Science-- there's something for everyone

Tuesday, November 30, 2010

First confirmed planet from another galaxy

Over 500 exoplanets have been found within our own galaxy, but no confirmed extragalactic planets have been identified. Until now. Johny Setiawan and his colleagues from the Max Planck Institut have discovered a planet orbiting a star of extragalactic origin.

The star in question, HIP 13044, is currently in our galaxy, having been swallowed by the Milky Way about six to nine billion years ago. At the time of its formation however, it was part of a nearby dwarf galaxy. That means that both it and its planet (HIP 13044 b) which was detected by observing the gravitational wobble of the star, are of extragalactic origin.

To make HIP 13044 b even more interesting, it apparently survived its star’s red giant phase. This is a late stage of stellar evolution in which stars about the size of our sun, having depleted their hydrogen reserves, go through an enormous expansion (the sun will expand to encompass the entire orbit of the Earth) and then contract again. Perhaps due to this expansion event, HIP 13044 b is currently extremely close to its star.

This artist's impression shows HIP 13044 b, an exoplanet orbiting a star that entered our galaxy, the Milky Way, from another galaxy. This planet of extragalactic origin was detected by a European team of astronomers using the MPG/ESO 2.2-metre telescope at ESO's La Silla Observatory in Chile

Credit: ESO/L. Calçada

Monday, November 29, 2010

Sonar for bubbly water

Standard sonar devices, which work by using the echoes of sound pulses to identify objects, are blinded by clouds of bubbles. This makes them ineffective in shallow water where waves are breaking, or near the wakes of ships. Timothy Leighton and his colleagues from the University of Southampton have invented a way to solve this problem. Their method, called twin inverted pulse sonar (TWIPS) can see through bubbles.

TWIPS uses two inverted sound pulses emitted a fraction of a second apart. In combination, the pulses enhance the scatter from a target while simultaneously suppressing clutter from interfering bubbles.

Leighton and his team tested TWIPS both in a large tank and at sea. They were able to detect objects despite interference from lab-created bubbles or oceanic waves. In either case, TWIPS outperformed standard sonar devices.

Interestingly, Leighton got the idea of developing a sonar device that could see through bubbles by observing wild dolphins. Some dolphins use their sonar to make bubble nets to confuse and trap prey. However, if dolphin sonar worked like conventional man-made sonar, this would mean that the dolphins were blinding themselves to the prey within their own bubble nets, an unlikely prospect. There had to be a way to counteract the bubbles. Because no one has taken sonar recordings of bubble-net hunting dolphins, it’s not clear whether they use a system like TWIPS or something completely different. In either case, observing the dolphins provided the spark that lead to Leighton’s breakthrough.

Tim Leighton with dolphin.

Credit: Image courtesy of National Oceanography Centre, Southampton (UK)

Sunday, November 28, 2010

Bacteria fight with toxic darts

Researchers at the University of California—Santa Barbara have found that some bacteria conduct advanced warfare on their competition. They inject toxic darts into their opponents.

The bacteria in question, which include some common pathogens, have cell surface proteins that contain toxic dart tips. The toxic dart is delivered into the victim cell in a process called ‘contact dependent growth inhibition’. In other words, the two cells must be touching to trigger this response. The attacked cell is sometimes killed, but often is simply prevented from further growth and reproduction (similar to many of our synthetic antibiotics). For example, the toxin might enter the enemy cell and chop up RNA, preventing protein synthesis. In any case, the attacked cell is removed from competition for resources.

As with all types of biological warfare, there are countermeasures. Some bacteria have an immunity protein on their cell surface that acts as a shield against the toxin. This ‘contact dependent growth inhibition immunity’ inactivates the toxic dart.

Up to 50 distinct toxic-tip proteins have been discovered, each with its own antidote (at a minimum, each bacteria carries the shield against its own toxin). The biologists hope that this discovery will yield an advantage in the war against pathogens, especially in this era of increasing antibiotic resistance.

Saturday, November 27, 2010

Trapping antimatter

For the first time, physicists at Swansea University have been able to trap anti-hydrogen for study. This Anti-hydrogen Laser Physics Apparatus (ALPHA) project at CERN will allow researchers to directly compare anti-matter and matter, and perhaps yield insights into why the universe looks the way it does.

ALPHA experiment fully assembled.

