Building blocks of DNA and RNA could have appeared together before life began on Earth

Did RNA and DNA arise at around the same time in the first life forms?

Scientists for the first time have found strong evidence that RNA and DNA could have arisen from the same set of precursor molecules even before life evolved on Earth about four billion years ago.

The discovery, published April 1 in Nature Chemistry, suggests that the first living things on Earth may have used both RNA and DNA, as all cell-based life forms do now. In contrast, the prevailing scientific view -- the "RNA World" hypothesis -- is that early life forms were based purely on RNA, and only later evolved to make and use DNA.

"These new findings suggest that it may not be reasonable for chemists to be so heavily guided by the RNA World hypothesis in investigating the origins of life on Earth," says co-principal investigator Ramanarayanan Krishnamurthy, PhD, associate professor of chemistry at Scripps Research.

Krishnamurthy and his lab worked on the study with the lab of John Sutherland, DPhil, of the UK Medical Research Council's Laboratory of Molecular Biology at Cambridge, as part of the New York-based Simons Foundation's Collaboration on the Origins of Life.

RNA (ribonucleic acid) and DNA (deoxyribonucleic acid) are chemically very similar, but chemists have never been able to show how the one could have been converted to the other on the early Earth, except with the help of enzymes produced by early organisms. Due in part to this lack of a demonstrated pre-life or "pre-biotic" chemical path connecting RNA to DNA, researchers in this field have been inclined to think that the simpler, more versatile one, RNA, was the basis for the first life forms -- or at least for an early stage of life prior to the emergence of DNA. RNA is able to store genetic information as DNA can, is able to catalyze biochemical reactions as protein enzymes can, and otherwise probably could have performed the basic biological tasks that would have been necessary in the first life forms.

Although origin-of-life researchers in recent decades have largely come to embrace the RNA World hypothesis, Sutherland, Krishnamurthy, Harvard's Jack Szostak and others have accumulated evidence that RNA and DNA may have arisen more or less all at once in the first life forms.

In a study published in 2017 for example, Krishnamurthy and colleagues at Scripps Research identified a compound that plausibly was present on the pre-biotic Earth and could have performed the crucial task of linking RNA building blocks into larger, chain-like RNA strands -- and could have done the same for the building blocks of DNA and proteins.

In the new study, the scientists combined insights from that investigation with recent findings from Sutherland and his lab on a compound called thiouridine. The latter was likely present on Earth before life arose, and could have been a chemical precursor of the nucleoside building blocks of early RNAs. The team showed that in a few chemical-reaction steps, which plausibly could have occurred in a pre-biotic world, they could convert this precursor of an RNA building-block into a DNA building block -- deoxyadenosine, which forms the letter "A" in the modern, four-letter DNA code. Alternatively they could convert thiouridine into deoxyribose, which is very closely related to deoxyadenosine and may also have been a precursor of early DNA building blocks.

The finding should make it easier for scientists to accept the possibility that DNA and RNA arose together and were included in the first life forms. Some researchers including Sutherland have suggested that RNA and DNA might even have been mixed together to make the first genes. No such organism is known to occur naturally now, but a recent paper by Scripps Research's Peter Schultz, PhD and colleagues described an engineered bacterium that can survive with genes made of an RNA/DNA mix.

Krishnamurthy suspects that, however life arose, RNA and DNA with their respective strengths and shortcomings would swiftly have sorted themselves into the rather strict division of labor seen in all cells today: DNA for the stable long-term storage of genetic information, and RNA for its own special set of tasks including the short-term storage and transport of genetic information and the making of proteins.

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Researchers tap rare pristine air to reveal pollution's impact

Data was collected by a research aircraft zigzagging between pristine air over the Amazon rainforest and polluted air nearby.

Five years ago, researchers spent three hours packed aboard a steamy Gulfstream-1 research aircraft as it zig-zagged between pristine air over the Amazon rainforest and polluted air nearby. It was like a trip back (and forth) through time, as scientists weaved between the two vastly different settings, snagging air samples characteristic of today's industrial environment as well as samples of unpolluted air, like that before the industrial age.

An international team of scientists led by Manish Shrivastava of the U.S. Department of Energy's Pacific Northwest National Laboratory has analyzed some of the data and found that human-caused pollution spurs the production of climate-changing particles known as secondary organic aerosols much more than previously thought. The team published its results in Nature Communications.

