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A potato affected by P. infestans, the pathogen responsible for the Irish Potato Famine. The exact strain involved in the 1840s famine has now been identified for the first time. Image via USDA

For nearly 150 years, starting in the late 17th century, millions of people living in Ireland subsisted largely off one crop: the potato. Then, in 1845, farmers noticed that their potato plants’ leaves were covered in mysterious dark splotches. When they pulled potatoes from the ground, most were shrunken, mushy and inedible. The blight spread alarmingly quickly, cutting yields from that year’s harvest in half. By 1846, harvest from potato farms had dropped to one quarter of its original size.

The disease—along with a political system that required Ireland to export large amounts of corn, dairy and meat to England—led to widespread famine, and nearly all of the few potatoes available were eaten, causing shortages of seed potatoes that ensured starvation would continue for nearly a decade. Ultimately, over one million people died, and another million emigrated to escape the disaster, causing Ireland’s population to fall by roughly 25 percent; the island has still not reached its pre-famine population levels today.

At the time, the science behind the blight was poorly understood, and most believed it was caused by a fungus. During the twentieth century, scientists determined that it was caused by an oomycete (a fungus-like eukaryote) called Phytophthora infestans. However, without access to the 1840s-era specimens, they couldn’t identify exactly which strain of the organism was responsible.

Now, an international group of scientists has gone back and sampled the DNA of Irish potato leaves preserved in the collections of London’s Kew Gardens since 1847. In doing so, they discovered that a unique, previously unknown strain of P. infestans that they call HERB-1 caused the blight.

Irish potato leaves from 1847, the height of the famine, used as part of the study. Image via eLife/Kew Gardens

The researchers, from the Sainsbury Laboratory in the UK and the Max Planck Institutes in Germany, came to the finding as part of a project sequencing DNA from 11 different preserved historial samples and 15 modern ones to track the evolution of the pathogen over time, published today in the journal eLife [PDF].

Currently, P. infestans is distributed worldwide, with the vast majority comprised of the destructive strain US-1. Most of the other strains of P. infestans occur only in Mexico’s Toluca Valley, where wild potato varieties are indigenous, so scientists long believed that US-1 had been responsible for the 1840s famine.

But when the researchers extracted small pieces of intact DNA from the old dried-out potato leaves, originally collected from from Ireland, Great Britain, Europe and North America, and compared them with present-day P. infestans specimens, they found that the strain responsible for the famine differed slightly from today’s US-1.

Based on their analysis of the genetic variation between the two strains and the other historical samples, they suggest that sometime in 1842 or 1843, the ancestor of the HERB-1 strain of P. infestans made it out of Mexico to North America and then to Europe, perhaps contained within the potatoes that ships carried as food for their passengers. Soon, it spread across the world, triggering famine in Ireland, and persisting until the 1970s, when it died out and was largely replaced by the US-1 strain. The two strains likely split apart sometime soon after their common ancestor made it out of Mexico.

The study is the first time that the genetics of a plant pathogen have been analyzed by extracting DNA from dried plant samples, opening up the possibility that researchers can study other plant diseases based on the historical collections of botanical gardens and herbaria around the world. Better understanding the evolution of plant diseases over time, the team says, could be instrumental in figuring out ways to breed more robust plant varieties that are resistant to the pathogens that infect plants today.

Our bodies convert asparagusic acid into sulfur-containing chemicals that stink—but some of us are spared from the pungent aroma. Photo by Gunnar Magnusson

If you’ve ever noticed a strange, not-entirely-pleasant scent coming from your urine after you eat asparagus, you’re definitely not alone.

Distinguished thinkers as varied as Scottish mathematician and physician John Arbuthnot (who wrote in a 1731 book that “asparagus…affects the urine with a foetid smell”) and Marcel Proust (who wrote how the vegetable “transforms my chamber-pot into a flask of perfume”) have commented on the phenomenon.

