Just for fun: Hubble's 20th anniversary

The Hubble Space Telescope celebrated its 20th anniversary on April 24, 2010.

Carina Nebula

Credit: NASA, ESA, and M. Livio and the Hubble 20th Anniversary Team (STScI).

You can see lots more images here. Some of the images (like the one above) are 'zoomable'.

Or check out this NASA video:

Circular polarization used by beetles

Certain types of jewel scarab beetles utilize circularly polarized light (CP light) to both hide from predators and to find each other. In particular, Chrysina gloriosa beetles (above left) are camouflaged among the juniper bushes they prefer, unless viewed with circularly polarizing filters.

As shown in the diagram on the top right, CP light travels in a circular pattern. It is commonly used to create 3D movie affects. Because humans can’t perceive CP, we have to wear special glasses during 3D movies. In fact, only one other creature is known to be able to see CP light, and that’s the mantis shrimp.

Parrish Brady and Molly Cummings of The University of Texas, Austin, confirmed that Chrysina gloriosa can detect CP light by observing the insects’ responses to various light cues. They contrasted the behavior of C. gloriosa with that of the closely related C. woodi (beetles that do not have CP reflecting carapaces). Perhaps not surprisingly, the C. woodi beetles could not detect CP light.

The researchers speculate that C. gloriosa use CP light not only to hide from predators (which most likely can not see that type of light) and to find each other, but also to communicate with each other. They are conducting further tests to see exactly how this might work.

Human gene expression map

Now that we have the sequence of the human genome, the next step is figuring out what all those genes actually do. Alvis Brazma and his team from the European Molecular Biology Laboratory have taken an important step in doing just that. They have produced a global map of human gene expression.

The data was collected from over 5000 human samples representing a wide assortment of tissue types and diseases. 163 different labs around the world participated in the research.

In order to make sense of all the data, the scientists divided the samples into six major groupings, called ‘continents’. These continents contained cells from the following origins: brain, muscle, blood related (hematopoietic), incompletely differentiated cells, solid tissue cells, and cell lines. You can see the gene expression clusters within each of these groupings in the graph below.

If you’re interested in checking out the expression of your favorite gene under varying circumstances, you can do that here, or try the beta interface here.

This image shows the 5,372 samples as dots colour-coded for the six major clusters identified by comparing gene expression profiles. The left and right panels of the figure are projections of the same three-dimensional shape viewed from two different perspectives.

(Credit: Brazma / EMBL)

Magnetic limb extender

A magnetic limb extender was successfully used at Texas Children’s Cancer Center to lengthen a little girl’s leg. In late March, 2010, nine-year-old Morgan LaRue had a cancerous (due to an osteosarcoma) section of her left upper leg bone removed. Rather than amputating the leg, the bone was replaced with a prosthetic device called a ‘Stanmore Implants Extendable Distal Femoral Replacement’. Prosthetics have, of course, been used for centuries, but what made this particular device unique was that it was not only extendable, but also magnetic.


Without these properties, a growing child like Morgan would face multiple operations to replace or extend her prosthesis so that her two legs could remain the same length. In her case, her left leg was simply placed within a donut shaped magnet that lengthened the prosthesis without surgery.


Although this device has been used regularly in Europe, it has not yet been approved for use within the U.S. Morgan’s doctors, Rex Marco and Lisa Wang received a ‘compassionate use’ exception to give her the prosthesis.

Dimming moon reflectors

Forty years ago, Apollo astronauts Neil Armstrong and Buzz Aldrin left ‘lunar laser ranging retroreflector arrays’ in precise locations on the moon. The arrays contain glass prisms called ‘corner-cube reflectors’, a type of mirror that always reflects incoming light straight back to the original source. The prisms have been used for a variety of purposes, most notably to give us an accurate measurement of the distance from the Earth to the moon.

Caption: Apollo astronauts left arrays of corner-cube prisms, like the one shown here, on the moon 40 years ago. Now light bouncing back from these reflectors appears to have dimmed. Scientist think dust is to blame.

Credit: UC San Diego

In recent years, the amount of light coming back from the reflectors has decreased significantly. According to Tom Murphy of the University of California San Diego, we’re now receiving only one tenth as much light as we should. The possible culprit? Moon dust.