The findings illustrate how pollution from cars, power plants and other sources combines with natural emissions from trees in the Amazon to spur a marked increase in tiny particles that can reflect or absorb sunlight, help create clouds, change rainfall patterns, and determine how carbon flows between the land and atmosphere -- all with dramatic effects on our planet.

The result comes from a research campaign, known as GOAmazon, led by the Atmospheric Radiation Measurement Research Facility, a Department of Energy Office of Science user facility. The campaign focused on the region near and around Manaus, a Brazilian city of more than 2 million people that is surrounded by tropical forests for hundreds of miles. Scientists refer to the vast forest canopy around Manaus as a "Green Ocean," giving the campaign's name its first letters.

The region offers a research environment hard to find anywhere else on earth. On one side of an undefined boundary is a straight-up tropical rainforest with crystal-clear air and levels of 300 aerosol particles per cubic centimeter; on the other side is the air over Manaus, with particle concentrations 100 times higher due to human activity.

"To really understand how pollution has influenced the atmosphere, we need to compare today's atmosphere with times before the industrial age," said Shrivastava. "This is challenging; of course, we cannot go back in time. But the Amazon is one of the few places on earth where we can study atmospheric chemistry both past and present simultaneously."

On that sunny day five years ago, the ARM aircraft ambled from one side of the boundary to the other, flying about the length of a football field every second, taking air samples from the pristine and then the polluted.

"The region provides a wonderful natural laboratory to understand how anthropogenic emissions have an impact on atmospheric chemistry and climate," said Shrivastava.

While only a tiny sliver of our planet provides the unique opportunity for this study, the findings apply to atmospheric chemistry that takes place everywhere on earth every moment.

This chemistry is behind the refreshing scents of a forest meadow or fresh flowers. When those scents hit our olfactory nerve, we're actually sensing an array of gases, such as carbon-containing isoprene and terpenes, which are given off naturally by trees and other vegetation. The gases contribute to ozone and other forms of haze that affect the amount of sunlight reaching the earth.

When these natural carbon emissions interact in sunlight with nitrogen oxide -- naturally emitted from soils but also a common product largely emitted by human activity -- one result is the formation of tiny particles known as secondary organic aerosols. Though aerosols are tiny, much smaller than the width of a human hair, they are no bit players when it comes to earth's climate. They're an important component in the planet's energy and carbon cycles, determining in part the fate of the planet's vast reservoir of carbon and how it flows between the land and the atmosphere.

Shrivastava and colleagues sought to learn how anthropogenic emissions increase the production of these naturally occurring carbon particles -- just how extensive the effects of human activity are in spurring the transformation of gases ejected from vegetation to these powerful climate-changing particles.

The team integrated this data with other laboratory measurements to develop an advanced computer model to simulate chemical reactions that form particles in the atmosphere. The model does double duty, reproducing both pre-industrial and present-day chemistry. Most models have largely been created based on present-day conditions; the Amazon measurements provide information about pre-industrial chemistry conditions that improved the model's predictive abilities.

The team found that nitrogen oxide emitted from human activities like traffic and oil refineries promotes the creation of these particles from natural forest carbon much more than previously thought, causing an average increase of anywhere from 60 to 200 percent and even up to 400 percent in some cases. That's compared to the 20 percent previously estimated by scientists based on data in more polluted continental locations.

The team also showed that most of these secondary carbon-containing particles were formed by this phenomenon.

"The impact of pollution in creating secondary organic aerosols has been very difficult to tease out," says Shrivastava. "Our findings indicate the earth's atmosphere in many continental locations has already been substantially altered by human activities, and there's a much larger and widespread impact than has been appreciated."

In their paper, Shrivastava and the other authors conclude: "Our results provide a clear picture of how anthropogenic emissions are likely to have greatly modified biogenic SOA [secondary organic aerosol] formation since preindustrial times over the Earth, and imply that rapid urbanization in future years might substantially enhance biogenic SOA formation in the pristine forested regions of the Amazon."

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Dark matter is not made up of tiny black holes

The Milky Way galaxy (left) and the Andromeda galaxy (right) are separated by 2.6 million light years. Compared with the areas where stars are clustered together, dark matter is believed to be distributed over a much larger volume.

An international team of researchers has put a theory speculated by the late Stephen Hawking to its most rigorous test to date, and their results have ruled out the possibility that primordial black holes smaller than a tenth of a millimeter make up most of dark matter. Details of their study have been published in this week's Nature Astronomy.

