The Stochastic Scientist

How E. coli grows so fast

2012-02-10T04:00:00.000-08:00

Even for bacteria, Escherichia coli (E. coli) can multiply at a prodigious rate. In fact, they can divide faster than they can replicate their DNA. Although this seems impossible, E. coli have a neat trick for accomplishing this feat.

First, let’s look at how cells normally divide. In order to duplicate itself, a single-celled organism like E. coli first makes a copy of its DNA, then divides in two. Each resultant daughter cell receives one copy of the DNA. You can see an animation of DNA replication below:

It takes about forty minutes to make one complete copy of the E. coli genome. Therefore, each generation of E. coli should last just under an hour. Instead, E. coli can divide (under ideal conditions) in as little as 20 minutes. How is this possible?

It turns out that E. coli can begin a new round of DNA replication before the previous round is complete. When the cell splits in two, each daughter cell receives a strand of DNA that is already in the process of being copied. That is, the daughter cell receives DNA that is halfway prepared for the eventual granddaughter cells.

Replication pattern of rapidly growing E. coli wild-type cells. Cells (yellow) with chromosomes (blue lines) and origins (black squares) are drawn schematically to show the number of replication forks and origins at different stages of the cell cycle. In this example, initiation of replication occurs at four origins at the same time as cell division (bottom). A young cell therefore contains four origins and six replication forks (upper left). As replication proceeds, the oldest pair of forks reach the terminus and the two sister chromosomes segregate. The cell then contains four origins and four replication forks (upper right). Initiation then occurs again at 4 origins and generates 8 new forks giving a total of 12 forks, as cell division approaches (bottom).

EMBO J. 2007 October 31; 26(21): 4514–4522.

As you can imagine, this requires tight control. The bacterium can’t divide until it has at least two complete and separate genomes, regardless of how much extra replication is going on. An international team of scientists led by Matthew Grant from the University of Cambridge has found that specific factors govern just how this occurs. This might give researchers a better handle on controlling bacterial cell growth.

New ways to assess infant pain

2012-02-09T04:00:00.000-08:00

It can be difficult to assess pain in very young and premature infants. Simply watching for changes in posture or expression isn't always enough to indicate how much discomfort a newborn is feeling. Therefore, researchers from University College London were looking for a better way to determine how much pain a baby is feeling.

They used electroencephalography (EEG), electrocardiography (ECG) and electromyography (EMG) to indirectly detect evidence of pain. These non-invasive devices record electrical activity in the brain, the heart and in muscle, respectively. Infants were hooked up to the devices and recordings were made of three events: a heel tap with a rubber bung, a touch with a lancet that did not pierce the skin, and a medically required heel lance to collect blood. EEG, ECG and EMG results were compared for the three events. The electrical data correlated well with presumed pain levels.

Aside from providing information to people who must care for infants, this study is interesting because it was published in the Journal of Visualized Experiments. You can watch a video demonstrating exactly how the experiments were conducted, and what the results were. Warning, the video includes a close up of an infant receiving a heel lance.

Just for fun: Checking in with Project Steve

2012-02-08T04:00:00.000-08:00

In 2001, a creationist group called the Discovery Institute issued a statement called 'Scientific Dissent from Darwinism'. It included a purported list of scientists who don't accept common descent as the explanation for the diversity of life on Earth. On closer scrutiny, most of the signatories later denied having that view, and those that did were not biologists, with very few exceptions. Nonetheless, this list and others like it have have been circulated as evidence against evolution.

In a counter move, the National Center for Science Education (NCSE) produced its own list of scientists who do support evolution. However, their list was made of entirely of people with the first name Steve (or a derivation thereof), which they estimate make up about 1% of scientists. Within a month, they had over 200 signatories.

As of last month, NCSE had almost 1200 Steves on its list. You can see the Steve-O-Meter on their website. If you're a scientist named Steve and you'd like to be an NCSE Steve, you can contact the NCSE to be added to their list.

By the way, the NCSE has recently begun to also defend the teaching of global warming in U. S. classrooms. They say they don't plan to start a new Project Steve for it, but I hope they do come up with something as funny and catchy.

Silk microneedles

2012-02-07T04:00:00.000-08:00

Anyone who’s ever had an injection would welcome the replacement of normal syringes with ‘microneedles’. These micron-sized needles only penetrate the outer layer of the skin. This means that they deliver their drug payload without contacting any nerve cells, ensuring that the process is entirely painless. Fiorenzo Omenetto and his team from Tufts University have improved the delivery system by making their microneedles out of silk.

Silk has several advantages over metal and the other materials that have been tried in microneedles. Unlike metal, silk is biodegradable. Because the silk protein can be molded into appropriate shapes at room temperature, drugs can be incorporated directly into the pre-formed silk matrix without loss of potency. This allows the embedded drug to be released slowly as the silk biodegrades, rather than being injected all at once.

The researchers successfully tested their silk microneedles both in vitro (observing the diffusion of enzymes into a gel pad and delivering antibiotics to a tissue culture) and in vivo (using the microneedles on mice). They were able to control the rate of drug delivery by manipulating the consistency of the silk matrix.

Of course, a slower release of drugs, while advantageous in many ways, would require a longer exposure to the apparatus. Rather than one quick injection, a patient might have to place a microneedle patch on his arm for as long as 30 minutes. On the other hand, perhaps people could apply the microneedles themselves at home.

How your drug got its name

2012-02-06T04:00:00.000-08:00

If you take any kind of medication, either prescription or over-the-counter, chances are your drug has at least three different names. It will have a brand name, a generic name and a chemical name. If water were a drug, its three names might be 'Refresh', 'water' (some names are grandfathered in), and 'dihydrogen monoxide'. The latter two names must follow strict naming conventions.

Taking them in reverse order, the chemical name is decided on by the International Union of Pure & Applied Chemistry (IUPAC). This name specifies the chemical nature of the active ingredient—that is, the composition of the actual molecule. Unless you were a chemist, and probably not even then, you would have no idea what a drug did based on this name. For example, can you guess what you’d take (RS)-2-(4-(2methylpropyl)phenyl)propanoic acid for? If you said fever and aches, you’d be right, because it’s the IUPAC name of ibuprofin (Motrin or Advil).

The generic name of a drug, which must be approved by the United States Adopted Name (USAN) Council, is chosen not just for its physical structure, but also for its physiological function. The USAN keeps a list of word stems that can be strung together to create each new drug name. If you consulted this list, you might be able to figure out what the drug would be used for. You could see that pantoprazole contains the suffix ‘prazole’ which indicates that it’s an anti-ulcer agent. And in fact, pantoprazole is the generic name of a drug used to treat gastroesophageal reflux disease.

Finally, the brand name is selected by the pharmaceutical company that invented the drug. This choice is often a matter of market research.

To do well in school, sign a contract

2012-02-05T04:00:00.000-08:00

Most people are familiar with traditional classes in which the teacher chooses and grades assignments. However, there is another grading system known as ‘contract grading’, that, though rarely used, seems to have a number of benefits. Dana Lindermann and Colin Harbke of Western Illinois University found that contract grading significantly outperformed traditional grading among a small group of college freshmen.

There are a few key components to a contract grading system, most notably that the student decides which grade he or she is aiming for and signs a contract to that effect. After that, the student can usually choose from a number of assignments, each of which is graded pass or fail at the discretion of the instructor. Students are sometimes allowed to resubmit assignments or exams. The number of satisfactorily completed assignments determines the final grade.

Forty first-year university students were randomly divided into two groups. Each group of twenty took the same introductory psychology class with the same instructor and the same exams and assignments. One group (traditional) received points for each assignment and a final grade based on the total number of points received. Members of the second group (contract) were asked to sign a contract specifying which grade they planned to achieve and what that would require. For example, to get an A, a student would need to get at least 80% on four exams, and complete three writing and three activity assignments. B’s, C’s and D’s required fewer assignments. Interestingly, one of the contract choices specified what to do ‘if you want to earn an F’. I wonder how many students chose that option.

The amount of work and mastery required to get an A was equivalent in both groups. Nevertheless three times as many students in the contract group received an A. The contract students also graded their instructor, the course and themselves more highly than the traditional students. Remember, all students had the same instructor and assignments.

The authors suggest that the difference was largely due to the fact that the contract students felt more in control of their own learning. However, they don’t discount the possibility that the traditional group, in noticing that some of their peers were allowed to choose and resubmit assignments, simply became demoralized.

For better child health, exercise safely

2012-02-04T04:00:00.000-08:00

Many parts of the world are experiencing an epidemic in childhood obesity and its concomitant ill health. One obvious way to alleviate this problem is to encourage children to get more exercise. Unfortunately, according to researchers from Johns Hopkins and the Centers for Disease Control and Prevention, programs that encourage fitness generally do not give enough advice on avoiding injury.

Personally, I'm not so sure this kind of advice is necessary. Yes, pedestrian injury is the second leading cause of death in the U.S. for kids ages 5 to 14. Injury in general is the leading cause of death for those under 44 years old. This study does outline measures that can be taken to decrease injuries both prior to and during exercise. For example, cities can design safe walking and biking zones and put fences around public pools. They can also provide play equipment with proper surfacing and guard rails.

On the other hand, the study also discusses ways that participants can work to keep themselves safe. Do we really need a study telling us that people engaged in water sports should learn to swim?

Possible cure for graft versus host disease

2012-02-03T04:00:00.000-08:00

Bone marrow is a rich source of hematopoietic (blood-forming stem cells). Consequently, blood disorders and cancers are sometimes treated by the administration of donated bone marrow cells. In fact, tens of thousands of bone marrow transplants take place worldwide each year. Unfortunately, graft-versus-host disease (GVHD), a potentially life-threatening complication in which white blood cells from the donor attack the recipient’s tissues, can make this treatment a perilous option.

Luckily, researchers from the University of Michigan and from the Ben-Gurion University of the Negev may have found a way to defeat GVHD. By administering the peptide alpha-1-antitrypsin (AAT), the scientists were able to significantly decrease the mortality rate in mice receiving bone marrow transplants.

Current therapies to prevent GVHD often involve powerful suppression of the immune system, putting the patient at great risk of infection. In contrast, AAT carries no such risk and is already approved for use in humans (though not for GVHD) with minimal side effects. The authors are hoping to begin clinical trials with AAT in human transplant cases.

GRAIL satellites get new names

2012-02-02T04:00:00.000-08:00

If you’re a lunarphile, you know that NASA recently launched twin lunar satellites as part of its Gravity Recovery and Interior Laboratory (GRAIL) mission. The objective of that mission was to precisely study the gravity of the moon. You may not know that gravity can vary across a planetary surface, depending on both surface structures (water or mountains) and internal construction (local mineral contents). The two GRAIL spacecraft get closer or further from each other as they detect pockets of greater or lesser lunar gravity beneath them.

Until recently, the two spacecraft were unimaginatively dubbed ‘GRAIL-A’ and ‘GRAIL-B’. Luckily, NASA is no stranger to naming contests, and they asked for students across the nation to provide better choices. 890 classrooms accepted that challenge. As a result, the two craft now have the monikers ‘Ebb’ and ‘Flow’. The winning entry was provided by Nina DiMauro’s fourth grade students from Emily Dickinson Elementary School, Bozeman, Montana.

In addition to studying gravity, Ebb and Flow also carry cameras that can focus on specific regions of the moon, as requested by students. Aside from some well-deserved pride of place, DiMauro’s students will have the privilege of choosing the first camera images.

Artist's Rendition of satellites formerly known as GRAIL A and B.

Not to Scale.

