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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):
Today is the last day! I know most of my readers are donating to Obama this year, but still, my challenge is on the very bottom of the Scienceblogs.com list….
All of us who grew up before World War II are immigrants in time, immigrants from an earlier world, living in an age essentially different from anything we knew before.
- Margaret Mead
I am sure that you have already heard about the despicable TV ad that Elizabeth Dole aired against Kay Hagan. You probably heard about it online, perhaps on Twitter or FriendFeed or blogs. Here’s a quick selection:
My godless money. Take it or leave it.
The Worst Insult of All?
Thou shalt not bear false witness
NC: Hagan responds to ‘Godless’ ad; Dole’s immigrant bashing
Elizabeth Dole ad falsely suggests opponent Kay Hagan is ‘Godless.’
North Carolina Senate Race Degenerates Into Shouting Match About Atheists
Sen. Liddy Dole (R-NC) attacks Sunday school teacher: ‘There is no God’
Sen. Dole vs. the atheists
With friends like these…
Also, we aren’t tax exempt, so: Vote Obama
You Know Your Senator Is Getting Desparate When…
North Carolina Watch
Don’t you call me an atheist, you
There is No God!
Is Elizabeth Dole Godless?
Elizabeth Dole accuses her opponent of atheism!
Will Elizabeth Dole Ad Have A Subliminal Effect On Young Viewers
Liddy Dole is an asshole
Calling someone an atheist is apparently slander
A pox on them all
Liddy Dole’s Desperate Bigotry
Godless isn’t immoral (a letter to Raleigh News & Observer)
….and many more….
But, if this happened four years ago, you would not have heard about it in the mainstream media. This year, you do:
What changed in four years?
Ari Melber thinks it’s the Web: blogs, social networks, YouTube:
Everyone can hear it now. This Internet-driven, hyperactive presidential race is forcing accountability on two of the oldest tricks in politics: dog whistles and secret smears.
Partisan and muckraking bloggers now fight political operatives’ efforts to keep unseemly attacks below the radar. Take automated “robo” phone calls, which often deploy the sharp attacks that campaigns don’t want exposed in the mass media. Previously, the calls were obscure, rarely drawing major media coverage, let alone sustained criticism. Now they can be recorded, uploaded and dissected in a single news cycle. Sites like TalkingPointsMemo and Daily Kos use crowd-sourcing by readers to track the attacks and pin them squarely on John McCain. Insider political sites, like Ben Smith’s Politico blog, also disseminate the audio recordings to media and political elites, converting a “targeted” message into a mass broadcast. And organized campaigns like the National Political Do Not Call Registry use the web, Twitter and e-mail to track and map every call.
Once exposed, McCain’s robocalls were unpalatable even to his allies in the party and the media, adding another “Hey, Rube” squabble to his already contentious campaign. Republican senators condemned the calls. Fox News’s Chris Wallace pressed McCain on the issue, reminding the senator that he once denounced such tactics. Even Sarah Palin felt compelled to respond to criticism of the campaign’s robocalls, telling reporters that while she did not renounce them, she would prefer to do personal and retail campaigning instead.
All this online activity has been amplified by the rapidly shifting landscape of political television. The increasingly opinionated cable news programs, always in search of conflict and fresh content, now treat debates over these tactics as a major campaign issue. This emphasis is bleeding into the broader campaign discourse, which includes minute dissection of attacks that were once considered unmentionable. A whole range of smears against Obama, for example, have been exposed under the glare of nationally televised debates. Sometimes that process has angered his supporters–as when the ABC News primary debate focused on smears regarding “patriotism” and Islam. In one of the general election debates, CBS moderator Bob Scheiffer was credited for playing a corrective role when he pressed both candidates to answer for attacks from their supporters. That is a stark contrast to the previous two presidential races, when even the most incendiary attacks drew scant calls for accountability at the candidate level.
“Thanks to YouTube–and blogging and instant fact-checking and viral emails– it is getting harder and harder to get away with repeating brazen lies without paying a price, or to run under-the-radar smear campaigns without being exposed,” contends Arianna Huffington, whose website pulses with a constant, two-way debate of news and opinion. “The McCain campaign hasn’t gotten the message,” she added, “hence the blizzard of racist, alarmist, xenophobic, innuendo-laden accusations being splattered at Obama.”
This new media environment undermines political attacks that turn on coded meanings and hidden messages, because now anything can be exposed and cheaply disseminated. Observers used to worry that the web would fragment our media consumption into private little silos–that famous “Daily Me.” Yet in presidential politics, an inverse dynamic is emerging. Small groups of people are using the web to expose the targeted appeals of the analog world, and then injecting them into the mass media for the whole nation to assess. And many voters do not like what they see.
Perhaps Liddy Dole, by airing this TV ad, provoked exactly the kind of storm that, amplified through both the New and Old Media, will lead to a public shift in perception of atheists. If everyone and their grandmother starts talking about it and seeing this ad as despicable – not for tainting Hagan but for denigrating atheists (sorta like what Colin Powell did to the idea that calling someone a Muslim is a smear) – then we as a society have just made another step in the right direction.
