Misc media.

Busy preparing for the start of the semester, so to tide you over here are some links of things to check out.

1) In our genes, old fossils take on new roles
by David Brown, Washington Post

It turns out that about 8 percent of the human genome is made up of viruses that once attacked our ancestors. The viruses lost. What remains are the molecular equivalents of mounted trophies, insects preserved in genomic amber, DNA fossils.

2) Gaming evolves
by Carl Zimmer, New York Times

Evolutionary biologists like Dr. Near and Dr. Prum, who have had a chance to try the game, like it a great deal. But they also have some serious reservations. The step-by-step process by which Spore’s creatures change does not have much to do with real evolution. “The mechanism is severely messed up,” Dr. Prum said.

Nevertheless, Dr. Prum admires the way Spore touches on some of the big questions that evolutionary biologists ask. What is the origin of complexity? How contingent is evolution on flukes and quirks? “If it compels people to ask these questions, that would be great,” he said.

I may have to check out this game.

3) Research raises questions about DNA barcoding methodology
by Andrea Anderson, GenomeWeb Daily News

This one is about the PNAS article by Song et al. that at first seemed like it was going to get a lot of hype (it did from NSF, but other venues decided it wasn’t worth a story). A lot of silliness going on with this one that I can’t really talk about, but suffice it to say I am not impressed with this paper or the conduct of the authors. I’ll just quote from the linked story.

“Sadly, the authors of this paper do not understand barcoding protocols,” Paul Hebert, director of the Biodiversity Institute of Ontario at the University of Guelph, told GenomeWeb Daily News. Calling the title of the paper misleading, he said barcoders have been aware of nuclear pseudogenes for years and have already designed some strategies for dealing with the problems described in the paper.

“Given that pseudogenes were reported 25 years ago, it’s not new news to us,” Hebert said. He said the team focused on species in which numts are particularly common and drew conclusions based on these eight species. Barcoding projects such as iBOL, he said, include data from thousands of species and are carried out using methods that differ from those described in the paper.
Hebert emphasized that the Barcoding of Life Data Systems, or BOLD, database scours sequences for indels, stop codons, and other tell-tale pseudogene signs. Barcoding sequences are also screened against a pool of sequences representing known contaminants, he said. Sequences that raise red flags are then set aside for further assessment, including longer sequence analysis or RT-PCR.
And, he noted, large barcoding studies typically amalgamate DNA barcode data with information provided by taxonomy, morphology, ecology, and other biological measures. “We’ve never advocated that sequence information alone is declarative for species boundaries,” he said.

For his part, Crandall conceded that large barcoding projects such as iBOL “have excellent strategies for quality control of data” and are already applying many of the steps he and his colleagues recommended. Still, he said, even though some people are already worrying about numts does not mean everyone in the field is addressing the problems appropriately.