RealClearScience Journal Club

Science Figures Interpreted and Analyzed by RealClearScience

Will Propane-Making Bacteria Revolutionize Energy?

Alex B. Berezow - September 2, 2014

Fire up the grill!

Propane is the fossil fuel of red-blooded Americans. What poolside or tailgating experience would be complete without firing up the gas grill and torching some meat? (I know, I know... there are charcoal devotees out there.) Even metropolitan mass transit systems are getting in on the excitement. Fleets of buses that run on "LPG" (liquefied petroleum gas) are burning a mixture of propane and butane.

Currently, propane is extracted from natural gas or crude oil. But, in the long run, this is neither a sustainable nor an environmentally friendly practice. Burning propane extracted from the earth is also not carbon-neutral, though it is better than combusting oil or coal. Thus, researchers are looking for ways to produce renewable "fossil fuels" through the use of alternative technologies, such as synthetic biology. Last year, for instance, scientists engineered E. coli to churn out a biofuel that resembled gasoline.

A team of researchers led by Patrik Jones of the University of Turku in Finland, however, believes they have invented a better method. Instead of gasoline, they focused on propane. Why? Because propane has the distinct advantage of being easily converted from gas to liquid (and back). Thus, as the bacteria release gaseous propane, the authors argue it should be easy to capture and store it as a liquid. Additionally, because propane does not build up in the culture medium, it will not inhibit the growth of the bacteria.

To create their tiny fuel manufacturers, the authors had to design a propane biosynthetic pathway that does not exist in E. coli. To do so, they borrowed genes from multiple bacteria: Bacteroides fragilis, Mycobacterium marinum, Bacillus subtilis, and Prochlorococcus marinus. (The pathway they created is shown below. Black letters denote chemical compounds, while red letters denote enzymes and proteins.)

The pathway shows that their genetically engineered E. coli can be fed glucose (sugar) and crank out propane. The next step is scaling up for large-scale industrial production. Their current platform is inadequte for that, but some preliminary data suggests reason for optimism. They would also like to transfer the pathway into a photosynthetic microbe, which would essentially convert the energy of sunlight into propane.

There are three big lessons from this research:

First, it is time for anti-GMO activists to grow up and accept biotechnology. The future of everything from food and medicine to renewable energy and high-tech materials will rely on it.

Second, the potential of synthetic biology (recently discussed in the journal Nature Reviews Molecular Cell Biology) may be limited merely by our imagination. Already, synthetic biology has been used by bioengineers to create genetic logic gates -- a useful technology for biosensors and biological computers -- and by systems biologists to further decipher the complexity of the cell.

Finally, the benefit of basic research is unforeseeable. Most likely, the scientists who figured out how these obscure metabolic pathways worked never became famous nor expected their research to change the world. And yet it just might.

Source: Pauli Kallio, Andras Pasztor, Kati Thiel, M. Kalim Akhtar, & Patrik R. Jones. "An engineered pathway for the biosynthesis of renewable propane." Nature Communications. Published 2-Sep-2014. DOI: 10.1038/ncomms5731

Can a Scientist's Writing Style Reveal Fraud?

Ross Pomeroy - August 28, 2014

Diederick Stapel was one of the most celebrated and published scientists in the field of social psychology. But in 2011, it was revealed that much of his career was built on fraud. He had tweaked or completely fabricated data in no fewer than 55 of his 125 published papers! Stapel lost his title as a respected professor and became known for what he truly is: an academic "con man."

Three years after Stapel's deception was revealed, two Cornell researchers, David Markowitz and Jeffrey Hancock, have put Stapel's misconduct to good use. In an analysis published to PLoS ONE, the pair compared the linguistics in 24 of Stapel's confirmed fraudulent papers with the linguistics in 25 of his genuine ones, seeking to find out if Stapel's writing differed between his honest and deceptive efforts. When a scientist hands you lots of lemons, why not make lemonade?

The results of Markowitz and Hancock's study are fascinating.

"The analysis revealed that Stapel’s fraudulent papers contained linguistic changes in science-related discourse dimensions, including more terms pertaining to methods, investigation, and certainty than his genuine papers. His writing style also matched patterns in other deceptive language, including fewer adjectives in fraudulent publications relative to genuine publications," the authors write.