Scientists know that 85 per cent of the matter in the Universe is made up of dark matter. Its gravitational force prevents stars in our Milky Way from flying apart. However, attempts to detect such dark matter particles using underground experiments, or accelerator experiments including the world's largest accelerator, the Large Hadron Collider, have failed so far.

This has led scientists to consider Hawking's 1974 theory of the existence of primordial black holes, born shortly after the Big Bang, and his speculation that they could make up a large fraction of the elusive dark matter scientists are trying to discover today.

An international team of researchers, led by Kavli Institute for the Physics and Mathematics of the Universe Principal Investigator Masahiro Takada, PhD candidate student Hiroko Niikura, Professor Naoki Yasuda, and including researchers from Japan, India and the US, have used the gravitational lensing effect to look for primordial black holes between Earth and the Andromeda galaxy. Gravitational lensing, an effect first suggested by Albert Einstein, manifests itself as the bending of light rays coming from a distant object such as a star due to the gravitational effect of an intervening massive object such as a primordial black hole. In extreme cases, such light bending causes the background star to appear much brighter than it originally is.

However, gravitational lensing effects are very rare events because it requires a star in the Andromeda galaxy, a primordial black hole acting as the gravitational lens, and an observer on Earth to be exactly in line with one another. So to maximize the chances of capturing an event, the researchers used the Hyper Suprime-Cam digital camera on the Subaru telescope in Hawaii, which can capture the whole image of the Andromeda galaxy in one shot. Taking into account how fast primordial black holes are expected to move in interstellar space, the team took multiple images to be able to catch the flicker of a star as it brightens for a period of a few minutes to hours due to gravitational lensing.

From 190 consecutive images of the Andromeda galaxy taken over seven hours during one clear night, the team scoured the data for potential gravitational lensing events. If dark matter consists of primordial black holes of a given mass, in this case masses lighter than the moon, the researchers expected to find about 1000 events. But after careful analyses, they could only identify one case. The team's results showed primordial black holes can contribute no more than 0.1 per cent of all dark matter mass. Therefore, it is unlikely the theory is true.

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'Molecular surgery' reshapes living tissue with electricity but no incisions

A new noninvasive process can alter the curve of a cornea from that seen in blue in a) to the new position seen in red in b) to fix vision problems.

Traditional surgery to reshape a nose or ear entails cutting and suturing, sometimes followed by long recovery times and scars. But now, researchers have developed a "molecular surgery" process that uses tiny needles, electric current and 3D-printed molds to quickly reshape living tissue with no incisions, scarring or recovery time. The technique even shows promise as a way to fix immobile joints or as a noninvasive alternative to laser eye surgery.

The researchers will present their results today at the American Chemical Society (ACS) Spring 2019 National Meeting & Exposition.

"We envision this new technique as a low-cost office procedure done under local anesthesia," says Michael Hill, Ph.D., one of the project's principal investigators, who will discuss the work at the meeting. "The whole process would take about five minutes."

Hill, who is at Occidental College, became involved in this project when Brian Wong, M.D., Ph.D., who is at the University of California, Irvine, asked for help in developing a noninvasive technique to reshape cartilage. Such a method would be useful for cosmetic surgery procedures, such as making a nose more attractive. But the method also could help fix problems, such as a deviated septum, or conditions for which no good treatments exist, such as joint contractures caused by stroke or cerebral palsy. Having suffered through painful deviated septum surgery himself, Hill understands what patients go through, and was excited to join a project to develop a better strategy.

Wong was already an expert in one alternative technique that uses an infrared laser to heat cartilage, making it flexible enough to reshape. "The problem is, that technique is expensive, and it's hard to heat the cartilage enough so that it's malleable without killing the tissue," Hill says. To find a more practical approach, Wong's team began experimenting with passing current through cartilage to heat it up. The method indeed allowed them to reshape tissue, but, curiously, not by warming it. Wong turned to Hill to determine just how the new method was working and to refine it to prevent tissue damage.

Cartilage is made up of tiny rigid fibers of collagen loosely woven together by biopolymers. Its structure resembles spaghetti that's been randomly dumped on a counter, with the individual strands tied together with thread. "If you picked it up, the strands wouldn't fall apart, but it would be floppy," Hill says. Cartilage also contains negatively charged proteins and positively charged sodium ions. Cartilage with a greater density of these charged particles is stiffer than cartilage with a lower charge density.

