No Bones About It: Scientists Recover Ancient DNA From Cave Dirt

Sifting through teaspoons of clay and sand scraped from the floors of caves, German researchers have managed to isolate ancient human DNA — without turning up a single bone.

Their new technique, described in a study published on Thursday in the journal Science, promises to open new avenues of research into human prehistory and was met with excitement by geneticists and archaeologists.

“It’s a bit like discovering that you can extract gold dust from the air,” said Adam Siepel, a population geneticist at Cold Spring Harbor Laboratory.

“An absolutely amazing and exciting paper,” added David Reich, a genetics professor at Harvard who focuses on ancient DNA.

Until recently, the only way to study the genes of ancient humans like the Neanderthals and their cousins, the Denisovans, was to recover DNA from fossil bones.

But they are scarce and hard to find, which has greatly limited research into where early humans lived and how widely they ranged. The only Denisovan bones and teeth that scientists have, for example, come from a single cave in Siberia.

Looking for these genetic signposts in sediment has become possible only in the last few years, with recent developments in technology, including rapid sequencing of DNA.

An entrance to the archaeological site of Chagyrskaya Cave, Russia. The only Denisovan bones and teeth that scientists have come from a single cave in Siberia.CreditRichard G. Roberts

Although DNA sticks to minerals and decayed plants in soil, scientists did not know whether it would ever be possible to fish out gene fragments that were tens of thousands of years old and buried deep among other genetic debris.

Bits of genes from ancient humans make up just a minute fraction of the DNA floating around in the natural world.

But the German scientists, led by Matthias Meyer at the Max Planck Institute for Developmental Biology in Tübingen, have spent years developing methods to find DNA even where it seemed impossibly scarce and degraded.

“There’s been a real revolution in technology invented by this lab,” Dr. Reich said. “Matthias is kind of a wizard in pushing the envelope.”

Scientists began by retrieving DNA from ancient bones: first Neanderthals, then Denisovans.

To identify the Denisovans, Svante Paabo, a geneticist at the Planck Institute and a co-author of the new paper, had only a child’s pinkie bone to work with.

His group surprised the world in 2010 by reporting that it had extracted DNA from the bone, finding that it belonged to a group of humans distinct from both Neanderthals and modern humans.

But that sort of analysis is limited by the availability of fossil bones.

“In a lot of cases, you can get bones, but not enough,” said Hendrik Poinar, an evolutionary geneticist at McMaster University.

“If you just have one small piece of bone from one site, curators do not want you to grind it up.”

Finding and analyzing ancient DNA in dirt is far more difficult than getting it out of bone. The idea was not new, noted Viviane Slon, a member of Dr. Meyer’s group and the first author of the new paper.

Other groups of researchers have found DNA in sediment, including Dr. Poinar and Michael Hofreiter, his former student. Using a tablespoon of dirt from a cave in Colorado, his team discovered traces from 16 animal species that had lived there. It took two weeks to do it.

Researchers who had scoured that cave for bones had spent 20 years there and had sifted through two metric tons of dirt to find bones, teeth or skin of 20 animal species — including the 16 that Dr. Poinar’s group later identified.

The new study involved searching for ancient DNA in four caves in Eurasia where humans were known to have lived between 14,000 and 550,000 years ago.

Dr. Meyer and his colleagues figured out which DNA in the cave sediment was prehistoric by looking for telltale signs of degradation at the ends of the molecules.

They then plucked out DNA from Neanderthals and Denisovans by using molecular hooks to snare genes in mitochondria — the cells’ energy factories — that are unique to these humans.

The scientists also built a robotic system to analyze the samples quickly; the old way, pipetting by hand, required several days to analyze only a fraction as many samples.

The group needed that efficiency. From different dirt samples, they recovered between 5,000 and 2.8 million DNA fragments. The number of DNA fragments per sample that were from ancient humans was minuscule and ranged from 0 to 8,822, depending on the site in the cave.

Svante Paabo, a geneticist at the Planck Institute and a co-author of the new paper, showing the location of a sediment sample collected from a layer where a 560,000-year-old human tooth was discovered in 2015.CreditChristian Perrenoud

The discovery that it is now possible to do all this, Dr. Reich said, is just “an amazing, amazing thing.” The questions that can now be addressed seem almost endless.

Researchers could feasibly begin searching for bones in caves where DNA in the dirt indicates habitation by ancient humans. And they are likely to begin learning much more about human prehistory.

The Denisovans, for example: Tiny pieces of genes inherited from them have been found in modern humans in Papua New Guinea. How did they get there? And why these people, and not humans closer to Siberia?

With the new technique, one way to try to verify the presence of humans would be to look for ancient human DNA at the site where the bones were found or in areas nearby.

“A natural thing to do is start looking in sediments,” said Jonathan Pritchard, a professor of genetics and biology at Stanford.

Another application of the discovery, said Dr. Reich, would be to start looking for evidence of ancient human DNA in open air sites, instead of looking for bones in caves.

