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.

paris The ‘globalization’ of investment in industrial research and development is complicating the link between a nation's public science base and its economic competitiveness, according to an OECD report.

/pdf/global-r-d-spread-clouds-locaal-analyses-tbgexbz6k9.pdf

Global R&D spread clouds locaal analyses

Plans to launch a Europe-based global website for the scientific literature, E-Biosci, were unanimously endorsed by research organizations, commercial publishers and the European Commission in Heidelberg last week.

/pdf/all-parties-keen-to-press-on-with-europe-based-science-224i7jzdky.pdf

All parties keen to press on with Europe-based science website.

A better balance in the contributions to joint projects of researchers from industrialized and developing countries could be achieved by an international code of professional ethics, says the head of a French research agency.

/pdf/call-for-north-south-code-of-research-ethics-ya2ewpnofa.pdf

Call for North/South code of research ethics.

The United States is facing bitter recriminations over its tactics at an international meeting on biological weapons in Geneva. The talks to review the 1972 Biological Weapons Convention (BWC) collapsed on 7 December without agreement. A unanimous vote to adjourn the conference until next November followed a move by the United States to block new means for verifying compliance with the BWC’s terms. As the meeting finished, negotiators from European Union (EU) states openly condemned the US tactics — echoing the deep divisions that characterized international conferences on topics such as global warming before the 11 September terrorist attacks. The EU delegation was sufficiently annoyed that it refused to sit with its US allies during the closing session of the meeting. Critics of the Bush administration say it has committed a sizeable diplomatic blunder, alienating its closest allies and also failing in its bid to stop the BWC parties from attempting fresh negotiations for a verification protocol in the future. But the administration believes that it succeeded in postponing the difficult issue of international agreement on bioweapons, without sustaining any real political damage. The adjournment leaves the BWC in disarray. But some observers say that the enforced ‘cooling off ’ period, together with the galvanization of opposition at the meeting to the Bush administration’s position, may ultimately result in greater international impetus towards an expanded BWC agreement. Less than two hours before the scheduled end of the conference, the United States tabled a demand that other countries were always going to reject: the formal abolition of a remit requiring parties to the BWC to agree on legally binding measures to ensure compliance. In July, the United States had said that it would veto a draft protocol allowing for inspections of facilities, arguing that this would not catch bioweapons proliferators, and would open up US biodefence establishments and biotechnology companies to espionage (see Nature 412, 365; 2001). From the outset, it was recognized that discussion of this remit at the meeting would probably result in the breakdown of the talks, which required unanimous consent to proceed. So parties representing the BWC’s 144 signatory states had tacitly agreed to ignore the issue, negotiators say. Instead, the talks sought consensus on two other issues. One was the nature of future BWC review meetings. To get around US opposition to formal discussion of verification protocols, the EU proposed ad hoc meetings alongside the five-year review conferences. The other was the question of how to deal with signatories suspected of running covert, offensive biological weapons programmes. Initially, the United States demanded that five named states — including Iran and Iraq — “terminate their offensive biological weapons programmes and fully comply with their obligations”. This irked some parties because it ignored eight other nations — including Russia, China and Israel — that the United States acknowledges as having similar programmes. On the last morning of the meeting, the United States offered a concession, asking instead that parties express “grave concern that compliance...has been subject to doubt in certain cases”. This was expected to win the meeting’s support, negotiators say. But with agreement in sight, the United States abandoned its position, saying that it would only agree to the compromise if the news

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Declan Butler

Papers

Global R&D spread clouds locaal analyses

All parties keen to press on with Europe-based science website.

Call for North/South code of research ethics.

Bioweapons treaty in disarray as US blocks plans for verification.

Slow release of data adds to BSE confusion.