Science-- there's something for everyone

Sunday, January 31, 2010

Handedness affects perception

In many languages, the word ‘right’ is often associated with positive and correct things, while ‘left’ can often mean inadequacy or wrongness. But do those associations hold true for both right and left-handed people? Daniel Casasanto of the Max Planck Institute for Psycholinguistics has conducted a series of experiments to test those perceptions.

In one experiment, volunteers were given a cartoon of a character standing between two empty boxes. They were told that this person goes to the zoo, and that he loves zebras and thinks they’re good, but hates pandas and thinks they’re bad (the order of the animals and their natures were switched around randomly). The volunteers were then asked, if the character wishes to place one animal in the good box, and the other in the bad box, where should he put them?

Right-handed people placed the animal described as ‘good’ on the right side of the page, but left-handed people placed it on the left. If these experiments were conducted on right-handers who had had their right hands restrained for a period of time, making them effectively left-handed, their tendency to assign the good animal to the left box increased five times.

In other experiments, subjects were asked to rate pairs of objects or people for traits like attractiveness, intelligence, honesty, or to decide which item they would buy or hire. Universally, right-handed people preferred the object on the right, whereas left-handed people gave higher marks to the object on the left.

Only 14% of the test subjects noticed any correlation between their choice and their handedness. These data show that our sensory-motor experiences can strongly but subconsciously influence our perceptions of the world.

Saturday, January 30, 2010

Just for fun: More size comparisons

Click here to see the entire universe from yoctometer to Yottameter.

Caveat: size and in some cases existence of items smaller than electrons is speculative.

Hat tip: Bad Astronomy

True green vaccines

You wanted green vaccines? You got it!

Henry Daniell and his colleagues from the University of Florida have successfully tested a plant-grown vaccine for cholera and malaria in mice.

Article Main Picture

Henry Daniell works with a variety of plants in his research lab. Photo credit: Jacque Brund.

The team genetically engineered tobacco and lettuce chloroplasts to express the subunits from both cholera toxin and malarial antigens as a dual vaccine against both cholera and malaria. Chloroplasts were used to ensure that the engineered plants could not pass on their new traits via their pollen. The mice were presented (either by injection or orally) with freeze-dried plant cells containing the antigens and then subjected to cholera toxin or to malaria-causing Plasmodium.

Sadly, the untreated mice quickly died. On the other hand, the luckier vaccinated mice acquired immunity that lasted over 300 days (half a normal mouse lifespan).

Clinical trials on humans have not yet begun, but the researchers are optimistic. If this vaccine does prove to be effective in humans, it will be a huge boon. Currently, the only cholera vaccine is extremely expensive and only effective for three years. At present, there is no malaria vaccine.

Daniell’s lab has previously created plant vaccines against black plague and anthrax using similar methods. His lab is also working on making insulin-producing plants as a cure for diabetes.

Friday, January 29, 2010

Dishevelled cilia move to the left

Although mammals tend to be largely left/right symmetrical, there are differences between the two sides, particularly in the placement of internal organs. This ‘left-right symmetry breaking’ occurs very early in embryonic development. How do developing embryos differentiate in this way? Surprisingly, it is the movement of amniotic fluid across the developing embryo that creates the asymmetry.

Hiroshi Hamada and colleagues at Japan’s Osaka University have previously demonstrated that beating cilia on the early embryonic cells can cause the differential movement of amniotic fluid. The cilia are positioned so that they create a leftward flow of amniotic fluid.

A scanning electron micrograph of mouse embryo node cilia

For a more detailed explanation plus pictures, look here.

New research by Hamada and his team has identified a set of genes in mice that are involved in directing the placement of the cilia. They looked at genes from the ‘Dishevelled’ family (don’t you love geneticists?) and found that mutations in these genes did in fact prevent the cilia from migrating to the proper position on the cell. Mouse embyros with these mutations did not display the normal left-right symmetry breaking.

This finding could impact research on human birth defects.

Thursday, January 28, 2010

Faster than light speed?

Researchers at the Joint Quantum Institute (JQI) have made light appear to move faster or slower.

