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Lost and found

You know I love this stuff:

A lost city thought to be more than 1,000 years old has been discovered in Ethiopia and may offer insight into Islam’s origins in the country.

The settlement, located near Ethiopia’s second largest city of Dire Dawa, in the east of the country, consisted of buildings constructed with large stone blocks, which gave rise to a local myth that giants lived there. Researchers believe it may date back as early as the 10th century.

Archaeologists discovered a 12th-century mosque in the settlement at Harlaa, as well as evidence of Islamic burials and headstones. The team, from the University of Exeter and the Ethiopian Authority for Research and Conservation of Cultural Heritage, also found artifacts from as far afield as India and China, suggesting that the region functioned as a hub for foreign traders.

Understanding tornadoes: 5 questions answered

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Tornado seven miles south of Anadarko, Oklahoma, May 3, 1999.
OAR/ERL/National Severe Storms Laboratory/Flickr, CC BY

Paul Markowski, Pennsylvania State University and Yvette Richardson, Pennsylvania State University

Editor’s note: May and June are typically peak months for tornadoes in North America. We asked Penn State meteorology professors Paul Markowski and Yvette Richardson to explain why tornadoes form, how to stay safe if you’re near one and whether climate change is affecting tornado patterns.

1. Where are tornadoes most likely to occur?

Most headline-making tornadoes are spawned by what are known as supercell thunderstorms. These are large, intense storms characterized by an updraft (rising air) that rotates.

Thunderstorms develop when warm, humid air near the surface lies beneath a thick layer of air in which the temperature decreases rapidly with height. We call this type of atmosphere “unstable,” meaning that when air is nudged upward, the water vapor that it contains condenses. This releases heat, making the air warmer than its surroundings. The air becomes buoyant and rises, creating the towering clouds we associate with thunderstorms.

The second key condition for supercell formation is wind shear – large changes in wind at different levels. Winds at different altitudes blowing at different speeds and/or from different directions is associated with horizontally spinning air, like a rolling pin. As this horizontally spinning air flows into the updraft, the spin is tilted into the vertical, creating a rotating updraft.

Time lapse video of a supercell thunderstorm near Booker, Texas.

Tornadoes are especially likely to be spawned by supercell thunderstorms when the lowest altitudes are particularly humid and possess exceptionally strong wind shear. These conditions are more likely to come together in certain locations, such as the U.S. Great Plains and Southeast.

2. How do actual tornadoes form?

Not all supercell thunderstorms produce tornadoes. Once wind shear has created a rotating updraft in our supercell thunderstorm, other processes develop rotation near the ground, in the cool air underneath the storm, which we call its “cold pool.” The cold pool is produced mostly by the evaporation of rain.

Within and beneath the storm, warm air is rising and cooler air is descending. As air descends and flows through the cold pool, the horizontal differences in temperature and acceleration of air along the ground combine to produce more horizontal spin. If there is strong upward suction from the overlying rotating updraft of the supercell storm, and the air in the cold pool is not too cold, the horizontally spinning air can be tipped toward the vertical and sucked upward. It also can be contracted inward and spin faster, just as skaters increase the speed of their spins by pulling in their arms. This forms the tornado.

Scientists’ present understanding of how a tornado develops in a supercell thunderstorm.
Paul Markowski, Author provided

3. How precisely can we predict tornado strikes?

In the past decade, forecasters have become skillful at identifying conditions that can support strong tornadoes – those rated EF2 or higher on the Enhanced Fujita Scale. The National Weather Service’s Storm Prediction Center routinely predicts large outbreaks days in advance. “High-risk” outlooks capture most major tornado events, and strong tornadoes rarely occur outside of tornado watches. We have less ability to forecast tornadoes in more marginal situations, such as within non-supercell storms.

Even if the environment is extremely favorable for supercell tornadoes, forecasters have limited ability to say when or if a specific storm will produce a tornado. Researchers are studying triggers for tornado production, such as small-scale downdraft surges and descending precipitation shafts on a supercell storm’s rear flank, and processes that sustain tornadoes once they form.

We don’t understand tornado maintenance well, or how tornadoes might be affected by interactions with obstacles such as terrain and buildings. This means that when a tornado is occurring, forecasters have limited ability to tell the public how long they expect it to last.

4. What should I do during a tornado warning?

Basements, storm cellars or “safe rooms” that meet federal guidelines provide excellent protection. If none of these is available, the best strategy is to go to the lowest floor of a sturdy building and put as many walls between you and the tornado as possible. In other words, shelter in an interior room, such as a closet or bathroom. Also, make sure you are wearing good shoes. If your area takes a direct hit, you do not want to walk through a debris field barefoot.