Stapel tended to fortify his methods section with extra description and employ words like ‘‘profoundly,’’ ‘‘extremely,’’ and ‘‘considerably’’ to make his results sound more convincing and dramatic. At the same time, he also used fewer terms that might downplay significance, such as "less," "somewhat," and "merely."

"Stapel presumably attempted to emphasize the novelty and strength of his findings, which ended up being 'too good to be true.'"

Using their findings, Markowitz and Hancock put together a simple model for detecting fraud, and, when tested on Stapel's papers, found it to be 71.4% accurate. Not bad, but still nowhere good enough to be feasible in other contexts. Moreover, the writing patterns found to indicate fraud in Stapel's writing may not apply to other scientists. It would be very interesting to see if they do -- something to examine in a future study!

Source: Markowitz DM, Hancock JT (2014) Linguistic Traces of a Scientific Fraud: The Case of Diederik Stapel. PLoS ONE 9(8): e105937. doi:10.1371/journal.pone.0105937

First Observation of Death Valley's Sliding Rocks

Alex B. Berezow - August 27, 2014

A dry lake in Death Valley, called Racetrack Playa, is home to the famous "sailing stones." These large rocks, some of which weigh up to 700 pounds, leave behind long trails in the dirt, indicating that something -- or someone -- has been moving them. (See photo above.) But how?

Conspiracy theorists and others with active imaginations have implicated aliens (of course), powerful magnetic fields, or just plain old magic as the culprit behind the mysterious phenomenon. More serious speculators suggested dust devils or a combination of rain and strong wind. These explanations, however, are wrong.

Last year, Live Science (and several other outlets) reported that the mystery was solved. Researcher Ralph Lorenz had discovered that a rock with a ring of ice around it is buoyant (PDF). When placed in a shallow pool of water, Dr. Lorenz found that he could move the rock simply by blowing on it. Additionally, if there is sand at the bottom of the shallow pool, the rock scrapes out a visible path. But, as it turns out, this explanation isn't quite right, either.

Now, in a new paper published in PLoS ONE, Dr. Lorenz and a team of researchers led by Richard Norris and Brian Jackson have definitively demonstrated how the rocks move. They placed 15 GPS-equipped limestone rocks on Racetrack Playa. They also installed a weather station nearby, as well as several cameras. Then, the researchers monitored the rocks from late November 2013 to early February 2014.

The team found that their rocks moved on two different days, December 4 and December 20. The most impressive rock weighed in at 36.6 pounds and made a trail 215 feet long, but its speed topped out at a sluggish 0.22 mph. (One of their rocks is pictured below.)

The rocks were located in a shallow pool of water that froze many of the nights. The next morning, when the temperature rose, the large sheet of ice would crack and pools of water would form. Large chunks of ice could then freely move around, dragging the rocks along with them, as the wind blew. In contrast to their hypothesis, the rocks did not become buoyant. Instead, the ice sheets -- which were only a few millimeters thick, but several meters across -- could exert a force large enough to move the rocks.

Not only did the authors collect data on their GPS-equipped rocks, but their cameras also captured several indigenous rocks gliding about.

The authors note that it would be difficult personally to watch the rocks in action due to their glacial pace. Also, the rocks move only on rare occasions; i.e., when a shallow pool of water is present along with freezing conditions and wind. Complicating matters for would-be enthusiasts is the fact that the ice would block anyone's view of the trail, which is formed in the mud below. Only after the water is blown away by the wind do the trails become visible.

Still, people who enjoy the sport of curling also may be inclined toward rock-watching. Now that the conditions under which the rocks can move are known, avid rock-watchers should plan a winter camping trip to Death Valley. Just be sure to pack some extra patience.

Source: Norris RD, Norris JM, Lorenz RD, Ray J, Jackson B (2014) Sliding Rocks on Racetrack Playa, Death Valley National Park: First Observation of Rocks in Motion. PLoS ONE 9(8): e105948. doi:10.1371/journal.pone.0105948

(Photo: Death Valley's "sailing stones" via PLoS ONE)

A World Cup in Qatar's Heat Won't Be Safe for Players or Even Spectators

Ross Pomeroy - August 21, 2014

Qatar is currently scheduled to host the FIFA World Cup in the summer of 2022. There are many reasons why this is a terrible idea, but for now, let's just focus on one of them: the heat.

