5,000-Year-Old Beer Recipe Had Secret Ingredient

A stove fragment from the Mijiaya site that was probably used to heat the fermenting grain mash during the beer-brewing process.

Barley might have been the “secret ingredient” in a 5,000-year-old beer recipe that has been reconstructed from residues on prehistoric pots from China, according to new archaeological research.

Scientists conducted tests on ancient pottery jars and funnels found at the Mijiaya archaeological site in China’s Shaanxi province. The analyses revealed traces of oxalate — a beer-making byproduct that forms a scale called “beerstone” in brewing equipment — as well as residues from a variety of ancient grains and plants. These grains included broomcorn millets, an Asian wild grain known as “Job’s tears,” tubers from plant roots, and barley.

Barley is used to make beer because it has high levels of amylase enzymes that promote the conversion of starches into sugars during the fermenting process. It was first cultivated in western Asia and might have been used to make beer in ancient Sumer and Babylonia more than 8,000 years ago, according to historians.

The researchers said it is unclear when beer brewing began in China, but the residues from the 5,000-year-old Mijiaya artifacts represent the earliest known use of barley in the region by about 1,000 years. They also suggest that barley was used to make beer in China long before the cereal grain became a staple food there, the researchers noted.

Surprising ingredient

The prehistoric brewery at the Mijiaya site consisted of ceramic pots, funnels and stoves found in pits that date back to the Neolithic (late Stone Age) Yangshao period, around 3400 to 2900 B.C., said Jiajing Wang, a Ph.D. student at Stanford University in California and lead author of a new paper on the research, published today (May 23) in the journal Proceedings of the National Academy of Sciences.

Wang told Live Science that the discovery of barley in such early artifacts was a surprise to the researchers.

Barley was the main ingredient for beer brewing in other parts of the world, such as in ancient Egypt, she said, and the barley plant might have spread into China along with the knowledge of its special use in making beer.

“It is possible that when barley was introduced from western Eurasia into the Central Plain of China, it came with the knowledge that the grain was a good ingredient for beer brewing,” Wang said. “So it was not only the introduction of a new crop, but also the knowledge associated with the crop.”

The ancient art of beer

The Mijiaya site was discovered in 1923 by Swedish archaeologist Johan Gunnar Andersson, Wang said. The site, located near the present-day center of the city of Xi’an, was excavated by Chinese archaeologists between 2004 and 2006, before being developed for modern residential buildings.

After the full excavation report was published in 2012, Wang’s co-author on the new paper, archaeologist Li Liu of Stanford, noticed that the pottery assemblages from two of the pits could have been used to make alcohol, mainly because of the presence of funnels and stoves.

Wang said that some Chinese scholars had suggested several years ago that the Yangshao funnels might have been used to make alcohol, but there had been no direct evidence until now.

In the summer of 2015, the Stanford researchers traveled to Xi’an and visited the Shaanxi Institute of Archaeology, where the artifacts from the Mijiaya site are now stored.

The scientists extracted residues from the artifacts, and their analysis of the residues turned out to prove their hypothesis: that “people in China brewed beer with barley around 5,000 years ago,” Wang said.

Reconstructing the recipe

The researchers found yellowish remnants in the wide-mouthed pots, funnels and amphorae that suggested the vessels were used for beer brewing, filtration and storage. The stoves in the pits were probably used to provide heat for mashing the grains, according to the archaeologists.

The beer recipe used a variety of starchy grains, including barley, as well as tubers, which would have added starch for the fermentation process and sweetness to the flavor of the beer, the researchers said.

Wang and her co-authors wrote that barley had been found in a few Bronze Age sites in the Central Plain of China, all dated to around or after 2000 B.C. However, barley did not become a staple crop in the region until the Han dynasty, from 206 B.C. to A.D. 220, the researchers said.

“Together, the lines of evidence suggest that the Yangshao people may have concocted a 5,000-year-old beer recipe that ushered the cultural practice of beer brewing into ancient China,” the archaeologists wrote in the paper. “It is possible that the few rare finds of barley in the Central Plain during the Bronze Age indicate their earlier introduction as rare, exotic food.”