Under the best conditions, astronomers can only expect to intercept one photon out of every 100 million billion sent to the moon from earthbound telescopes. Much of the outgoing light never hits the lunar reflectors, having been scattered by Earth’s atmosphere on the way out, and the photons that do arrive on target are dispersed over a wide area on the way back. Still that small amount of light has yielded some valuable information. For example, it turns out that moon is receding away form the earth by just under four centimeters per year.

The 2.7 meter Harlan J. Smith Telescope of the McDonal Observatory (USA) is used to point a laser beam to a mirror stationed on the surface of the moon.

The astronomers aren’t sure exactly what is causing the low return problem, but they suspect that dust is involved. Not so much because the surface of the reflectors are dirty, but because the dust causes uneven heating of the glass prisms, affecting the returning laser pulses. How is the dust accumulating on an atmosphereless, windless moon? Small amounts of dust could be attracted to the prisms by electrostatic forces. Alternatively, micrometeorites landing nearby could be kicking up dust.

If the problem is one of uneven heating, that should be made clear by making observations during a lunar eclipse. While the moon is in Earth’s shadow, the reflectors won’t be heated by the sun. The astronomers are waiting for a fair weather eclipse to test their theories.

Titanium ink origami

Jennifer Lewis from the University of Illinois and her team have developed a novel way to ‘print’ complex three-dimensional shapes. They used flat sheets of titanium hydride ink, and folded them.

Solid objects can be ‘printed’ by laying out each layer of ink in precise sequence. The inks contain metal, plastic or ceramic particles. When the desired shape is reached, the liquid ink is evaporated, leaving the particles annealed into a solid structure. Unfortunately, if too many layers are added, the entire structure can start to sag or even collapse. Lewis and her colleagues decided to start with a flat sheet of ink and fold it into the desired shape.

These structures were folded from flat sheets of direct-printed titanium hydride ink, a new technique pioneered by University of Illinois researchers.

Credit: Bok Yoep Ahn (a postdoctoral researcher in the Lewis lab).

This required some fiddling to get the right ink consistency. Some ink solvents dry too quickly, making the sheets too brittle for consecutive folds. Other solvents don’t dry quickly enough, allowing the structures to fall apart. A happy medium left the sheets pliable enough to fold, but stiff enough to hold their shape throughout the folding and annealing process.

The ability to make tiny precise objects would have many uses, particularly in medicine and electronics.

To see a slideshow of some of the printed origami creations, look here.

Exercise required for weight loss

We’ve all heard the standard weight loss mantra: eat less and exercise more. However, some weight loss programs rely entirely on the first part, lowering caloric intake, without focusing at all on activity levels. New research by Elinor Sullivan and Judy Cameron shows why this doesn’t work.

The researchers gave monkeys a low calorie diet and monitored their activity levels. As the calories decreased, so did the activity level of the animals. In effect, the animals were compensating for the lack of food by using up less energy. After one month, there was no significant weight loss among the monkeys. An alternate group of monkeys were trained to run on a treadmill for an hour a day and that group of monkeys did lose weight.

This decrease in activity may be a natural coping mechanism for creatures that don’t always have access to ample food. If this data applies to humans (and there’s no reason to think it wouldn’t), it means dieting alone is unlikely to be sufficient for weight loss. The natural inclination to use less energy as food intake decreases must also be overcome.

Just for fun: Casey Dunn videos

Casey Dunn of Brown University creates both live action and cartoon videos about animals.

Here are two examples:

An un-narrated video of siphonophores:

And a claymation video explaining certain aspects of multicellularity:

Wrong way planets

The origin of solar systems was thought to be well understood. That is, until the discovery of planets which orbit their stars in the wrong direction.

Artist's rendition of newly found planet WASP 8b orbiting its star at a reverse angle compared to the star's rotation.

credit: ESO/L. Calçada

The prevailing theory is that solar systems begin as clouds of rotating gas and dust. The center of the cloud condenses into the star, and the remnants of material collect into planets of various sizes and distances. But the important point is that because the original cloud rotated in one direction, the ensuing star and planets should all continue to rotate in that same direction. Apparently, not so. In fact, there are now six known cases of planets that do not rotate in the same direction as their star.