Even Benjamin Franklin took note, stating in a 1781 letter to the Royal Academy of Brussels that “A few Stems of Asparagus eaten, shall give our Urine a disagreable Odour” (he was trying to convince the academy to “To discover some Drug…that shall render the natural Discharges of Wind from our Bodies, not only inoffensive, but agreable as Perfumes”—a goal that, alas, modern science has still not achieved).

But modern science has, at least, shed some light on why this one particular vegetable has such an unusual and potent impact on the scent of urine. Scientists tell us that the asparagus-urine link all comes down to one chemical: asparagusic acid.

Asparagusic acid, as the name implies, is (to our knowledge) only found in asparagus. When our bodies digest the vegetable, they break down this chemical into a group of related sulfur-containing compounds with long, complicated names (including dimethyl sulfide, dimethyl disulfide, dimethyl sulfoxide and dimethyl sulfone). As with many other substances that include sulfur—such as garlic, skunk spray and odorized natural gas—these sulfur-containing molecules convey a powerful, typically unpleasant scent.

All of these molecules also share another key characteristic: They’re volatile, meaning that have a low enough boiling point that they can vaporize and enter a gaseous state at room temperature, which allows them to travel from urine into the air and up your nose. Asparagusic acid, on the other hand, isn’t volatile, so asparagus itself doesn’t convey the same rotten smell. But once your body converts asparagusic acid into these volatile, sulfur-bearing compounds, the distinctive aroma can be generated quite quickly—in some cases, it’s been detected in the urine of people who ate asparagus just 15-30 minutes earlier.

Of course, the whole asparagus-urine scent issue is complicated by an entire separate issue: Some people simply don’t smell anything different when urinate after they eat asparagus. Scientists have long been divided into two camps in explaining this issue. Some believe that, for physiological reasons, these people (which constitute anywhere from 20 to 40 percent of the population) don’t produce the aroma in their urine when they digest asparagus, while others think that they produce the exact same scent, but somehow lack the ability to smell it.

On the whole, the evidence is mixed. Initially, a pair of studies conducted in the 1980s with participants from France and Israel found that everyone produced the characteristic scent, and that a minority of people were simply unable to smell it. People with the ability to detect the scent, though, were able to smell it even in the urine of those who couldn’t smell it, indicating that the differences were rooted in perception, not production.

More recent studies, though, suggest the issue is a bit more complicated. The most recent study, from 2010, found that differences existed between individuals in both the production and detection of the scent.

Overall, scientists now conclude that most of the difference is in perception—that is, if your urine doesn’t seem to smell any differently after you eat asparagus, it’s likely that you simply can’t perceive the sulfurous compounds’ foul odor, but there’s a small chance it’s because your body digests asparagus in a way that reduces the concentration of these chemicals in your urine.

It’s still unclear why some people don’t produce the smell, but we do seem to have a clear explanation of why some people don’t perceive it. In 2010, the genetic sequencing company 23andMe conducted a study in which they asked nearly 10,000 customers if they noticed any scent in their urine after eating asparagus, and looked for genetic similarities among those who couldn’t. This peculiarity—which you might consider useful if you eat asparagus frequently—appears to stem from a single genetic mutation, a switched base-pair among a cluster of 50 different genes that code for olfactory receptors.

We’re still waiting for some enterprising team of scientists to attempt gene therapy to convert smellers into non-smellers—but given other priorities to use genetic modification to cure blindness and breast cancer, it seems likely that those suffering from asparagus-scented urine might have to wait a while.

By combining genes from different bacteria species, scientists created E. coli that can produce diesel fuel from fat. Image via Marian Littlejohn/PNAS

Over the past few decades, researchers have developed biofuels derived from an remarkable variety of organisms—soybeans, corn, algae, rice and even fungi. Whether synthesized into ethanol or biodiesel, though, all of these fuels suffer from the same limitation: They have to be refined and blended with heavy amounts of conventional, petroleum-based fuels to run in existing engines.