“If it worked, it would provide a much richer picture of the geographic distribution and migration patterns of ancient humans, one that was not limited by the small number of bones that have been found,” he said.

“That would be a magical thing to do.”

Advertisements

Scientists Create Artificial Womb That Could Help Prematurely Born Babies

An illustration of a fetal lamb inside the “artificial womb” device, which mimics the conditions inside a pregnant animal.

The Children’s Hospital of Philadelphia

Scientists have created an “artificial womb” in the hopes of someday using the device to save babies born extremely prematurely.

So far the device has only been tested on fetal lambs. A study published Tuesday involving eight animals found the device appears effective at enabling very premature fetuses to develop normally for about a month.

“We’ve been extremely successful in replacing the conditions in the womb in our lamb model,” says Alan Flake, a fetal surgeon at Children’s Hospital of Philadelphia who led the study published in the journal Nature Communications.

“They’ve had normal growth. They’ve had normal lung maturation. They’ve had normal brain maturation. They’ve had normal development in every way that we can measure it,” Flake says.

Flake says the group hopes to test the device on very premature human babies within three to five years.

“What we tried to do is develop a system that mimics the environment of the womb as closely as possible,” Flake says. “It’s basically an artificial womb.”

Inside an artificial womb

The device consists of a clear plastic bag filled with synthetic amniotic fluid. A machine outside the bag is attached to the umbilical cord to function like a placenta, providing nutrition and oxygen to the blood and removing carbon dioxide.

“The whole idea is to support normal development; to re-create everything that the mother does in every way that we can to support normal fetal development and maturation,” Flake says.

Other researchers praised the advance, saying it could help thousands of babies born very prematurely each year, if tests in humans were to prove successful.

Jay Greenspan, a pediatrician at Thomas Jefferson University, called the device a “technological miracle” that marks “a huge step to try to do something that we’ve been trying to do for many years.”

The device could also help scientists learn more about normal fetal development, says Thomas Shaffer a professor of physiology and pediatrics at Temple University.

Enlarge this image

Alan Flake, a fetal surgeon at the Children’s Hospital of Philadelphia, led the study published in the journal Nature Communications.

/Ed Cunicelli/The Children’s Hospital of Philadelphia

“I think this is a major breakthrough,” Shaffer says.

The device in the fetal lamb experiment is kept in a dark, warm room where researchers can play the sounds of the mother’s heart for the lamb fetus and monitor the fetus with ultrasounds.

Previous research has shown that lamb fetuses are good models for human fetal development.

“If you can just use this device as a bridge for the fetus then you can have a dramatic impact on the outcomes of extremely premature infants,” Flake says. “This would be a huge deal.”

But others say the device raises ethical issues, including many questions about whether it would ever be acceptable to test it on humans.

“There are all kinds of possibilities for stress and pain with not, at the beginning, a whole lot of likelihood for success,” says Dena Davis, a bioethicist at Lehigh University.

Flake says ethical concerns need to be balanced against the risk of death and severe disabilities babies often suffer when they are born very prematurely. A normal pregnancy lasts about 40 weeks. A human device would be designed for those born 23 or 24 weeks into pregnancy.

Only about half of such babies survive and, of those that do, about 90 percent suffer severe complications, such as cerebral palsy, mental retardation, seizures, paralysis, blindness and deafness, Flake says.

About 30,000 babies are born earlier than 26 weeks into pregnancy each year in the United States, according to the researchers.

Potential ethical concerns

Davis worries that the device is not necessarily a good solution for human fetuses.

“If it’s a difference between a baby dying rather peacefully and a baby dying under conditions of great stress and discomfort then, no, I don’t think it’s better,” Davis says.

“If it’s a question of a baby dying versus a baby being born who then needs to live its entire life in an institution, then I don’t think that’s better. Some parents might think that’s better, but many would not,” she says.

And even if it works, Davis also worries about whether this could blur the line between a fetus and a baby.

“Up to now, we’ve been either born or not born. This would be halfway born, or something like that. Think about that in terms of our abortion politics,” she says.

Some worry that others could take this technology further. Other scientists are already keeping embryos alive in their labs longer then ever before, and trying to create human sperm, eggs and even embryo-like entities out of stem cells. One group recently created an artificial version of the female reproductive system in the lab.

“I could imagine a time, you know sort of [a] ‘Brave New World,’ where we’re growing embryos from the beginning to the end outside of our bodies. It would be a very Gattaca-like world,” says Davis, referring to the 1997 science-fiction film.

There’s also a danger such devices might be used coercively. States could theoretically require women getting abortions to put their fetuses into artificial wombs, says Scott Gelfand, a bioethicist at Oklahoma State University.

Employers could also require female employees to use artificial wombs to avoid maternity leave, he says. Insurers could require use of the device to avoid costly complicated pregnancies and deliveries.

“The ethical implications are just so far-reaching,” Gelfand says.

Barbara Katz Rothman, a sociologist at the City University of New York, says more should be done to prevent premature births. She worries about the technological transformation of pregnancy.

