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Archaeologists now have a handy new tool for analyzing paleo-poop

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Enlarge / Ancient poo samples: H35 (Ash pit number 35) coprolites from Xiaosungang archaeological site, Anhui Province, China.

Jada Ko, courtesy of the Anhui Provincial Institute of Cultural Relics and Archaeology

Combing through samples of ancient feces probably isn’t going to be many people’s idea of a roaring good time. However, for archaeologists keen on learning more about the health and diet of past populations—as well as how certain parasites evolved, the evolutionary history of the microbiome—such samples can be a veritable gold mine of information.

Yet it can be difficult to determine whether fecal samples are human or were produced by other animals, particularly dogs. Now an international team of scientists has devised a new method of doing so that combines host DNA and gut microbiome analysis with open-source machine learning software, according to a new paper in the journal PeerJ.

The challenge of determining whether paleofeces and coprolites are of human or animal origin dates back to the 1970s. Usually, only those samples found with human skeletons or mummies could be designated as being of human origin with any certainty. Exceptions could be made for samples found in ancient latrines, since they are highly likely to be human; samples found in trash deposits, however, are more ambiguous. 

Subsequent work to document the morphology of mammal feces has made it easier to separate human from animal samples, since there are enough differences to make such distinctions. The exception is dog poo, which bears a striking close resemblance to human feces in both size and shape, is frequently found at the same archaeological sites, and has a similar composition. And frankly, some ancient societies routinely ate dog meat, while dogs are known to nibble on human feces. So DNA from both can be present in the same archaeological sample.

There are some helpful clues. For instance, ancient dog poo samples “typically contain masses of short, nibbled dog hairs and odd inclusions, such as fragments of clothing and rope,” the authors of the PeerJ paper wrote. The presence of specific parasites can also indicate whether a sample is human or canine, such as eggs from pinworms (Enterobius vermicularis), which are typically only present in human feces. Scanning electron microscopy (SEM) can also be useful for identifying plant remains (such as pollen grains) in ancient samples. Rehydrating the samples can also help make the distinction, since human feces will turn the rehydration solution dark brown or black; animal samples typically remain clear or turn yellow.

Dog or human?

This new coprolite identification method, dubbed coproID, combines host DNA analysis with analysis of the distinct colonies of microbes living inside humans and dogs. The scientists used their open source software to analyze both a previously sequenced modern fecal dataset, as well as a newly sequenced dataset of paleo-poop specimens, and sediments from archaeological digs.

For the latter dataset, there were 20 archaeological samples (13 paleofeces, 4 sediments, and 3 sediments take from human pelvic bone) from ten sites, spanning periods from the prehistoric era to the medieval era, 17 of which were newly sequenced. They got their modern fecal samples from a long-term Boston type 1 diabetes study, as well as from a broader study on human gut microbiome biodiversity being conducted in villages in the West African Republic of Burkina Faso. Per the authors, “Feces were collected fresh and stored frozen until analysis.”

The researchers found that, using the method, they could distinguish between fecal and non-fecal samples, as well as human and canine fecal samples. “One unexpected finding of our study is the realization that the archaeological record is full of dog poop,” said co-author Christina Warinner of the Max Planck institute for the Science of Human History.

“One unexpected finding is the realization that the archaeological record is full of dog poop.”

Specifically, coproID correctly identified seven of the 13 samples of paleo-poop (five human, two canine), and flagged the non-fecal sediments as “unknown.”  Of the six fecal samples the software couldn’t identify, three did not have sufficiently preserved microbiome components to make a determination. The other three uncertain samples hailed from a prehistoric archaeological site in the Rio Zape Valley in Durango, Mexico, and showed both high levels of dog DNA, and microbiome profiles more typical of humans.

The Rio Zape samples “could have originated from a human who consumed a recent meal of canine meat,” the authors suggest. “Dogs were consumed in ancient Mesopotamia, but further research on the expected proportion of dietary DNA in human feces is needed to determine whether this is a plausible explanation.” The alternative is that the samples came from dogs with a different microbiome profile than the microbiome data used in the study, derived from a single study of labrador retrievers and beagles.

