Demographics of the review process

Grod et al. (2008) Systematic variation in reviewer practice according to country and gender in the field of ecology and evolution. PLoS ONE 3(9): e3202.

An inverse relationship between publication output and beer consumption

Grim T. (2008) A possible role of social activity to explain differences in publication output among ecologists. Oikos 117(4): 484-487.

Attack of the flies!

The 12 genomes are out!

Check out the relevant papers in Nature, Genome Research, PLoS Genetics, PLoS Biology, Genome Biology.

What's the impact factor got to do with paper quality?

Postma E. (2007) Inflated impact factors? The true impact of evolutionary papers in non-evolutionary journals. PLoS ONE 2(10):e999.

Too much ado about high impact factor journals. Evolutionary papers in lower-ranking non-specialized journals are undervalued. A call for a more elaborate journal classification system including field-oriented impact factors.

Intense sweetness surpasses cocaine reward

Lenoir et al. (2007) Intense sweetness surpasses cocaine reward. PLoS ONE 2(8):e698.

A cool experiment showed that rats prefer saccharin-sweetened water (calorie-free) to intravenous cocaine. The authors speculate that intense sweetness being a supernormal stimulus can override homeostatic and sel-control mechanisms and lead to addiction – greater than cocaine addiction! In most mammals sweet taste perception is primarily owed to the existence of two G-protein-coupled receptors (T1R2 & T1R3) that evolved in sugar-free ancestral environments not adapted to really sweet conditions.

Nature Editorial: ERC not disclosing the state-members distribution of its grants shortlist

Nature 448, 727-728 (16 August 2007)

Division of labour: The European Research Council shouldn't be coy about saying who will get its first set of grants.

The first Europe-wide research agency to distribute funding purely on the basis of scientific merit is working with commendable efficiency. Its officials have just ploughed through more than 9,000 first-stage applications for the inaugural programme of grants and asked 559 of them to submit a complete application. Around half of these shortlisted candidates will eventually win five-year grants worth up to euro dollar400,000 (US$550,000) per year.

The European Research Council (ERC) has done well to get so far within eight months of its official creation. But it is already facing criticism for its reluctance to reveal the exact distribution of nationalities on the shortlist. The ERC's decision to keep this information to itself for the time being can be read two ways: as a failure to be transparent or as a pragmatic response to a tricky political environment.

The ERC's mission is perhaps unprecedented in the brief history of the European Union (EU). It has to distribute large amounts of European money — building up to euro dollar1 billion a year within a few years — to the best research proposals, regardless of nationality or other political criteria. Both the EU member states and the European parliament have fully signed up to this mission.

Nonetheless, the young agency's leadership can expect to take some political heat if, as is likely, most of its grants go to those EU countries that are already most established scientifically. A comparable dilemma has been encountered in the past by the US National Science Foundation (NSF), an agency that, perhaps more than any other, the ERC seeks to emulate. NSF grants have always flowed disproportionately to certain states, such as Massachusetts and California, where US scientific excellence is most heavily concentrated. The agency has dealt with the political challenge that this presents by publishing reams of relevant data upfront, while developing programmes (at the prompting of Congress) that assist researchers in the states that do less well with their applications. It has done this without compromising its criteria for grant selection.

One of the council's top priorities is to make sure that it establishes a reputation for excellence in its processes. It must do this to win the solid support of European scientists ahead of its first formal evaluation by the EU authorities, which will take place in just two years' time. For now, the council is still negotiating the details of the final EU executive agency within which it will eventually operate. Evaluation of grant proposals, meanwhile, is being overseen by a modest number of staff, most of whom have been seconded from national research agencies.

It is in this fragile context that the ERC is eager to avoid rocking political boats by publishing a national breakdown of who is being considered for its first grants. Instead, it has broken down the shortlist into the groups of nations that joined the EU at different stages of its evolution.

So it has revealed that 45% of the applicants, and 53% of the winners, come from Belgium, Germany, France, Italy, Luxembourg and the Netherlands — the six original members of the European Economic Community, as it was then known. The nine countries that joined after 1973, but before the entry of the former communist states, account for 36% of applications and 27% of the winners. The 12 members who have joined since 2004 did not do so well, putting in 9% of the applications and winning 5%. (Nine 'associated countries', such as Russia and Israel, as well as participants from farther afield account for the rest of the applications.)