“The problem is a baby raised in a machine is denied a human connection,” Rothman says. “I think that’s a scary, tragic thing.”

Flake says his team has no interest in trying to gestate a fetus any earlier than about 23 weeks into pregnancy.

“I want to make this very clear: We have no intention and we’ve never had any intention with this technology of extending the limits of viability further back,” Flake says. “I think when you do that you open a whole new can of worms.

Flake doubts anything like that would ever be possible.

“That’s a pipe dream at this point,” Flake says.

Scientists Find That Babies Who Are Given DTP Vaccine Are up to 10 Times More Likely to Die

http://www.renegadetribune.com/scientists-find-babies-given-dtp-vaccine-10-times-likely-die/

 

Research conducted by a team of Scandinavian scientists came to a startling conclusion regarding the DTP vaccine, which is supposed to protect children from diphtheria, pertussis, and tetanus. Though they found that the vaccine can prevent those diseases, it does so at a terrible cost.

The research, which was partly funded by the Danish government, derived its data from a vaccination campaign conducted in the African nation of Guinea Bissau during the 1980’s. Initially, the campaign offered parents the opportunity to have their babies weighed every 3 months, and in 1981 they started giving out DTP vaccines during these sessions. Because the babies were only allowed to be vaccinated at a certain age, some were not vaccinated, which created the perfect control group.

It turns out that the babies who were vaccinated had a mortality rate that was on average, five times higher than the unvaccinated infants. The vaccinated girls were 9.98 times more likely to die after being vaccinated, and the boys were 3.93 time more likely to die.

These numbers were derived from kids who also had a polio vaccine. Strangely, they had a much lower mortality rate. The kids who only received the DTP vaccine had on average, a mortality rate that was 10 times higher than the control group. The researchers believe that the vaccine must have stifled the immune systems of these children, opening them up to mutliple infections.

The researchers wrote that It should be of concern that the effect of routine vaccinations on all-cause mortality was not tested in randomized trials.  All currently available evidence suggests that DTP vaccine may kill more children from other causes than it saves from diphtheria, tetanus or pertussis.  Though a vaccine protects children against the target disease it may simultaneously increase susceptibility to unrelated infections.”

The study only looked at children who were healthy before being vaccinated. Because of that, the researchers noted “The estimate from the natural experiment may therefore still be conservative.”

Delivered by The Daily Sheeple

We encourage you to share and republish our reports, analyses, breaking news and videos (Click for details).


Contributed by Daniel Lang of The Daily Sheeple.

Trillions of Plastic Bits, Swept Up by Current, Are Littering Arctic Waters

The world’s oceans are littered with trillions of pieces of plastic — bottles, bags, toys, fishing nets and more, mostly in tiny particles — and now this seaborne junk is making its way into the Arctic.

In a study published Wednesday in Science Advances, a group of researchers from the University of Cádiz in Spain and several other institutions show that a major ocean current is carrying bits of plastic, mainly from the North Atlantic, to the Greenland and Barents seas, and leaving them there — in surface waters, in sea ice and possibly on the ocean floor.

Because climate change is already shrinking the Arctic sea ice cover, more human activity in this still-isolated part of the world is increasingly likely as navigation becomes easier. As a result, plastic pollution, which has grown significantly around the world since 1980, could spread more widely in the Arctic in decades to come, the researchers say.

Andrés Cózar Cabañas, the study’s lead author and a professor of biology at the University of Cádiz, said he was surprised by the results, and worried about possible outcomes.

Fragments of fishing lines found in Arctic surface waters by the research team. CreditAndres Cozar

“We don’t fully understand the consequences the plastic is having or will have in our oceans,” he said. “What we do know is that this consequences will be felt at greater scale in an ecosystem like this” because it is unlike any other on Earth.

Every year, about 8 million tons of plastic gets into the ocean, and scientists estimate that there may be as much as 110 million tons of plastic trash in the ocean. Though the environmental effects of plastic pollution are not fully understood, plastic pollution has made its way into the food chain. Plastic debris in the ocean was thought to accumulate in big patches, mostly in subtropical gyres — big currents that converge in the middle of the ocean — but scientists estimate that only about 1 percent of plastic pollution is in these gyres and other surface waters in the open ocean.

Another model of ocean currents by one of the study’s authors predicted that plastic garbage could also accumulate in the Arctic Ocean, specifically in the Barents Sea, located off the northern coasts of Russia and Norway, which this study demonstrates.

The surface water plastic in the Arctic Ocean currently accounts for only about 3 percent of the total, but the authors suggest the amount will grow and that the seafloor there could be a big sink for plastic.

This particular part of the ocean is important in the thermohaline circulation, a deepwater global current dictated by differences in temperature and salinity around the world. As that current brings warm surface water up to the Arctic, it seems to be bringing with it plastic waste from more densely populated coastlines, dumping the now-fragmented pieces of plastic in the Arctic, where landmasses like Greenland and the polar ice cap trap them.