“Our findings imply that early beer making may have motivated the initial translocation of barley from western Eurasia into the Central Plain of China before the crop became a part of agricultural subsistence in the region 3,000 years later,” the researchers wrote.

Read more at Discovery News

Stonehenge: Easier Done Than Said

How did prehistoric Britons manage to move Stonehenge’s stones? Each rock weighed an average of 25 tons and stood as tall as 30 feet, and the first tractor was still five millennia away, so clearly they must have endured great pains to build the monument, right?

Much of the mystery around the site comes from the questions of how Stonehenge was built and why. A recent experiment by archaeologists at University College London provides a hint to that first part anyway.

As back-breaking a task as building a monument of dump truck-sized stones without the aid of modern machinery might seem, the demonstration held in London’s Gordon Square suggests it wasn’t that difficult at all.

Last week, University College London doctoral candidate Barney Harris put out a call for volunteers to see how many people it would take to pull a stone about half the size as the smallest rock at Stonehenge, which is about one metric ton. Harris anticipated it would take a team of at least 15 people to move the stone, and as many as 40 to 50 to lift it.

Instead, 10 people were able to get the stone going at a rate of roughly 10 feet (3 meters) every five seconds, or around one mile (1.6 kilometers) per hour. A team twice the size would be able to move a small piece of Stonehenge.

Devoting the kind of human capital needed for what may appear to be a frivolous effort for a Neolithic society isn’t all that far-fetched considering settlements in the area at the time numbered in the thousands, so there were plenty of other members of the society to carry on with the more life-sustaining activities, such as farming, hunting or child-rearing.

Made of rope, a wooden track and a sycamore sled, the design of the rig used in the experiment mirrors others found throughout the ancient world. “We know that pre-industrialized societies like the Maram Naga in India still use this kind of sledge to construct huge stone monuments,” Harris told The Telegraph. “And similar y-shaped sleighs have been found dating back to 2000 B.C. in Japan which we know were used to move megaliths.”

Recreating even at a small scale how the rocks used at Stonehenge were transported can provide researchers an estimate of how long it took to complete the entire site.

Beginning around 5,000 years ago, the first stones were lain at Stonehenge. The monument was built in two phases with two different kinds of stones. The largest stones are called sarsens, a local sandstone, placed around 2400 B.C. The circle of rocks at the center, known as bluestones, were erected 500 years earlier, around 2900 B.C.

Read more at Discovery News

Loss of Y Chromosome Linked to Alzheimer's

About one in five men over age 80 lose the Y chromosome from their blood cells, and this condition has now been linked to an increased risk of Alzheimer’s disease, researchers said.

The condition known a loss of Y, or LOY, is the most common genetic mutation acquired during a man’s lifetime.

Previous research has shown LOY can raise the likelihood of cancer and is more frequently found in smokers.

Now, researchers say the condition may serve as a predictive biomarker for a wider range of health problems.

For the study in the American Journal of Human Genetics — led by Lars Forsberg and Jan Dumanski of Uppsala University in Sweden, along with colleagues Britain, France, the United States and Canada — researchers examined cases of LOY in more than 3,200 men with an average age of 73.

Around 17 percent showed LOY in blood cells.

Those who had been already diagnosed with Alzheimer’s had a higher degree of LOY, they found.

Also, those who had not yet been diagnosed with dementia but had LOY were more likely to develop Alzheimer’s in subsequent years.

“Having loss of Y is not 100 percent predictive that you will have either cancer or Alzheimer’s,” cautioned Forsberg.

Some men with LOY in the study lived with no symptoms well into their 90s.

“But in the future, loss of Y in blood cells can become a new biomarker for disease risk and perhaps evaluation can make a difference in detecting and treating problems early.”

According to Chris Lau, professor in the department of medicine at the University of California, San Francisco, the study sheds little light on why Alzheimer’s risk may be elevated in these men.

Read more at Discovery News

Mystery Plumes: Did the Sun Bruise Mars?

In recent years, the Red Planet has been doing something quite weird and scientist are stumped.

