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.

/pdf/europe-extends-biotech-grants-experiment-1fyum7lju0.pdf

Europe extends biotech grants 'experiment'

paris Documents from the mid-1980s reveal that the French agency that later carried out investigations into the 'contaminated blood' affair was aware at the time that blood products were contaminated with HIV.

/pdf/anomalies-in-french-blood-inquiry-over-misleading-report-8broepoifp.pdf

Anomalies in French blood inquiry over 'misleading' report.

Internet users spur on request for independent science evaluation.

Bloggers rally for liberation of the 'Tripoli Six'

Palaeoanthropologists are falling out over who should have access to data on the most prized fossils of our human ancestors, once they have been discovered in the field. The National Science Foundation (NSF), which funds most work in the discipline by US researchers, is preparing guidelines on when and how data should be released for general analysis by researchers other than those who find the fossils. But the community is bitterly divided over what the rules should say. Those who discover hominids during expeditions, often in Africa, want to keep first rights to analyse and document their work. But those who do analytical work at universities say the discipline would benefit if all photographs and measurements were made openly available as soon as possible after discovery. Among those wanting quicker access to the fossil data is Ian Tattersall, anthropology curator at the American Museum of Natural History in New York City. “If you are taking public money to go out and find fossils, you have to make them available,”he says. But Brenda Benefit, a palaeoanthropologist at New Mexico State University in Las Cruces, thinks that such access would take advantage of field research teams who spend years in dangerous conditions investigating sites. “I find it appalling that scientists who make no such commitment wish to gain from the personal sacrifices of others,”she says. Mark Weiss and John Yellen, two NSF officials responsible for physical anthropology and archaeology, respectively, have been working on the guidelines since last year. They are reviewing about 80 letters from researchers received in response to a request for comments, and expect to produce final guidelines later this year, but they are treading carefully.“I have tried to be as equitable and reasonable as possible,”says Weiss. Some researchers say that the pair are relying too heavily for advice on Harvard palaeoanthropologist David Pilbeam, who has helped to process the researchers’comments, and whom critics regard as averse to fieldwork. In a day-long trek in Pakistan many years ago, Pilbeam wouldn’t leave the truck “to walk 50 metres to a rich hominid site”,says Martin Pickford,a palaeoanthropologist at the National Museum of Natural History in Paris. “He told me he didn’t like wide-open spaces.” Pilbeam acknowledges that he doesn’t care for fieldwork but says this won’t affect his advisory role at the NSF. Weiss says that Pilbeam is “as objective as anyone could be”. When hominids are discovered, their skulls, teeth and major bones are often encased in stone and shattered into hundreds of pieces. These must be painstakingly separated from the rock and pieced together, which can take years. Researchers typically report a new hominid species or genus in a short report in publications such as Nature or Science after most of the reconstruction is done, and then publish a much fuller analysis in a lengthy, definitive monograph some years later. Tattersall, who wants data for the books he publishes on hominids, says researchers should have full access to the specimens immediately after initial publication. But Timothy White, a palaeoanthropologist at the University of California, Berkeley, whose team has made some of the biggest discoveries in Ethiopia, disagrees. “We don’t think laboratory workers or book publishers should dictate our publication schedule,” he says. “We’re the ones who seek, find, clean, restore and study the fossils, and put them into context.” The NSF’s task is complicated by the question of whether it should even be publishing guidelines on the handling of specimens that belong to the nation where they are found, such as Ethiopia or Kenya. Museums there often demand approval from the discoverer before they grant other researchers access. ■ news

/pdf/gates-grant-helps-africa-develop-science-academies-2mp5panhko.pdf

Gates grant helps Africa develop science academies

/pdf/mozambique-prime-minister-tipped-for-global-health-post-ntpy19idzl.pdf

Declan Butler

Papers

Europe extends biotech grants 'experiment'

Anomalies in French blood inquiry over 'misleading' report.

Bloggers rally for liberation of the 'Tripoli Six'

Gates grant helps Africa develop science academies

Mozambique prime minister tipped for global health post.