f(R) modified gravity

Realistic simulations of galaxy formation in f(R) modified gravity

Nature Astronomy (2019)

Future astronomical surveys will gather information that will allow gravity to be tested on cosmological scales, where general relativity is currently poorly constrained. We present a set of cosmological hydrodynamical simulations that follow galaxy formation in f(R) modified gravity models and are dedicated to finding observational signatures to help distinguish general relativity from alternatives using this information. The simulations employ the IllustrisTNG model and a new modified gravity solver in AREPO, allowing the interplay of baryonic feedback and modified gravity to be studied in the same simulation, and the degeneracy between them in the matter power spectrum to be resolved. We find that the neutral hydrogen power spectrum is suppressed substantially in f(R) gravity, which allows this model to be constrained using upcoming data from the Square Kilometre Array. Disk galaxies can form in our f(R) gravity simulations, even in the partially screened regime, and their galaxy stellar properties are only mildly affected. We conclude that modified gravity allows the formation of realistic galaxies and leaves observable signatures on large scales.

 

Debate over Hubble constant

Debate intensifies over speed of expanding universe

By Joshua Sokol |

This week, leading experts at clocking one of the most contested numbers in the cosmos—the Hubble constant, the rate at which the universe expands—gathered in hopes that new measurements could point the way out of a brewing storm in cosmology.

No luck so far. A hotly anticipated new cosmic yardstick, reliant on red giants, has served only to muddle the debate about the actual value of the constant, and other measurements brought no resolution. “It was the craziest conference I’ve been to,” said Daniel Scolnic, an astrophysicist at Duke University in Durham, North Carolina. “Everyone felt like they were on this rollercoaster.”

The meeting, at the Kavli Institute for Theoretical Physics in Santa Barbara, California, was the latest episode in a saga stretching back to the 1920s, when Edwin Hubble established that the farther one looks into space, the faster galaxies are speeding away from Earth. Since then, scientists have devoted entire careers to refining the rate of that flow, Hubble’s eponymous constant, or H0. But recently, the problem has hardened into a transdisciplinary dispute.

On one side are cosmologists who gather data from the greatest distances, such as a map of the big bang’s afterglow recorded by the European satellite Planck. They compare the apparent size of features in that afterglow with their actual size, as predicted by theory, to calculate an H0 of about 67. That means distant galaxies should be flying away from the Milky Way 67 kilometers per second faster for every additional megaparsec astronomers gaze out into space.

But when astronomers look at actual galaxies, using delicate chains of inferences to make up for the universe’s frustrating lack of tick marks, they get a different number. Over the past few years, a team led by Nobel laureate Adam Riess from Johns Hopkins University in Baltimore, Maryland, has cataloged standard candles: astrophysical objects with a known brightness, whose distance can be calculated based on how bright they appear from Earth. The team uses the supernovae explosions of white dwarf stars as standard beacons to measure distances far out into the swelling universe; they calibrate the brightness of nearby supernovae by monitoring variable stars, called cepheids, in the same galaxies. The stars’ light waxes and wanes at a rate that signals their intrinsic brightness. Earlier this year, this team, dubbed SH0ES, reported an H0 of about 74, a standard-bearing measurement for the astronomers’ side.

If the discrepancy between the cosmologists and the astronomers can’t be chalked up to a subtle, hidden methodological flaw, modern physics itself could be due for a revision. Theorists, salivating at the possibility, have begun to dream up hidden ingredients in the early universe—new particles or interactions—that could patch over the gulf. But they haven’t found a fix that doesn’t cause new problems. With stakes that high, astronomers put their heads together in Santa Barbara to double and triple check the SH0ES result against other ways to measure the constant.

A team called H0LiCOW relied on gravitational lenses, freak cosmic alignments where the light from a very distant, flickering beacon called a quasar is bent into multiple images on the sky by the gravity of another, intervening galaxy. Each image is formed by light traveling along a different path across expanding space. Because of that, though, the flickers don’t all arrive at Earth at the same time. Based on the time delays and not-so-simple geometry, the team calculated the H0 from six different such systems and came up with a value of roughly 73—“very close” to the SH0ES results, says Geoff Chih-Fan Chen, a team member at the University of California, Davis. The team didn’t check its final number—published just before the meeting on the preprint server arXiv—until the very end of its analysis to avoid bias, Chen says. “Some people will unconsciously want to get the right answer.”

One point for possible new physics. But the meeting brought a twist. On the first evening, the Carnegie-Chicago Hubble Program team, led by Wendy Freedman, a veteran H0 measurer at the University of Chicago in Illinois, uploaded its own long-anticipated paper—already accepted to The Astrophysical Journal—to arXiv. Freedman’s team sought to develop a new type of standard candle. “If we put all our eggs in the cepheid basket,” Freedman says, “we will never uncover our unknown unknowns.”

Instead, her team looked toward old, swollen stars called red giants. These stars have already exhausted the hydrogen fuel at their hearts, converting it to a core of helium that sits, inert, as a hydrogen shell around the core continues to burn. The star, seen from afar, grows brighter and brighter. But at a certain, predictable limit the temperature and pressure in the core grow high enough to burn helium, too, generating an explosive flash of energy that rearranges the interior of the star, ultimately causing it to begin to dim. By finding the very brightest red giants in a distant galaxy—the ones that toe this theoretical limit—the team could use them as standard candles to calculate distances and its own H0.

One day after the paper appeared, Freedman presented the result to the meeting: a surprisingly low H0 of about 70. “It definitely felt like an album drop,” says Scolnic, a SH0ES team member. The value was stuck between the competing sides—and slightly favored the cosmologists. “It has caused at least some people to pause for a second, and say, ‘Well, maybe it’s not as clear cut,’” Freedman says.

The SH0ES team had huddled together as soon as Freedman’s paper came out, and members were ready to question some of her team’s underlying premises after her talk. They also pointed to a trio of other, if less-precise, Hubble results debuted in Santa Barbara that rely on independent astrophysical concepts—clouds of water circling the centers of faraway galaxies, other kinds of variable stars, and the rate at which the luminosities of galaxies fall off from their center to their edge.

A combined measurement that averaged all these astronomical results together still gave a value of 73. Unless hidden biases still lurk in the data, the gulf between that value and the cosmologists’ lower number remains near or above the 5σ statistical standard physicists use to divide possible flukes from the real deal.

In Riess’s mind, at least, astronomers are nearing a consensus that the Hubble gulf highlights a true difference between the ancient and more recent universe. “You’re left with a problem, discrepancy, crisis,” Riess says. “The biggest argument at the meeting, I thought, was about what word to use.”

 

Spektr-RG x-ray observatory

Telescope designed to study mysterious dark energy keeps Russia’s space science hopes alive

By Daniel Clery |

At 6:31 p.m. local time on 13 July, Russia’s Spektr-RG x-ray observatory was launched from the Baikonur Cosmodrome in Kazakhstan. It will begin a 4-year survey of the x-ray sky.