Though this is far from the only current problem with biofuels, a new approach by researchers from the University of Exeter in the UK appears to solve at least this particular issue with one fell swoop. As they write today in an article in Proceedings of the National Academy of Sciences, the team has genetically engineered E. coli bacteria to produce molecules that are interchangeable to the ones in diesel fuels already sold commercially. The products of this bacteria, if generated on a large-scale, could theoretically go directly into the millions of car and truck engines currently running on diesel worldwide—without the need to be blended with petroleum-based diesel.

The group, led by John Love, accomplished the feat by mixing and matching genes from several different bacteria species and inserting them into the E. coli used in the experiment. These genes each code for particular enzymes, so when the genes are inserted into the E. coli, the bacteria gains the ability to synthesize these enzymes. As a result, it also gains the ability to perform the same metabolic reactions that those enzymes perform in each of the donor bacteria species.

By carefully selecting and combining metabolic reactions, the researchers built an artificial chemical pathway piece-by-piece. Through this pathway, the genetically modified E. coli growing and reproducing in a petri dish filled with a high-fat broth were able to absorb fat molecules, convert them into hydrocarbons and excrete them as a waste product.

Hydrocarbons are the basis for all petroleum-based fuels, and the particular molecules they engineered the E. coli to produce are the same ones present in commercial diesel fuels. So far, they’ve only produced tiny quantities of this bacterial biodiesel, but if they were able to grow these bacteria on a massive scale and extract their hydrocarbon products, they’d have a ready-made diesel fuel. Of course, it remains to be seen whether fuel produced in this way will be able to compete in terms of cost with conventional diesel.

Additionally, energy never comes from thin air—and the energy contained within this bacterial fuel mostly originates in the broth of fatty acids that the bacteria are grown on. As a result, depending on the source of these fatty acids, this new fuel could be subject to some of the same criticisms leveled at biofuels currently in production.

For one, there’s the argument that converting food (whether corn, soybeans or other crops) into fuel causes ripple effects in global food market, increasing the volatility of food prices, as a UN study from last year found. Additionally, if the goal of developing new fuels is to fight climate change, many biofuels fall dramatically short, despite their environmentally-friendly image. Using ethanol made from corn (the most widely used biofuel in the U.S.), for example, is likely no better than burning conventional gasoline in terms of carbon emissions, and maybe actually be worse, due to all the energy that goes into growing the crop and processing it info fuel.

Whether this new bacteria-derived diesel suffers from these same problems largely depends upon what sort of fatty acid source is eventually used to grow the bacteria on a commercial scale—whether it would by synthesized from a potential food crop (say, corn or soy oil), or whether it could come from a presently-overlooked energy source. But the new approach already has one major advantage: Just the steps needed to refine other biofuels so they can be used in engines use energy and generate carbon emissions. By skipping these steps, the new bacterial biodiesel could be an energy efficient fuel choice from the start.

Image via NASA/NOAA/GSFC/Suomi NPP/VIIRS/Norman Kuring

Last year, to celebrate the 42nd Earth Day, we took a look at 10 of the most surprising, disheartening, and exciting things we’d learned about our home planet in the previous year—a list that included discoveries about the role pesticides play in bee colony collapses, the various environmental stresses faced by the world’s oceans and the millions of unknown species are still out in the environment, waiting to be found.

This year, in time for Earth Day on Monday, we’ve done it again, putting together another list of 10 notable discoveries made by scientists since Earth Day 2012—a list that ranges from specific topics (a species of plant, a group of catfish) to broad (the core of planet Earth), and from the alarming (the consequences of climate change) to the awe-inspiring (Earth’s place in the universe).

Even the supposedly pristine Antarctic landscape is marred by trash heaps. Image via Germany Federal Environment Agency Report (PDF)

1. Trash is accumulating everywhere, even in Antarctica. As we’ve explored the most remote stretches of the planet, we’ve consistently left behind a trail of one supply in particular: garbage. Even in Antarctica, a February study found (PDF), abandoned field huts and piles of trash are mounting. Meanwhile, in the fall, a new research expedition went to study the Great Pacific Garbage Patch, counting nearly 70,000 pieces of garbage over the course of a month at sea.