There are 33 new articles in PLoS ONE today. 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:
The Political Gender Gap: Gender Bias in Facial Inferences that Predict Voting Behavior:
Throughout human history, a disproportionate degree of political power around the world has been held by men. Even in democracies where the opportunity to serve in top political positions is available to any individual elected by the majority of their constituents, most of the highest political offices are occupied by male leaders. What psychological factors underlie this political gender gap? Contrary to the notion that people use deliberate, rational strategies when deciding whom to vote for in major political elections, research indicates that people use shallow decision heuristics, such as impressions of competence solely from a candidate’s facial appearance, when deciding whom to vote for. Because gender has previously been shown to affect a number of inferences made from the face, here we investigated the hypothesis that gender of both voter and candidate affects the kinds of facial impressions that predict voting behavior. Male and female voters judged a series of male and female political candidates on how competent, dominant, attractive and approachable they seemed based on their facial appearance. Then they saw a series of pairs of political candidates and decided which politician they would vote for in a hypothetical election for President of the United States. Results indicate that both gender of voter and candidate affect the kinds of facial impressions that predict voting behavior. All voters are likely to vote for candidates who appear more competent. However, male candidates that appear more approachable and female candidates who appear more attractive are more likely to win votes. In particular, men are more likely to vote for attractive female candidates whereas women are more likely to vote for approachable male candidates. Here we reveal gender biases in the intuitive heuristics that voters use when deciding whom to vote for in major political elections. Our findings underscore the impact of gender and physical appearance on shaping voter decision-making and provide novel insight into the psychological foundations underlying the political gender gap.
Living soil invertebrates provide a universal currency for quality that integrates physical and chemical variables with biogeography as the invertebrates reflect their habitat and most ecological changes occurring therein. The specific goal was the identification of “reference” states for soil sustainability and ecosystem functioning in grazed vs. ungrazed sites. Bacterial cells were counted by fluorescent staining and combined direct microscopy and automatic image analysis; invertebrates (nematodes, mites, insects, oligochaetes) were sampled and their body size measured individually to allow allometric scaling. Numerical allometry analyses food webs by a direct comparison of weight averages of components and thus might characterize the detrital soil food webs of our 135 sites regardless of taxonomy. Sharp differences in the frequency distributions are shown. Overall higher biomasses of invertebrates occur in grasslands, and all larger soil organisms differed remarkably. Strong statistical evidence supports a hypothesis explaining from an allometric perspective how the faunal biomass distribution and the energetic flux are affected by livestock, nutrient availability and land use. Our aim is to propose faunal biomass flux and biomass distribution as quantitative descriptors of soil community composition and function, and to illustrate the application of these allometric indicators to soil systems.
Individual mice have a unique odor, or odortype, that facilitates individual recognition. Odortypes, like other phenotypes, can be influenced by genetic and environmental variation. The genetic influence derives in part from genes of the major histocompatibility complex (MHC). A major environmental influence is diet, which could obscure the genetic contribution to odortype. Because odortype stability is a prerequisite for individual recognition under normal behavioral conditions, we investigated whether MHC-determined urinary odortypes of inbred mice can be identified in the face of large diet-induced variation. Mice trained to discriminate urines from panels of mice that differed both in diet and MHC type found the diet odor more salient in generalization trials. Nevertheless, when mice were trained to discriminate mice with only MHC differences (but on the same diet), they recognized the MHC difference when tested with urines from mice on a different diet. This indicates that MHC odor profiles remain despite large dietary variation. Chemical analyses of urinary volatile organic compounds (VOCs) extracted by solid phase microextraction (SPME) and analyzed by gas chromatography/mass spectrometry (GC/MS) are consistent with this inference. Although diet influenced VOC variation more than MHC, with algorithmic training (supervised classification) MHC types could be accurately discriminated across different diets. Thus, although there are clear diet effects on urinary volatile profiles, they do not obscure MHC effects.
Despite their prevalence in nature, echoes are not perceived as events separate from the sounds arriving directly from an active source, until the echo’s delay is long. We measured the head-saccades of barn owls and the responses of neurons in their auditory space-maps while presenting a long duration noise-burst and a simulated echo. Under this paradigm, there were two possible stimulus segments that could potentially signal the location of the echo. One was at the onset of the echo; the other, after the offset of the direct (leading) sound, when only the echo was present. By lengthening the echo’s duration, independently of its delay, spikes and saccades were evoked by the source of the echo even at delays that normally evoked saccades to only the direct source. An echo’s location thus appears to be signaled by the neural response evoked after the offset of the direct sound.