Image credit: NASA/JPL-Caltech

Just for fun: 60 second adventures in thought

2012-02-01T04:00:00.000-08:00

The iTunes U team at The Open University presents famous thought experiments. Here's one example:

More examples can be found here.

Meet the X prize

2012-01-31T04:00:00.000-08:00

You may be familiar with the Ansari X PRIZE, awarded to the first private team to build a spacecraft capable of taking three people to 100 kilometers above the surface of the Earth. Burt Rutan and Paul Allen took that $10 million prize in 2004 for their SpaceShip One.

SpaceShip One in flight, from Rokits XPrize gallery.

However, you may not know that the X PRIZE Foundation has lots of other huge prizes for meeting technological challenges. For example, they offer $10 million for rapid and accurate human genome sequencing, $1 million for cleaning up oil spills, and $30 million for the first private team to send a robot to the moon. There’s also a $10 million prize for building a medical tricorder like the ones on Star Trek.

In each case, the X prize is designed to encourage engineers and scientists to push the limits of what's possible. The tricorder X prize is no exception. On the TV shows, doctors wave a small instrument over a patient’s body and instantly know all that ails him. The prize-winning apparatus would have to diagnose at least 15 diseases and weigh no more than five pounds. The task of creating such a device may not be as daunting as it seems. Researchers from the Singapore Agency for Science, Technology and Research and from the Imperial College London may be on their way to collecting the prize by developing a new way to create electromagnetic Terahertz waves (T-rays). T-rays are often used in airport scanners, and could be modified for use in medical scanners as well.

I hope all these prizes do get awarded. When they do, we all win.

Tiny wasp will travel

2012-01-30T04:00:00.000-08:00

A few months ago, I wrote a post about how some fairyfly wasps had managed to shrink to lilliputian sizes by shedding nuclei. Although this wasp (Gonatocerus ater) is much larger (though still miniscule), it too had a trick up its antenna. It made its way across the country in less than a year.

Gonatocerus ater.

Credit: Jason Mottern, UC Riverside Department of Entomology.

In August, 2010, the first North American specimen of this species was discovered by Serguei Triapitsyn (principal museum scientist from the University of California, Riverside) in upstate New York. By August, 2011, it was found in Irvine, California. Three thousand miles is pretty far to travel in one year when you’re only a millimeter long. That’s almost 5 billion body lengths. If the tiny insects had journeyed under their own power, they’d have had to move millions of body lengths each day, the equivalent of a six-foot man traveling well over ten thousand miles a day. Of course, it’s much more likely that G. ater hitched a ride to the west coast, just as it originally must have done from Europe.

The good news is that G. ater isn’t likely to be an ecological threat, and may even be a boon. Like all fairywasps, G. ater makes its living by laying its eggs inside the eggs of larger insects. I’m sure I don’t need to tell you what happens to the hosts. In this case, the victim of choice is most likely a leafhopper (Rhytidodus decimaquartus), a pest that feeds on Lombardy poplar trees. In fact, the researchers suggest that G. ater was transported within leafhopper eggs that were themselves attached to sticks.

The sex life of fungi

2012-01-29T04:00:00.000-08:00

Fungi don’t have physical differences in gender the way animals do. Instead, they have specific regions of their genomes that code for sexual identity. These sites determine with which other fungi they are compatible. But here’s the rub: there can be more than just two forms of mating type genes (alleles), so fungi can have more than two sexes.

Ronny Kellner and Dominik Begerow from Ruhr-Universität Bochum and Evelyn Vollmeister and Michael Feldbrügge from Heinrich-Heine University Düsseldorf have been studying a type of parasitic fungus called a ‘grass smut’. This fungus parasitizes grass crops such as wheat, but only after mating. Thus, grass smuts must find compatible sexual partners before they can proceed through their life cycle. Fortunately for them, they have three distinct mating types. To be clear, this does not mean that the fungi require two partners to procreate, but rather that each fungus can successfully mate with either of the other two sex types.

And that's not a grass smut's only reproductive advantage. They can also successfully mate across species lines. That may not seem unusual until you note that the species in question diverged over a hundred million years ago, which is about how long ago humans diverged from elephants. This loose sexual selection gives the fungus access to more genetic variety, which can allow it to parasitize more freely and to evade biological counterattacks.

In case you think having three sexes is extreme, you may want to consider the fungus Schizophyllum commune. Because S. commune has close to 400 different mating genes spread between two locations on its genome, this little organism comes in about 28,000 sexual forms, each of which can mate with any other form.

Google Flu Trends for the win

2012-01-28T04:00:00.000-08:00

Google Flu Trends (GFT) is a tool for predicting where and when the flu will strike, based on the number of people doing Google searches for flu-like terms and symptoms. The number of flu searches correlates surprisingly well with the number of actual flu cases. In fact, a new study led by Andrea Dugas of Johns Hopkins showed that GFT could predict emergency room visits.

Traditionally, doctors’ offices and hospitals rely on reports from the Centers for Disease Control (CDC) to prepare for influxes of flu patients. Because these reports are based on actual hospital admissions and laboratory tests, by the time a community hears from the CDC about flu epidemics in their area, it may be too late. In contrast, clinicians can access the data from GFT in real time. A regional spike in interest in the flu tells local health care providers to prepare for incoming flu patients.

Like citizen science projects, GFT relies on the power of the community of internet users. However, unlike other projects, participants don’t need to sign up for anything or get any kind of instruction. Simply by using Google however they like, they end up advancing science and benefiting their neighbors. It makes me feel all warm inside.

Why primates don’t all look alike

2012-01-27T04:00:00.000-08:00

As you can see from the illustration below, primate faces are extremely variable. Sharlene Santana, Jessica Alfaro and Michael Alfaro of the University of California, Los Angeles were interested in how that diversity came about. They found that both local environments and population size were driving factors in facial evolution.

Eleven species of Neotropical (Central and South American) primates were compared. In each case, two to ten photographs of adult males were studied. Each face was divided into fourteen sections which were graded for colors and patterns of hair and skin.

Primates from Central and South America. (1) Cacajao calvus, (2) Callicebus hoffmansi, (3) Ateles belzebuth, (4) Alouatta caraya, (5) Aotus trivirgatus, (6) Cebus nigritus, (7) Saimiri boliviensis, (8) Leontopithecus rosalia, (9) Callithrix kuhli, (10) Saguinus martinsi and (11) Saguinus imperator.

Illustrations by Stephen Nash, courtesy of University of California - Los Angeles.

Interestingly, they found that primates that live in small groups have more complex facial patterns (varying colors, alternating areas of hair and skin) than those that live in large social groups. As Santana says:

We found very strong support for the idea that as species live in larger groups, their faces become more simple, more plain.

In case you’re wondering what this says about humans, by the criteria of this study, we have extremely plain faces. But don’t feel bad. The authors suggest that plainness correlates with expressiveness. Emotional content can be read more easily on a plain face, which is much more important for individuals living in large groups.

Among the additional findings, species that live near other members of the same genus had more complex facial features than primates with no closely related neighbor species. Presumably, this helps to avoid hybridization between similar species. Also, colorization of specific facial regions correlated well with latitude and forestation. Monkeys living at higher latitudes had lighter crowns but darker nose and mouth patches than those at lower latitudes, those in forested regions had darker crowns and eye patches than those in open areas.

Taken together, the data suggest that facial differences did not arise by random chance but are selected for based on behavior (group size) and location.

You can see a slide show of monkey faces (not necessarily the ones in this study) presented by BBC Nature here.

HPV vaccine does not cause autoimmune disease

2012-01-26T04:00:00.001-08:00

The human papillomavirus (HPV) is responsible for virtually all cervical cancers, and for some other cancers as well. Fortunately, there is now a vaccine (called HPV4, because it contains antigens to four major types of HPV) that can prevent those diseases. You may know the vaccine by its trade name Gardasil. Thus far, it has had an outstanding record of safety and efficacy. Thanks to a new study conducted by Kaiser Permanente researchers, we can now also eliminate any connection between HPV4 and sixteen different autoimmune diseases (AID), including lupus, Guillain-Barré syndrome and rheumatoid arthritis.

Researchers examined the medical records of almost 200,000 young women who received at least one dose of HPV4 from 2006 to 2008. The subjects were followed for six months after each injection for signs of AID. The number of new cases of AID during any time period was the same for vaccinated and unvaccinated women, strongly indicating that the vaccine had no effect whatsoever on the development of AID.

Oh, and by the way, HPV4 doesn’t cause mental retardation either.

Just for fun: Digitizing books with reCAPTCHA

2012-01-25T04:00:00.001-08:00

Luis von Ahn of Carnegie Mellon not only invented captcha (those exasperating squiggly words that tell websites you are a human), he reinvented it. ReCaptcha is now a tool for digitizing books. Ever since I learned that, I've found them much less annoying. Well, okay, a bit less annoying.

Here's an excerpt from NOVA ScienceNow explaining reCaptcha.

You can watch von Ahn's TED talk here.

New magnetic bacteria

2012-01-24T04:00:00.000-08:00

Magnetotactic bacteria produce magnetic crystals within their cells. They use these crystals to orient themselves, but we can use them for drug delivery and medical imaging. Up until now, scientists have only been able to culture bacteria that produce magnetite (iron oxide) crystals. For the first time, Dennis Bazylinski at the University of Nevada and his colleagues have been to grow bacteria that can also produce greigite (iron sulfide) crystals.

Bacteria BW-1 were isolated from deepwater samples in Badwater Basin, Death Valley National Park. They have the genes to make either magnetite or greigite crystals, a useful advantage in the uncertain environment in which it finds itself. Because iron oxides have slightly different properties than iron sulfides, BW-1 may turn out to be more useful than standard magnetotactic bacteria.

Below are some magnetotactic bacteria swirling back and forth as an external magnet is moved (you may need to watch this clip on youtube).

Are marathons bad for your heart?

2012-01-23T04:00:00.000-08:00

In most cases, the answer is no. However, researchers led by Andre La Gerche of the University of Melbourne have found that endurance exercise (marathons, alpine bike races and triathlons) can damage the right ventricles of a small subset of athletes. To be clear, this study did not address sudden cardiac arrest during a race, for which marathoners are at no greater risk than any other athletes. Rather it looked at whether asymptomatic damage could be detected in extreme athletes. The short answer is that although such damage does occur, it seems to be reversible for most people.

Forty experienced volunteers (having finished in the top 25% of a recently competed race) with no known heart problems were asked to run a race for science. Each person had complete heart work-ups a few weeks before the race, within an hour of finishing, and about a week later. The tests included cardiac MRIs, echocardiographs and blood tests.

Immediately after intense endurance exercise, the athletes did show changes in the shape and function of their hearts. Specifically, they had a significant reduction in function in their right ventricles, which was corroborated by biomarkers in the blood tests. The left ventricles did not appear to be affected, which was consistent with previous studies showing that the right ventricle is under greater stress than the left during intense exercise.

The good news is that for most of the athletes, that change was completely reversed by the one week follow up. Only one out of eight people still showed signs of damage at that time. And those people may have simply required a slightly longer recovery time.

The researchers are quick to point out that their small study in no way negates the positive effect of exercise on human health.

According to La Gerche:

To draw an analogy, some tennis players develop tennis elbow. This does not mean that tennis is bad for you; rather it identifies an area of susceptibility on which to focus treatment and preventative measures.

So, to summarize, this study may just indicate that ultra-athletes should give their hearts time to recover between events. However, just to be on the safe side, I’ve decided to forego running marathons.

MRNA kill switch

2012-01-22T04:00:00.000-08:00

One of the ways in which cells regulate their metabolic functions is to control how much of each protein is made. Robert Singer and his colleagues from the Albert Einstein College of Medicine and the National Cancer Institute have found that some mRNAs have an internal ‘stability switch’ which causes them to decay when no longer needed.

