and ailments, for example, pneumonia is caused by bacteria, AIDS and influenza are caused by viruses, and malaria is caused by parasites. Replicating pathogens can lead to a rapid demise of the host if left unchecked. There are two aspects to the problem that the immune system faces: the identification or detection of pathogens, and the efficient elimination of those pathogens while minimizing harm to the body, from both pathogens and the immune system itself. The detection problem is often described as that of distinguishing “self” from “nonself” (which are elements of the body, and pathogens/toxins, respectively). However, many foreign micro-organisms are not harmful, and an immune response to eliminate them may damage the body. In these cases it would be healthier not to respond, so it would be more accurate to say that the problem faced by the immune system is that of distinguishing between harmful nonself and everything else [7, 8]2. Once pathogens have been detected, the immune system must eliminate them in some manner. Different pathogens have to be eliminated in different ways, and the components of the immune