On a handful of occasions bizarre “plumes” have been observed protruding from Mars’ upper atmosphere. A 2012 event was spotted by amateur astronomers and the phenomenon persisted for several days. Even the Hubble Space Telescope has been witness to a plume.

At first it was assumed some form of high-altitude cloud may be to blame, or maybe a storm kicked up dust into the upper atmosphere. But each hypothesis had its flaws and planetary scientists were left confused.

Now, European Space Agency scientists heading the Mars Express mission have studied this Martian oddity and found pretty strong evidence that the plumes aren’t produced by the planet’s weather; they’re likely sparked by space weather.

Interactions between the sun and planetary environments are well known. As highly energized particles from the solar wind hit Earth’s global magnetic field, for example, they can get trapped in the magnetosphere and funneled to high latitude regions. This influx of solar wind ions will collide with high-altitude atmospheric gases, causing them to glow, creating auroras. Where ever there’s a magnetic field and an atmosphere, the sun can kick off a dazzling lightshow and we’ve seen auroras throughout the solar system, including Jupiter, Saturn and even Venus.

The 2012 plume as seen by amateur astronomers.

But solar interactions are not limited to auroras. When Earth is hit by coronal mass ejections — basically bubbles of magnetized plasma ejected from the sun’s lower atmosphere — the entire planet’s magnetic configuration can feel its effects, setting up powerful electrical currents through the atmosphere and energizing our ionosphere.

Mars, however, does not possess a global magnetic field to deflect the worst the sun can throw at it. When a CME hits Earth, the magnetosphere protects the atmosphere, but on Mars, lacking this magnetic shield, it suffers atmospheric erosion. Though it is thought Mars once had a thicker atmosphere, over billions of years, the constant flow of solar wind particles have stripped it away. Mars’ atmosphere is, literally, leaking into space.

If space weather has such a powerful influence on Mars’ atmospher loss, could it also be to blame for these odd plumes? Mars Express scientists have turned to their veteran Mars orbiter for answers.

The 2012 Mars plume made world headlines and Mars Express was there collecting data of the local space environment. Did a space weather event occur around the time the plume was observed?

“Our plasma observations tell us that there was a space weather event large enough to impact Mars and increase the escape of plasma from the planet’s atmosphere,” said David Andrews of the Swedish Institute of Space Physics in an ESA news release. “But we were not able to see any signatures in the ionosphere that we can categorically say were due to the presence of this plume.”

There is circumstantial evidence that Mars’ ionosphere — an upper layer of the atmosphere filled with charged particles, or ions — was in some way influenced by a space weather event, such as the impact of a CME. But because of the plume’s location, it is a challenge acquire additional observations of the event, so just because there is some evidence a CME-triggered event is at play, it’s circumstantial at best.

Now scientists are looking over archival data in the hope of finding occasions when a plume occurred during a CME hit. In 1997, for example, a Mars plume was spotted by Hubble and at around the same time, a fast CME was recorded as hitting Earth. Unfortunately there was no information from any Mars mission as to how that CME impacted the Red Planet’s atmosphere, if it affected it at all.

Read more at Discovery News

Squid - 'Weeds of the Sea' - on the Rise

Squid, octopus and cuttlefish are on the rise, finds new research on these animals, which are collectively known as cephalopods.

Nicknamed the “weeds of the sea,” these animals have experienced impressive population growth over the past 60 years and at a time when many fish species have been declining in numbers, according to the new study, which is published in the journal Current Biology.

“Our analyses showed that cephalopod abundance has increased since the 1950s, a result that was remarkably consistent across three distinct groups,” lead author Zoë Doubleday, a researcher at the University of Adelaide’s Environment Institute and School of Biological Sciences, said in a press release.

“Cephalopods are often called ‘weeds of the sea’ as they have a unique set of biological traits, including rapid growth, short lifespans and flexible development,” Doubleday continued. “These allow them to adapt to changing environmental conditions (such as temperature) more quickly than many other marine species, which suggests that they may be benefiting from a changing ocean environment.”

