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New and Exciting in PLoS ONE

There are 15 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. You can now also easily place articles on various social services (CiteULike, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week - you go and look for your own favourites: Web Queries as a Source for Syndromic Surveillance: In the field of syndromic surveillance, various sources are exploited for outbreak detection, monitoring and prediction. This paper describes a study on queries…

Darwin: Discovering the Tree of Life

According to an opinion poll from late 2004, only 13% of all Americans think that humans evolved without any guidance from an all-powerful divine being. In view of this surprising lack of knowledge, I think it is essential that the public is presented with more details about evolution, and this is exactly what this book strives to accomplish. To celebrate the 200th anniversary of Charles Darwin's birth on 12 February 2009, Niles Eldredge, curator of the American Museum of Natural History, designed a wonderful traveling exhibition that documents and discusses the development of Darwin's…

Donors, Disasters, and Disease

When severe flooding in Pakistan left millions of people without food, shelter, and water, I wrote a post wondering why that disaster was getting less attention than Haiti's earthquake. I suspected the gradual nature of the disaster was part of the problem, and commenters had additional suggestions, ranging from Haiti's closeness to the US to the US public's overall view of Pakistan as a nation. Last week, The New York Times' Lydia Polgreen put some numbers on the Haitian earthquake vs. Pakistani floods comparison and delved into reasons for the disparity: In all, $3.4 billion has been…

CSI: Durham

As anybody who has read my comments on basketball knows, I have an intense dislike of the Duke men's basketball team, mostly due to their fans, who combine the arrogance typical of fans of a dominant program with a sort of snobbery regarding their own class and cleverness. This is particularly aggravating given the institutional contrast between Duke's status as an elite private university and their main competitors' status as larger, more diverse public institutions-- it pushes my class consciousness buttons, and makes their antics all the more annoying. In a weird way, this has prevented me…

Senior on Lapham and Blumenthal

Jennifer Senior has this essay, reviewing new anti-Bush books by Lewis Lapham and Sidney Blumenthal, in a recent issue of The York Times Book Review. Her verdict? Now, just in time for the midterm elections, the collected columns of two passionate Bush critics, Lewis H. Lapham and Sidney Blumenthal, are landing in bookstores. Both, to varying degrees, suffer from a distorting case of Bush-phobia. Of Lapham specifically she writes: People who are serious about politics don't just preen. They report, explain, explore contradictions, struggle with ideas, maybe even propose suggestions. If…

Climate Change, Sea Level Rise, and The Biggest Blogathon Evah!

There is a relationship between how much CO2 is in the atmosphere and sea level. More CO2 means a warmer atmosphere and that means less long term (glacial) ice and that means more sea water. Also, a warmer planet means the ocean water is warmer, and thus it expands, and that also contributes to sea level rise. However, there is something of a falsehood generated when we read estimates of sea level rise. The straight forward link between CO2 and sea level (via heating oceans and melting ice) leads to estimates that are very small for sea level rise. We see things like “1.8 mm per year” which…

Ruin On An Islet

Christian Loven's plan of Landsjö Islet with letters marking on-going fieldwork. Landsjö castle is on a high islet in the lake next to the modern manor house. Nobody ever goes there. The ruins are covered by vegetation and they're in bad shape: only along the western side of the islet do they rise even a metre above the rubble and accumulated forest mulch. Visible is a 59-metre N-S stretch of perimeter wall with a preserved corner at either end, and a shorter W-E stretch of perimeter wall from the south-western corner. Along the inside of the visible wall are vague suggestions of two…

May Pieces Of My Mind #1

Learned a joke from a German on Twitter. It works in English as well. Q: What do you call a Nazi sitting on a high voltage cable? A: National resistance. Played "Hoochie Coochie Man" to Jrette to explain where the anonymous piano riff she uses as a ring tone comes from. And mightily did she groove to it. My wife asks me how come I'm familiar with a certain sociologist she's reading for her second degree. "Because I have annoying colleagues who cite sociologists needlessly all the time." When I copy or move information from one document to another, I usually put the goal document to the right…

GMO Virus: Long-term success treating Hemophilia B

One of my favorite stories is the tale of a GMO virus deployed to treat Hemophilia B: Gene therapy for Hemophilia B ... Hemophilia B is a disease in males caused by point mutations/deletions/etc in the clotting Factor IX gene. If you dont make Factor IX, you wont clot properly, and will have all of the health issues we associate with hemophilia. ... The scientists in this paper took six Hemophilia B patients, and treated them with an Adeno-Associated Virus-8 (two at low, medium, and high doses of virus) that contained a functional copy of the Factor IX gene. Four of them of them bumped up…

A new, out-of-left-field way to fight HIV. Maybe?

