November 8, 2013
In 1854, in response to a devastating cholera epidemic that was sweeping through London, British doctor John Snow introduced an idea that would revolutionize the field of public health: the epidemiological map. By recording instances of cholera in different neighborhoods of the city and plotting them on a map based on patients’ residences, he discovered that a single contaminated water pump was responsible for a great deal of the infections.
The map persuaded him—and, eventually, the public authorities—that the miasma theory of disease (which claimed that diseases spread via noxious gases) was false, and that the germ theory (which correctly claimed that microorganisms were to blame) was true. They put a lock on the handle of the pump responsible for the outbreak, signaling a paradigm shift that permanently changed how we deal with infectious diseases and thus sanitation.
The mapping technology is quite different, as is the disease, but there’s a certain similarity between Snow’s map and a new project conducted by a group of researchers led by Henry Kautz of the University of Rochester. By creating algorithms that can spot flu trends and make predictions based on keywords in publicly available geotagged tweets, they’re taking a new approach to studying the transmission of disease—one that could change the way we study and track the movement of diseases in society.
“We can think of people as sensors that are looking at the world around them and then reporting what they are seeing and experiencing on social media,” Kautz explains. “This allows us to do detailed measurements on a population scale, and doesn’t require active user participation.”
In other words, when we tweet that we’ve just been laid low by a painful cough and a fever, we’re unwittingly providing rich data for an enormous public health experiment, information that researchers can use to track the movement of diseases like flu in high resolution and real time.
Kautz’ project, called SocialHealth, has made use of tweets and other sorts of social media to track a range of public health issues—recently, they began using tweets to monitor instances of food poisoning at New York City restaurants by logging everyone who had posted geotagged tweets from a restaurant, then following their tweets for the next 72 hours, checking for mentions of vomiting, diarrhea, abdominal pain, fever or chills. In doing so, they detected 480 likely instances of food poisoning.
But as the season changes, it’s their work tracking the influenza virus that’s most eye-opening. Google Flu Trends
has similarly sought to use Google searchers to track the movement of flu, but the model greatly overestimated last year’s outbreak, perhaps because media coverage of flu prompted people to start making flu-related queries. Twitter analysis represents a new dataset with a few qualities—a higher geographic resolution and the ability to capture the movement of a user over time—that could yield better predictions.
To start their flu-tracking project [PDF], the SocialHealth researchers looked specifically at New York, collecting around 16 million geotagged public tweets per month from 600,000 users for three months’ time. Below is a time-lapse of one New York Twitter day, with different colors representing different frequencies of tweets at that location (blue and green mean fewer tweets, orange and red mean more):
To make use of all this data, his team developed an algorithm that determines if each tweet represents a report of flu-like symptoms. Previously, other researchers had simply done this by searching for keywords in tweets (“sick,” for example), but his team found that the approach leads to false positives: Many more users tweet that they’re sick of homework than they’re feeling sick.
To account for this, his team’s algorithm looks for three words in a row (instead of one), and considers how often the particular sequence is indicative of an illness, based on a set of tweets they’d manually labelled. The phrase “sick of flu,” for instance, is strongly correlated with illness, whereas “sick and tired” is less so. Some particular words—headache, fever, coughing—are strongly linked with illness no matter what three-word sequence they’re part of.
Once these millions of tweets were coded, the researchers could do a few intriguing things with them. For starters, they looked at changes in flu-related tweets over time, and compared them with levels of flu as reported by the CDC, confirming that the tweets accurately captured the overall trend in flu rates. However, unlike CDC data, it’s available in nearly real-time, rather than a week or two after the fact.
But they also went deeper, looking at the interactions between different users—as represented by two users tweeting from the same location (the GPS resolution is about half a city block) within the same hour—to model how likely it is that a healthy person would become sick after coming into contact with someone with the flu. Obviously, two people tweeting from the same block 40 minutes apart didn’t necessarily meet in person, but the odds of them having met are slightly higher than two random users.
As a result, when you look at a large enough dataset of interactions, a picture of transmission emerges. They found that if a healthy user encounters 40 other users who report themselves as sick with flu symptoms, his or her odds of getting flu symptoms the next day increases from less than one percent to 20 percent. With 60 interactions, that number rises to 50 percent.
