Science-- there's something for everyone

Monday, January 31, 2011

For pills, color matters

I’ve written a few stories about how important the placebo effect is when taking medication. It turns out that the color and/or shape of a pill can have dramatic effects on patient outcomes. At the very least, the physical attributes of the pills affect patient compliance in taking the medication.

R.K. Srivastava and Aarti More of the University of Bombay surveyed 600 consumers’ perceptions of a variety of OTC (over the counter) pharmaceutical products. They found that differences in color greatly affected what the participants thought of the drugs, as well as whether they remembered to take them.

Among their findings:

  • 14% thought pink pills were sweeter than red.
  • 11% thought white or blue bills were bitter.
  • 10% said orange pills were sour.
  • Many people thought yellow pills were salty.
  • Middle-aged people and women liked red pills more than young people or men did.
  • Many people said the color and/or shape of the pills helped them remember to take them.

Remember there were no actual differences in taste among these different colors. Needless to say, these findings have implications not only for pharmaceutical companies trying to sell their wares, but also for health professionals trying to ensure compliance in their patients.

Sunday, January 30, 2011

Want to learn something? Memorize!

What’s the best way to learn new material? According to a study by Jeffrey Karpicke and Janell Blunt of Purdue University, practicing memory retrieval is much more effective than any other study method.

Practicing memory retrieval simply involves repeatedly testing yourself to see what you remember after you put your notes away. In order to see how memorization practice compares with other kinds of study practice, the researchers enlisted 200 students to study a variety of science subjects. One group prepared elaborate concept maps explaining the material, whereas the other group simply read the texts and practiced memory retrieval. No one was more surprised than the students themselves when one week later the retrieval team showed a 50% greater improvement compared to the concept map team. This was true even when the students were tested on connections and inferences that weren’t explicitly in the text. In other words, practicing retrieval led not only to more complete memorization, but more importantly to a better understanding of the material.

As I stated, this went counter to the students’ own predictions. Most of them assumed that constructing concept maps and using other study tools would be more effective than merely practicing retrieval of the material. It’s certainly not the result I would have expected, but one I’m glad to know about for the next time I try to learn something new.


Saturday, January 29, 2011

Penguin tagging not so innocuous


Tagging animals in order to study them is a common practice. Much information has been gained about behavior and migration patterns thanks to various labeling techniques. But do the tags have any negative effects? If you’re using flipper bands on king penguins, the answer is ‘yes’.

Claire Saraux led a team from the Université de Strasbourg and the University of Oslo in investigating the long term effects of banding on a colony of king penguins. 100 birds were implanted with electronic tags, and half of these were also fitted with flipper bands. The birds were observed over the next ten years. Compared to the birds with only electronic tags, the banded birds reared 39% fewer chicks and had a 16% lower survival rate. The increased mortality and decreased reproductivity continued throughout the entire ten-year period, indicating that the birds were not acclimating to their banded flippers as researchers had thought they would.


King Penguins (Aptenodytes patagonicus) at Edinburgh Zoo.

Photo by SeanMack, 2006.

The banded birds as a group tended to show up late to their breeding grounds, possibly because they were taking longer to forage for food. This hypothesis is born out by observations that the differences between banded and non-banded birds was minimized in years with more favorable environmental conditions.

Personally, I’ve always wondered how tagging affects an animal’s long term survival. If nothing else, it seems like the odd smell, appearance and/or texture would have to impact mating success. Prior to this study, I’d never seen any mention of this issue. Biologists always seemed to assume that their tags have a null affect on their study subjects. I should point out that one of the reasons for using wing bands rather than electronic tags is that the bands can be seen from a greater distance, presumably decreasing the stress of close human contact. This study shows that, at least for king penguins, electronic tags are preferable.

Hat tip and more details: Not Exactly Rocket Science.

Friday, January 28, 2011

Just for fun: Another optical illusion

Here's an optical illusion made by youtuber Rxe08.



Cool, huh?

Hat tip:
Bad Astronomy.

