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.

Statistics on scientific investment and performance are lacking across the Muslim world. Declan Butler analyses the best of what is available.

/pdf/islam-and-science-the-data-gap-1r4i264h67.pdf

Islam and Science: the data gap.

Public Library of Science (PLoS), the poster child of the open-access publishing movement, is following an haute couture model of science publishing — relying on bulk, cheap publishing of lower quality papers to subsidize its handful of high-quality flagship journals. Since its launch in 2002, PLoS has been kept afloat financially by some US$17.3 million in philanthropic grants. An analysis by Nature of the company’s accounts shows that PLoS still relies heavily on charity funding, and falls far short of its stated goal of quickly breaking even through its business model of charging authors a fee to publish in its journals. In the past financial year, ending 30 September 2007, its $6.68-million spending outstripped its revenue of $2.86 million, according to the publicly available accounts. But its financial future is looking brighter thanks to a cash cow in the form of PLoS One, an online database that PLoS launched in December 2006. PLoS One uses a system of ‘light’ peer-review to publish any article considered methodologically sound. In its first full year of operation in 2007, PLoS One published 1,230 articles, which would have generated an estimated $1.54 million in author fees, around half of PLoS’s total income that year. By comparison, the 321 articles published in PLoS Biology in 2007 brought in less than half this amount. From the outset, the company consciously decided to subsidize its top-tier titles by publishing second-tier community journals with high acceptance rates that would be cheaper to produce. In addition to its premium titles — PLoS Biology and PLoS Medicine, which have low acceptance rates and high overheads, and charge author fees of $2,750 — it has launched four lower-cost journals that are run by volunteer academic editorial teams rather than in-house staff. At $2,100, the fees to authors for publishing in these journals — PLoS Computational Biology, PLoS Genetics, PLoS Pathogens and PLoS Neglected Tropical Diseases — are almost as much as those for its top journals. But this combination has generated much less income than PLoS envisaged. “It’s very clear that the reality is very far from PLoS’s original plan,” says John Ewing, executive director of the American Mathematical Society. In particular, PLoS’s initial projections overestimated by an order of magnitude the number of articles that both its topand second-tier journals would attract, tax-record data obtained by Nature reveal. PLoS also grossly underestimated the cost of producing its top-tier journals. “If the original model was to be self-sustaining through author fees, it seems that PLoS is not even half-way there,” says Bernard Rous, deputy director of publications of the Association for Computing Machinery, the world’s largest educational and scientific computing society. Nevertheless, Rous endorses PLoS’s strategy of tapping multiple revenue sources and cross-subsidizing to allow open access to all its titles. Faced with an increasingly dire financial situation, PLoS hiked all its author fees in 2006, from $1,500 to as much as $2,500 for its top two journals, and has since increased them further. This has helped to boost revenue, but the effect of the increase has been minor compared with the new cash flowing from the flood of articles appearing in PLoS One. Since it launched, PLoS One has published 2,526 articles — more than PLoS Biology has published in its five years of existence, and that growth shows no signs of abating. PLoS One has published 1,158 papers since the beginning of this year, which is almost as many as it published during the whole of 2007. Another factor is that it costs authors only $1,250 to publish in PLoS One. “It’s fair to say that the community-run journals, including PLoS One, are contributing very well to our overall financial picture, says Peter Jerram, chief executive of PLoS, adding: “PLoS is on track to be self-sustaining within two years. In the interim some philanthropic support will be needed. “It’s tremendous to see how the progress that PLoS has made over the years has been mirrored by the great strides taken towards openaccess to research more broadly,” Jerram says. Papers submitted to PLoS One are sent to a member of its editorial board of around 500 researchers, who may opt to review it themselves or send it to their choice of referee. But referees only check for serious methodological flaws, and not the importance of the result. The board members who Nature spoke to were generally positive about the overall quality of the papers they had received to review and the referees reports they solicited. “There’s so much in PLoS One that it is difficult to judge the overall quality and, simply because of this volume, it’s going to be considered a dumping ground, justified or not, says John Hawley, executive director of the freeaccess Journal of Clinical Investigation. “But nonetheless, it introduces a sub-standard journal to their mix.” Hawley says it’s unsurprising that the PLoS business model has come under scrutiny. “PLoS trumpeted its business model as being better than everyone else’s, as being ‘the one’.” The tack taken by BioMed Central, a Londonbased open-access company, of publishing mostly lower-impact journals in a wide variety of disciplines “is probably closer to what works in open access”, he says. BioMed Central has an estimated annual revenue of around £10 million ($20 million). It is already “pleasantly profitable”, according to a science-publishing consultant who asked to remain anonymous. “BioMed Central knows well that much of the journal middle order is more profitable than the great brands because of the lower editorial costs and the cheaper marketing costs for bundles of journals. I suspect that PLoS One is a result of learning the same lesson,” he adds. BioMed Central is now up for sale, which will be a “fascinating first market test of what people will pay for an open-access company”. ■ Declan Butler PLoS stays afloat with bulk publishing

/pdf/plos-stays-afloat-with-bulk-publishing-3ra07dfrgq.pdf

PLoS stays afloat with bulk publishing.

A world population analysis reveals the locations that could put the most people in danger should a nuclear accident occur.

Nuclear safety: Reactors, residents and risk.

/pdf/verbal-autopsy-methods-questioned-2bh0n14ik6.pdf

Verbal autopsy methods questioned.

Across the developed world, birth rates are plummeting. Is this just a social phenomenon, or is our biological fertility also declining? We don't yet know, and that is worrying, says Declan Butler.

Declan Butler

Papers

Islam and Science: the data gap.

PLoS stays afloat with bulk publishing.

Nuclear safety: Reactors, residents and risk.

Verbal autopsy methods questioned.

The fertility riddle