© Niels Madsen, ALPHA, CERN

Antimatter is the mirror image of regular matter in terms of charge and other subatomic properties. Whereas normal hydrogen is composed of a proton and an electron, anti-hydrogen is composed of an antiproton and a positron. Antimatter has been predicted for nearly a century, and experimentally produced for nearly a decade. However, until now, there has been no way to affectively study antimatter. This is because antimatter is instantly annihilated upon contact with regular matter. In other words, there hasn’t been any possible container for long-term study of antimatter.

Enter Mike Charlton and his colleagues. They devised a way of cooling and slowing anti-particles (antiprotons and positrons) so that they can form anti-hydrogen. This part wasn’t new. The innovation was in using magnetic coils to trap the anti-hydrogen after it’s created.

These sorts of experiments have a very long lead time. The physicists involved expect to begin running experiments on their anti-hydrogen atoms in about five years. I’ll try to keep you posted.

Friday, November 26, 2010

Just for fun: ESO images

The European Southern Observatory has a list of its top 100 images. Number one, 'The hidden fires of the Flame Nebula', is shown below. The rest are just as stunning.

The hidden fires of the Flame Nebula

Credit:ESO/J. Emerson/VISTA. Acknowledgment: Cambridge Astronomical Survey Unit

Hat tip: Bad Astronomy.

Thursday, November 25, 2010

Finding a pain gene

An international team of scientists has identified a gene that is implicated in the sensation of pain. In particular, this gene allows both insects and mammals to sense dangerous levels of heat.

In an attempt to find genes involved in feeling pain, the researchers altered nearly 12,000 fruit fly genes, and then tested the resulting mutant flies to see which ones failed to flee from areas of excessive heat. 600 possible candidate genes passed the first round of experiments. Eventually, the team narrowed their focus to a single gene called alpha2delta3, which encodes part of a calcium channel. Calcium and other ion channels are critical for nerve signal conduction, so it’s not surprising that they form an integral part of pain sensation.

The scientists next examined mice that were missing the same alpha2delta3 gene and found that they too lacked the heat avoidance behavior. MRI study of the mouse brains showed that rather than sending the pain signal to the cortex for processing, that signal was activating other senses, such as vision, smell or hearing. This sort of cross-activation of senses, also known as synesthesia, occasionally occurs in humans, though the connection to pain sensation has not previously been noted.

Finally, the molecular biologists examined 189 healthy human volunteers who had variations in or around their alpha2delta3 genes. Some of the mutations did result in reduced sensitivity to pain. Among another 169 patients who had undergone back surgery, the ones with these same mutations were much less likely to have persistent chronic pain.

The scientists hope that by identifying genes involved in sensing pain, doctors will be able to tailor analgesics to more closely fit patients’ needs.

Wednesday, November 24, 2010

Stochastic Scientist hits 10,000!

It’s been just under a year since I wrote my first blog post (about RNA self-assembling itself). Almost 400 posts later, I’ve reached over 10,000 people. Along the way, I’ve learned a great deal, both about putting together a blog and about the myriad topics I try to cover. I’d like to thank my readers, who I hope share my love of science in all its wondrous variety. I’ll keep going if you will!

Tuesday, November 23, 2010

Genetic boundaries between species

Our knowledge about living creatures has skyrocketed since the adoption of commonplace DNA sequencing. However, at the same time, that new information calls into question how species should be categorized. In other words, how should we define a species? Emma Vodoti from the University of Gothenburg has just completed a thesis that attempts to answer that question.

In the old days, pre 1980 or so, species were delineated purely by phenotype (physical or behavioral characteristics). If it looked different enough or if it displayed a unique behavior, particularly in mate attraction or selection, then it was labeled as a different species. With the advent of genome sequencing, biologists could compare organisms on the inside as well as on the outside. They’ve found some surprising things. It turns out that some organisms that look and act identical to one another are genetically unrelated. Case in point, the Atlantic horse mussel (Modiolus modiolus) was thought to be the same species as the identical looking Pacific variety. Upon finding that they are genetically distinct, one of the varieties will need a new scientific name.

Caption: Emma Vodoti conducts field studies.

Credit: Erik Boström

This brings us back to our question of how to define a species. Clearly, if two organisms have different enough genomes, they must be considered separate species. But what is ‘different enough’? This is the same question that was previously asked about physical appearance. When does a creature look different enough to be classified as a different species? There may never be an absolute dividing line. For one thing, as with phenotypic differences, some types of organisms can tolerate a greater degree of variety. Just look at dogs. For another, the delineations between species are manmade not natural, so there simply aren’t any sharp divisions between living creatures. Still, it’s an interesting exercise in cataloguing, particularly since genetic sequencing is bound to provide many more surprises.

