Science-- there's something for everyone

Monday, May 31, 2010

Small forest patches are worth saving

As the human population spreads across the globe, forested areas become more and more fragmented. There has been some question as whether the tiny patches of green interspersed between urban areas are sufficient to sustain the animals that once lived in those areas. For one little bird, the answer appears to be ‘yes’.

Swainson’s thrushes (Catharus ustulatus) migrate between Canada and South America. Along the way, they require refueling stopovers where they fill up on insects and berries. Paul Rodewald and Stephen Matthews from The Ohio State University trapped and radio-tagged the birds while they were migrating north through Columbus Ohio, and released them into seven woodlots, ranging in size from one hectare (1.7 acres) to about 38 hectares (93.9 acres). The researchers then observed whether the birds remained within the small forest patches where they were originally placed until ready to continue migrating, or moved to other nearby regions. It turned out that almost all the birds found sufficient food in even the smallest sites.

A researcher attaches a radio transmitter to the back feathers of a Swainson’s Thrush.
Photo by Ken Chamberlain, Ohio State University.

Obviously, this finding does not translate to all species. In particular, large predators are unlikely to find enough food in small fragmented patches of forest. However, it is nice to know that saving green areas between housing developments can allow some species to continue to thrive.

Sunday, May 30, 2010

Just for fun: Air Jelly

Festo, a company specializing in pneumatic and electric drive technolog, has developed the 'AirJelly'.

While you're at it, you might want to check out Aqua Jelly.

Hat tip: Pharyngula.

Saturday, May 29, 2010

New scramjet successfully tested

The U.S. Air Force has successfully tested an experimental aircraft called the X-51A Waverider. This unmanned vehicle traveled at Mach 6 (six times the speed of sound) for 200 seconds, crushing the 12 second flight record of earlier models.

The X-51A, built by Boeing with a Pratt & Whitney Rocketdyne engine, is a supersonic version of a ramjet. This type of craft is therefore dubbed a ‘scramjet’. Unlike conventional jets, which use fans to compress air in the engine prior to igniting it, ramjets use the aircraft’s speed to compress the incoming air. Ramjets have to slow the incoming air to subsonic levels, whereas scramjets use supersonic airflow through their engines.

Obviously, this was only a preliminary test with an unmanned vehicle. However, to put this kind of speed into perspective, if an equivalent manned scramjet could safely fly for an extended period, it could take its passengers from New York to London in about three quarters of an hour.

According to Charlie Brink, a X-51A program manager with the Air Force Research Laboratory at Wright-Patterson Air Force Base:

We equate this leap in engine technology as equivalent to the post-World War II jump from propeller-driven aircraft to jet engines.
The X-43 is the previous model of scramjet.

Friday, May 28, 2010

Keeping everything in focus

Keigo Iizuka of the University of Toronto, in collaboration with David Wilkes, president of Wilkes Associates, has developed the ‘Omni-focus Video Camera’. This novel device keeps both background and foreground objects in continuous sharp focus.

First, Iizuka had to invent a new distance-mapping camera (the Divergence-ratio Axi-vision Camera, or Divcam). The Divcam measures the distance from itself to each pixel in the intended image. An array of video cameras, each containing an integrated Divcam, makes up the entire Omni-focus system. Information from the different cameras is compiled to form one focused image.


Figure 1a: Image taken with prototype Omni-focus system using two color video cameras

Figure 1b. Same image with conventional camera

Credit: University of Toronto

The system is still in the initial development phase. When perfected, the researchers anticipate a range of uses for the Omni-focus Video Camera including improved coverage of televised events where background and foreground performers are simultaneously in focus.

Iizuka also thinks the device could be useful in the field of medicine:

I'd like to apply the principle of the Omni-focus Video Camera to the design of a laparoscope. It would help doctors at the operating table, if they can see the entire view without touching optics of the laparoscope, especially if dealing with a large lesion.

Thursday, May 27, 2010

Gulp your food to grow big and strong

Martin Sander of the University of Bonn, Germany and a large group of German scientists have uncovered clues as to how sauropod dinosaurs were able to grow so large. It turns out that one important advantage was that they did not chew their food.

