Convoluted title, cool paper in #PLoSGenetics on relative of insect mutualists causing a human infection

Saw this tweet a few minutes ago:

The title of the paper took me a reread or two to understand.  But once I got what they were trying to say I was intrigued.  And so I went to the paper:  PLOS Genetics: A Novel Human-Infection-Derived Bacterium Provides Insights into the Evolutionary Origins of Mutualistic Insect–Bacterial Symbioses.  And it is loaded with interesting tidbits.  First, the first section of the results details the history of the infection in a 71 year old male and his recovery and the isolation and characterization of a new bacterial strain.  Phylogenetic analysis revealed this was a close relative of the Sodalis endosymbionts of insects.

And then comparative genomics revealed a bit more detail about the history of this strain, it’s relatives, and some of the insect endosymbionts.  And plus, it allowed the authors to make some jazzy figures such as

And this and other comparative analyses revealed some interesting findings.  As summarize by the authors

Our results indicate that ancestral relatives of strain HS have served as progenitors for the independent descent of Sodalis-allied endosymbionts found in several insect hosts. Comparative analyses indicate that the gene inventories of the insect endosymbionts were independently derived from a common ancestral template through a combination of irreversible degenerative changes. Our results provide compelling support for the notion that mutualists evolve from pathogenic progenitors. They also elucidate the role of degenerative evolutionary processes in shaping the gene inventories of symbiotic bacteria at a very early stage in these mutualistic associations.

The paper is definitely worth a look.

Oh the irony – new #OpenAccess #PLoSOne paper on Research Blogs doesn’t share data behind analyses.

Interesting new paper: PLoS ONE: Research Blogs and the Discussion of Scholarly Information. All about the new world of science blogging.  Much of the context here relates to openness.  Yet as far as I can tell, the data collected that make up the meat of the analyses in the paper, are not shared.  Uggh.

Is there something I am missing here? Shouldn’t a prerequisite of publishing this kind of paper be sharing the information / data used in the analyses?  Shouldn’t that be released with the paper?

Definitely time to start “Open Data Watch” where people have a place to complain about lack of open availability of data behind papers (I came up with the name as a mimic of Ivan Oransky’s diverse watch sites like Retraction Watch).  Originally in thinking about doing this I had been thinking about genomic data.  But I am sure this is a problem in other areas.  Consider paleontology, where openness to fossils and other samples is, well, not as common as it should be.  It is not that hard anymore to find a place to share one’s data.  With places like Data Dryad and Biotorrents and FigShare and Merritt and 100s of others it is really inexcusable not to share the data behind a paper in most cases.  Certainly, in some cases there maybe privacy issues but that is not the case here (I think) and not an issue in most cases.

Come on people.  If scientific papers are to be reproducible and testable, you need to give people access to the data you used. Shema, H., Bar-Ilan, J., & Thelwall, M. (2012). Research Blogs and the Discussion of Scholarly Information PLoS ONE, 7 (5) DOI: 10.1371/journal.pone.0035869