Summary
1. Here, I present a new, multifunctional phylogenetics package, phytools, for the R statistical computing environment.

2. The focus of the package is on methods for phylogenetic comparative biology; however, it also includes tools for tree inference, phylogeny input/output, plotting, manipulation and several other tasks.

3. I describe and tabulate the major methods implemented in phytools, and in addition provide some demonstration of its use in the form of two illustrative examples.

4. Finally, I conclude by briefly describing an active web-log that I use to document present and future developments for phytools. I also note other web resources for phylogenetics in the R computational environment.

/pdf/phytools-an-r-package-for-phylogenetic-comparative-biology-yli0omoidd.pdf

phytools: an R package for phylogenetic comparative biology (and other things)

Associations between modifiable exposures and disease seen in observational epidemiology are sometimes confounded and thus misleading, despite our best efforts to improve the design and analysis of studies. Mendelian randomization-the random assortment of genes from parents to offspring that occurs during gamete formation and conception-provides one method for assessing the causal nature of some environmental exposures. The association between a disease and a polymorphism that mimics the biological link between a proposed exposure and disease is not generally susceptible to the reverse causation or confounding that may distort interpretations of conventional observational studies. Several examples where the phenotypic effects of polymorphisms are well documented provide encouraging evidence of the explanatory power of Mendelian randomization and are described. The limitations of the approach include confounding by polymorphisms in linkage disequilibrium with the polymorphism under study, that polymorphisms may have several phenotypic effects associated with disease, the lack of suitable polymorphisms for studying modifiable exposures of interest, and canalization-the buffering of the effects of genetic variation during development. Nevertheless, Mendelian randomization provides new opportunities to test causality and demonstrates how investment in the human genome project may contribute to understanding and preventing the adverse effects on human health of modifiable exposures.

/pdf/mendelian-randomization-can-genetic-epidemiology-contribute-vb0zjyrtxf.pdf

‘Mendelian randomization’: can genetic epidemiology contribute to understanding environmental determinants of disease?

In recent months there has been an explosion of interest in using the Web to create, assemble, and disseminate geographic information provided voluntarily by individuals. Sites such as Wikimapia and OpenStreetMap are empowering citizens to create a global patchwork of geographic information, while Google Earth and other virtual globes are encouraging volunteers to develop inter- esting applications using their own data. I review this phenomenon, and examine associated issues: what drives people to do this, how accurate are the results, will they threaten individual privacy, and how can they augment more conventional sources? I compare this new phenomenon to more traditional citizen science and the role of the amateur in geographic observation.

/pdf/citizens-as-sensors-the-world-of-volunteered-geography-phibl484h3.pdf

Citizens as sensors: the world of volunteered geography

We review the recent rapid progress in the statistical physics of evolving networks. Interest has focused mainly on the structural properties of complex networks in communications, biology, social sciences and economics. A number of giant artificial networks of this kind have recently been created, which opens a wide field for the study of their topology, evolution, and the complex processes which occur in them. Such networks possess a rich set of scaling properties. A number of them are scale-free and show striking resilience against random breakdowns. In spite of the large sizes of these networks, the distances between most of their vertices are short - a feature known as the 'small-world' effect. We discuss how growing networks self-organize into scale-free structures, and investigate the role of the mechanism of preferential linking. We consider the topological and structural properties of evolving networks, and percolation and disease spread on these networks. We present a number of models demonstrat...

/pdf/evolution-of-networks-27h4ny8xbi.pdf

Evolution of networks

Yuelong Shu1, John McCauley2 1. WHO Collaborating Center for Reference and Research on Influenza, Chinese National Influenza Center, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China 2. WHO Collaborating Centre for Reference and Research on Influenza, Crick Worldwide Influenza Centre, the Francis Crick Institute, London, United Kingdom

GISAID: Global initiative on sharing all influenza data - from vision to reality.

Iter means ‘the way’ in Latin — but ‘lost its way’ might be a more apt description of the international fusion project that bears the name. A technical assessment intended to break a stalemate over where to site the facility has itself ended in deadlock,with the six partners blaming each other for the lack of progress. Negotiations over ITER’s site have been stalled since a ministerial meeting in Washington last December, when the United States and South Korea backed the Japanese site at Rokkasho, and China and Russia supported the European Union’s site at Cadarache in France. The US$5-billion project seeks to show that heating plasma in a magnetic field can produce fusion energy. But a meeting of experts in Vienna, Austria, on 12 and 13 March ended in discord. Supporters of the European site insisted that the meeting should publish a technical comparison of the two sites — which they claim would have shown up their strengths. Supporters of the Japanese site, including the United States, countered that the technical discussions were meant to feed into a wider political decision on a site. The outcome of the meeting — privately described as ‘fiery’ by participants — was a bland statement that it had agreed to disagree. No further meetings have been scheduled to decide on a site, and plans to consider making the experimental reactor part of a broader, international fusion-research package remain just plans. One Japanese government official put a brave face on the situation. “We’re going up the stairs one step at a time,”he says.“There’s no such thing as an endless staircase, so eventually we’ll get there.”A European fusion scientist close to the talks disagreed: “We’re not going anywhere.” US sources familiar with the negotiations say that the government there wants to take a backseat, in the hope that Europe and Japan can come to an agreement. But many researchers wonder if an accord can be reached.“People in the United States have no idea how this will get resolved,” says Stephen Dean, head of Fusion Power Associates, a Washington-based advocacy group for fusion research. Others worry that a decision on location will not be reached by the summer, when US researchers are set to re-evaluate the nation’s role in the project. “Europe and Japan have to arrive at a decision, otherwise this could go on forever,”says Dale Meade,a physicist at the Princeton Plasma Physics Laboratory in New Jersey. An eight-person European Union delegation went to Tokyo this week to seek agreement with Japanese experts and government officials. One European scientist privately branded the trip “mission impossible”. But despite the deadlock, India last week became the latest nation to say it might join the project. According to science secretary Valangiman Ramamurthy, it accepted an offer from David King, science adviser to Prime Minister Tony Blair,to join ITER as a partner of Britain, which will cost India less than joining the project as a full partner. ■

/pdf/partners-fail-to-find-common-ground-for-fusion-project-3gxnarpzfu.pdf

Partners fail to find common ground for fusion project.

paris Draft plans to overhaul France's 27,000-strong national research agency (CNRS) have run into a storm of protest from the labour unions representing scientific staff.

French researchers kick up a storm over CNRS ‘reforms’

/pdf/diplomatic-talks-spur-hope-in-libya-hiv-case-2k2ebx9jsq.pdf

Diplomatic talks spur hope in Libya HIV case.

/pdf/political-initiatives-contributed-to-crisis-1u1a50k0sc.pdf

Political initiatives contributed to crisis

paris French laws banning human embryo research should be eased, according to the country's national bioethics committee and its National Academy of Medicine

/pdf/pressure-grows-for-relaxation-of-french-embryo-research-laws-3d0tozk0e2.pdf

Declan Butler

Papers

Partners fail to find common ground for fusion project.

French researchers kick up a storm over CNRS ‘reforms’

Diplomatic talks spur hope in Libya HIV case.

Political initiatives contributed to crisis

Pressure grows for relaxation of French embryo research laws.