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The players in a mutualistic symbiosis: insects, bacteria, viruses, and virulence genes.

One of the many problems farmers of various kinds of legumes need to deal with is the pea aphid. They reproduce incredibly fast and live by sucking the sap out of the plants, an electron micrograph of one in action. However, while they are terrifying parasites of legumes, they have their own yet more horrific parasites, a parasitoid wasp. Here is a really nice close up picture of one doing its thing, a video of the act, and here is a brain meltingly horrific video of a dissection of the mummified aftermath 8 days later. Essentially, these wasps deposit their eggs in a pea aphid and the growing larva feeds on it, developing there for about a week, and then consuming the host from the inside out like a Xenomorph. When it’s done, the wasp larva dries the aphid’s cuticle into a papery brittle shell and an adult wasp emerges from the aphid mummy. Legume farmers love them, and you can even order their mummies online these days. However, farmers noticed that the wasps didn't work as effectively on all of the aphids, and so researchers went to work figuring out why. It turns out that all aphids have a primary bacterial endosymbiont living inside their cells, in addition to and just like a mitochondria, and that many have some combination of five other secondary endosymbionts. Interestingly, two of those other five, Hamiltonella defensa and Serratia symbiotica have been shown to confer varying levels of resistance to the parasitoid wasp, allowing the aphid to survive infection. However, it turns out that there is yet one more layer to this story, [more inside]
posted by Blasdelb on Oct 22, 2012 - 50 comments

The Puzzle of Plastid Evolution

The Puzzle of Plastid Evolution: A comprehensive understanding of the origin and spread of plastids remains an important yet elusive goal in the field of eukaryotic evolution. Combined with the discovery of new photosynthetic and non-photosynthetic protist lineages, the results of recent taxonomically broad phylogenomic studies suggest that a re-shuffling of higher-level eukaryote systematics is in order. Consequently, new models of plastid evolution involving ancient secondary and tertiary endosymbioses are needed to explain the full spectrum of photosynthetic eukaryotes. [Full Text HTML] [Full Text PDF] [more inside]
posted by Blasdelb on Oct 20, 2012 - 8 comments

Mitigating Mutational Meltdown in Mammalian Mitochondria

Mitigating Mutational Meltdown in Mammalian Mitochondria PLoS Biol 6(2): e35. [The PDF, where you can read the paper in its much prettier intended format.]
Mitochondria are remarkable microorganisms. About two billion years ago, their distant free-living ancestors hooked up with a truly foreign lineage of archaebacteria and started a genomic merger that led to the most successful coevolved mutualism on the planet: the eukaryotic cell. Along the way, evolving mitochondria lost a lot of genomic baggage, entrusted their emerging hosts with their own replication, sorted out genomic conflicts by following maternal inheritance, and have mostly abstained from sex and recombination. What mitochondria did retain was a subset of genes that encode critical components of the electron transport chain and ATP synthesis enzymes that carry out oxidative phosphorylation. Because mitochondria house the biochemical machinery that requires us to breathe oxygen, it was first assumed that mitochondrial genes would show very slow rates of molecular evolution. So it was big news almost 30 years ago when mitochondrial DNA (mtDNA) evolution was observed to be quite rapid [1]. How could the genes for a highly conserved and critical function sustain the consequences of high mutation pressure and permit rapid rates of nucleotide substitution between species? Without the benefits of recombination, where offspring can carry fewer mutations than either parent, mutations should accumulate in mitochondrial genomes through the random loss of less-mutated genomes, a process referred to as Muller's ratchet [2,3]. How have mitochondria avoided a mutational meltdown, or at least significant declines in fitness?
Here is a jaw droppingly beautiful 3D animation of what Mitochindria look like in action. [more inside]
posted by Blasdelb on Oct 19, 2012 - 37 comments

Constitutive formation of caveolae in a bacterium.