“Identifying human coprolites should be the first step for ancient human microbiome analysis,” said co-author Maxime Borry. “With additional data about the gut metagenomes of non-Westernized rural dogs, we’ll be better able to classify even more ancient dog feces as in fact being canine, as opposed to ‘uncertain.'”

DOI: PeerJ, 2020. 10.7717/peerj.9001  (About DOIs).

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What’s the best design for splash-free urinal? Physics now has the answer

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Enlarge / Can you spot the urinal design with the optimal splash-reducing angle? It’s the one second from right.

Mia Shi/University of Waterloo

Scientists at the University of Waterloo have determined the optimal design for a splash-free urinal: a tall, slender porcelain structure with curves reminiscent of a nautilus shell, playfully dubbed the “Nauti-loo.” That’s good news for men tired of having urine splash onto their pants and shoes—and for the poor souls who have to regularly clean up all the splatter. Bonus: It’s quite an aesthetically appealing design, giving this workhorse of the public restroom a touch of class.

“The idea originated exactly where you think it did,” Waterloo’s Zhao Pan told New Scientist. “I think most of us have been a little inattentive at our post and looked down to find we were wearing speckled pants. Nobody likes having pee everywhere, so why not just create a urinal where splatter is extremely unlikely?” His graduate student, Kaveeshan Thurairajah, presented the results of this research during last week’s American Physical Society (APS) meeting on fluid dynamics in Indianapolis.

It’s not the first time scientists have attempted to address this issue. Pan is a former graduate student of Tadd Truscott, a mechanical engineer who founded the so-called “Splash Lab” at Utah State University. In 2013, the Splash Lab (then at Brigham Young University) offered a few handy tips on how men could avoid staining their khaki pants with urine splashback while relieving themselves in restrooms. “Sitting on the toilet is the best technique, since there’s less distance for the pee to cover on its journey to the bowl,” I wrote previously at Gizmodo. “If you opt for the classic standing technique, the scientists advised standing as close to the urinal as possible, and trying to direct the stream at a downward angle toward the back of the urinal.”

For those who lack optimal anti-splash technique, another of Truscott’s graduate students, Randy Hurd, presented an optimal design for a splash-free urinal insert at the 2015 APS fluid dynamics meeting. There are three basic types of inserts. One employs absorbent cloth to keep splashing to a minimum; another uses a honeycomb structure—a raised layer (held up by little pillars) with holes—so urine droplets pass through but splash doesn’t come out; and a third type featuring an array of pillars. However, absorbent fabrics can’t absorb liquid quickly enough and soon become saturated, while the honeycomb and arrayed pillar structures don’t prevent urine pools from gradually forming.

In 2013, the Splash Lab demonstrated that reduced urine splash could be achieved by aiming at a vertical surface, moving closer to the urinal, and by decreasing the impact angle.

Hurd and Truscott’s insert design drew inspiration from a type of super-absorbent moss (Syntrichia caninervis) that thrives in very dry climates and thus is very good at collecting and storing as much water as possible. And they found that the manmade material called “VantaBlack” mimicked the moss’ absorbent properties. They copied that material’s structure for their urinal insert and found it successfully blocked droplets of pee from escaping—effectively acting as a “urinal black hole.”

Nor have the ladies been left out of this scientific (ahem) pissing contest. Women, too, suffer from urine spillage, most notably when required to pee into a cup for medical testing purposes. In 2018, the Splash Lab conducted a series of experiments involving a model of an anatomically correct female urethra. (They used a soft polymer to model the labia.) The results inspired the (patented) design of the “Orchid,” a funnel-shaped attachment for urine cups that reduces spillage. The research could lead to devices that allow women to pee standing up, which would be a boon to women in the military or female academics working in the field.

