I can't think of anything more startling, more promising, and more intractable in biology than the business of endogenous retroviruses. They seem to be ubiquitous in both invertebrates and vertebrates, and even in plants. In humans, they make up at least 8% of the genome, plus some bits and pieces. They are ancient; in our lineage they go back perhaps 100 million years. Let's face it, if we hadn't been told about them, we could never have conjured up such a strange story. It’s like hearing that you possess a limb or an organ that you didn't know about.
The very existence of endogenous retroviruses (ERVs) touches us in a number of ways. How is evolution shaped by the acquisition of such viral packets of genes? How often has it happened? Did it arise by infection, as seems likely? Is this an ongoing process that leads to further evolution? What does this have to do with the evolution of viruses? What does it reveal about the regulation of gene expression? On balance, do they do more good or more harm? All these questions have arisen elsewhere, but they are brought to the fore by these strange entities.
There is much to be learned, but certain facts stand out. A striking example of the good ERVs have done is seen in the case of the syncytin gene, whose product is involved in some essential way in the development of the placenta. It is thought that ERVs may also play a role in the immunosuppression needed to avoid fetal rejection by the mother. On the other hand, can they cause cancer? With some laboratory-induced exceptions, ERVs have not been found in tumors. On the other hand, ERVs in humans and great apes control the formation of a protein (GTAp63) that protects the germ line from cancers. In addition, ERVs may contribute to resistance to exogenous retroviruses. So much for viruses being “bad.”
It follows that knowing about endogenous retroviruses should be part of the education of all biologists, not just retrovirologists. I recommend a review by Jonathan Stoye entitled Studies of Endogenous Retroviruses Reveal a Continuing Evolutionary Saga. Here you will find a clearly written account of ERV genomic architecture, reproductive cycle, and phylogeny. Also discussed are some of the consequences of their presence, including the expression of viral proteins, the control of host processes by ERVs, and their cost-benefit balance. The complex subject of controlling retroviral replication is explained with clarity, as is the evolutionary interplay between the ERVs and their host. You might as well start somewhere, and this is a good place for it.