Understanding mechanisms responsible for changes in tooth morphology in the course of evolution is an area of investigation common to both paleontology and developmental biology. Detailed analyses of molar tooth crown shape have shown frequent homoplasia in mammalian evolution, which requires accurate investigation of the evolutionary pathways provided by the fossil record. The necessity of preservation of an effective occlusion has been hypothesized to functionally constrain crown morphological changes and to also facilitate convergent evolution. The Muroidea superfamily constitutes a relevant model for the study of molar crown diversification because it encompasses one third of the extant mammalian biodiversity. Combined microwear and 3D-topographic analyses performed on fossil and extant muroid molars allow for a first quantification of the relationships between changes in crown morphology and functionality of occlusion. Based on an abundant fossil record and on a well resolved phylogeny, our results show that the most derived functional condition associates longitudinal chewing and non interlocking of cusps. This condition has been reached at least 7 times within muroids via two main types of evolutionary pathways each respecting functional continuity. In the first type, the flattening of tooth crown which induces the removal of cusp interlocking occurs before the rotation of the chewing movement. In the second type however, flattening is subsequent to rotation of the chewing movement which can be associated with certain changes in cusp morphology. The reverse orders of the changes involved in these different pathways reveal a mosaic evolution of mammalian dentition in which direction of chewing and crown shape seem to be partly decoupled. Either can change in respect to strong functional constraints affecting occlusion which thereby limit the number of the possible pathways. Because convergent pathways imply distinct ontogenetic trajectories, new Evo/Devo comparative studies on cusp morphogenesis are necessary.
An observation we’ve heard repeated in Obama offices across America, Crandall emphasized how beneficial the contested primary had been for building the foundation for record turnout. “We had real hints of it in the primary,” Crandall said. The first-time voters the campaign energized for the May 6 vote foreshadowed what North Carolina is seeing today. Crandall remembers thinking “these are NOT your typical primary voters.”
By far I see more Obama stickers and signs in my town, including a hilarious “Tina Fey in 2008″ sign next to an Obama sign on one yard in Durham. What have you seen in your area? Take a stab at the proportion of Obama to McCain signs and stickers.
With only a short time to go, the Obama campaign is tightening up with information and statistics, and most of our questions for numbers were met with referrals to already-published newspaper stories. Still, when asked what kinds of numbers the data-obsessed field teams were seeing in the early voting precinct-by-precinct statistics, Cox said “in terms of the early vote, we feel very comfortably that we’re in a good position.”
While there was no way to predict a win, Cox gave off the vibe of a man who was liking what he saw in the numbers. With more votes cast already at the halfway point than in all of 2004, and registered Democrats holding a huge double-digit lead in those ballots, the campaign here is already in full fledged GOTV mode.
It’s a simliar story in North Carolina, which last voted for a Democratic presidential candidate in 1976, when Jimmy Carter was running. A new poll suggests Obama has a six-point lead over McCain, 52 percent to 46 percent. Obama was up by four points in our last poll, conducted last week. “Other polls are showing North Carolina is essentially tied, but our poll shows Obama picking up support among younger voters and the blue-collar segment. Those are two reasons the race in North Carolina has gone from a 49-49 tie in early October to a 52-46 edge for Obama, at least in our results,” Holland said.
Hillary Stookey wouldn’t tell us her age. “60 and holding” and a big smile was all we got. But on her birthday, Hillary Stookey canvassed Wilmington, North Carolina for Barack Obama from 1:30 until 8:00 pm. That’s three hours past the time the Republican office had closed.
I’m told that electoral votes are based on popular votes. Well I’ll be damned. If that’s the case, then I really don’t see what the big whoopie is about people being against electoral votes. Unless the elector doesn’t vote with popular vote. I still don’t believe NC will swing, but the probability becomes a lot larger from a mathematical stand point. The place where it fails is the historical trend data pulls it to the red still from a predictability factor.
According to the State Board of Elections, more than 1.4 million votes had been cast in North Carolina through Oct. 27–23 percent of the 6.2 million registered voters. The figure eclipsed the total 984,000 early votes in the 2004 election–with five days to go.
In heavily Democratic Durham and Orange counties, the numbers were even higher: About one-third percent of voters in Durham and Orange had cast early ballots by Oct. 27.
That turnout jibed with the state elections board report that 58 percent of the early voters statewide are registered Democrats, while just 25 percent are registered Republicans. And the statewide turnout was heavily African-American, the board reported: Black voters accounted for 28 percent of early voters, though they make up 21 percent of the population; they accounted for just 18.5 percent of the turnout four years ago.
In 2008, it’s the Democrats who can’t wait to vote, especially black Democrats, since Obama is on course–the polls say–to become the first African-American president.
New African-American voter registrations comprise 31 percent of the total in the state since the start of the year–271,000 out of 875,000 total new registrants through last Thursday.
Conspicuously absent from the mall voting experience were political candidates, their supporters and party volunteers, who normally greet voters and hand out campaign literature. Security officers have ousted politicians and their supporters attempting to campaign, including one who was warned that his car would be towed. Confusion surrounding mall voting rules has allegedly prompted at least one election worker to enforce policies that contradict election law. Outcry over the policy prompted picketing and a boycott effort by critics who say it violates the First Amendment.
This year marks North Carolina’s first experiment with mall voting. As officials ponder whether that experiment is successful, they should also consider whether the promise of higher turnout trumps the right of voters to receive information–and the right of candidates to provide it.