Constitutive formation of caveolae in a bacterium. [Full Text]
Caveolin plays an essential role in the formation of characteristic surface pits, caveolae, which cover the surface of many animal cells. The fundamental principles of caveola formation are only slowly emerging. Here we show that caveolin expression in a prokaryotic host lacking any intracellular membrane system drives the formation of cytoplasmic vesicles containing polymeric caveolin. Vesicle formation is induced by expression of wild-type caveolins, but not caveolin mutants defective in caveola formation in mammalian systems. In addition, cryoelectron tomography shows that the induced membrane domains are equivalent in size and caveolin density to native caveolae and reveals a possible polyhedral arrangement of caveolin oligomers. The caveolin-induced vesicles or heterologous caveolae (h-caveolae) form by budding in from the cytoplasmic membrane, generating a membrane domain with distinct lipid composition. Periplasmic solutes are encapsulated in the budding h-caveola, and purified h-caveolae can be tailored to be targeted to specific cells of interest.
Elio Schaechter writes in plain English about how fantastically amazing and unexpected the researchers actually pulling this off is, and he also talks about it in more detail in his podcast.
posted by Blasdelb on Oct 18, 2012 - 22 comments

Provirophages and transpovirons as the diverse mobilome of giant viruses

Provirophages and transpovirons as the diverse mobilome of giant viruses
Abstract: A distinct class of infectious agents, the virophages1 that infect giant viruses of the Mimiviridae family, has been recently described. Here we report the simultaneous discovery of a giant virus of Acanthamoeba polyphaga (Lentille virus) that contains an integrated genome2 of a virophage (Sputnik 2), and a member of a previously unknown class of mobile genetic elements3, the transpovirons4. The transpovirons are linear DNA elements of ∼7 kb [kilobases]5 that encompass six to eight protein-coding genes, two of which are homologous6 to virophage genes. Fluorescence7 in situ hybridization8 showed that the free form of the transpoviron replicates within the giant virus factory and accumulates in high copy numbers inside giant virus particles, Sputnik 2 particles, and amoeba cytoplasm. Analysis of deep-sequencing data showed that the virophage and the transpoviron can integrate9 in nearly any place in the chromosome of the giant virus host and that, although less frequently, the transpoviron can also be linked to the virophage chromosome. In addition, integrated fragments of transpoviron DNA were detected in several giant virus and Sputnik genomes. Analysis of 19 Mimivirus strains revealed three distinct transpovirons associated with three subgroups of Mimiviruses. The virophage, the transpoviron, and the previously identified self-splicing introns10 and inteins11 constitute the complex, interconnected mobilome12 of the giant viruses and are likely to substantially contribute to interviral gene transfer.
[Full Text PDF] and two explanations in English [more inside]
posted by Blasdelb on Oct 16, 2012 - 28 comments

if the shoe fits

You can accurately judge a person just by looking at their shoes, psychologists say. "Researchers at the University of Kansas found that people were able to correctly judge a stranger's age, gender, income, political affiliation, emotional and other important personality traits just by looking at the person's shoes." Virginia Postrel responded: "The study made a solid contribution to research on first impressions, but it was hardly earthshaking. By getting so much attention, however, it demonstrated a sociological truth: People love to talk about shoes. Even those who dismissed the research as silly often felt compelled to call radio stations or comment on websites, providing details about their own choices. Why this fascination with footwear? " [more inside]
posted by flex on Oct 15, 2012 - 159 comments

"Please state where and when this card was found and then put it in the nearest Post Office."

Oldest message in a bottle found. The bottle was released as part of a research project tracking deep ocean currents. (Via socimages, via boingboing.)
posted by NoraReed on Oct 15, 2012 - 25 comments

Acoustic Barcodes from CMU

Researchers from Carnegie Mellon have created what they are calling "acoustic barcodes". These barcodes can be decoded by a computer with a microphone attached, and their video presents several potential use cases including an interactive whiteboard, cell phone mode controls, and children's toys.
posted by eak on Oct 14, 2012 - 22 comments

thinking logarithmically

What number is halfway between 1 and 9? New research lends credence to the Weber-Fechner law.
posted by aniola on Oct 10, 2012 - 138 comments

*This* is the science of sound and matter.

