Notes from the biomass

The editorial to PLoS Computational Biology sounded like it would solve the questions that I was always afraid to ask. While it clarifies the situation to some extent, Ten Simple Rules for Reviewers leaves me down on those issues that usually cross my mind when submitting a review.

1. How much time should you plan for reviewing a paper?
I have seen both reviews solely stating “Not enough novelty” as well as verbose prose the length of the original manuscript. An overly lengthy review is more showing off than an aid in the editorial decision in my eyes but how much information does the editor really want? The number of words would provide at least a rough guide. I typically reserve four hours for a review, which I found sufficient to review a paper thoroughly, if the paper is in my field but allocated time will vary for each referee.

2. Was my review useful?
Bourne and Korngreen make the point that your review will reflect on you in the round of editors. I often wonder whether my reviews in the current form were useful to the editors. They always say so (why do I complain) but the lack of any feedback makes it quite difficult to improve. A rating by the editor (as in reviews on Amazon) obviously does not make too much sense but two lines of critical feedback could prove useful.
A recurring remark in the editorial was the blank statement to consult the editors if questions arise. A little less formality in the process might be a good move to improve the situation. Maybe one should simply ask.

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?

Just like with every other hype, the immediate, applicable results of the community metagenomics studies based on random sequencing were not apparent despite the promises made. For instance, the handful of enzymes unraveled in a study of the human intestine in Science hardly justify the efforts; we learn much more from 16S-RNA studies of this extremely complex environment was my take-home message.
A recent study of a gutless worm and its four unculturable symbionts, available from the AOP pages of Nature, however demonstrates the power of community sequencing studies. The background is comparably simple, allowing unexpected findings and real questions can be answered using sequence comparisons and metabolic reconstruction. The technical aspects of the work are worth the read alone, even if you have a gut. Once we understand the simple systems we can apply these techniques to complex environments - but it’ll take its time. Just like with every other hype.

After summer school and workshops, I finally get back to blogging. The access stats were absurd, peaking at about 50 times the average for about two weeks despite almost no posts. The vast majority came from Flags & Lollipops analysis of hot science bloggers. I came in 5th, which probably means that there less than 6 science bloggers out there that have identifiable pictures in Technorati. Nonetheless, F&L send scores of people here to check the typo-riddled me-too entry that was leading the blog for those two weeks. The referrer stats tell me that there is still some traffic through that route.

Still, I refrain from finding and applying an adequate translation for “Klickvieh” and rather shower in my newly won yet fading prominence. The happy picture which send you here, was taken at 4 am in the morning of my stag night in the Nachtcafe in Munich. Hence, I am married and pictures of me are not exactly breathtaking even under these circumstances.
The good news? Number three is still available.

Refuting phylogenetic relationships, published recently in Biology Direct is a peculiar paper in several ways. Bucknam, Bucher and Bapteste suggest a novel way of assessing phylogenies. Rather than searching the most probable of a species tree given a concatenated alignment, unsupported phylogenies are rejected, leaving possible ones and not inferring more than what the data delivers. The method appears powerful in removing weak hypothesis more strictly than classical methods do in difficult cases.

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Shortly after the tear proteome, Genome Biology publishes the urine proteome. Neither study is the first of its kind but both show substantial increase in the number of proteins detected. The large number of proteins (~1500) stands out as the fluid is of an overall low content of protein, and about half of the annotated proteins are membrane associated. Many of these proteins might have been missed in analyses of more complex samples.

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