New, weird, out-of-left-field, ideas-- we need them to stop HIV. This one makes sense, in retrospect, but I wouldnt have thought to try what these folks did: Targeting α4β7 integrin reduces mucosal transmission of simian immunodeficiency virus and protects gut-associated lymphoid tissue from infection Background info: HIV loves to rip through CD4+ T-cells in gut-associated lymphoid tissue. Early in infection, HIV tears those cells up, and anything HIV doesnt kill, it digs in as a latent reservoir to pop out more babby viruses later. Doesnt matter if you ultimately take anti-retrovirals, the…

It Figures: The Historical Aesthetics of Scientific Publishing

Steve Hsu has a post comparing his hand-drawn diagrams to computer-generated ones that a journal asked for instead: He's got a pretty decent case that the hand-drawn versions are better. Though a bit more work with the graphics software could make the computer ones better. This reminded me, though, of something I've always found interesting about scientific publishing, namely the evolution in the use of figures through the years. Whenever I need to do literature searching, I always suspect you could guess the approximate date of a paper's publication by looking at the figures. If you go back…

The Giants' Shoulders # 8

"The Giants' Shoulders" is a monthly science blogging event, in which authors are invited to submit posts on "classic" scientific papers. Information about the carnival can be found here. The last Giants' was hosted at The Questionable Authority, here. The next issue will be hosted at The Evilutionary Biologist: All Science, All The Time, which resided here. Since this is Darwin Month in Darwin Year and almost, indeed, Darwin Day, we start with ... Paleontology. We'll get to Darwin at the end. Early palaentologists and the Giant killer lungfish from Hell as well as the Revenge of…

My Silly Cat

My cat, Emily, tends to get a bit sulky when I leave her for long periods of time. So when I returned home from New York the other day, having been gone for a week, I was not surprised when she did not greet me at the door. Par for the course, I thought. She'll appear on her own in five to ten minutes. When fifteen minutes went by and she still had not appeared I decided to go hunting. My first pass around the house was unsuccessful. Emily was not in any of her usual hiding places. Then I heard meowing. It was weird since it sounded like it was coming from directly underneath the floor…

Teacher Self Management vs. Going to the Dark Side

The New York Times has an article about the opening of a teacher-run school in The City. It sounds like an interesting experiment: Shortly after landing at Malcolm X Shabazz High School as a Teach for America recruit, Dominique D. Lee grew disgusted with a system that produced ninth graders who could not name the seven continents or the governor of their state. He started wondering: What if I were in charge? Three years later, Mr. Lee, at just 25, is getting a chance to find out. Today, Mr. Lee and five other teachers -- all veterans of Teach for America, a corps of college graduates who…

Amazing Laser Application 3: Lunar Laser Ranging!

What's the application? Measuring the distance from the Earth to the Moon by bouncing a laser off one of the retro-reflector arrays left there by the Apollo missions. What problem(s) is it the solution to? 1) "How does the distance from the Earth to the Moon vary over time due to things like tidal drag?" 2) "Does the strength of gravity change over time?" 3) "What can we do with a laser to really cheese off people who think the Moon landings were fake?" How does it work? This concept is simplicity itself. You simply point a laser at the Moon, fire off a short pulse of light, and wait for it…

Rover Ants (Brachymyrmex patagonicus), an emerging pest species

As if we didn't already have enough pest ants to worry about, here is a relatively new one. The rover ant Brachymyrmex patagonicus, a tiny South American species, has been working its way under the radar across the southern United States. Its presence is now large enough that pest control companies are reporting a sudden increase in requests. According to gardeners I've talked to, these ants emerged in huge numbers here in Tucson about 5 years ago. Given the interest in this species, I thought I'd post a summary of what we know of this emerging pest and how to reliably identify it.…