Russia’s beleaguered space science program is hoping for a rare triumph this month. Spektr-RG, an x-ray satellite to be launched on 21 June from Kazakhstan, aims to map all of the estimated 100,000 galaxy clusters that can be seen across the universe. Containing as many as 1000 galaxies and the mass of 1 million billion suns, the clusters are the largest structures bound by gravity in the universe. Surveying them should shed light on the evolution of the universe and the nature of the dark energy that is accelerating its expansion.

First proposed more than 30 years ago as part of a Soviet plan for a series of ambitious “great observatories” along the lines of NASA’s Hubble Space Telescope, Spektr-RG fell victim to cost cutting in cash-strapped, post-Soviet Russia. But roughly €500 million satellite, which will carry German and Russian x-ray telescopes, was reborn early last decade with a new mission: not just to scan the sky for interesting x-ray sources, such as supermassive black holes gorging on infalling material, but to map enough galaxy clusters to find out what makes the universe tick. The new goal meant further delays. “There have been many ups and downs,” says Peter Predehl, leader of the team at the Max Planck Institute for Extraterrestrial Physics (MPE) in Garching, Germany, that built one of the satellite’s two telescopes. “Whenever we thought we were out of the woods, a new one came along.”

Spektr-RG was born in the late 1980s. Glasnost was encouraging Soviet researchers to collaborate with Western colleagues, and studies of SN 1987A, the nearest supernova in modern times, had demonstrated the power of x-rays for tracing such violent events. Rashid Sunyaev of Moscow’s Space Research Institute (IKI) proposed an x-ray observatory to orbit above Earth’s atmosphere, which blocks x-rays. The 6-ton mission soon bristled with five telescopes and involved 20 institutes in 12 countries including the United States. But after the collapse of the Soviet Union, Roscosmos struggled to keep its Mir space station aloft and contribute to the growing International Space Station (ISS). “They told us the spacecraft was too large for Russia, too ambitious,” says Sunyaev, now at the Max Planck Institute for Astrophysics in Garching. “It just died.”

Resurrection began in 2003 with plans for a smaller mission with a U.K.-built all-sky x-ray monitor and MPE’s x-ray survey telescope, called ROSITA—which had been destined for the ISS but was grounded by the Challenger space shuttle disaster. The new impetus was cosmology. Studies of distant supernovae in the 1990s had revealed that the expansion of the universe is accelerating. Researchers wanted to know more about dark energy, the mysterious force that was causing it, and whether it varied in space or over time. Galaxy clusters are among the best indicators, says x-ray astronomer Andrew Fabian of the Institute of Astronomy (IoA) in Cambridge, U.K. “Clusters are the most massive objects in the universe, the pinnacle of galaxy formation, and are very sensitive to cosmological models.”

They are best seen in x-rays because the gaps between galaxies are filled with gas that is heated to millions of degrees as the galaxies jostle together to form a cluster. By mapping the clusters, says Esra Bulbul of the Harvard-Smithsonian Center for Astrophysics in Cambridge, Massachusetts, who recently joined the MPE team, Spektr-RG “will study the evolution of the structure of the universe.”

The challenge was to boost the capabilities of the existing ROSITA telescope, which could only garner up to 10,000 galaxy clusters. Discussions led to a €90 million “extended” eROSITA, paid for by MPE and the German Aerospace Center, DLR. It is an array of seven identical telescopes with five times the effective collecting area of the original instrument. Russia and Germany signed an agreement in 2007 with launch penciled in for 2012.

But mission development was not smooth. The U.K. instrument failed to win funding and was replaced with a Russian telescope, called ART-XC, which will complement eROSITA by detecting scarcer high energy x-rays. Though harder to collect, the higher energy photons are particularly useful for seeing the supermassive black holes at galactic centers, because they pierce the clouds of gas and dust that shroud them.

Making the mirrors for eROSITA also proved much harder than expected. Because x-rays would penetrate a traditional flat telescope mirror, focusing them requires cylindrical mirrors that gather x-ray photons in glancing, low-angle reflections off inner surfaces. Each of eROSITA’s seven scopes contains 54 gold-plated cylindrical mirrors, nested inside one another, that must be shaped precisely to bring the photons to a focus. Making them proved so difficult that the MPE team had to fire its main contractor part way through. “It almost killed us,” Predehl says.

A decision to site the telescope at a quiet, gravitationally balanced point beyond the moon, outside the shelter of Earth’s magnetic field, meant electronics had to be hardened against solar radiation. Incompatibility between the German and Russian electronics delayed the launch, as did problems with the spacecraft’s communications system and a change in launch rocket.

Now that Spektr-RG is finally ready, expectations are high. “It’s going to be revolutionary in terms of numbers,” says IoA astronomer George Lansbury, taking x-ray studies into “the big data regime.”

It may also be a rare high point for Russia’s great observatories program. Previously, only one has made it into orbit: 2011’s Spektr-R, a radio astronomy mission that fell short of expectations and could not be revived after malfunctioning earlier this year.

Astronomers may face a long wait for Spektr-RG’s successors: the ultraviolet telescope Spektr-UV and Spektr-M, a millimeter-wave radio telescope. Spektr-UV has survived moments of near-death, most recently in 2014 when Russia’s annexation of Ukraine’s Crimean peninsula caused major Ukrainian partners to withdraw. The mission is now slated for a 2025 launch, but, Sunyaev says, some collaborators, including a German team supplying a spectrograph, have dropped out. Spektr-M, which would come next, is not yet fully funded, he says. And in the meantime, rival telescopes launched by other countries may scoop up the science the Russian missions aim to do.

“Russia is doing as much as possible with the budget available,” says Spektr-RG chief Mikhail Pavlinsky of IKI. He notes that Roscosmos’s lean budget, worth $20.5 billion over 10 years, faces multiple demands. Russia is building the landing system for the European ExoMars rover, due to launch next year, and like other countries it hopes to return to the moon with the Luna 25 lander in 2021. For Russia’s astrophysicists, Pavlinksy says, “It means slow progress.”

 

HD 139139: A Bizarre Star

Astronomers Don’t Know What to Make of This Incredibly Bizarre Star

Unusual dips of light observed by the Kepler space telescope have so far confounded attempts at an explanation.

Here in this isolated corner of the Milky Way, our Earth-bound human lives might seem tiny and parochial on a galactic scale. But the universe—vast, deep and presumably infinite—can always be counted on to deliver the unexpected.

Within the bounty of information from the Kepler space telescope, a now-retired exoplanet-hunting observatory, astronomers have spotted a peculiar star whose characteristics defy many of their preconceived notions. After staring at the data about it for more than a year, the team who discovered the strange object, named HD 139139, still does not know what to make of it.