The team also looked at interactions on Twitter itself, isolating pairs of users who follow each other and calling them “friendships.” Even though many Twitter relationships exist only on the Web, some correspond to real-life interactions, and they found that a user who has ten friends who report themselves as sick are 28 percent more likely to become sick the next day. In total, using both of these types of interactions, their algorithm was able to predict whether a healthy person would get sick (and tweet about it) with 90 percent accuracy.
We’re still in the early stages of this research, and there are plenty of limitations: Most people still don’t use Twitter (yes, really) and even if they do, they might not tweet about getting sick.
But if this sort of system could be developed further, it’s easy to imagine all sorts of applications. Your smartphone could automatically warn you, for instance, if you’d spent too much time in the places occupied by people with the flu, prompting you to go home to stop putting yourself in the path of infection. An entire city’s residents could even be warned if it were on the verge of an outbreak.
Despite the 150 years we’re removed from John Snow’s disease-mapping breakthrough, it’s clear that there are still aspects of disease information we don’t fully understand. Now, as then, mapping the data could help yield the answers.
November 6, 2013
Brain-machine interfaces were once the stuff of science fiction. But the technology—which enables direct communication between a person or animal’s brain and an external device or another brain—has come a long way in the past decade.
Scientists have developed interfaces that allow paralyzed people to type letters on a screen, let one person move another’s hand with his or her thoughts and even make it possible for two rats to trade thoughts—in this case, the knowledge of how to solve a particular task—when they’re located in labs thousands of miles apart.
Now, a team led by Miguel Nicolelis of Duke University (the scientist behind the rat thought-trading scheme, among other brain-machine interfaces) has created a new setup that allows monkeys to control two virtual arms simply by thinking about moving their real arms. They hope that the technology, revealed in a paper published today in Science Translational Medicine, could someday lead to similar interfaces that allow paralyzed humans to move robotic arms and legs.
Previously, Nicolelis’ team and others had created interfaces that allowed monkeys and humans to move a single arm in a similar fashion, but this is the first technology that lets an animal to move multiple limbs simultaneously. “Bimanual movements in our daily activities—from typing on a keyboard to opening a can—are critically important,” Nicolelis said in a press statement. “Future brain-machine interfaces aimed at restoring mobility in humans will have to incorporate multiple limbs to greatly benefit severely paralyzed patients.”
Like the group’s previous interfaces, the new technology relies upon ultra thin electrodes that are surgically embedded into the cerebral cortex of monkeys’ brains, a region of the brain that controls voluntary movements, among other functions. But unlike many other brain-machine interfaces, which use electrodes that monitor brain activity in just a handful of neurons, Nicolelis’ team recorded activity in nearly 500 brain cells distributed over a range of cortex areas in the two rhesus monkeys who were test subjects for this study.
Then, over the course of a few weeks, they repeatedly set the monkeys in front of a monitor, where they saw a pair of virtual arms from a first-person perspective. Initially, they controlled each of the arms with joysticks, and completed a task in which they had to move the arms to cover up moving shapes to receive a reward (a taste of juice).
As this happened, the electrodes recorded the brain activity in the monkeys that correlated with the various arm movements, and algorithms analyzed it to determine which particular patterns in neuron activation were linked with what sorts of arm movements—left or right, and forward or back.
Eventually, once the algorithm could accurately predict the monkey’s intended arm movement based upon the brain patterns, the setup was altered so that the joysticks no longer controlled the virtual arms—the monkeys’ thoughts, as recorded by the electrodes, were in control instead. From the monkeys’ perspective, nothing had changed, as the joysticks were still put out in front of them, and the control was based on brain patterns (specifically, imagining their own arms moving) that they were producing anyway.
Within two weeks, though, both the monkeys realized they didn’t need to actually move their hands and manipulate the joysticks to move the virtual arms—they only had to think about doing so. Over time, they got better and better at controlling the virtual arms through this machine-brain interface, eventually doing it just as effectively as they’d moved the joysticks.
