# 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  
The immune system of jawed vertebrates includes a similar strategy. In this case, the genetic information of interest is not from the process of inheritance, but instead originates from a foreign source, such as a virus or bacterium, which may infect and lead to changes in the host organism. To deter these foreign invaders, a jawed vertebrate has cellular processes that search for intracellular and extracellular proteins, whether the source is foreign, or from itself, for detection and identification of proteins that are specific to a pathogen, and to potentially activate a pathway to eliminate the infected host cells. A virus is defined as a pathogen that is dependent on a host cell for genetic replication, and to generate proteins (Figure 5). After intracellular infection, the viral proteins are produced in the cells of the host, so these proteins and their sequences are available for host detection. This involves a pathway which has similarities to the information processing in the genetic inheritance of cellular organisms. The protein information, a sequence of amino acids, is processed by the host to a set of subsequences. These subsequences are small in size as compared to the original sequence, and they are further combined with a type of specialized cell-surface receptor [60, 61]. This combination of biological molecules leads to a cellular presentation of its corresponding three-dimensional shape, so the one-dimensional protein subsequence has been converted to a three-dimensional arrangement, and this latter arrangement, in combination with the receptor, is used in detection by specific immune cells that are surveilling the surface of host cells [62]. This mechanism of cellular surveillance, by these \"specific immune cells\", involves another cell-surface protein receptor (Figure 5D). This receptor is also formed by an informational process with similarities to the mechanisms of genetic inheritance. It is formed by different combinations of proteins that have undergone genetic-level processes that include mutation and recombination, thereby modifying the protein sequences, and changing the resultant receptor shape, which leads to a very large diversity of receptor types as compared to the genetic instructions that code for the initial receptor [63]. This increased diversity of host receptor types has a greater potential for detecting many types of pathogens, including those that are novel to the host. This pathway is a probabilistic solution to the evolution of a pathogen that can escape host detection [64]. There is an additional layer of complexity that occurs in this process, where many different cellular receptors are mutually acting in detection of an intracellular pathogen. This overall process may be considered optimal in the efficient use of genetic information that is derived from the pathogen, along with high precision in detection of proteins that are pathogen specific [64], while avoiding reactions to host-specific proteins, because otherwise host cells without infection would be eliminated by host immunity [65]. The contest between survival of the host and that of the intracellular pathogen is dependent on the generation of these pathogen-specific protein subsequences by the host. The length of the relevant portion of these subsequences is typically short. For the intracellular case, they are often about nine amino acids in sequence [63]. This short length is expected for efficiency in the host detection of a pathogen. For example, if the pathogen is rapidly evolving, such as by the mechanisms of mutation and recombination, then its genetic sequence is expected to become unrecognizable to the host immune system. However, the evolutionary process is not likely to act on every portion of the genetic sequence of the virus, so subsequences are expected to remain unmodified over time, and likewise, a shorter-length subsequence is more likely to remain unmodified than one of longer length.