Scientists aboard the research vessel Tara lower nets into the water to collect plankton and microplastics.CreditAnna Deniaud/Tara Expeditions Foundation

The scientists sampled floating plastic debris from 42 sites in the Arctic Ocean aboard Tara, a research vessel that completed a trip around the North Pole from June to October 2013, with data from two additional sites from a previous trip. They scooped up plastic debris and determined the concentration of particles by dividing the dry weight of the plastic collected, excluding microfibers, by the area surveyed.

Almost all of the plastic, measured by weight, was in fragments, mostly ranging from 0.5 millimeters to 12.6 millimeters. The rest of the plastic appeared in the form of fishing line, film or pellets. This mix of plastic types is roughly consistent with the kinds of plastic that collect in the subtropical gyres, though those parts of the ocean amasses a higher concentration of fishing line.

The researchers did not find many large pieces of plastic, nor did they find much plastic film, which breaks down quickly, suggesting that the plastic has already been in the ocean for a while by the time it gets to the Arctic.

If the plastics were coming directly from Arctic coastlines, it would mean that people in the sparsely populated Arctic were depositing many more times the plastic in the ocean than people in other parts of the world, which is unlikely. Shipping is also relatively infrequent there and, the authors write, there is no reason to think that flotsam or jetsam in the Arctic would be so much higher than in other parts of the world.

The lesson from the study, Dr. Cózar Cabañas said, is that the issue of plastic pollution “will require international agreements.”

“This plastic is coming from us in the North Atlantic,” he said. “And the more we know about what happens in the Arctic, the better chance we have” of solving the problem.

Human umbilical cord blood helps aging mice remember, study finds

Decades ago, scientists surgically attached pairs of rats to each other and noticed that old rats tended to live longer if they shared a bloodstream with young rats.

It was the beginning of a peculiar and ambitious scientific endeavor to understand how certain materials from young bodies, when transplanted into older ones, can sometimes improve or rejuvenate them.

From the beginning, the findings were exciting, complex and, sometimes, contradictory. For example, scientists have shown that young blood can restore cell activity in the muscles and livers of aging mice. They’ve also found that linking old mice to young ones helped reverse heart muscle thickening.

On the other hand, researchers weren’t able to replicate those findings and another study concluded that, in mice that swapped blood without being connected surgically, the negative effects of being exposed to old blood outweighed the benefits of getting young blood.

What was clear was that, like humans, as mice age their bodies and their behavior change on a fundamental level. For example, older mice stop building nests, and they tend to become forgetful, taking a long time to remember how to escape from a maze.

“We see a pretty dramatic difference between young and aged mice in terms of their performance,” says Joe Castellano, a neuroscientist at Stanford University School of Medicine.

Castellano and his colleagues wondered if young human blood might have beneficial effects for aging mice.

Now, they report in the journal Nature that they’ve found a protein in human umbilical cord blood that improved learning and memory in aging mice. It’s an exciting find in the field of regenerative medicine.

But, scientists caution, it does not mean people should start ordering umbilical cord blood online. There is no indication that it would work in humans.

For their study, Castellano and his colleagues collected plasma, which is the watery part of blood, from people of different ages. Some were in their 60s and 70s, others in their 20s. They also collected plasma from human umbilical cords.

Then, they injected human plasma from those different age groups and from umbilical cord blood into mice several times over the course of a couple of weeks.

The mice were 12 and 14 months old, which is approximately the mouse equivalent of being in your late 50s or 60s.

When they dissected the mouse brains and inspected the hippocampi, they found that certain genes linked to making new memories had been turned on in some of the mice.

“So, we had a hint early on that one of these donor groups, specifically the [umbilical] cord plasma, might be having an effect on the brain itself,” he says.

Next, they injected more aging mice with human plasma and tested the animals’ ability to remember things.

For example, they watched how long it took the mice to escape from a maze the mice had done before, using visual cues to choose an exit that would lead to safety.

Castellano says it’s basically like observing a person try to navigate through a crowded garage to locate their parked car.

Before being injected with umbilical cord blood, Castellano says, “their performance wasn’t very impressive.” It took them a long time to learn and remember the location of the escape hole, and some of them didn’t manage at all. “But after cord plasma treatment, both the time [it took to] find it, the rate at which they’d find it and the fact that they do find it was improved and changing,” he says.

Similarly, mice treated with human umbilical cord blood performed better on a second memory test. That test involved introducing mice to a chamber and then delivering a little shock to their feet. Mice that remembered the unpleasant experience would, when reintroduced to the chamber, freeze in anticipation of the shock. A forgetful mouse, on the other hand, would go about its usual business.

Castellano says the mice that had received umbilical cord plasma froze more often.

“We were, first of all, surprised and excited that there was something in human plasma, and more specifically there’s something exciting about cord plasma,” he says.

After a series of other experiments, Castellano and his colleagues concluded that one protein, called TIMP2, in human umbilical cord blood was likely responsible for the improvement.