Future advances in this sort of interface could be enormously valuable for people who’ve lost control of their own limbs, due to paralysis or other causes. As high-tech bionic limbs continue to develop, these types of interfaces could eventually be the way they’ll be used on a daily basis. A person with a spinal cord injury, for example, could learn how to effectively imagine moving two arms so that an algorithm could interpret his or her brain patterns to move two robotic arms in the desired way.
But brain-machine interfaces could also someday serve a much broader population, too: users of smartphones, computers and other consumer technology. Already, companies have developed headsets that monitor your brainwaves so that you can move a character around in a video game merely by thinking about it, essentially using your brain as a joystick. Eventually, some engineers envision that brain-machine interfaces could enable us to manipulate tablets and control wearable technology such as Google Glass without saying a word or touching a screen.
October 22, 2013
If you traveled to the town of Kalgoorlie, in Western Australia, then headed about 25 miles north, you’d eventually reach a grove of large eucalyptus trees, some more than 30 feet tall, scattered across a dusty, arid landscape. Examining the dirt at your feet would reveal no trace of the gold deposits that lie roughly 100 feet underground, due to the thick layers of clay and rock that sit atop the precious metal.
But, scientists recently learned, if you peered closely enough at the eucalyptus trees—specifically, using X-rays to detect nanoparticles—you’d find that there’s gold in them thar leaves. As detailed in a study published today in Nature Communications, a group of researchers from Australia’s Commonwealth Scientific and Industrial Research Organisation has shown that plants can absorb gold particles deep underground and bring it upward through their tissues—a finding that could help mineral exploration companies mine for gold.
“In Australia, we’re faced with this problem of trying to explore through thick layers of sediments and weathered rock to reach valued minerals,” says Melvyn Lintern, an Earth scientist and lead author of the study. “At the same time, we’d previously heard from mining engineers that, in some places, they’d found eucalyptus roots going down to 30 meters [98 feet] or deeper in the mines.” With this observation in mind, and the knowledge that plants can absorb and transport minerals from the surrounding soil and bedrock all the way up to their leaves, Lintern and his colleagues were struck with an idea: Why not test eucalyptus leaves to see if they could indicate underground gold deposits?
To do so, they visited two Australian sites with known gold deposits deep underground (as revealed by exploratory drilling) that were covered by thick layers of rock and on top of which grew tall eucalyptus trees. When they tested leaves that grew on or had fallen from the large trees in both areas, they indeed found minute traces of gold—up to 80 parts per billion, compared with the 2 parts per billion they found in leaves that had grown 650 feet away from the underground deposit.
Other researchers had detected gold particles in plants and leaf litter before, but it was unclear whether they’d been transported all the way from underground deposits. “We were concerned that the gold might have been occurring as dust particles on the outside of these leaves, so it was important for us to locate the gold within the plant,” says Lintern.
His team did so by analyzing the leaves in even further detail (using a specialized X-ray microprobe located at the Australian Synchrotron research facility) and confirmed that the gold particles were located within the plant’s vascular tissue, indicating that they were moving naturally within the leaves. They also conduced greenhouse experiments and found that eucalyptus saplings, grown in soil laced with similar levels of gold, absorbed it and transported detectable levels into their leaves. These separate streams of evidence, they say, shows that the wild eucalyptus trees were indeed sucking up gold from deep underground.
“The eucalyptus acts like a hydraulic pump,” using its roots to suck ground water upward, crucial in an arid environment, Lintern says. “The plants, of course, are searching for water, not gold, but it just so happens that there’s gold dissolved in it.”
The fact that the gold has been found in the leaves, in fact, might be evidence that the eucalyptus is actively trying to get rid of it—after all, it’s a toxic heavy metal—by transporting it to its extremities. Additionally, the gold particles in the leaves were often found located near calcium oxalate crystals, theorized to be part of the removal pathway for toxic chemicals.
Lintern’s group plans to conduct further research into which plants are capable of transporting gold particles in this way and what environmental factors affect the rate of uptake. Mining companies in Canada, he mentions, have already toyed with the idea of using plants as mineral indicators, so this first scientific evidence for the process is likely to accelerate adoption of the method.