As stated by Andrew Cameron of the University of St. Andrews, Scotland (hmm… wonder why he picked that school):

The new results really challenge the conventional wisdom that planets should always orbit in the same direction as their stars spin.

Did these planets start out orbiting their stars in the normal fashion and get knocked off course? Or is an entirely different mechanism for solar system formation required? One possibility is that planets can migrate into solar systems from other regions of space.

Hat tip and more detailed explanation: Bad Astronomy.

Anaerobic multicellular organisms

Roberto Danovaro and his team from Polytechnic University of Marche, Italy, have discovered the world’s first known multicellular anaerobic (non-oxygen using) organisms. The creatures are as yet unnamed specimens from the phylum Loricifera. The microscopic creatures were found in the deep L’Atalante basin of the Mediterranean Sea. This basin is so salty and dense that the deep waters do not mix with the oxygenated waters closer to the surface.

The researchers proved that the organisms were metabolically active by observing their uptake of radioactive tracers. Unlike other multicellular creatures, the new specimens appear to completely lack mitochondria, but instead have organelles called hydrogenosomes, hitherto found only in single-celled obligate anaerobic organisms. Whereas mitochondria utilize oxygen as an energy source, hydrogenosomes use hydrogen.

Light microscopy image of the undescribed species of Spinoloricus, phylum Loricifera (stained with the protein-binding stain Rose Bengal) The bright pink cap is about 150 µm (ten thousandths of a centimeter) in length.

Image Credit: R. Danovaro et al., BMC Biology

This discovery could shed light on the development of multicellular creatures on the early Earth before oxygen was plentiful.

Hat tip: The Skeptics' Guide to the Universe.

Sibling bacteria fight to the death

It’s not surprising that colonies of bacteria use chemical attacks to prevent rival colonies from encroaching on their territory. What is surprising is that these attacks occur even between colonies of the same species, and even between colonies that were started from the same parent cell.

Avraham Be’er and Harry Swinney of the University of Texas and Eshel Ben-Jacob of UC San Diego and Tel Aviv University have been studying just how this intrafamily warfare is conducted. The scientists inoculated Petri plates with the bacteria Paenibacillus dendritiformis. Normally, this bacterium grows in colonies that spread out in fine branches in every direction. However, when two seemingly identical colonies were placed on the same plate, they left a conspicuous void between them.

Poisons are unleashed when colonies of bacteria get too close and create a toxic "no-man's land" in between.

Credit: Eshel Ben-Jacob

Upon further study, the researchers found that the empty space was created not but any lack of nutrients, but by the addition of a protein subsequently named ‘sibling lethal factor’. This protein actually starts as a gene product that is two-thirds larger and harmless. After being trimmed down to size by the protease ‘subtilisin’, the newly discovered factor kills any bacterium that wanders too close.

Just why these sibling colonies would lash out at each other rather than simply blending into one super-colony is not clear. As explained by Ben-Jacob:

It supports the notion that each colony is a superorganism, a multicellular organism with its own identity.

Ink jet skin grafts

Researchers at Wake Forest University working with the U.S. Armed forces Institute of Regenerative Medicine have invented spray-on skin. They modified ordinary ink jet printers to spray precisely calibrated layers of skin cells onto burn victims.

It's critical to cover burn wounds as quickly as possible in order to avoid infection. Currently, burns are surgically covered by skin grafts, a slow and painful process. Being able to quickly 'bandage' wounds with skin cells sprayed from a printer would be a tremendous advantage.

To use the printer, skin cells such as fibroblasts and keratinocytes are cultured and then placed in separate sterile ink jet cartridges. After a laser-generated 3D image of the wound is produced, the printer deposits the cells over the wound in a process called ‘bioprinting’.

Thus far, the system has been successfully tested on mice.

Hat tip: The Skeptics’ Guide to the Universe.

Orange ears

Torbert Rocheford and his team from Purdue University have been breeding orange ears of corn. The orange corn is high in carotenoids, such as beta-carotene, which humans convert into vitamin A.

The intense orange color of high pro-vitamin A maize is caused by high carotenoid content.

Credit: Purdue University photo/Debra J. Skinner

Vitamin A deficiency causes up to 500,000 children to go blind worldwide each year, half of whom die within the first year. The researchers hope that the new type of corn, among other enhanced grains, will prevent these tragedies.