Thursday, January 27, 2011

Informed consent

What kind of informed consent should be required for medical study participants? Is a one-time consent sufficient, or should volunteers be given multiple opportunities to opt out of studies? This question is particularly important for people donating genetic samples and/or information that might later be used in unexpected ways. Bioethicists led by Susan Brown Trinidad from the University of Washington have been tackling this issue.

There are two main questions that the panel attempted to address. First, does consent to provide a genetic sample to one group of researchers give that group implied or explicit permission to give that sample to anyone else who may want it? Today, laboratories are pooling genetic information to an unprecedented extent. Many studies rely on large pools of information, and often the original sample collectors could not have predicted how the data would one day be used.

Second, should the biospecimen donators be informed of each study or usage to which their data is put so that they can choose to opt out at any point? Should they perhaps get a yearly summary? For example, 'in 2011, your tissue sample was used in a cancer study, a geneology study, and for suturing practice.' Needless to say, this would require an enormous database and may not even be feasible. Researchers not only don’t know but in many cases are forbidden to know the personal information about the origins of their samples.

When participants in a bioethics study were asked about their preferences, 90% of them were willing to supply tissue and genetic samples to research biobanks. They were divided almost evenly about whether a one-time consent would be sufficient or if they preferred to re-consent to each new usage.

Gathering large pools of biological and genetic data can only benefit the public. Doing so without trampling individual rights is an even worthier goal.

Wednesday, January 26, 2011

Algae that lives in fresh and salt water

Biologists from Dalhousie University, the University of Exeter, and the Monterey Bay Aquarium Research Institute have discovered a new type of algae called a 'rappemonad' with a variety of highly unusual characteristics. For one thing, rappemonads can live in both fresh and salt water. Most organisms are exclusively adapted to one or the other of these environments. In addition, the algae were found in habitats ranging from 52 to 79 degrees Fahrenheit, again, an unusual ability. Finally, the rappemonads are so different from other types of algae living in the same environments that scientists believe they may form an entirely new group of microorganisms.

What I find particularly interesting about this story isn’t the unusual survival abilities of rappemonads, but rather the fact that it took researchers twenty years to actually see them. Back in 1990, a paper was published containing the DNA sequence of this new, as yet unnamed, type of algae. Based on that DNA evidence, the algae were named rappemonads (after Michael RappĂ©, the author of that paper). But the algae themselves had never been observed.

More recently, the biologists mentioned above analyzed water from a variety of fresh and salt water sources and found DNA evidence that the algae was present. However, that’s still all they found, just the DNA. It was as if all the wildlife in a patch of forest were gathered into a sack and then the contents were analyzed (a bit of blackbird, some ants, a squirrel, etc.) based on the DNA in the bag without ever having seen any of those creatures.

In any case, the researchers did eventually see the rappemonads. They used the known DNA sequences to make fluorescent probes, and then were able to photograph the lit up organisms. You can see the results below:


stained rappemonad cells


A collection of rappemonad cells photographed by a high-powered microscope. Each cell contains at least two chloroplasts (green dots) and a nucleus (blue dots).

Images: from Kim, Harrison, Sudek et al. PNAS 2010.

Tuesday, January 25, 2011

Partition values are fractal

Ken Ono of Emory University and his colleagues have solved a centuries old problem in mathematics: how to predict and make sense of partition values. The mathematicians have discovered that partition values are fractal in nature. Perhaps that means as little to you as it did to me upon first reading. Let me explain.

Any positive integer will equal one or more added smaller integers. The number of ways that the original integer can be created by adding is that integer’s partition value. For example, 4 = 3 + 1 = 2 + 2 = 2 + 1 + 1 = 1 + 1 + 1 + 1. There are five ways to come up with the number 4 by adding, so there are 5 partitions of 4. The partition value of 4 is 5. Partition values form the basis of our adding and counting system.

Sounds simple enough right? Well, while it may be easy to figure out partition values for very small integers this rapidly becomes impossible. The number 100 has more than 190,000,000 partitions! Before 1937, no one had been able to accurately predict partition values for integers above 200. Since then, extremely tedious methods have been designed, but they generally require adding infinitely many numbers with infinitely many decimal points. Mathematicians wanted a finite formula for the problem.