When they removed TIMP2 from cord plasma and injected the plasma into mice, they didn’t observe any improvement on the memory tests. And when they injected plasma containing TIMP2 into elderly mice, they again observed improvement in memory and learning tasks.

“The really exciting thing about this study, and previous studies that have come before it, is that we’ve sort of tapped into previously unappreciated potential of our blood — our plasma — and what it can do for reversing the harmful effects of aging on the brain,” says Castellano.

It’s an intriguing hint at how potential therapies might someday work to prevent age-related illness, including Alzheimer’s disease, from developing.

“The desired outcome is overall whole body rejuvenation,” says Aubrey de Grey, a biomedical gerontologist who founded the SENS Research Foundation.

The study by Castellano and colleagues, he says, is an “excellent” starting point.

“The only thing, of course, is that it’s a mouse experiment and mouse experiments often don’t actually translate faithfully into the human setting,” he says.

And Castellano agrees that this finding does not mean that people should start sprinkling TIMP2 protein on their cereal or signing up for umbilical cord transfusions.

First off, he says, there’s no evidence that elderly humans would experience the same effects as the mice did in this study. It’s also unclear what would happen to mice if they received the plasma for more than just a few weeks.

There’s also the nagging worry that, while proteins like TIMP2 may be beneficial for developing babies, they could be harmful in older humans.

“Maybe there’s a reason that older brains aren’t exposed to certain proteins any longer,” says Castellano.

And Irina Conboy, who studies aging and degenerative diseases at the University of California, Berkeley, points out that the TIMP2 protein is actually present in higher levels in people with Alzheimer’s disease.

That runs counter to the argument made by Castellano and colleagues that TIMP2 is associated with improved memory and learning, and that TIMP2 levels would drop as people age.

“TIMP2 is a very well-known protein,” she says. She also notes that one of Castellano’s co-authors, Tony Wyss-Coray, is the board chair for a company called Alkahest, which has separately studied plasma injections as a potential treatment for Alzheimer’s.

And, Conboy says, there is no indication that the TIMP2 Castellano and colleagues detected in mouse brains actually came from the injections of human plasma. It’s unclear, she says, whether a protein in plasma could actually make its way from a mouse’s bloodstream into its brain, or that, once there, it could actually impact brain function.

Last year, Conboy published a study in which she and colleagues swapped half of the blood in old mice with that of young mice, and vice versa. They saw signs of regeneration in the muscles and liver.

But, says Conboy, “There was zero positive effect on the brain. The mice were not smarter. They did not learn better.”

Such conflicting results reflect two fundamentally different ways of thinking about aging.

From the point of view of Castellano and colleagues, aging involves a loss of beneficial materials; for example, diminishing amounts of proteins that were once present in the plasma.

To Conboy, however, “The problem is not that you run out of positive things, but that you accumulate negative things.”

She and others hold that proteins likely accumulate with old age, sometimes inhibiting certain functions, including the growth of new cells.

“We have hundreds of proteins that change with age,” she says, and finding a way to reduce the effects of aging will likely require tinkering with a huge bouquet of them.

“If you are looking for miracles, it will not come from [injecting] bodily fluids,” she says. “There will not be one silver bullet.”

Scientists find giant, elusive clam known as ‘the unicorn of mollusks’

For hundreds of years, biologists knew of the giant shipworm only from shell fragments and a handful of dead specimens. Those specimens, despite being preserved in museum jars, had gone to mush. Still, the shipworm’s scattered remains made an outsize impression on biologists. Its three-foot-long tubular shells — the shipworm isn’t technically a worm but a bivalve — were so striking that Swedish taxonomist Carl Linnaeus included the animal in his book that introduced the scientific naming system “Systema Naturae.”

And yet no one could get their hands on a living example of the giant shipworm, or Kuphus polythalamia. Unlike with other shipworms, named because they ate their way into the sides of wooden boats, no one knew where the giant shipworm lived.

“It’s sort of the unicorn of mollusks,” Margo Haygood, a marine microbiologist at the University of Utah, told The Washington Post.

The habitat of the world’s longest clam is a mystery no longer. As Haygood and her colleagues reported Monday in the Proceedings of the National Academy of Sciences, the search for the giant shipworm has come to an end.

Television news in the Philippines dealt the mortal blow to the shipworm’s near-mythical status. A TV station aired a short documentary segment about strange shellfish living in a lagoon. The show filmed the mollusks growing in the muck, as though someone had planted rows of elephant tusks. As luck would have it, a colleague of Haygood’s in the Philippines caught wind of the segment. Researchers investigated the lagoon, where they plucked a live shipworm from the mud, slipped it along with some seawater into a PVC pipe and shipped the animal to a laboratory.

“I’ve been studying shipworms since 1989 and in all that time I had never seen a living specimen of Kuphus polythalamia,” Daniel Distel, a co-author of the new study and the director of Northeastern University’s Ocean Genome Legacy Center, wrote in an email. “It was pretty spectacular to lift that tube out of its container for the first time.”