What sparked the research was an observed decline of a species that’s iconic down under: the giant Australian cuttlefish.

Doubleday explained that researchers started to notice fewer of these cuttlefish at the cephalopod’s world-renowned breeding ground in South Australia’s Spencer Gulf.

The scientists compiled a global-scale database of cuttlefish, as well as squid and octopus. Not only did the study reveal that the giant Australian cuttlefish is already making a major comeback, but also that most other related animals have been increasing in numbers over the past six decades.

Like weeds taking over a garden, however, the news isn’t all good.

Co-author Bronwyn Gillanders said large-scale changes to the marine environment, brought about by human activities, could be driving the global increase in cephalopods.

Read more at Discovery News

Iconic Art Shows Disease Unknown for a Century

Science's most famous picture, Joseph Wright's "An Experiment on a Bird in the Air Pump," contains the accurate representation of a skin rash that is indicative of a disease recognized more than a century later, according to a new study of the iconic painting.

Depicting an 18th century scientific demonstration of the properties of the vacuum, the 1768 painting may also feature the first ever picture of dermatomyositis. This is a rare inflammatory disease of the muscle, skin and blood vessels that was clinical described in the last decades of the 19th century.

The painting, currently on a National Gallery loan to Tate Britain, is widely recognized as an artistic milestone that reflects the Enlightenment era where modern society's exposure to science had been initiated. It portrays a wizard-Iike scientist, surrounded by spectators, pumping air out of flask containing a poor cockatoo.

The candlelit scene shows the moment when the bird will either die or be allowed to revive by the demonstrator, who looks straight out of the picture and doesn’t appear to be emotionally connected to the dying bird.

“Additionally two young lovers fail to notice the experiment due to their intoxication with each other, whilst a father consoles his two horrified children who cannot bear to experience the death of the bird despite the scientific lesson,” Hutan Ashrafian, a surgeon at Imperial College London, wrote in the journal Clinical Rheumatology.

But aside from containing a prominent metaphor of the role of scientists and the different attitudes around scientific facts, Wright's masterpiece may now be celebrated for its representation of real-life pathology.

“When we look at the painting with much higher detail, it is clear the father character has a skin rash that is consistent with the disease of dermatomyositis,” Ashrafian told Discovery News. “The dermatopathology on the hand is most characteristic of Gottron’s papules, which is indicative of dermatomyositis."

This diagnosis is also consistent with the rash on the subjects other hand and face.

Such red bumps overlying the knuckles of the fingers were first described by German dermatologist Heinrich Adolf Gottron in 1931, some 163 years after Wright's depiction in "The Air Pump."

Dermatomyositis is a systemic inflammatory neuromuscular disorder that was first described a bit earlier, in 1891, by Heinrich Unverricht.

“The depiction of the disease is so clear and accurate in the painting that it must have reflected the actual existence of an underlying disease in the portrayed father character,” Ashrafian said.

The finding remarks Wright's skill in painting exactly what he saw, but also adds a powerful metaphor.

Read more at Discovery News

Ancient 'Mad Libs' Papyri Contain Evil Spells

Ancient, magical spells of love, subjugation and sex: It may sound like a “Game of Thrones” episode, but these evildoings are also found on two recently deciphered papyri from Egypt dating to around 1,700 years ago.

One spell invokes the gods to “burn the heart” of a woman until she loves the spell caster, said Franco Maltomini of the University of Udine in Italy, who translated the two spells. Another spell, targeted at a male, uses a series of magical words to “subject” him, forcing him to do whatever the caster wants.

The two spells were not targeted at a specific person. Rather, they were written in such a way that the person who cast the spell would only need to insert the name of the person being targeted — sort of like an ancient “Mad Libs.”

Researchers date the two spells to the third century A.D., but the names of the ancient spell writers are unknown. The spells are written in Greek, a language widely used in Egypt at the time.

Archaeologists Bernard Grenfell and Arthur Hunt discovered the spells in Oxyrhynchus, Egypt, more than 100 years ago, among a haul of hundreds of thousands of papyri. Over the past century, scientists have gradually studied and translated the papyri. Many of them are now owned by the Egypt Exploration Society and are housed and studied at the University of Oxford in England.

