Elementary, my dear Cameron

I read two papers recently that reminded me of this ingenuity. The first describes the application of a highly abstract and academic discipline, molecular phylogenetics, to support two convictions for assault [1] and the second the application of a spin-off from immunology to determine the age of a person from a sample of their blood alone [2].The weapon in the assault cases [1] was, despite its small size, a deadly one - the virus HIV-1. The question being asked was about the direction of transmission of the virus among a set of infected individuals: in particular, does the phylogenetic evidence support the hypothesis that the defendant (who knew himself to be HIV-positive in each case) was responsible for the infections carried by a number of his sexual partners? Two aspects of HIV-1 biology were exploited in order to address this: first, the virus has a high mutation rate (about 3 × 10-5 per base per replication cycle) and so, during proliferation within an infected person, a diverse set of HIV-1 sequences arises; and second, when one person infects another, the population of viruses goes through a strong genetic bottleneck, so that three-quarters of new infections are each established by a single virus.In each case the sample identity was blinded and parts of the HIV-1 genome sequenced in the putative offender and victims. A phylogenetic tree showed that sequences from one DNA donor contained subsets that were more closely related to the sequences carried by other donors than they were to other subsets in the same donor. This property ('paraphyly') demonstrates that one DNA donor is the source of the infections in the others. In each case the inferred source was revealed to be the defendant and the DNA evidence contributed to the conviction.The second paper [2] exploits the curious fact that, as a person ages, their thymus shrinks. This organ is the home of T-lymphocyte development and, as these cells mature, they rearrange the genes encoding T-cell receptors (T