It’s no surprise that larger animals require more food. African elephants, weighing up to 12 tons, devote sixteen hours per day to eating. How were 50 ton sauropods able to find the time to gather the amount of food they must have required each day? The answer lies in their long necks. The long necks allowed these animals to gather vegetation by sweeping their heads across vast regions, rather than by expending the energy required to move their enormous bodies.

Unfortunately, most animals cannot support their heads on long stalk-like necks. Elephants, to go back to our earlier example, have massive heads supporting huge grinding molars. These molars are essential for chewing and crushing the elephants' food. Sauropods got around this obstacle by not bothering to chew their food. Gulping down vegetation without chewing allowed sauropods to evolve tiny, light heads, which could easily be supported by their long necks.

Chewing does have advantages, not least of which that it allows greater absorption of nutrients, especially from plants. Apparently, the sauropods were able to get enough calories to sustain themselves even with less complete digestion.

Sauropod diagram by Dinoguy2, August 8, 2007

Wednesday, May 26, 2010

Possible drug treatment for one type of autism

Before I report on this story, I’d like to caution my readers that this treatment is only in the earliest stages of testing. Still, it’s pretty exciting news. Joseph Buxbaum of the Seaver Autism Center for Research and Treatment at Mount Sinai School of Medicine and his colleagues have successfully improved nerve cell connections in mice by giving them a derivative of insulin-like growth factor-1 (IGF1).

The mice in question have a gene mutation called SHANK3, which is associated with Phelan-McDermid Syndrome (an autism spectrum disorder). In humans, along with physical abnormalities, the SHANK3 mutation causes language delays and other autistic symptoms. Mice with the same mutation have nerve cells that cannot communicate with each other properly, leading to neurological symptoms.

As an aside, Gudrun Rappold and his team from Heidelberg University Hospital have now implicated the SHANK2 gene in autism as well. The Shank proteins are molecular scaffolds, meaning they function as support structures that hold other proteins or factors in their proper places. They appear to be critical to the structure and function of nerve synapses.

But back to our SHANK3 mouse studies. Buxbaum and his team treated the mice with IGF1. In only two weeks, the mice had improved nerve cell communication and were able to react normally to stimuli. The hope is that by restoring nerve function, autism spectrum symptoms would be diminished or eliminated. The scientists plan to continue observing the mice to determine what specific neuronal changes were caused by the IGF1 injections.

As I said, this treatment is not yet ready for human trials. However, these preliminary tests are promising, especially since IGF1 is already approved for human use (to treat growth failure), and thus is likely to be relatively safe.

Tuesday, May 25, 2010

Youth is in the jawline

It’s not only surface features that cause a person to look older. New research by Rochester Medical Center doctors shows that it’s the underlying bones that are most responsible for aging looks.

The physicians used facial computed tomography (CT) scans of 60 men and 60 women, evenly divided among three age groups (20-36, 41-64, and 65 and up), to compare jawbone length, width and angle. They found that in older individuals, the jaw angle was significantly increased while the jaw height and length was decreased. Overall, the older subjects had a much smaller total jaw volume, leading to less support for the facial soft tissues. This, in turn, leads to a general softening and sagging in facial appearance.

Significant changes in facial bones -- particularly the jaw bone -- occur as people age and contribute to an aging appearance.

Credit: Image courtesy of University of Rochester Medical Center

Study author Robert Shaw concludes:

The future of facial cosmetic procedures to restore a youthful look may include methods to suspend soft tissue -- such as chin and cheek implants -- to rebuild the structure that time has worn away, in addition to lifting and reducing excess skin.

I conclude that I’m glad I never plan to have a facelift, because now I also don’t have to have reconstructive jaw surgery to go with it.

Monday, May 24, 2010

Light at a weird angle, is invisibility next?

Harry Atwater and Stanley Burgos of Caltech, and Rene de Waele and Albert Polman of the Center for Nanophotonics, Amsterdam, have invented a way to bend visible light the 'wrong' way. This may be a first step toward creating an invisibility cloak.

