Decaying for science

Living hagfish

This image shows the remains of a hagfish after 20 days of decay. Only the head skeleton, notochord and parts of the liver are left.

Credit: University of Leicester

Paleontologists examine fossil remains to discover clues about long-extinct organisms. Unfortunately, such creatures were mostly soft-bodied and left few fossils behind. Those traces that have been found are difficult to identify. In order to provide a framework for interpreting these remains, Robert Sansom, Sarah Gabbott and Mark Purnell of the University of Leicester have been studying the decay of modern fishes.

In particular, the team has been leaving out carcasses of lampreys and hagfishes, both cartilaginous jawless fishes. As the fish decompose, their bodies take on distinctive appearances (and odors, apparently). The scientists can then compare those remnants to the fossils of ancient soft-bodied animals. The data is already improving the reconstructions of early vertebrate fossils.

According to Gabbott:

Our macabre experiments are grisly and smelly but they have revealed, for the first time, what characteristic vertebrate features look like when they are partially decomposed.

1000 Genomes Project

The first human genome was completely sequenced a decade ago. Since then, genetic information about humans and other animals has been added at an astounding rate. Now a particularly ambitious genetic project is underway: the 1000 Genomes Project. Over 75 Universities around the world are participating in this effort to catalogue every human variation and mutation.

The first part of the study has just been published. Thus far, the molecular biologists have sequenced the genomes of about 900 people from different regions of the globe.

Among the preliminary findings:

• Each person’s genome contains about 250 to 300 ‘loss-of-function’ mutations, meaning the affected gene cannot encode a viable protein.
• Each person’s genome contains 50 to 100 mutations that have been implicated in inheritable diseases.
• The de novo mutation rate (the rate at which mutations spontaneously arise) is 10^-8 per base pair per generation.

In addition, the sequencing project has lead to innovations in the handling of genomes. For example, much of the variation in human genomes is due to ‘copy number’. Certain genes may be represented anywhere from only once to hundreds and hundreds of times, and not always at the same location, or even on the same chromosome. It has been extremely difficult to be sure the number of these genes was ‘counted’ correctly. Researchers working with the 1000 Genomes consortium have now developed a method for tackling this problem.

The next phase of the study will be to sequence the DNA of an additional 2500 people.

Just for fun: NASA Earth mission

Many people think NASA exclusively points its telescopes at the sky. In fact, NASA has an important Earth-studying mission as well. For example, NASA satellites are instrumental in detecting and studying hurricanes. Here's a recent example:

Caption: GOES-13 image of Tropical Storm Richard at 1732 UTC (1:32 p.m. EDT) on Oct. 22 showing Richard's clouds over the Honduras/Nicaragua border as it heads toward Belize.

Credit: NOAA/NASA GOES Project

Much of our climate change data also comes from NASA satellites, which measure everything from temperature, to greenhouse gases to rainfall. A new suite of these satellites is pictured below:

Artist's Concept of the A-Train constellation of satellites. Credit: NASA

Playtime

Play is an accepted form of mammalian behavior, particularly in the young. However, Gordon Burghardt of the University of Tennessee claims that play is universal across the animal kingdom, in reptiles, fish and even in insects!

To establish this claim, Burghardt first had to define play, something much harder to do than it seems. Since no one is entirely sure of the purpose of play, how do you distinguish play from other activities? Burghardt decided on the following five criteria:

• Play is not fully functional in the form or context in which it is expressed.
• Play is spontaneous, voluntary, and/or pleasurable, and is likely done for its own sake.
• Play is incomplete, exaggerated, or precocious.
• Play is repeated but not in exactly the same way every time, as are more serious behaviors.
• Play is initiated when animals are well fed, healthy, and free from acute or chronic stressors.

Based on these criteria, researchers have categorized activities such as the manipulation of balls by turtles or fish as ‘play’. Jennifer Mather of the University of Lethbridge believes that octopuses squirting at floating pill bottles are being playful. Elisabetta Palagi of the University of Pisa even wonders whether off-season non-lethal dominance battles between female wasps could be a form of play-fighting.

Skeptics aren’t convinced. After all, play implies a state of mind, and it’s impossible to tell what an animal is thinking when it wields an object. You can see some examples of these activities in the video below and decide for yourself whether you think the animals involved are really playing.

Willpower is all in the mind

Do people require breaks from difficult tasks to ‘recharge’? Popular opinion is that people will eventually lose the ability to concentrate when working hard or studying. However, Veronika Job from the University of Zurich and Carol Dweck and Gregory Walton from Stanford University found that the willpower required to keep going is not a limited resource. It’s only the belief that willpower can be depleted that limits it.