Hill's group discovered that passing current through cartilage electrolyzes water in the tissue, converting the water into oxygen and hydrogen ions, or protons. The positive charge of the protons cancels out the negative charge on the proteins, reducing charge density and making the cartilage more malleable. "Once the tissue is floppy," he says, "you can mold it to whatever shape you want."

The team tested the method on a rabbit whose ears normally stand upright. They used a mold to hold one ear bent over in the desired new shape. If they had then removed the mold without applying a current, the rabbit's ear would have sprung back into its original upright position, just like a human ear would. But by inserting microneedle electrodes into the ear at the bend and pulsing current through them with the mold in place, they briefly softened the cartilage at the bend site without damage. Turning off the current then allowed the cartilage to harden in its new shape, after which the mold was removed.

To achieve this outcome with traditional methods, a surgeon would have to cut through the skin and cartilage and then stick the pieces back together. That can lead to formation of scar tissue at the joint. That scar tissue must sometimes be removed in subsequent operations, Hill says. By avoiding this mechanical damage to the cartilage, the molecular surgery technique causes no scarring and no pain.

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Researchers find ancient Maya farms in Mexican wetlands

UC assistant professor Christopher Carr examines an ancient quarry in Yaxnohcah, Mexico.

Archaeologists with the University of Cincinnati used the latest technology to find evidence suggesting ancient Maya people grew surplus crops to support an active trade with neighbors up and down the Yucatan Peninsula.

They will present their findings at the annual American Association of Geographers conference in Washington, D.C.

The Mayan civilization stretched across portions of Mesoamerica, a region spanning Mexico and Central America. The oldest evidence of Maya civilization dates back to 1800 B.C., but most cities flourished between 250 and 900 A.D. By the time Spanish ships arrived in the 1500s, some of the biggest cities were deserted. Researchers at UC are trying to piece together the life history of the Maya before the Spanish conquest.

Nicholas Dunning, a professor of geography in UC's McMicken College of Arts and Sciences, was part of a research team that found evidence of cultivation along irregular-shaped fields in Mexico that followed the paths of canals and natural water channels at a place called Laguna de Terminos on the Gulf of Mexico. The archaeologists expect to find evidence of habitation when they begin excavations.

The extensive croplands suggest the ancient Maya could grow surplus crops, especially the cotton responsible for the renowned textiles that were traded throughout Mesoamerica.

"It was a much more complex market economy than the Maya are often given credit for," Dunning said.

Local workers brought the Laguna de Terminos site to the attention of researchers about seven years ago.

"A forester working in the area said there seemed to be a network of ancient fields," Dunning said. "I looked on Google Earth and was like, 'Whoa!' It was an area in the Maya Lowlands that I'd never paid any attention to. And obviously not a lot of other people had, either, from the perspective of looking at ancient agriculture."

Satellite images revealed a patchwork quilt of blocks along drainage ditches that suggested they were built. Archaeologist also studied imagery NASA created of the region using a tool called Light Detection and Ranging, or LIDAR, that can depict the contours of the ground beneath the leafy canopy of trees and vegetation. Their review confirmed Dunning's suspicions: the area was covered in ancient farm fields.

"It appears they developed fairly simply from modifications of existing drainage along the eastern edge of the wetlands," Dunning said. "They probably deepened and straightened some channels or connected them in places, but then further expanded the fields with more sophisticated hydro-engineering."

LIDAR gives scientists a never-before-seen picture of the Earth's surface even after centuries of unchecked jungle growth conceals the remains of ancient structures. Researchers look for telltale signs of human activity: squares and rectangles indicating old foundations and circular pits from human-made reservoirs and quarries where the chert used in stone tools was mined. On the LIDAR maps, any hidden structures pop out, including ancient roads and former villages.

"That's the magic of LIDAR," UC assistant research professor Christopher Carr said.??Carr spent a career practicing engineering before returning to UC to study and eventually teach in the geography department. He approaches questions about the ancient Maya from an engineer's perspective.

Carr pointed to a map of Yaxnohcah, Mexico, showing a small reservoir the ancient Maya apparently dug in a wetland far from cultivated fields or known settlements.

"What were my ancient counterparts thinking when they built that water reservoir? What did they want to accomplish?" he asked.

Carr also used the LIDAR imagery in the project to follow an ancient Maya road that perhaps hasn't been traveled in more than 1,000 years. The road is perfectly visible on the LIDAR map but is virtually impossible to discern when you are standing right on it, Carr said.

