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The Month in Blogs, February 2008


In the past month, bloggers have been abuzz about the 1,000 genomes project, Venter's latest foray in synthetic biology, the value of impact factors, and collaborative science.

1,000 Genomes Project

In January, a consortium led by NHGRI, Sanger, and the Beijing Genomics Institute announced the 1,000 genomes project, a next-gen sequencing initiative. The news was a bit confusing, but the blogosphere cleared that up. At Genetic Future, Daniel MacArthur noted that the project will only be sequencing about 200 complete genomes, and then performing exon sequencing on portions of the rest. Ultimately, the goal is to catalog variants at as little as one percent frequency across the genome. Adaptive Complexity's Michael White responded to the news, saying that while it's a great start, creating useful, high-res catalogs of rare genetic variants might necessitate sequencing a lot more than 1,000 genomes.

Learning to Share

The blogosphere was chattering about everything open access and open notebook. Scientific American had a long piece about the pros and cons of collaborative scientific research and blogger Pedro Beltrao announced he'd be leading an open notebook study, the data for which he's depositing at Google Code. In the New York Times, an opinion piece wondered whether cancer researchers shouldn't be required to open their data archives for other investigators' benefit. Moreover, with the Protocol for Implementing Open Access Data announced at Science Commons in December, blogger Deepak Singh wondered how this will change the way scientific information is distributed.

Venter Builds a Synthetic Genome

Not surprisingly, Craig Venter and his colleagues were all over the news for creating the longest synthetic genome. In response to the media coverage of what some people considered a non-event, the blogosphere couldn't hold its tongue. Carl Zimmer at The Loom acknowledged the technical challenge of creating a synthetic Mycobacteria genitalium genome, but notes that scientists have yet to boot it up in a live cell. As an added twist, Venter's team encoded several watermarks in the genome, which a Wired blog reported to be the names of the scientists themselves. MIT synthetic biologist Drew Endy commented that the watermarks would likely disappear through random mutations, making them more like graffiti than distinguishing engravings.

Impact Factors Take a Hit

Impact factors definitely got a bad rap this past month, as did the analysts behind them at Thomson Scientific. Rockefeller University scientists wrote an opinion piece in the Journal of Cell Biology, slamming the process that Thomson uses to rank publications as well as the lack of transparency in the rating process. In turn, Thomson replied with an editorial defending its methods and saying that the Rockefeller crew based its stance on misinterpreted information. Blogger Neil Saunders opined that impact factors are outmoded, while a Nature Network blog encouraged alternatives such as the SCImago Journal Rank indicator.

The Scan

Study Reveals New Details About Genetics of Major Cause of Female Infertility

Researchers in Nature Medicine conducted a whole-exome sequencing study of mote than a thousand patients with premature ovarian insufficiency.

Circulating Tumor DNA Shows Potential as Biomarker in Rare Childhood Cancer

A study in the Journal of Clinical Oncology has found that circulating tumor DNA levels in rhabdomyosarcoma may serve as a biomarker for prognosis.

Study Recommends Cancer Screening for Dogs Beginning Age Seven, Depending on Breed

PetDx researchers report in PLOS One that annual cancer screening for dogs should begin by age seven.

White-Tailed Deer Harbor SARS-CoV-2 Variants No Longer Infecting Humans, Study Finds

A new study in PNAS has found that white-tailed deer could act as a reservoir of SARS-CoV-2 variants no longer found among humans.