Aug 11, 2004
Apes and humans share a common ancestor.
How do we know? There are several lines of evidence--genetics, physiology, fossils, behavioral observation... read about them here.
Some of the strongest independent evidence, though, consists of endogenous retroviruses. The standard conception of viral activity goes something like this: a virus overtakes cellular machinery, producing copy after copy of itself until the cell bursts and the newly-freed viruses romp about looking for more mischief. Endogenous retroviruses go a few steps further, producing DNA and inserting it into the cell's genome. (More detail here.)
If this process occurs in a germ cell (sperm or ovum), the retrovirus's DNA will become a part of the organism's genetic inheritance, passed on to its progeny.
Humans and apes share many gene sequences inserted by endogenous retroviruses. One might object, saying that certainly, this is expected, since viruses like HIV are known to infect both humans and simians alike. However, the sequences in question are found in the exact same regions of human and ape genes, rather than scattered in a more random fashion among species, as probability and chemistry would dictate. Furthermore, non-apes do not share these insertions, allowing evolutionary biologists to construct plausible divergence scenarios, going back to the time when the common ancestor of both apes and humans was genetically modified by microscopic replicants. (Sample study here.)
More amazingly, over time, some retroviral sequences have become an integral part of hominoid development. (This particular functional sequence is "preserved in the orthologous loci isolated from chimpanzee, gorilla, orangutan, and gibbon.")
Read more about endogenous retroviruses, and see a nifty graphic rendition, here.
Update (8 26 04): More articles worth reading. DNA is more plastic than we think. How to construct primate phylogenies from retroviral sequences.