Monday, November 22, 2010

Identifying risk-taking males by their finger length

Risk-taking behavior in men is closely associated with levels of testosterone. Erin Stenstrom and his colleagues from Concordia University found that not only did testosterone levels in the womb affect men’s proclivity for risk-taking, but that those prenatal testosterone levels could be predicted by looking at men’s finger length.

The researchers surveyed 413 male and female students for finger length and risky behavior, such as aggressive sports play. They found correlations for the men, but not for the women. In particular, the length of the index finger in comparison to the other finger lengths tells the tale. Baby boys who were exposed to higher amounts of testosterone in the womb had smaller ratios of index finger length to ring finger length, and of index finger length to the length of the other four fingers combined

As to why the effect is only seen in men, Gad Saad explains:

A possible explanation for the null effects in women is that they do not engage in risky behavior as a mating signal, whereas men do.

Sunday, November 21, 2010

First Human Methylome

UPDATE: It's been brought to my attention that other groups have previously completed partial and complete methylomes of human cell lines. To name two examples, Ryan Lister's group from the Salk Institute and Josesh Costello from the University of California, San Francisco have completed methylomes in 2009. I want to thank my readers for catching this error. Please keep correcting me!

For the first time, Chinese researchers have identified every methylated site in a human genome. This collection of methylation sites, known as a ‘methylome’ is already yielding valuable information about gene regulation and inheritance.

A person’s genome determines exactly which genes he or she will have. Many genes come in different alleles, or flavors, which explain some of the variability between people. However, it’s not just enough to have a gene, that gene must be expressed. It turns out that gene expression is largely controlled by non-genetic or epigenetic factors, a principal one of these being DNA methylation. At certain places along the DNA strand, predominantly on the cytosine in cytosine guanine pairs, a methyl group is added. This addition has consequences in gene expression and regulation.

Because the scientists studied the methylome of a man whose genome had previously been sequenced, they were able to compare the methylation of the genes he’d inherited from his mother with those inherited from his father. They found that many alleles were differentially methylated between the two parents, and that this affected which version was manifested in the offspring.

This methylome was sequenced in only one man, and in only one type of cells (peripheral blood mononuclear cells). Methylation undoubtedly varies in different tissue types, and definitely varies among different individuals (since even the two parents of the man under study showed different methylation rates). Nonetheless, this is an important first step in understanding how epigenetic factors make us who we are.

Saturday, November 20, 2010

The space-time cloak

Researchers from Imperial College London have thought of a way to use metamaterials to construct what they call a ‘space-time cloak’ that could conceal events.

Metamaterials are artificial materials that distort light or sound waves in particular ways. Martin McCall and his team got the idea of using metamaterials to speed up or slow down light. Light ordinarily varies in speed as it passes through different materials. By carefully controlling that speed, a window of invisibility can be created.

As McCall explains:

The leading half of the light speeds up and arrives before an event, whilst the trailing half is made to lag behind and arrives too late. The result is that for a brief period the event is not illuminated, and escapes detection.

Credit: Imperial College London

Although the researchers suggests that such a device could create the illusion of transporting people or objects instantaneously, a more likely usage would be in signal processing. For example, the space-time cloak could be used to temporarily interrupt a data channel in order to conduct a priority calculation. To an observer, it would appear as if there had been no interruption.

Alberto Favaro, a researcher on the project, gives the following analogy:

Imagine computer data moving down a channel to be like a highway full of cars. You want to have a pedestrian crossing without interrupting the traffic, so you slow down the cars that haven't reached the crossing, while the cars that are at or beyond the crossing get sped up, which creates a gap in the middle for the pedestrian to cross. Meanwhile an observer down the road would only see a steady stream of traffic.

Most of the applications remain theoretical at this stage, though a proof of concept design using optical fibers has been constructed.

Friday, November 19, 2010

Just for fun: Be the neurosurgeon

Here's your chance to be a virtual brain surgeon. The program designed by Edheads, a nonprofit educational organization, is called Deep Brain Stimulation. In this 'game', you actually get to practice drilling holes in peoples' heads. Warning, this game is quite graphic with pictures of actual brain surgery. For the squeamish, Edheads also presents Design a Cell Phone and other games.

Visit Edheads Deep Brain Stimulation!
Visit Edheads Design a Cell Phone!

Like all their products, Deep Brain Stimulation is free of teachers, students and parents.

Thursday, November 18, 2010

If it’s smooth, bats think it’s water

Bats use echolocation to locate insect prey and to navigate. Sources of water, which reflect the bats echolocation calls like a mirror, are particularly important both for drinking and for finding insects. Stefan Greif and Björn M. Siemers of the Max Planck Institute have found that bats will mistake any smooth surface for water.