Policy-makers might benefit from fuller information about the geographical distribution of both those who apply and those who make the shortlist, if only as a snapshot of how excellence in European science is currently distributed.

Cell phone microwaves affect transcription and protein stability

Friedman et al. (2007) Mechanism of short-term ERK activation by electromagnetic fields at mobile phone frequencies. Biochemical Journal 405(3):559–568.

Abstract: The exposure to non-thermal microwave electromagnetic fields generated by mobile phones affects the expression of many proteins. This effect on transcription and protein stability can be mediated by the MAPK (mitogen-activated protein kinase) cascades, which serve as central signalling pathways and govern essentially all stimulated cellular processes. Indeed, long-term exposure of cells to mobile phone irradiation results in the activation of p38 as well as the ERK (extracellular-signal-regulated kinase) MAPKs. In the present study, we have studied the immediate effect of irradiation on the MAPK cascades, and found that ERKs, but not stress-related MAPKs, are rapidly activated in response to various frequencies and intensities. Using signalling inhibitors, we delineated the mechanism that is involved in this activation. We found that the first step is mediated in the plasma membrane by NADH oxidase, which rapidly generates ROS (reactive oxygen species). These ROS then directly stimulate MMPs (matrix metalloproteinases) and allow them to cleave and release Hb-EGF [heparin-binding EGF (epidermal growth factor)]. This secreted factor activates the EGF receptor, which in turn further activates the ERK cascade. Thus this study demonstrates for the first time a detailed molecular mechanism by which electromagnetic irradiation from mobile phones induces the activation of the ERK cascade and thereby induces transcription and other cellular processes.

Automation and evaluation of NCPA

Following up on the previous posting on two programs that automate the inference process of Nested Clade Phylogeographic Analysis (NCPA), Panchal & Beaumont create a framework of automated NCPA. Their simulations show that NCPA has a high tendency for false positives. More research is needed, of course, on real-life data.

Panchal M, Beaumont MA. (2007) The automation and evaluation of Nested Clade Phylogeographic Analysis. Evolution 61(6):1466-1480.

Automating Nested Clade Analysis

TCS and GeoDis are the programs to use for NCA, but recently two programs came out that automate NC inference: AUTOINFER and ANeCA.

Addendum (30 Oct 2007)
Panchal & Beaumont (2007) of ANeCA report that Ai-bing Zhang of AUTOINFER has noted that there are some issues in the program that require resolution and that it has temporarily been withdrawn.

2 new journals for 2007

Two new journals are to be launched in 2007:

Evolutionary Biology, following the book serial originally founded by Theodosius Dobzhansky.

HFSP Journal - Frontiers of Interdisciplinary Research in the Life Sciences, published by the Human Frontier Science Program. Six months following publication, papers will be open-access, leaving the publication copyright to the authors.

"Beer goggles" effect explained

Beauty is in the eye of the beer-holder. A formula built by researchers at the University of Manchester, UK, spits out a score ranking the drinkers' (mis)perception of beauty. The calculation factors in not only the the amount of booze consumed, but also the light conditions, the amount of smoke in the room, visual acuity, and distance from the person of interest.

BBC News online article

Selection in murid noncoding DNA

In the November issue of PLoS Genetics Gaffney & Keightley present results from their in silico examination of the rat and mouse genomes. They find selection to be acting three times more (in absolute number of sites) in noncoding than in coding sites. Most of these constrained noncoding sites are found more than 5kb away from known protein-coding genes. Intron sites believed to be functionally important are observed to be more concentrated near the 5'-end of genes, providing more evidence for a role of such intron parts in gene regulation. Intergenic regions appear to be harboring twice the number of deleterious mutations found in genes.

Gaffney DJ, Keightley PD. (2006) Genomic selective constraints in murid noncoding DNA. PLoS Genetics 2(11):e204.

Supergene controls color in buterflies

In the October issue of PLoS Biology Joron et al. report that a "supergene" locus controls color patterning in three Heliconius butterfly species.

Joron et al. (2006) A conserved supergene locus controls colour pattern diversity in Heliconius butterflies. PLoS Biology 4(10):e303.