“We’ve never seen anything like this in Kepler, and Kepler’s looked at 500,000 stars,” says Andrew Vanderburg, an astronomer at the University of Texas at Austin and co-author of a new paper on the star, posted to the preprint server ArXiv.

The space-based Kepler telescope, which ended its mission in October 2018, examined light from stars for periodic dips in their brightness—which are usually presumed to indicate a planet passing in front of their face. Astronomers analyze the observatory’s data using algorithms that search for these repeating eclipses of starlight.

But some of these patterns are too complex for computers to tease out; volunteer citizen scientists also comb through the Kepler catalogue, using the human brain’s power to uncover surprising signals. In the spring of 2018 some of these layperson astronomers contacted Vanderburg and told him to check out HD 139139, a sunlike star roughly 350 light-years away.

“When I got that e-mail, I looked more closely and said, ‘okay, this definitely looks like a multiplanet system. But I can’t find any [planets] that appear to line up,'” he recalls.

The star had 28 distinct dips in its light, each of which lasted between 45 minutes and 7.5 hours—and none of which seemed to repeat. The patterns looked more like noise than signal, and at first the team thought it might be some kind of instrument glitch. Yet after careful reanalysis, the data seemed to check out as real.

The first astronomical explanation was that HD 139139 was surrounded by a bunch of planets, at least 14 and perhaps as many as 28—an astounding number, far greater than any known system. Based on their almost-identical light curves, these worlds would all be nearly the same size: slightly bigger than Earth.

The issue is that the extremely short duration of the dips in light suggested that any putative exoplanets would be passing quickly in front of the star, indicating close-in orbits. For none of them to repeat in the 80 days Kepler stared at the star strained credulity.

Another possibility was that a second body—a large planet or unseen star—was tugging gravitationally on the obscurants, causing them to sometimes hasten or delay their eclipsing and produce what looked like a random pattern. But such an object would also be pulling on the central star. After observing HD 139139 with ground-based telescopes, the team found no indication it was being tugged in this way.

The researchers looked into the idea that a planet might be disintegrating in front of the star, producing clouds of dust that would sometimes create dips and other times would not. Such cases have been seen in a small handful of systems, but in all of those examples astronomers were still able to identify the evaporating planet’s orbital period.

Finally, the team wondered if there were short-lived starspots (cooler patches analogous to sunspots) that suddenly appeared and disappeared on HD 139139’s face—a situation nobody had really seen before. Vanderburg says this idea was considered mostly because he and his colleagues felt uncomfortable writing up a paper that did not include some kind of natural explanation.

He says one more possibility was left out of the paper, albeit an extremely unconventional one: an extraterrestrial mega-engineering project blocking the star’s light. Similar speculations arose in 2015, when citizen scientists discovered a Kepler star with odd patterns and notified astronomer Tabetha Boyajian at Louisiana State University at Baton Rouge. The light dips in that case looked intriguing enough that astrophysicist Jason Wright of Pennsylvania State University organized a campaign to listen to the object, eventually nicknamed Tabby’s star, for leaking radio transmissions. The undertaking ultimately turned up nothing unusual.

“When people in our community hear about something like this, the running joke is it might be aliens,” Vanderburg says. The possibility crossed his mind, he adds, as the seemingly-random dips reminded him of the scene in the film Contact in which Jodie Foster’s character begins hearing blips from outer space that trace out a prime number sequence.

The newly noticed star will certainly be added to the list of those investigated for signs of technological activity, Wright says. But he considers it more likely astronomers will eventually settle on an explanation that does not involve intelligent extraterrestrials.Boyajian agrees. “I think we have to consider all options before we go there,” she says. “This is one of those systems where it’s probably not going to be figured out without more data.”

Yet few other observatories can match Kepler’s extreme precision. Most ground-based telescopes are not sensitive enough to see the involved light dips, and it is difficult for researchers to reserve the relatively long stretches of time they would require on a powerful orbiting instrument such as the Hubble Space Telescope. NASA’s recently launched Transiting Exoplanet Survey Satellite (TESS) is not scheduled to look at HD 139139 during its primary campaign, though perhaps if the satellite receives an extended mission it could.

Vanderburg says he and his colleagues are hoping someone in the astronomy community will think of something they have not. In the meantime, the situation remains another example of the universe’s never-ending diversity.

“This put us in our place,” Boyajian says. “It humbles us and reminds us that we really don’t know everything.”

The Random Transiter — EPIC 249706694/HD 139139

We have identified a star, EPIC 249706694 (HD 139139), that was observed during K2 Campaign 15 with the Kepler extended mission that appears to exhibit 28 transit-like events over the course of the 87-day observation. The unusual aspect of these dips, all but two of which have depths of 200±80 ppm, is that they exhibit no periodicity, and their arrival times could just as well have been produced by a random number generator. We show that no more than four of the events can be part of a periodic sequence. We have done a number of data quality tests to ascertain that these dips are of astrophysical origin, and while we cannot be absolutely certain that this is so, they have all the hallmarks of astrophysical variability on one of two possible host stars (a likely bound pair) in the photometric aperture. We explore a number of ideas for the origin of these dips, including actual planet transits due to multiple or dust emitting planets, anomalously large TTVs, S- and P-type transits in binary systems, a collection of dust-emitting asteroids, “dipper-star” activity, and short-lived starspots. All transit scenarios that we have been able to conjure up appear to fail, while the intrinsic stellar variability hypothesis would be novel and untested.

 

Hayabusa2 collected 2nd sample

In a first, a Japanese spacecraft appears to have collected samples from inside an asteroid

By Dennis Normile |

Japan’s Hayabusa2 successfully completed its second touchdown on the asteroid Ryugu and probably captured material from its interior that was exposed by firing a projectile into the asteroid earlier this year. It is the first collection of subsurface materials from a solar system body other than the moon.

Engineers and technicians in the spacecraft’s control room near Tokyo could be seen erupting into cheers and applause on a YouTube live stream when Project Manager Yuichi Tsuda proclaimed the operation a success just before 11 a.m. local time.

At an afternoon press briefing, Tsuda said, “Everything went perfectly.” He joked that if a score of 100 indicated perfection, “I would give this a score of 1000.”

Hayabusa2 was launched by the Japan Aerospace Exploration Agency’s Institute of Space and Astronautical Science in Sagamihara, near Tokyo, in December 2014 and reached Ryugu in June 2018.

Since then it has conducted remote observations, released several rovers that hopped around on the asteroid, and made a February touchdown to retrieve surface samples. To get interior material, Hayabusa2 in April released a tiny spacecraft that exploded and sent a nonexplosive, 2-kilogram copper projectile into Ryugu, creating a crater. Subsequent remote examination of the site indicated material ejected from the crater had accumulated about 20 meters to one side.