Microraptor - the dinosaur that flew like a biplane

Many of us believe dinosaurs to be extinct but in truth, they surround us every day. All the world's birds, from the pigeons of our cities to the gulls of our seasides, are descended from dinosaurs, and modern science now classifies the birds with their long-dead kin. The gulf between dinosaurs and modern birds may seem huge, but the discovery of several feathered dinosaurs are seriously blurring the line between the two. And now, new research on the feathered dinosaur Microraptor reveals that birds may have evolved from dinosaur ancestors that flew not on two wings, but on four. The link…

Pollution and Human Life in West Virginia

This is a first-person commentary by Rebecca Harding Davis on life at the Iron Mills of West Virginia. I paste it below for your reading. Incidentally, it's from 1861. A cloudy day: do you know what that is in a town of iron works? The sky sank down before dawn, muddy, flat, immovable. The air is thick, clammy with the breath of crowded human beings. It stifles me. I open the window, and, looking out, can scarcely see through the rain the grocer's shop opposite, where a crowd of drunken Irishmen are puffing Lynchburg tobacco in their pipes. I can detect the scent through all the foul…

Prehistoric carving is oldest known figurative art

Image by Nicholas Conard This sculpture may look a little bit like a roast chicken, but don't let that distract you - it's an incredibly important artistic find. This small figurine is arguably the oldest representation of the human body yet discovered. The figure is clearly human, with short arms ending in five, carefully carved fingers, and a navel in the right position. But its most obvious features show that it depicts a woman, and very explicitly at that. She has large protruding breasts, wide hips and thighs, accentuated buttocks and pronounced vulva between her open legs. In contrast…

Babies' gestures partly explain link between wealth and vocabulary

Babies can say volume without saying a single word. They can wave good-bye, point at things to indicate an interest or shake their heads to mean "No". These gestures may be very simple, but they are a sign of things to come. Year-old toddlers who use more gestures tend to have more expansive vocabularies several years later. And this link between early gesturing and future linguistic ability may partially explain by children from poorer families tend to have smaller vocabularies than those from richer ones. Vocabulary size tallies strongly with a child's academic success, so it's striking…

Borges was a Webelo (and Other Book Jokes)

Happen you to need a diversion, check out The McSweeney's Joke Book of Book Jokes, why not? It's new, it's got about 70 stories (or entries, more properly), it has a picture of a chicken smoking a cigarette on the cover, and if you're not overwhelmed by the end, it even comes with a story I contributed about Borges. Come on, people've been griping for years about the dearth of Borges jokes. It's time. It's here. Admittedly, I would consider the contribution more melancholy than funny. More of a meditation or lament. About Borges. From his time in the Cub Scouts. He made it to Webelo.…

Hot cross-species toad sex

Hybrids are sort-of a mystery in evolutionary biology. In the strictest sense, they shouldn't exist because the offspring are often sterile or reproductively impaired. It is to a species evolutionary benefit to limit the number of hybrid offspring in most cases, so biologists often attribute hybrids to mistakes on the animal's part. The animal mistook a similar species for one of its own. However, Karin Pfennig, publishing in Science, shows that under some circumstances animal's will choose to mate across-species. Pfennig looked at two species of frogs from the American Southwest: Spea…

Why does the Catholic church allow Bill Donohue to speak for them?

This is a real mystery. Donohue is an angry guy with a fax machine who gets donations from affronted Catholics, which is nothing the church can do about, obviously…but he also pretends to be a defender of Catholicism while having no standing with the church and while making the most outrageous claims. You'd think someone in the hierarchy would take a moment to mention to journalists that the crazy ranting guy does not speak for them. I guess maybe the old guard thinks he does a good job representing their views, which makes him even worse. Donohue is waxing indignant again about church…

What a mess we've made! The 2008 International Coastal Cleanup Report

The results are in from the 2008 International Coastal Cleanup, and boy, do we make a mess of our oceans and beaches. The Ocean Conservancy had almost 400,000 volunteers worldwide picking up trash on land and off shore for the annual event. Last year, they picked up 6.8 million - that's 6,800,000 - pounds of trash in 104 countries (including 42 of US states). That's about 17 lbs of trash per volunteer! What they found was absolutely appalling. 3,216,991 cigarette butts, 1,377,141 plastic bags, and 942,620 food wrappers were littering the world's beaches and oceans. Worldwide, 11,439,086…