"There's vegetation everywhere. But when you've been doing this for a while, you notice little things," Carr said. "I'll have a LIDAR image on my smartphone that shows me where I am, but I don't see anything but rainforest. You just walk back and forth until you can feel something underfoot and follow it."

Identifying possible roads is important for another interest of the UC researchers: ancient Maya marketplaces. Dunning and Carr are working at Yaxnohcah with researchers such as Kathryn Reese-Taylor from the University of Calgary and Armando Anaya Hernandez from Universidad Autónoma de Campeche to unlock the mysteries of the ancient Maya economy. Additionally, they and graduate student Thomas Ruhl have been analyzing NASA's LIDAR imagery across the Yucatan Peninsula to identify more ancient marketplaces.

Unlike pyramids or even many homes, marketplaces had no foundations or permanent structures, researchers said. They were built on low platforms or cleared areas, perhaps like a seasonal fair or flea market. But they were an important part of life in Maya culture

Dunning said the presence of roads between Maya cities would lend credence to the value the ancient Maya placed on trade with their neighbors. He thinks some of the larger squares identified on the LIDAR maps represent these open markets.

"In some areas, they have this very distinct physical signature," Dunning said. "So far, we've identified several possible marketplaces. We don't know for sure that they're marketplaces, but they have an architectural layout that is suggestive of one."

Soil analysis at other locations identified evidence of ancient butcher shops and stone masons. Dunning solicited the help of UC's botanists who are conducting analyses that might shed light on his marketplace hypothesis. But the LIDAR maps themselves are instructive.

"I look at spatial patterns. If you look at these big structures and small pyramids, you can tell they're important structures," Carr said. "And then you have this 'lightweight' thing next to it. That's what a marketplace looks like to me."

Dunning said the ancient Maya likely sold perishable goods such as maize and a starchy tuber called manioc. And they traded "mantas," or bolts of the ornate and richly patterned textiles made from the cotton they grew. These were prized by the Spaniards who arrived in the 1600s.

"We don't have direct evidence of what the textiles look like in this area. But if you look at ancient paintings and sculptures, people were wearing very elaborate garments," Dunning said.

Dunning first explored the historic sites of the Yucatan Peninsula at age 14 when he and his older brother drove down to Mexico from Illinois.

"We took a train to the Yucatan and used public transportation to get around to the sites," Dunning said.

He applied to the University of Chicago partly because it offered a Mayan language class. Dunning returned to Mexico while in college to conduct his first field research. He's been back many times since.

"My interest in archaeology is in human-environment interactions, including agriculture," Dunning said.

Dunning is learning more about how ancient Maya people shaped their world to overcome challenges and take advantage of natural opportunities. Dunning's work also took him to a place called Acalan near the Gulf of Mexico.

"Roughly translated, Acalan means 'place of canoes' because it's very watery," Dunning said. "And getting around by water is far easier than any other means in that area."

Then as now the region is covered in thick tropical rainforest. Researchers have to be wary of cheeky monkeys that will throw fruit or worse from the treetops. Carr said one encounter left him sore for days.

"There was this aggressive spider monkey. He'd seen me a couple days earlier. And he's back shaking the trees," Carr said. "And all of a sudden, I'm lying flat on the ground. A branch hit me in the shoulder and knocked me to the ground."

Visiting archaeologists at Yaxnohcah stay at a former Army outpost that was converted into a staffed research station.

"Living conditions are actually luxurious by camping standards. You're in the field all day and you're dirty and tired. But you can take a shower. And when you're finished, someone has cooked you a meal," Carr said.

At Laguna de Terminos, UC researchers are working to collect clues about the ancient Maya before they are lost to development. Many of the wetlands are being drained or plowed up for grazing pasture.?

Dunning said ironically these low-yield pastures provide far less economic value to today's farmers than the seeming bounty of crops the ancient Maya derived from them more than 1,000 years ago. Their study warns the land-use practices are causing environmental damage to some of these valuable wetlands.

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Climate change is a threat to dolphins' survival

This is a dolphin mother and calf in Shark Bay.

An unprecedented marine heatwave had long-lasting negative impacts on both survival and birth rates on the iconic dolphin population in Shark Bay, Western Australia. Researchers at UZH have now documented that climate change may have more far-reaching consequences for the conservation of marine mammals than previously thought.

