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Monthly Archives: October 2008
After making several potential designs in silico, my daughter chose one and we carved it. In order to participate in the Happy Hallo-Meme, we brought out the camera – first picture immediately after, the second once the darkness arrived and we lit up the candle inside:
Of course, Juno in costume was a hit with neighbors….
It’s the most famous chord in rock ‘n’ roll, an instantly recognizable twang rolling through the open strings on George Harrison’s 12-string Rickenbacker. It evokes a Pavlovian response from music fans as they sing along to the refrain that follows:
It’s been a hard day’s night
And I’ve been working like a dog
The opening chord to A Hard Day’s Night is also famous because for 40 years, no one quite knew exactly what chord Harrison was playing. Musicians, scholars and amateur guitar players alike had all come up with their own theories, but it took a Dalhousie mathematician to figure out the exact formula.
OK, that is all very nice – but: where is the chord!? I want to play it. Now. Come on, don’t be selfish – publish it somewhere online for all of us!
So, let’s see what’s new in PLoS Genetics, PLoS Computational Biology, PLoS Pathogens, PLoS ONE and PLoS Neglected Tropical Diseases this week. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. Here are my own picks for the week – you go and look for your own favourites:
Curling Up with a Story: An Interview with Sean Carroll:
To meet Sean Carroll on his home turf in the early spring of Wisconsin is like encountering a bear cuddled up in his lair, waiting out the cold winter. I burrowed into the softly lit cave of small offices, with stalactites of yellow post-its dripping from every imaginable surface. Tiptoeing over misaligned stacks of books and reprints, I had to resist the urge to pick up one of the worn works, settle into a corner, and join in the reverie.
Carroll is an expert in the field known as “evo devo,” an amalgam of developmental molecular biology as applied to the workings of animal evolution. Following his initial work with fushi tarazu (ftz)–one of the segmentation genes in the Antennapedia complex of Drosophila–he has been instrumental in elaborating the developmental regulation and interaction of a variety of genes, at first in the developing embryo, and later in the genesis of leg and wing appendages. A chance encounter fueled his long-standing interest in evolution and prompted him to re-tool his lab for the study of butterfly wing development; comparison between the two species led to groundbreaking insights into the subtle evolutionary changes that can give rise to spectacularly different appearances.
Cholera, a life-threatening diarrhoeal disease, has afflicted human beings and shaped human history for over two millennia. The disease still kills thousands of people annually. Vibrio cholerae, the etiologic agent of cholera, is endemic to aquatic environments , but despite intensive research efforts its ecology remains an enigma. The fatal effects of cholera are mainly due to the toxin produced by specific serogroups (O1 and O139) of V. cholerae . Strains of V. cholerae that belong to serogroups other than O1 and O139, collectively referred to as the non-O1, non-O139 V. cholerae, have also been implicated as etiologic agents of moderate to severe human gastroenteritis . The disease is endemic in Southern Asia and in parts of Africa and Latin America, where outbreaks occur widely and are closely associated with poverty and poor sanitation. The epidemic strains spread across countries and continents over time, giving rise to cholera pandemics . It has been suggested that zooplankton function as a carrier of V. cholerae via ocean currents. However, the mechanism that enables V. cholerae to cross freshwater bodies within a continent, as well as oceans between continents, remains unknown. Here, we put forward a strongly neglected hypothesis that deserves more attention, and discuss evidence from the scientific literature that supports this notion: migratory water birds are possible disseminators of V. cholerae within and between continents.
There is considerable interest from the wider scientific community in the heritability of epigenetic states across generations, and this has arisen as a result of a series of studies in mice ,, flies , plants ,, and yeast  over the past decade. These studies have identified genetic elements at which epigenetic states appear to be inherited through meiosis. The Lamarckian implications of these findings are hard to avoid. Transgenes, transposons, and other “foreign DNA” appear to be particularly prone to transgenerational epigenetic inheritance (reviewed in ). In this issue of PLoS Genetics, Singh et al.  describe the identification of a locus in the genome of maize at which a transposon, silenced by an RNAi-based mechanism, becomes reactivated over subsequent generations. This article reports an activating “position effect,” i.e., an integration site that is associated with the reversal of a previously established silent state in plants.
The coevolution of genes and languages has been a subject of enduring interest among geneticists and linguists. Progress has been limited by the available data and by the methods employed to compare patterns of genetic and linguistic variation. Here, we use high-quality data and novel methods to test two models of genetic and linguistic coevolution in Northern Island Melanesia, a region known for its complex history and remarkable biological and linguistic diversity. The first model predicts that congruent genetic and linguistic trees formed following serial population splits and isolation that occurred early in the settlement history of the region. The second model emphasizes the role of post-settlement exchange among neighboring groups in determining genetic and linguistic affinities. We rejected both models for the larger region, but found strong evidence for the post-settlement exchange model in the rugged interior of its largest island, where people have maintained close ties to their ancestral lands. The exchange (particularly genetic exchange) has obscured but not completely erased signals of early migrations into Island Melanesia, and such exchange has probably obscured early prehistory within other regions. In contrast, local exchange is less likely to have obscured evidence of population history at larger geographic scales.