Atheist rights

Hank Fox at Unscrewing the Inscrutable has posted an Atheist Declaration of Rights. With two minor changes I reprint it below the fold. Nonreligious Declaration of Rights 1. Freedom from Fear and Hate: In every part of a secular society, the nonreligious have the right to live free of fear for their personal safety, their homes, pets and possessions. The nonreligious have the right to be safe from public hate speech and vilification. 2. Freedom of Speech: The nonreligious have the right to freely speak of atheism in public, or to publicly display characteristic messages or symbols, without…

Possible herbal medicine contribution to mushroom poisoning recoveries

A thoughtful reader of mine and Kevin MD's just brought to my attention the plight of six members of a California family who apparently ingested Amanita phalloides (deathcap) mushrooms following a New Year's Day outing. Jondi Gumz of the Santa Cruz Sentinel reported today on the circuitous route the attending physicians took to obtain a source and FDA emergency approval to try an intravenous formulation of an herbal medicine from Europe. Using Google Scholar, a search engine of scholarly literature, he [Dr Todd Mitchell] found a promising avenue of treatment: Extract from milk thistle, a…

Do kids recognize emotion in music?

Music can be used to convey a range of emotion, from sadness to happiness, from anger to fear. We use music to help fall asleep at night, and to wake up in the morning. Its effect on our mood may be enough to improve our performance on a range of intellectual tasks. But where do these effects come from? Are we born with an association between music and emotion, or does it develop as we grow older? Studies have found some evidence for an appreciation of music even in infants. Babies as young as 9 months old prefer musical scales to monotonic scales—the notes in the western musical scale do not…

Does involving parents really help students learn? Depends on how they're involved

One of things I was taught over and over again when I was in education school was the importance of getting parents involved in kids' learning. If you get the parents on your side, my professors insisted, then you're going to be much more able to get through to the students. I didn't last long enough as a teacher to see how well this advice worked, but as a parent, I've certainly experienced the process from the other end. From an early age, our kids were given "homework" that they couldn't possibly do without the help of their parents. Sometimes it seemed as if these assignments were really…

Edward Lorenz, father of Chaos Theory and the Butterfly Effect, has died.

He was 90 and worked at MIT. From the MIT press release: Edward Lorenz, an MIT meteorologist who tried to explain why it is so hard to make good weather forecasts and wound up unleashing a scientific revolution called chaos theory, died April 16 of cancer at his home in Cambridge. He was 90. A professor at MIT, Lorenz was the first to recognize what is now called chaotic behavior in the mathematical modeling of weather systems. In the early 1960s, Lorenz realized that small differences in a dynamic system such as the atmosphere--or a model of the atmosphere--could trigger vast and often…

Blogger vs Big Media

So I was reading this thread on John Quiggin's blog when the discussion turned to Tim Blair's policy of banning any dissenters from commenting on his blog. (See here for an example of the sort of comment that will get you banned.) Now Blair doesn't have to support comments from people that disagree with him, but there are free commenting systems available, so I set up Haloscan so that people could comment without being banned. I also wrote a little CGI proxy script that people could use to add links to the Haloscan comments under each of Blair's posts. Tim Blair got rather upset,…

With-gun defense polls

Peter Boucher writes: Just in case anyone's interested. Copied from Kleck/Gertz, here are the polls from table 1 (minus those with no estimate of annual DGUs): Survey, Where, What year, What kinds of guns, # DGUs Field, California, 1976, just handguns, 3.1M Bordua, Illinois, 1977, all guns, 1.4M DMIa, U.S., 1978, all guns, 2.1M DMIb, U.S., 1978, all guns, 1.1M Hart, U.S., 1981, just handguns, 1.8M Ohio, Ohio, 1982, just handguns, 0.8M Mauser, U.S., 1990, all guns, 1.5M Gallup, U.S., 1991, all guns, 0.8M Gallup, U.S., 1993, all guns, 1.6M L.A.Times, U.S., 1994, all guns, 3.6M Tarrance, U.S.,…