Shark Bay in Western Australia in early 2011: A heatwave causes the water temperatures to rise to more than four degrees above the annual average. The extended period caused a substantial loss of seagrass, which drives the Shark Bay ecosystem, in this coastal area, a UNESCO world heritage site.

Researchers from UZH have now investigated how this environmental damage has affected survival and reproduction of dolphins. They used long-term data on hundreds of animals collected over a ten-year period from 2007 to 2017. Their analyses revealed that the dolphins' survival rate had fallen by 12 percent following the heatwave of 2011. Moreover, female dolphins were giving birth to fewer calves -- a phenomenon that lasted at least until 2017.

Negative influence of the heatwave is unprecedented

"The extent of the negative influence of the heatwave surprised us," says Sonja Wild, former PhD candidate at the University of Leeds and first author of the study. "It is particularly unusual that the reproductive success of females appears to have not returned to normal levels, even after six years." There are several possible explanations for this phenomenon, for instance neglect of calves, increased newborn mortality, delayed sexual maturity or a combination thereof, but researchers have not yet been able to investigate them in detail.

Tool-using dolphins are less affected

Interestingly, the heatwave did not have the same effect on all dolphin groups. Dolphins that use sponges as tools -- a socially learned foraging technique that helps dolphins to locate food in deep water -- were not as badly affected as those that do not use this technique. "Nevertheless, our work raises concerns that such sudden events might have quite negative long-term effects even in groups of marine mammals that are known to adapt usually well to novel environmental conditions," says Sonja Wild.

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Complex artefacts don't prove brilliance of our ancestors

Artefacts such as bows and arrows do not necessarily prove our ancestors had sophisticated reasoning and understanding of how these tools worked, new research suggests.

Artefacts such as bows and arrows do not necessarily prove our ancestors had sophisticated reasoning and understanding of how these tools worked, new research suggests.

Instead, such items could have emerged from an "accumulation of improvements made across generations" -- with each generation understanding no more than the last.

The new study, by the University of Exeter and the Catholic University of Lille, does not question humanity's capacity for "enhanced causal reasoning" -- but argues this did not necessarily drive the development of technologies such as bows, boats and houses.

Researchers used "chains" of volunteers to tackle an engineering problem, with each volunteer able to learn from the last. Solutions improved with each "generation" -- but those at the end of the chain had no more understanding of key concepts than their predecessors.

"We tend to explain the existence of complex technologies by saying humans have big brains and superior causal reasoning abilities," said Dr Maxime Derex, of the University of Exeter and the Catholic University of Lille.

"But -- as our study shows -- you don't have to understand how something works in order to improve it.

"Artefacts from hundreds or thousands of years ago do not necessarily show that their makers had a plan or a theory about how something would work."

The study used 14 chains of five French university students, each aiming to optimise a wheel that rolled down a track -- moving faster or slower depending on the adjustment of moveable weights on its four spokes.

Each participant had five attempts to minimise the time it took for the wheel the reach the end of the track, and all but the first participant in each chain got details of the last two configurations used by the previous person.

Afterwards, researchers tested each participant's understanding by asking them to predict which of two wheels would cover the distance faster.

The study found: "The average wheel speed increased across generations while participants' understanding did not."

A further 14 chains of students completed the same process, but this time they could write down a theory to pass to the next participant.

Wheel speed rose at a similar rate as that seen in groups who passed on no written instructions, but once again understanding "barely changed across generations."

The researchers said: "Most participants actually produced incorrect or incomplete theories despite the relative simplicity of the physical system."

The findings prove the power of "cultural transmission, without the need for an accurate causal understanding of the system," they said.

"Our experiment indicates that one should be cautious when interpreting complex archaeological materials as evidence for sophisticated cognitive abilities such as reasoning, problem solving or planning, since these abilities are not the sole driver of technological sophistication," said Dr Alex Mesoudi, of the University of Exeter.

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Calculating temperature inside moon to help reveal its inner structure

The moon.

Little is known about the inner structure of the Moon, but a major step forward was made by a University of Rhode Island scientist who conducted experiments that enabled her to determine the temperature at the boundary of the Moon's core and mantle.

She found the temperature to be between 1,300 and 1,470 degrees Celsius, which is at the high end of an 800 degree range that previous scientists had determined.