Enter Ono, who had a mathematical epiphany while hiking with his student Zach Kent. The two of them realized that partition values are fractal in nature. In other words, partition values form part of a repeating pattern. This knowledge allowed the mathematicians to devise an algebraic formula for calculating partition values. I haven't included that formula here, but you can find it by following the links if you're so inclined.


Emory mathematician Ken Ono.

Photo by Carol Clark.

Okay, I admit that this story still may not mean that much to many of you. Probably only mathematicians can truly appreciate the scope of this discovery. Nevertheless, I think it’s a fascinating glimpse into the kinds of inquiry some people are exploring.

Monday, January 24, 2011

Quick and easy anti-bacterial drug testing

Researchers from the University of Michigan have managed to test drug susceptibility in individual bacteria. Because there is no need for the bacteria to grow into a visible colony before testing, results can be obtained in minutes, rather than in days. The scientists, led by Raoul Kopelman, managed this feat by bypassing the need to see the bacteria with a microscope.

Currently, in order to tell what sort bacterial infection a person has, doctors have to allow the microorganisms time to grow into a visible culture. This can take hours or even days. Testing whether a culture is susceptible to a particular drug can take just as long as researchers wait to see whether bacteria have died or stopped dividing.

Rather than trying to observe bacteria through a microscope, Kopelman and his colleagues used a device called an asynchronous magnetic bead rotation (AMBR) sensor. Simply put, the scientists attach a single bacterium to a spinning magnetic bead. If the bacterium grows (divides in two), the increased drag slows the bead down. On the other hand, if the bacterium dies (after administration of a drug, for example), the bead speeds up. The changes in speed can be detected for size differences as small as 80 nanometers, one third the limit of the most powerful light microscope and easily small enough to register the addition or subtraction of a single bacterium.

You can watch the following animation to see how this works:



The researchers expect this technique to be useful not only for identifying and treating bacterial infections, but for treating cancer as well. After all, cancer cells can be attached to an AMBR sensor and subjected to a variety of drugs and treatments just as well as bacteria can.


Sunday, January 23, 2011

First confirmed rocky exoplanet

Although hundreds of exoplanets have been found, most have been gas giants. The search is on to find a truly Earth-like planet: one with a solid surface that is the right distance from its star to contain liquid water. Last year, NASA launched the Kepler mission with the goal of finding just such a planet. They came pretty close with the discovery of Kepler-10b.

Kepler-10b was discovered using the ‘transit method’. The Keck Observatory in Hawaii recorded the miniscule dip in light caused by the planet passing in front of its star, Kepler-10. Information about the size of the planet and distance from its star were calculated based on the time between those periodic light dips.

It turns out that Kepler-10b zips around its star in less than a day, indicating that it is 20 times closer to its star than Mercury is to ours. Needless to say, this is not within the habitable zone. However, as a confirmed rocky planet only about 4.5 times the size of the Earth, Kepler-10b’s discovery means that the Kepler mission is on track to find other, even more Earth-like planets.

You can see an explanation by lead astronomer Natalie Batalha below:



Until the discovery of Kepler-10b, the closest thing to an Earth-like planet has been Gliese 581g. This planet is about the right size and does lie within the habitable zone, but may be gaseous instead of rocky. In addition, Gliese 581g is tidally locked to its star, Gliese 581, meaning that it no longer rotates. Instead, one side of the planet has perpetual daylight, and the other, perpetual night. It’s not clear whether such an arrangement would preclude life.

UPDATE: A new look at the data calls into question whether Gliese 581g even exists! You can read more about this controversy on the Bad Astronomy website.


Saturday, January 22, 2011

Streets without left turns

City planners who wish to increase traffic efficiency and safety would do well to consider designing ‘superstreets’ according to a study by researchers at North Carolina State University.

Superstreets are roads that are designed to eliminate left turns. Rather than making a left at an intersection, drivers must first turn right and then make a u-turn. Although this sounds counterintuitive it actually saves time. In fact, travel time on superstreets is 20% less than on conventional streets. Even more important, superstreet intersections lead to 50% fewer collisions.