The cognitive scientists tested their theory on Stanford college students. Some of the students were primed to believe that they would eventually run out of willpower and have to quit. Other students were told that they had unlimited willpower, that how long they could continue a task was entirely within their control. Not surprisingly, the group that thought they would hit a concentration wall performed worse on concentration tests after having already performed a tiring task. Those same students also ate more junk food and procrastinated more prior to college exams.

To be clear, these results don’t mean that people can work nonstop. Obviously, there are biological limits to how long people can continue without food or rest. The point is that there is no cognitive limit. We don’t reach a point at which we just can’t think anymore… unless we think we will.

According to Walton:

This is an example of a context where people's theories are driving outcomes. Willpower isn't driven by a biologically based process as much as we used to think. The belief in it is what influences your behavior.

Uncontrolled placebo controls

The gold standard for proper medical experiments is the double-blind placebo-controlled study. Beatrice Golomb of the University of California San Diego and her colleagues are arguing that that standard isn’t good enough, if researchers don’t disclose what’s in their placebos.

Placebos, sometimes referred to as ‘sugar pills’, are sham treatments. A good placebo replicates the actual medicine or procedure so closely that no one can tell the difference. For example, a placebo pill should look and taste like the medicinal pill in the study, but not contain any active ingredients. Placebo injections or placebo surgeries must feel like the real things. ‘Double blind’ means that neither the patient nor the doctor knows whether the patient is getting the real treatment or the placebo. It’s actually another level of placebo control, because patients will tend to feel better if their doctor is confident that his treatment will help them.

These careful controls are essential because many people will improve, at least temporarily, from almost any condition even with no treatment. If you give a group of people a medical intervention and many of them improve, you can’t know whether they would have improved anyway unless you have these controls.

The placebo itself is presumed to be inert, meaning that it has no effect. But is it? Golomb and her colleagues found that researchers rarely disclose the exact contents of their placebos. In addition, they argue that placebos themselves haven’t been properly tested to make sure they really don’t have any effect. To take an extreme example, suppose a placebo really were a sugar pill. Couldn’t a dose of sugar have some affect on people suffering from certain conditions? Remember, it’s the comparison to the placebo that tells how effective a drug is. If 60% of patients improve when taking the drug, and 62% improve when taking the placebo, then the drug is deemed ineffective. Therefore, it’s critical to know what if any effect the placebo has on its own.

The authors suggest that in future, researchers take care to disclose the exact contents of their placebos as well as of their treatments. They would also like to see studies done comparing different placebo compositions. Only then will placebo-controlled studies be properly controlled.

Blind people have superior hearing and touch

Josef Rauschecker of Georgetown University lead a team of neuroscientists in comparing people who had been blind from birth to sighted people. The blind people had adapted parts of their visual cortex for use in hearing and touch, making those senses more acute.

The visual cortex is composed of about forty different modules. Each module is used for a specific task, such as orienting an object in space. For people with normal vision, these modules are only associated with vision, they aren’t activated to interpret sounds or other sensory input. People who are blind from birth use these modules differently.

The researchers hooked up twelve blind and twelve sighted people to an fMRI machine. While connected, the volunteers were asked to report from which direction certain sounds were emanating. In the blind but not the sighted subjects, the sounds activated the spatial module of the visual cortex. In fact, the more strongly that module was activated, the better the person was at figuring out the direction of the sound. When the same group of subjects was asked which finger was being gently stimulated, again the blind volunteers used parts of their visual cortexes to interpret the sensation.

The blind people were using not only the parts of the brain normally associated with sound or touch, but also the visual cortex, something sighted people cannot do. This gives the blind an edge in processing their other senses. It’s important to note that this study was done with people who had been blind from birth. In other words, their visual cortexes have never had any visual cues to process. It’s not clear to what extent the brain can be rewired in people who become blind later in life.

Quick and easy star measurement

Artist’s concept of an exoplanet and its moon transiting a sun-like star. Such a system could be used to directly weigh the star. Credit: David A. Aguilar (CfA)

David Kipping, an astronomer at University College London has devised a new way to accurately measure stars. All it takes is a transiting planet with its own moon, and Kepler’s laws of motion.

Many exoplanets (planets that orbit stars other than our sun) have been found by using the transit method. Briefly, the planet is directly observed passing in front of its star. If that planet also has a moon, astronomers have the three data points they need to figure out the mass of the star. They can directly measure the orbital periods (time it takes to complete an orbit) of the moon and planet, the size of those orbits relative to the star, and the size of the moon and planet themselves relative to the star. Taken together, these data can be used to determine the size of the star. You need all three objects (star, planet and moon) for this method to work though.

You may be wondering, as I was, how many transiting exoplanets also have moons. The answer is none. So far, not a single ‘exomoon’ has been found. That does make Kipping’s method a bit less useful, but he isn’t discouraged:

"When they're found, we'll be ready to weigh them.”