The average summer temperature in Qatar is 106 degrees Fahrenheit. In sweltering heat like that, nobody should be in direct sunlight for very long, let alone playing soccer at a world-class level for ninety minutes. But don't worry, the Qataris have a plan for reducing the pitch temperature to a less frightening 87 degrees in all of their open-roof stadiums: giant fans... lots of them. Good luck with that, wealthy oil tycoons.

The simple fact is that playing soccer outdoors in a Qatari summer isn't safe for players, and, according to a new report in the International Journal of Biometeorology, it might not even be safe for spectators.

Researchers Andreas Matzarakis and Dominik Fröhlich of Albert-Ludwigs University in Freiburg, Germany gathered weather data for Doha -- Qatar's capital and the designated home for 6 of the 13 World Cup stadiums -- and distilled the collection into a metric called physiological equivalent temperature (PET). PET takes variables like wind, humidity, and solar radiation into account to produce what's essentially an estimated indoor temperature. For example, on an 80-degree day with copious amounts of sunlight and high humidity, the PET might be 95 or higher. Walking around outside would feel like being inside if the temperature were 95 degrees.

When all the numbers were crunched, Matzarakis and Fröhlich actually were forced to update the standard PET table created back in 1996. Here is the original table:

And here are the two levels added in order to fit a Qatari summer:

The 2022 FIFA World Cup in Qatar will be outlandishly, mind-bogglingly, barbeque-liciously hot. And that's putting it mildly. Check out this figure showing the calculated PET by time of day for Doha over the course of a year.

 

You're reading that graph correctly. Between 7 A.M. and 2:30 P.M.* during the time of the World Cup, the average PET will be between 45 and 50 degrees Celsius or higher. Converted to Fahrenheit, that's between 113 and 122 degrees! At PETs like that, heat stroke, where the body's temperature rises above 104 degrees Fahrenheit, can occur in a manner of hours or less, Matzarakis says, depending on factors like age, clothing, and alcohol intake. Heat stroke can result in permanent organ damage or even death.

"The results show that this kind of event may be not appropriate for visitors," Matzarakis and Fröhlich simply stated.

Not wanting to ruffle any feathers, they also added:

"It is not the aim of this study to show that Doha City is inappropriate for the FIFA 2022 but to find a time period with the most suitable thermal conditions for visitors and tourists. According to the results, this is the time from November to February."

FIFA is currently considering rescheduling Qatar's World Cup to the winter months to avoid the life-threatening heat, but that may not even be necessary. Qatar's successful World Cup bid is widely thought to be the result of bribery, and a report assessing those allegations is due this fall. If claims of bribery are substantiated, it is highly likely that the 2022 World Cup will be relocated to the second place country, the United States.

(*Correction 8/22: Adjusted upper limit from 3 P.M. to 2:30 P.M. to more accurately reflect the figure.)

Source: Matzarakis A, Fröhlich D. "Sport events and climate for visitors-the case of FIFA World Cup in Qatar 2022." Int J Biometeorol. 2014 Aug 14.

Narcolepsy May Be an Autoimmune Disease

Alex B. Berezow - August 18, 2014

Fans of the 2001 movie Rat Race will remember that Rowan Atkinson's character suffered from narcolepsy. Moments before claiming the $2-million cash prize, he fell asleep. In real life, not only do narcoleptics suffer from irresistible daytime sleepiness, but they also have trouble sleeping at nighttime and may physically collapse from sudden muscle weakness, a symptom known as cataplexy. But, what causes it?

Evidence over the past few years has suggested that narcolepsy is an autoimmune disorder. However, the evidence is rather scattered; some data implicates environmental triggers, while others suggest genetic factors. Last December, a report linking an influenza vaccine with narcolepsy supposedly provided confirmation of the underlying autoimmune nature of the disease, but the article was later retracted due to a failure to replicate key findings. Still, the suspicion about narcolepsy remained.

Now, a new study in PNAS provides very strong evidence that some cases of narcolepsy are indeed due to autoimmunity. The authors report that human antibodies (immune proteins that attack foreign substances) from narcoleptics bind to molecules in rat brains, specifically neuropeptides, which are signaling molecules. (See chart. Note: OSRD = other sleep-related disorders; HCs = healthy controls; MC = military controls; A, B, and C refer to different patterns of antibody binding in the brain.)