The scientists engineered a ‘metamaterial that has a negative index of refraction, causing entering light waves to exit at an unexpected angle. This part has been done before. What's new is that Atwater's negative-index metamaterial (NIM) was effective for a wide range of incoming light angles and polarization levels. In other words, this new NIM is the first optical material to be able to negatively refract light in the visible spectrum. According to Atwater, among other applications, this could open the door to invisibility cloaking.

Another advantage over earlier NIM's is that the new material consists of only a single layer, making it easier to manufacture. In addition, the new NIM is tunable to different incoming wavelengths and outgoing angles. Atwater and his team believe that their new metamaterial will be especially useful for collecting sunlight for use in solar cells.

Arrays of coupled plasmonic coaxial waveguides offer a new approach by which to realize negative-index metamaterials that are remarkably insensitive to angle of incidence and polarization in the visible range.
Credit: Caltech/Stanley Burgos.

Sunday, May 23, 2010

Just for fun: The Elements song

This song, entitled
The Elements for obvious reasons, was written and song by Tom Lehrer in 1959.

Youtube user TimwiTerby created the animation to go with it in 2008.

By the way, news of element 112, named Copernicium, has now reached Harvard.

Saturday, May 22, 2010

Creation of artificial bacteria

Craig Venter and his team from the J. Craig Venter Institute have built the first bacterial cell with an entirely artificial genome. They placed a synthetic Mycoplasma mycoides genome into a Mycoplasma capricolum cell.

The bacteria M. mycoides was chosen because not only does it have one of the smallest genomes of any living organism, but it doesn’t even need all the genes it does have. Over a fifth of its genes can be disrupted without affecting the bacteria’s growth. Therefore, only about a million base pairs of DNA were required to create a functional synthetic M. mycoides genome.

This was still a daunting procedure, as the best DNA synthesizers cannot construct DNA strands longer than a few thousand base pairs. Thus, the entire genome was created in thousands of sections that then had to be stitched together in the correct order. In addition to the M. mycoides genes, some markers were added to help the scientists identify correctly spliced and functional DNA strands.

Finally, the entire genome was inserted into an M. capricolum cell that had no DNA of its own. These cells served as a host body for the synthetic genome. The newly created hybrid cells grew and reproduced. By any criteria you choose, they were alive.

A few caveats are in order here. First, it’s a far cry from a million base pair bacteria to a couple of billion base pair mammal. Splicing together a million segments of DNA in the correct order is just not within our grasp right now. Second, even if we could synthesize that much DNA and put it together, the error rate is still much too high to expect any viable results. The new bacteria cells, for example, contained eight single base pair changes, an 85 base pair duplication, and an E. coli transposon. In other words, don’t expect to see living synthetic dogs anytime soon.

It's also important to note that the synthetic cells were not really 'new' life forms, since Venter and his associates simply copied an existing genome. Still, this does open the door to creating new types of bacteria by altering the DNA before inserting it.

Friday, May 21, 2010

Seeing the hidden picture

Over the centuries, either to save space or because of changing social mores, many church murals have been painted over. Michael Panzner and other scientists at the Fraunhofer Institute for Material and Beam Technology IWS in Dresden have found a way to use terahertz (THz) radiation to uncover the hidden treasures underneath newer coats of paint.

THz radiation can penetrate multiple layers of paint and lime wash to reveal many consecutive paintings, something other forms of radiation, such as microwaves or UV, cannot do. Unlike more conventional methods, the THz scanner does not damage the more recent top paintings, which are sometimes also valuable.

The scanner consists of two main parts. A femtosecond laser scans over the wall mural, producing short bursts of THz radiation. By the way, a femtosecond is 10 − 15 of a second, so I do mean short. A separate detector scans the same wall picking up the radiation pulses reflected from the wall. Each layer and/or pigment on the wall reflects those pulses differently, and those differences are used to reconstruct the entire art history of that wall.

The technique has been successfully tested in the lab. Panzer and his team are eager to try their device, which they’ve dubbed the ‘reveal-all-scanner’, in a church.