Deceptive beauties take two

Orchids use a number of strategies to lure in pollinators. Besides docilely offering nectar like most other flowers, they often mimic the scents or appearance of other insects, particularly females of the pollinating species. Johannes Stökl from the Max-Planck Institute and his colleagues from Max-Planck, Haifa University and the University of Ulm have added a new kind of orchid deception to the list. Epipactis veratrifolia lures predatory insects by producing the alarm pheromones of their prey.

Hoverflies need to lay their eggs on plants containing aphids, the food source for their young. When aphids are in danger, they produce specific chemicals to warn other aphids away from the area. Hoverflies hone in on these signals and lay their eggs nearby. E. veratrifolia can make these same chemicals, inducing female hoverflies to approach close enough to collect and transfer pollen. Male hoverflies are also coerced into helping the plant as they hopefully wait for females.

The researchers suspect that the orchids first used the aphid pheromones as a way to prevent aphids from eating them. The plants are remarkably free of aphids, so this does seem to be an effective strategy. Only later were the same chemicals used to attract pollinators. There are a couple of lines of evidence for this. E. veratrifolia offers its pollinators a small amount of nectar, indicating that it doesn’t rely entirely on its deceptive tactics. Also, by luring the hoverflies to lay their eggs on aphid-free flowers, the orchids are ensuring the death of the next generation of their own pollinators, an evolutionarily unstable relationship.

Caption: Eastern marsh helleborine (Epipactis veratrifolia), an orchid species, has successfully lured a hoverfly of the genus Ischiodon by mimicking alarm pheromones usually emitted by aphids.

Credit: MPI Chemical Ecology, Johannes Stökl

Just for fun: Census of marine life

An international team of 2700 scientists from over 80 nations has spent the past ten years surveying the oceans in a massive ‘Census of Marine Life’. Over the course of 540 expeditions, the researchers have catalogued and counted everything from whales to plankton, discovering thousands of new species along the way. In addition to identifying types of organisms, this first ever marine census is yielding valuable information about species distribution and abundance, as well as about the diversity of different marine environments.

You can see images from the survey here.

New method for finding exoplanets

An international team of astronomers has successfully tested a novel way to find extrasolar or exoplanets. By using a special lens called an Apodizing Phase Plate (APP), they were able to cancel out the light of the star Beta Pictoris and directly see its planet Beta Pictoris b.

Caption: The planet Beta Pictoris b imaged using the Apodizing Phase Plate coronagraph. The "bad" (bright) side of the image is visible to the right while the central bright regions of the central star (Beta Pictoris) have been masked out to enable the viewer to clearly see the planet to the left of the star.

Credit: European Southern Observatory (ESO)

Close to 500 exoplanets (planets orbiting stars other than our sun) have already been discovered with more being found all the time. A variety of methods are used to find these planets, among them direct observation. However, in order to see a planet in the vicinity of its star, which may be a million times brighter than the planet, special lenses have to be employed. In the past, coronagraphs have been used to physically block starlight. These devices have to be lined up exactly right and are limited to detecting planets at least 30 astronomical units (about the distance from Neptune to the sun) from their stars.

Thanks to some complicated mathematics that I won’t even try to decipher, the new APP lens causes the light from the star to cancel itself out, leaving only the background visible. The astronomers were able to see Beta Pictoris b even though it’s only seven astronomical units from Beta Pictoris. This new method will make it easier to find Earth-like planets that might contain life.

Caption: The Apodizing Phase Plate causes light waves coming from a star to interfere with each other, exposing the faint glow of a nearby planet. Shown here is an early version.

Credit: University of Arizona

Football players may have overlooked head injuries

Football players are well known to be at risk for concussion. For this reason, players are routinely screened for signs of concussion after receiving blows to the head. Athletes who do not display the classic signs of concussion (dizziness, confusion, vision problems, slurred speech, or loss of consciousness) are cleared to continue playing. However, Thomas Talavage and his colleagues from Purdue University have discovered that many athletes who don’t display the usual concussion symptoms are in fact suffering from brain injury.

The researchers outfitted twenty-one high school football players with helmets containing accelerometers to measure the degree of impacts they suffered. Eleven of the boys suffered high numbers of impacts or one or more unusually hard impact and were subsequently evaluated for brain injury, using both MRI and cognitive tests. Of these 11, only three were diagnosed with concussion based on their symptoms. Four other boys who were not diagnosed with concussions, and thus would have been okayed for further play, nevertheless displayed serious brain deficits. In other words, a significant number of football players could be playing despite suffering from brain injury. Personally, I wonder whether James Eckner’s concussion stick could identify these players.

Based on the accelerometer data, the athletes who did not display any of the trademarks of concussion yet were suffering from brain impairment were the ones who received a disproportionate number of blows to the top and front of the head. These data could be used to determine recovery times for players who have been hit, as well as to design more protective helmets.

A diagram of the forces on the brain in concussion.

