Was everyone a "little bit right" after all?

On the opposing views of the self-nonself discrimination by the immune system

Today's generally accepted view of the self-nonself discrimination was voiced by Miller(1) in 2004 in a thought-provoking essay. In spite of its popularity, this position has its limitations, which are analyzed here with a view toward establishing an interactive discussion that hopefully will culminate in agreed upon decisive experiments. The inadequacies of Miller's view of the self-nonself discrimination and their resolution under the associative recognition of antigen model are analyzed.

A biological context for the self-nonself discrimination and the regulation of effector class by the immune system

An effective immune response to an antigen requires two sets of decisions: Decision 1, the sorting of the repertoire, and Decision 2, the regulation of effector class. The repertoire, because it is somatically generated, large, and random, must be sorted by a somatic mechanism that subtracts those specificities (anti-self) that, if expressed, would debilitate the host, leaving a residue (anti-nonself) that, if not expressed, would result in the death of the host by infection. The self-nonself discrimination is the metaphor used to describe Decision 1, the sorting of the repertoire. In order to be functional, the sorted repertoire must be coupled to a set of biodestructive and ridding effector functions, such that the response to each antigen is treated in a coherent and independent manner. Although a reasonably complete framework for Decision 1 exists, Decision 2 lacks conceptualization. The questions that must be considered to arrive at a proper framework are posed. It should be emphasized that manipulation at the level of Decision 2 is where clinical applications are likely to be found.

An alternative to current thinking about positive selection, negative selection and activation of T cells

Given that recognition by the T-cell receptor (TCR) of allele-specific determinants on major histocompatibility complex (MHC)-encoded restricting elements (Rs) is germline encoded, whereas recognition of peptide (P) is somatically encoded, two combining site repertoires, anti-R and anti-P, are implied. As a consequence, the three pathways of T cells, positive selection, negative selection and activation, must be signalled by qualitatively distinct interactions engaging the TCR. These are spelled out as they provide an alternative to the current thinking that these pathways depend on affinity-based quantitatively distinguishable interactions.

Away with words: commentary on the Atlan-Cohen essay 'Immune information, self-organization and meaning'

Drawing on metaphors from linguistics and information theory, Atlan and Cohen challenge us to take a very different view of the immune system, one that engages in constant chatter among the constituents and allows the immune system to arrive at a decision about what to, and not to, destroy. Our commentary responds to this challenge and points out many logical biological flaws in their view. We seem to agree that specificity is important, and that there is some kind of somatic selection process at work to distinguish self from non-self. Our analysis of models depends on the basis of how self and non-self are separated. There are only two possibilities, time or space; and space-based models are all but ruled out. There are two major kinds of time-based model, one based on the time taken for an organism to develop from embryo to adult, the other based on the time taken for a cell to differentiate from one state to another. With so many ambiguities in the metaphors and so little attention to mechanism, the Atlan and Cohen challenge is, we suspect, based on time measured in cell differentiation units. They also make the common mistake of assuming repertoires that are transcendental in size (>10(10)), making it impossible to have a functional immune system in animals smaller than a rabbit--a feature that does not instill confidence in the biological relevance of such models.