That area became the target for the second touchdown, which occurred this morning. Engineers moved the spacecraft into position above the target site over the previous day and then placed it into autonomous mode. As the craft touched down, it fired a tantalum bullet into the surface, likely kicking dust and rock fragments into a collection horn. The craft then ascended.

The team won’t know for certain what is in the sample return capsule until it returns to Earth in December 2020. “But we expect that we obtained some subsurface samples,” said project scientist Seiichiro Watanabe, a planetary scientist at Nagoya University in Japan. They will be able to compare these subsurface samples with those collected from the surface. The team believes comparing the surface samples subjected to eons of space weathering and the more pristine material from the interior will provide clues to the origins and evolution of the solar system.

Watanabe noted that NASA’s in-progress Origins, Spectral Interpretation, Resource Identification, Security, Regolith Explorer mission also plans to bring samples from an asteroid, named Bennu, back to Earth in 2023. But at least for the near future, Japan is the only nation that will have acquired samples from both the surface and interior of an asteroid, Watanabe said. The samples “will have great significance scientifically,” he said.

Hayabusa2 will continue remote observations until December 2020. “We shouldn’t waste even a single day,” Tsuda said.

Japanese spacecraft snags second sample from asteroid

Scientists celebrated another success with Japan’s Hayabusa 2 spacecraft late Wednesday (U.S. time), when the robot explorer accomplished a second pinpoint touch-and-go landing on asteroid Ryugu, this time to collect a sample of pristine dust and rock excavated by an explosive impactor earlier this year.

Using rocket thrusters to control its descent, and guided by a laser range finder, Hayabusa 2 glacially approached Ryugu on autopilot Wednesday, slowing to a relative speed of about 4 inches per second (10 centimeters) per second in the final phase of the landing.

Hayabusa 2 maneuvered over a bright navigation aid released on the asteroid’s surface earlier this year to mark the landing site, then went in for the final descent, with the probe’s sampling horn extending from the front of the spacecraft.

Telemetry data and imagery downlinked from Hayabusa 2 show the spacecraft briefly touched down on the asteroid at 9:06 p.m. EDT Wednesday (0106 GMT; 10:06 a.m. Japan Standard Time Thursday), and began climbing away from Ryugu seconds later, pulsing its thrusters to counteract the half-mile-wide (900-meter-wide) asteroid’s feeble gravity.

In a press conference around four hours later, officials hailed the brief landing as a perfect success, following the mission’s first touch-and-go landing on Ryugu in February.

“Hayabusa 2 today executed a second touchdown, and we were able to obtain (information about) the history of the solar system,” said Yuichi Tsuda, Hayabusa 2’s project manager at the Japan Aerospace Exploration Agency.

Ground teams cheered when data streaming back from the spacecraft, currently orbiting the sun in lock-step with Ryugu more than 151 million miles (244 million kilometers) from Earth, confirmed the touchdown.

Launched in December 2014, Hayabusa 2 is Japan’s mission to travel to an asteroid and collect samples for return to Earth. Scientists are eager to analyze specimens from Ryugu, a dark asteroid rich in carbon, a critical building block of life.

Researchers will study the samples for clues about the formation of the solar system 4.6 billion years ago, and perhaps the origin of water and life on Earth.

Mission managers last month decided to send Hayabusa 2 on a second sampling run to gather bits of rock and dust from a second location on Ryugu, providing scientists with more varied materials to examine when the mission returns to Earth late next year.

Hayabusa 2’s sampling mechanism works by firing a metal bullet into the asteroid once the probe’s sampler horn contacts the surface. The projectile is designed to force bits of rock and dust through the sampler horn into a collection chamber inside spacecraft.

Takanao Saiki, Hayabusa 2’s project engineer and flight director at JAXA, told reporters in a press briefing Thursday that data downlinked by the spacecraft showed the temperature rose in the projectile’s firing mechanism at the time of landing, suggesting the system functioned as intended.

Three images taken by a camera on-board Hayabusa 2 showed the sampling horn contacting the asteroid, then violently blasting away debris from the surface. Countless tiny asteroid fragments were visible around the spacecraft in the final snapshot in the three-image sequence released by JAXA.

“The third picture is really amazing,” said Makoto Yoshikawa, Hayabusa 2’s mission manager “It’s really awesome, a large amount of chips of rocks are flying off.”

“This is a wonderful picture, I think,” Tsuda said. “Hayabusa 2 touched the surface of Ryugu, so this is evidence.”

A different view of the landing site taken by Hayabusa 2’s navigation camera shows a cloud of debris left behind moments after the spacecraft took off from the asteroid.

With its second and final sample collection complete, Hayabusa 2 started to climb back to a “home position” roughly 12 miles (20 kilometers) from the asteroid. The spacecraft closed the lid to the sample catcher device containing the asteroid pay dirt, and ground teams will later send commands to seal it inside the re-entry canister that will carry the material through Earth’s atmosphere at the end of the mission.

“There’s nothing I need to complain about, everything moved perfectly,” Tsuda said through a translator. “It was a perfect operation, so … it’s a 1,000 score out of 100.”

Not only did the specimens gathered Wednesday come from a different location on Ryugu than the first sampling run, scientists say the newly-captured materials originated from underneath the asteroid’s surface, where they may have escaped radiation and other space weathering effects for billions of years.

The pristine samples were exposed during a daring, unprecedented bombing run by the Hayabusa 2 spacecraft in April. The probe deployed an explosive charge to fire into the asteroid at high speed, carving a fresh crater and ejecting buried materials around the impact site, ripe for retrieval by Hayabusa 2.

“We decided to obtain the samples in this particular area so that we would be able to sample the subsurface materials … and because our operation was perfectly conducted, therefore, we can observe that we obtained some subsurface samples,” said Seiichiro Watanabe, Hayabusa 2’s project scientist from Nagoya University.

“Bringing the subsurface materials (back to Earth) will be something no other country can do in the coming 20 years or so,” Watanabe said.

Hayabusa 2’s sampler carrier has three chambers to separate materials gathered from each landing. Officials decided to press ahead with the second sampling run after assessing the scientific benefits and engineering risks of the maneuver, but with two samples now on-board the spacecraft, mission managers do not plan to attempt a third sampling run.

While Hayabusa 2 explores Ryugu, NASA’s OSIRIS-REx mission is surveying asteroid Bennu before moving in to collect a sample there in 2020 for return to scientists on Earth in 2023.

OSIRIS-REx is designed to bring home at least 60 grams, or 2.1 ounces of samples from Bennu, significantly more than Hayabusa 2. But OSIRIS-REx is only expected to collect a single sample from one location on Bennu’s surface.

NASA and JAXA agreed in 2014 to share their asteroid samples.

Named for a dragon’s palace in a famous Japanese fairy tale, asteroid Ryugu completes one circuit of the sun every 1.3 years. Its path briefly brings it inside Earth’s orbit, making Ryugu a potentially hazardous asteroid.