Maltomini is part of a larger group of editors and contributors from multiple institutions who analyzed and translated the most recent batch of these magical texts, which will be published in an upcoming volume of “The Oxyrhynchus Papyri,” a series a books devoted to publishing the papyri from Oxyrhynchus.

A love spell

The deciphered love spell invokes several gnostic gods. (Gnosticism was an ancient religion that incorporated elements of Christianity.) It says that the spell caster should burn a series of offerings in the bathhouse (the names of the offerings didn’t survive degradation) and write a spell on the bathhouse’s walls, which Maltomini translated as follows:

“I adjure you, earth and waters, by the demon who dwells on you and (I adjure) the fortune of this bath so that, as you blaze and burn and flame, so burn her (the woman targeted)whom (the mother of the woman targeted) bore, until she comes to me…”

Then, the spell names several gods and magical words. It goes on to say, “Holy names, inflame in this way and burn the heart of her…” until she falls in love with the person casting the spell.

Read more at Discovery News

Solar Superflares Set Stage for Life on Earth

Scientists may have cracked a 40-year-old mystery about how early Earth grew warm enough for water to pool on its surface — a condition believed to be necessary for life – despite meager warming from a young sun.

The key, says a team of NASA astronomers, is a phenomena known as superflares, which are massive and frequent solar flares that blasted high-energy particles toward baby Earth and its sibling planets.

Computer models show that near-daily deluges of energetic particles streaming from the sun would have compressed Earth’s magnetic bubble and caused gaps to open over the polar regions.

The particles could then penetrate into the atmosphere, setting off a cascade of chemical reactions that created the extremely potent greenhouse gas nitrous oxide, as well as hydrogen cyanide, an essential compound for life, a study published in this week’s Nature Geoscience shows.

Earth would have grown warm enough for liquid water as far back as 4 billion years ago, the study shows.

The first signs of microbial life appear as fossilized rock dating back to about the same time.

Scientists have tried for decades to solve the so-called “faint young sun” paradox, an issue raised by astronomers Carl Sagan and George Mullen  in 1972.

“It’s perplexing because it is unclear why Earth was not permanently glaciated under the less luminous sun,” Cornell University’s Ramses Ramirez writes in a related commentary in Nature Geoscience.

The new theory extrapolates data collected by the Kepler space telescope, whose primary mission was to look for planets orbiting sun-like stars.

Temporary dips in the amount of light coming from target stars could be caused by planets flying across the face of their parent stars, relative to Kepler’s line of sight. But the changes also could be caused by other events, including, it turns out, superflares.

“Kepler observed the superflares of young stars, resembling our sun at the time when life started on Earth … We used these as proxies,” astrophysicist Vladimir Airapetian, with NASA’s Goddard Space Flight Center in Greenbelt, Maryland, told Discovery News.

The superflares turn out to be three times more powerful than the biggest flare in recent history, the so-called Carrington event in 1859, which caused Northern Lights auroras as far south as Miami.

“A very, very conservative number is that one of these events occurred every single day, and each event lasts for two or three days, so that suggests the Earth was under constant attack from these powerful coronal mass ejections,” Airapetian said.

Coronal mass ejections, or CMS, release massive amounts of solar particles and electromagnetic radiation into space.

Ramirez, for one, already is putting Airapetian’s theory to test by using the atmospheric chemistry data in another computer model.

Read more at Discovery News

Rich coral communities discovered in Palamós Submarine Canyon in the Northwestern Mediterranian Sea

A scientific team has found in La Fonera canyon, also known as the Palamós canyon in the Northwestern Mediterranian Sea, deep-water coral communities, a marine ecosystem which is very vulnerable to human activity.

The findings are explained in an article published in the magazine PLOS ONE signed by the researchers Galderic Lastras, Miquel Canals and Anna Sánchez Vidal, from the Research Group on Marine Geosciences (GRC) from the Faculty of Geology of the UB, together with Enric Ballesteros (Blanes Centre for Advanced Studies, CEAB-CSIC) and Josep-Maria Gili (Institute of Marine Sciences, ICM-CSIC).

