Lab report: An edited sequence

Genomes are popularly regarded as the instructions for making an organism. The sequences of genes encode the composition of proteins, which are the body’s chemical workhorses and the primary fabric of muscle, skin, tendon, nerves and bone. Since the early days of modern genetics, the central dogma has been that information flows more or less inexorably from genes, via the intermediary RNA molecule, to proteins.

Far from merely filling in the details of that process, molecular biology has gradually revealed its shortcomings. The picture remains true in essence, but has many loopholes and exceptions. Much can happen to the information between the gene and the protein: not only must it be stripped of junk, but it can also be edited and modified at the RNA stage, so that for example the instructions in a single gene can be adapted further downstream to encode several different proteins. Much of the information never gets beyond RNA, yet seems to play a crucial and mostly still mysterious role.

Even against this background of caveats and complications, the new results reported in Science by a US team led from the University of Pennsylvania are too shocking to be believed by some of their peers. They find that the message of the genes is edited and altered to a far greater extent than was thought. Such editing may be the norm, rather than the exception.

Some researchers suspect, even hope, that the finding might turn out to stem from flaws of technique or analysis. Others say they have happened upon similar findings in their own genomic studies. Among other things, the degree of mismatch between the DNA sequence and the RNA sequence that is supposed to mirror it would imply that there are previously unknown mechanisms for making the edits.

Why would these edits be made? One possibility is that it helps to boost diversity, which can be beneficial in evolutionary terms. It could cause wide variations in individuals’ susceptibility to disease, and might help to explain why it has been unexpectedly difficult to link the heritability of disease with specific gene mutations. Maybe some of the heritability comes from inherited differences in the extent of RNA editing and not from the sequences in the disease-linked genes at all. In short, maybe genomics is not just about genes.

High water

Giant waves that rise out of placid seas, swallow ships and vanish again sound like the premise of a bad film. But it seems they really occur. In 2001 the Caledonian Star passenger ship was hit in the South Atlantic by a wave estimated to have been 30 metres high. It narrowly survived, but such rogue waves have been blamed for the mysterious disappearance of ships in the past.

The bigger the wave, the rarer it should be: waves as big as the 2001 one should appear only once in several millennia. Yet radar soundings from North Sea oilfields have recorded hundreds—like the 26-metre monster that hit the Draupner rig in 1995. Not only do they defy statistics, but rogue waves seem peculiarly robust, solitary walls of water that move without spreading out. This makes them akin to solitons: isolated waves that remain tightly focused as they move, which were first seen in a Scottish canal in the 19th century. Solitons are a generic feature of wave physics, produced by the interactions of acoustic or light waves as well as water waves.

Four years ago, analogues of rogue waves were seen in light confined in optical fibres, showing that the theory of how they form as a tight, brief concentration of wave energy is correct. But only now has a rogue wave been generated by scientists; a team in Germany and Australia created a wave two and a half times taller than average height in a 15-metre long tank. Odd as it may seem, the rogue waves emerge in theory as a solution of the so-called nonlinear Schrödinger equation, a variant of the probability density equation concocted by Erwin Schrödinger—for after all, a wave is a wave, whether in water or in electron clouds.

Model behaviour

All Watched Over By Machines of Loving Grace, the latest documentary by Adam Curtis (BBC2), was a dish of thought-provoking and contentious fare with a sprinkling of the plain misleading. Over-reliance on and excessive faith in computers is a problem worth airing—but it was not the cause of the financial crisis. “The machines,” Curtis told us, “created mathematical models that parcelled out the loans and then hedged and balanced them so that there was no risk.” The machines did nothing of the sort. The models were created by financial engineers and it was their assumptions and inputs that proved so damaging. All Watched Over intended to blame financiers and economists for the crash—but they are presumably delighted to see the blame deflected. Computers did not cause the crash. They might be needed to build a better alternative.