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.

As outbreak enters its second year, relief bodies move to roll out vaccine for the first time.

/pdf/no-quick-fix-for-haiti-cholera-50oaumcw4q.pdf

No quick fix for Haiti cholera

paris A leading scientist is applying to the US National Institutes of Health for funds to challenge the ban on federal funding for research into the culturing and differentiation of human embryonic stem cells.

/pdf/breakthrough-stirs-us-embryo-debate-3299dtzf22.pdf

Breakthrough stirs US embryo debate...

/pdf/vaccine-campaign-to-target-deadly-childhood-diarrhoea-3qtoljvj0c.pdf

Vaccine campaign to target deadly childhood diarrhoea.

Technology will soon allow the world to be mapped in near-real time and at high resolution. Declan Butler investigates the potential for operational monitoring of the planet.

/pdf/earth-monitoring-the-planetary-panopticon-1x9o3abnw3.pdf

Earth monitoring: the planetary panopticon.

parasites will develop resistance to artemisinin because almost half of both its manufacturers and malaria-affected countries are failing to comply with World Health Organization (WHO) demands to sell it only in combination with other drugs. Artemisinin and its derivatives are the leading treatments for the disease, being the only antimalarials that have not yet seen widespread resistance in malaria parasites. The full scale of the problem is revealed in a soon-to-be-published WHO briefing seen by Nature, “Stop the marketing of oral artemisinin monotherapies”, which calls for governments to empower national drug-regulatory authorities to clamp down on offending companies. Treatments that use only artemisinin need to be taken for seven days to kill all parasites, but patients often stop treatment after a few days when they begin to feel much better. This leaves the remaining parasites in contact with low levels of the drug — a recipe for resistance. The WHO recommended in January 2006 that artemisinin should always be given in combination with other drugs for at least three days, because a cocktail reduces the chances of resistance. The need to move away from monotherapies has become all the more urgent with recent reports of resistance arising in Cambodia. Although artemisinin-based combination therapies (ACTs) have become the treatment of choice for malaria, with a three-day programme curing more than 95% of patients, monotherapies are cheaper to produce and sell. Of the 69 manufacturers of artemisinin monotherapies that the WHO has identified, 21 have withdrawn monotherapies, and 14 say they intend to comply with the WHO’s recommendations. But the remaining 34 have not yet disclosed their intentions. Many have not even replied to multiple WHO e-mail Malaria drug-makers ignore WHO ban As Francis Collins prepares to take the helm of the US National Institutes of Health (NIH), opinions are divided about how the geneticist will steer the agency through its extraordinary funding boom. Following President Barack Obama’s longanticipated nomination of Collins on 8 July, Harold Varmus, NIH director from 1993 to 1999, and now president and chief executive of the Memorial Sloan-Kettering Cancer Center in New York, described him as “a terrific scientist, inspirational leader, superb manager, and adept politician. I have great confidence in his ability to lead the NIH in complicated times.” But some believe that Collins has focused too much on genomics to the detriment of other approaches to improving health. Collins directed the NIH’s National Human Genome Research Institute (NHGRI) for 15 years until 2008, led the public effort to sequence the human genome and was a co-discoverer of the gene responsible for cystic fibrosis (see Nature 460, 164–169; 2009). “The genetic approach is extremely important, but it is a tool, it is not the be all and end all,” says Fran Visco, president of the Washington-based National Breast Cancer Coalition, which has called on the NIH to back more research on the environmental causes of breast cancer. There are also concerns about whether Collins’s very public expressions of his evangelical Christian faith will affect his job. He laid out his beliefs in a 2006 book, The Language of God: A Scientist Presents Evidence for Belief, and last year founded the BioLogos Foundation, which aims to help Christians integrate their faith with contemporary science. Steven Pinker, a psychologist at Harvard University, says he has “serious misgivings” about the nomination. “Collins is an advocate of profoundly anti-science beliefs, and it is reasonable for the scientific community to ask him how these beliefs will affect his administration of the NIH and his efforts on behalf of the scientific enterprise.” Several scientists close to Collins say that his faith will not affect his NIH duties. “In all the years that I worked with Francis — and there were a lot of years — I never once saw evidence where his religious faith was in conflict with his scientific judgement,” says developmental biologist Shirley Tilghman, president of Princeton University in New Jersey, who sat on Collins’s advisory council when he directed the NHGRI. “We would count him as an ally,” adds Joshua Rosenau, a policy analyst at the National Center for Science Education, a non-profit organization in Oakland, California, that defends the teaching of evolution in schools. “It is helpful to have scientists like Francis Collins speaking out about how they personally reconcile science and religion.” The BioLogos Foundation has confirmed that Collins would step down from his role there before taking up the reins at the NIH. It’s the right move, says Varmus. “Discussion about the foundation and his involvement with it could readily become a distraction from the business of running the NIH,” he told Nature. NIH nominee draws scrutiny

/pdf/malaria-drug-makers-ignore-who-ban-27l39j22zb.pdf

Declan Butler

Papers

No quick fix for Haiti cholera

Breakthrough stirs US embryo debate...

Vaccine campaign to target deadly childhood diarrhoea.

Earth monitoring: the planetary panopticon.

Malaria drug-makers ignore WHO ban.