First, a quick primer on light and refractivity. Light travels about 300,000 kilometers per second or 186,000 miles per second, but it can only reach this velocity in a vacuum. This maximum speed is known by the value ‘c’. When traveling through other substances, such as glass or water, light can be slowed down considerably. Under those conditions, the speed of light is referred to as ‘v’ for velocity. The ratio between c and v (in other words, how close to its maximum speed light can achieve when passing through a substance) is called the refractive index. The higher the refractive index, the slower light passes through that material.

One more thing: light is made of photons, which exhibit properties of both particles and waves. Don’t ask.

OK, on to the good stuff.

The team of scientists made a 30 layer thick stack of dielectric materials, alternating between high and low refractive index. Each layer was about 80 nm thick (about 1/4 of the wavelength of the light they were testing). They passed photons through this stack and measured the time it took for the photons to reach a detector on the other side. This turned out to be about 12.84 fs (femtosecond, or 10-15 of a second). They then added one more layer onto the end of the stack. For reference, based on the additional distance, adding a single layer should have increased the transit time by 0.58 fs.

Yet, when they added a low refractive index layer to the end of the stack, the transit time increased to 16.36 fs. Even more surprisingly, when they added a single high refractive index layer, the total transit time decreased to only 5.34 fs.


What’s going on?

I mentioned that light is made of both particles and waves. It is the quantum properties of the light waves interfering with each other at each boundary between the layers that creates the illusion of faster than light speed. If all the photons made it all the way through, the speed would be exactly as expected.


Got that? I’ll let Paul Lett, one of authors of this study, have the last word:

A key strangeness of quantum mechanics is that it lets a particle tunnel through a barrier and appear on the other side. Even stranger is that the time it takes to appear on the other side of the barrier can be independent of the thickness. This leads to apparent travel times that can be faster than the speed of light.

Diagram credit: JQI

Wednesday, January 27, 2010

Four winged early glider

Microraptor gui was an unusual creature. It was a small dromaeosaurid (bird-like) dinosaur that lived about 125 million years. It had four wings rather than two, with its hind legs forming the second pair. Microraptor was assumed to be a glider, but the configuration of the four wings during gliding was a mystery. Were the first wings held above the leg wings in a biplane formation (see illustration at right), or were all the wings kept in a single plane like a dragonfly’s wings?

Both sides have proponents. Sankar Chatterjee of Texas Tech University is the strongest advocate of the biplane configuration, stating that Microraptor could not have bent its hips around into the dragonfly conformation. More recently, a joint team from the University of Kansas and from Northeastern University in China came to the opposite conclusion. They built an exact replica of a Microraptor based on some exquisitely preserved fossils. This team, led by David Alexander, used their model to show that not only could Microraptor have rotated its hind legs into a monoplane, but that that configuration provided for more efficient gliding.

Model of Microraptor as a monoplane glider, created by scientists at the University of Kansas.

Two interesting questions arise from this controversy. One is whether two pairs of wings were a precursor to the single pair seen in modern birds. Interestingly, this would have mirrored the technological evolution of human flight. Alternatively, the double pair of wings may have been a side shoot rather than a main branch of the evolutionary tree.

The second question is whether these findings can lay to rest the longstanding controversy over the evolution of bird flight. There are two predominant theories as to how avian flight developed. One theory postulates that ancestral birds lived in trees, and used their proto-wings to glide from limb to limb and to parachute down to the ground. A second theory says that bird-like creatures ran around on the ground and may have flapped their stumpy wings to aid them in hopping up after insect prey.

In other words, did flight begin from the top down, or from the bottom up? Although this question is not settled to everyone’s satisfaction, it is clear that Microraptor could not have spent much time on the ground. The seven-inch long feathers and curvy claws on its feet would have precluded such a possibility. So, in this case at least, flight must have begun in the trees.

Tuesday, January 26, 2010

Water keeps to itself

Scientists from Oregon State University and the Environmental Protection Agency used stable isotope analysis to ‘fingerprint’ water in the Cascade Range of Oregon and Washington, and keep track of exactly where it goes. They found that in dry areas, the first precipitation after a period of draught does not mix freely with older ground water. Instead, the new water is held by the soil surrounding plant roots.