First, a molecular biology primer. Very briefly, DNA contains genes that code for proteins. Those genes are transcribed into mRNA, which is then translated into protein. The amount of each protein that can be made depends largely on the number of mRNA strands that are available. To immediately stop protein production, a cell would have to eliminate any existing mRNA strands.

The researchers used the proteins Clb2 and Swi5 because they are tied to the cell cycle. In fact, the mRNA transcripts of these proteins decay 30 times faster during mitosis (cell division) than at other times. To figure out what was causing the CLB2 and SWI5 mRNAs to self-destruct so rapidly, the researchers tried swapping bits of those genes with bits from other genes whose mRNAs don’t decay during mitosis. Surprisingly, swapping the internal regions of the genes (the part that tells which amino acids will be in the protein) had no effect, but replacing the promoter (the start code for RNA transcription) completely changed the mRNA turnover rate.

The researchers suggest that as CLB2 and SWI5 are being transcribed, a specific factor is loaded onto the mRNA strand that, under the right environmental signals, initiates decay of that transcript. In other words, each mRNA strand carries its own kill switch along with it. Although this work was done on yeast cells (using a fluorescent microscopy technique that allowed the scientists to label and observe individual mRNA molecules), it could have implications for human cell division diseases like cancer.

New fronts in the war against malaria

2012-01-21T04:00:00.000-08:00

Over the past year, there’s been some encouraging work done on preventing malaria, a disease caused by a parasitic protozoan (Plasmodium) with a complicated lifecycle involving both human and mosquito hosts (see video below).

Here are just three of the many drug or vaccine targets under current investigation, all involving Plasmodium falciparum, the species responsible for the most lethal form of malaria. Nine out of ten of the hundreds of thousands of annual malarial deaths can be attributed to this little pest.

Joseph Jez of Washington University and his colleagues have isolated a membrane protein (phosphoethanolamine methyltransferase, or PfPMT) that is critical for the growth and survival of P. falciparum within human blood cells. Not only did Jez and his team isolate the protein, but they were also able to determine its exact structure and function. Even more importantly, this particular protein is not found in mammals, making it an ideal drug target.

University of Oxford biologists led by Alexander Douglas have identified a different blood-stage antigen (reticulocyte-binding protein homologue 5, or RH5) that, unlike most of the other P. falciparum proteins, is highly conserved among all strains of the protozoa. This means that an immune response generated against this protein should be effective against all strains of the bug. Scientists have begun testing a vaccine against this particular protein with promising results thus far.

Finally, David Cavanagh and his colleagues from the University of Edinburgh chose to focus on merozoite surface protein 1 (MSP-1), a protein that makes up about 40% of the surface area of the merozoite life stage of P. falciparum. Because MSP-1 is highly variable the researchers constructed an artificial gene containing elements from all the major types of the proteins. In animal tests, this elongated hybrid protein produced a good immune response.

Deep-sea vent discoveries

2012-01-20T04:00:00.000-08:00

An international team of scientist explorers, led by Douglas Connelly of the National Oceanography Centre, Southhampton, UK and Jonathan Copley of the University of Southhampton, have discovered two new deep-sea hydrothermal vent fields. The first is the deepest and hottest to date, and the second is in a place no one thought to look before.

Both hydrothermal vents are located on the Caribbean Sea floor. The first, dubbed the Beebe Vent Field (after Charles William Beebe, the first scientist to descend to the deep sea), is almost five kilometers down in the Cayman Trough. The plume of smoke that rises from its chimneys goes up over a thousand meters, suggesting that water is exiting the vent at close to 500°C.

Next to the Cayman Trough is an undersea mount called Mount Dent. If transported to land, Mount Dent would rise almost three thousand meters. As it is, the summit of Mount Dent is still a few thousand feet below sea level. A second set of hydrothermal vents (named the Von Damm Vent Field after Karen Von Damm, a renowned marine geochemist) has been found on the upper slopes of this mountain, a location thought to preclude that possibility.

Prior expeditions to deep-sea vents have yielded creatures unknown to science, and this enterprise was no exception. The team discovered a new species of shrimp with no eyes but with a light-sensing organ on its back.

The scientists present the following videos of their discovery. Note: HyBIS is the name of the deep-sea submarine, and also the name given to the new shrimp, Rimicaris hybisae.

Stem cells are in the eyes of the beholder

2012-01-19T04:00:00.000-08:00

And in everyone else’s eyes as well. According to new research led by Sally Temple and her colleagues from Rensselaer, our retinal pigment epithelial (RPE) cells not only allow us to see, but also harbor multipotent stem cells.

The RPE, shown at the bottom of the retina (pigmented layer), is made up of a single layer of pigmented cells. These cells are essential for nourishing the light sensitive photoreceptors within the retina. Among their other talents, entire retinas can be regrown from a few RPE cells… At least in salamanders. Of course, salamanders can also regenerate entire limbs. Nevertheless, Temple and her team set out to determine whether human RPEs could be induced, if not to entirely regrow retinas, at least to repair them.

The researchers obtained RPE cells from cadavers ranging from 22 to 99 years old at the time of death. After trying assorted growth mediums, they discovered that about ten percent of the cells had the ability to differentiate into a variety of cell types, including neurons and bone cells. This was true even for cells derived from eyes that had been nearly a hundred years old.

Needless to say, this work has implications for treating many diseases, not the least of which is retinal repair. Before you despair that you’d have to be a cadaver to benefit from this, you should know that RPEs can easily be removed from living persons as well.

As Temple cheerfully explains:

You can literally go in and poke a needle in the eye and get these cells from the subretinal space.

Art is in the label of the expert

2012-01-17T04:00:00.000-08:00

Here’s a story that should surprise no one: people react differently to art depending on whether they believe it is authentic or fake. But did you know those differences are visible in brain scans?

Researchers from the University of Oxford placed 14 participants (labeled ‘human participants’ in the paper, no doubt to avoid provoking the wrath of the NIH over inappropriate use of chimpanzees) in an fMRI brain scanner while they viewed 50 portraits, half of which were painted by Rembrandt and half of which were fakes. Each image was accompanied by the verbal description ‘authentic’ or ‘copy’ regardless of the actual nature of the painting. In fact, half the paintings were mislabeled. As the volunteers were not art experts, they presumably believed whatever description was given for each portrait. In any case, different regions of their brains were activated when they viewed what they believed to be forgeries regardless of the actual origin of the piece.

If this is true, I’m going to attempt to delude myself into thinking every art piece I encounter has been crafted by a grand master. I plan to start with anything created by my daughter.

Researchers to stop using chimpanzees

2012-01-16T04:00:00.002-08:00

The National Institutes of Health (NIH) has decided to all but eliminate the use of chimpanzees in biomedical or behavioral studies. This decision follows the release of a new report from the Institute of Medicine and the National Research Council, led by committee chair Jeffrey Kahn of Johns Hopkins.

Chimpanzees not only share 98% of our genes, but they also display many of the behaviors and cognitive abilities that we once thought set us apart from the rest of the animal kingdom. Chimps solve problems, display altruism, and feel pain and sorrow. For this reason, the NIH came up with the following strict guidelines limiting the usage of chimpanzees in research.

The knowledge gained must be necessary to advance the public’s health.
There must be no other research model by which the knowledge could be obtained, and the research cannot be ethically performed on human subjects.
The animals used in the proposed research must be maintained either in ethologically appropriate physical and social environments or in natural habitats.

Very few studies meet these criteria. For example, one possibility is for the development of a vaccine against the hepatitic C virus (HCV). Only chimps and humans are susceptible to HCV, which infects 17,000 Americans per year, many of whom will require liver transplants. Even so, the committee was split on allowing that usage of chimps in HCV studies.

Laboratories already using chimpanzees will not be immediately cut off from NIH funding. Instead, they will be encouraged to find other methods of continuing their studies. As there were only 53 chimpanzee projects funded by the NIH last year (out of more than 94,000 total study projects), it should be possible to completely eliminate the usage of research chimps within a few years.

To evade mosquitoes, cultivate more skin bacteria

2012-01-15T04:00:00.001-08:00

Our bodies are coated inside and out with microorganisms. By some estimates, you are ten times as much microbe as you are you. In fact, it’s the bacteria on our bodies that give our sweat its scent, essential for identification by dogs and for attracting mosquitoes. But not all bacterial films are created equal.

According to a new study by Niels Verhulst of Wageningen University and Research Centre and an international group of colleagues, people with a lower diversity of bacteria on their skin are more attractive to the Anopheles gambiae mosquito. As this little menace is responsible for much of the malarial transmission in Africa, this finding could have implications in preventing disease.

The researchers compared the foot odor, a known A. gambiae attractant, of 48 male volunteers. You may be relieved to read that these subjects did not have to stick their feet into a mosquito chamber. Instead, glass beads were rubbed against their feet to collect volatiles, and then mosquitoes were allowed to approach the beads of their choice. At the same time, the total number and the diversity of bacteria on the men’s feet were determined.

Men with more total bacteria but less diversity were more attractive to the mosquitoes. Specific genera of bacteria correlated well with attractiveness (some were liked and some disliked by the mosquitoes). The authors speculate that this information could be used to develop mosquito traps and repellants.

For more information, Ed Yong includes a microbiology slide show on his post about this study.

Don’t eat out of your bathroom drain

2012-01-14T04:00:00.001-08:00

You most likely don’t make a habit of using your bathroom sink as a salad-mixing bowl. But in case you’ve ever been tempted to snatch a contact lens out of the drain and put it back in your eye, you should know that sink drains are ripe with fungi, many of which can cause severe human infections.

Dylan Short of Pennsylvania State College and his colleagues sampled almost 500 bathroom sink drains in 131 buildings (ranging from homes to dorms to public facilities) across eight U.S. states. 82% of the buildings and 66% of the sinks harbored at least one type of Fusarium, a genus of fungus known to cause infections in humans and agricultural plants. In fact, plumbing systems were most likely the culprit behind an outbreak of fungal eye infections among contact lens wearers six years ago.

It may not all be bad news. Although 70% of the Fusarium species found in sink drains were associated with human disease, the other 30% may actually play some beneficial roll. At least, that’s the optimistic view of author David Geiser. Either way, don’t skimp on the contact lens cleaner, and don’t drop your toothbrush in the drain.

Will a satellite fall on your head?

2012-01-13T04:00:00.002-08:00

The satellite in question is a Russian space probe called Phobos-Grunt. Designed to grab and return with a surface sample of Phobos (one of Mars’ moons), it encountered trouble soon after its initial launch on November 8, 2011. The rocket system that would have taken it to Mars malfunctioned, leaving it stranded in a low Earth orbit. Since then, all attempts to communicate with the probe have failed, and the entire thing is destined to plunge to Earth in the coming days.

The final architecture of the Phobos-Grunt spacecraft and its major components as of 2011.

Credit: IKI

Unfortunately, because Phobos-Grunt was supposed to go to all the way to Mars, it retains a full payload of highly toxic rocket fuel. The good news is that almost all of the satellite is expected to burn up in the atmosphere, including the fuel. Only a couple of dozen fragments are expected to survive reentry.

We don’t yet know exactly when or where the satellite will land, but an early estimate puts it over the Indian Ocean on Sunday afternoon.

First animal without a centrosome

2012-01-12T04:00:00.001-08:00

Planarians are a favorite lab animal. Among their talents, these cross-eyed little flatworms display an amazing ability to regenerate, even when carved into pieces. And that’s not all that’s remarkable about these tiny creatures. Apparently, they also lack centrosomes.