Distel carefully chipped away at the giant shipworm’s massive shell. Smaller shipworms are fleshy pink, beige or white, as are most clams. Not the giant shipworm. Its body is black.

“To see this giant gunmetal black specimen was amazing,” Distel said. “On the one hand I was pretty excited to see what it looked like inside. On the other hand it was a little intimidating to dissect this incredibly rare specimen.”

ADVERTISING

A full-grown giant shipworm reaches up to three feet long, which means that when draped across the width of a twin bed, the clam would just barely fit. “It’s quite heavy. It’s like picking up a tree branch or something even heavier,” Haygood said. “The living animal is just magnificent.”

What’s more, the giant shipworm barely has a digestive system. “It’s not feeding in any normal way,” Haygood said.

The clam has a mouth and a small stomach, but its gills are supersize. Living within those gills are bacteria. That’s not unusual for shipworms: The clams, as a rule, have symbiotic relationships with microbes. Usually, though, the microbes help shipworms digest wood.

In the case of the giant shipworm, the scientists found grains of sulfur packed into the bacteria. The marine biologists suspect that, at some point in the shipworm’s evolution, the animal traded its wood-digesting bacteria for bacteria that feed off sulfur compounds.

The study “provides a fascinating example of symbiont displacement, a phenomena we are only just beginning to observe more regularly in nature, thanks to advances in sequencing which have provided us with the tools to unravel the evolutionary history of microbes,” said Nicole Dubilier, director of the Max Planck Institute for Marine Microbiology, who was not involved in the study. “What we are now seeing is unexpected: symbioses are not as stable as we previously assumed.”

The symbiotic arrangement between microbe and giant shipworm was similar to one found in deep-sea hydrothermal vents. Thousands of feet below the surface, beyond the reaches of sunlight, tube worms also get their nutrients from bacteria that consume sulfides. Despite their similar names, though, tube worms and shipworms aren’t close relatives. Tube worms are annelids — they’re actual worms, like earthworms, not clams.

CONTENT FROM THE NATIONAL ASSOCIATION OF REALTORS®
Quiz: What do today’s homebuyers really care about?
Learn what matters most to them and see how you stack up.

But the symbiotic bacteria in both deep-sea worms and the lagoon-living clams are related to each other. “So this is a case of convergent evolution,” Distel said. That is, both the worms and clams independently arrived at the same conclusion: Housing bacteria inside their bodies was a fine way to stay nourished.

Haygood said the presence of the sulfide-consuming bacteria suggested that the lagoon, perhaps filled with rotting wood or other organic matter, produced hydrogen sulfide.

The discovery lends support to a hypothesis proposed by Distel in 2000 about the origins of animals that live in deep-sea vents. In Distel’s theory, mussels that lived in wood and harbored the sulfide-eating bacteria might have sunk to the vents. Far below, they flourished on sulfide released from the vents.

“Wood provided an ecological bridge, helping them to invade the vents,” he said. The discovery of the new shipworm indicated that shallow lagoons could have served as the location for the switch in bacteria types: First the wood served directly as food for clams. But once the clams began to take in the sulfur-loving bacteria, the wood provided a source of the hydrogen sulfide for the microbes.

“This is an extremely rare example where we were actually able to find fairly direct evidence about how this particular symbiosis evolved,” in which the clams traded one type of bacteria for the other, Distel said.

Researchers Find A New Way To Make Water From Thin Air

Researchers have come up with a new way to extract water from thin air. Literally.

This isn’t the first technology that can turn water vapor in the atmosphere into liquid water that people can drink, but researchers from the Massachusetts Institute of Technology and the University of California, Berkeley, say their approach uses less power and works in drier environments.

The new approach makes use of a substance called a MOF, a metal-organic framework. As the name suggests, these are materials made of metals mixed with organic compounds. Powders made from MOFs are very porous, so researchers have proposed using them to store hydrogen or methane fuels or to capture carbon dioxide.

MIT’s Evelyn Wang and her Berkeley colleague Omar Yaghi decided to try using MOFs to capture water. MOF powders can not only suck up liquid water, they can also absorb water vapor.

And there’s plenty of water vapor in the atmosphere. Even in the driest place on the planet there are tons of water molecules floating overhead.

The researchers built a small prototype water collector that contains a thin layer of MOF powder. The powder absorbs water vapor until it is saturated.

“Once you achieve that maximum amount,” Wang says, “you apply some type of heat to the system to release that water.”

And when the water is released, it collects in the bottom of the prototype.

There are other compounds that can suck water from the air, zeolites for example, but Wang says it takes a significant amount of energy to get these materials to release the water. Not so with a MOF device. “The amount of energy required is very low,” she says.

In the prototype, the heat needed to drive the water out of the MOF comes from ambient sunlight — no external power supply is needed.

As they report in the journal Science, Wang and her colleagues tested the prototype of their MOF-based device on the roof of a building at MIT, and it worked great.

But it’s just a prototype. It only used a fraction of an ounce of the MOF powder. “So the amount of water that we’ve shown is also pretty small,” says Wang.