The orbit also made Ryugu an attractive candidate for a sample return mission.

The Hayabusa 2 spacecraft arrived at Ryugu in June 2018, and deployed three mobile scouts to hop around the asteroid’s surface last September and October, achieving another first in space exploration.

Hayabusa 2 will depart Ryugu in November or December and fire its ion engines to head for Earth, where it will release a re-entry capsule protected by a heat shield to land in Australia in December 2020.

“We have captured the samples,” Tsuda said. “We must make sure that it comes back to Earth, so we need to continue with the operations properly.”

Follow Stephen Clark on Twitter: @StephenClark1.

 

Cheap solar power

Giant batteries and cheap solar power are shoving fossil fuels off the grid

By Robert F. Service |

This month, officials in Los Angeles, California, are expected to approve a deal that would make solar power cheaper than ever while also addressing its chief flaw: It works only when the sun shines. The deal calls for a huge solar farm backed up by one of the world’s largest batteries. It would provide 7% of the city’s electricity beginning in 2023 at a cost of 1.997 cents per kilowatt hour (kWh) for the solar power and 1.3 cents per kWh for the battery. That’s cheaper than any power generated with fossil fuel.

“Goodnight #naturalgas, goodnight #coal, goodnight #nuclear,” Mark Jacobson, an atmospheric scientist at Stanford University in Palo Alto, California, tweeted after news of the deal surfaced late last month. “Because of growing economies of scale, prices for renewables and batteries keep coming down,” adds Jacobson, who has advised countries around the world on how to shift to 100% renewable electricity. As if on cue, last week a major U.S. coal company—West Virginia–based Revelation Energy LLC—filed for bankruptcy, the second in as many weeks.

The new solar plus storage effort will be built in Kern County in California by 8minute Solar Energy. The project is expected to create a 400-megawatt solar array, generating roughly 876,000 megawatt hours (MWh) of electricity annually, enough to power more than 65,000 homes during daylight hours. Its 800-MWh battery will store electricity for after the sun sets, reducing the need for natural gas–fired generators.

Precipitous price declines have already driven a shift toward renewables backed by battery storage. In March, an analysis of more than 7000 global storage projects by Bloomberg New Energy Finance reported that the cost of utility-scale lithium-ion batteries had fallen by 76% since 2012, and by 35% in just the past 18 months, to $187 per MWh. Another market watch firm, Navigant, predicts a further halving by 2030, to a price well below what 8minute has committed to.

Large-scale battery storage generally relies on lithium-ion batteries—scaled-up versions of the devices that power laptops and most electric vehicles. But Jane Long, an engineer and energy policy expert who recently retired from Lawrence Livermore National Laboratory in California, says batteries are only part of the energy storage answer, because they typically provide power for only a few hours. “You also need to manage for long periods of cloudy weather, or winter conditions,” she says.

Local commitments to switch to 100% renewables are also propelling the rush toward grid-scale batteries. By Jacobson’s count, 54 countries and eight U.S. states have required a transition to 100% renewable electricity. In 2010, California passed a mandate that the state’s utilities install electricity storage equivalent to 2% of their peak electricity demand by 2024.

Although the Los Angeles project may seem cheap, the costs of a fully renewable–powered grid would add up. Last month, the energy research firm Wood Mackenzie estimated the cost to decarbonize the U.S. grid alone would be $4.5 trillion, about half of which would go to installing 900 billion watts, or 900 gigawatts (GW), of batteries and other energy storage technologies. (Today, the world’s battery storage capacity is just 5.5 GW.) But as other cities follow the example of Los Angeles, that figure is sure to fall.

 

Forest against global warming

Adding 1 billion hectares of forest could help check global warming

By Alex Fox |

Global temperatures could rise 1.5° C above industrial levels by as early as 2030 if current trends continue, but trees could help stem this climate crisis. A new analysis finds that adding nearly 1 billion additional hectares of forest could remove two-thirds of the roughly 300 gigatons of carbon humans have added to the atmosphere since the 1800s.

“Forests represent one of our biggest natural allies against climate change,” says Laura Duncanson, a carbon storage researcher at the University of Maryland in College Park and NASA who was not involved in the research. Still, she cautions, “this is an admittedly simplified analysis of the carbon restored forests might capture, and we shouldn’t take it as gospel.”

The latest report from the United Nations’s Intergovernmental Panel on Climate Change recommended adding 1 billion hectares of forests to help limit global warming to 1.5° C by 2050. Ecologists Jean-Francois Bastin and Tom Crowther of the Swiss Federal Institute of Technology in Zurich and their co-authors wanted to figure out whether today’s Earth could support that many extra trees, and where they might all go.

They analyzed nearly 80,000 satellite photographs for current forest coverage. The team then categorized the planet according to 10 soil and climate characteristics. This identified areas that were more or less suitable for different types of forest. After subtracting existing forests and areas dominated by agriculture or cities, they calculated how much of the planet could sprout trees.

Earth could naturally support 0.9 billion hectares of additional forest—an area the size of the United States—without impinging on existing urban or agricultural lands, the researchers report today in Science. Those added trees could sequester 205 gigatons of carbon in the coming decades, roughly five times the amount emitted globally in 2018.

“This work captures the magnitude of what forests can do for us,” says ecologist Greg Asner of Arizona State University in Tempe, who was not involved in the research. “They need to play a role if humanity is going to achieve our climate mitigation goals.”

Adding forests wouldn’t just sequester carbon. Forests provide a host of added benefits including enhanced biodiversity, improved water quality, and reduced erosion. Estimates of how much forest restoration on this scale would cost vary, but based on prices of about $0.30 a tree, Crowther says it could be roughly $300 billion.

Exactly how much carbon future forests could store may not be crystal clear, but Duncanson says NASA has new instruments in space—like the Global Ecosystem Dynamics Investigation (GEDI) aboard the International Space Station—that will use lasers to create high-resolution 3D maps of Earth’s forests from canopy to floor. These data will add much-needed precision to existing estimates of aboveground carbon storage.

“With GEDI we can take this paper as a stepping stone and inform it with much more accurate carbon estimates,” Duncanson says. “There have always been large uncertainties on large-scale carbon totals, but we have richer data coming soon.”

 

Atmosphere of Gliese 3470 b

Astronomers probe atmosphere of alien world that’s a cross between Earth and Neptune

By Katie Camero |

Gliese 3470 b isn’t like anything in our solar system. The strange world—midway between Earth and Neptune in mass—orbits a star about half the mass of the sun roughly 100 light-years away. Now, astronomers have taken a detailed look at Gliese 3470 b’s atmosphere, the first time researchers have done so for a planet like this.