According to Pan, the key to optimal splash-free urinal design is the angle at which the pee stream strikes the porcelain surface; get a small enough angle, and there won’t be any splashback. Instead, you get a smooth flow across the surface, preventing droplets from flying out. (And yes, there is a critical threshold at which the urine stream switches from splashing to flowing smoothly, because phase transitions are everywhere—even in our public restrooms.) It turns out that dogs have already figured out the optimal angle as they lift their legs to pee, and when Pan et al. modeled this on a computer, they pegged the optimal angle for humans at 30 degrees.

Marcel Duchamp's "La Fontaine," photographed by Alfred Stieglitz at the 291 art gallery following the 1917 Society of Independent Artists exhibit.
Enlarge / Marcel Duchamp’s “La Fontaine,” photographed by Alfred Stieglitz at the 291 art gallery following the 1917 Society of Independent Artists exhibit.

Pan and his team also conducted a series of experiments with dyed fluids sprayed in jets of varying speeds into a range of faux-urinal designs (see top photo) made of dense, epoxy-covered foam—including the standard commercial shape and a urinal similar to the one Marcel Duchamp used in his famous (and controversial) 1917 art installation “La Fontaine.” All produced varying degrees of splashback, which the scientists wiped up with paper towels. They weighed the wet towels and compared that to how much the paper towels weighed when dry to quantify the amount of splash. The more the wet towels weighed, the bigger the splashback.

The next step was to figure out a design that would offer that optimal urine stream angle for men across a wide range of heights. Instead of the usual shallow box shaped like a rectangle, they landed on the curved structure of the nautilus shell. They repeated the simulated urine stream experiments with the prototypes, et voila! They didn’t observe a single droplet splashing back. By comparison, the other urinal designs produced as much as 50 times more splashback. There was one round design with an opening shaped like a triangle that performed even better than the Nauti-loo in the experiments, but Pan et al. rejected it because it wouldn’t work across a wide range of heights.

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A most “abnormal” Atlantic hurricane season officially ends this week

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Enlarge / Hurricane Ian, as seen from the International Space Station.

NASA

The Atlantic hurricane season officially ends on Wednesday, bringing to a close the six-month period when the vast majority of tropical activity occurs in the Atlantic Ocean, Gulf of Mexico, and Caribbean Sea.

Prior to the season, forecasters generally expected a busier-than-normal season. However, six months later, overall activity this year has come in slightly below normal. One of the more scientifically rigorous measurements of seasonal activity—based on the length and intensity of storms—is Accumulated Cyclone Energy. This year’s value, 95, is about three-quarters of the normal value of 126.

That bland statistic belies the fact that this was an odd season. After three weak early-season storms, the Atlantic basin produced zero named storms between July 3 and August 31. This was the first time since 1941 that the Atlantic had no named storm activity during this period. Then, a light came on. Four hurricanes formed in September, along with three more in November. This brought seasonal activity to near-normal levels.

“This season was really bizarre,” said Phil Klotzbach, one of the world’s foremost seasonal hurricane forecasters. “I’m giving a talk to the American Meteorological Society on Tuesday about the season, and I’m referring to it as the most abnormal ‘normal’ season on record.”

What happened

So what caused this? It’s a question that Klotzbach and his research team at Colorado State University have been investigating since the anomalously quiet August. The season’s sputtering start was all the more surprising because this is a La Niña year, a pattern that typically leads to lower-than-average wind shear across the Atlantic. This favors increased tropical activity.

In August, however, wind shear was higher than average in the region of the Atlantic Ocean where tropical systems commonly form. These crosswinds at varying altitudes disrupt the circulation of rotating storms, such as tropical storms and hurricanes. Another big factor this August was the incursion of dry air from the mid-latitudes. Dry air, of course, saps the thunderstorms that are essential to forming a tropical cyclone.

The shear and dry air appear to have had their origins in the mid-latitudes, the area between 30 degrees and 60 degrees north of the equator. And this higher wind shear and increased amount of dry air may have been transported southward into the tropical Atlantic Ocean due to a phenomenon called “wave breaking,” Klotzbach told Ars.