The freshwater flatworm Schmidtea mediterranea lives in southern Europe and Northern Africa is the first animal ever discovered without a crucial structure inside its cells known as the centrosome.

Image credit: UCSF/J.Azimzadeh

Here’s an abbreviated explanation of the way animal cells usually divide: Prior to cell division, each chromosome (DNA package) divides in two. The centrosome, an organelle composed of two microtubule bundles called centrioles, also divides. The two centrosomes migrate to opposite ends of the cell, each drawing a full complement of chromosomes toward that end of the cell. Once this process is complete, the cell cleaves in two. Without centrosomes, DNA cannot be split evenly between the resulting daughter cells.

Or so we thought. According to Juliette Azimzadeh from the University of California, San Francisco and her colleagues, the planarian Schmidtea mediterranea does not have centrosomes. The researchers discovered this odd fact when trying to see what effect eliminating centrosomes would have on the millimeter long flatworms’ ability to regenerate. Answer: no effect at all, given that S. mediterranea never had any centrosomes to begin with. This makes planarians the only known animals to lack centrosomes.

Obviously, this changes much of what we thought we knew about cell division. Author Sánchez Alvarado also wonders why centrosomes are found in all other types of animals, if they aren’t necessary:

There may be another function for centrosomes that is still obscured.

Just for fun: The next e-reader

2012-01-11T04:00:00.002-08:00

Professor Howon Lee and his team from the Korea Advanced Institute of Science and Technology (KAIST) has developed a new e-reading system. The new technology allows readers to skim and jump around just like they could with a paper book.

Wolf reintroduction for the win

2012-01-10T04:00:00.000-08:00

In 1995, after a seventy-year absence, wolves were reintroduced into Yellowstone National Park. How have they fared? According to a study by William Ripple and Robert Beschta of Oregon State University, not only have the wolves thrived, but their presence has wrought a cascade of favorable changes in the park. Wolf predation has altered both the population and behavior of elk, which in turn has allowed entire habitats to recover.

The Gibbon wolf pack in Yellowstone.

Without wolves, elk had been allowed free reign to browse where they liked. This resulted in the decimation of many types of bushes and trees and caused changes to the entire Yellowstone ecosystem. In particular, critical habitats within and around streams were annihilated by the elimination of adjacent trees. Now that the elk are held in check, the plant life has rebounded. With them has come a resurgence in a great many species, including songbirds, beaver and fish, all of whom rely on healthy streams.

It seems that reintroducing the wolves has been a win-win for almost all the species within Yellowstone. Although the elk might dissent from this view, their numbers are still holding strong as well.

Here’s a description by Ripple (that unfortunately cuts off abruptly at the end):

Temporal cloaking

2012-01-09T04:00:00.001-08:00

Physicists from Cornell University have managed to create what they call a ‘temporal cloak’. Their proof of concept demonstration shows that events can be made invisible to normal observation. If you have a nefarious deed to hide that takes place in less than 50 picoseconds (trillionths of a second), this may be the system for you.

Briefly, the researchers took advantage of the fact that different frequencies of light (colors) move at different speeds. The team, led by Alex Gaeta, shot a laser through a fiber optic cable. That beam of light passed through a ‘split-time lens’, a device that increases the speed of the blue elements of the light beam and decreases the speed of the red elements. As the light beam progressed through the cable, a gap opened up between the red and blue parts of the light. The beam then passed through a second split-time lens that reversed the effects of the first lens, stitching the light beam back together. Any event that occurred at the precise time and place of that light gap was undetectable.

Top: Experimental configuration for cloaking an event in time using two identical split time-lenses (STLs).

Bottom: The wavelength of the probe beam as a function of time.

(a) before first STL

(b) after the first STL;

(c) temporal hole

(d) before second STL

(e) after the second STL.

When both STL's are in operation the event becomes invisible.

Used by permission.

By the way, the event you're attempting to conceal must not only occur within only a few trillionths of a second, but must be illuminated only by the beam of light you're using. Not exactly a recipe for bank robbing.

For a much more detailed (and probably clearer) explanation, check out Skull in the Stars and a video made by Rose Eveleth.

Cancer breath

2012-01-08T04:00:00.001-08:00

It turns out that it’s not just onions that linger our breath. Each time we exhale, we exude a complex mixture of volatile organic compounds (VOCs). Interestingly, these VOCs differ depending on the state of our health. For years, doctors have been attempting to use specific VOCs to diagnose cancer. Peter Mazzone of the Cleveland Clinic and his colleagues from that clinic, from the University of Illinois and from Florida Hospital have now used that technique to not only identify cancer patients but to discriminate between types of cancer.

For their study, the researchers used a colorimetric sensor array. This device, designed by the Metabolomx company, is calibrated to determine the concentration of VOCs in a person’s breath. Encouragingly, the colorimetric test accurately picked out the lung cancer patients over 80% of the time. Of the people who tested positive for cancer, the test was also about 80% accurate in discriminating between different types and stages of cancer.

This study only involved 229 people, but more experiments are being done. Obviously, doctors cannot yet rely on a breath test over other methods of diagnosis. However, analysis of VOCs may one day be used in conjunction with other tests, or as an initial screening tool.

Two reasons neutrinos can’t go faster than light

2012-01-07T04:00:00.001-08:00

A few months ago, I posted an article about faster-than-light (FTL) travel. While that data has yet to be refuted, most physicists are certain that it soon will be. Here are just two reasons why FTL travel is impossible, even for neutrinos.

The pion problem:

First, let's take an extremely simplified look at how those speedy neutrinos were created. Physicists produced subatomic particles called ‘pions’. The pions were sent down a long tunnel, along the way decaying into neutrinos and other particles. Those neutrinos, being able to pass through solid objects, continued their merry way through the Earth to Gran Sasso, Italy, where they were clocked at superluminal speeds.

Here’s the problem: To have the energy required to travel that fast, the neutrinos had to inherit that energy from the pions from whence they came. But if those pions had had that kind of energy in the first place, they’d have lasted longer, which means they would have spent more of their energy before decaying into neutrinos. In other words, you just can’t get parent pions to decay into neutrinos that retain enough energy for FTL travel.

The supernova problem:

In 1987, we observed a supernova (SN1987A) that showered the Earth with both neutrinos and light from 160,000 light years away. If those neutrinos had traveled at the same speed as the FTL neutrinos in the CERN experiment, they would have arrived four years before we saw the explosion. Needless to say, this did not happen.

So those are just two reasons why there must be some error in the FTL conclusion. By the way, even scientists who adamantly deny that FTL travel is possible think the physicists at CERN did the right thing by publishing. At the least, we will probably gain some new understanding about subatomic particles.

Acquiring the Knowledge can change your brain

2012-01-06T04:00:00.000-08:00

In case you aren’t familiar with this term, 'the Knowledge' is the map of London streets that every local taxi driver must memorize. If you live in a planned community, this might not seem so daunting. However, if you’re a London taxi driver, you must deliver your customers through streets that have been cobbled together, in some cases literally, over the past two millennia. The result is a mass of information that takes three or four years to master, if you’re in the 50% of trainees who make it that far.

What does this have to do with brains? A lot. London cabbies, who by definition have passed a test on the Knowledge, have larger posterior hippocampuses than the rest of us mere mortals. To test whether this intensive learning actually altered people’s brains (perhaps successful London cab drivers simply have larger hippocampuses to begin with), Katherine Woollett and Eleanor Maguire of University College London got their hands on a group of 79 would-be taxi drivers and 31 controls.

All participants were given brain scans and memory tests both at the start of the Knowledge training and four years later. By then, 39 of the trainees had passed their tests and become cab drivers. Before training, there was no difference between the three groups (fully trained, partially trained and not trained). After training, only those people who had fully acquired the Knowledge and qualified as taxi drivers had larger posterior hippocampuses.

Interestingly, the qualified taxi drivers performed worse at other types of memory tasks, such as recalling complex visual information, than either the disqualified trainees or the controls.

By the way, if you think the Knowledge is soon to be replaced by satellite navigation (GPS systems), here's a dissenting view:

For more on this story, check out Ed Yong's blog, Not Exactly Rocket Science.

Credit where credit is due

2012-01-05T04:00:00.001-08:00

Although women from previous centuries were just as capable as women today, that fact was not always recognized. A case in point was the eighteenth century French botanist Jeanne Baret. She should have been an obvious choice for the 1766 expedition led by Louis Antioine de Bougainville, but women at that time were prohibited from sailing on French naval vessels. So she went anyway, dressed as a man.

Baret and her mentor, Philibert Commerson, participated in the first French circumnavigation of the Earth. Along the way, they collected and catalogued thousands of plants, over seventy of which were named for Commerson. Even the captain got a plant named after him (three guesses what that was). But Baret went unrecognized. Until now.

University of Utah and University of Cincinnati botanist Eric Tepe heard an NPR story about Jeanne Baret and decided to give credit where it’s due. To that end, he and his colleagues Glynis Ridley (author of the book The Discovery of Jeanne Baret) and Lynn Bohs have named a plant after Baret. You can see pictures of Solanum baretiae below.

Just for fun: Ant crushers

2012-01-04T04:00:00.001-08:00

What's more fun than Philip Gith's bearded dragon getting a high score on Ant Smasher?

How about an African Bull Frog doing the same?

Millipede border patrols

2012-01-03T04:00:00.000-08:00

Millipedes are surprisingly particular about maintaining their own territories. Robert Mesibov of Queen Victoria Museum and Art Gallery discovered that two species of Tasmanian millipedes, Tasmaniosoma compitale and Tasmaniosoma hickmanorum, maintain a border that is about 230 kilometers long. At places, the no-millipede’s land between the two regions is only about 100 meters across.

Caption: These are Tasmaniosoma hickmanorum and Tasmaniosoma compitale, preserved in alchohol.
Credit: Bob Mesibov.

It’s not uncommon for two similar species to maintain non-overlapping territories. However, this practice, known as parapatry, usually involves insurmountable physical barriers. For example, two species may live on opposite sides of a river or cliff face. In contrast, T. compitale and T. hickmanorum don’t appear to have any physical reason for their enforced separation.

Although 100 meters is pretty wide for a creature that’s only a few centimeters long, it’s narrow compared to the size of the entire territory. With no environmental impediments separating the two species, you’d expect them to intermingle. Even Mesibov is not sure why they don’t, as you can see from the report below.

Babies won’t imitate liars

2012-01-02T04:00:00.000-08:00

We’ve all taken pleasure in enticing babies to imitate us. It turns out that very young children are much more discriminating than previously thought at deciding who to copy. According to a study by Diane Poulin-Dubois and her colleagues at Concordia University, Montreal, children as young as 14 months are skeptical of people with an unreliable track record.

Researchers were paired with 60 babies, aged 13 to 16 months. Each adult exclaimed excitedly while peering inside a container. Upon further exploration of the container, babies either found a desirable toy (reliable adult) or nothing inside (unreliable adult). Having thus established their credibility, the same experimenters then demonstrated turning on a light with their foreheads, rather than with their hands. 61% of the babies who had been paired with a reliable adult imitated the forehead technique. In contrast, only 34% of the children who had been misled were willing to copy their adult’s behavior.

Next time I find one of my young nieces or nephew eyeing me suspiciously when I try to get them to do something, I’ll have to think back to see how often I’ve misled them in the past.

Living neon signs

2012-01-01T04:00:00.001-08:00

For your New Year’s pleasure, bacteria coaxed into performing a light show. Okay, that’s not the main purpose behind the work of Jeff Hasty and his colleagues from the University of California, San Diego. The researchers are using similar methods to create living sensors of arsenic and other toxins.