Astronomers used NASA’s Hubble and Spitzer space telescopes to measure which frequencies of starlight Gliese 3470 b absorbs and reflects as it circles around its star. The planet has a relatively thin atmosphere comprised primarily of hydrogen and helium, NASA announced yesterday. That’s similar to the atmosphere of the sun, with the exception of heavy elements such as oxygen and carbon. The planet (above) also has a hefty rocky core, the analysis reveals.

Gliese 3470 b appears to have formed close to its star, where it still sits today. This might explain why the planet was able to develop its unconventional atmosphere. One hypothesis is that it was able to corral gases from a primordial disk of gas surrounding its star. Typically when this happens, planets become giant gas worlds known as “hot Jupiters.” But Gliese 3470 b stayed relatively small, perhaps because the disk of gas dissipated before the planet was able to bulk up, the team speculates.

NASA’s new James Webb Space Telescope—Hubble’s successor set to launch in 2021—will penetrate the planet’s atmosphere to greater depths. Until then, astronomers have to solve another mystery about Gliese 3470 b: whether to call it a “super-Earth” or a “sub-Neptune.”

 

Epigenetics – not just genes

Epigenetics – It’s not just genes that make us

Written for the BSCB by Dr Ian Cowell, Institute for Cell and Molecular Biosciences, University of Newcastle-Upon-Tyne, UK

In its modern sense, epigenetics is the term used to describe inheritance by mechanisms other than through the DNA sequence of genes. It can apply to characteristics passed from a cell to its daughter cells in cell division and to traits of a whole organism. It works through chemical tags added to chromosomes that in effect switch genes on or off.

Researchers studying the microscopic roundworm Caenorhabditis elegans recently discovered a set of mutations that extended the worms’ normal 2-3 week lifespan by up to 30%. This was exciting, not least because discoveries in animals such as roundworms can sometimes help us understand processes like ageing in humans. This was not the end of the story though, as the researchers found that the descendants of the long-lived roundworms could also live longer than normal, even if they only inherited the non-mutated version of the genes from their parents. This doesn’t seem to make sense at first; surely characteristics such as hair colour, height and even how long we or a microscopic worm could potentially live are carried in the DNA sequence of the genes that we inherit from our parents. So how can we solve the conundrum of how the roundworms inherited the long lived characteristic, without inheriting the DNA sequence that initially caused it? The answer is epigenetics.

It’s not all in your DNA

In a nutshell, epigenetics is the study of characteristics or “phenotypes” that do not involve changes to the DNA sequence; and the long-lived roundworms are just one of many examples. Others, as we will see below, include how queen and worker honey bees can appear so different despite being genetically identical, how starvation in human populations may affect the health and longevity of the next generation, why all tortoiseshell cats are female and even how we all develop from a single cell (a fertilized egg) to end up with bodies containing many different types of specialised cells but which all contain the same genes and DNA sequence.

How does epigenetics work?

So epigenetics is about how genes are expressed and used, rather than the DNA sequence of the genes themselves, but how does this work? Many researchers have been studying epigenetics over the past few decades, and it is currently an area of intense research activity. We know that a part of how epigenetics works is by adding and removing small chemical tags to DNA. You can think of these tags as post-it notes that highlight particular genes with information about whether they should be switched on or off. In fact the chemical tag in question is called a methyl group (see Diagram 1) and it is used to modify one of the four bases or “chemical letters”, A, C, T and G, that makes up the genetic code of our DNA. The letter that is tagged is C or cytosine and when it is modified, or methylated it is called 5-methyl cytosine. Methyl groups are added to DNA by enzymes called DNA methyl transferases (DNMTs).

Diagram 1. Two chemical tags, methyl and acetyl groups that are central to epigenetic phenomena and the chemical structure of cytosine and 5-methyl cytosine in DNA. The pentagonal part of the molecule forms the continuous “backbone” of the DNA . Only one of the two strands of DNA that makes up the familiar double helix is shown.

Queen bee status is partly determined by fewer methyl tags

In most cases, more methylated Cs in the DNA of a gene results in the gene being switched off. Honey bees provide us with a good example of how this can work. Worker bees and the queen have very different bodies; the queen is much larger, longer lived, has an enlarged abdomen and lays many thousands of eggs, while the smaller workers are sterile but have complex foraging and communication skills. Despite this, the queen and workers in a hive are female and genetically identical. The clue to how this comes about lies in royal jelly, a secretion that is fed to some developing larvae, and which results in these larvae becoming queens rather than workers. We will come back to royal jelly and its queen-making properties later, but a fascinating piece of research showed that if the amount of the methyl group adding DNMT enzyme was artificially reduced in bee larvae, then the larvae developed into queens, even if they weren’t fed royal jelly. Thus, the switch between queen and worker can be flipped by the abundance of methyl tags on the bee larvae’s DNA. Fewer methyl tags leads to switching on of a special gene or genes in the developing larvae that results in the development of the larvae into queens and not workers.

Tags on tails also operate gene switches

DNA methyl tags are only one part of the story though. In the cells of all plants and animals, DNA is packaged or wrapped up into nucleosomes where the DNA double helix is wrapped around a central core of protein (see Diagram 2). About 150 letters-worth of DNA (or base-pairs) is wrapped around each nucleosome, and this helps package the 3 billion base pairs of genetic code into each of our cells. Nucleosomes are too small to see using conventional microscopes, but biologists use a technique called X-ray diffraction to work out the shape and organisation of objects like nucleosomes, and in 1997 this technique revealed the beautiful structure of nucleosomes at high resolution – see (http://www.rcsb.org/pdb/explore/explore.do?structureId=1aoi).

Diagram 2. The familiar DNA double helix (blue) is wrapped around nucleosomes (grey cylinders) in cells. The string of nucleosomes can be coiled into a thicker filament, called the 30 nm fibre and this can be further coiled into a still thicker chromatin fibre. When genes are switched on their nucleosomes are more uncoiled like the 10nm fibre.

Nucleosomes are compact, but the ends or “tails” of the proteins that make up the nucleosome, which are called histones, stick out from the otherwise compact nucleosome structure. Like the methyl tags on DNA, small chemical tags can also be added to these histone tails  (see Diagram 3). Two of the chemical tags that are added to these tails are acetyl groups and methyl groups. Methyl, acetyl and a few other types of tags can be added to the tails in a large number of combinations and this effects whether an underlying gene is switched on or off. In fact genes can be switched right off (this is called silencing), full on, or somewhere in between by DNA methyl tags and histone tail tags. The combination of DNA and histone tags can also effect how easily a gene is turned on or off.

Diagram 3. Chemical tags can be added to the “tails” of the histone proteins that make up nucleosomes. Grey cylinder, nucleosome; curved black lines, histone tails; green circles, methyl tags; red triangles, acetyl tags; mauve hexagons, other types of tag.