Don’t chase tornadoes without professional training. Observations from spotters are valuable to forecasters who are issuing warnings, but they can be made from a distance. We don’t need people driving in harm’s way to know that a dangerous storm is approaching.

Missouri Gov. Eric Greitens surveys damage to homes in Oak Grove that were destroyed by a tornado on March 6, 2017.
AP Photo/Charlie Riedel

5. Is climate change making tornadoes bigger or more frequent?

It’s hard to say. Reliable U.S. records of tornadoes go back only to roughly 1950, and records outside of the United States are even less complete. Thanks to storm chasing and the spread of camera phones, more tornadoes are counted today compared with yesteryear, but that does not necessarily mean that more are occurring. And there’s a lot of natural variability from year to year. Over the past decade, the annual U.S. tornado count has ranged from 886 to 1,690 storms per year.

Estimates of wind speeds based on post-storm damage surveys can be off by 50 percent or more. And many tornadoes in remote areas leave no clues as to how strong their winds were.

The ConversationMost climate models predict that there will be more days per year when the atmosphere would have sufficient instability and wind shear to support tornadoes. But we need to be careful in interpreting this result. Climate models don’t capture tornadoes, their parent thunderstorms or nuances in the lowest level of the atmosphere that affect tornado formation. So it is hard to say whether there will be more tornadoes, even if tornado-supporting environments become more common.

Paul Markowski, Professor of Meteorology, Pennsylvania State University and Yvette Richardson, Professor of Meteorology, Pennsylvania State University

This article was originally published on The Conversation. Read the original article.

Digging up Troy

This was a really interesting piece about how Heinrich Schliemann found ancient Troy but didn’t know it:

The story that he told about the day he and Sophia found the treasure has long been repeated in introductory archaeology textbooks, although it is unlikely to be true. Schliemann later admitted that he lied about Sophia’s role in his story. She wasn’t even at the dig on the day that he claims to have found the treasure. Some scholars have also suggested that Schliemann didn’t find the treasure all in one place. Instead, they think he gathered the best of his finds from the entire season and announced to a gullible public that he had found them all together as a single treasure. Moreover, since the objects were found in Troy II, they are a thousand years too early to have belonged to Priam.

Schliemann continued to dig at Troy throughout the 1870s and 1880s, though he also was digging at Mycenae at that time, looking for material remains of King Agamemnon. To help him at Troy, he hired Wilhelm Dörpfeld, an architect with some previous archaeological experience, who eventually persuaded Schliemann that he had been wrong and that it was actually the layers called Troy VI or Troy VII at Hissarlik that he should have been investigating all along. Schliemann began to make plans for an additional attack on the mound, focused on these later levels, but on Christmas Day in 1890, he collapsed on a street in Naples and died the next day.

It was left to Dörpfeld to carry on. And so he did, with the financial assistance of Sophia Schliemann, who wanted him to continue her husband’s work at the site. He concentrated on excavating the remains that Schliemann had left untouched, mostly around the edges of the mound. As it turned out, those remains were extremely impressive. He unearthed tall stone walls, each several meters thick, that would have stymied any attackers, and large gateways allowing entrance to the interior, but only after one got past the guards.

One of the reasons I’m fascinated by archaeology is that it’s very easy to get it wrong, and I’ve no doubt that much of what is thought to be settled knowledge really isn’t. From being a reporter, and seeing how five different journalists can come up with five different versions of events, I’m well aware that perspective is everything.

Here’s a fun little exercise. Look at random items around your house, and imagine how the archaeologists of the future would interpret them as artifacts of a long-gone civilization.

Medieval medical books could hold the recipe for new antibiotics

Tổng quan về bệnh đau dạ dày

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A recipe for an eyesalve from ‘Bald’s Leechbook.’
© The British Library Board (Royal MS 12 D xvii)

Erin Connelly, University of Pennsylvania

For a long time, medieval medicine has been dismissed as irrelevant. This time period is popularly referred to as the “Dark Ages,” which erroneously suggests that it was unenlightened by science or reason. However, some medievalists and scientists are now looking back to history for clues to inform the search for new antibiotics. The Conversation

The evolution of antibiotic-resistant microbes means that it is always necessary to find new drugs to battle microbes that are no longer treatable with current antibiotics. But progress in finding new antibiotics is slow. The drug discovery pipeline is currently stalled. An estimated 700,000 people around the world die annually from drug-resistant infections. If the situation does not change, it is estimated that such infections will kill 10 million people per year by 2050.