2. Climate change could erode the ozone layer. Until recently, atmospheric scientists viewed climate change and the disintegration of the ozone layer as entirely distinct problems. Then, in July, Harvard researcher Jim Anderson (who won a Smithsonian Ingenuity Award for his work) led a team that published the troubling finding that the two might be linked. Some warm summer storms, they discovered, can pull moisture up into the stratosphere, an atmospheric layer 6 miles up. Through a chain of chemical reactions, this moisture can lead to the disintegration of ozone, which is crucial for protecting us from ultraviolet (UV) radiation. Climate change, unfortunately,  is projected to cause more of these sorts of storms.

3. This flower lives on exactly two cliffs in Spain. In September, Spanish scientists told us about one of the most astounding survival stories in the plant kingdom: Borderea chouardii, an extremely rare flowering plant that is found on only two adjacent cliffs in the Pyrenees. The species is believed to be a relic of the Tertiary Period, which ended more than 2 million years ago, and relies on several different local ant species to spread pollen between its two local populations.

4. Some catfish have learned to kill pigeons. In December, a group of French scientists revealed a phenomenon they’d carefully been observing over the previous year: a group of catfish in Southwestern France had learned how to leap onto shore, briefly strand themselves, and swim back into the water to consume their prey. With more than 2,000,000 Youtube views so far, this is clearly one of the year’s most widely enjoyed scientific discoveries.

5. Fracking for natural gas can trigger moderate earthquakes. Scientists have known for a while that whenever oil and gas are extracted from the ground at a large scale, seismic activity can be induced. Over the past few years, evidence has mounted that injecting water, sand and chemicals into bedrock to cause gas and oil to flow upward—a practice commonly known as fracking—can cause earthquakes by lubricating pre-existing faults in the ground. Initially, scientists found correlations between fracking sites and the number of small earthquakes in particular areas. Then, in March, other researchers found evidence that a medium-sized 2011 earthquake in Oklahoma(which registered a 5.7 on the moment magnitude scale) was likely caused by injecting wastewater into wells to extract oil.

6. Our planet’s inner core is more complicated than we thought. Despite decades of research, new data on the iron and nickel ball 3,100 miles beneath our feet continue to upset our assumptions about just how the earth’s core operates. A paper published last May showed that iron in the outer parts of the inner core is losing heat much more quickly than previously estimated, suggesting that it might hold more radioactive energy than we’d assumed, or that novel and unknown chemical interactions are occurring. Ideas for directly probing the core are widely regarded as pipe dreams, so our only options remains studying it from afar, largely by monitoring seismic waves.

The berries of Pollia condensata were found to produce the most intense color in the natural world. Image via PNAS

7. The world’s most intense natural color comes from an African fruit. When a team of researchers looked closely at the blue berries of Pollia condensata, a wild plant that grows in East Africa, they found something unexpected: it uses an uncommon structural coloration method to produce the most intense natural color ever measured. Instead of pigments, the fruit’s brilliant blue results from nanoscale-size cellulose strands layered in twisting shapes, which which interact with each other to scatter light in all directions.

8. Climate change will let ships cruise across the North Pole. Climate change is sure to create countless problems for many people around the world, but one specific group is likely to see a significant benefit from it: international shipping companies. A study published last month found that rising temperatures make it probable that during summertime, reinforced ice-breaking ships will be able to sail directly across the North Pole—an area currently covered by up to 65 feet of ice—by the year 2040. This dramatic shift will shorten shipping routes from North America and Europe to Asia.

9. One bacteria species conducts electricity. In October, a group of Danish researchers revealed that the seafloor mud of Aarhus’ harbor was coursing with electricity due to an unlikely source: mutlicellular bacteria that behave like tiny electrical cables. The organisms, the team found, built structures that traveled several centimeters down into the sediment and conduct measurable levels of electricity. The researchers speculate that this seemingly strange behavior is a byproduct of the way of the bacteria harvests energy from the nutrients buried in the soil.