As shown, 27% of narcoleptics and 22.5% of people with other sleep-related disorders had antibodies which could bind to various molecules within the rat brain, compared to just 10.4% of healty controls and 10% of military recruits. This means that narcoleptics (and those with other sleep disorders) are twice as likely to have autoreactive antibodies as healthy people.

The authors then injected antibodies from two narcoleptics and a healthy control into rats. The narcoleptics' antibodies altered the rats' sleeping patterns, for instance, by causing them to exhibit fragmented sleep. However, the rats did not fall asleep uncontrollably (the main symptom of narcolepsy), perhaps because the researchers only injected them once with the antibodies, rather than multiple times (which would mimic a chronic condition).

The data provides very strong evidence that a proportion of narcoleptic patients, as well as those who suffer other sleep disorders, are suffering from an underlying autoimmune condition. However, the data also suggests that this applies to only 1/4 of all narcoleptics, meaning that, most likely, there are multiple causes for this mysterious disorder.

Source: Peter Bergman et al. "Narcolepsy patients have antibodies that stain distinct cell populations in rat brain and influence sleep patterns." PNAS. Published online before print: 18-Aug-2014. doi: 10.1073/pnas.1412189111

First Interstellar Dust Brought Back to Earth

Ross Pomeroy - August 14, 2014

Fifteen years ago, the Stardust spacecraft blasted off from Cape Canaveral with the goal of collecting the tiny particles adrift in the ocean of space: cosmic dust.

In 2000 and 2002, Stardust opened its aerogel collectors wide in the hopes of catching some of that dust. Two years later, the spacecraft encountered the comet Wild 2 and began tailing the object like a bicyclist drafting a competitor. With its collectors open once again, the spacecraft basked in the nebulous coma of the comet, aiming to catch any particles shedding away.

When Stardust passed by Earth in 2006, the vessel dropped off a precious package, a capsule containing the aerogel collectors, hopefully plastered with dust particles from beyond our solar system. "Dropped" is a bit of an understatement. The capsule plummeted through Earth's atmosphere at a velocity of 12.9 kilometers per second, the fastest reentry speed ever achieved by a man-made object. Peak deceleration was measured at 34 gs. Luckily, the collectors were packed nice and tight; they were just fine. NASA scientists took them to a specially designed clean room to minimize contamination and found a million microscopic specks of dust embedded in the aerogel. A tad overwhelmed, they opened up the process of analyzing the specks to citizen scientists via Stardust@Home. Naming themselves "Dusters," the volunteers scanned magnified images to identify trails in the aerogel much thinner than a human hair. Once the trails were identified, NASA scientists extracted and analyzed them.

Today, after eight years, the Stardust team has officially announced in the journal Science that seven of those one million tiny specks are -- very probably -- interstellar dust.

The seven particles, all on the picogram scale (one-trillionth of a gram!) are incredibly diverse. One, named "Sorok," is composed of magnesium and iron-rich silicates. Two others, "Hylabrook" and "Orion," sport an olivine core surrounded by other trace elements like silicon and manganese. The larger pieces are fluffy like snowflakes, lead author and UC-Berkeley physicist Andrew Westphal said.

Additional tests are underway that will further confirm that the particles are of interstellar origin. 

The universe is in a constant state of recycling, and cosmic dust allows us to trace the process. Often exploded from supernovae or exuded from waning red giant stars, dust particles can later join together to form new planets and stars.

Besides allowing us to characterize the properties of interstellar dust, NASA believes that the miniscule grains described today could help reveal the secrets of the stars and elucidate the creation of chemical elements.

Source: Westphal et. al. "Evidence for interstellar origin of seven dust particles collected by the Stardust spacecraft." Science. 15 Aug 2014. VOL 345 ISSUE 6198

(Images: NASA, Anna Butterworth)

Identify a Bomb from 1 Kilometer Away

Alex B. Berezow - August 11, 2014

One of the problems with bomb detection is that bombs tend to explode. It would be advantageous for a bomb squad to be able to positively identify the contents of a purported bomb before attempting to dismantle it. Existing techniques, however, are inefficient or of limited utility.