The mobile scanner at work on a test wall. A software system reveals the structure of the concealed paintings.
Credit: Copyright Fraunhofer IWS

Thursday, May 20, 2010

Autism symptoms not improved by removing gluten or casein

A common treatment plan for autistic children calls for removing gluten and/or casein from their diets. Although there is anecdotal support for this diet, there haven’t been very many controlled tests. Susan Hyman and her colleagues from the University of Rochester conducted just such study and found no affect from gluten or casein.

In this study, autistic children were placed on a completely gluten-free, casein-free diet for at least four weeks. Prior to and during the test, the children were carefully evaluated for vitamin deficiencies. Children who tested positive for milk or wheat allergies or for celiac disease were removed from the study. The children all underwent similar behavioral treatments.

After the four weeks had passed, the children were given a once-a-week snack that contained gluten, casein, both or neither. The snacks were carefully prepared so as to be both palatable and indistinguishable. In other words, neither the kids, nor the parents, nor the research staff nor the teachers knew which snack was which. Each child received each type of snack three times, in random order.

Before each snack, and at two and twenty-four hours after each snack, parents, teachers and research assistants filled out detailed information about each child’s behavior and sleep and bowel habits. Play sessions were videotaped to evaluate social interaction and language skills.

When challenged with gluten and/or casein, the children exhibited no change in attention, activity, sleep patterns or bowel movements. This strongly suggests that gluten and casein have no affect on autism. Granted, this study was only completed by fourteen children. The authors also caution that some children, such as celiac sufferers, may get real benefits from excluding certain types of food from their diets. However, for most autistic children, it looks as though removing gluten and casein is not helpful, and may even be harmful if the children end up with nutritional deficiencies.

This study will be presented at the 9th International Meeting for Autism Research in Philadelphia.

Wednesday, May 19, 2010

Better vision while you sleep

As part of a master’s thesis at the UPC-Barcelona Tech’s College of Optics and Optometry, Jaume PaunĂ© developed a new kind of contact lens that improves vision while you sleep.

Using removable contact lenses rather than refractive surgery (permanent reshaping of the cornea) to correct vision problems is known as orthokeratology (ortho-K). The technique has been used for the last few years to treat myopia, (nearsightedness, or the inability to see far away objects clearly). PaunĂ©’s innovation was to create lenses that also work for hyperopia. Hyperopia (farsightedness) prevents a person from focusing on nearby objects.

The custom-made ortho-K lenses are worn only at night, effectively correcting vision during sleep. The lenses don’t actually touch the cornea, they alter its shape by applying slight pressure to the tear film covering the cornea. This temporary alteration results in improved vision the next morning. I should point out that hyperopia is usually genetic and not the same as age-related farsightedness (presbyopia). The new lenses are not meant to work for presbyopia, more's the pity.

Tuesday, May 18, 2010

College students invent salad spinner centrifuge

Rice University undergraduates Lila Kerr and Lauren Theis turned an ordinary salad spinner into a device for diagnosing anemia.

Caption: Rice University students Lauren Theis, left, and Lila Kerr created the Sally Centrifuge as part of a class on global health, and will take it overseas this summer for testing in developing countries.

Credit: Jeff Fitlow/Rice University

Ordinarily, anemia is diagnosed by spinning blood samples in a centrifuge until the heavier red blood cells separate from the rest of the liquid, or plasma. The ratio of red blood cells to total volume (hematocrit) can be used as a tool in diagnosing a number of diseases, such as malaria or HIV/AIDS. However, centrifuges are expensive and require an energy source. Salad spinners are cheap, light, and run solely on muscle power.

The two students were given the task of coming up with an anemia test that didn’t require an external power source by their Introduction to Bioengineering and World Health class professor, Rebecca Richards-Kortum. They assembled the device, named ‘Sally Centrifuge’ (in honor of the Sallyport archway at Rice), from a salad spinner, plastic lids, cut up combs, and yogurt containers. The entire thing cost about $30.

The prototype spinner performed as well as a real centrifuge. Besides the low cost, the Sally Centrifuge has the advantage of being made entirely of plastic, making it light and sturdy. If something does break off of one, you can always hot glue it back in place.