The idea of eliminating left turns is not new. Roundabouts, junctions that allow drivers to circle around to the left or right without making an abrupt turn, have been shown to be safer and more efficient than right-angle intersections. They are currently more common in Europe and Asia, but are becoming more popular in North America.

Even on traditional streets, some companies have initiated ‘no left turn’ policies for their drivers. Again, it seems like eliminating left turns would require time-consuming circuitous routes. Not so. UPS, for example, claims to save three million gallons of gas each year by eliminating lefts. UPS drivers do rely on route-planning software to get them to their destinations efficiently. You can’t get that kind of time and energy savings by blindly turning right instead of left at each intersection.

Here's an example of a superstreet interesection:


Friday, January 21, 2011

Just for fun: SETI Gurls

SETI is the Search for ExtraTerrestrial Intelligence. The undergraduates and interns working at the SETI Institute seem to have a little too much free time. I'm sure that will change if they ever find what they're looking for.


Hat tip: Skepchick.

Thursday, January 20, 2011

Genetic basis of hair color

Manfred Kayser of Erasmus MC led a team of scientists in accurately tying genetic makeup to hair color. The team was 90% accurate in identifying red and black hair, and 80% accurate in identifying brown or blond hair.

Kayser and his colleagues used the genetic and hair color information from hundreds of Europeans to find the hair color genes. They narrowed the possibilities to 13 DNA markers, found in 11 different genes. Different combinations of these markers result in the different shades of hair color.

The researchers expect forensic scientists to make use of this new identification tool in the near future. Personally, I’m not sure this information will be all that helpful. Of all genetically-encoded physical traits, hair color must be the easiest to alter. Information on a suspect’s age, which can now be determined from markers in blood, seems a lot more useful to me.

Paris wig shop, by Arnaud de Gramont, 2009.



Wednesday, January 19, 2011

New weapon against cancer

We may be one step closer to a cure for cancer. Researchers from the Wake Forest University School of Medicine have found that a small peptide called angiotensin-(1-7), or Ang-(1-7) was effective in reducing breast tumors in mice. Not only that, but the peptide decimated the non-tumorous support cells that nurture the tumor.

Ang-(1-7) is a seven amino acid long hormone initially shown to inhibit the growth of the muscle cells surrounding blood vessels. These smooth muscle cells are involved in regulating blood pressure. People treated with drugs that increase Ang-(1-7), in an effort to lower blood pressure, were serendipitously found to have a lower cancer risk. Based on this data, Patricia Gallagher and Ann Tallant tested Ang-(1-7) on lung tumors. In mice, Ang-(1-7) reduced the size of both the tumor itself and of supporting blood vessels.

The team next tested Ang-(1-7) on breast tumors in mice. This time, the peptide inhibited the growth of the tumor and of cancer-associated fibroblasts (support cells in the tumor’s immediate environment that provide a scaffold for the tumor). Gallagher likens the two-pronged attack to killing seeds and destroying the soil around the seeds.

The scientists hope to go to clinical trials with Ang-(1-7) soon. The fact that it works in more than one type of mouse tumor is very exciting. Let's hope it's as effective in humans.

Tuesday, January 18, 2011

Safer driving for seniors

For a number of reasons, including poorer eyesight and slower reflexes, older people are a greater danger on the roads than young people. Can anything be done to remedy this situation? Researchers from Université Laval believe that a training program including a simulator can improve driving safety for senior citizens.

In their study, participants were tested on the road both before and after a coaching session with a driving simulator. During the simulator session, any errors made on the road were highlighted, along with ways of coping with those situations. Not surprisingly, the seniors improved considerably on their next road test.

Unfortunately, this kind of training session is not widely available to seniors who wish to make use of it. In many regions, nothing more than vision tests are available to older drivers. At best, seniors may take driving tests with no attached coaching sessions. Study author Normand Teasdale hopes that will change.

In the meantime, here’s a video clip from a simulator exercise. Wouldn’t you like to know what the man is saying at the end of the clip?