The scientists didn’t simply pick the orangest ears of corn for breeding, however. They focused on a gene called ‘beta-carotene hydroxylase 1’ (crtR-B1). When highly active, this gene, through a series of steps including hydroxylation, decreases the amount of beta-carotene in the corn. For this reason, the researchers are careful to select ears that display little crtR-B1 activity for dissemination to parts of the world where children suffer from vitamin A deficiency.

On the other hand, although crtR-B1 decreases the amount of beta-carotene, the gene actually increases the amount of zeaxanthin in the corn. Zeaxanthin is a major component of the central macula of the human eye. Thus, active crtR-B1 could protect people from macular degeneration, the leading cause of blindness in seniors living in industrialized nations.

Ultimately, Rocheford and his team hope to be able to prevent blindness in the young and the old by tailoring their orange ears of corn to fit particular needs. In the meantime, I can think of someone who’d be pretty happy to find this offering on the dinner menu. You know who you are.

Drought resistant plants

Some plants can survive almost total dehydration. Ronald Balsamo and Bradley Layton of Villanova University and Drexel University respectively, and their colleagues, have been studying a plant known as the ‘resurrection fern’ (Polypodium polypodioides) that can survive a 95% loss of water. For reference, corn (maize) will die from a 20 to 30% loss of water. Humans can develop symptoms of dehydration after losing only 2% of our water.

The scientists discovered that the ferns contain large amounts of a class of proteins aptly named ‘dehydrins’. These extremely hydrophilic molecules cluster near the plant’s cell walls, attracting what little water is left to those areas. In this way, the dehydrins appear to act as a lubricant, preventing the plant cells from becoming too brittle.

The researchers hope that by transferring the dehydrin gene to crops, they’ll be able to increase the drought resistance of those plants.

Just for fun: First genome

In 1995, Haemophilus influenzae was the first organism to have its genome completely sequenced. Since then hundreds of creatures have been added to the list, including humans. Here's that first complete genome, a beautiful merger of art and science.

"Whole-genome random sequencing and assembly of Haemophilus influenzae Rd." Science: 1995 Jul 28;269(5223):496-512.

By the way, Haemophilus influenzae is a bacteria, not one of the viruses that causes the flu (it was falsely accused of that crime at the time it was discovered and named, back in 1892).

Hat tip: The Loom

Haploid plants

Simon Chan and Maruthachalam Ravi from the University of California, Davis have invented a way to breed haploid plants.

Normally, plants are diploid (they can sometimes be tetraploid, but leave that aside for now), meaning they have two of each type of chromosome, one from the male parent and one from the female. Scientists and crop farmers prefer plants that ‘breed true’: plants that produce offspring with identical traits to those found in the parents. This can be tricky to achieve with diploid plants. On the other hand, a haploid plant with only one set of chromosomes will breed true by definition. They only have one version of each gene. Although haploid plants have been created in the past, the methods used were expensive and only worked some of the time.

Ravi and Chan were studying a particular histone called CENH3. Histones are the proteins that package loose strands of DNA into tightly packed chromosomes. CENH3 is located at the centromere, the region of the chromosome where homologous chromosomes pair up and where the chromosome is pulled into daughter cells as the cell divides.

Ravi damaged and fluorescently tagged CENH3 in Arabidopsis thaliana (frequent readers of this blog will have seen this plant before), and bred the mutants with wild-type (normal) plants. He expected to see plants containing both a gene for normal CENH3 and a gene for mutant CENH3. Instead, the offspring only had the normal gene (no fluorescence). It turned out that the resultant plants were all haploid. Because the centromeres could not line up properly, half the chromosomes were eliminated in a process called ‘genome elimination’. This technique of creating haploids by breeding wild-type plants with CENH3 deficient plants should be applicable to most plant species.

Of course, haploid plants cannot produce germ cells, so the plants must double their chromosomes before reproducing. This is accomplished by ‘meiotic non-reduction’ in which the chromosomes replicate as during cell division, but the cell itself never actually divides.

As an aside, CENH3 is found in animals as well as plants, but unlike most essential genes, which tend to be highly conserved, CENH3 shows great variability. Ravi and Chan speculate that differences in centromeres may prevent different species from interbreeding.