The students will be taking their spinners abroad this summer to test them in the field; Kerr to Ecuador and Theis to Swaziland.

Monday, May 17, 2010

Formula is not the same as breastmilk

A team of researchers from Texas A & M University, University of Illinois, and Mead Johnson Nutrition have developed a new way to detect differences between formula-fed and breastfed infants. The scientists, led by Robert Chapkin of Texas A & M, have discovered a host of intestinal genes that are expressed differently in the two groups.

Very quickly after birth, infants have to ‘learn’ not to mount immune attacks against their food or their newly acquired intestinal flora, but to attack potentially deadly pathogens. For this reason, Chapkin and his team decided to see whether the type of food received by the babies had any affect on their intestinal development.

The researchers got the novel idea of collecting shed intestinal cells from infants’ diapers, and extracting mRNA from those cells. This, in turn, would tell the scientists exactly which proteins were being made and in what amounts. To this end, the mothers of 12 breastfed and 10 formula-fed infants collected fecal samples from their children at ages one, two and three months, and delivered the samples to the scientists for processing.

The difference between the two groups of children was striking. For example, breastfed newborns had far more of a protein involved in protecting them from necrotizing enterocolitis, a type of intestinal gangrene that causes about 650 deaths in the U.S. annually.

According to Sharon Donovan of the University of Illinois:

For the first time, we can see that breast milk induces genetic pathways that are quite different from those in formula-fed infants. Although formula makers have tried to develop a product that's as much like breast milk as possible, hundreds of genes were expressed differently in the breast-fed and formula-fed groups.
In other words, breastmilk not only contains immune-protective elements, but it also moderates the development of the child's own immune and digestive systems.

Sunday, May 16, 2010

Just for fun: Illusion of the Year

Kokichi Sugihara of t
he Meiji Institute for Advanced Study of Mathematical Sciences, Japan, has won first prize for Illusion of the Year, given by the Vision Sciences Society. His piece is shown below. You can see all the top entries for 2010 here.

And if you're so so inclined you can find directions for making this illusion here (if this pdf file does not load, try here).

Saturday, May 15, 2010

Universal common ancestry confirmed

Universal common ancestry (UCA), also called universal common descent, is the theory, first proposed by Charles Darwin 150 years ago, that all creatures alive on Earth today are the descendents of one single-celled progenitor species. Douglas Theobald of Brandeis University recently confirmed this theory.

Although the huge amounts of genetic inter-relatedness between different species has lead to wide acceptance of the UCA theory, alternate theories were still possible. For example, it could have been that all multicellular organisms arose from one ancestor, and all microorganisms from another. More specifically, life could have arisen independently in each of the three main domains of life: Bacteria, Archaea, and Eukarya (including us).

To distinguish between these possibilities, Theobold compared the sequences of 23 essential proteins from organisms ranging from humans to flies to a variety of microorganisms. He was careful to use creatures from each of the three big domains listed above. All the tested organisms contained all 23 proteins, though with slight variations between them. He then asked whether the probability of finding that pattern of variation was most likely if the UCA model were true, or if one of the alternate models were true.

Based on his data, he concluded that the UCA theory was astronomically more probable than any multi-lineage theory. In other words, all life on Earth arose from a single progenitor species. In particular, the probability that humans did not descend from the same ancestor species as all other species on Earth was computed to be 1 in 10 to the 6000th power.

This does not mean that life cannot ever have arisen independently in Earth’s history. Life could have arisen multiple times, but only one version left descendents.

Friday, May 14, 2010

Flower petal bee nests

Teams of entomologists in both Turkey and Iran have discovered a solitary bee that lays its eggs in flower petal nests.

Although we tend to think of bees as living in large colonies, nearly 75% of bee species are completely solitary. Those queens must find or make suitable nests each time they lays eggs. Osima (Ozbekosima) avoseta females build their nests out of flower petals.

The nests begin with a layer of flower petals laid into a small vertical chamber in the ground. The queen adds a thin layer of mud, and then a second layer of petals. The nest is now ready to be provisioned with nectar and pollen. That done, the queen lays one egg inside, folds the petals at the top to seal the chamber, and caps the whole thing with mud.