Prior to this study, it was assumed that as new precipitation entered the soil, it became indistinguishably mixed with older water and trickled into nearby streams. Renée Brooks and her colleagues found that when the ground is dry, most of the precipitation that falls gets trapped in tiny pores surrounding plant roots. This water never mingles with ground water, but remains trapped in place until the plants draw it out via transpiration.

For example, after the first large rainstorm of the fall, 96% of the falling water was held around plant roots, and only 4% made its way into a stream. Later, after many rains had saturated the soil, 55% of falling water ended up in streams. Regardless of when the precipitation occurred, water that was originally held in soil around plant roots never ended up mixing and entering streams.

In other words, water can be divided into two separate ‘populations’ of molecules. This totally unexpected finding requires researchers to rethink everything from the movement of nutrients and pollutants through soil to how streams function.

Photo credit: Jina Lee, May 2007.

Monday, January 25, 2010

Just for fun: Crystal Cave

Iain Stewart from the University of Plymouth
takes us on a tour of the Naica Mine's crystal cavern. This working silver mine is located in Chihuahua, Mexico. In 2000, the brothers Juan and Pedro Sanchez discovered the 'Cave of Crystals' while drilling a new mine tunnel.

Stewart has to wear a special suit and breathing apparatus to combat the extreme heat and humidity (50 C or 122 F, and 100% respectively). Would you brave those conditions to see this?

Hat tip: Nancy Trump.

Could humans run 40 miles/hour?

Usain Bolt won the Olympic gold medal by running 23 miles per hour. How close to the human limit is that?

Runners push down on the ground with each step and that force propels them forward. A greater force against the ground equates to greater speed. Until recently, scientists thought that running speed depended entirely on this strike force. Elite sprinters can strike the ground with up to 1000 pounds of force at every step. This was thought to be the human limit. However, a new study by Peter Weyand of Southern Methodist University and his colleagues calls that into question.

Weyand and his team used a specialized treadmill that could go over forty miles per hour while making precise measurements of the foot forces on the running surface. Male and female runners were tested running at their top speeds forward, backward, and hopping on one foot.

The researchers found that the runners were striking the ground with considerably more force while hopping. This is not to say that the gold medal sprinters at the London games in 2012 will be hopping across the finish line. But clearly, humans are capable of much greater foot forces than was previously suspected. In other words, the amount of force applied to the running surface is not the limiting factor after all.

Instead, the researchers found that it’s the speed of the foot strike that is biologically limiting. This was corroborated by the fact that the foot-ground contact time was essentially identical for runners going forward or backward. The human top speed for ground contact appears to be less than a tenth of a second.

Matthew Bundle, an assistant professor at the University of Wyoming and one of the authors on the paper, said:

Our simple projections indicate that muscle contractile speeds that would allow for maximal or near-maximal forces would permit running speeds of 35 to 40 miles per hour and conceivably faster.

In a previous post, I mentioned that Oscar Pistorius’s artificial ‘cheetah legs’ gave him an advantage because they allowed him to reposition his legs more quickly. This new study confirms that foot strike speed is indeed the limiting factor. How humans can learn to increase that speed by over 50% is not clear.

Statue of Shirley Strickland outside the Melbourne Cricket Ground. Sculptor: Louis Laumen, photo by Melburnian, Oct. 2006.

Sunday, January 24, 2010

Double-tailed star nursery

The Elephant's Trunk Nebula, taken by NASA's Spitzer Space Telescope. NASA/JPL-Caltech/W. Reach (SSC/Caltech)

Thanks to some spectacular pictures like the one above, we now know that stars are formed in ‘molecular clouds’. These are spectacularly beautiful and immense clouds of gas and dust, also referred to as ‘stellar nurseries’.