Last year, the state legislature voted to allow non-public buildings to serve as early voting sites–a move Wake County election officials clamored for. The goal was to make early voting more convenient and get more voters to the polls, especially in areas where there are few public buildings that can absorb thousands of voters over the course of two weeks.
The irony, of course, is that it only matters in America. The day the bad news about Senator Johnny began to make the rounds, we were eating lunch with a Chilean businessman, husband of an old friend of my wife’s. “In Chile, anywhere in Europe or Latin America, no one would have known about this,” he said. “And if they knew, no one would care.”
“What’s the big deal?” asked the Chilean, in the presence of his wife. But Edwards was no Candide. He knew what we all know about America’s double standard. Our private morals might make rabbits blush, but the standards we impose on public servants have changed very little since the Mayflower dropped anchor. Nowhere else in the world is there such a hypocritical discrepancy between private and public morality. Edwards knew the risk and took it. That’s where hubris comes in, as a sense of entitlement and immunity that comes with uncommon success.
I admit to a certain sympathy for this ruined man, this outcast. I don’t make political contributions, but I wouldn’t be surprised if my wife, who knows Edwards’ wife and is not bound by my scruples, has sent a check or two in their direction. I liked many of the things Edwards was saying during the primaries; some of them have even more bite now that corporate avarice and irresponsibility have brought the American economy to its knees.
I met him a couple of times. He had the nerve, rare among North Carolina politicians with more than local ambitions, to show up at holiday parties for the staff of the notorious Independent Weekly, once denounced by a Republican as “Left-wing attack media from hell.” Last spring I sat next to him at a small fund-raising luncheon and confess that I was unnerved by his boyish appearance–he could pass for 35 in the right light–and surreptitiously inspected his profile for signs of the plastic surgeon’s hand, or the hair-restorer’s.
In the end, I could not make it to the Obama rally in Raleigh, but other bloggers did.
If I did, I would have been one of the 28000 people to be the first to hear the “peanut butter and jelly” thing:
I think this is great framing – getting your mind back to the time you were a child. Who do you want to play with: a kid who shares his toys, or the old man who shouts “Get off my lawn!”? Do you prefer a parent who beats you every day, or a parent who teaches you how to get along with others?
Ed Cone interviews the security guru Bruce Schneier about voting machines:
There are a couple of reasons that things like automatic teller machines and gas pumps are more secure. The first one is, there’s money involved. If someone hacks an ATM, the bank loses money. The bank has a financial interest in making those ATMs secure. If someone hacks a voting machine, nobody loses money. In fact, half the country is happy with the result. So it’s much harder to get the economic incentives aligned.
The other issue about voting machines is that ballots are secret. A lot of the security in computerized financial systems is based on audits, based on being able to unravel a transaction. If you go to an ATM and you push a bunch of buttons and you get out ten times the cash you were supposed to, that’s a mistake, but that mistake will be caught in audit, and likely, you will be figured out as the person who got the money by accident, and it will be taken out of your account. Because ballots are secret, a lot of the auditing tools that we in the community have developed for financial systems don’t apply.
This is interesting:
But voter behavior is only part of the change drawing political attention to North Carolina. Presidential contenders are increasing their focus here because the state has more clout on the national stage than it did as recently as the 1980s. The same population boom that has helped alter the political landscape in North Carolina has also led to an increase in the number of electoral votes the state is allotted in the presidential election. While some states (such as Illinois and Pennsylvania) have been given fewer and fewer electoral votes since 1980, North Carolina has been on the rise. North Carolina now has 15 electoral votes, up from 13 in 1988. While that is fewer than Ohio’s 20, it is more than some of the other traditional swing states such as Missouri, which has 11.
In fact, only eight states have more electoral votes than North Carolina (New Jersey and Georgia are tied with North Carolina at 15 votes). In an election where only 270 electoral votes are needed to win, the Tarheel State matters.
The Great Limbaugh Con by Charles M. Kelly, published in 1994, is even more current and up-to-date than it was then. And it is not really about Limbaugh himself – he serves only as a starting point. There are many Limbaughs out there now who parrot the same stuff and what he pioneered in the early 1990s is now a big industry for the Right.
Furthermore, some of the right-wing rhetoric that Rush invented is now not just a standard GOP advertising lingo, but also deeply ingrained in the nation’s psyche and will take a lot of effort to neutralize. The book describes, for instance, exactly how Limbaugh demonized Hillary Clinton as early as 1991., and how some of the same tropes about her survive till today and made her presidential bid just that much harder.
But what is most important about the book is that Kelly uses Limbaugh’s rhetoric to discuss some of our erroneous preconceptions about the world, especially economics and how it works. For instance, Chapter 6 analyzes the phrase “trickle-down economics”, and Chapter 12 explains how liberals and conservatives have a very different definition of the word “work”. If the two sides of the political spectrum use different definitions of the same word, then the target audience – the low-information independent voters – will be confused. Or, depending how it is framed, the audience will understand the message to use one definition, while it really uses the other – the basis for Orwellian spin of the Right.
As far as I know, this is the first book that seriously talks about the role of language and ‘frames’ (though the word never appears in the text – too early in history for that) in the modern American politics. And it does it well.