Palin Glenn Beck Talking Points Email Data Mining

Data mining of the more than 24,000 Gov. Sarah Palin's emails released June 10 is an interesting test case in national news media using crowd sourcing to mine a large database. The example I found today is interesting indeed, providing insight into the preparation process of a politician for a news media interview - in this case with Glenn Beck. Source Crivella West. Unknown From: gov.sarah@yahoo.com Sent: Monday, June 23, 2008 7:25 AM To: Morgan; Katryn L (GOV) Cc: Perry; Kristina Y (GOV) Subject: Fw: Talking Points for National Interviews Importance: High Pis print Sent from my…

Peripatetic Paroxysms - Linkin Park Live VIDEO, Madison Square Garden

Source. Linkin Park's Chester Bennington / Photo by Ian Witlen. If the radiance of a thousand suns were to burst at once into the sky, that would be like the splendor of the mighty one... Now, I am become Death, the destroyer of worlds. Bhagavad Gita From the first moment of "Requiem" from A Thousand Suns, ripples of peripatetic paroxysms began to spread across the sold out Madison Square Garden arena the evening of February 4. Peripatetic, because the source of LP's music was dynamic, shifting from percussion to keyboards to the trading lead rapid-fire vocals of rapping Mike Shinoda to…

On Being Rated

Amongst the other TAs and the lab coordinators in my department, I have a reputation of being a tough grader. At the end of the semester, when the course admins calculate grades, my students invariably get a few points added to their lab scores -- this is done to bring lab scores more in line with lecture exam scores. Does that mean I'm a bad teacher who doesn't explain the material well enough, but grades as if it were explained clearly? Or do I explain the material perfectly fine, but expect too much from my students? Because I'm such a hard-ass, I often get complaints from my students --…

Oil Spills for Dummies

So, at a Sunday news briefing, British Petroleum's CEO, Tony Hayward, announced that there are no underwater plumes of oil resulting from the April accident at the company's Deepwater Horizon rig in the Gulf of Mexico. Why? Well, first BP's testing hasn't found any such evidence. And second, Hayward reminds us that, you know, oil floats. Or if we didn't get that: "Oil has a specific gravity that's about half that of water. It wants to get to the surface because of the difference in specific gravity." Let's give the man this: there is definitely oil floating on the surface…

Microbial Bioprospecting in the Deep Sea by Peter J. McCarthy,

The Johnson-Sea-Link manned submersible (Photo courtesy of Chip Baumberger) Nature provides a treasure-trove of chemicals that can be used in chemical manufacturing processes, or developed into drugs for the treatment of human disease. Since the discovery of penicillin in 1929 and its impact on the treatment of infections, the pharmaceutical industry has used terrestrial microorganisms as a productive source of new therapeutic agents. In fact, the majority of antibiotics currently used in clinical practice are derived from microbial products. The intensity of this research led to a dramatic…

A Deep Sea Mutualism in Response to Predation

Sometimes we just need a little help to get by in life. A nudge, some encouragement or a simple pat on the back will suffice. Being stuck to a rock is not a real good way to avoid predators, unless that rock can move. Symbioses between sea anemones and snails have been well known for over a century, yet it is not entirely clear where the lines are drawn in this relationship. Are the anemones just happening to settle on the backs of snails as they would any hard substrate or is the anemone mafia running some protection racket? In the latest issue of the Journal of Experimental Marine Biology…

Just One Thing Challenge #6

As I write this post and sipping on my Organic Nueva Esperanza Coffee, I am happy. Part of it stems 3 cups of coffee previous to this one now flowing through my system. Mostly, it stems from knowing that my choice to drink this cup of coffee makes a difference in conserving the oceans. I firmly believe in the power of an individual to make impacts, both small and great, through daily choices. I also believe in the power of consumer choices as indicated by my previous challenges. The Request: This week I ask you to think about your choices surrounding your coffee (or tea) consumption and…

Mythbusters and WANTED - curved bullet

I have been wanting to look at this whole curved bullet thing, but I wasn't sure how to approach it. In case you are familiar with the myth, this is from the movie WANTED (which I did not see). Apparently, some people learn how to make bullets curve by moving their gun. Here is a shot of a bullet curving in front of someone. Maybe the picture doesn't do the clip justice, but it is enough for you to get an idea. Before I do an analysis, this reminds me of a great educational activity. In the activity, you give groups of students a full sheet of paper with lines that look something like…