In a new PNAS paper, American researchers propose using a variation of Raman spectroscopy to detect bombs from a safe distance. This technique relies on detecting slight changes in a molecule's vibrational energy. Most molecules vibrate in some sort of fashion; atoms move back and forth as if the bonds holding them together are actually springs. Firing photons from a laser at molecules can either increase the vibration of the molecule (thus, decreasing the energy of the photon), or decrease the vibration of the molecule (thus, increasing the energy of the photon). Such photons are said to be "scattered," and the resulting patterns serve as fingerprints to identify particular molecules.

Traditional Raman spectroscopy, however, produces a very weak signal that is difficult to detect. So, the authors used a powerful laser, but unfocused it slightly, to create a larger spot on the target. The large spot trapped the Raman scattered light inside of the target, causing it to glow even brighter. This allowed them to detect explosives, such as potassium nitrate, from 400 meters away. Various tweaks suggested that they could actually detect explosives from 1 km away.

In the figure above, the authors demonstrate the possibility of using aircraft to detect explosives. The airplane would carry a spectrometer that fires a laser (green arrow) at an unknown and possibly explosive substance. This would induce Raman scattering, and the photons would bounce back toward the aircraft (red arrow). The energy of these photons would reveal the identity of the substance.

The authors claim this technology may also help detect the sorts of molecules that would indicate the presence of extraterrestrial life. Indeed, that would be the bomb.

Source: Brett H. Hokr, Joel N. Bixler, Gary D. Noojin, Robert J. Thomas, Benjamin A. Rockwell, Vladislav V. Yakovlev, and Marlan O. Scully. "Single-shot stand-off chemical identification of powders using random Raman lasing." PNAS Early Edition. DOI: 10.1073/pnas.1412535111

(AP Photo)

Scientists Create Autonomous Transformer

Ross Pomeroy - August 7, 2014

In the latest action-packed Transformers film, scientists manipulate an element unsurprisingly dubbed Transformium to create their own metamorphosing robots. Mayhem, mediocre acting, and gratuitous product placement ensues.

Transformium is unlikely to be discovered anytime soon (or ever, for that matter), but that hasn't stopped real-life roboticists from trying to devise their own transformers. So far, most of their advances have been limited to the nanoscale, require significant manual assembly, or create only simplistic geometric shapes. Not exactly Optimus Prime.

While Decepticons and Autobots are still firmly in the realm of science fiction, engineers at Harvard University and the Massachusetts Institute of Technology have taken transforming robots to a new level, creating an origami inspired robot that can transform from a flat piece of material to an insect-like walking robot with no outside interference. The team's efforts are detailed in the journal Science.

To accomplish the feat, the engineers devised a five-layered composite material composed of two layers of paper, one of polyimide with a copper circuit, and two of prestretched polystyrene. The latter material is designed to bend in one direction when heated to 100 degrees Celsius. When completely folded, heat is removed and the new joint hardens. The complete transformation takes four and a half minutes and finishes after five steps. Small motors then kick in which allow the robot to crawl at speeds of about 5.4 centimeters per second.

Three robots were created. Two failed to transform completely due to the failure of a single fold. But the third was a success.

"The robot self-assembled in 270 seconds, after which time it was able to walk without further manual intervention," the researchers describe.

The folding process can be accelerated as well. By applying larger current at a higher voltage, folds could take three seconds instead of forty-five. The robot could be up and walking in under a minute.

Apart from creating cool-looking robots and arousing the hopes of nerds everywhere, the technique does have practical potential. The researchers hope to build satellites that assemble themselves in space, adapt the technique to create rapid prototypes of electrical or mechanical systems, or -- and this is the big one -- create IKEA-style furniture that assembles itself!

Sadly, giant, laser-toting transformers are still a ways off. However, the engineers unintentionally (or intentionally?) embedded a bit of an Easter egg in their printed circuit board design, which conspicuously resembles the Autobot insignia...

