Notes from the biomass

As a science publication, the journal Nature is held in highest regard; to me it shines even more for its science journalism, which is the focus of a new experiment. Somewhat modest in the light many activities at NPG and probably not entirely novel in publishing, the editors have selected three publications in journals outside the usual scope and the reader gets to select one of the topics to be investigated further. I have never heard of the journals before and one of the articles even seem to be a couple of months old but they all appear to be curious little stories, discovered by people who read more than the press releases. Last week’s story covers the genome of a giant bacterium and is freely accessible from what I can see. Let’s hope that there will always be a market that supports science journalism targeted at scientists rather than just a large crowd that wants to read hear about the latest cure for cancer.

Most of my dear readers will have either noticed or written about the lack of comments on scientific articles, for instance at the BMC journals and most notably at PLoS ONE, which was designed for interaction of author and reader.
At this point, there’s not too much to add to the conclusions: It’s takes to much time to comment on a scientific article properly, there’s no incentive (can’t put it in your CV) or honor to be gained (no one asked me to review this) and they are not written to be discussed (open/pragmatic) but supposed to discuss the results thoroughly themselves. However, despite all the comments on the matter, trying to study the phenomenon on the web is difficult due to the lack of strong keywords: Searching for “comments on publications” does not take you to very informative resources.
Similar discussions were underway in the Usenet and a particular consideration on the lack of comments made into Wikipedia as Warnock’s dilemma, which I stumbled across by chance. The term did not stick but it’s a worthwhile keyword for research in communication in blogs and scientific publications. Most of the considerations listed can be applied to all forms of written electronic communication.

Next: The careful analysis of the source for the scarcity of my blog output. A killer post.

Philica is an attempt at academic publishing with very few restrictions. Journalology (my source) is critical as is Archaeoastronomy. I too doubt whether the initiators do much good to academic publishing by releasing work on divination methods.

Infections caused by Mycobacterium tuberculosis kill 2 million people each year; tuberculosis is the most important disease caused by a bacterium. Despite the introduction of vaccines in the 1920s and promising antibiotics in the 1950s, it remains one of the major health issues in developing countries.

News@nature has a special, summarizing the current state of research, accompanying the current issue of Nature Medicine that focuses on tuberculosis. The extensive material is both introduction and overview, helpful to those new in the field (like me).

Most of you will have heard of the launch of PLoS ONE, a new publishing platform promising many changes to the way scientific work is communicated. A important aspect distinguishing One from many journals is the strong commitment to increase participation of the readership.
Several bloggers (e.g. Deepak and Pedro) and probably many observers out there are somewhat concerned that the participation of scientists will not be intense, particular in the light of the Nature Peer Review trial that only received few comments.
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The Nature correspondence section called brief communications is to disappear from Nature print issues. What could be spun like a move forward for the added flexibility reads like an unfortunate, forced demise in the editorial. The high number of unsuitable submissions, given as a principal reason for the move, might result from the evaluation of this type of publication as a Nature paper by many scientists. Compare the scores of submissions to the low number of comments that Nature got in its peer review trial - researchers simply don’t make a sound unless there an impact factor can be attached. Ideally, the (peer reviewed) communications and bloggish comments should be combined but do we want to start formal reviews of comments?

The next big thing of the Public Library of Science, the journal PLoS ONE has just opened its online submission portal. PLoS ONE is a PLoS journal with broad scientific scope and a community based editorial board (instead of a few dedicated editors in traditional journals), amongst other small improvements. Several features, such as  interactive papers are announced but from what the site has to offer now, it is difficult to perceive how they will be implemented, particularly the ranking system(!). Other improvements are pretty typical. Every journal claims fast publication within weeks, and an objective rather than subjective editorial process. Despite the claim for a broad scope, most of the members on the editorial board are people who made the mark in the modern life science research as far as I can see. The peer review process itself appears to be highly similar to other PLoS journals. The most important innovation might be the chance to update your publication with new results or to tie in other findings. The publishing formats are kept broad. I had hoped for more possibilities, such as short papers, meta-analyses or hypotheses though. (more…)

The latest issue of Nucleic Acid Research contains work that finds non-orthologous proteins in about one third of the COG database from the NCBI.
The work by Christophe Dessimoz et al. from the ETH Zürich entitled “Detecting non-orthology in the COGs database and other approaches grouping orthologs using genome-specific best hits” is low in voice and avoids clevering. Eugene Koonin, one of the inventors of the resource, admitted that the resource had some flaws in this respect.
The examples convince (e.g. for COG0508) as they follow up the screening for paralogs by a phylogenetic consensus tree.
However, the large number seems a bit worrying - I always thought that COGs would be rather too stringent and not contain many paralogs that could in principle be resolved. The finding that the majority of the wrongly included proteins have metabolic functions was likewise surprising.

The finding has only major implications if the majority of the non-orthologous can be shown to be functionally divergent, which I doubt. And can one use the procedure to provide a resource of the same quality as COG?