The Science of Discworld IV

scrambled around its roots because of a process called horizontal gene transfer. Bacteria, archaea and viruses swap genes with gay abandon, and they can also insert them into the genomes of higher animals, or cut them out. So a gene in one type of bacterium might have come fromanother type of bacterium altogether, or from an archaean, or even from an animal or a plant.
    The major agents of this swapping are viruses, and there are lots of them on the planet, probably ten times as many virus particles as all other forms of life added together. Now, it might appear that with all this swapping, it would be virtually impossible to work out lineages, the heredity of individual bacteria. Even more so, it would seem impossible to work out the lineages of the viruses doing the swapping. Surprisingly, this is not the case; well, not altogether. There are clues in the order in which specific genes appear in many viruses, and there are useful clues as to which organisms the viruses parasitise. Some parasitise both bacteria and archaeans, suggesting strongly that they have been doing so since before these groups diverged. Moreover, these are viruses with RNA genetics. So Brüssow proposes quite convincingly that these particular viruses may be relics of a former RNA world. Going further: infection by ancient DNA viruses could have imported DNA into the heredity of all of the familiar creatures whose genomes we now make such a fuss about. So some of the mavericks, and physicists, might have been right all along, even if it was for the wrong reasons.
    If that is the case, we need to look with new eyes at all the ways in which RNA is involved in modern life forms. According to the standard story, which has not changed for some time, RNA serves as a humble messenger that carries the all-important DNA sequence to the ribosomes, huge molecular structures in which proteins are assembled. There are also small RNAs that transfer amino acids to the ribosomes for protein assembly. Ribosomes in turn are made of several kinds of RNA, and several people have suggested that they are the central mechanism of protein construction in cells, their most important function.
    This story may soon have to change.
    There has been a revolution in nucleic acid biology over the last ten years, and almost all of it has been about RNA. MessengerRNA and transfer RNA are merely the most prosaic jobs that RNA performs in cells. But RNA does many more important – perhaps having said ‘prosaic’ we should now say ‘poetic’ – jobs too. When DNA was considered the most important molecule in the cell, and protein construction the most important function (many textbooks still think so), strings of DNA that specified proteins by transcribing messenger RNA were called
genes
. The strings of DNA upstream and downstream, which did not specify proteins, were mostly thought to be ‘junk DNA’ of no importance to the organism. Junk DNA was just there as an accidental by-product of past history, but because it didn’t cost much to replicate it, there was no evolutionary reason to eliminate it.
    Indeed, there are plenty of remnants of old genes, and quite a lot of sequences from ancient viral attacks, which really might be junk. However, it turns out that although it doesn’t specify proteins, nearly all DNA between genes does transcribe RNA molecules. These RNA molecules form the main control system of cells: they control which genes are activated and when, and how long different messenger RNAs last before destruction. In bacteria they also control genes, but a subset of them protects the bacterial cell against attack by viruses. This is a simple kind of immune system. So DNA may be the soloist, but RNA is the orchestra.
    With that established, we can return to ribosomes, the molecular factories that assemble proteins. They are tiny particles, mostly of RNA. In bacteria, archaea, animals, plants and fungi, every cell has its own complement of ribosomes; moreover, much the same RNA occurs, though with different proteins, right across the span of life.
    Marcello Barbieri is a leading exponent of biosemiotics, a relatively new science concerned with the
codes
of life. You have probably heard of the genetic code, the way in which triplets of DNA nucleotides are turned into different amino acids in proteins – by the ribosome. Barbieri has pointed out that there are hundreds of other codes; they range from insulin anchoring itself to receptors on thecell surface and