You can read the entire book online on Google Books or buy yourself a cheap used copy on amazon.com. Even if you disagree with Kelly on some details, it will make you think differently and it will make you think next time you hear a right-wing hack in the media use some of those phrases – they do not mean what you think they mean.
“Would you get on a plane with a pilot who has never flown?” the announcer asks. Yes, if the only other option is the guy who has proven repeatedly that he cannot keep his plane in the air:
(cartoon from The Star)
I and the Bird #87 is up on Ecobirder
Tangled Bank #117 is up on Neural Gourmet
Gene Genie #39 is up on Genetics & Health
The new Carnival of Education is up on Leading From The Heart
Change of Shift, Volume 3, Issue 9 is up on This crazy mircale called Life
Carnival of Homeschooling #148 is up on Why Homeschool
No man will ever bring out of the Presidency the reputation which carries him into it…To myself, personally, it brings nothing but increasing drudgery and daily loss of friends.
- Thomas Jefferson
Far more important is this: Science is a way of governing, not just something to be governed. Science offers a methodology and philosophy rooted in evidence, kept in check by persistent inquiry, and bounded by the constraints of a self-critical and rigorous method. Science is a lens through which we can and should visualize and solve complex problems, organize government and multilateral bodies, establish international alliances, inspire national pride, restore positive feelings about America around the globe, embolden democracy, and ultimately, lead the world. More than anything, what this lens offers the next administration is a limitless capacity to handle all that comes its way, no matter how complex or unanticipated.
Sen. Obama’s embrace of transparency and evidence-based decision-making, his intelligence and curiosity echo this new way of looking at the world. And that is what we should be weighing in the voting booth. For his positions and, even more, for his way of coming to them, we endorse Barack Obama for President of the United States.
Let’s look at few other sessions on the Program – on topics that are rarely seen at either tech or science meetings:
Art and science — online and offline:
This session is moderated by Jessica Palmer and Glendon Mellow:
Art is not just illustration. And it is not the opposite of science (“Two Cultures”). How can the two work together and help each other?
Why is History of Science important for scientists? How to blog about it. How does Open Access and the Web in general (Google Books in particular, for example) help/hinder the work of professional historians of science?
Science fiction has inspired curiosity and enthusiasm in generations of children. How can science bloggers draw on SF’s power to entertain and educate? What science can we find in fiction beyond the old multi-page calculations of rocket trajectories? What does the practice of science look like in SF? In the past, scientists like Asimov and Clarke were the ones writing SF. Who’s producing the good stuff these days, and what makes a good bad example? Many modern SF writers blog too. What opportunities exist for cross-promotion and educating the writers? And which bloggers are already doing it all right?
We have got but one life here. It pays, no matter what comes after it, to try and do things, to accomplish things in this life and not merely to have a soft and pleasant time.
- Theodore Roosevelt
Here is the fourth interview in the series on Miss Baker’s Biology class blog – Samantha’s interview with Erica Tsai.
Previously in this series:
ScienceOnline09 – an interview with…me!
ScienceOnline09 – an interview with Eric Roston
ScienceOnline09 – an interview with Clinton Colmenares
There are 25 new articles in PLoS ONE today. 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:
If you are coming to ScienceOnline09, it’s time for you to reserve a hotel room, find a room-mate if you want, and organize your travel – do all of that here.
If you’ll be in town on Thursday evening, please sign up for the Early Bird Dinner so we can figure out the numbers and reserve the appropriate amount of space at Town Hall Grill.
Web journals ‘narrowing study’ by Linda Nordling:
Online publishing has sparked an explosion in the number of places where academics can showcase their work. Today, no field of study is too obscure to have its own dedicated title. But have platforms such as the Journal of Happiness Studies or Archaeoastronomy and Ethnoastronomy News made academic publishing more democratic?
Far from it, says Alex Bentley, an anthropologist at Durham University. “We’re just producing so much wordage that nobody has time to read anything. It makes academic publishing, and even science itself, a bit like trying to get hits on blogs or try to make yourself the Britney of science.”
Although the internet puts information at our fingertips, we have no time to trawl it. As a result, we trust sites like Digg.com to guide us through the information jungle. This phenomenon is called “herding” by economists, who use it to explain, say, fashion trends and stockmarket bubbles.
SEO can, however, make articles tedious to read. A headline that once read “Of mice and men” for a study that discussed the suitability of mice when testing drugs for humans might now say “Suitability of mice for in vivo drug testing” or something even more jargon-laden.
But those who fear an end to eloquence in research articles should stop worrying, says Bora Zivkovic, community manager at open access publisher PLoS One and author of the blog Around the Clock (http://scienceblogs.com/clock). According to him, today’s dull SEO writing is a passing phase. The open access movement will tear down the walls between academic publishing and the rest of the internet, making eye-catching titles not only optional but downright necessary.