Cold-water corals, known for ages by the Norwegian fishermen, have been observed in different latitudes around the world, and are considered to be the cold-water "cousins" of the coral reefs from tropical regions. These kind of corals create fragile and branched colonies, which boost marine biodiversity related to their relation to the life cycle of lots of marine organisms.

Deep cold-water coral colonies in the Mediterranean

The first cold-water coral communities discovered in the Iberian Peninsula were found in 2010 in the Avilés canyon, in the Cantabrian Sea. In the west Mediterranean sea, teams of the University of Barcelona and CSIC had found living colonies in Cap de Creus canyon, a scientific finding that represents one of the best documented examples of this kind of deep ecosystem in all the Mediterranean.

It is estimated that the new communities which were discovered by the research team in La Fonera canyon -- at 130-370 m water depth- lie around 400,000 square metres. Video images testifying the discovery were obtained using a submarine remotely operated vehicle (ROV). In this specific submarine habitat, the most abundant species are Madrepora oculata corals (white coral) and Dendophyllia cornigera (yellow coral). "These new habitats expand the cold-water coral province of the northwest Mediterranea to the south even more than before: they had been seen in the Cap de Creus canyon and other canyons in the Gulf of Lion" said the teacher Galderic Lastras, main author of the article and member of the GRC on Marine Geosciences.

Preserving a habitat threatened by human activity

La Fonera canyon, outside the Catalan coast waters, shows a very abrupt terrain, with great depths near the coast. The north part of the canyon, where trawling is usually done, shows a softer terrain compared to the southern part, which is more abrupt. Like Professor Miquel Canals -head of Research Group on Marine Geosciences of the UB- said, "Trawling greatly modifies the submarine terrain so the landscape goes from having a cliff terrain to having a benthic terrain shape, following isobathic or level curves."

These cold-water coral communities have been found in the most harbour-like northern areas. They show clear symptoms of human impact. "The bigger coral colonies are in areas which are inaccessible for trawling, like vertical walls and abrupt areas, where there is also Corallium rubrum (red coral). However, these coral colonies are usually shattered with fishing gears and plastics or partially covered by sediment, especially the ones closer to areas where trawling is practised" warns Galderic Lastras.

Read more at Science Daily

Chemists settle longstanding debate on how methane is made biologically

The chemical reaction that a biological catalyst uses to make methane involves the rare-in-nature methyl radical, unusual because it is based on carbon.

Like the poet, microbes that make methane are taking chemists on a road less traveled: Of two competing ideas for how microbes make the main component of natural gas, the winning chemical reaction involves a molecule less favored by previous research, something called a methyl radical.

Reported today in the journal Science, the work is important for understanding not only how methane is made, but also how to make things from it.

"Methane is an interesting substance because it's both a fossil fuel and a potentially renewable fuel that can come from microbes," said study lead Stephen Ragsdale of the University of Michigan, Ann Arbor. "In addition, detailed knowledge of the chemical steps involved in making methane could lead to major breakthroughs in designing energy efficient catalysts for converting methane into liquid fuels and other chemicals."

This study demonstrates one of a very few known instances of nature using a highly reactive methyl radical in its biological machinations.

"We were totally surprised," said computational chemist Simone Raugei, a coauthor at the Department of Energy's Pacific Northwest National Laboratory. "We thought we'd find evidence for other mechanisms."

Origins story

More than 90 percent of methane is (and has been) generated by microbes known as methanogens, which are members of the archaea, a group of microbes that are similar to bacteria. To make the gas, methanogens use a particular protein known as an enzyme. Enzymes aid chemical reactions in living organisms like synthetic catalysts do in industrial chemical conversions. Also, the enzyme can run the reaction in reverse to break down methane for energy consumption.

Scientists know a lot about this microbial enzyme. It creates the burnable gas by slapping a hydrogen atom onto a molecule called a methyl group. A methyl group contains three hydrogens bound to a carbon atom, just one hydrogen shy of full-grown methane.