I am part of the Ancientbiotics team, a group of medievalists, microbiologists, medicinal chemists, parasitologists, pharmacists and data scientists from multiple universities and countries. We believe that answers to the antibiotic crisis could be found in medical history. With the aid of modern technologies, we hope to unravel how premodern physicians treated infection and whether their cures really worked.

To that end, we are compiling a database of medieval medical recipes. By revealing patterns in medieval medical practice, our database could inform future laboratory research into the materials used to treat infection in the past. To our knowledge, this is the first attempt to create a medieval medicines database in this manner and for this purpose.

Bald’s eyesalve

In 2015, our team published a pilot study on a 1,000-year old recipe called Bald’s eyesalve from “Bald’s Leechbook,” an Old English medical text. The eyesalve was to be used against a “wen,” which may be translated as a sty, or an infection of the eyelash follicle.

Human white blood cells (in blue) take on Staphylococcus aureus bacteria.
Frank DeLeo, National Institute of Allergy and Infectious Diseases

A common cause of modern styes is the bacterium Staphylococcus aureus. Methicillin-resistant Staphylococcus aureus (or MRSA) is resistant to many current antibiotics. Staph and MRSA infections are responsible for a variety of severe and chronic infections, including wound infections, sepsis and pneumonia.

Bald’s eyesalve contains wine, garlic, an Allium species (such as leek or onion) and oxgall. The recipe states that, after the ingredients have been mixed together, they must stand in a brass vessel for nine nights before use.

In our study, this recipe turned out to be a potent antistaphylococcal agent, which repeatedly killed established S. aureus biofilms – a sticky matrix of bacteria adhered to a surface – in an in vitro infection model. It also killed MRSA in mouse chronic wound models.

Medieval methods

Premodern European medicine has been poorly studied for its clinical potential, compared with traditional pharmacopeias of other parts of the world. Our research also raises questions about medieval medical practitioners. Today, the word “medieval” is used as a derogatory term, indicating cruel behavior, ignorance or backwards thinking. This perpetuates the myth that the period is unworthy of study.

During our eyesalve study, chemist Tu Youyou was awarded the Nobel Prize in Physiology or Medicine for her discovery of a new therapy for malaria after searching over 2,000 recipes from ancient Chinese literature on herbal medicine. Is another “silver bullet” for microbial infection hidden within medieval European medical literature?

Certainly, there are medieval superstitions and treatments that we would not replicate today, such as purging a patient’s body of pathogenic humors. However, our work suggests that there could be a methodology behind the medicines of medieval practitioners, informed by a long tradition of observation and experimentation.

One key finding was that following the steps exactly as specified by the Bald’s eyesalve recipe – including waiting nine days before use – was crucial for its efficacy. Are the results of this medieval recipe representative of others that treat infection? Were practitioners selecting and combining materials following some “scientific” methodology for producing biologically active cocktails?

Further research may show that some medieval medicines were more than placebos or palliative aids, but actual “ancientbiotics” used long before the modern science of infection control. This idea underlies our current study on the medieval medical text, “Lylye of Medicynes.”

A medieval medicines database

The “Lylye of Medicynes” is a 15th-century Middle English translation of the Latin “Lilium medicinae,” first completed in 1305. It is a translation of the major work of a significant medieval physician, Bernard of Gordon. His “Lilium medicinae” was translated and printed continuously over many centuries, until at least the late 17th century.

The text contains a wealth of medical recipes. In the Middle English translation, there are 360 recipes – clearly indicated with Rx in the text – and many thousands more ingredient names.

As a doctoral student, I prepared the first-ever edition of the “Lylye of Medicynes” and compared the recipes against four extant Latin copies of the “Lilium medicinae.” This involved faithfully copying the Middle English text from the medieval manuscript, then editing that text for a modern reader, such as adding modern punctuation and correcting scribal errors. The “Lylye of Medicynes” is 245 folios, which equates to 600 pages of word-processed text.

I loaded the Middle English names of ingredients into a database, along with translations into modern equivalents, juxtaposed with relationships to recipe and disease. It is very time-consuming to format medieval data for processing with modern technologies. It also takes time to translate medieval medical ingredients into modern equivalents, due in part to multiple synonyms as well as variations in modern scientific nomenclature for plants. This information has to be verified across many sources.

With our database, we aim to find combinations of ingredients that occur repeatedly and are specifically used to treat infectious diseases. To achieve this, we are employing some common tools of data science, such as network analysis, a mathematical method to examine the relationships between entries. Our team will then examine how these patterns may help us to use medieval texts as inspiration for lab tests of candidate “ancientbiotic” recipes.