“Titles that go ‘the effect of x and y is z’ are perfect for machines right now, but the machines are getting better and advances in technology will mean that search engines are going to find the important keywords in the text,” he says. But catchy titles and readable writing will be necessary to draw in lay people, journalists and bloggers, who will have a much bigger role in determining what research is read. “Google loves blogs, so if your work is being blogged about, it will generate interest in your paper.”
“Google Scholar initially wasn’t very good, but now it is,” he adds. “It covers more of the literature than Web of Science [another, older academic search engine].” However, the big difference about Google Scholar is that you don’t have to be a rocket scientist to use it, he says. It is intuitive and will lead you to a free version of an article if one exists.
As search engines get more sophisticated, the technology will hopefully result in better ways of measuring research quality, says Bentley. “Citations have always been important. But they have never been as ridiculously important as they are now,” he says. “I think that people are recognising this and that we will see more evaluation mechanisms that are based on actually reading the articles.”
Approximately two-thirds of Americans voting in the November Presidential election will cast their votes on paper ballots. How can voters be assured their votes are counted and kept private?
A historian at the University of Liverpool has uncovered extensive archive material detailing the activities of the ‘scuttlers’ – one of Britain’s earliest youth cults.
Youth in their late teens who live in poor neighbourhoods are four times more likely to attempt suicide than peers who live in more affluent neighbourhoods, according to a new study from Canada’s Universite de Montreal and Sainte-Justine Hospital Research Center, as well as Tufts University in the U.S. The researchers also found youth from poor neighbourhoods are twice as likely to report suicidal thoughts.
In a time lacking in truth and certainty and filled with anguish and despair, no woman should be shamefaced in attempting to give back to the world, through her work, a portion of its lost heart.
- Louise Bogan
On the 13th of October in 2003, with the first issue of PLoS Biology, the Public Library of Science realized its transformation from a grassroots organization of scientists to a publisher. Our fledgling website received over a million hits within its first hour, and major international newspapers and news outlets ran stories about the journal, about science communication in general, and about our founders–working scientists who had the temerity to take on the traditional publishing world and who pledged to lead a revolution in scholarly communication (see, for example, [1,2]). It was not only scientists and publishers who wanted to see what this upstart start-up was doing; we had somehow captured the imagination of all sections of society. Not all of the reactions were positive, of course, especially from those in the scientific publishing sector with a vested interest in maintaining the subscription-based system of journal publishing. But thanks in no small part to the efforts of the founders–Pat Brown, Mike Eisen, and Harold Varmus–and an editorial team that included a former editor of Cell and several from Nature, our call for scientists to join the open-access revolution [3,4] did not go unheeded. Five years on, the publishing landscape has changed radically. How much have PLoS Biology and PLoS contributed to that change and what might the future hold for us and for publishing?
PLoS Biology is the flagship journal that gave PLoS its initial credibility as a publisher, paving the way for the equally successful launch of the flagship medical journal PLoS Medicine, four leading subject-specific journals (PLoS Computational Biology, PLoS Genetics, PLoS Pathogens and PLoS Neglected Tropical Disease), and its most radical, interdisciplinary peer-reviewed upstart, PLoS ONE
Just got this e-mail earlier today:
This Wednesday, October 29th, please join Barack Obama in Raleigh, where he will talk about his vision for creating the kind of change we need.
Early Vote for Change Rally
with Barack Obama
300 North Salisbury Street
Raleigh, NC 27603
Wednesday, October 29th
Doors Open: 10:00 a.m.
Pre-program Begins: 11:15 a.m.
This event is free and open to the public. Tickets are not required; however, an RSVP is strongly encouraged.
For security reasons, do not bring bags or umbrellas. Please limit personal items. No signs or banners allowed.
He is finally coming close enough for me to consider going to see him live (ah, the beauty of living in a battleground state – who would have thunk NC would be one!). I am thinking about bringing the kids along (they want to go), but I am not sure that the venue is large enough for everyone who will probably want to be there. Four years ago, when Kerry picked Edwards as running mate they came to Raleigh and used a bigger venue on the NCSU campus – it was full (25,000-40,000 people, depending who counted). This year, the crowd should be at least twice as big – how about 100,000? I have no idea how that many people will fit downtown. And where should one park? Probably far away, then walk or take a bus.
Any folks from Chapel Hill, Carrboro or Durham interested in car-pooling?
The Feminist Press with IBM have just launched UnderTheMicroscope.com, a new site to involve young women in science and to encourage them to pursue careers in science, technology, engineering and math. The site is part of the Women Writing Science, a project initiated by The Feminist Press at the City University of New York and funded by the National Science Foundation.
The site features personal stories of women scientists, role models, and mentors; tips for parents and teachers; links to related women and science sites; videos; and networking. Some of these features are available now, and others will come later this year as noted in the press release below
On the website they have also started a promising-looking blog.