Monday, January 17, 2011

Ancient club-winged bird

Nicholas Longrich from Yale University and Storrs Olson from the Smithsonian Institute have discovered a novel fighting strategy in an extinct ibis. Apparently, the birds would bludgeon each other with their club-like wings.

Xenicibis xympithecus lived in Jamaica about ten thousand years ago. A flightless member of the ibis family, Xenicibis was about the size of a large chicken. Newly discovered skeletons revealed that the bird had wing bones unlike any seen before. Rather than being greatly reduced like most flightless birds, the wings contained thick curved hand bones hinged at the wrist joint. In two cases, the bones showed obvious signs of combat, including broken hand and arm bones. The paleontologists concluded that the birds would batter their rivals with their cudgel-like wings.

This behavior was so unprecedented that, in referring to the skeletal discoveries, Longrich stated,

When I first saw it, I assumed it was some sort of deformity. No one could believe it was actually that bizarre.


The prehistoric Xenicibis used its wings like two clubs hinged at the wrist joint in order to swing at and attack one another.

Credit: Nicholas Longrich/Yale University.



Sunday, January 16, 2011

Watching proteins fold


We now have the human genome completely sequenced. However, that information isn’t particularly useful unless we also know something about the proteins that our genomes encode. Unfortunately, predicting the final structure of a protein (which is critical for that protein’s function) from its DNA sequence has been challenging, not least of which because the folding process takes place in under a millisecond. Enter Michael Gross, Jiawei Chen and Don Rempel of Washington University, who have invented a way to observe proteins folding.


Example of a protein going from linear strand to three dimensional folded enzyme.

The researchers used a protein called ‘barstar’ as a model. This small (110 amino acids long) has a known primary structure (linear sequence of amino acids) and a known tertiary structure (the final, fully folded polypeptide). What was not known was the exact folding process required to go from one to the other. Here’s what the researchers did:

Samples of cold (unwound) barstar were placed in extremely thin hollow fibers, along with hydrogen peroxide (H2O2). The mixture was hit with two rapid laser pulses. The first pulse warmed up the solution enough for the protein strands to begin to fold. The second pulse broke up the H2O2, creating the highly reactive hydroxyl (-OH) radical. This radical added oxygen atoms to the exposed portions of the barstar protein. As Gross explains,

Imagine that you suspended a styrofoam model of a partially folded protein and spray-painted it blue. The outside parts would be painted blue; those buried within would remain white.

A microsecond after the second laser pulse, the excess –OH was removed. The protein was then ‘weighed’ in a mass spectrometer to see how much oxygen had been added.

This process was repeated 500 times in rapid succession, giving the scientists snap shot views of the protein in the processing of folding. The technique was successful with barstar, and may lead to helpful insights about other proteins as well.

Saturday, January 15, 2011

Border collie understands over 1000 words

John Pilley and Alliston Reid of Wofford College have determined that their border collie Chaser can understand more than a thousand words. Not only that, but the dog can distinguish nouns from verbs, and even understand categorizing labels.

Chaser’s owners taught her the names of over a thousand different toys over a three-year period. In order to determine whether Chaser understood that the nouns were in fact the names of the objects and not simply orders to fetch that particular object, they combined the names with different kinds of verbs like ‘take’ or ‘paw’ (nudge with your foot). Chaser was able to match the correct action with the correct object.

Pilley and Reid found that Chaser could also group her toys into broader categories like ‘ball’ or ‘frisbee’. And even more amazing, she could infer the name of a new object by excluding previously used names.

Here’s an example of a testing/training session.

When I hear stories like this, I always wonder if these results are more or less representative of the whole species, or if the animal in question is some sort of super genius. There certainly is a wide range of cognitive ability in humans, why not in other species as well? If the animal is not representative, does that tell us more or less about the species?


Friday, January 14, 2011

Just for fun: Google Science Fair

Any young scientists out there? If you are between 13 and 18 years old, you can submit a science project to Google's Science Fair. Projects can be designed by individuals or by teams of up to three people. The grand prize is a trip to the Galapagos and a $50,000 scholarship! So get cracking, the entry deadline is April 4, 2011.



