Nature round-up

A few highlights from the Nov. 9 issue.

• It’s the junk that makes us human – news summary of recent ncRNA research
• Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia
• Crystal structure of a rhomboid family intramembrane protease – first crystal structure of an intramembrane protease
• An exceptional Devonian fish from Australia sheds light on tetrapod origins

The curse of amino acid alphabets revisited

I’ve discussed previously the problem of writing Perl to deal with rogue sequences. I think this is what makes writing biological software challenging; you never know what you’re going to encounter in an input file until it throws an error message, at which point you can devise a fix for that particular anomaly. Recently I’ve encountered a problem with the way in which Bioperl deals with alphabets.

Do you have any Neanderthal in you?

The answer (never mind the punchline) might be “yes”, according to a paper in PNAS this week. Comment and review is available in Science and at evolgen.

The authors have used a technique called the interhaplogroup divergence test to analyse a gene named MCPH1, which regulates brain size. They present evidence that this gene is derived from “archaic Homo populations”. Neanderthals are a possibility given that we think there was a long period of coexistence between them and modern humans, but the paper does state that this is speculation and that the Neanderthal lineage is “a potential (although by no means only) candidate”. It would be great if those Neanderthal genome guys at the Max Planck Institute could sequence this gene from ancient DNA.