# A Perspective on Information Optimality in a Neural Circuit and Other Biological Systems
## 4 Discussion
### Information Processing as an Algorithm in Biological Systems
#### 4.2.3 Cellular Immunity in Jawed Vertebrates
Furthermore, a pathogen population is constrained in its evolvability, since genetic change may lead to loss of biological function, such as in the change of a protein sequence, which may lead to changes in essential regions of its three-dimensional shape. This is a further constraint on the evolution of a pathogen for escaping host immune detection. In addition, the typical protein subsequence length is sufficiently long for high precision in detection by the host; otherwise, a very short subsequence would likely originate from another source, including from the host itself. This process is further regulated by its dependence on sampling a variety of pathogenic protein subsequences in order to evoke a strong immune response. Lastly, a pathogen population must replicate and spread to multiple hosts in a host population, otherwise the pathogen will cease to replicate and exist. So, the virus must encounter many host immune systems, along with the corresponding potential of the host population to generate a larger number of immune-cell receptor types  
Figure 5: One simplified pathway of jawed vertebrate immunity—from intracellular pathogenic protein to its detection by a host cell. (**A**) Shape of viral protein in three dimensions; (**B**) protein is spliced into protein subsequences; (**C**) subsequence of viral protein is combined with a host cell receptor; (**D**) the protein subsequence and receptor from (**C**) are bound to the surface of a host cell (on the left). A specific immune cell (on the right) with a cell-surface receptor scans the host cell for evidence of pathogenic protein subsequences. Positive detection of a pathogenic protein may contribute to an immune response, so that host cells infected with a pathogen are eliminated by the immune system. than any single individual by itself. Therefore, the host population employs a strategy of pathogen detection at multiple levels, each one additive or multiplicative in its generation of molecular diversity toward the process of pathogen detection. From the perspective of the pathogen population, its genetic changes, including recombination within and between populations, may lead to evasion of host immunity, such as in the above example. The pathogen can avoid detection along the steps of the pathway of intracellular host immunity (Figure 5). One method is by interruption of the path as shown in Figure 5B, so that a previously spliced protein subsequence is no longer spliced by the host. Another method is by interruption of the path in Figure 5C, so that a spliced protein subsequence is no longer adequately combined with the host-cell receptor [66]. A third method is by the path in Figure 5D, so that the specific immune cell and its receptor no longer has recognition of the combinational pattern on a host cell, where the combinational pattern is defined as the protein subsequence bound with a cellular receptor [67]. In essence, for this pathway, the host is detecting the pathogen by sampling protein subsequences, while the evolution of the pathogen would tend to favor genetic change to evade host immunity. These favorable genetic changes in the pathogen are likely to lead to changes in its proteins, and therefore increasing its chance of evasion of host immunity; but these particular genetic changes, which lead to modified protein shapes, and possibly loss of biological function, are not favored in the pathogen population. The above process is considered optimal, since the host is sampling information of sufficiently high complexity in identification of a pathogen, while avoiding detection of itself. Furthermore, the host-pathogen interactions are a dynamical process, and these population dynamics may persist over a long time-period, since each of the two populations has the potential to adapt to the other's strategy, in which the host population is learning the genetic sequence of the pathogen and the pathogen is evolving for evasion of the outcome of this learning process by the host.