Patrick J. Lynch, medical illustrator

Rescue breathing not necessary for bystander CPR

CPR, or cardio-pulmonary resuscitation is used to assist victims who are not breathing. Traditionally, CPR has included both rescue breathing (to keep the lungs ventilated and supplied with oxygen) and chest compressions (to maintain blood flow to the vital organs). Bentley Bobrow of the Arizona Department of Health Services led a team of doctors from Universities and Hospitals throughout Arizona in challenging that combination. According to them, it’s more effective for bystanders to forego rescue breathing altogether, and concentrate on chest compressions alone.

The scientists examined the records of patients who had been hospitalized for cardiac arrest. Because the scientists were interested in advising the lay population, they excluded patients who had been treated in the field by medical professionals. Of those remaining, some received standard CPR from an untrained bystander, some received chest compressions but no rescue breathing, and some got no CPR until arrival at the hospital.

Not surprisingly, those who received some form of CPR faired better than those who received none. What was surprising was that the group that did not receive rescue breathing had a slight advantage over the group that got chest compressions plus rescue breathing.

The researchers believe that one explanation for this is that the benefit of supplying the lungs with oxygen is more than offset by the drawback of having the blood flow temporarily interrupted. In other words, it’s best not to pause the chest compressions for anything, not even to ventilate the lungs.

Bacteria walk to infection site

Gerard Wong and his colleagues from UCLA, the University of Houston, the University of Illinois and University of Notre Dame have discovered one method bacteria use to move to a new site of infection. They ‘walk’ there.

The microbiologists studied Pseudomonas aeruginosa, a leading cause of death in patients with cystic fibrosis. These bacteria can exist as free-swimming individual bacteria, a state in which they do relatively little harm, or as part of a biofilm. Not only do these biofilms form an impenetrable coating, but the bacteria within them often excrete completely new and toxic substances. But how do bacteria transition between the two states?

Wong and his teammates made a breakthrough in answering this question when they discovered that P. aeruginosa can effectively walk upright. Each rod-shaped bacterium orients itself vertically and uses its type IV pili (tiny hairlike projections) to propel it across a surface. The bacterium hasn’t become part of a biofilm, nor is it free-swimming. It is, however, in the unique position of being able to forage over a surface, or to detach completely. In other words, a 'walking' bacterium appears to be in a transitional state between the free-swimming and biofilm phases.

The scientists expect this new data to answer questions not only about biofilms, but also about infectivity in general.

Walking bacterium

Artists representation of a bacterium "walking."

Largest eukaryotic genome

Biologists from the Royal Botanic Gardens, Kew, have discovered the world’s largest eukaryotic genome known to date. That distinction belongs to the Paris japonica, a small white flower native to Japan. At 152 billion base pairs in its haploid genome, this little plant has about 50 times more DNA than humans do.

Scientists have known for almost a century that genome size does not correlate with either number of chromosomes or with number of genes. For example, the haploid human genome has about three billion base pairs, which are divided into 23 chromosomes. In comparison, an aquatic rat called Anotomys leander has 46 chromosomes in its haploid genome. Granted, chromosomes are fairly arbitrary divisions of DNA. More importantly, those 3 billion base pairs in the human genome are divided into about 23,000 genes. That makes it seem rather odd that the nematode worm Caenorhabditis elegans has a genome containing over 20,000 genes. This seems to be implying that it takes nearly as many genes to make a 1 mm long worm as to make a human.

The previous eukaryotic record holder was the marbled lung fish Protopterus aethiopicus, weighing in at about 133 billion base pairs. Like all organisms with huge genomes, P. aethiopicus and P. japonica face a steep penalty for their massive amounts of DNA. Because it takes so long to replicate their DNA, they grow very slowly, making them unsuited for certain habitats. It’s known that creatures with very large genomes are less able to tolerate extreme environmental conditions.

As I stated, P. japonica is the award winner among the eukaryotes. You may be surprised to learn that the organism with the largest genome of all is an amoeba called Polychaod dubium. Its genome weighs in at whopping 670 billion base pairs. Why an amoeba would need that much genetic information is a mystery, at least to me.

Men sweat, women perspire

It turns out that there actually are differences in the way men and women sweat. According to Yoshimitsu Inoue and his team from Osaka International University, men really do sweat more than women.

The researchers compared roughly equal numbers of physically trained and untrained men and women. Each volunteer was asked to ride an exercise bicycle for an hour. For both men and women, physically fit individuals sweated more than their untrained cohorts. However, men sweated more than women in both the trained and untrained groups, and men showed a greater increase in sweating with physical training.

The authors speculate that the difference in the sexes may have to do with the lower total fluid volume of women. A less efficient cooling system may have been an evolutionary trade-off for staving off dehydration. In any case, this finding has implications for both female athletes and for women in extremely hot environments.