According to Wang’s calculations, a full-sized system using about 2 pounds of MOF powder could deliver close to three quarts of water per day.

And she expects scaling up the prototype won’t be all that expensive. Although MOFs are a relatively new material, “there are companies that already make various MOFS at very large bulk scales,” she says.

There are many steps before a mass-produced MOF-based water collector becomes a reality. It hasn’t been shown, for example, that the water released by the MOF powder is free of contaminants.

But it’s conceivable that someday if you’re visiting Death Valley, one of the driest places in the United States, you’ll be able to wet your whistle with a device based on Wang and Yaghi’s concept.

No Ant Left Behind: Warrior Ants Carry Injured Comrades Home

This wounded ant (Megaponera analis), with two termites clinging to it, is alive but likely too exhausted after battle to get back to the nest without help.

Frank et al./Science Advances

Leave no man behind. That’s an old idea in warfare — it’s even part of the Soldier’s Creed that Army recruits learn in basic training.

And never leaving a fallen comrade is also the rule for some warriors who are ants, according to a report published Wednesday in the journal Science Advances.

These ants, Megaponera analis, hunt and eat termites. Scouts will go out, find a group of termites, and then return to the ant nest to muster the troops.

Biologist Erik Frank explains that 200 to 500 ants will march out in formation. “Like three ants next to each other, in a 2-meter-long column,” he says. “It’s very peculiar and it looks like a long snake walking on the ground.”

When the termites spot this invading army, they try to escape, but the fighting is fierce.

“And after roughly 20 minutes the battle is over,” says Frank, a doctoral student with the University of Würzburg in Germany who is researching animal behavior and evolution. “You have a lot of termites lying dead on the ground,” he says, “and the ants start collecting the termites to return.”

A few years ago, Frank was working at a field station in the Ivory Coast when he noticed that some of the ants marching home after battle weren’t carrying termites. Instead, they were carrying other ants.

“And I was wondering, ‘What exactly was going on there? Why were they carrying some of the ants?'” he recalls.

It turns out, those transported ants weren’t dead — they were injured.

Ants sometimes lose a leg or two, which makes it hard for them to walk. Or, they can be weighed down by a dead termite whose jaws had clamped onto them. Either way, they’re slower than uninjured, unburdened ants.

By marking these injured ants with paint, Frank learned that in nearly all cases, they made a full recovery after being carried home to recuperate. They learn to walk with fewer legs, and their ant buddies apparently will pull off stuck termites. It doesn’t take long for an ant that’s been hurt to once again be ready for action.

Ant Rescue

An injured ant (circled in red) that’s missing two legs is carried back by nestmates during the return journey from a termite raid.

“We saw them again, participating in hunts the next day,” says Frank.

He and his colleagues did some experiments to see what would happen to injured ants that weren’t carried home. It turns out that these poor ants couldn’t march fast enough. So they fell behind — and frequently got eaten by spiders and other predators, the researchers report.

It’s not so far-fetched, says Frank, to compare these ant rescue missions to those performed by human soldiers.

“One big difference I would say, though, is that these ants are not doing it out of the goodness of their heart,” says Frank.

He says they’re just responding to a chemical signal from the injured ants, rather than being motivated by empathy.

Peggy Mason, a neurobiologist at the University of Chicago who has studied how rats will rescue other rats from traps, says this is a great study that confirms that ants will rescue each other in certain situations.

“Does it remind me of mammalian helping? Well, not really,” she says, noting that the ants don’t seem to be intentionally helping each other.

“One reason why one might think that they’re not is that if they encounter that same injured ant on the way to the hunt, they ignore it,” Mason says. Wounded ants only get carried home if they’re encountered after the battle.

Rats, in contrast, seem to have some sort of emotional response that triggers helping. Mason and her colleagues have found that giving rats an anti-anxiety drug seemed to take away their urge to release a distressed rat from a trap.

“None of them helped,” she says. “They didn’t help. They didn’t see a problem.”

It’s clear that bringing injured warriors home has huge benefits for the ant colony.

“The number of ants that are saved by this behavior is about equivalent to the number of ants that are born each day in that colony.” Mason says. “So they’re making this substantial contribution to the ant colony through this rescue behavior. That’s probably what drove this behavior to be selected for, and to evolve into a stable behavior.”

After all, she notes, “this is an army. They’re going off to attack the termites. It’s a battle. And the more numerous you are, the more successful you are.”

Octopuses can basically edit their own genes on the fly

You’re a complex organism. You socialize with family and friends, you solve puzzles and make choices. Humans may be some of the most cerebral animals on the planet, but we know we’re not alone in having this sort of behavioral complexity. Crows use tools. Primates create incredible social structures. Whales congregate.

But all of these critters have one thing in common: they’re vertebrates. Members of our subphylum share more than just a backbone; our common ancestor gifted us with the sort of structure and central nervous system that lends itself to behavioral complexity.