Although these molecular clouds can take many different shapes, astronomers were amazed to find one with a double X-ray tail stretching more than 200,000 light years. Part of this tail is located in the ESO 137-001 galaxy, (219 million light years from the Milky Way), but it extends past that galaxy’s borders, a hitherto unknown possibility. It had been thought that star formation had to be limited to the interior of galaxies.

Photo of double-tailed glass cloud, courtesy of the Chandra X-Ray Observatory.

Michigan State University astronomer Megan Donahue led the international team of astronomers who discovered this anomaly. The first tail had been seen three years ago, but the discovery of the second tail, made by the Chandra X-ray Observatory, surprised everyone.

According to Donahue:

The double tail is very cool – that is, interesting – and ridiculously hard to explain. It could be two different sources of gas or something to do with magnetic fields. We just don’t know.

Saturday, January 23, 2010

Speedier vaccine production

Flu vaccines are safe and effective for most people. However, the usual production method does have disadvantages.

Currently, flu vaccines require a multistep process. To begin with, chicken eggs are inoculated with both the virulent flu virus, and also with a harmless but related virus. The two viruses are allowed to recombine, and the resulting hybrids are tested. The ones that contain the outer proteins from the virulent virus (so the immune system can learn to recognize it) but the inner proteins from the harmless virus (so it can not infect) are chosen for the vaccine. At this point, large scale production can begin, with the vaccine strain of virus grown in more eggs, harvested, purified and inactivated. Over a billion were used for the H1N1’s 3 billion doses.

It’s immediately clear that one liability is the amount of time required to make the vaccine. At best, the process takes five months, and can take much longer. Among other problems, slower than usual viral growth or a shortage of eggs can cause substantial delays. Another drawback is the fact that people who are allergic to eggs cannot use the vaccine.

To circumvent these issues, several labs are studying the use of virus-like particles (VLPs) as a means to make vaccines. These are particles that are similar to viruses because they have protein shell like a virus, but lack components essential for infection. For the purposes of vaccine production, the VLPs do not contain any nucleic acid, but are simply antigenic shells that can trigger an immune response.

Rather than waiting for the CDC to send out the inactivated hybrid virus before they can begin vaccine production, companies like Novavax can begin wide scale vaccine production as soon as the viral genetic sequence is known. For example, Novavax has created a H1N1 VLP vaccine by injecting insect cells with the three flu genes for making the VLP shell and for the antigenic proteins coating its surface. The cells then assemble the VLPs. The entire process takes weeks rather than months.

Novavax has already begun clinical trials with their VLP version of the H1N1 vaccine.

Friday, January 22, 2010

Seeing takes time

Weizmann Institute scientists and doctors led by Rafael Malach found that recognizing a visual object coincided with a burst of neural activity. That recognition was not instantaneous, however, but required a minimum amount of time.

The experiments were performed on epileptic volunteers with pre-surgical electrodes implanted in their brains. These subjects were shown a screen shot of a recognizable image, called the ‘target’, consisting of a face, house or other man-made object. At different time intervals after the target image, a meaningless picture, called the ‘mask’ was put on the screen. The researchers could compare the electrical signals from the brain with the subjects’ claims of recognition of the target image.

Malach states:

We found that there was a rapid burst of neural activity occurring in the high-order visual centers of the brain – centers that are sensitive to entire images of objects, such as faces – whenever patients had correctly recognized the target image.

The volunteers were able to recognize the target and have the corresponding burst of neural activity if the target was left on the screen for at least 150 milliseconds.

Thursday, January 21, 2010

Where should the HiRISE look?

The HiRISE camera on board the Mars Reconnaissance Orbiter has been taking some spectacular pictures of Mars. Now they're giving the public a chance to choose where to aim the camera. If you want to put in your two cents, go
here, sign in and tell them what you'd like to see photographed.
Image: Layers in the lower portion of two neighbouring buttes within the Noctis Labyrinthus formation on Mars.

Thanks to Phil Plait's Bad Astronomy Blog.

That's knot light

Always thought light traveled in a straight line? That’s only when it isn’t being tied in knots. A team of physicists working at the universities of Bristol, Glasgow and Southampton recently did just that.