Thursday, January 13, 2011

For accurate dosing, don’t split tablets

Splitting tablets to achieve lower doses of medication is a common practice. Unfortunately, according to a new study by Ghent University researchers, it’s one that should be discouraged.

Between them, the five researchers split 3600 pills into halves or quarters, using various methods, including a pill-splitter. Some of the pills were pre-scored, others were not. The scientists found that splitting tablets very often results in uneven dosages. For one thing, tablets are often not split into exactly equal parts. For another, some material is usually lost at the cut site, making the total of the remaining pieces less than the original was. Even under the best conditions, a sizeable fraction of the resulting fragments were up to one quarter bigger or smaller than expected.

Although this may not matter for some medications, others require tightly controlled dosing. For this reason, the researchers suggest that whenever possible patients use either pills formulated to their exact dosage or liquids, rather than splitting pills. If pills must be split, using a pill-splitter rather than a knife or other implement yielded the most accurate results.


Wednesday, January 12, 2011

When humans began to wear clothing

At some point in our distant past, humans gained the habit of wearing clothing rather than walking around naked. Certainly, clothing became essential once humans left Africa for colder climates. But how long ago did this occur? David Reed of the University of Florida and his colleagues used a novel method for answering that question: they studied lice.

Lice that make their living on human bodies currently come in three flavors: head lice, body or clothing lice, and pubic lice. This was not always so. Before humans lost their body hair, there was only one type of human louse that was free to roam from head to toe. Without body hair, the desert of bare skin confined lice to specific regions, namely the head and pubic area. Lice finding themselves stranded in these regions evolved apart from each other. Later, when humans began to wear clothing, head lice found a new way to make a living by hiding in the folds and creases of clothing. From these safe havens, they could venture forth to make a meal on the hairless regions of the human form. As with the pubic lice, body lice diverged from head lice until they became the two independent species they are today.

Reed and his team used genetic analysis to determine when head lice and body lice diverged, and came up with a range of 83,000 to 170,000 years ago. Therefore, humans began wearing clothing during approximately the same time period. This corresponds well to some of the known human migrations out of Africa.

One final note: this method looked at modern head and body lice to determine when the two species diverged. In other words, it could only answer the question of when modern humans began to wear clothing. We don’t have any head or body lice from Neanderthals, although they were known to be living in cold climates far earlier than modern humans. Extinct human species may well have taken to wearing clothing many thousands of years before modern humans did.


Tuesday, January 11, 2011

Faster brain scans

A team of researchers from the University of Minnesota, Universities of California Berkeley and San Francisco, Washington University and Oxford, as well as from Advanced MRI Technologies has reduced the time required for full 3D fMRI brain scans over five fold.

Briefly, functional magnetic resonance imaging (fMRI) uses pulses of radio waves to measure the amount of oxygen being delivered to specific neurons. Neurons that are actively firing require more oxygen than those that are quiescent. Therefore, by using fMRI, researchers can actually watch people think. Naturally, the faster images can be taken, the more accurate the picture of how people are using their brains.

The team combined two novel techniques, each of which reduces scan time over conventional means. The first technique was to send the radio pulses out in multiple bands. The second was to make use of echoes to multiply the amount of information gained from each pulse. Taken together, these two innovations allow scans to be made in less than half a second, rather than in the two or three seconds required by conventional methods.


Caption: The new technique accelerates diffusion MRI as well as functional MRI. The colored tracks show the direction of nerve fiber bundles, providing a 3-D image of the axonal pathways in the white matter (cortex) of a resting human brain. A normal structural cross sectional image of the brain (fMRI) bisects the diffusion 3-D fibertrack image. The entire 3-D image was scanned in 8.5 minutes instead of 30 minutes.

Credit: David Feinberg

Besides helping doctors map specific brain disorders, the researchers are hopeful that this increase in processing speed will be a major boon for the Human Connectome Project. The goal of this project is to map every neural connection in the human brain, and thereby understand what makes us who we are. You can watch a video explaining this here.