Two elements: tempo and volume. Researchers at the Sundance Research Facility have finally discovered how to turn sound into matter.
posted by Dr. Fetish on Oct 4, 2012 - 12 comments

"Cocaine for Snowblindness"

You're about to be the base doctor at Halley Research Station in Antarctica for a year. For ten months, no one gets in or out. Fourteen lives are in your hands, including your own. What do you put in your medical kit? And how do your choices differ from those of your predecessors (Eric Marshall and Edward Wilson) a century ago?
posted by zarq on Oct 2, 2012 - 8 comments

Cute Overload: Now with more productivity!

The Power of Kawaii: Viewing Cute Images Promotes a Careful Behavior and Narrows Attentional Focus This is interpreted as the result of a narrowed attentional focus induced by the cuteness-triggered positive emotion that is associated with approach motivation and the tendency toward systematic processing.
posted by EvaDestruction on Oct 1, 2012 - 19 comments

Something fishy with the math

Why did one newspaper, in a story copied by several other UK newspapers, somewhat underestimate the number of adult cod in the North Sea by a factor of...
posted by Wordshore on Sep 29, 2012 - 66 comments

Red Pill or Blue Pill? First, take off those 3D glasses.

The drugs don't work : a modern medical scandal - "The doctors prescribing the drugs don't know they don't do what they're meant to. Nor do their patients. The manufacturers know full well, but they're not telling."
posted by Gyan on Sep 22, 2012 - 76 comments

No more Windex

The Sponsor Effect: Breaking through the Last Glass Ceiling (pdf) Women aren't making it to the top. Despite gains in middle and senior management, they hold just 3 percent of Fortune 500 CEO positions. In the C-suite, they're outnumbered four to one. What's keeping women under the glass ceiling? High-performing women simply don't have the sponsorship they need to reach the top. The study found that women underestimate the role sponsorship plays in their advancement. And those who do grasp its importance fail to cultivate it. It's also a classic catch-22: a woman's personal choices, whatever they may be, brand her as not quite leadership material. What will it take to promote sponsorship?
posted by infini on Sep 20, 2012 - 33 comments

The Hamming Ambiguity (among other things)

Beyond the 10,000 Hour Rule: Richard Hamming and the Messy Art of Becoming Great
posted by infini on Sep 13, 2012 - 20 comments

Modern Times: The Way of All Flesh (1997)

A documentary by Adam Curtis on Henrietta Lacks and HeLa cell line created from her cells. Previously. Previously.
posted by hat_eater on Sep 4, 2012 - 7 comments

Marinexplore

Have you ever wondered what the water temperature off the Kamchatka Peninsula is? What about the wind speed in the Andaman Sea? Or maybe you’re losing sleep over the chlorophyll levels in the South Pacific. Fortunately, all of that information –- and 450 million other data points collected from oceanographic instruments around the world –- is freely and easily accessible thanks to the Marinexplore project. [more inside]
posted by Egg Shen on Aug 28, 2012 - 3 comments

There are fewer microbes out there than you think

There are fewer microbes out there than you think. New estimate reduces the number of microbes on Earth by around half. [more inside]
posted by Blasdelb on Aug 28, 2012 - 38 comments

"And beauty slandered with a bastard shame:"

'Dark Lady' of Shakespeare's sonnets 'finally revealed to be London prostitute called Lucy Negro' [dailymail.co.uk] "New research claims The 'Dark Lady' of Shakespeare's sonnets was a notorious London prostitute named Lucy Negro or Black Luce - a dark-skinned madam who ran a licentious house in Clerkenwell."
posted by Fizz on Aug 28, 2012 - 94 comments

Well, nobody's perfect. But at least we have cameras.