"In order to understand the interior structure of the Moon today, we needed to nail down the thermal state better," said Ananya Mallik, a URI assistant professor of geosciences who joined the University faculty in December 2018. "Now we have the two anchor points -- the core-mantle boundary and the surface temperature measured by Apollo -- and that will help us create a temperature profile through the Moon. We need that temperature profile to determine the internal state, structure and composition of the Moon."

The surface temperature of the Moon is approximately -20 C.

According to Mallik, the Moon has an iron core, like that of Earth, and previous research using seismic data had found that between 5 and 30 percent of the material at the boundary of the core and mantle was in a liquid or molten state.

"The big question is, why would we have some melt present in the Moon at that depth," Mallik said.

To begin to answer this question, Mallik conducted a series of experiments in 2016 at the Bavarian Research Institute of Experimental Geochemistry and Geophysics in Germany using a multi-anvil device that can exert the high pressures found deep inside the Moon. She prepared a tiny sample of material similar to that found on the Moon, squeezed it in the device at 45,000 times the Earth's atmospheric pressure, which is the pressure believed to exist at the Moon's core-mantle boundary, and used a graphite heater to raise the temperature of the sample until it partially melted.

"The goal was to determine what temperature range would produce a 5 to 30 percent melt, which would tell us the temperature range of the core-mantle boundary," she said.

Now that the temperature range at the boundary has been narrowed, scientists can begin to develop a more precise temperature profile of the Moon and proceed to determine a profile of the minerals that make up the mantle from its crust to its core.

"It's important that we know the composition of the Moon to better understand why it has evolved as it has," Mallik said. "The histories of the Earth and Moon have been intertwined since the beginning. In fact, both are the product of a great collision between proto-Earth and an approximately Mars-sized body that occurred over 4.5 billion years ago. So to understand our Earth better, we have to know our nearest neighbor because we all had a common start.

"Earth is complicated," she continued. "Any similarity in the composition between Earth and the Moon can give us insight into how these two planetary bodies were formed, what were the energetics of the collision, and how elements were partitioned between them."

The URI geoscientist noted that Earth has evolved through the process of plate tectonics, which is responsible for the distribution of the continents, the topography of Earth's surface, the regulation of long-term climate, and perhaps even the origin of life. But there is no evidence of plate tectonics on the Moon.

"Everything on Earth happens because of plate tectonics," she said. "What does this tell us about our own planet when the Moon doesn't experience this process? It's the same argument for why we study Mars and Venus. They are our next closest neighbors, and we all had a common start, but why are they so different from our planet?"

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Biophysicists use machine learning to understand, predict dynamics of worm behavior

Caenorhabditis elegans.

Biophysicists have used an automated method to model a living system -- the dynamics of a worm perceiving and escaping pain. The Proceedings of the National Academy of Sciences (PNAS) published the results, which worked with data from experiments on the C. elegans roundworm.

"Our method is one of the first to use machine-learning tools on experimental data to derive simple, interpretable equations of motion for a living system," says Ilya Nemenman, senior author of the paper and a professor of physics and biology at Emory University. "We now have proof of principle that it can be done. The next step is to see if we can apply our method to a more complicated system."

The model makes accurate predictions about the dynamics of the worm behavior, and these predictions are biologically interpretable and have been experimentally verified.

Collaborators on the paper include first author Bryan Daniels, a theorist from Arizona State University, and co-author William Ryu, an experimentalist from the University of Toronto.

The researchers used an algorithm, developed in 2015 by Daniels and Nemenman, that teaches a computer how to efficiently search for the laws that underlie natural dynamical systems, including complex biological ones. They dubbed the algorithm "Sir Isaac," after one of the most famous scientists of all time -- Sir Isaac Newton. Their long-term goal is to develop the algorithm into a "robot scientist," to automate and speed up the scientific method of forming quantitative hypotheses, then testing them by looking at data and experiments.

While Newton's Three Laws of Motion can be used to predict dynamics for mechanical systems, the biophysicists want to develop similar predictive dynamical approaches that can be applied to living systems.

For the PNAS paper, they focused on the decision-making involved when C. elegans responds to a sensory stimulus. The data on C. elegans had been previously gathered by the Ryu lab, which develops methods to measure and analyze behavioral responses of the roundworm at the holistic level, from basic motor gestures to long-term behavioral programs.