The performance art required the development of two components. First, the bacteria had to be engineered. Microbes that glow on command do not exist in nature. To get them to do so, the biologists tied genes involved in fluorescence to each cell’s biological clock. By introducing the right chemical signals, Hasty and his team were able to synchronize the firing of those genes and get the bacteria to glow in unison.

The second component was the apparatus in which to place the bacteria. For this, the bioengineers built microfluidic chips, no larger than a microcscope cover slide. Each chip contains up to 13,000 individual chambers with about 5000 bacteria per chamber. Collectively, the bacteria in each chamber make up one point of light, dubbed a biopixel. By sending the right signals to each chamber, the millions of bacteria in the chip can be induced to perform a dance of light, or to spell out your alma mater.

A microfluidic chip

Credit: UCSD

It’s not all pretty pictures though. The bacteria can be further tweaked so that they flash more slowly in the presence of arsenic or other harmful substances. Hasty predicts that biosensors will one day be used to monitor samples for toxins.

You can see the bacteria in action below:

140 new species in 2011

2011-12-31T04:00:00.000-08:00

Over the past year, researchers at the California Academy of Sciences added 140 new species to the Earthly index. This effort took the scientists deep into the oceans and to every continent except Antarctica.

Although the species were spread through many phyla, there were some clusters. Just over half the new species were arthropods, and 43 of those were ants. There were 14 vertebrates, all but one of which were fish, the fourteenth being a tortoise. There were also 11 plants. You can peruse the entire list here.

Spanning six continents and three oceans, new discoveries add to the family tree of life on Earth.

Credit: Image courtesy of California Academy of Sciences.

The results of this survey have been published in 33 different papers. Aside from adding to our knowledge about our fellow inhabitants on this planet, the data helps conservators plan how best to protect critical areas.

Meet the Kepler space telescope

2011-12-30T04:00:00.000-08:00

I’ve mentioned the Kepler space telescope (pictured left) in lots of posts, so I thought it was high time we got a closer look at it.

Kepler is the name of both the telescope and the mission that uses it. Named after the 17^th century astronomer Johannes Kepler, the Kepler telescope was launched in March of 2009 with the goal of finding Earth-like planets.

Kepler finds planets via the ‘transit method’. If, from our vantage point, a planet passes in front of its star, we’ll see a compensatory dimming in the light from that star. Because several of these transits are required to confirm the presence of a planet, it can take years to verify each finding. As a comparison, an alien civilization looking in our direction would wait four years to see as many transits of the Earth across the Sun.

The Kepler telescope is not rotated to view different aspects of the sky. Instead, it monitors a single patch of sky, continuously observing the same 100,000 plus stars. How successful is this strategy? As of the beginning of this month, the Kepler mission has found over two thousand candidate planets and confirmed thirty-three of them. You can see a list of these planets along with their properties here.

Where exactly is the Kepler space telescope? Orbiting the sun, as you can see from the following animation. Note, objects in this video are not to scale.

In reality, the Kepler telescope is about 3 meters by 5 meters. In contrast, the Hubble Space Telescope, launched in 1990, orbits the Earth rather than the sun and is about 13 meters by 4 meters.

Calendar reform

2011-12-29T04:00:00.001-08:00

Here’s a problem you didn’t know needed fixing: our calendar differs from year to year. Steve Hanke and Richard Henry of Johns Hopkins would like to change that. They propose a new calendar, called the ‘Hanke-Henry Permanent Calendar’ that would be identical from year to year. Your birthday would fall on the same day of the week from now on, so better hope it’s a weekend.

You can see what 2012 would look like using both the old and the new calendar here. All the months would have either 30 or 31 days, and there would be an extra week every five or six years to compensate for the fact that the Earth takes 365 and 1/4 days to circle the sun.

Not only would Hanke and Henry simplify the calendar, but they would do away with time zones as well. Under their system, every place on Earth would be set to Greenwich Mean Time. It would be noon for everyone on Earth at the same time. Of course, for some people, that would be in the middle of the night.

Hanke and Henry make the case that these changes would be an asset in our global economy, greatly simplifying international business transactions. The researchers are confident that they can convince people to adopt this new system. They recommend that people begin using it on a voluntary basis this January 1st, and have set a date for universal adoption at the start of 2017. I’m sure they will have no trouble convincing shop owners in California to open their doors at 1 am, especially if it's called 9 am.

Just for fun: Olympus Bioscapes 2011

2011-12-28T04:00:00.001-08:00

For the past eight years, Olympus America has sponsored the Bioscapes Competition for the most beautiful and/or extraordinary microscopic images. The winning photographs must "depict subjects that are, or at one time were, living".

Here's the 2011 Grand prize winner, by Charles Krebs of Issaquah, Washington, USA:

Specimen: Rotifer Floscularia ringens feeding. Its rapidly beating cilia (hair-like structures) bring water containing food to the rotifer
Technique: Differential interference contrast microscopy

I happen to like this Honorable Mention entry by Gerd Guenther of Duesseldorf Germany:

Specimen: Stem section of Fragesia sp., garden bamboo, showing a vascular bundle
Technique: Fluorescence, ca. 200x

You can see the full gallery of winners here.

The deadline for next year's contest is Sept. 30, 2012. If you're interested in entering, you can read the rules here.

Hospital isolation and delirium

2011-12-27T04:00:00.000-08:00

Some hospital patients must be kept in isolation, either for their own safety or for the safety of others. They might be severely immuno-compromised, or extremely contagious. In either case, keeping such patients apart can save lives. Unfortunately, such precautions may come at a cost. It turns out that patients who become isolated are 1.75 times as likely to develop delirium.

For this retrospective study, Hannah Day and her colleagues from the University of Maryland School of Medicine examined the records of over 42,000 non-psychiatric patients admitted to a hospital over a two-year period. Those that had to be transferred to isolation wards suffered from delirium more often than their non-isolated cohorts. Interestingly, patients who began their hospital stay with contact precautions were not more likely to develop delirium.

There are a number of possibilities for this finding. First, patients who are transferred to isolation wards midstay may be sicker than those who are isolated at admission. After all, patients who require such a transfer have evidently taken a turn for the worse. Second, it may be more traumatic for patients to suddenly find themselves in isolation when they weren’t expecting to need those precautions. By the way, delirium is not a permanent condition like dementia. It's a temporary state of confusion.

In any case, I wonder if the Trinity Medical Center’s duct tape system would be able to alleviate some of these problems.

Flight evolution via stability flapping

2011-12-26T04:00:00.000-08:00

Denver Fowler and his colleagues from Montana State University and from Brown University have some new theories about the habits of a group of theropod dinosaurs called Deinonychus. Their ideas, which form the basis of their ‘Raptor Prey Restraint (RPR)’ model, have implications not only for the behavior of these meat-eating dinosaurs, but possibly for the evolution of flight as well.

Skeleton of Deinonychus at the Field Museum in Chicago.

You may be familiar with Deinonychus’s cousin, Velociraptor from the Jurassic Park movies. These are smallish dinosaurs with giant claws on their second toes. In popular mythology, the claws are used to slash prey. However, Fowler and his team compared the feet of Deinonychus to those of living raptors (hawks and eagles). These birds also have large talons, but they use them to immobilize their prey, not to disembowel their victims. In the same way, the paleontologists propose that Deinonychus used its claws to grip large prey, which could then be eaten alive.

Further study of living birds of prey shows that they will sometimes flap their wings while gripping prey that is too large to carry off. They do so in order to stabilize their position on top of their struggling quarry. Although Deinonychus would have been incapable of flight, its stubby wings would have been more than up to the job of helping it maintain its balance while subduing its dinner. In other words, flapping as a means to stabilize position while feeding could have preceded powered flight.

You can see an example of this sort of behavior displayed by an Eurasian Sparrowhawk below. Note: if you're sensitive about watching animals eat each other, you may want to skip this.

By the way, how cool is it that a person who studies bird evolution is named 'Fowler'?

What to do with your discarded wrapping paper?

2011-12-25T04:00:00.001-08:00

Turn it into biofuel! At least, that’s what Richard Murphy and his colleagues from Imperial College London would like us all to do. They studied the feasibility of converting many kinds of waste paper into ethanol and found that almost any kind of paper can be used.

According to graduate student Lei Wang:

The fermentation process could even cope with festive paper and card which has been 'contaminated' with the likes of glitter and sellotape [adhesive tape like Scotch brand for us Yanks].

The fuel derived from the Christmas cards and wrapping paper from within the United Kingdom alone would be more than enough to send a fleet of 250 double-decker buses on a trip around the circumference of the Earth. If all countries adopted this method to deal with paper waste, it could be an important step in replacing fossil fuels.

Less blood needed

2011-12-24T04:00:00.000-08:00

Most healthy people have hemoglobin levels that fall between 12 and 18 grams per deciliter of blood (g/dl). Currently, patients undergoing surgery are routinely given blood transfusions if their hemoglobin levels drop below 10 g/dl or if they have any of a number of other risk categories, such as old age or heart disease. Jeffrey Carson of Robert Wood Johnson Medical School and a large team of colleagues tested whether these rules could be safely relaxed for patients undergoing hip surgery. This turned out to be the case, even for elderly patients.

Matched patients around eighty years old who required hip surgery were randomly assigned to two groups of about a thousand people each. The liberal group automatically received blood transfusions if their hemoglobin levels dropped below 10 g/dl. The restricted group did not receive blood unless their hemoglobin levels fell below 8 g/dl, or they showed clinical signs of anemia. All patients were allowed transfusions at the discretion of their doctors.

Thirty and sixty days later, the patients were surveyed on their ability to walk. The doctors hypothesized that maintaining a higher hemoglobin level might have allowed patients to work harder at their rehabilitation, resulting in greater independence two months after surgery. Other consequences, such as rates of heart attack, pneumonia and death were also determined for the two groups.

As I’m sure you’ve guessed, there were no significant differences between the two groups in either ability to walk unassisted, length of hospital stay or clinical outcomes. However, the patients in the restricted group used 65% fewer units of blood. This is important because many hospitals suffer from a critical lack of transfusable blood. If most surgical patients could safely be given little or no blood, it would free up the supply for patients who truly need transfusions.

Prevention of HIV infection

2011-12-23T04:00:00.001-08:00

By starting anti-retroviral medicines early, heterosexual HIV patients can avoid giving the disease to their partners. This information could drastically decrease the transmission rate of HIV, turning it from a pandemic to a manageable disease.

Myron Cohen of the University of North Carolina, Chapel Hill and his colleagues screened over 10,000 AIDS patients to find heterosexual couples composed of one HIV-infected and one uninfected partner. Half of the HIV-positive partners in those 1763 couples were immediately started on a regimen of three daily anti-retrovirals, and the other half did not begin treatment until they became symptomatic.

Over the next three and a half years, there were 28 transmissions of HIV from infected to previously uninfected partners. Of those, all but one occurred among the couples in the delayed treatment group. That’s a difference of over 96% between the two treatment groups. This result was so significant that the study was ended three years early (it was to have run through 2015), and all HIV-infected participants were offered anti-retroviral therapy. In fact, Science magazine called this study the breakthrough of the year.

I have two comments about this study. First, you may be wondering why doctors don’t routinely start their HIV patients on anti-retrovirals immediately upon diagnosis. It simply was not known whether the drugs would be more effective at later stages of the disease. Also, many of these drugs have powerful side effects which patients may wish to avoid as long as possible.

Second, because all the participants in this study were given standard care and counseling, including free condoms, I find it a bit disconcerting that any of the uninfected partners ended up with AIDS. At least we now know how to limit that transmission.