To generate methane, the enzyme pulls the methyl group from a helper molecule called methyl-coenzyme M. Coenzyme M's job is to nestle the methyl group into the right spot on the enzyme. What makes the spot just right is a perfectly positioned nickel atom, which is largely responsible for transferring the last hydrogen.

How the nickel atom does this, however, has been debated for decades in the highly complex world of chemical reactions. Different possible paths create different fleeting, ephemeral intermediate molecules, but the reaction happens too fast for scientists to distinguish between them.

The path chemists have most sided with involves the nickel atom on the enzyme directly attacking the methyl group and stealing it from coenzyme M. The methyl-nickel molecule exists temporarily, until the methyl in its turn steals a hydrogen atom from another molecule in the enzyme's workspace, coenzyme B, and becomes methane.

Many experiments lend support for this idea, which creates an intermediate methyl-nickel molecule.

A second possibility, according to a much smaller group of supporters, is via a methyl radical. Radicals (aka free radicals) are unstable molecules that have an unpaired electron. They can do a lot of damage by breaking down weaker bonds in molecules.

It's that unpaired electron that causes problems. Bonds between atoms routinely involve two electrons, like a pair of ballroom dancers. The unpaired electron will do everything in its power to find a second, just as a single dancer in search of a partner will cut into another couple.

In this path to methane, the nickel atom bonds to a sulfur atom in coenzyme M rather than the methyl group. This knocks the methyl away and sends it off sans an electron. Hungry and irritated, the methyl radical immediately snags a hydrogen atom from coenzyme B, generating methane.

Process of elimination

To find out which mechanism was correct, the UM-PNNL team of researchers came up with a way to rule out one or the other. The first thing they had to do was slow down the reaction. They slowed it down a thousand times by hobbling the second half of the path to methane, after the intermediate came alive. Doing so let the intermediate build up.

Then, they performed a biochemical analysis called electron paramagnetic resonance spectroscopy at the University of Michigan that allowed them to distinguish between the two intermediate molecules. If the reaction created the methyl-nickel molecule, methyl-nickel would show up as a blip on their EPR system. If the reaction created a methyl radical that sauntered off, the molecule remaining with the protein -- nickel bound to coenzyme M -- would not register at all.

The team found no blip in the EPR profile of the post-reaction products, making the most likely intermediate the methyl radical. But, to be sure, the team performed additional biochemical analyses that ruled out other potential molecules. They also performed another biochemical test and showed that the structure of the major intermediate was the nickel stuck to coenzyme M, the expected result if the reactions took the methyl radical path.

"The impact of radicals on living matter, such as biological material, can be devastating, and involvement of a methyl radical, one of the most unstable radicals, is truly surprising," said Raugei, "For this to happen and make methane 100 percent of the time, the protein has to perform and control this reaction with an extremely high degree of precision, placing that methyl radical specifically beside only one atom -- the hydrogen atom bound to the sulfur of coenzyme B."

Energy block

To further substantiate their results, the team modeled the reaction computationally. They zoomed in on the action within the enzyme, known as methyl-coenzyme M reductase.

"We found that the methyl radical required the least amount of energy to produce, making that mechanism the frontrunner yet again," said Bojana Ginovska, a computational scientist on the PNNL team.

In fact, one of the other intermediates required three times as much energy to make, compared to the methyl radical, clearly putting it out of the running.

Modeling the reaction computationally also allowed the team to look inside the reductase. Experiments showed that the reaction happens faster at higher temperatures and why: Parts of the protein that helped move the reaction along would move the nickel closer to the methyl-coenzyme M. Shorter distances allowed things to happen faster.

The team used high performance computing resources at two DOE scientific user facilities: EMSL, the Environmental Molecular Sciences Laboratory at PNNL, and NERSC, the National Energy Research Computing Center, a DOE Office of Science User Facility at Lawrence Berkeley National Laboratory.

The results might help researchers, including Ragsdale and Raugei, learn to control methane synthesis -- either in the lab or in bacteria that make it in places like the Arctic -- and how to break it down.

Read more at Science Daily