C. elegans is a well-established laboratory animal model system. Most C. elegans have only 302 neurons, few muscles and a limited repertoire of motion. A sequence of experiments involved interrupting the forward movement of individual C. elegans with a laser strike to the head. When the laser strikes a worm, it withdraws, briefly accelerating backwards and eventually returning to forward motion, usually in a different direction. Individual worms respond differently. Some, for instance, immediately reverse direction upon laser stimulus, while others pause briefly before responding. Another variable in the experiments is the intensity of the laser: Worms respond faster to hotter and more rapidly rising temperatures.

The researchers fed the Sir Isaac platform the motion data from the first few seconds of the experiments -- before and shortly after the laser strikes a worm and it initially reacts. From this limited data, the algorithm was able to capture the average responses that matched the experimental results and also to predict the motion of the worm well beyond these initial few seconds, generalizing from the limited knowledge. The prediction left only 10 percent of the variability in the worm motion that can be attributed to the laser stimulus unexplained. This was twice as good as the best prior models, which were not aided by automated inference.

"Predicting a worm's decision about when and how to move in response to a stimulus is a lot more complicated than just calculating how a ball will move when you kick it," Nemenman says. "Our algorithm had to account for the complexities of sensory processing in the worms, the neural activity in response to the stimuli, followed by the activation of muscles and the forces that the activated muscles generate. It summed all this up into a simple and elegant mathematical description."

The model derived by Sir Isaac was well-matched to the biology of C. elegans, providing interpretable results for both the sensory processing and the motor response, hinting at the potential of artificial intelligence to aid in discovery of accurate and interpretable models of more complex systems.

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Seeds inherit memories from their mother

This is a seed of Arabidopsis thaliana at the beginning of germination.

Seeds remain in a dormant state -- a temporary blockage of their germination -- as long as environmental conditions are not ideal for germination. The depth of this sleep, which is influenced by various factors, is inherited from their mother, as researchers from the University of Geneva (UNIGE), Switzerland, had previously shown. Today, they reveal in the journal eLife how this maternal imprint is transmitted through small fragments of so-called 'interfering' RNAs, which inactivate certain genes. The biologists also reveal that a similar mechanism enables to transmit another imprint, that of the temperatures present during the development of the seed. The lower this temperature was, the higher the seed's dormancy level will be. This mechanism allows the seed to optimize the timing of its germination. The information is then erased in the germinated embryo, so that the next generation can store new data on its environment.

Dormancy is implemented during seed development in the mother plant. This property allows the seeds to germinate during the appropriate season, to prevent all the offspring of a plant from developing in the same place and competing for limited resources, and to promote plant dispersal. Seeds also lose their dormancy at variable times. "Subspecies of the same plant can have different levels of dormancy depending on the latitudes at which they are produced, and we wanted to understand why," explains Luis Lopez-Molina, Professor at the Department of Botany and Plant Biology of the UNIGE Faculty of Science.

The paternal gene is silenced

Like all organisms with sexual reproduction, the seed receives two versions of each gene, a maternal and a paternal allele, which may have different levels of expression. The UNIGE biologists had shown in 2016 that the dormancy levels of Arabidopsis thaliana, a model organism used in laboratories, are inherited from the mother. Indeed, in the seed, the level of expression of a dormancy regulating gene called allantoinase (ALN) is the same as that of the maternal allele. This implies that it is the maternal allele of ALN that is mainly expressed, to the detriment of the paternal allele.

In the current study, the researchers show that this maternal imprint is transmitted by an epigenetic mechanism, which influences the expression of certain genes without altering their sequence. The paternal allele of ALN is 'silenced' by biochemical modifications called methylations, which are carried out in the promoter region of the gene in order to inactivate it.

"These methylations are themselves the result of a process in which different enzymatic and factor complexes are involved, as well as small fragments of so-called 'interfering' RNA. This is a unique example of genomic imprinting, because it is made in the absence of the enzyme usually responsible for methylation," says Mayumi Iwasaki, researcher in the Geneva group and the first author of the article.

The imprint of past cold prevents the seed from awakening

The environmental conditions present during the seed formation also leave their mark, as its dormancy level increases with decreasing temperatures. "We have discovered that, in this case, both alleles of the ALN gene are strongly repressed in the seed. This is due to a similar epigenetic mechanism, but not all of the actors are the same as those used to silence the paternal allele," says Luis Lopez-Molina.

This imprint of the cold enables the seed to keep information on past temperatures, in order to include them in the choice of the optimal time of germination. After germination, the ALN gene is reactivated in the embryo. The memory of the cold will then be cleared, allowing the counters to be reset for the next generation.

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