Word cloud from the Lylye of Medicynes.
Erin Connelly

In March, we tested a small portion of the database to ensure that the method we developed was appropriate for this data set. At present, the database contains only the 360 recipes indicated with Rx. Now that the proof-of-concept stage is complete, I will expand the database to contain other ingredients which are clearly in recipe format, but may not be marked with Rx.

We are specifically interested in recipes associated with recognizable signs of infection. With Bald’s eyesalve, the combination of ingredients proved to be crucial. By examining the strength of ingredient relationships, we hope to find out whether medieval medical recipes are driven by certain combinations of antimicrobial ingredients.

The database could direct us to new recipes to test in the lab in our search for novel antibiotics, as well as inform new research into the antimicrobial agents contained in these ingredients on the molecular level. It could also deepen our understanding of how medieval practitioners “designed” recipes. Our research is in the beginning stages, but it holds exciting potential for the future.

Erin Connelly, CLIR-Mellon Fellow for Data Curation in Medieval Studies, University of Pennsylvania

This article was originally published on The Conversation. Read the original article.

Enzymes versus nerve agents: Designing antidotes for chemical weapons

US Official: Russia knew Syrian chemical attack was coming

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Enzymes, the catalysts of biology, can engulf and break down hundreds of nerve agent molecules per second.
Image: Pymol. PDB 4E3T, CC BY-ND

Ian Haydon, University of Washington

A chemical weapons attack that killed more than 80 people, including children, triggered the Trump administration’s recent missile strikes against the Syrian government. The use of illegal nerve agents – apparently by the Assad regime – violated international law; President Trump said he was moved to act by images of the victims’ horrible deaths. The Conversation

But there’s another path to mitigate the danger of chemical weapons. This route lies within the domains of science – the very same science that produced chemical weapons in the first place. Researchers in the U.S. and around the world, including here at the University of Washington’s Institute for Protein Design, are developing the tools needed to quickly and safely destroy nerve agents – both in storage facilities and in the human body.

Nerve agents, a class of synthetic phosphorous-containing compounds, are among the most toxic substances known. Brief exposure to the most potent variants can lead to death within minutes. Once nerve agents enter the body, they irreversibly inhibit a vitally important enzyme called acetylcholinesterase. Its normal job within the nervous system is to help brain and muscle communicate. When a nerve agent shuts down this enzyme, classes of neurons throughout the central and peripheral nervous systems quickly get overstimulated, leading to profuse sweating, convulsions and an excruciating death by asphyxiation.

U.S. Marine Corps specialists performing decontamination procedures.
Sgt. Keonaona Paulo

Chemical weapons are often associated with wars of the previous century – mustard gas in WWI, Zyklon B in WWII. But the worst variety, nerve agents, were never deployed in the world wars, though Nazi scientists developed the first generation of these compounds. Gerhard Schrader, the so-called father of nerve agents, didn’t begin life as a Nazi scientist – he was developing new pesticides to combat world hunger when he accidentally synthesized the first organophosphorus nerve agent. Later, he led the research team that produced sarin, or GB, the most toxic of the all the so-called G-series nerve agents. The U.S. government stated with “very high confidence” that sarin was used in the recent attack near Idlib, Syria.

Beginning in 2013, teams from the Organization for the Prohibition of Chemical Weapons went to Syria and, with help from the Danish, Norwegian, Russian, Chinese and U.S. government, destroyed all declared stockpiles of Syrian chemical weapons. It seems that either not all of Assad’s stockpiles were in fact declared and destroyed, or that new nerve agents arrived in Syria – either via the black market or chemical synthesis – in the intervening years.

Empty sarin containers at Pine Bluff Arsenal.
U.S. Army

Clearing chemical weapons

Twenty-first-century chemists, biochemists and computer scientists are working right now to sap chemical weapons of their horrifying power by designing counter agents that safely and efficiently destroy them.

Sarin sitting in a container – as opposed to in a human body – is relatively easy to destroy. The simplest method is to add a soluble base and heat the mixture to near-boiling temperatures. After several hours, the vast majority – more than 99.9 percent – of the deadly compound can be broken apart by a process called hydrolysis. This is how trained specialists dispose of chemical weapons like sarin.

Nerve agents that make their way inside the body are a different story. For starters, you clearly cannot add a near-boiling base to a person. And because nerve agents kill so quickly, any treatment that takes hours to work is a nonstarter.

There are chemical interventions for warding off death after exposure to certain chemical weapons. Unfortunately, these interventions are costly, difficult to dose properly and are themselves quite toxic. The chemical antidotes pralidoxime and the cheaper atropine were deployed after recent attacks in Syria, but doctors in the area worry their dwindling supplies offer little protection against possible future attacks.

