Notes from the Biomass

Pedro Beltrao wonders how he should distribute his time between bench and computer screen. Interesting discussion in development there.

Publishing longer articles and trains of thought, which are updated over weeks, is difficult using blogs due to their lack of versioning systems. These measures would both enhance the quality of posts, and ensure a little more persistence as well as take out the need to publish something new constantly. I would like to go back to ideas I had earlier, update the post (or work) and publish it online. In principle, you can do that well in a Wiki but I miss the comments (to particular versions) and I would like to have the edits offline and only release versions that contains significant updates and generally prefer the no-frills blog platforms to wikis.

Many blogs carry links to posts that were selected as highlights but it would be nicer to update them, wouldn't it? Taking that idea a little further, Spreeblick, an influential German blog introduced a feature that departed further from its classical diary form and introduced persistence by what is called 'Main Feature' in its redesign in November. Instead of having one line of articles, articles of higher relevance remain longer visible to the casual visitor and don't get replaced by shorter, entertaining entries or the 'one line, one link'-posts.

It is very unlikely that I am the only one who has come up with that idea. I checked for plugins for WordPress and Serendipity but did not find the Subversion like behavior that I am looking for. All hints are very welcome.

Let's face it - the current way of blogging favours new posts over development of concepts and ideas. Better non-peer reviewed scientific communication (and even the chitchat) over the internet needs enhancements to its platform too.

The current cloning scam is taking its toll on the publishers. I was surprised how outspoken Benjamin Lewin (the one with the book), founder and former editor of Cell, critized Science recently. From the NY Times article:

"It sounds as though their processes were rather sloppy," said Dr. Benjamin Lewin, the founder and former editor of Cell, a biology journal known for its rigor. "At a minimum, Science should have been more careful and should never have reached the stage of publishing a paper with identical photos," he said, referring to the fact that some photos of cell colonies in Dr. Hwang's 2005 article were duplicates of one another.

Dr. Lewin said that a journal editor needed to develop an intimate knowledge of his reviewers' strengths and weaknesses, and that "Nature and Science don't have the reputation for rigorous review."

However, digging a little I realized that this is not the first time that Lewin critizes Science harshly. It seems as if the quarrel is going back more than 20 years as can see from this discussion on press embargoes in Science from 1998. Lewin also appeared as an outspoken critic of the publication of the first cloned sheep Dolly a year earlier.
Unfortunately, Cell too has had to retract research publications due to fraud in 2004.

Any publication process has to compromise relevance, timeliness and thoroughness and I don't see a one size fits all approach to the problem - even if it leads to occasional publication of oversold or fabricated results.

[Update: In the Pipeline hast the story too, providing additional view points.]

You need to study molecular evolution longer than most of bioinformaticians grasp of it between writing Perl scripts designing XML interfaces before you can comment on progress in the understanding of molecular evolution. However, the forthcoming edition of Molecular Biology and Evolution includes a publication authored by Michael Lynch that has all the features of a landmark. It puts the view forward that evolution of the eukaryotic genome is largely dominated by the small population sizes that permits the creation and fixation of structures such as introns and long intergenic regions.

Or in Lynch's words:

However, by establishing an essentially permanent change in the population-genetic environment permissive to the genome-wide repatterning of gene structure, the eukaryotic condition also promoted a reliable resource from which natural selection could secondarily build novel forms of organismal complexity. Under this hypothesis, arguments based on molecular, cellular, and/or physiological constraints are insufficient to explain the disparities in gene, genomic, and phenotypic complexity between prokaryotes and eukaryotes.

According to Eike Staub, who notified me of the work, it gained much attention when it was presented at last year's conference of European Society for Evolutionary Biology in Krakow.
In addition to the hypothesis, the work builds upon a encompassing overview of the current state of our knowledge of molecular evolution and I can but recommend to take a couple of quiet hours to delve into it if you are interested in molecular evolution. And who isn't?

Usually, I don't read Nature Neuroscience. I've got nothing much to do with neurons.
Usually, I don't have post about pictures that display cuddly animals.
Usually, I don't link to German sites as I assume the majority of my readership prefers to read in the science pidgin that I use for communication on this site.
However, Riesenmaschine, the blog whose consumption will repay all your pain in having learned German, tells us about this fine work on how dopamin levels affect monogamy in praerie voles and I simply can't resist.

Where was my head in December? I missed two interesting additions to our life science blogosphere (will the term still be accepted in 2006?).

For one, Pierre Evry, a virologist/bioinformatician writes at Yakafokon about "Bioinformatics, Semantic Web and Social Networks". Its blogroll links to Declan Butler's blog, who is a reporter with Nature and authored a recent article on bloggers in the sciences. Seems like he found something convincing, he became a blogger himself thereafter.