Under certain conditions, light can be twisted into a helix around its travel axis. In that case, the light along the axis itself is cancelled out, and the light appears to be corkscrewing rather than traveling in a straight line. This twirling light pattern is called an ‘optical vortex’.

Lead author Mark Dennis and his team took this one step further. They used knot theory (a hitherto purely abstract branch of mathematics begun by Lord Kelvin in 1867 and inspired by… well… knots) to design holograms that could direct the flow of light into optical vortex knots.

The researchers are confident that this new laser technology will find wide usage in a variety of industries.

Illustrations: The coloured circle represents the hologram, out of which the knotted optical vortex emerges.

Wednesday, January 20, 2010

Rewiring the Brain

There is a growing body of evidence that autistic spectrum disorders (ASD) are the result of miswiring within the developing brain, leading to connectivity problems. To test this hypothesis, Mustafa Sahin and his team at Children's Hospital Boston studied a rare disorder called tuberous sclerosis complex (TSC) which is often associated with ASD.

TSC is caused by defects in either the TSC1 or TSC2 genes. It is now known that the TSC1 and TSC2 gene products inactivate an enzyme called mTOR, which in turn controls neural growth. This corroborates Sahin’s data from 2008 showing that disrupting TSC1 and TSC2 caused neurons to sprout two or more axons, rather than the single one that normal neurons have. More recently, they found that disrupting TSC2 prevented mouse retinal axons from mapping correctly from the retina to the visual area of the brain. Instead, the neurons continued to grow past the point where they should have stopped.

The next step was to examine the brains of humans. Sahin and his colleague Simon Warfield used diffusion tensor imaging (a type of MRI) to examine the brains of 10 TSC patients, (7 with autism or developmental delay), and 6 unaffected controls. The researchers found abnormal and poorly myelinated axons in the TSC sufferers.

Can anything be done with this new data? Possibly. There is a drug called rapamycin which is an inhibitor of mTOR. In fact, mTOR stands for ‘mammalian Target of Rapamycin’.

Rapamycin is already FDA approved to prevent organ rejection in transplant patients. In mouse studies, abnormal neurons that had been growing multiple axons reverted to only growing one axon when presented with rapamycin. Rapamycin even normalized myelination in mice.

Although these results seem promising, we won’t know whether this treatment will yield any benefits until more data is collected. Sahin plans to launch a clinical trial of rapamycin in TSC patients later this year.

Tuesday, January 19, 2010

Galaxy Questions

Galaxies can have as few as a couple of millions stars or as many as a trillion. They come in three basic shapes, now called the ‘Hubble sequence’ after the American astronomer Edwin Hubble: spiral with a round center, barred spiral (with an elongated center), and elliptical with a more or less uniform distribution of stars and no visible arms. By this definition, our own Milky Way is a barred spiral.

Hubble sequence by Ville Koisinen: elliptical galaxies on the left, spirals top right, barred spirals bottom right.

There are two interesting puzzles regarding galaxy formation. One is why there are so many ‘dwarf’ galaxies containing far fewer stars than would be expected. The other is why galaxies come in these distinct shapes.

To answer the first question, Fabio Governato from the University of Washington and his international team ran simulations of galaxy formation on supercomputers. After millions of hours of computing time (the equivalent of several centuries), they uncovered evidence that it was the explosion of massive new stars into supernovas that was limiting the number of stars in those galaxies. As the stars exploded, the blast waves swept away huge amounts of gas that could have been made into other stars.

Governato’s results are also consistent with the cold dark matter theory, which, among other things, states that galaxies form within haloes of dark matter.

This brings us to the second question of why galaxies have the particular shapes they have.

Andrew Benson of the California Institute of Technology (Caltech) and Nick Devereux of Embry-Riddle University in Arizona postulated that the nascent galaxies merged in different ways with their surrounding haloes of dark matter. The final galactic shape depended on the number and type of these mergers. For example, the barred spiral of our own Milky Way would have resulted from some minor collisions with its halo, followed by the collapsing of the inner disk into a bar.