How to make a supernova

2011-12-22T04:00:00.000-08:00

Two international teams of astronomers have confirmed a leading theory about how type Ia supernovae form. This is significant not only for supernova aficionados, but for anyone trying to understand the nature of the universe. Type Ia supernovae were used to demonstrate the expansion of the universe and the existence of dark energy.

Caption: This is SN 2011fe in the Pinwheel Galaxy (M101) at maximum brightness, a composite of optical data from the Las Cumbres Observatory Global Telescope Network 0.8m Byrne Observatory Telescope at the Sedgwick Reserve and (purple) hydrogen emission data from the Palomar Transient Factory.

Credit: B.J. Fulton (LCOGT) / PTF

The current theory is that type Ia supernovae require a binary system. The exploding star is thought to be a white dwarf, the normally quiescent stage at the end of a small star’s lifetime. When a star below a certain mass runs out of fuel, it first expands dramatically and then collapses into a dense package that can no longer generate energy. This is the fate that awaits our Sun, in about five billion years.

For most white dwarfs, this is the end of the line, a quiet retirement of slowly dissipating heat and energy. However, if the white dwarf has a companion star (thought to be a red giant), it can steal matter from that star, effectively rebooting itself. If it steals too much energy too quickly, the white dwarf will explode into a type Ia supernova.

In August, there was a supernova in the Pinwheel galaxy that we were lucky enough to observe just eleven hours after the explosion. Actually, since supernova SN 2011fe is 21 million light years away, the event really occurred 21 million years minus eleven hours ago, last August. Don’t you love cosmology?

In any case, analysis of the event showed that the explodee couldn’t have been more than a tenth of the radius of the Sun. In other words, it was indeed a white dwarf. On the other hand, while the identity of the companion star is not known, it was definitely not a red giant, as previously assumed. This means that although type Ia supernovae do appear to involve white giants in binary systems, the second star in the system may be more variable than expected.

Just for fun: Red Tide

2011-12-21T04:00:00.000-08:00

Man's Best Media produced this Red Tide video. The surfer stirs up the bioluminescent phytoplankton Lingulodinium polyedrum to produce the stunning effects.

Hat tip: Jennifer Ouellette.

Exoplanet in the habitable zone

2011-12-20T04:00:00.000-08:00

NASA’s Kepler mission is specifically designed to search for habitable planets. Among the thousands of candidate planets found in the past few years is Kepler-22b, the first non-solar planet confirmed to orbits within the habitable zone of its star.

Let’s be clear about what this means. This does not mean that Kepler-22b contains life, or even that it could sustain life. All it means is that the planet orbits at the correct distance from its star so that liquid water could form on its surface. We don’t yet know if there’s any water actually there. In fact, we don’t even know whether the planet is rocky or gaseous, though at only 2.4 times the radius of the Earth, it could well have a solid surface.

This diagram compares our own solar system to Kepler-22, a star system containing the first "habitable zone" planet discovered by NASA's Kepler mission.

Image credit: NASA/Ames/JPL-Caltech

Because NASA requires three transits (views of the planet passing in front of its star) of an exoplanet to confirm its existence and position, it can take years to verify a finding. In this case, Kepler-22b was first seen by William Borucki and his team at NASA Ames Research Center just three days after the launch of the Kepler mission, back in 2009. The third transit was not observed until the end of 2010.

Gene therapy for hemophilia

2011-12-19T04:00:00.001-08:00

There may be a cure in sight for hemophilia patients. Researchers led by Amit Nathwani of University College London, along with colleagues from many other institutions have successfully used gene therapy to treat hemophiliacs. This amazing development would not only extend and improve the lives of hemophiliacs, but could be the beginning of a new era of treatments for other genetic diseases.

Hemophilia is a blood-clotting disorder caused by a genetic defect. Specifically, people with hemophilia B (also called ‘Christmas disease’ after Stephen Christmas, a young sufferer of this condition) are born with a mutation in the gene for the protein factor IX (FIX). Because this gene is located on the X chromosome, the disease occurs almost exclusively in boys. To be a hemophiliac, a girl would have to be the misfortunate product of a hemophiliac father and a carrier mother.

Hemophilia patients need regular infusions of the clotting agents they lack in an effort to alleviate symptoms. In contrast, gene therapy, the replacement of faulty or mutated genes with normal versions of those same genes, would permanently cure the patients. Although a promising idea, little progress has been made due to a number of difficulties, including the problem of providing genetic material in a way that won’t adversely affect other genes or alert the immune system.

The researchers got around these problems by using a modified adenovirus, to which most people do not exhibit strong immune reactions, as a vector. Six patients with hemophilia B, each of whom had required supplementation with FIX protein between one and three times per week, were infused with the FIX-adenoviruses. After treatment, their FIX levels remained stable at between 2 and 12% of normal (all had been below 1% prior to the treatment) for up to 15 months. Some of the patients did require extra FIX protein, but at a much lower rate than before the treatment.

This was obviously an extremely small study. Much more work must be done before gene therapy can be approved for general usage. For one thing, the optimal dosage for delivering FIX must be determined. Also, it’s too early to tell how long the treatment will last, or whether it will produce any unforeseen consequences. For now, the doctors and patients alike have reason to celebrate.

How to heal a broken bone

2011-12-18T04:00:00.000-08:00

Is it better to rest an injured limb completely or to begin using it as soon as possible? According to a study by Robert Guldberg and his colleagues from the Georgia Institute of Technology, the answer is a little of both. The best choice is to immobilize a broken bone for about four weeks, and then to start applying compressive forces to the injury. At least, that’s the case for rats.

The scientists created gaps in rat limb bones and then seeded those gaps with a potent bone growth factor (human bone morphogenetic protein-2). All the rats had plates screwed onto their injured legs to protect them from mechanical forces. Some of those plates were rigid, whereas others had a release mechanism that allowed the bone to be compressed.

Rats whose broken bones were immediately subjected to compressive loads did not heal very well. The mechanical forces applied at the very beginning of the treatment prevented blood vessels from spreading into the injured area. These rats suffered up to a 75% loss in bone formation. However, the benefit of having the rigid plate only lasted for the first four weeks of healing. After that time, the rats with the compressible plates began to fair better.

Micro-computed angiography reconstructions of blood vessel formation in the area of the defect

Top: when it experienced no mechanical force for seven weeks

Bottom: when mechanical forces were exerted on the injury site beginning after four weeks for a duration of three weeks.

Credit: Joel Boerckel.

If this data applies to humans, it suggests that broken bones should only be immobilized for a few weeks after an injury. And I certainly hope it does apply to humans since I’d hate to think of these rats going through these procedures for nothing.

Don’t eat raw cookie dough

2011-12-17T04:00:00.000-08:00

Just when you were congratulating yourself on saving time on your holiday baking, news that prepackaged raw cookie dough can make you ill. Karen Neil and her colleagues from the Centers for Disease Control (CDC) linked 77 cases of Escherichia coli O157:H7 back in 2009 to ready-to-bake commercial cookie dough. Luckily, none of the afflicted people died, though several had to be hospitalized.

I had heard that you should not consume raw cookie dough in order to avoid the Salmonella that can lurk in raw eggs. However, manufacturers of commercial cookie dough use pasteurized eggs in their mixes. The scientists at the CDC instead suspect that the E. coli infection originated in a contaminated batch of flour. Unfortunately, they were not able to confirm this hypothesis. Although 94% of the patients who became ill with E. coli O157:H7 over a few weeks in 2009 reported having eaten raw cookie dough, testing revealed very few product samples contaminated with the bacteria. It’s not clear how the cookie dough became contaminated, if in fact it was the dough that was at fault.

Still, the doctors at the CDC recommend that people not consume raw cookie dough, especially of the prepackaged commercial kind. Seeing that this advice is unlikely to find much compliance (some of the patients admitted that they had had no intention of baking cookies when they bought the raw dough), doctors are asking manufacturers to make their product safe for raw consumption. Some companies have responded by switching to heat-treated flour.

Glob of raw cookie dough, by Ginny, July 25, 2008.

Are chimps synesthetes?

2011-12-16T04:00:00.000-08:00

A new study by Vera Ludwig of Humboldt-Universität zu Berlin and Ikuma Adachi and Tetsuro Matsuzawa from Kyoto University suggests that chimpanzees can be synesthetes. If true, this implies that synethesia predates the evolutionary split between humans and chimpanzees, about six million years ago.

Synesthesia is a cross-firing of the senses. For example, a person may perceive particular digits to have specific colors, sounds, shapes or even personalities. Although only about 1% of the population identify as synesthetes, most people display mild symptoms of the condition. For example, people tend to associate high-pitched tones with light colors and low-pitched tones with dark colors.

Ludwig and her team gave 33 humans and 6 chimps touchscreens and asked them to select a large square that was the same color (black or white) as a small indicator square. The apes were given fruit treats for correct answers. It’s not clear what the human subjects were given.

As each new set of squares appeared, either a high tone or a low tone was played. Although all the participants did extremely well, humans and chimps were quicker at picking the right square when the sound matched the color. In the video below, you can see the chimp hesitate briefly before picking the correct black square when a high tone is played.

Is this really synesthesia? Some researchers, such as Danko Nikolic, at the Max Planck Institute are skeptical. I have to agree with him. I think it would only truly be an example of synesthesia if the subjects heard a high tone when presented with a white square even if no sound was actually playing, something that would be exceedingly difficult to test in chimps.

Just for fun: Fun Science

2011-12-15T04:00:00.000-08:00

Charlie McDonnell self-describes himself as 'an English twenty-something who makes videos'. He's being way too modest. Here's one of his offerings about time travel.

Hat tip: Bad Astronomy.

BTW, Charlie also has videos about his visit to the Doctor Who set, which automatically makes him my hero.

Finding the Higgs Boson

2011-12-14T04:00:00.001-08:00

Two separate teams (ATLAS and CMS) have found evidence of the elusive Higgs Boson, whose existence is theorized to explain why things have mass. While this is not conclusive proof that the Higgs exists, the new data does make it much more likely that we will eventually confirm the existence of this subatomic particle.

The Higgs Boson, if it exists, was expected to have a mass of about about 125 gigaelectronvolts (in particle physics, this is a measurement of both energy and mass; remember E = mc²), and both teams found a signal bump in exactly that range. At this time, the chance of error (that the signal they found is not from the Higgs but is merely background noise) is only a few percent. That may seem definitive, but physicists won’t claim success unless they can lower the error rate to less than 0.0001%, something that may be done as more experiments are done.

As a refresher on the Higgs and on the Large Hadron Collider (where all the action is), I’m reposting this 2008 LHC rap:

For more details, here's an explanation by Phil Plait.

A rediscovered bumblebee

2011-12-13T04:00:00.000-08:00

Here’s a bit of good news about bees. Researchers at the University of California, Riverside have rediscovered an extremely rare bumblebee that hasn’t been seen in over fifty years. The Cockerell’s Bumblebee was discovered in 1913 and, until its rediscovery in August of this year, hadn’t been encountered since 1956.

A Cockerell’s Bumblebee.

Credit: G. Ballmer, UC Riverside

Not only is the Cockerell’s Bumblebee rare today, it was never abundant. Only 23 specimens had ever been found, all within about 300 square miles in the White Mountains of New Mexico. In fact, entomologists once thought the bee was merely a color variant of a more common bumblebee. Genetic tests have now shown the bee to be a unique species, though little is known about how it makes its living.

Considering the widespread die-outs of many bee populations in recent years, I think it’s nice to hear about a bee that made a come back.

Inadvertent fecal transplants

2011-12-12T04:00:00.000-08:00

If you read yesterday’s post, you know that fecal transplants can be effective weapons against microbial pathogens. That’s good news considering that medical students do not know when to wash their hands.