What makes a memorable movie quote memorable?
A news summary of how they went about it.
A short audio version (via NPR) of the story and research summary.
A Wikipedia list: AFI's 100 years, 100 quotes.
A short list of advertising slogans that fit the research model for movie quote memorability.
The research paper (automatic PDF download). [more inside]
posted by iamkimiam on Aug 15, 2012 - 65 comments

two Erics summarize SCIENCE! for life improvement & greater understanding

Barking Up The Wrong Tree distils scientific research, focused on its motto: "I want to understand why we do what we do and use the answers to be awesome at life." With a gradual shift to more digest posts packed with links to summaries & sources, a sampling of the past couple weeks includes: What are 10 things you should do every day to improve your life? - What are 10 things you should do every week to improve your life? - 25 research-based ways to increase your intelligence - What are 7 things that can make you happier in 7 seconds? - 7 steps to never procrastinating again. Another blog along the same lines but less glib & immediate is Peer-Reviewed By My Neurons; recently: How confusion facilitates learning - The science of coming on too strong - Want to be creative? Play Dungeons & Dragons [more inside]
posted by flex on Aug 5, 2012 - 39 comments

LSD absolutely had helped them solve their complex, seemingly intractable problems

"The Heretic: For decades, the U.S. government banned medical studies of the effects of LSD. But for one longtime, elite researcher, the promise of mind-blowing revelations was just too tempting." [more inside]
posted by andoatnp on Jul 30, 2012 - 113 comments

Whither the university?

Terran Lane's short blog post explaining why he is leaving academia (for a post at google) offers concise and damning insight into problems at US research universities. I find the analysis resonates with the Canadian experience as well (though I'm a grad student not a professor)..
posted by chapps on Jul 25, 2012 - 72 comments

SitOrSquat: Cheeta Camp

Mapping Toilets in a Mumbai Slum. As part of an initiative by the Harvard School of Public Health, a team of students is researching life in the Mumbai slum, Cheeta Camp. They started by studying sanitation and water use. Their results? This map of toilets.
posted by bluefly on Jul 24, 2012 - 8 comments

And a 1 and a 2, a 1, 2, 3, 3.984

"People prefer music that deviates from perfection in a natural way." Researchers into rhythm are trying to figure out the nature of these deviations, and what implications this has for audio engineering and neuroscience.
posted by EvaDestruction on Jul 23, 2012 - 50 comments

The Longest Time (Coral Triangle Edition)

Billy Joel has now officially endorsed - The Longest Time (Coral Triangle Edition), by the Barber Lab Quartet [more inside]
posted by Blasdelb on Jul 18, 2012 - 17 comments

Why we can't have nice research reporting

Just because you don't like a study doesn't mean it's wrong. Gawker takes the rest of the blog world to task for misinterpreting this new paper on women who watch televised sports. [more inside]
posted by DiscourseMarker on Jul 17, 2012 - 34 comments

Does anesthesiology have a problem? Final version of report suggests Fujii will take retraction record, with 172

In the wake of a very thorough and damning statistical analysis of 168 of his papers, published in March, Japanese investigators have concluded that Yoshitaka Fujii, fabricated his results in at least 172 published studies; shattering the previous record for most retracted papers. Considered an expert in postoperative nausea and vomiting, his "incredibly nice" findings drew scrutiny in 2000, but he continued to publish prolifically for more than a decade. Here are the published results of the Japanese Society of Anesthesiology's Special Investigation Committee, with an annotated list of all of his papers (PDF). The Retraction Watch also considers not only the depth of Fujii's betrayal but also whether the discipline of anesthesiology itself has a problem as it weighs in. [more inside]
posted by Blasdelb on Jul 8, 2012 - 33 comments

“The arc of the moral universe is long, but it bends towards justice”

A quarter-century of responses to the Pew Research Center's American Values survey statements show some surprising trends when graphed over time. A sampling: Data is also broken down by religious and political affiliation, gender, age, race, education and income.
posted by Bora Horza Gobuchul on Jul 4, 2012 - 86 comments

Turn your house into a giant battery.