Buckyballs can be toxic

Fullerenes, also known as ‘buckyballs’ or ‘buckminster fullerenes’ all after the late Buckminster Fuller, are spherical molecules composed of carbon atoms. Fullerenes are interesting because the carbon atoms form a molecular cage that can be used to transport drugs or other chemicals into living tissues. The balls themselves were assumed to be biologically inert. Rashi Iyer and his team from Los Alamos National Laboratory put that assumption to the test. They found that certain fullerene derivatives are actually toxic.

Specifically, the team tested fullerene C₆₀ (a molecule composed of 60 carbon atoms), hexa carboxyl fullerene (hexa-C₆₀, a variation with six molecular branches coming off one hemisphere of the ball), and tris carboxyl fullerene (tris-C₆₀, another variation with only three molecular branches). Upon applying the three types of fullerenes to human skin cells, they found that the tris configuration caused premature senescence in the cells, but that the plain or hexa configurations had no effect.

Senescence in cells is basically a shutting down of the cell cycle. Although the cells aren’t technically dead, they don’t perform any of their cellular functions. Obviously, this is not generally a desired result of treatment. For this reason, the researchers suggest that therapists avoid using tris-C₆₀ as delivery molecules. On the other hand, there are certain diseases, such as Parkinson’s in which nerve cells die or degenerate prematurely. Perhaps putting these damaged nerve cells into premature senescence might actually be helpful.

Clearly more research should must be done. For one thing, cells in tissue culture don't always behave the same way as cells within a living body. Los Alamos National Laboratory plans to continue studying exposure to nanomaterials.

Opportunity for software update

Simulated view of Opportunity in "Endurance Crater."

When the robotic rover Opportunity landed on Mars in January, 2004, the engineers who designed it hoped that it would last at least 90 Martian days (sols) and run for up to one kilometer. Six years later, it’s still functioning and has traveled over 20 kilometers. With the new software that was recently uploaded, the rover has become even more useful.

Displaying NASA’s love of acronyms, the new upgrade is called Autonomous Exploration for Gathering Increased Science (AEGIS). It allows the rover to autonomously choose promising rocks or other targets for further study, based on programmable selection criteria, rather than first transmitting images to the rover team on Earth and awaiting instructions. Because it takes about a day to collect data from the rovers and send back new instructions, giving Opportunity the ability to proceed alone is a huge advantage.

The first rover-selected study object was a tan football-sized rock. Opportunity chose this rock out of a field of more than fifty objects visible to its camera. Tara Estlin, a rover driver and senior member of the Jet Propulsion Laboratory’s artificial intelligence group, was pleased with this choice:

It found exactly the target we would want it to find. This checkout went just as we had planned, thanks to many people's work, but it's still amazing to see Opportunity performing a new autonomous activity after more than six years on Mars.

Preventing liver metastasis

Unfortunately for cancer patients, many kinds of cancers eventually spread to the liver, at which point they are often no longer curable. George Miller and his colleagues from the New York University School of Medicine believe they have found out why. Metastasis to the liver is controlled by the immune system.

The scientists observed the course of pancreatic and colon cancers in mice. They found that the livers of these mice started producing immune-suppressing cells. In particular, the cells were suppressing T-cells activation, preventing the liver from recognizing and killing tumor cells.

Based on this new data, the researchers hope to find new therapies for preventing liver cancer. By targeting the liver’s immunosuppressive cells, other cancers may be prevented from spreading to the liver.

Seeing the backside of a supernova

Chandra X-ray Observatory image of the supernova remnant Cassiopeia A.The red, green, and blue regions in this image show where the intensity of low, medium, and high-energy X-rays, respectively, is greatest.

Credit: NASA/CXC/MIT/UMass Amherst/M.D.Stage et al.

When cosmologists study the skies, they can only do so from the vantage point of the solar system. But a new detection method developed by Armin Rest of Harvard University and his colleagues have allowed scientists to see the back side of cosmic events.

The team has been studying a supernova called Cassiopeia A. Most of the observable light from that event went straight toward the solar system 330 years ago. However, a small amount of light first bounced off some clouds of interstellar dust, and then rebounded towards us. In other words, the dust clouds acted like giant mirrors, reflecting the back or sides of the supernova back towards us.