In the wild, an extended echo-mirroring region is unlikely to be anything but a stretch of water. However, in urban and rural areas, many surfaces can create that illusion. The scientists simulated water surfaces with smooth plates of metal, wood or plastic to test how easily bats could be fooled. It turns out the bats were surprisingly easy to trick. Fifteen different species of bats all consistently tried to drink from the smooth plates and did not seem to learn that the plates were not water.

A Schreiber's bat (Miniopterus schreibersii), trying to drink from a smooth metal plate.

Credit: Image by Stefan Greif.

Greif and Siemers experimented with bats raised in their lab from an age at which they would never have seen water. The young bats also mistook the smooth regions for water, demonstrating that the behavior was innate, not learned.

Many of the drinking attempts took place under conditions where the bats could clearly see that the surface they were approaching was not water. In order to determine whether the bats used their other senses at all, the researchers ran the same experiments in the dark. With no visual cues, the bats increased their attempts to drink from 100 times to 160 times in ten minutes. Although the bats were using their other senses, they relied much more heavily on their echolocation.

The authors would like to test bats in rural settings next, to see how much they are affected by manmade horizontal mirrors such as car or roof tops. Do the bats eventually learn to ignore those surfaces, or do they die of exhaustion and thirst?

Wednesday, November 17, 2010

Stone tool advancements

Left: Oldowan stone tool; Right: Acheulean stone tool

Starting about 2.5 million years ago, early hominids developed the technology to shape simple stone knives. After that, there was no advancement for almost two million years. Then, about 500,000 years ago, the hand axe was developed. Why did it take so long to achieve this technological breakthrough? According to new research lead by Aldo Faisal of Imperial College, London, humans had to wait for their brains to catch up with their hands.

There had been a couple of prevailing theories as to why there was such a long lag time between the development of the first stone tools and the creation of more sophisticated axes and knives. One view was that early hominids lacked the manual dexterity and precision required to fashion the more delicate items. The other view was that we simply didn’t have the computing power needed to visualize and plan complex tool-making.

Faisal and his team outfitted an experienced flint-knapper (someone proficient at making stone tools) with a specialized ‘cyberglove’ that recorded data on grip and movement. The flint-knapper created both simple (Oldowan) stone tools and more complex (Acheulean) tools. He also performed a variety of manual activities that involved sorting and gripping items. The researchers found that the manual dexterity required to make both simple and complex tools was the same. In other words, the limiting factor in early tool use was not physical, but cognitive. Perhaps not coincidentally, the mental leap to the manufacture of complex tools coincided with the development of language.

By the way, it's not clear exactly which hominid species was responsible for inventing these different tools. Oldowan tools have been associated with some Australopithecines, and also with some early Homo species. Acheulean tools have been found with the remains of Homo erectus.

You can watch Dietrich Stout, an Emory archeologist and one of the authors on the study, discuss the making of stone tools below.

Tuesday, November 16, 2010

Real-time 3D holograms without glasses

A team of optical scientists lead by Nasser Peyghambarian from the University of Arizona, and by scientists from the Nitto Denko Technical Corporation, has improved the hologram. Most significantly, their device is capable of refreshing every two seconds, a hitherto impossible achievement.

Briefly, holograms rely on light interference patterns. One beam of light illuminates the object. The light scattered from this illumination is detected by the recording medium. At the same time, another beam of light strikes the recording medium. The interference pattern between the two light sources creates the hologram.

Currently, holographic recording media cannot be updated in any meaningful way. It just takes too long to generate each individual image. This new method will allow someone to send a constantly changing hologram via the Ethernet to a distant location. In addition, although holograms are currently monochromatic, the team has demonstrated the capability to make their holograms multicolor 3D displays with refresh rates that approach those of TV images.

The researchers anticipate wide use for their device in areas as divergent as business or medical presentations, 3D mapping, and entertainment.

Monday, November 15, 2010

Helping the blind see

German researchers have developed and tested a retinal implant that allows blind people to see shapes and objects. This breakthrough may allow blind people to have a much greater degree of independence.

The device was tested on three individuals suffering from retinitis pigmentosa, a degenerative genetic eye disorder. The light receptors of patients afflicted with this disease eventually cease to function, resulting in incurable blindness. The scientists got the idea of implanting artificial light receptors beneath the patients’ retinas. In this way, the device could use the natural, undamaged image processing capabilities of the eye, rather than rely on external cameras and processors, as is the case for implants that lie outside the retina.