“I think a lot of the shear and dry air had mid-latitude origins and was associated with vigorous wave breaking,” he said. “Wave breaking is associated with upper-level low pressure systems that have anomalous upper-level westerlies on their southern periphery. These upper-level westerlies increase vertical wind shear. Also, mid-latitude air is typically drier than tropical air, stifling thunderstorm development and effectively choking African easterly waves.”

Chart showing

Chart showing “normal” Accumulated Cyclone Energy (in black) versus what happened this year (in light blue).

Colorado State University

Klotzbach said he has been working with Jhordanne Jones, who graduated from his research group last year and got her PhD studying the predictability of mid-latitude wave breaking. The goal is to better understand the predictability of this phenomenon and incorporate it into seasonal forecasting.

“The predictors that she found did hint at some increased potential for wave breaking this year, but not as much as was anticipated,” Klotzbach said. “We’ll certainly be spending more time looking at prediction of wave breaking for our forecasts in the future.”

Blowing up

After the quiescent period in August, the Atlantic tropics came alive in September, beginning with the formation of Tropical Storm Danielle on September 1. Five additional storms followed in the next three weeks, with Hurricane Ian being the strongest of them. With maximum sustained winds of 150 mph at landfall along the southwestern coast of Florida, Ian is tied with five other hurricanes for the fifth strongest continental US hurricane landfall on record.

Another surprise came in November, when the late-season Hurricane Nicole formed. It eventually made landfall along the southeast coast of Florida as a Category 1 hurricane.

Both of these storms—Ian and Nicole—proved disruptive for NASA and its Artemis I program. Ian’s fury forced the space agency to roll the Space Launch System rocket and its Orion spacecraft back into the Vehicle Assembly Building to protect it from the storm in September. Less than two months later, facing another hurricane, NASA opted to remain at the launch pad.

It proved a smart decision, as less than a week later, the Artemis I rocket had safely launched Orion toward the Moon.

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The evolution of whales from land to sea

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Enlarge / Whales and their kin evolved from land-dwelling mammals, a transition that entailed major physiological and morphological changes—which geneticists have begun to parse.

Hayes Baxley/National Geographic for Disney+

Around 400 million years ago, the ancestor of all four-limbed creatures took its first steps onto dry land. Fast-forward about 350 million years, and a descendant of these early landlubbers did an about-face: It waded back into the water. With time, the back-to-the sea creatures would give rise to animals vastly different from their land-trotting kin: They became the magnificent whales, dolphins, and porpoises that glide through the oceans today.

Going back to being aquatic was a drastic move that would change the animals inside and out, in the space of about 10 million years—an eyeblink in evolutionary terms. Members of this group, now called cetaceans, dropped their hind limbs for powerful flukes and lost nearly all their hair. For decades, their bizarre body plans perplexed paleontologists, who speculated they might have arisen from creatures as varied as marine reptiles, seals, marsupials like kangaroos, and even a now-extinct group of wolf-like carnivores.

“The cetaceans are on the whole the most peculiar and aberrant of mammals,” one scientist wrote in 1945.

Then, in the late 1990s, genetic data confirmed that whales were part of the same evolutionary line that spawned cows, pigs, and camels—a branch called Artiodactyla. Fossils from modern-day India and Pakistan later fleshed out that family tree, identifying the closest ancient relatives of cetaceans as small, wading deer-like creatures.

But their body plans are just the start of cetaceans’ weirdness. To survive in the sea, they also had to make internal modifications, altering their blood, saliva, lungs, and skin. Many of those changes aren’t obvious in fossils, and cetaceans aren’t easily studied in the lab. Instead it was, once again, genetics that brought them to light.

With an increasing availability of cetacean genomes, geneticists can now look for the molecular changes that accompanied the back-to-water transition. While it’s impossible to be certain about the influence of any particular mutation, scientists suspect that many of the ones they see correspond to adaptations that allow cetaceans to dive and thrive in the deep blue sea.