The researchers have already discovered that the different sides of the supernova explosion were not symmetrical. Gas from the explosion is zooming away in one particular direction much faster than in any other way. Meanwhile, the neutron star that resulted from the collapse of the star’s core is careening away in the direction opposite this gaseous surge.

By combining this new light-echo data with X-ray data, the cosmologists have been able to construct a 3D computer model of the supernova. You can watch a simulation here.

A new hominid ancestor

In 2008, paleontologist Lee Berger's nine year old son found an interesting fossil in a South African cave. Consequently, study showed that the fossil was from one of two partial hominid skeletons belonging to a hitherto unknown species, now named Australopithecus sediba. ‘Sediba’ means ‘fountain’ or ‘wellspring’ in the local language of Sotho.

Australopithecus sediba

CREDIT: L. BERGER ET AL., SCIENCE

Researchers used uranium-lead radiometric dating (by two independent labs), as well as paleomagnetic dating of the sediments around the fossils to date the skeletons to just under 2 million years old, making them over a million years younger than Lucy, an Australopithecus afarensis.

The specimens have traits in common with the older Australopithecines as well as with the earliest Homo species. In fact, the scientists believe that Au. sediba descended from Au. africanus (itself a descendent of Au. afarensis), and may be an ancestor of Homo erectus or Homo habilis.

I should point out that the hominid family tree is extremely ‘bushy’. There are a large number of species on the tree, many of which were once thought to lead directly to Homo sapiens sapiens (us), but which now appear to be side branches that were eventually trimmed off by evolution. Add to that the fact that many species existed for long stretches of time, overlapping later species, and it becomes extremely difficult to establish an exact evolutionary timetable. For example, because Au. sediba has certain traits in common with Homo erectus but not with Homo habilis, Au. sediba may replace H. habilis as our ancestor. On the other hand, both species may be ancestors of ours, but may need to be temporally realigned.

Besides the Au. sediba skeletons, at least 25 other species were found in the same cave. The scientists researchers were able to make a detailed analysis of the surrounding conditions, and speculate that the hominids and other creatures may have entered the cave looking for water and then either fell to their deaths or gotten hopelessly lost.

The two skeletons are of boy and an adult woman. The children of South Africa have been invited to give the juvenile skeleton a common name.

Just for fun: Science Tattoo Emporium

Carl Zimmer, a science writer with seven popular science books under his belt, is collecting pictures of science based tattoos on his blog The Loom.

Here's an example of a chloroplast, displayed by a University of Minnesota botanist.

There are about 250 more, some of them truly amazing.

Dinosaurs rose from the ashes of volcanoes

One of Earth's mass extinction events occurred at the end of the Triassic period, giving rise to the age of dinosaurs. But what caused this lucky break for the dinosaurs? A new study led by Jessica Whiteside of Brown University shows that it was volcanic activity.

At that time, about 200 million years ago, the Earth contained one giant land mass called Pangea, which eventually broke up into the modern continents. For a long time, scientists have suspected that this breakup was somehow connected to the Triassic/Jurassic mass extinction. By studying plant and animal fossils as well as carbon isotope ratios, Whiteside and her team have documented evidence proving that this was so.

In a nutshell, as the American and African tectonic plates separated creating the basin of the Atlantic ocean, there was tremendous volcanic activity throughout this enormous fissure. This area, called the Central Atlantic Magmatic Province (CAMP) and covering a region about the size of the continental United States, experienced volcanic eruptions over a period of about 600 thousand years. Even more deadly than the lava flows and shaking were the tremendous amounts of carbon dioxide and other greenhouse gases released into the atmosphere. These gases were responsible for killing half the species alive at that time.

Among the evolutionary losers in this mass extinction were the dominant predators on the planet, the large crurotarsans (relatives of modern crocodiles and alligators). And among the winners were a group of small theropod dinosaurs that eventually gave rise to Tyrannosaurus rex and its ilk.

Pencil drawing of Gracilisuchus stipanicorum. Gracilisuchus (meaning "gracile crocodile") is the name given to a tiny (30 cm long) genus of crurotarsan (a group which includes the ancestors of crocodilians) from the Middle Triassic of Argentina.

Drawing by Nobu Tamura, Dec 25, 2006, Modified May 15, 2007

Of course, if you want to take a longer view, there still are 23 species of crocodilians alive today, and T. rex, not so much.