Cognitive Dissonance: A Mitt Romney Case Study

There was something particularly infuriating about Mitt Romney's concession speech. He's clearly a smart guy - once upon a time, he was a socially moderate, pragmatic Republican - and yet the address was filled with utter nonsense like this: Europe is facing a demographic disaster. That's the inevitable product of weakened faith in the Creator, failed families, disrespect for the sanctity of human life, and eroded morality... It's time for the people of America to fortify marriage through a constitutional amendment, so that liberal judges cannot continue to attack it... Today we are a nation…

Saami not descended from Swedish Hunter-Gathers

A few weeks ago I posted on a paper, Genetic Discontinuity Between Local Hunter-Gatherers and Central Europe's First Farmers.Another one is out in the same vein, Ancient DNA Reveals Lack of Continuity between Neolithic Hunter-Gatherers and Contemporary Scandinavians: The driving force behind the transition from a foraging to a farming lifestyle in prehistoric Europe (Neolithization) has been debated for more than a century...Of particular interest is whether population replacement or cultural exchange was responsible...Scandinavia holds a unique place in this debate, for it maintained one of…

Genetic distance between populations

In the comments below on the post on human population structure there was some request for a bigger global perspective. Below the fold I've placed a table with FST values which compare each population to the other. This an older population genetic statistic derived from the work of Sewall Wright, but you are almost certainly familiar with the talking point that "85% of variation is within races, and only 15% between." That is an FST insight. The higher the FST the greater the proportion of genetic variation which can be attributed to between population differences, so it serves as a rough…

March of the (small, plastic) pelicans

No time. Too busy. Toy pelicans from Marwell Zoo. Accompanying thoughts from Dave Hone here; involves azhdarchids. Bye now, sorry for lack of substantive content.

Water Dance

From the "just because it's beautiful" department, have a look at the image sequence below. Thanks again to APOD! Water Dance from Alex Cherney on Vimeo.

What a difference two days makes

The view from my back door in Cambridge on Monday: The view from my hotel balcony in Marco Island this afternoon: Subscribe to Genetic Future.

Another reason not to work with vertebrates...

From CNN... A woman sunbathing on a boat died after a stingray leaped from the water off the Florida Keys on Thursday and struck her, officials said.

It Never Stops: Another Silly Creationist Argument

As I've mentioned before, I get lots of email from all sorts of people. Lots of it is interesting, and lots of it is stupid. This morning, when I was checking my mail, I found an email from a creationist in my mailbox, which puts forth an "proof" against atheism that I hadn't seen before. It's about as idiotic as most creationist arguments are, but it's one that I've never seen before, and it's interesting to shred it from the viewpoint of mathematical logic. Here's his argument: Now to the main point, and somewhat more interesting stuff. I recently ran across a proof (perhaps not in the…

Pure Hypomanics: Living Zippedy Doo Dah Lives?

tags: hypomania, bipolar disorder, manic depression, mood disorders, mental health, psychology Image: Michael Witte/NYTimes [larger view]. Have you ever met a person who seems to be on a perpetual caffeine high, without all the shaking? You know the type, those few hyperactive extroverts who are always doing things or meeting people, who have an expansive and optimistic mood yet are easily irritated, and who have an overactive libido or who enjoy really risky pastimes, like jumping out of airplanes or climbing buildings. According to some reading I've been doing, these are apparently…

Will the real DNA sequence please stand up?

Sometimes asking a question can be a mistake. Especially when your question leads to more questions and having to question things that you didn't want to question, and pretty soon you begin to regret ever opening the file and looking at the data and asking the question in the first place. Sigh. Take a deep breath. Yesterday through a twist of fate, I ended up taking a look at the DNA sequences produced by two different base calling programs from the same chromatogram file, from an ABI 3730 DNA sequencing instrument. I thought they would be the same, or at least similar. tags: DNA…

Lincoln's smallpox?

I think it must be difficult to study infectious disease without having some kind of interest in history. The field is so rich in stories from decades and centuries past, and infectious disease has played an enormous role in shaping our societies today. As with many fields, I believe our understanding of the present can be improved if we view it through the lens of the past--realizing as much as we can the historical influences and legacies that have brought us to where we are today. I mentioned a few weeks back that, despite its eradication in the natural world, the smallpox virus still…