Functional scheme of subretinal implants.

Credit: © Retina Implant AG.

Thus far, the device has exceeded expectations. One volunteer was able to identify objects on a table, read a clock and differentiate between shades of gray.

Sunday, November 14, 2010

Improved malaria treatment

An international team of scientists and doctors, lead by Nick White of the Wellcome Trust-Mahidol University-Oxford Tropical Medicine Research Programme in Bangkok, has conducted one of the largest clinical studies ever done on malarial patients. They found that the drug quinine should be replaced whenever possible by a drug called artesunate.

This is interesting for a two reasons. First, this breakthrough gives us an important advantage in the battle against a millennium-old foe. Malaria (a mosquito-born illness) kills almost a million people each year, mostly pregnant women and young children. Artesunate was found to decrease the malarial death rate by 22% when compared with quinine. In addition, fewer side affects were experienced by patients receiving artesunate, including fewer comas and seizures.

The second point I’d like to make is that this is how science is supposed to work. Quinine and artesunate are both nominally herbal remedies. Quinine is derived from Cinchona tree bark and artesunate is derived from an herb called qinghao (Artemisia annua), shown here. Quinine had been the malarial treatment of choice for centuries when qinghao was first proposed as a malaria treatment. Although researchers were skeptical at first, they proceeded to test artesunate, culminating in the enormous African Quinine v. Artesunate Malaria Trial (AQUAMAT) just completed. Without this sort of rigorous comparison, doctors would still be prescribing quinine for their malarial patients.

Even with artesunate, the death rate is still 8.5%, so there is plenty of room for improvement. The next drug candidates should now be tested against artesunate, rather than quinine.

Saturday, November 13, 2010

Bees solve traveling salesman problem

The traveling salesman problem is a common mathematical exercise. The hypothetical salesman must take the shortest possible route to visit a number of customers. Most people use computers to figure out which route is the most economical, but Mathieu Lihoreau, Lars Chittka and Nigel Raine of Queen Mary University of London found that bees can do it just as well.

The researchers presented bees with four patches of flowers placed in a non-optimal order. If the bees chose to return to the flower patches in the order in which they first found those flowers, they’d be covering a much longer distance than if they could optimize their route. Not only could the bees quickly figure out the shortest route to all four flower patches, but the next day the bees remembered that optimal route. Apparently, bees are constantly calculating energy saving routes rather than simply retracing their flights to flower sources.

As Raine points out:

Despite their tiny brains bees are capable of extraordinary feats of behavior. We need to understand how they can solve the Traveling Salesman Problem without a computer. What short-cuts do they use?

Friday, November 12, 2010

Just for fun: Electron microscopy

Martin Oeggerli is a master at photographing the extremely small. His camera is the electron microscope, and with it he has captured everything from blood cells to insect eyes. National Geographic is currently running a slide show of his spectacular photographs of insect eggs.

You look through his photo gallery here, or watch a slide show of his stunning work below.

Thursday, November 11, 2010

Changing skin cells into blood cells

For the first time, scientists have been able to change one mature type of cell directly into another type of cell, bypassing the potentially cancerous pluripotent stage. Mickie Bhatia lead a team of researchers from McMaster University in transforming human skin cells into blood cells.

Every cell in our bodies contains the same genome as every other cell. However, not all those genes are turned on in all cell types. Specific combinations of gene activation, as well as environmental factors such as nutrients and hormones, determine what kinds of cells will develop. The hard part is figuring out exactly which combinations will create the desired effect. After much trial and error, the researchers discovered that turning on the gene OCT4 was sufficient to reprogram skin cells into becoming blood cells. In addition, playing around with specific growth factors allowed them to manufacture different types of blood cells. For example, leaving out erythropoietin caused the skin cells to change into neutrophils and macrophages (white bloods cells)

In the past, human skin cells have been converted to other types of tissues through a two-step process. First, the skin cells are converted into pluripotent stem cells. Next, these pluripotent cells are programmed to change into any kind of cell, including blood cells. One major drawback of this method is that the pluripotent cells often become cancerous. This new process bypasses the pluripotent stage, and hopefully the ability to form tumors.

The scientists plan to start clinical trials as early as 2012. If those tests are successful, this cell conversion method will be enormously beneficial. Anyone needing blood products, whether due to injury, surgery or cancer treatment will be able to rely on their own skin cells to provide those products. Besides obviating the need to rely on donors, there would be zero risk of rejection.