"You could turn your home into a battery," said researcher Neelam Singh. Researchers at Rice University have created paints that act as rechargeable lithium-ion batteries. They can be painted onto virtually any surface, and can be charged with a solar cell. Full paper.
posted by stoneweaver on Jun 29, 2012 - 42 comments

The Viable Zombie

“[...] it took more than a dozen calls to work out the details of her zombie contagion. “After about the 17th time,” says McGuire, “I called and said, ‘If I did this, this, this, this, this, this and this, could I raise the dead?’ And got, ‘Don’t … don’t do that.’ And at that point, I knew I had a viable virus.”
posted by batmonkey on Jun 27, 2012 - 70 comments

We're here to convert you

Obama evolved. The NAACP evolved. The NCLR has evolved. How do you get your friends and family to evolve into support for LGBT rights? The Movement Advancement Project's excellent Talking About LGBT Issues series gives research-driven rhetorical and messaging frameworks that work best for meeting reluctant folks where they are. They include warnings about civil rights framings, how to hit emotional marks that emphasize commonality and cover things like adoption, marriage, transgender etiquette and employment protections.
posted by klangklangston on Jun 25, 2012 - 17 comments

Too many trainee positions in biomedical research

The U.S. National Institute of Heath has urged steps to curb growth in "training" positions in biomedical research (report). [more inside]
posted by jeffburdges on Jun 16, 2012 - 39 comments

Kyle McDonald Explains FaceTracker

FaceTracker is an example of a complex technique that builds on top of a series of computer vision, image processing, and machine learning functions in order to achieve its result. Here's an interview with Kyle McDonald, artist and researcher in New York with a background in computer science and philosophy. He released FaceOSC, a tool for prototyping face-based interaction. Kyle has a growing body of work that uses face tracking in an artistic context, notably Face Substitution.
posted by netbros on Jun 2, 2012 - 12 comments

Greenbacks

Last week, I wrote about how urban trees—or the lack thereof—can reveal income inequality. After writing that article, I was curious, could I actually see income inequality from space? It turned out to be easier than I expected.
posted by infini on Jun 1, 2012 - 43 comments

Ringing in the ears?

New hope for tinnitus sufferers. [more inside]
posted by digitalprimate on May 26, 2012 - 41 comments

The Weight of a Nation

Consequences, Choices, Children in Crisis, Challenges. HBO’s multi-part research documentary The Weight of the Nation examines obesity in America in four parts, marshaling leading doctors, epidemiologists, economists, researchers, and community leaders to understand and explain the individual costs and public solutions to a multi-faceted social and individual problem. The documentary both explores large picture statistics, while giving voice “to those that often too seek to be invisible: members of the nearly 70 percent of Americans currently diagnosed as overweight or obese. (AV Club Review)” [more inside]
posted by stratastar on May 16, 2012 - 42 comments

Publish or Perish

Are bias and fraud damaging the existing public trust in scientific and medical research? (previously) [more inside]
posted by jeffburdges on May 13, 2012 - 35 comments

The Avian Flu: Transparency vs. Public Safety

"Experimental adaptation of an influenza H5 HA confers respiratory droplet transmission to a reassortant H5 HA/H1N1 virus in ferrets." After an extensive, months-long debate, one of two controversial papers showing ways the H5N1 "avian" influenza virus could potentially become transmissible in mammals with only 3 or 4 mutations was published in Nature today. The journal included an editorial on the merits and drawbacks of "publishing risky research" with regard to biosafety. The debate included an unprecedented recommendation by The US National Science Advisory Board for Biosecurity (NSABB) to block publication -- a decision they later reversed. (Via: 1, 2) Nature's special report has additional articles, including interviews with the teams behind both papers.
posted by zarq on May 3, 2012 - 37 comments