There are 13 new articles published Friday night and 10 new articles tonight in PLoS ONE today. 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:
Implication of the F-Box Protein FBXL21 in Circadian Pacemaker Function in Mammals:
In mammals, the circadian clock relies on interlocked feedback loops involving clock genes and their protein products. Post-translational modifications control intracellular trafficking, functionality and degradation of clock proteins and are keys to the functioning of the clock as recently exemplified for the F-Box protein Fbxl3. The SCFFbxl3 complex directs degradation of CRY1/2 proteins and Fbxl3 murine mutants have a slower clock. To assess whether the role of Fbxl3 is phylogenetically conserved, we investigated its function in the sheep, a diurnal ungulate. Our data show that Fbxl3 function is conserved and further reveal that its closest homologue, the F-Box protein Fbxl21, also binds to CRY1 which impairs its repressive action towards the transcriptional activators CLOCK/BMAL1. However, while Fbxl3 appears to be ubiquitously expressed, Fbxl21 expression is tissue-specific. Furthermore, and in sharp contrast with Fbxl3, Fbxl21 is highly expressed within the suprachiasmatic nuclei, site of the master clock, where it displays marked circadian oscillations apparently driven by members of the PAR-bZIP family. Finally, for both Fbxl3 and Fbxl21 we identified and functionally characterized novel splice-variants, which might reduce CRY1 proteasomal degradation dependent on cell context. Altogether, these data establish Fbxl21 as a novel circadian clock-controlled gene that plays a specific role within the mammalian circadian pacemaker.
Specification of primordial germ cells (PGCs) results in the conversion of pluripotent epiblast cells into monopotent germ cell lineage. Blimp1/Prmt5 complex plays a critical role in the specification and maintenance of the early germ cell lineage. However, PGCs can be induced to dedifferentiate back to a pluripotent state as embryonic germ (EG) cells when exposed to exogenous signaling molecules, FGF-2, LIF and SCF. Here we show that Trichostatin A (TSA), an inhibitor of histone deacetylases, is a highly potent agent that can replace FGF-2 to induce dedifferentiation of PGCs into EG cells. A key early event during dedifferentiation of PGCs in response to FGF-2 or TSA is the down-regulation of Blimp1, which reverses and apparently relieves the cell fate restriction imposed by it. Notably, the targets of Blimp1, which include c-Myc and Klf-4, which represent two of the key factors known to promote reprogramming of somatic cells to pluripotent state, are up-regulated. We also found early activation of the LIF/Stat-3 signaling pathway with the translocation of Stat-3 into the nucleus. By contrast, while Prmt5 is retained in EG cells, it translocates from the nucleus to the cytoplasm where it probably has an independent role in regulating pluripotency. We propose that dedifferentiation of PGCs into EG cells may provide significant mechanistic insights on early events associated with reprogramming of committed cells to a pluripotent state.
Previous work by our group has shown that the scaling of reach trajectories to target size is independent of obligatory awareness of that target property and that “action without awareness” can persist for up to 2000 ms of visual delay. In the present investigation we sought to determine if the ability to scale reaching trajectories to target size following a delay is related to the pre-computing of movement parameters during initial stimulus presentation or the maintenance of a sensory (i.e., visual) representation for on-demand response parameterization. Participants completed immediate or delayed (i.e., 2000 ms) perceptual reports and reaching responses to different sized targets under non-masked and masked target conditions. For the reaching task, the limb associated with a trial (i.e., left or right) was not specified until the time of response cuing: a manipulation that prevented participants from pre-computing the effector-related parameters of their response. In terms of the immediate and delayed perceptual tasks, target size was accurately reported during non-masked trials; however, for masked trials only a chance level of accuracy was observed. For the immediate and delayed reaching tasks, movement time as well as other temporal kinematic measures (e.g., times to peak acceleration, velocity and deceleration) increased in relation to decreasing target size across non-masked and masked trials. Our results demonstrate that speed-accuracy relations were observed regardless of whether participants were aware (i.e., non-masked trials) or unaware (i.e., masked trials) of target size. Moreover, the equivalent scaling of immediate and delayed reaches during masked trials indicates that a persistent sensory-based representation supports the unconscious and metrical scaling of memory-guided reaching.
Sodalis glossinidius, a maternally transmitted bacterial endosymbiont of tsetse flies (Glossina spp.), uses an acylated homoserine lactone (AHL)-based quorum sensing system to modulate gene expression in accordance with bacterial cell density. The S. glossinidius quorum sensing system relies on the function of two regulatory proteins; SogI (a LuxI homolog) synthesizes a signaling molecule, characterized as N-(3-oxohexanoyl) homoserine lactone (OHHL), and SogR1 (a LuxR homolog) interacts with OHHL to modulate transcription of specific target genes. We used a tiling microarray to analyze the S. glossinidius transcriptome in the presence and absence of exogenous OHHL. The major finding is that OHHL increases transcription of a large number of genes that are known to be involved in the oxidative stress response. We also show that the obligate symbiont of the rice weevil, Sitophilus oryzae (SOPE), maintains copies of the quorum sensing regulatory genes that are found in S. glossinidius. Molecular evolutionary analyses indicate that these sequences are evolving under stabilizing selection, consistent with the maintenance of their functions in the SOPE symbiosis. Finally, the expression studies in S. glossinidius also reveal that quorum sensing regulates the expression of a cryptic, degenerate gene (carA) that arose from an ancient deletion in the last common ancestor of S. glossinidius and SOPE. This oxidative stress response is likely mandated under conditions of dense intracellular symbiont infection, when intense metabolic activity is expected to generate a heavy oxidative burden. Such conditions are known to arise in the bacteriocytes of grain weevils, which harbor dense intracellular infections of symbiotic bacteria that are closely related to S. glossinidius. The presence of a degenerate carA sequence in S. glossinidius and SOPE indicates the potential for neofunctionalization to occur during the process of genome degeneration.