Biogeographic patterns of species invasions hold important clues to solving the recalcitrant ‘who’, ‘where’, and ‘why’ questions of invasion biology, but the few existing studies make no attempt to distinguish alien floras (all non-native occurrences) from invasive floras (rapidly spreading species of significant management concern), nor have invasion biologists asked whether particular habitats are consistently invaded by species from particular regions. Here I describe the native floristic provenances of the 2629 alien plant taxa of the Eastern Deciduous Forest of the Eastern U.S. (EUS), and contrast these to the subset of 449 taxa that EUS management agencies have labeled ‘invasive’. Although EUS alien plants come from all global floristic regions, nearly half (45%) have native ranges that include central and northern Europe or the Mediterranean (39%). In contrast, EUS invasive species are most likely to come from East Asia (29%), a pattern that is magnified when the invasive pool is restricted to species that are native to a single floristic region (25% from East Asia, compared to only 11% from northern/central Europe and 2% from the Mediterranean). Moreover, East Asian invaders are mostly woody (56%, compared to just 23% of the total alien flora) and are significantly more likely to invade intact forests and riparian areas than European species, which dominate managed or disturbed ecosystems. These patterns suggest that the often-invoked ‘imperialist dogma’ view of global invasions equating invasion events with the spread of European colonialism is at best a restricted framework for invasion in disturbed ecosystems. This view must be superseded by a biogeographic invasion theory that is explicitly habitat-specific and can explain why particular world biotas tend to dominate particular environments.
Duncan Hull and colleagues just published an excellent, must-read article – Defrosting the Digital Library: Bibliographic Tools for the Next Generation Web:
Many scientists now manage the bulk of their bibliographic information electronically, thereby organizing their publications and citation material from digital libraries. However, a library has been described as “thought in cold storage,” and unfortunately many digital libraries can be cold, impersonal, isolated, and inaccessible places. In this Review, we discuss the current chilly state of digital libraries for the computational biologist, including PubMed, IEEE Xplore, the ACM digital library, ISI Web of Knowledge, Scopus, Citeseer, arXiv, DBLP, and Google Scholar. We illustrate the current process of using these libraries with a typical workflow, and highlight problems with managing data and metadata using URIs. We then examine a range of new applications such as Zotero, Mendeley, Mekentosj Papers, MyNCBI, CiteULike, Connotea, and HubMed that exploit the Web to make these digital libraries more personal, sociable, integrated, and accessible places. We conclude with how these applications may begin to help achieve a digital defrost, and discuss some of the issues that will help or hinder this in terms of making libraries on the Web warmer places in the future, becoming resources that are considerably more useful to both humans and machines.
The paper goes through each of the services, one by one, explains the pros and cons of each, and makes suggestions for the future development, as well as pointing out barriers and possible ways to overcome those. A couple of listed services are almost there – but are you using them? If so, why? If not, why not?
Apart from the rhetoric, apparently not:
The election is right around the corner, and voters around the country have been subjected to politicians, pundits and commercials laden with allegations of class warfare and claims about which candidates cater to the rich and which candidates will best serve the interests of the poor and the middle class. But a new study, co-authored by North Carolina State University researcher Dr. Chris Ellis, shows that it would be impossible for Congress and the White House to cater solely to any socioeconomic group – because people’s preferences tend to be overwhelmingly similar when it comes to how the federal government should spend its money.
In the study, Ellis and his co-author Dr. Joseph Ura used data from the long-running General Social Survey to measure public opinion on government spending from 1973 to 2006 and found that political sentiment was very similar between the various socioeconomic groups. Basically, trends toward becoming more liberal or more conservative tended to take place at the same time among rich, poor and middle-class voters. Ellis explains that the trends happened at the same time because both rich and poor responded to changes in the nation’s economic health, or the actions of the federal government, in broadly similar ways. Ellis is an assistant professor of political science at NC State. Ura is an assistant professor of political science at Texas A&M University.
We are busy preparing for The Open Laboratory 2008. The submissions have been trickling in all year, and a little bit more frequently recently, but it is time now to dig through your Archives for your best posts since December 20th 2007 and submit them. Submit one, or two, or several – no problem. Or ask your readers to submit for you.
Then take a look at your favourite bloggers and pick some of their best posts – don’t worry, we can deal with duplicate entries. Do not forget new and up-coming blogs – they may not know about the anthology – and submit their stuff as well.
As we did last year, we encourage you to also send in original poems and cartoons.
Keep in mind that the posts will be printed in a book! A post that relies heavily on links, long quotes, copyrighted pictures, movies, etc., will not translate well into print.
The deadline is December 1st, 2008. – just one month to go!
Below are submissions so far. Check them out and get inspired. If you see that one of your posts is at an old URL and you have since moved, re-submit with the new URL (perhaps re-post it if necessary):