To test their hypothesis, Benson and Devereux used the infrared Two Micron All Sky Survey (2MASS) to track the formation of galaxies since the Big Bang. After crunching the numbers, they found that their computations could account for both the shape and relative numbers of galaxies.

Monday, January 18, 2010

Just for fun: Size comparisons

Unfortunately, I could not embed this, but have a look

The slider on the bottom takes you from a coffee bean to a carbon atom. Fun for everyone.

Desirable objects are further than they appear.

In five related sets of experiments, Emily Balcetis from New York University and David Dunning from Cornell University tested how desire affects perception.

In the first set of experiments, researchers asked volunteers (half of whom had been eating salty pretzels) to estimate the distance to a water bottle. As a group, the thirstier subjects all thought the water was closer than did their unsalted counterparts.

In another set of experiments, volunteers were asked to toss a beanbag onto a gift card that was worth either $0 or $25. They threw the beanbag much farther if the card wasn’t worth anything. The $25 cards seemed to be closer.

All the experiments confirmed that estimates of physical proximity are affected by desire. The researchers suggest that our brains perceive desired objects as being closer in order to increase our motivation to go and get it.

Sunday, January 17, 2010

Caffeine OK for tinnitus sufferers

It is a commonly held assumption that caffeine makes tinnitus worse. Lindsay St. Claire of the University of Bristol set out to test this hypothesis.

Sixty-six tinnitus-suffering volunteers who normally consume at least 150 mg per day of caffeine took place in a thirty-day trial. They were divided into two groups. One group consumed their usual amount of caffeine for 15 days, was weaned off caffeine over three days, and then had no caffeine for the remaining time. The second group was weaned off caffeine over the first three days, spent the next 11 days without caffeine, and then was brought back to their normal levels. Neither group ever knew whether or not they were receiving caffeine that day.

The volunteers recorded their tinnitus experiences throughout the month. The conclusion of the study was that tinnitus severity was not affected by caffeine consumption.

Saturday, January 16, 2010

Wasp genome sequenced

The genomes of three species of parasitic wasp, all from the genus Nasonia, have been sequenced. John Werren of the University of Rochester was one of the team leaders of the international consortium of scientists who achieved this multiyear project.

Why is this finding significant?

Parasitic wasps are major predators of insects. There are 600,000 different species of parasitic wasp, each of which has a specific preferred prey. Being able to raise wasps could be a huge boon to agriculturalists and environmentalists who prefer to limit pesticide usage. In addition, the venoms employed by these tiny creatures (Nasonia or 'jewel' wasps are no more than 2 mm long) could prove to have a range of pharmaceutical uses.

The value of this data goes far beyond simply using the wasps for pest control. Now that we have its entire genome sequenced, Nasonia may be an even more valuable animal model than that gold standard of insects models, Drosophila melanogaster (the fruit fly). For one thing, the genomic analysis has uncovered almost 7000 wasp genes that have recognizable equivalents in humans.

For another, unlike flies, the male wasps have only a single set of chromosomes. This makes genetic analysis much simpler. In diploid organisms such as ourselves, you may need to alter both copies of a gene to see any differences. With only one copy of each gene, the effects of a single change can be immediately visible.

Also unlike flies but like humans, wasps use methylation to regulate their genes. It is becoming increasing evident that methylation plays a major role in development and regulation.

Another advantage is that the different species of wasp can crossbreed with each other. Researchers can use this ability to finesse out the causes of speciation. A major controversy in evolutionary biology is whether regulatory changes (changes in non-coding regions) or protein changes (alterations in the coding portions of genes) are more often responsible for differences between species. The first experiments to test this are already underway. For example, Werren and his colleagues found that the non-coding regions of DNA are responsible for wing size differences between two Nasonia species.

One last point of interest to come from this data: Werren and his colleagues found bacterial and viral genes in Nasonia.

Werren says:

“We don’t yet know what these genes are doing in Nasonia, but the acquisition of genes from bacteria and viruses could be an important mechanism for evolutionary innovation in animals, and this is a striking potential example.”

Image of female Nasonia vitripennis (one of the three sequenced species) by M.E.Clark.