“Essentially, we’re tapping into a natural process,” Lintern says. In an age when most of the readily accessible gold near the planet’s surface has been mined, it makes sense to harness the natural mineral exploration plants are already engaging in when they drive their roots deep into the ground. Doing so might even reduce the number of exploratory mines we’re forced to drill—and consequently, lead to less environmental destruction of these plants’ habitats as a result of mining.
September 10, 2013
Rising gas prices and a dangerously low world panda population–what if someone told you that we soon could have one solution to both these problems? If it seems too good to be true, think again; scientists at Mississippi State University are conducting research on the feasibility of using pandas to help solve our biofuel woes, a step that could lead to a bump in conservation efforts and a drop in fuel expense. The secret to the solution? It’s all in the panda’s poop.
When it comes to biofuels, the market is dominated by one word: ethanol, a biofuel made from corn. Though ethanol is the most widely used biofuel, it isn’t necessarily touted as a perfect replacement for fossil fuels–in fact, the benefit of ethanol is been hotly debated since its creation.
The debate goes a little something like this: in order to fill the tank of an SUV with ethanol fuel, you need to use enough corn to feed a single person for an entire year. A 2012 paper published by the New England Complex Systems Institute cites ethanol as a reason for the increasing price of crops since 2005. And even environmental groups steer clear of ethanol, citing the massive amounts of fossil fuel needed to render corn a useable biofuel product and the propensity of companies to buy land in developing countries to grow the lucrative biofuel rather than food for local consumption.
Ashli Brown, a researcher at Mississippi State University, thinks she’s found the answer to this alternative fuel conundrum. By taking corn byproducts–the husks, the stems and cobs–ethanol could be created without dipping into the edible parts of corn, reducing the chance of a food shortage and price spike. The issue is that to break down these materials, which are extremely high in lignocellulose, or dry plant matter, a special pretreatment process is required. The process is extremely costly and not very time-efficient, using high temperatures, high pressures and acid to break down the dry plant matter before it can become ethanol. To circumvent this problem, Brown and other researchers have been looking for a natural solution–bacteria, which could help with the breakdown of the lignocellulose material.
Biofuel companies have been seeking a natural method to break down plant material for a while; so far, termites have been a favorite for chewing through the woody material. But it turns out there might be a better–and cuter–animal that can help produce biofuel
. The intestines of pandas are remarkably short, a physical attribute which means their intestines have come to contain bacteria with unusually potent enzymes for breaking down their woody diet of bamboo in a short amount of time.
“The time from eating to defecation is comparatively short in the panda, so their microbes have to be very efficient to get nutritional value out of the bamboo,” Brown, the researcher heading the work, said. “And efficiency is key when it comes to biofuel production—that’s why we focused on the microbes in the giant panda.”
The study began more than two years ago, when Brown and a team of researchers began looking at panda feces. In 2011, they identified these super-digesting microbes are present in panda feces, but they had yet to specify the type and amount of microbes present until now. Using the poop from two giant pandas–Ya Ya and Le Le in the Memphis Zoo–Brown and her team performed DNA sequencing on microbes in their samples, identifying more than 40 microbes in the panda feces that could be useful to the breakdown and creation of biofuels.
To grow these microbes on an industrial scale
, Brown believes that scientists could put the genes that produce those enzymes into yeasts--these yeasts could then be mass-produced and harvested for biofuel production. The process would go something like this: Large pits of corn husks, corn cobs, wood chips, and other forms of discarded fibrous material are covered with the genetically altered yeasts. As the microbes digest woody substances, they quickly turn it into sugar, which would then be allowed to ferment. Over time and after filtering out solids and any excess water, you would have ethanol, distilled from woody waste products.
Pandas aren’t the only animal that subsists on a grassy diet, but their physiology makes them a unique candidate for breaking down plant byproducts in a hyper-efficient way. Pandas have the same digestive track as any other bear; unlike cows or other herbivores, pandas don’t have an extra stomach where hard lignocellulostic material is pretreated before being digested. Instead, they have the intestinal system of a carnivore, and yet manage to extract enough nutrients from their herbaceous diet to survive.