When cells divide

When cells divide, the entire DNA sequence from the original cell (3 billion base pairs contained in 23 pairs of chromosomes in a human cell) is duplicated so that both daughter cells receive an exact copy. What, you might ask, happens to all those epigenetic tags? We have known for some time that the DNA-methyl tags are copied too, so that both daughter cells have the same pattern of DNA methylation. We now know that the pattern of histone tags is also mostly duplicated as cells divide, although this is currently less well understood. Nevertheless, cell division is also a time when epigenetic tags can most easily be changed.

Return of the long-lived worm

Right at the beginning we came across the story of the long-lived microscopic worms thatpassed on their longevity to their offspring even if the individual offspring did not inherit the variant gene (mutation) that originally caused the extended lifespan. We are now in a position to explain this apparently strange result. In most cases genes contain the information to make a protein molecule, and the protein molecules might be enzymes that carry out chemical reactions in the cell, or parts of the structure of the cell itself. It turns out that the genes that were mutated in the worm study make proteins that work together to add a methyl tag to nucleosomes. This tag is an on-switch. When one or more of the genes were mutated this tag was absent and several genes that should be on, including some involved in ageing,  were switched off and the worms had a longer lifespan. The unexpected thing is that the epigenetic tags were thought to be completely erased or reset during the formation of sperm and egg, and so unlike the genes themselves they shouldn’t be passed on to the next generation. But this result and other research that shows that this is not always the case and that sometimes, the pattern of epigenetic tags are passed on.

How to make a queen

Whether a larval honey bee becomes a worker or a queen depends on an epigenetic switch, and this switch seems to be “flipped” by royal jelly. But what is it about royal jelly that leads a larva that would otherwise grow up to be a worker, to become a queen? The answer lies in understanding that the individual chemical tags that are added to the histone tails of nucleosomes are constantly being revised by the cell. Acetyl tags are added by enzymes called histone acetyl transferases and they are removed or erased by a second group of enzymes called histone deacetylases (HDACs). Both of these enzymes are present in most cells and this allows genes to be switched on or off over time.

More acetyl tags help deliver queen bee status

Recently, researchers set out to identify compounds in royal jelly that could alter this process, and what they found was something known as an HDAC inhibitor. This was a relatively simple chemical compound that is present in royal jelly and that stops the action of HDAC enzymes that normally remove acetyl tags from histones. This results in a build-up of acetyl tags in the cells of the bee embryos, and like the reduction in DNA-methyl groups described previously, this is thought to switch on key genes required for development of a queen. Without the HDAC inhibitor in the royal jelly, the larvae follow a “default” set of genetic instructions and develop into workers.
HDAC inhibitors are not only important to queen bees, but are also part of a small but growing number of  medically useful drugs that target epigenetic tags and which are useful in treating some kinds of cancer. Furthermore HDACs also have a role in the way our brains form memories, and novel drugs that affect histone acetylation may have a role in the future in treating memory impairment in elderly patients.

The environment and epigenetics

We have seen how the difference between a queen and worker bee is determined by exposure to a chemical that directly alters epigenetic tags such as acetyl groups; but are there examples where nutrition or other aspects of the environment affect human populations in a way that can be explained by epigenetics? Obviously we can’t do experiments on human populations as we can on microscopic worms or bees, but sometimes human history or natural phenomena do it for us. One such example is what is known as the Dutch Hunger Winter. In the last year of the Second World War in Europe, a food embargo imposed by occupying German forces on the civilian population of the Netherlands resulted in a severe famine, coinciding with a particularly harsh winter. About 20,000 people died from starvation as rations dropped to below 1000 kilocalories per day. Despite the chaos of war, medical care and records remained intact allowing scientists to subsequently study the effect of famine on human health. What they found was that children who were in the womb during the famine experienced a life-long increase in their chances of developing various health problems compared to children conceived after the famine. The most sensitive period for this effect was the first few months of pregnancy.  Thus, something appears to happen early in development in the womb that can affect the individual for the rest of their lives.

Epigenetic effects can sometimes pass to grandchildren

Even more surprisingly, some data seems to suggest that grandchildren of women who were pregnant during the Hunger Winter experience some of these effects. From what we have already discussed, this strongly suggests an epigenetic mechanism. In fact, research with the Dutch Hunger Winter families continues, and a recent study looking at a gene galled IGF2 found lower levels of the methyl tag in the DNA of this gene in individuals exposed to the famine before birth. Although IGF2 may not itself be involved in the increased risk of poor health in these people, it shows that epigenetic effects (i.e. reduction of the number of methyl tags on particular genes) that are produced before birth can last for many decades. Studies in animals have also found that the diet of the mother can have effects on her offspring. For example, feeding sheep a diet lacking the types of food required to make methyl groups leads to offspring with altered patterns of DNA methylation and which have higher than expected rates of certain health problems.

Epigenetics and imprinting, why genes from Mum and Dad are not always equivalent

We all have 23 pairs of chromosomes in our cells. For each pair, one came from mother and one from father.  Thus, we inherit one copy of each gene from each parent and we generally assume that the function of the gene does not to depend on which parent it came from. However, for imprinted genes things are different. For these genes, either the maternal or paternal copy of the gene is active, while the other one is kept silent. There are at least 80 imprinted genes in humans and mice, many of which are involved in growth of the embryo or the placenta. How can one copy of a gene be switched off, while the other copy in the same cell is switched on? The answer is epigenetics. Probably the most studied imprinted gene is IGF2(see above). One part of IGF2 operates as a switch.  If the DNA is methylated here the IGF2 gene can be expressed. The switch is only methylated in Dad’s copy of the gene and so only this copy is expressed, while the maternal copy is silent. This switch is thought to be set up in the gametes (eggs and sperm) so right from the start, genes received from Mum and those from Dad are labelled differently with epigenetic tags and so are not equivalent.

Imprinting and mental disorders

Angelmann and Prader-Willi syndromes are two distinct genetic conditions with different symptoms, both caused by loss of a part of chromosome 15. Children who inherit one copy of this faulty chromosome develop either Angelmann or Prader-Willi syndrome, despite having a normal copy of the chromosome from their other parent. So how does the same mutation (loss of part of chromosome 15) lead to these two different conditions? The answer lies in the discovery that this particular piece of chromosome 15 contains a number of genes that are imprinted, so only the paternal or maternal copy of these gene are expressed; which of the two syndromes appears depends on whether the deletion was in the maternal or paternally inherited chromosome. When the faulty chromosome is inherited from Dad, there is no functional copy of the imprinted genes that are switched off on the maternal chromosome 15 and the result is Angelmann syndrome and vice versa for Prader-Willi syndrome. This is quite unlike most genetic conditions such as cystic fibrosis, where an effect on development or health is only seen when a mutated gene or genes is inherited from both parents.