It seems a shame that a creature that raises eyeless larvae in the dark would be the one to choose flower petals for a nursery, but there you are.

Flower petal nests.
Pictures by J. G. Rozen.

Thursday, May 13, 2010

Mirror neuron system not responsible for autism

It has been hypothesized that autism results, at least in part, from a defect in the mirror neuron system of the brain. Ilan Dinstein, formerly from New York University, and his colleagues have now shown that this hypothesis is most likely false. Autistic people do not show significant differences in their mirror neuron systems.

Mirror neurons are found in two distinct regions of the brain. As their name implies, they ‘mirror’ or mimic actions performed by others. For example, if I scratch my nose, particular neurons in my brain will fire. If I observe you scratching your nose, those same neurons will fire just as if I were scratching my own nose. Why is this important? It literally allows me to put myself in your place, to feel your pain, as it were. Without mirror neurons, it might be impossible to understand other people’s behavior or intentions.

It had been thought that because autistic people often have difficulty in interpreting the intentions of other people, they might have a defect in their mirror neuron system. Preliminary research has backed this up, though not always consistently. Dinstein and his colleagues decided to look specifically at movement-selective neurons, the neurons that distinguish between thumbs up and thumbs down, for instance. Like other neurons, these neurons adapt to repeated identical stimulation by fading (firing less strongly). The researchers hypothesized that if autistic people have functional mirror neurons, those neurons will display the same degree of adaptation to repeated stimulation as the neurons of their non-autistic cohorts. This is exactly what they found. Functional magnetic resonance imaging (fMRI) studies on both autistic people and non-autistic controls showed the same pattern of fading.

This finding is controversial for a number of reasons, not least because it contradicts some previous data. Dinstein and his colleagues suggest that those studies were inconclusive. Also, this new study only looked at a subgroup of mirror neurons, those responsible for interpreting and mimicking specific motions. There is probably more to mirror neurons than just recognizing actions, and those other functions might still be affected in autistic individuals. Clearly, more work is required in this field.

Watch a video explaining these results here.

Wednesday, May 12, 2010

Strategies of parasitic brooders

Brood parasites are birds that lay their eggs in other birds’ nests, tricking the host parents into feeding and caring for the parasitic offspring. Common examples of brood parasites include cuckoos and cowbirds. Different birds seem to adopt different strategies for getting their young raised by unwitting foster parents, depending largely on how long the host/parasite relationship has existed.

Eastern Phoebe nest with one Brown-headed Cowbird egg
By Galawebdesign, June 2007.
Consider the brown-headed cowbird (Molothrus ater), which chooses from among over two hundred host species. The cowbird appears to make little effort to disguise its eggs, and given the wide range of hosts it uses, it wouldn’t make much difference if it did. There seem to be two factors involved in keeping cowbird eggs safely tucked into their host nests. One, the cowbird-host relationship is relatively young, evolutionarily speaking, and the hosts haven’t yet learned to be suspicious of odd-looking eggs. Second, cowbirds are known to retaliate against hosts who reject their eggs by destroying the entire host nest. Would more ancient parasitic relationships require different strategies?
Claire Spottiswoode and Martin Stevens of the University of Illinois chose as their study animal, the cuckoo finch (Anomalospiza imberbis), which has been sneaking its eggs into tawny-flanked Prinia (Prinia subflava) nests for the past twenty million years. Unlike the hosts employed by the cowbirds, Prinias are very good at spotting and rejecting interloping eggs. The scientists discovered that Prinias use many visual cues, including patterning, color, and luminance to detect the forgeries. But just as the hosts have gotten better at picking out the fakes, the cuckoos have gotten better at mimicking the originals. Thus, compare the counterfeiting ability of the cuckoo finch below, with that of the cowbird above.

Left: Researchers are in the process of setting up the egg rejection experiment, taken by Tim Dee.
Right: Prinia eggs in left column and cuckoo finch eggs in right column, taken by Claire Spottiswoode.