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 Controversy has erupted over a deal giving a French biotechnology company access to a DNA bank that contains samples of DNA taken from centenarians built up for longevity research.

/pdf/tensions-grow-over-access-to-dna-bank-1imrn8rtuc.pdf

Tensions grow over access to DNA bank.

Grenoble, France. Future prospects for research into the structure of matter took a major step forward last week with the opening in Grenoble of the 6-GeV European Synchrotron Radiation Facility (ESRF) which extends the wavelength range of synchrotron radiation from 'soft' to 'very hard' X-rays. The FFr3 .6-billion (US$681-million) ESRF is the first of the so-called thirdgeneration synchrotrons, which produce fine and brilliant beams of X-rays at chosen wavelengths almost an \"X-ray laser\", says Yves Petroff, director general ofESRF. The United States will also open a 7-GeV machine ( the Advanced Photon Source) at Argonne in 1996--97, and Japan an 8-Ge V machine, the SP-8, at Kobe a year later. Synchrotron radiation was first observed in 194 7 by researchers at General Electric in the United States. They found that each time the trajectory of high-energy electrons in a circular accelerator was bent by magnets, the electrons emitted a cone of electromagnetic radiation, similar to the cone of light from the headlights of a car turning a bend. accelerators. Only in the 1960s did scientists recognize the potential of synchrotron radiation for overcoming the problems of the conventional Coolidge X-ray tube, which emits relatively feeble and direction-less Xrays that are intense only at a few wavelengths, and cannot be focused or polarized. First-generation synchrotrons amounted simply to crude X-ray beams clipped on to existing particle accelerators. What sets ESRF The ESRF: 'almost an X-ray laser'. apart from previous purpose-built synchro300-metre-circumference synchrotron. The trons such as the second-generation 2electrons are then fed into the 844-metreGe V machine at the Daresbury Laboratory circumference storage ring (see photo). in Warrington, in the United Kingdom-is Here we find the big third-generation its threefold higher energy, the consequent innovation the addition of 'insertion deability to attain wavelengths thousands of vices'. Existing synchrotrons produce ratimes shorter, and the much higher (up to diation only when high-energy electrons five orders of magnitude) brilliance of its pass bending magnets in the storage ring. X-ray beams. But ESRF also produces radiation at 29 Initially, scientists saw this synchrotron radiation as simply a curious nuisance that reduced the energy of electrons in particle ESRF's high energies are obtained by insertion devices, each of which creates an first accelerating electrons to 200 Me V in a oscillating magnetic field that forces eleclinear accelerator, and then to 6 GeV in a trons to slalom about the linear part of their r--------------------------------~ trajectory. ESRF as 'a model of collaboration'

/pdf/esrf-as-a-model-of-collaboration-1868u8ky0v.pdf

ESRF as 'a model of collaboration'

/pdf/ministers-prepare-to-back-neuroscience-network-2ctguq3vm0.pdf

Ministers prepare to back neuroscience network.

paris French geneticists are concerned about the likely distribution of a FF1.5 billion boost to genome research said to be under consideration by the government.

/pdf/french-geneticists-raise-worries-over-use-of-new-genome-5b77tbu90x.pdf

French geneticists raise worries over use of new genome funds

/pdf/pope-condemns-immoral-embryo-research-175ydtznr1.pdf

Declan Butler

Papers

Tensions grow over access to DNA bank.

ESRF as 'a model of collaboration'

Ministers prepare to back neuroscience network.

French geneticists raise worries over use of new genome funds

Pope condemns `immoral' embryo research