For a medical intervention to work after nerve gas exposure, it has to work fast. If a first responder administers a sarin-destroying molecule, each therapeutic molecule must be capable of breaking down through hydrolysis hundreds of nerve agent molecules per second, one after another.

Enzymes, the genetically encoded catalysts of biology, are up for such a task. Famous enzymes include lactase, which breaks down milk sugars in those who are lactose tolerant. Another known as RuBisCO is vital to the process of carbon fixation in plants. The most efficient enzymes in your body can perform a million reactions per second, and do so under chemically mild conditions.

Aside from their astonishing speed, enzymes often display an equally impressive selectivity. That is, they react with only a small number of structurally similar compounds and leave all other compounds alone. Selectivity is useful in the context of the chemical soup that is the cell but problematic when it comes to xenobiotics: those compounds which are foreign to one’s biology. Man-made organophosphates such as sarin are xenobiotics. There are no enzymes that hydrolyze them well – or so we thought.

When farmers spray pesticides, much of it ends up on the ground. Soil bacteria living nearby are challenged by high doses of these potent foreign chemicals. It turns out that efficient detoxifying enzymes have recently evolved inside some of these microbes as a result.

Scientists have identified and isolated a small number of these enzymes and tested them on a range of nasty compounds, including nerve agents, which are structurally similar to some pesticides. A select few did indeed show hydrolytic activity.

Scientists are using computers to design a new generation of proteins to solve 21st-century problems.
UW Institute for Protein Design, CC BY-ND

Improving on the discovery

Researchers have taken these naturally occurring enzymes as raw material. Then, using computer modeling and controlled evolution in the lab, we’ve bolstered the efficiency of the originally found anti-nerve agent enzymes. Enzymes that initially showed only modest activity have been turned into potential therapeutics against VX – a chemical cousin of sarin and the most toxic nerve agent of all.

In a proof-of-concept study conducted jointly by researchers in Germany and Israel in late 2014, guinea pigs under anesthesia were exposed to lethal doses of VX, followed by optimized VX-destroying proteins. Low doses of the protein drug, even after a 15-minute delay, resulted in survival of all animals and only moderate toxicity.

Despite these promising advances, no enzyme yet exists which is efficient enough for lifesaving use in people. Scientists are refining these microscopic machines, and new paradigms in computer-aided protein engineering are unlocking the door to this and other applications of biomolecular design. We may be only a few years away from developing the kind of therapeutics that would make chemical weapons a worry of the past.

As the world grieves over the latest attacks in Syria, it is worth keeping in mind the awesome and often complex power of science. In trying to combat hunger, one might accidentally invent liquid death. In studying soil microbes, one might discover a tool to prevent atrocities.

Ian Haydon, Doctoral Student in Biochemistry, University of Washington

This article was originally published on The Conversation. Read the original article.

Mysterious chambers found hidden in ancient Giza structure


Two scientists say they’ve uncovered hidden chambers in the Great Pyramid of Giza. Discovered using an advanced X-ray technique the chambers are completely isolated from all other tombs and passages in the 4,500 year-old structure.

The discovery was made by Scan Pyramids, a research project involving universities and advanced scientific instruments. Using a combination of thermography, 3D simulation and radiography imaging, the team discovered anomalies in the structure indicating the presence of holes beneath the rock.

From the expert’s mouth

Chimpanzé (Pan troglodytes)

In this Atlantic piece on how candidates will do in the debates:

“In many ways the performances of Donald Trump remind me of male chimpanzees and their dominance rituals,” Jane Goodall, the anthropologist, told me shortly before Trump won the GOP nomination. “In order to impress rivals, males seeking to rise in the dominance hierarchy perform spectacular displays: stamping, slapping the ground, dragging branches, throwing rocks. The more vigorous and imaginative the display, the faster the individual is likely to rise in the hierarchy, and the longer he is likely to maintain that position.”

In her book My Life With the Chimpanzees, Goodall told the story of “Mike,” a chimp who maintained his dominance by kicking a series of kerosene cans ahead of him as he moved down a road, creating confusion and noise that made his rivals flee and cower. She told me she would be thinking of Mike as she watched the upcoming debates.

“Vigorous and imaginative displays on Trump’s part and steady error avoidance on Clinton’s are the stories of their progress through the primary-cycle debates. Clinton is her party’s nominee independent of anything that happened in the 10 Democratic debates and town halls, and with minimal effect from them on her financial, endorsement, and name-recognition advantages. Trump is his party’s nominee largely because of the Republicans’ 20-some debates, town halls, forums, and other live-television displays.

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