And then there are cephalopods. They can solve a shocking number of complex puzzles, suggesting a cognition that rivals those found in the vertebrate world—even though they last shared a common ancestor with us at least 500 million years ago. In the world of invertebrates, octopuses, squid, and cuttlefish stand apart.

We may finally have some idea why. According to a study published in Cell, these creatures have an uncanny ability to manipulate the instructions found within their DNA. An unprecedented panache for RNA editing may explain why cephalopods are so bright and adaptable.

You probably remember RNA from your high school biology class. DNA is like a blueprint of genetic instructions laid out for us at conception. DNA is stable and sequestered (mostly) in the nucleus, keeping genetic information safe to pass it on to the next generation, while its single-stranded sibling RNA translates those directions into marching orders. When DNA says “we should produce these proteins at this time”, RNA goes out into the world of the cytoplasm and makes it happen.

But sometimes RNA rebels. Sometimes enzymes intervene, pulling out the RNA adenosine bases that code for certain proteins and replacing them with inosine bases instead. When this happens, the RNA can be ‘edited’ to produce a different protein than the one called for by the DNA.

“About 25 years ago, people identified the first example of RNA editing in mammals. There were a few cases where you’d see the DNA saying one thing and then see the actual protein was different,” says study co-author Eli Eisenberg, a biophysicist at Tel Aviv University in Israel. Eisenberg co-lead the study with Joshua Rosenthal at the Marine Biological Laboratory, though both point to Tel Aviv’s Noa Liscovitch-Brauer as the driving force behind the research.

For a couple decades, Eisenberg says, study of this phenomenon was limited to a handful of cases found by accident. But in recent years, scientists have made a more systematic approach—and found that humans occasionally use this genetic trick, too. But for us, it’s a rare occurrence. We have many sites where editing could occur, but most are located on parts of the genome with ‘junk’ DNA that doesn’t code for anything. Of the 1,000 or so coding sites where editing could take place, only a few dozen exist in places where the editing would likely have an important impact.

Squid, which have the same number of genes, have around 11,000 of these useful sites.

The new study, which tracked down the RNA editing sites in several species of cephalopod, built upon earlier research that found that octopuses use RNA editing to rapidly adapt to temperature changes, and that extensive editing occurs in squid neural tissue. In examining additional species, the researchers determined that this boon of editable RNA is almost universal among cephalopods—and the exceptions that prove the rule provide some fascinating clues.

All members of the “coleoid” subclass—squid, cuttlefish, octopuses—that the researchers examined had this boost in RNA editing. But the chambered nautilus, which is considered a primitive beast in comparison to its whip-smart cousins, had much lower levels of RNA editing. An even more distant mollusk cousin (not a cephalopod) tested for comparison had similarly low levels.

Because so much of the RNA editing occurs in brain tissue, the researchers think this correlation could indicate that the process helps give some cephalopods their smarts. Exactly how or why this process occurs is a question for future studies. But one thing is for certain: RNA editing can make a species incredibly flexible.

“For us, generally when we have a gene, the coding can be improved through mutation. That’s the general picture of evolution, where a mutation comes along to adapt the protein to the needs of the organism,” Eisenberg says. “But when you change the DNA, it’s hardwired. You change it, and that’s that.”

The process of RNA editing is much more adaptable.

“You might edit the RNA in one tissue, say, the brain, and not in another, like the muscle,” Eisenberg explains. “You can have the old protein produced under normal conditions, and a new one when you’re under stress. You can edit it or not to varying levels—you can have the edited and unedited version in the same cell, working together.”

Researchers have already seen that octopuses who have to adapt to changing temperatures use RNA editing to do so, but the possibilities are truly endless. Eisenberg and his colleagues hope to investigate other environmental changes—like ocean acidification, a growing concern in the age of climate change—to see what kind of whacky adaptations a cephalopod might implement as needed.

So if RNA editing is such a cool trick, why don’t humans do it more often?

“That’s a question we can just now start to answer, because now we have these animals who do it all the time to compare ourselves to,” Eisenberg says. “But we do have some idea of the price that they pay.”

It seems likely that cephalopods have made a serious evolutionary trade-off: In order to maintain the flexibility of extensive RNA editing, they may have given up the ability to make hardwired genetic changes by way of mutation. In other words, their evolution may be stunted. This is because the structures that allow RNA editing to occur are complex and must sit in precisely the right part of the genome. The sorts of mutations that help humans adapt and survive from generation to generation would likely hinder a cephalopod’s ability to undertake on-the-fly editing with such aplomb.

“These results fit well with what has been characterized previously in cephalopods, but are otherwise unexpected from what we know about other animals, highlighting the importance of studying many different organisms to learn about how biological systems work,” says Carrie Albertin, a researcher at the University of Chicago who was not involved in the new study. Albertin, part of the team that sequenced the octopus genome for the first time, hopes the results can help give us insight into the largest brains in the invertebrate world. “These findings are very exciting.”

So basically, cephalopods continue to be weird as hell. Hopefully future studies can help us figure out just how and when they undertook this fascinating evolutionary strategy—and whether it truly is the secret to their brilliance.