A dramatic expansion of road building is underway in the Congo Basin fuelled by private enterprise, international aid, and government aspirations. Among the great wilderness areas on earth, the Congo Basin is outstanding for its high biodiversity, particularly mobile megafauna including forest elephants (Loxodonta africana cyclotis). The abundance of many mammal species in the Basin increases with distance from roads due to hunting pressure, but the impacts of road proliferation on the movements of individuals are unknown. We investigated the ranging behaviour of forest elephants in relation to roads and roadless wilderness by fitting GPS telemetry collars onto a sample of 28 forest elephants living in six priority conservation areas. We show that the size of roadless wilderness is a strong determinant of home range size in this species. Though our study sites included the largest wilderness areas in central African forests, none of 4 home range metrics we calculated, including core area, tended toward an asymptote with increasing wilderness size, suggesting that uninhibited ranging in forest elephants no longer exists. Furthermore we show that roads outside protected areas which are not protected from hunting are a formidable barrier to movement while roads inside protected areas are not. Only 1 elephant from our sample crossed an unprotected road. During crossings her mean speed increased 14-fold compared to normal movements. Forest elephants are increasingly confined and constrained by roads across the Congo Basin which is reducing effective habitat availability and isolating populations, significantly threatening long term conservation efforts. If the current road development trajectory continues, forest wildernesses and the forest elephants they contain will collapse.
Here is the third interview in the series on Miss Baker’s Biology class blog – William’s interview with Clinton Colmenares.
Previously in this series:
ScienceOnline09 – an interview with…me!
ScienceOnline09 – an interview with Eric Roston
GOODVOTE.ORG gives advice and collects media coverage of potential voter suppression:
GOODVOTE.ORG is a group of volunteers from the technology community and blogosphere who simply want the will of the voters to be reflected in the result of the 2008 election. Our only purpose is to make sure that when legitimate voters are challenged they know who to turn to for help.
The sum of the expertise of the people in the audience is greater than the sum of expertise of the people on stage.
But, there will be a few exceptions. First, there will be several quick demos on Sunday morning.
But also, four of the sessions are meant to be more in a workshop mode, where we expect that the people on stage will actually have greater expertise than people in the audience and that the reason people will choose to attend these sessions will be to learn the skills they do not yet possess. But the audience should prepare nonetheless, at least by helping the session leaders by editing the session wiki-pages and adding questions and ideas. These sessions are:
Blogging101 – how to get started:
This session will be moderated by Pal,MD:
You have heard about blogs, perhaps read some blogs, have spent a whole day yesterday hearing about how great blogs are, so now you have finally decided to try to write one yourself. Bring your laptop and we’ll help you, step-by-step, start your own WordPress.com blog during this session.
You have been blogging for a while, but want to make it better – we’ll help you choose and install applications and widgets, help you make your blog look better, be more functional and, hopefully, more popular.
What does it take to make your blog better?
Tell me what you want to know. Let’s get semantics out of the way. What do you mean by “better”? Prettier? Easier to navigate? More visibility in search engines? More relevant content?
Let’s discuss all these and more. What ideas do you have for our session?
Take this workshop by a couple of professional artists and get started on illustrating your blog with your own art.
Not just text – image, sound and video in peer-reviewed literature:
This session is moderated by Moshe Pritsker and Apryl Bailey:
Moving publishing from paper to the Web will change the format of the scientific paper. Things that are impossible to do in print are easy online. What are some of the first strides and what is the future of multimedia as an integral part of a scientific report?
Tamara Fletcher is currently studying science communication at the University of Queensland. As part of her course she is conducting a research project under the supervision of Dr Joan Leach from the School of English, Media Studies and Art History and she needs your help:
The form of the project is a short survey and analysis of scientists’ perceptions of scientific blogging. As your participation in science blogging suggests you are aware, it is important to explore as blogging has the potential to act as a medium for two-way dialogue between scientists and the public, without intermediaries such as professional communicators or journalists, and is an ever growing area of communication
Many possible factors contribute to how blogging is perceived. The way in which scientists perceive science blogs the will ultimately determine the use of this medium as a mainstream tool of science communication.
As such I am seeking science bloggers (as well as academic staff and graduate students in various schools in science at UQ) to complete the short survey, at the following url:
Its really important to be able to compare and contrast bloggers and non-bloggers, and as such I would be especially grateful to anyone at scienceblogs.com who can give up <10 minutes of their time to complete the survey.
So, if you are a science blogger, please do the survey – it is really short and fast. Just click on “scienceblogs.com” when given the choices at the beginning.