Eighty-five medical students at Hannover Medical School who were about to begin clinical studies (meaning that they were to begin examining and treating real patients) were given a questionnaire asking whether hand washing was required under various scenarios. For example, must you wash your hands after removing gloves? Answer: yes. How about after touching a patient’s bed? Also yes. Only a third of the students got all the answers right.

Interestingly, the medical students predicted that they would have better hand-washing compliance than nursing students, when in fact the reverse was true. Nursing students were much better at washing their hands than were medical students.

Needless to say, this was a small study at a single school. It does highlight the need for teaching students when to wash their hands and for ensuring that experienced health care professionals continue to exercise proper hand-washing protocols. As helpful as they may be, nobody wants unsolicited fecal transfers.

Something to look forward to—fecal transplants

2011-12-11T04:00:00.000-08:00

As unpleasant as it sounds, fecal transplants may be coming to a hospital near you. Specifically, the microorganisms within the donated fecal samples can be used to eliminate pathogens such as Clostridium difficile. No fewer than four studies about the efficacy of fecal transplants were presented at the 76th Annual Scientific Meeting of the American College of Gastroenterology last month.

C. difficile is a well named pathogen. Not only does it cause severe diarrhea, but it can also lead to a potentially life-threatening infection of the colon. In addition, C. difficile is often antibiotic-resistant. Normally, C. difficile is held in check by the ‘friendly’ bacteria in a person’s gut, but following antibiotic treatment, the good microbes are often decimated, leaving room for C. difficile to flourish. By seeding the gut with a new supply of good bacteria, C. difficile may again be outcompeted to the point of extinction. At least, that’s the reasoning behind the fecal microbe transfer, and it appears to hold true. In fact, over 90% of patients who undergo this procedure (many of whom have combated C. difficile unsuccessfully for years) have a full recovery.

One caveat: although the evidence is mounting that this procedure is safe and effective (to the point where investigator Lawrence Brandt of the Albert Einstein College of Medicine suggests it should be the first line of attack in treating C. difficile), it hasn’t been thoroughly tested. For one thing, it’s hard to get NIH grants to study feces.

And in case you were wondering, doctors who perform this procedure sometimes suggest that patients recruit their own donors, often from spouses or other family members. Now, that’s love.

No reason to switch to presumed consent

2011-12-10T04:00:00.000-08:00

There’s a severe shortage of organs available for donation in the United States. According to the U.S. department of Health and Human Services, there are over 100,000 people currently waiting for an organ. One suggestion for how to alleviate that situation has been to change our consent policy so that potential donors have to opt out rather than in. However, a new study led by Dorry Segev of Johns Hopkins suggests that this would be of little help.

In the U.S., we have an opt in system of donation consent. In other words, you have to actively agree to become a donor. Many other countries choose an opt out system, also called presumed consent. In those nations, each person is assumed to be a donor unless they specifically refuse while alive. At first glance, it seems that presumed consent would have to garner more donations since many people with no objection to donating organs may never have bothered to opt in. However, comparisons with donation rates in other countries show that this is not the case. In fact, the U.S. ranks third in donation rates, well above many countries with opt out policies.

Apparently, the type of legal consent obtained makes little difference. This may be because even in countries with presumed consent, family members are consulted prior to donation. Only in Portugal (with the second highest donation rates, below only Spain) would doctors ignore family objections.

Rather than switching to a presumed consent system, which would be costly and of dubious value, the authors suggest that the U.S. copy other aspects of Spain’s system. Spain has dedicated transplant physicians at hospitals, ready to approach families and to assess and prepare patients. Beyond that, the most important thing is to educate the public to discuss their wishes with their next of kin.

Virtual train dilemma

2011-12-09T04:00:00.000-08:00

David Navarrete and his colleagues from Michigan State wondered how people would react to moral dilemmas within a virtual world. They used the classic runaway train scenario for their test, but rather than presenting it as a hypothetical situation, they immersed their subjects in a three-dimensional virtual world. The change in venue made little difference.

The scenario runs as follows. An unstoppable train is heading down a track toward five people who have no chance to escape. There is a switch in the track that can divert the train onto a sidetrack just in time, but there’s one person on that sidetrack. You control the switch. Do you do nothing and let the train kill the five people, or do you throw the switch and let the train kill the single person?

If you’re like most people, you’ll throw the switch. In Navarrete’s virtual study, over 90% of people chose to sacrifice one person to save five, a percentage which is consistent with nonvirtual tests.

I have a problem with this study. Being in a virtual world, however realistic, does not change the fact that the subjects know that no one is really being killed. Thus, I don’t see how this is an improvement on simply asking people what they’d do. If anything, you might be testing how much participants want to see virtual people get hit by trains.

You can see a 2D adaptation of the test below.

Medical marijuana for the win

2011-12-08T04:00:00.000-08:00

Sixteen states have now passed medical marijuana laws (MML), allowing physicians to prescribe marijuana to patients who can either grow it themselves or obtain it from legal growers. Have there been any unforeseen consequences of this change? According to a preliminary report by Mark Anderson of Montana State University and Daniel Rees from the University of Colorado, Denver, legalizing marijuana may be significantly reducing traffic fatalities.

Traffic fatalities (as reported by the Fatality Analysis Reporting System) decreased by 9% after the implementation of MMLs. Why should this be so? After all, marijuana does have detrimental affects on one’s ability to drive. Distance perception, hand-eye coordination and reaction time are all adversely affected by marijuana usage, just as they are by alcohol consumption.

For one thing, unlike drunk drivers, who tend to speed and take risks, stoned drivers tend to compensate for their defect by driving more slowly and carefully. Therefore, using marijuana rather than alcohol would be of benefit to motorists (though obviously, using neither would be preferable). Data from the Beer Institute confirm that beer sales do fall upon the passage of MMLs, suggesting that some people switch from alcohol to marijuana when the latter is available.

Perhaps even more significantly, because people can legally drink in public places, they often find themselves in need of transportation home, which they may unwisely provide for themselves. The often problematic legal nature of medical marijuana ensures that it is primarily used in the home.

By the way, a 9% decrease in traffic fatalities is nothing to sneeze at. This is about the same savings in lives achieved by mandatory seat belt laws. It does make one wonder what would happen if all marijuana usage were decriminalized.

Just for fun: Small world competition

2011-12-07T04:00:00.001-08:00

Since 1974, Nikon has hosted the Small World Photomicrography Competition. Photographs must involve some type of light microscopy but can encompass any subject. Prizes are given for originality, informational content, technical proficiency and visual impact.

The 2011 grand prize winner was this submission by Igor Siwanowicz of the Max Planck Institute. In case you don't recognize the creature depicted below, it's a lacewing larva magnified 20x.

You can see all the winners and honorable mentions here. Personally, I like the following picture of a 630x magnification of freshwater ciliates undergoing conjugation, submitted by Gerd Guenther.

If you'd like to enter the contest next year, here are the rules. Make sure your entry is in by the April 30, 2012 deadline.

Hot flashes can persist for years after menopause

2011-12-06T04:00:00.000-08:00

This was the unfortunate conclusion of a study conducted by scientists from King’s College London and from the Gynecological Cancer Research Centre. If you are in the majority of women who will suffer from either hot flashes (HF) or night sweats (NS) during menopause, you may have over a decade of symptoms to look forward to.

The researchers sent questionnaires to 15,000 post-menopausal women, asking them about their menopausal symptoms. Of the over 10,000 respondents, 90% had experienced HF and/or NS on a regular basis, and over half of them were still experiencing those symptoms even though it had been an average of ten years since they went through menopause.

There are factors that can affect the severity of menopausal symptoms. Smoking, alcohol consumption, anxiety and weight all have negative effects on menopause. That’s no surprise. What's disconcerting is that the symptoms last for so long.

As author Myra Hunter states:

Health professionals need to be aware that women can still have hot flushes and night sweats in their late 50s and 60s.

Don’t be so quick to target invasive species

2011-12-05T04:00:00.000-08:00

Invasive species can wreak havoc on an ecosystem. A case in point is the notorious ship rat (Rattus rattus), which has been an unwelcome guest at every port visited by humans. The North Island of New Zealand can thank the ship rat for the nearly complete elimination of all native vertebrates. Unfortunately, many of the native plants relied on those vertebrates for pollination services. But don’t worry, this story does have a happy ending. A substitute pollinator has apparently taken over the duties vacated by the missing vertebrates. That creature is… the ship rat.

David Pattermore and David Wilcove of Princeton University studied the pollination of three native New Zealand plants growing on North Island and in a nature reserve called Little Barrier Island. Although the native vertebrate population had been depleted from North Island, it thrives in abundance on Little Barrier Island. Surprisingly, the pollination rate for the plants was similar in the two areas.

The primary pollinators on Little Barrier Island are the endemic birds and bats. On North Island, that job is done by ship rats and by an introduced species of bird known as the silvereye. Apparently, ship rats had replaced the very pollinators that they drove to extinction.

This creates a tricky problem for conservationists trying to hold back the flood of invasion by non-native species. Scourging ship rats from the North Island would do the native plants no favors. After all, the plants don’t care whether it’s a rat or a bat that carries their pollen around. The more that is understood about the current role of introduced species within an ecosystem, the better those locations can be managed. At the very least, every effort must be made to reintroduce native pollinators before removing invaders.

You can see Pattermore’s explanation below.

How to build a superheavy element

2011-12-04T04:00:00.000-08:00

Two teams (one from the University of Oslo and the other an American/Russian team from the Joint Institute for Nuclear Research, Dubna, Russia) are competing to create the world’s heaviest element with an atomic number of 119 (meaning that each nucleus contains that numbers of protons). Want to get in on the action? Here’s what you’ll need:

1. The ability to smash two smaller atoms together in such a way that they combine to form the new heavier element.
You’ll want a particle accelerator for this step.

2. The proper ingredients.

To create an element with 119 protons, you’ll need to start with some pretty heavy atoms. Such atoms themselves tend to be radioactive, meaning that they only last so long before decaying, an event measured in ‘half-lives’ (the amount of time required for half the substance to disappear). The labs working on the superheavy element race are trying to combine Berkelium (atomic number 97; half-life of 320 days) with titanium (atomic number 22).

3. The ability to detect any successful fusions.

The physicists don’t expect to create more than one atom of element 119 per month, each of which will have a half-life of less than a microsecond. You’ll need an ultrafast and powerful detector if you don’t want to miss one.

Of course, there is another way to create superheavy elements (those with atomic numbers above 104), but it requires starting with a supernova.

New and improved lithium ion batteries

2011-12-03T04:00:00.000-08:00

Lithium ion batteries are a common component of many consumer electronic products, such as cell phones. Unfortunately, current lithium ion batteries don’t last as long as we’d like. Innovations by Harold Kung and his colleagues from Northwestern University may soon change that. They’ve developed a battery that lasts ten times as long. It recharges much faster as well.

Briefly, lithium ion batteries work by shuttling lithium ions from the anode (negative end) to the cathode (positive end). Once all the lithium atoms have arrived at the cathode, the battery is dead and must be recharged by reversing the flow (which is done by applying a higher voltage to the battery). How long a battery lasts is limited by the number of lithium ions available to move through that battery.

Currently, anodes are constructed from layers of graphene, which is a form of carbon. Although carbon has the advantage of being stable, it takes six carbon atoms to hold each lithium ion. In contrast, you can pack four lithium ions onto every atom of silicon, a considerable improvement. Regrettably, pure silicon tends to shatter during charging. The solution? Combine the two materials.

The researchers placed clusters of silicon between layers of graphene. The new anode can hold many more lithium ions than plain graphene, but is much more stable than pure silicon. By adding some silicon to the anode, the scientists have created a much more powerful battery.