Diving into the depths

The first cetaceans lost a lot more than legs when they went back to the water: Entire genes became nonfunctional. In the vast of book of genetic letters that make up a genome, these defunct genes are among the easiest changes to detect. They stand out like a garbled or fragmented sentence, and no longer encode a full protein.

Such a loss could happen in two ways. Perhaps having a particular gene was somehow detrimental for cetaceans, so animals that lost it gained a survival edge. Or it could be a “use it or lose it” situation, says genomicist Michael Hiller of the Senckenberg Research Institute in Frankfurt, Germany. If the gene had no purpose in the water, it would randomly accumulate mutations and the animals would be no worse off when it didn’t function anymore.

Hiller and colleagues dove into the back-to-water transition by comparing the genomes of four cetaceans—dolphin, orca, sperm whale and minke whale—with those of 55 terrestrial mammals plus a manatee, a walrus, and the Weddell seal. Some 85 genes became nonfunctional when cetaceans’ ancestors adapted to the sea, the team reported in Science Advances in 2019. In many cases, Hiller says, they could guess why those genes became defunct.

For example, cetaceans no longer possess a particular gene—SLC4A9—involved in making saliva. That makes sense: What good is spit when your mouth is already full of water?

Cetaceans also lost four genes involved in the synthesis of and response to melatonin, a hormone that regulates sleep. The ancestors of whales probably discovered pretty quickly that they couldn’t surface to breathe if they shut off their brains for hours at a time. Modern cetaceans sleep one brain hemisphere at a time, with the other hemisphere staying alert. “If you don’t have the regular sleep as we know it anymore, then you probably do not need melatonin,” says Hiller.

The long periods of time that whales must hold their breath to dive and hunt also seem to have spurred genetic changes. Diving deep, as scuba divers know, means little bubbles of nitrogen can form in the blood and seed clots — something that was probably detrimental to early cetaceans. As it happens, two genes (F12 and KLKB1) that normally help kick off blood clotting are no longer functional in cetaceans, presumably lowering this risk. The rest of the clotting machinery remains intact so whales and dolphins can still seal up injuries.

Another lost gene—and this one surprised Hiller—encodes an enzyme that repairs damaged DNA. He thinks this change has to do with deep dives as well. When cetaceans come up for a breath, oxygen suddenly floods their bloodstreams, and as a result, so do reactive oxygen molecules that can break DNA apart. The missing enzyme—DNA polymerase mu—normally repairs this kind of damage, but it does so sloppily, often leaving mutations in its wake. Other enzymes are more accurate. Perhaps, Hiller thinks, mu was just too sloppy for the cetacean lifestyle, unable to handle the volume of reactive oxygen molecules produced by the constant diving and resurfacing. Dropping the inaccurate enzyme and leaving the repair job to more accurate ones that cetaceans also possess may have boosted the chances that oxygen damage was repaired correctly.

Cetaceans aren’t the only mammals that returned to the water, and the genetic losses in other aquatic mammals often parallel those in whales and dolphins. For example, both cetaceans and manatees have deactivated a gene called MMP12, which normally degrades the stretchy lung protein called elastin. Maybe that deactivation helped both groups of animals develop highly elastic lungs, allowing them to quickly exhale and inhale some 90 percent of their lungs’ volume when they surface.

Deep-diving adaptations aren’t all about loss, though. One conspicuous gain is in the gene that carries instructions for myoglobin, a protein that supplies oxygen to muscles. Scientists have examined myoglobin genes in diving animals from tiny water shrews all the way up to giant whales, and discovered a pattern: In many divers, the surface of the protein has a more positive charge. That would make the myoglobin molecules repel each other like two north magnets. This, researchers suspect, allows diving mammals to maintain high concentrations of myoglobin without the proteins glomming together, and thus high concentrations of muscle oxygen when they dive.

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