Kepler 62f, discovered yesterday, is the most promising exoplanet candidate yet in terms of its potential to harbor life. Image via NASA/Ames/JPL-Caltech

10. Our Earth isn’t alone. Okay, this one might not technically be a discovery about Earth, but over the past year we have learned a tremendous amount about what our Earth isn’t: the only habitable planet in the visible universe. The pace of exoplanet detection has accelerated rapidly, with a total of 866 planets in other solar systems discovered so far. As our methods have become more refined, we’ve been able to detect smaller and smaller planets, and just yesterday, scientists finally discovered a pair of distant planets in the habitable zone of their stars that are relatively close in size to Earth, making it more likely than ever that we might have spied an alien planet that actually supports life.

A mixture of plant oils, bacterial spores and ozone is responsible for the powerful scent of fresh rain. Image via Wikimedia Commons/Juni

Step outside after the first storm after a dry spell and it invariably hits you: the sweet, fresh, powerfully evocative smell of fresh rain.

If you’ve ever noticed this mysterious scent and wondered what’s responsible for it, you’re not alone.

Back in 1964, a pair of Australian scientists (Isabel Joy Bear and R. G. Thomas) began the scientific study of rain’s aroma in earnest with an article in Nature titled “Nature of Agrillaceous Odor.” In it, they coined the term petrichor to help explain the phenomenon, combining a pair of Greek roots: petra (stone) and ichor (the blood of gods in ancient myth).

In that study and subsequent research, they determined that one of the main causes of this distinctive smell is a blend of oils secreted by some plants during arid periods. When a rainstorm comes after a drought, compounds from the oils—which accumulate over time in dry rocks and soil—are mixed and released into the air. The duo also observed that the oils inhibit seed germination, and speculated that plants produce them to limit competition for scarce water supplies during dry times.

These airborne oils combine with other compounds to produce the smell. In moist, forested areas in particular, a common substance is geosmin, a chemical produced by a soil-dwelling bacteria known as actinomycetes. The bacteria secrete the compound when they produce spores, then the force of rain landing on the ground sends these spores up into the air, and the moist air conveys the chemical into our noses.

“It’s a very pleasant aroma, sort of a musky smell,” soil specialist Bill Ypsilantis told NPR during an interview on the topic. “You’ll also smell that when you are in your garden and you’re turning over your soil.”

Because these bacteria thrive in wet conditions and produce spores during dry spells, the smell of geosmin is often most pronounced when it rains for the first time in a while, because the largest supply of spores has collected in the soil. Studies have revealed that the human nose is extremely sensitive to geosmin in particular—some people can detect it at concentrations as low as 5 parts per trillion. (Coincidentally, it’s also responsible for the distinctively earthy taste in beets.)

Ozone—O_3, the molecule made up of three oxygen atoms bonded together—also plays a role in the smell, especially after thunderstorms. A lightning bolt’s electrical charge can split oxygen and nitrogen molecules in the atmosphere, and they often recombine into nitric oxide (NO), which then interacts with other chemicals in the atmosphere to produce ozone. Sometimes, you can even smell ozone in the air (it has a sharp scent reminiscent of chlorine) before a storm arrives because it can be carried over long distances from high altitudes.

But apart from the specific chemicals responsible, there’s also the deeper question of why we find the smell of rain pleasant in the first place. Some scientists have speculated that it’s a product of evolution.

Anthropologist Diana Young of the University of Queensland in Australia, for example, who studied the culture of Western Australia’s Pitjantjatjara people, has observed that they associate the smell of rain with the color green, hinting at the deep-seated link between a season’s first rain and the expectation of growth and associated game animals, both crucial for their diet. She calls this “cultural synesthesia”—the blending of different sensory experiences on a society-wide scale due to evolutionary history.

It’s not a major leap to imagine how other cultures might similarly have positive associations of rain embedded in their collective consciousness—humans around the world, after all, require either plants or animals to eat, and both are more plentiful in rainy times than during drought. If this hypothesis is correct, then the next time you relish the scent of fresh rain, think of it as a cultural imprint, derived from your ancestors.