Not only have the Northwestern researchers greatly increased the charge capacity of their batteries, but they also decreased the recharging time required. As I said, lithium ion batteries are recharged by forcing the flow of the lithium ions back from the cathode to the anode. The scientists effectively gave those ions a shortcut by cutting tiny holes in the graphene/silicon lattice through which the ions could plunge.

Taken together, we may soon have a battery that lasts much longer and recharges much more quickly than anything on the market today. Well, I say soon, but the authors predict that it will be at least three years.

Insect power

2011-12-02T04:00:00.000-08:00

You’ve seen the cartoons of engines powered by hamster wheel. Well, University of Michigan engineers led by Ethem Aktakka are designing motors that use green June beetle (Cotinis nitida) power. Specifically, they converted the kinetic energy of wing flapping into electricity. Each beetle can generate up to 115 µW of power, enough to power tiny sensors or cameras carried by the insect.

A piezoelectric beam attached to a Green June Beetle reveals the optimum location to scavenge energy and shows that up to 115 µW total power can be generated from the insect’s body movements.

Image credit: Aktakka, et al.

The beetles used for these tests were all tethered. The researchers attached piezoelectric beams to various parts of the insects’ bodies to see which configurations generated the most power. Of course, the point isn't to attach insects to treadmills for energy production. Eventually, the beetles would be free flying, taking their sensing payloads into small or dangerous spaces.

You may be wondering, as I was, how you persuade a beetle to investigate the exact locations you need visited. As you can see in the video below, it turns out that insects can be controlled rather handily by the application of a few implanted electrodes.

In fact, it turns out that it’s easier to manipulate a living insect into doing what you want than to build a robot to do the same thing. The green June beetles in this study were not asked for their commentary on this point.

Tiny wasps have lost their nuclei

2011-12-01T04:00:00.000-08:00

Fairy wasps (sometimes called fairyflies) are extremely small insects. At 200 micrometers in length, seven of these tiny parasites could fit across the head of a pin. So how does this multicellular wasp squeeze its cells into the space some organisms reserve for a single cell? In part, by shedding nuclei from their neurons.

Fairy wasp (Megaphragma mymaripenne) shown compared to a paramecium and an amoeba.

Credit: Alexey Polilov.

Alexey Polilov of Lomonosov Moscow State University compared the neurons of adult fairy wasps with those of fairy wasp pupae. Although the juvenile neurons appeared completely normal, up to 95% of the adult neurons were missing a nucleus. While there are cells that routinely lack a nucleus (red blood cells, for example), neurons are not usually among them.

Needless to say, this is rather odd. After all, neurons are pretty important cells. If an organism wanted to get rid of excess mass, I wouldn’t think it would do so by tampering with its neurons. Still, these insects are able to function perfectly well, so maybe nuclei are overrated.

Hat tip: Jennifer Ouellette.

Just for fun: Surgical robots

2011-11-30T04:00:00.001-08:00

I know someone who had his prostate removed via the Da Vinci surgical robot. I wonder if he would have felt better or worse watching Ramesh Thurairaja of Southmead Hospital use the Da Vinci to peel a grape?

Hat tip: Not Exactly Rocket Science.

False confessions lead to false evidence

2011-11-29T04:00:00.000-08:00

A surprising number of people unfairly accused of crimes will falsely confess to those crimes. The innocent people may be coerced into confessing, or they may simply be confused. As I reported earlier, they may even confess just to get out of the interrogation room. Unfortunately, for them, false confessions are often corroborated with otherwise poor or even fallacious evidence.

According to Saul Kassin from John Jay College of Criminal Justice, Daniel Bogart of the University of California, Irvine, and Jacqueline Kerner of Nova Southeastern University, possessing a confession can lead to a perfect storm of invalid evidence collection. Upon obtaining a confession, law enforcement officers begin amassing evidence that corroborates that confession and discarding disconfirming evidence.

This is not to say that officers of the law are deliberately trying to convict innocent people. It’s just that once they have a confession, they naturally place more credence on eyewitness accounts that place their suspect at the scene of the crime and less on evidence that contradicts the confession. In other words, the gathering of corroborating evidence may be corrupted by the very existence of the confession.

What can be done to ensure that the guilty are punished and the innocent go free? It’s clear that confessions and eyewitness accounts should be considered of secondary importance compared to forensic evidence (fingerprints, DNA, etc). But even more importantly, the people collecting that forensic evidence can't know who has or hasn't confessed. Each piece of evidence must be evaluated independently in order to eliminate preconceived biases.

Doorway of forgetfulness

2011-11-28T04:00:00.001-08:00

When I was in graduate school, my lab was divided between two rooms, each of which contained much used equipment and supplies. We referred to the passage between those rooms as the ‘Arch of Forgetfulness’. It was a common occurrence to find someone hesitating near an entrance with a puzzled look on her face. Apparently, this phenomenon is not restricted to graduate students. According to research by Gabrie Radvansky and her colleagues from the University of Notre Dame, forgetting why you entered a room is a universal experience.

The scientists conducted a series of experiments in which people progressed through either virtual or real rooms picking up objects (such as a white cone, or a blue cube) from one table and placing them on another table. Sometimes the tables were within the same room, but at other times the participants had to pass through a doorway before depositing their items. In all cases, the objects were hidden after being picked up (becoming invisible if virtual, or being concealed within a box if real). Along the way, the participants were asked to remember what they were carrying. In both the real and the virtual worlds, people did a better job remembering their objects if they hadn’t just crossed a doorway.

Returning to the starting position did not improve people’s memories either. This last result surprised me a bit, as I seem to recall that reentering the first room did jog my memory. Of course, upon returning to my lab bench I would have been faced with the same lack of ingredients that had set me on my journey to the other room in the first place. That’s quite different from trying to remember if I had last picked up a red wedge or an orange cylinder.

Something to look forward to

2011-11-27T04:00:00.000-08:00

That beautiful orthodontic-created smile may not last a lifetime. According to research done at Malmö University, Sweden, our jaws shrink as we age, resulting in the very crowding we fought against in our youth.

The researchers had taken plaster molds of the jaws of their dental students back in 1949. Molds were taken of these same people in 1959 and in 1989. As time progressed, people had less room in their jaws. The difference was not great, no more than a millimeter in most cases. However, even that small difference can lead to overcrowding, particularly among the lower teeth.

Despite this new data, I wouldn’t put down a deposit at your local orthodontist’s office for thirty years from now. For one thing, this was a very small study. By the forty-year mark, only 18 of the original students were still available. For another, assuming you had straight teeth in your youth, the crowding in your dotage probably won’t be severe enough to warrant correction. Besides, as I've written before, there are more severe changes to the jawline that come with aging.

Instead, the dental researchers suggest that orthodontists keep in mind the eventual shrinking of their patients’ jaws when they prescribe treatment plans.

Birds don’t like noise

2011-11-26T04:00:00.001-08:00

The amount of noise in an area affects the number of songbirds seen in that territory. Two studies from two different parts of the world show the same thing: birds don’t like noise. Although some species can be tolerant of noise, increased background noise levels lead to decreased diversity.

The first study took place in Puebla-Cholula, Mexico, and was run by scientists from the University of the Americas and from the Basque Institute for Agricultural Research and Development. The second study, conducted by researchers from the University of Extremadura, Spain, took place in the Iberian Peninsula. In both cases, the number of bird species in an area was adversely affected by the amount of background noise. In fact, noise levels were a greater predictor of species diversity than was size of test area, or human usage. For example, university campuses had many more species of songbird than urban parks.

The Spanish study suggested that the cut off for discouraging the more sensitive bird species was 50 decibels (dB). That’s about as loud as a normal conversation in a quiet location. A whisper is at about 30 dB and traffic sounds heard from inside your car are around 85 dB. All the regions studied had at least 38 dB of background noise, and some had over 70 dB.

What can be done to encourage birds to live alongside people? The authors of both studies propose that urban planners include acoustic barriers, such as wooded spaces, within city limits.

World’s lightest engineered material

2011-11-25T04:00:00.000-08:00

Researchers from Caltech, from the University of California, Irvine, and from HRL Laboratories have developed the lightest material in the world. Their new metal weighs less than 0.9 milligrams per cubic centimeter. The previous lightweight champion, weighing in at about 1.9 milligrams per cubic centimeter, was a substance called ‘aerogel’.

Just to put things in perspective, a typical bowling ball weighs somewhere between three and seven thousand grams. If it were made of aerogel, the same bowling ball would only weigh about ten grams, and if made of the new metal, it would weigh less than 5 grams. This is because both materials consist almost entirely of air trapped within a framework. Aerogel is 99.8% air and 0.2% silicon dioxide, whereas the new ultralight metal is 99.9% air within a latticework of metallic microtubes.

Left: Aerogel.

Right: New metal resting on a dandelion without damaging it.

Credit: Dan Little, HRL Laboratories LLC.

Just for fun: How not to cook a turkey

2011-11-24T04:00:00.001-08:00

Okay, maybe more of a public service announcement than something for fun. If you're considering deep frying your turkey this year, you may want to rethink that choice.

Hat tip: Greg Laden's Blog.

Practicing on toys

2011-11-23T04:00:00.000-08:00

It’s not only small children who get practice dealing with pets and other people through the handling of toys. According to a study led by Rikke Langebæk of the University of Copenhagen, veterinary students can also benefit from doctoring toy animals before they start operating on the real thing.

Veterinary students will one day be called upon to perform surgical procedures on people’s beloved pets and valuable lifestock. In preparation, they often practice on laboratory animals. However, this has several drawbacks. For one thing, the future vets understandably feel distress at causing these animals any unnecessary suffering. For another, the pressure of having to operate on living animals can make students anxious, never the best learning environment. And of course, there’s the cost of maintaining and caring for laboratory animals.

In order to alleviate these problems, Langebæk developed a skills laboratory in 2007 that uses toy animals instead of living animals. These are not your ordinary stuffed toys from Hallmark though. The toys contain organs and veins that simulate those found in real animals.

Thus far, students say the toys are a good model for learning surgical procedures, and that operating on the toys gives them confidence for moving on to the real thing.

Disgust by any other name is still disgust

2011-11-22T04:00:00.000-08:00

One controversy in cognitive research is whether language is critical for the perception of emotion. In other words, can you feel something just as strongly if you can’t label that feeling? According to scientists from the Max Planck Institute, the answer is yes.

The researchers compared German speakers to speakers of Yucatec Maya, a language spoken in the Yucatan Peninsula that has no separate word for ‘disgust’. When shown photographs of people displaying various emotions, Yucatec Maya speakers could not distinguish verbally between ‘disgust’ and ‘anger’. Does this mean that the Mayans do not perceive any difference between these two emotional states?

To answer this next question, the Germans and Mayans were shown a new set of photos. First, they were shown a person displaying a digitally fine-tuned mix of emotions, such as 80% angry, 20% disgusted. They were next presented with a pair of photos, the original and a picture of the same person but with a different mix of the same two emotions. In some cases, the dominant emotion was the same in both pictures, but in other pairs of pictures it was reversed (one picture mostly angry but a little disgusted, the other mostly disgusted but a little angry). The subjects were asked which of the two pictures was identical to the single picture they had just seen.

This task is easier for most people when the dominant emotions in the non-identical picture are reversed. But is that due to the verbal labels people place on those emotions (I’m looking for a picture of a disgusted person, and the person on the left is more angry than disgusted)? In that case, having labeled the angry and the disgusted person the same way, the Mayans should do more poorly in the matching game.

As I’m sure you’ve guessed, the Yucatec Maya speakers performed the task just as well as the German speakers. Mayans may not have a word for ‘disgust’, but they know it when they see it.