“Because their retention time is very short—they’re constantly eating and they’re constantly pooping—in order to get the material for nutrition, they have to be really quick at breaking it down and extracting the sugars,” Brown explained. “Many microbes produce celluloses that breakdown lignocellulostic biomass, but it’s about how efficiently or how effectively they do it.” When it comes to a panda, Brown notes, their microbes are some of the most efficient scientists have seen at breaking down the woody material of a plant.
And Brown thinks that using pandas for their poop could lead to more than a greener economy: it could also lead to increased conservation for the animals, who have seen their numbers in the wild drop to a dangerous 1,600 (though there has been recent luck with breeding pandas in captivity, like the new baby panda at the National Zoo). “These studies also help us learn more about this endangered animal’s digestive system and the microbes that live in it, which is important because most of the diseases pandas get affect their guts,” said Brown.
Brown notes that if the panda becomes valuable to the market for more reasons than its incredibly adorable demeanor, it might spark greater steps toward conservation–a move that could be mutually beneficial to pandas and humans alike.”It’s amazing that here we have an endangered species that’s almost gone from the planet, yet there’s still so much we have yet to learn from it. That underscores the importance of saving endangered and threatened animals,” she said. “It makes us think—perhaps these endangered animals have beneficial outputs that we haven’t even thought about.”
August 20, 2013
The saying goes that one person’s waste is another’s treasure. For those scientists who study urine the saying is quite literal–pee is a treasure-trove of scientific potential. It can now be used as a source of electric power. Urine-eating bacteria can create a strong enough current to power a cell phone. Medicines derived from urine can help treat infertility and fight symptoms of menopause. Stem cells harvested from urine have been reprogrammed into neurons and even used to grow human teeth.
For modern scientists, the golden liquid can be, well, liquid gold. But a quick look back in history shows that urine has always been important to scientific and industrial advancement, so much so that the ancient Romans not only sold pee collected from public urinals, but those who traded in urine had to pay a tax. So what about pee did preindustrial humans find so valuable? Here are a few examples:
Urine-soaked leather makes it soft: Prior to the ability to synthesize chemicals in the lab, urine was a quick and rich source of urea, a nitrogen-based organic compound. When stored for long periods of time, urea decays into ammonia. Ammonia in water acts as a caustic but weak base. Its high pH breaks down organic material, making urine the perfect substance for ancients to use in softening and tanning animal hides. Soaking animal skins in urine also made it easier for leather workers to remove hair and bits of flesh from the skin.
The cleansing power of pee: If you’ve investigated the ingredients in your household cleaners, you may have noticed a prevalent ingredient: ammonia. As a base, ammonia is a useful cleanser because dirt and grease–which are slightly acidic–get neutralized by the ammonia. Even though early Europeans knew about soap, many launderers preferred to use urine for its ammonia to get tough stains out of cloth. In fact, in ancient Rome, vessels for collecting urine were commonplace on streets–passers-by would relieve themselves into them and when the vats were full their contents were taken to a fullonica (a laundry), diluted with water and poured over dirty clothes. A worker would stand in the tub of urine and stomp on the clothes, similar to modern washing machine’s agitator.
Even after making soap became more prevalent, urine–known as chamber lye for the chamber pots it was collected in–was often used as a soaking treatment for tough stains.
Urine not only made your whites cleaner, but your colors brighter: Natural dyes from seeds, leaves, flowers, lichens, roots, bark and berries can leach out of a cloth if it or the dyebath aren’t treated with mordant, which helps to bind the dye to the cloth. It works like this: molecules of dye called chromophores get wrapped inside a more complex molecule or a group of molecules; this shell housing the dye then binds to the cloth. The central nugget of dye is then visible but is protected from bleeding away by the molecules surrounding it. Stale urine–or more precisely the ammonia in it–is a good mordant. Molecules of ammonia can form a web around chromophores, helping to develop the color of dyes as well as to bind it to cloth.
Specific chamberpots dedicated to urine helped families collect their pee for use as mordants. Urine was so important to the textile industry of 16th century England that casks of it–an estimated amount equivalent to the urine stream of 1000 people for an entire year–were shipped from across the country to Yorkshire, where it was mixed with alum to form an even stronger mordant than urine alone.