Source: S. Felton, M. Tolley, E. Demaine, D. Rus, R. Wood. "A method for building self-folding machines." Science 2014. DOI: 10.1126/science.1252610

(Images: Seth Kroll, Wyss Institute)

New Test Could Eliminate Allergy Skin Pricks

Alex B. Berezow - August 5, 2014

When I was a kid, I remember going to the allergist's office and having him stick me in the back with several dozen tiny needles, each filled with a common allergen such as cat hair. After a few minutes, my back became itchy, and patterns of bright red bumps emerged like this, indicating an allergic reaction. My doctor, along with my parents, stood over my back, pointing at all the pretty colors. He informed us that I was mildly allergic to dogs and terribly allergic to cats, but not at all allergic to goats. (We ended up getting a dog, anyway, and I spent the next several years getting allergy shots, too.)

This modern-day form of torture, however, soon may be coming to an end. Researchers report in the journal Nature Communications that a new blood test could eliminate the need for allergy skin prick assays. Its mechanism of action is nothing short of a cellular Rube Goldberg machine, built using the tools of synthetic biology.

Instead of jamming tiny needles into your back, an allergist would simply draw your blood and mix in a sample of allergen. (See middle panel.) If you are allergic to, say, cat hair, your blood will contain a type of antibody called IgE that will bind to it. IgE bound to the allergen will simultaneously bind to an IgE receptor on the surface of mast cells and basophils (left panel), triggering these two types of immune cells to release histamine. (That is why you take anti-histamines to treat allergies.)

Now, the authors' clever cell-based assay takes over. (See right panel.) Histamine will bind to a histamine receptor on the designer cells. This triggers a whole cascade of events, ultimately culminating in the production of Citrine, a protein that fluoresces yellow. The intensity of the fluorescence correlates with the severity of the allergic reaction.

Sickly children everywhere, rejoice!

Source: David Auslander, Benjamin Eggerschwiler, Christian Kemmer, Barbara Geering, Simon Auslander & Martin Fussenegger. "A designer cell-based histamine-specific human allergy profiler." Nat Commun 5:4408 (2014). DOI: 10.1038/ncomms5408

(Photo: Allergy skin test via Skoch3/Wikimedia Commons)

How the Color Red Screws with Men

Ross Pomeroy - August 1, 2014

"The color red distorts time perception for men, but not for women."

That's the intriguing title of a study published yesterday to Nature's Scientific Reports. Researchers Masahiro Shibasaki and Nobuo Masataka from the University of Kyoto's Primate Research Institute found that when male and female subjects were shown both red and blue screens on computers for varying amounts of time, men tended to overestimate the duration of the red screens.

"These results are consistent with those of previous studies indicating that red induces higher arousal levels than does blue," the researchers say. "It is plausible that the arousal induced by red increases the speed of the internal clock, resulting in the overestimation of the duration of a red screen."

Thirty-seven men and thirty-seven women participated in the experiment. Each subject sat in front of a computer screen and completed 126 trials in which either a red or blue screen was flashed in front of them for a duration of 400, 504, 635, 800, 1008, 1270, or 1600 milliseconds (equally spaced in logarithmic terms). In each trial, subjects selected whether the duration was closer to 400 or 1600 ms. 76% of men overestimated the duration of the red screen on average, while only 43% of women did.

The authors turned to a bit of evolutionary psychology to explain their findings, noting that red is a sign of anger and dominance in many primates. Since males of many species are biologically programed to compete for status, territory, and mates, they might be especially sensitive to the color red. Support for this explanation comes courtesy of an interesting study from 2005, which showed that male competitors at the 2004 Athens Olympics who were wearing red were more likely to win in boxing, taekwondo, Greco–Roman wrestling, and freestyle wrestling.

The color red also "makes men feel more amorous toward women." Women wearing red elicit more attention and are judged to be more attractive than women wearing other colors.

When previous research is considered, the effect of the color red on time perception is inconsistent, the authors admit. While there's little doubt that colors subtly influence our perception of the world, the effects are likely highly context-specific. In the current experiment, for example, it would be interesting to see if the results hold if the durations were longer or equally-spaced on a linear, instead of a logarithmic, timescale.

As far as the color red goes, the most specific thing science can say right now is that it attracts attention, which isn't all that surprising. Red is a relative rarity in most environments, sometimes only seen in times of danger or death.

Source: Shibasaki, M. & Masataka, N. The color red distorts time perception for men, but not for women. Sci. Rep. 4, 5899; DOI:10.1038/srep05899 (2014).

(Image: Shutterstock)

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