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.

/pdf/france-too-much-analysis-leads-to-paralysis-26uo4ozqw6.pdf

France: Too much analysis leads to paralysis

Axel Kahn’s is one of the most wellheeled genetics labs in France. As a pillar of the research establishment, he is not given to tempestuous announcements. But earlier this month, he threatened to resign as director of the Cochin Institute in Paris unless the government takes immediate and significant steps to boost French research. Kahn, together with many of the country’s top scientists, is a prominent member of a researchers’ revolt. The protesters, known as the Save Research movement, made their demands on 7 January in an online petition.They want the government to pay research agencies the millions of euros it owes them, to boost recruitment of young scientists,and to launch a national debate on science. To give teeth to their demands, signatories pledge to resign all administrative duties, an act that could bring the country’s research system to its knees. The seeds of revolt were sown last year, when the national research agencies bore the brunt of a 1.3% cut in the country’s €8.8billion (US$10-billion) research budget. At Kahn’s laboratory, for example, public funding fell 10%, and staff numbers dropped by 15 to around 150.“And we are one of the top labs in France,” he says. “Just imagine the situation elsewhere.” Faced with crushing public deficits, the finance ministry has also withheld millions from the agencies, bringing them close to bankruptcy. The CNRS, France’s national research agency, was until last week owed €172 million. The agency was only able to avoid going broke after the government freed up €103 million, promising to repay the rest in 2005. But it is the job situation that sparked the protests. At INSERM, the national biomedical research agency, staff numbers are being cut and only 30 new positions are available this year, compared with 90 in 2003. New threeto five-year contracts, paying €1,900 a month, are also being shunned by young scientists, as it is almost impossible to rent an apartment or get a loan on a short-term contract. Kahn says that anger among PhD students infected more senior staff, leading them to establish the petition, which has attracted more than 17,000 signatures. As a well-known public figure,Kahn feels obliged to go one step further than other signatories and resign his research position. He seems to be deadly serious about carrying this through: “I can’t allow myself to make threats that are not credible.” Last weekend, science minister Claudie Haigneré received Alain Trautmann, co-head of the biology department at the Cochin Institute and spokesman for the Save Research movement. Haigneré described the meeting as “constructive” and promised an interministerial meeting to discuss the demands.■ ➧ http://recherche-en-danger.apinc.org news

/pdf/resignation-threats-add-steel-to-french-revolt-4xxrlfywfe.pdf

Resignation threats add steel to French revolt.

/pdf/galapagos-tortoise-disease-contained-16zew1kkvq.pdf

Galapagos tortoise disease 'contained'.

Catholic Church ready to reject intelligent design.

/pdf/when-science-and-theology-meet-4796a9000y.pdf

When science and theology meet

Claude Allegre, France's minister of national education, research and technology, last week set the target of doubling the impact of French publications in the international scientific literature within four years. He also wants to triple the number of international patents held by French scientists, and to create several hundred stable high-technology companies.

/pdf/france-sets-high-targets-for-impact-factors-and-patents-gdl1lonw23.pdf

Declan Butler

Papers

France: Too much analysis leads to paralysis

Resignation threats add steel to French revolt.

Galapagos tortoise disease 'contained'.

When science and theology meet

France sets high targets for impact factors and patents