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.

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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.

E urope has never been particularly fond of genetically modified (GM) foods, but a startling research paper published last week looks set to harden public and political opposition even further, despite a torrent of scepticism from scientists about the work. The study 1 , published in the peer-reviewed journal Food and Chemical Toxicology , looked for adverse health effects in rats fed NK603 maize (corn), developed by biotech company Monsanto to resist the herbi-cide glyphosate and approved for animal and human consumption in the European Union, United States and other countries. It reported that the rats developed higher levels of cancers, had larger cancerous tumours and died earlier than controls. The researchers have not conclusively identified a mechanism for the effect. The rats were monitored for two years (almost their whole life span), making this the first long-term study of maize containing these specific genes. About a dozen long-term studies of different GM crops have failed to find such stark health effects 2. An earlier test of NK603 maize in rats in a 90-day feeding trial — the current regulatory norm — sponsored by Monsanto showed no adverse effects 3. The explosion of media coverage about the findings has energized opponents of GM food, especially in Europe. French Prime Minister Jean-Marc Ayrault said that, if the results are confirmed, the government will press for a Europe-wide ban on the maize. The European Commission has instructed the independent European Food Safety Agency (EFSA) in Parma, Italy, to assess the study. Many scientists, however, have already questioned the study's methodology and findings. They assert that the data presented in the paper do not readily allow the claims to be independently assessed, and they question the study's experimental design and its statistical analysis of any differences between the treated groups and controls. Other scientists point out that the Sprague-Dawley strain of rats used in the experiments has been shown to be susceptible to developing tumours spontaneously, particularly as they grow older, making it difficult to interpret the results. Monsanto itself said that the study \" does not meet minimum acceptable standards for this type of scientific research \". The €3.2-million (US$4.1-million) study was led by Gilles-Eric Séralini, a molecular biologist at the University of Caen, France, in collaboration with the Paris-based Committee for Research and Independent Information on Genetic Engineering (CRIIGEN), whose scientific board he heads. CRIIGEN bills itself as an \" independent …

/pdf/rat-study-sparks-gm-furore-4mf8nh97w4.pdf

Rat study sparks GM furore

/pdf/what-the-numbers-say-about-refugees-1yig36h4vp.pdf

What the numbers say about refugees

stockholm The traditional [subject-wise] organization of research institutions is stifling interdisciplinary research, scientists and research administrators were told at a symposium last week

Interdisciplinary research ‘being stifled’

paris The UK Ministry of Defence has admitted that it failed to heed warnings at the start of the 1991 Gulf War about the possible side-effects of a vaccine combination administered to British troops.

/pdf/admission-on-gulf-war-vaccines-spurs-debate-on-medical-3bv03tbd8n.pdf

Admission on Gulf War vaccines spurs debate on medical records

Mostafa Moin is a paediatrician and medical researcher who has served as Iran's minister for higher education and for science. He was a reformist candidate in Iran's presidential election last year, which was won by religious conservative Mahmoud Ahmadinejad. Declan Butler asks Moin about the prospects for science in Iran.

/pdf/islam-and-science-q-a-the-reformer-2fd0le4l1v.pdf

Declan Butler

Papers

Rat study sparks GM furore

What the numbers say about refugees

Interdisciplinary research ‘being stifled’

Admission on Gulf War vaccines spurs debate on medical records

Islam and Science: Q&A The reformer