Failing to succeed

The learning paradox is at the heart of “productive failure." While the model adopted by many teachers and employers when introducing others to new knowledge — providing lots of structure and guidance early on, until the students or workers show that they can do it on their own — makes intuitive sense, it may not be the best way to promote learning. [more inside]
posted by unSane on May 1, 2012 - 29 comments

The lady doth protest too much, methinks

Is Some Homophobia Self-Phobia? Many have suspected but now the Journal of Personality and Social Psychology has published empirical research on the subject. In the study, 20% of self-identified "highly-straight" participants demonstrated some level of same-sex attraction in reaction time tests. These individuals were significantly more likely than any other group of participants to favor anti-gay policies. Also in NYTimes.
posted by dave99 on Apr 28, 2012 - 100 comments

Research on happiness and profit

For my 250th post: There is a lot of interesting research going on in business schools, and some of it is even fun to watch. Wharton has been hosting 10 minute entertaining talks on cutting-edge research by faculty including: where inspiration comes from at work, how time relates to happiness, how to run an innovation tournament, socially responsible investing, learning from people who leave your company and what breakfast cereal and Steve Jobs have to tell us about the secret sources of innovation. If you want less academics in your business school mini-lectures, Stanford also has a collection of advice to entrepreneurs on many subjects that includes everyone from Mark Zuckerberg to Guy Kawasaki.
posted by blahblahblah on Apr 26, 2012 - 10 comments

From SIN to HEL in 11 hours

How Creativity Connects with Immorality Are creative types more likely to cross moral boundaries?
posted by infini on Apr 25, 2012 - 40 comments

Wanna see some dirty books?

A researcher at St. Andrews University is using a tool called a densitometer to measure which pages in medieval manuscripts are the dirtiest, and therefore the most frequently read. The complete (and well-illustrated) study is available online from the Journal of Historians of Netherlandish Art. [more inside]
posted by Horace Rumpole on Apr 24, 2012 - 12 comments

Computer Science: Still have Byte? Or Down to Bits?

While growth prospects in the field are incredibly high, recent trends, such as "tools grow[ing] more advanced" (see Adobe Flash Builder or MS Visual Studio) have had people wondering over the past few years if computer science has much room for growth left. Some question whether it is alive. Others, such as Carnegie Mellon, say not so fast. In any case, employment has been a bit iffy (/.). There is the possibility that Computer Science is simply growing up (PDF), then again the U of Florida decided to say good bye to it this past week. But hey, if you are not going to that University, and still are shooting for computer science, here are some tips.
posted by JoeXIII007 on Apr 23, 2012 - 57 comments

The character of an urban area

LiveHoods: Using Social Media and Machine-Learning to Study Cities [via mefi projects] [more inside]
posted by Potomac Avenue on Apr 20, 2012 - 6 comments

Tattoos, Piercings, and Alcohol Consumption

According to research recently published in Alcoholism: Clinical & Experimental Research[DOI: 10.1111/j.1530-0277.2011.01711.x], tattooed people drink significantly more than their peers (as well as other risky behaviours).
posted by wilful on Apr 19, 2012 - 63 comments

To read or not to read

How to read a paper is a series by Trisha Greenhalgh in BMJ, the British Medical Journal, that explains how to critically read and apply the biomedical literature. Deciding what the paper is about. Assessing methodological quality. Statistics for the non-statistician: parts I and II. Drug trials, diagnostic and screening tests, economic analyses, systematic reviews and meta-analyses (PDF), and qualitative research (PDF).
posted by grouse on Apr 19, 2012 - 14 comments

Want to find out more about that relative on the 1940 census? Good luck.

It's getting harder to do genealogical research using the SSDI, and this bill might make it impossible. [more inside]
posted by pernoctalian on Apr 5, 2012 - 18 comments

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