Pee makes things go boom: Had enough with cleansing, tanning, and dyeing? Then why not use your pee to make gunpowder! Gunpowder recipes call for charcoal and sulfur in small quantities, both of which for aren’t too hard to find. But the main ingredient–potassium nitrate, also called saltpeter–was only synthesized on a large-scale in the early 20th century. Prior to that, makers of gunpowder took advantage of the nitrogen naturally found in pee to make the key ingredient for ballistic firepower.
As detailed in the manual Instructions for the Manufacture of Saltpetre, written by physician and geologist Joseph LeConte in 1862, a person hoping to make gunpowder quickly would need “a good supply of thoroughly rotted manure of the richest kind” which is then mixed with ash, leaves and straw in a pit. “The heap is watered every week with the richest kinds of liquid manure, such as urine, dung-water, water of privies, cess-pools, drains, &c. The quantity of liquid should be such as to keep the heap always moist, but not wet,” he wrote. The mixture is stirred every week, and after a several months no more pee is added. Then “As the heap ripens, the nitre is brought to the surface by evaporation, and appears as a whitish efflorescence, detectible by the taste.”
Different regions of the world had their own recipes for gunpowder, but the scientific principle at work is the same: Ammonia from stagnant pee reacts with oxygen to form nitrates. These nitrates–negatively charged nitrogen-bearing ions–then search for positively charged metal ions in the pee-poo-ash slurry to bind with. Thanks to the ash, potassium ions are in abundance, and voila! After a little filtering, you’ve made potassium nitrate.
Urine gives you a whiter smile: Urine was a key ingredient in many early medicines and folk remedies of dubious effectiveness. But one use–and those who’ve tried it say it works–is as a type of mouthwash. While “urine-soaked grin” isn’t the insult of choice these days, a verse by Roman poet Catullus reads:
Egnatius, because he has snow-white teeth, smiles all the time. If you’re a defendant in court, when the counsel draws tears, he smiles: if you’re in grief at the pyre of pious sons, the lone lorn mother weeping, he smiles. Whatever it is, wherever it is, whatever he’s doing, he smiles: he’s got a disease, neither polite, I would say, nor charming. So a reminder to you, from me, good Egnatius. If you were a Sabine or Tiburtine or a fat Umbrian, or plump Etruscan, or dark toothy Lanuvian, or from north of the Po, and I’ll mention my own Veronese too, or whoever else clean their teeth religiously, I’d still not want you to smile all the time: there’s nothing more foolish than foolishly smiling. Now you’re Spanish: in the country of Spain what each man pisses, he’s used to brushing his teeth and red gums with, every morning, so the fact that your teeth are so polished just shows you’re the more full of piss.
The poem not only reveals that Catullus wasn’t a fan of Egnatius, but that Romans used urine to clean and whiten their teeth, transforming morning breath into a different smell entirely. The active ingredient? You guessed it: ammonia, which lifted stains away.
But perhaps one of the most critical uses of urine in history was its role in making the above home remedies obsolete. Urea, the nitrogen bearing compound in urine, was the first organic substance created from inorganic starting materials. In 1828, German chemist Friedrich Wöhler mixed silver cyanate with ammonium chloride and obtained a white crystalline material that his tests proved was identical to urea. His finding disproved a hypothesis of many leading scientists and thinkers of the time, which held that living organisms were made up of substances entirely different than inanimate objects like rocks or glass. In a note to a colleague, Wöhler wrote, “I can no longer, so to speak, hold my chemical water and must tell you that I can make urea without needing a kidney, whether of man or dog; the ammonium salt of cyanic acid is urea.”
Wöhler’s discovery showed that not only could organic chemicals be transformed and produced in the lab, but that humans were part of nature, rather than separate from it. In doing so, he began the field of organic chemistry. Organic chemistry has given us modern medicines, materials such as plastic and nylon, compounds including synthetic ammonia and potassium nitrate…and, of course, a way to clean our clothes or fire a gun without using our own (or someone else’s) pee.