Boys versus Girls, how to switch off a whole chromosome

A bit of genetics that most of us know about is what makes a boy a boy, and a girl a girl. It’s the X and Y chromosomes. At the very beginning of our existence each of us received one X chromosome from our Mums via the egg, and while the girls received another X chromosome from their dads, via the sperm, the boys got a Y chromosome. The Y chromosome in the cells of a male embryo directs it to develop into a boy, while with two X and no Y chromosome the female embryo develops into a girl. Now, you might notice that there is an imbalance here. We all have two each of all the other chromosomes, but for the sex chromosomes (X and Y) the girls have two Xs while the boys only have one X (and a Y). While the Y chromosome contains few genes, mostly involved in “maleness”, the X chromosome contains quite a few genes involved in important processes such as colour vision, blood clotting and muscle function. In order to even up the “dosage” of X chromosome genes between male and female cells, one entire X chromosome is switched off in female cells. This is called X-chromosome inactivation and happens very early in the womb. In this process cells randomly switch off either the paternal or maternal X chromosome, so that when a girl baby is born her body is a mixture or chimera of cells where either the maternal or paternal X-chromosome is switched off. The way that this happens involves the type of epigenetic tags that we have discussed and it has been known for decades that female cells contain one very compact X chromosome called the Barr body that can be seen under the microscope, and this is the inactive X chromosome.

The case of the tortoiseshell cat

We are probably all familiar with tortoiseshell cats and their mottled coats with patches of orange and black fur. What you might not know is that almost all cats with this type of coat are female! The reason for this is that a gene for coat colour is located on the cat’s X chromosome. There are two versions of this gene, called “O” and “o”; one gives ginger fur and the other black. Two copies of the same version in a female cat results in ginger or black fur respectively, but one copy of each gives a tortoiseshell effect. This is down to X-chromosome inactivation. The skin of these cats is composed of patches of cells where either the maternal or paternal X chromosome is inactivated. This results in skin with the O gene switched on and o silenced in some patches (orange fur) and o gene on and O silenced in other patches (black fur), hence the tortoiseshell pattern. Since the male cats only have one X chromosome, and no X-chromosome inactivation, they are either orange or black all over.

Epigenetic inheritance, can epigenetic states be passed from one generation to the next?

As we have seen from the roundworm example, epigenetic effects (in this case extended lifespan) can sometimes be passed from one generation to the next, although the effects only seem to last for a few generations. Are there examples where epigenetic effects carry over to subsequent generations in humans or other mammals? There is some evidence that the effects of the Dutch Hunger Winter affected grandchildren of women who were pregnant during the famine. Similarly, in a study of a 19th century northern Swedish population who underwent cycles of famine and plenty, the amount of food available appears to have affected the health and longevity of the next generation.

Hair colour in mouse can be determined by an epigenetic effect

Perhaps the best known example of transgenerational epigenetic effects is provided by the mouse Agouti gene. This gene controls hair colour, and is switched on at just the right time in hair follicle cells to produce a yellow stripe in the otherwise dark hairs, resulting in what is called an agouti coat. But mice with a particular variant of the Agouti gene called Avy have coats that are anywhere between yellow and the normal dark (agouti) pattern of wild-type mice. The yellow mice also become obese and suffer other health problems. So the Avy gene seems to have a variable effect (in fact the Avy stands for Avariable yellow). How this works has puzzled geneticists for years, but we can now recognise this as an epigenetic effect. The yellow fur occurs because Avy version of the Agouti gene has faulty controls and is switched on all the time. However, methyl tags are often added to the faulty control DNA sequence and this tends to switch the gene off, resulting in mottled or dark agouti fur in individual mice. Pups born to dams with the Avy gene range in colour from yellow to dark, but the proportion depends on the coat colour of the mother; litters of dark (agouti) females are more likely to contain dark pups. Furthermore, a higher proportion of dark offspring is observed if both the mother and the grandmother have the dark colouration. So the agouti colouration, which is determined epigenetically (by the number of methyl tags on the Avy gene) can to some extent, carry through from one generation to the next.

Eggs and sperm do not usually ‘carry over’ epigenetic effects

Although we can find cases where epigenetic effects apparently last from parents to offspring, this is not usually the case and almost all of the epigenetic switches or marks are reset in germ cells (eggs and sperm) and in the very earliest stages of development of an embryo. In fact if this wasn’t the case, the amazing development of a fertilised egg into a fully formed creature would be impossible.

Getting from a fertilized egg to a fully formed human, it’s all in the (epi) genome

So far we have described some specific cases of epigenetic regulation, but we now know that epigenetics in its broad sense, (how genes are expressed and used, rather than the DNA sequence of the genes themselves) is central to how a fertilised egg can eventually give rise to a whole organism and how cells of, let’s say your skin, remain skin cells and are different from your brain cells, despite containing exactly the same genes. Shortly after fertilisation, a developing human embryo consists of a ball of cells called embryonic stem cells. Each of these cells has the capacity to give rise to any of the types of cells in the body as the embryo grows (for example, brain cells, skin cells or blood cells). By contrast, 9 months later when a baby is born, most of the cells making up his or her body are committed to be a specific type of cell with specific functions. So as the cells divide, the ball of embryonic stem cells gradually develops into all the cell types and structures of the baby at term.  For this to happen, thousands of genes must be switched on or off at just the right times and in the right cells as an embryo grows. For example, genes that make the fibrous keratin protein that gives our skin its strength, are only switched on in skin cells and not in the developing brain and genes required for brain cells to develop and make their interconnections are on in the brain but not in the skin.

During development genes have to be switched ‘on’ and ‘off’. Epigenetic tags help with this

A very big area of research today concerns how all this gene switching on an off works, and a large part of this process uses the epigenetic chemical tags, especially acetyl and methyl histone tags. In order for those embryonic stem cells to be able to give rise to all of the other types of cells, their epigenetic switches are (almost) completely reset compared to adult cells. I have put “almost” in brackets as we know from imprinted genes and transgenerational epigenetic inheritance that there are exceptions.

Epigenetics, Dolly the sheep and friends

In February 1997, a sheep called Dolly became the most famous example of her species, briefly even becoming a TV celebrity. The reason for her fame is that she was the first mammal to be “created” by a process called somatic cell nuclear transfer, or in other words the first man-made clone (man-made to be distinct from identical twins, who are natural clones). The process leading to her birth required a mature oocyte (a unfertilised egg) from one female sheep and an ordinary cell from the udder of a second sheep. First the nucleus (the part containing the DNA) was removed from the oocyte. This was done using a special microscope as although oocytes are quite big compared to other cells, they are still too small to see with the naked eye. Then the nucleus from the udder cell was inserted into enucleated oocyte. Thus, Dolly had three “mothers”: the donor of the oocyte, the donor of the udder cell and the sheep that carried the developing embryo to term. No father was involved. Although this process was, and remains, very inefficient it was the first proof that the genes from an adult mammalian cell can be “epigenetically reprogrammed” back to the state of the embryonic stem cells that can develop into any other type of cell. Subsequently the same process has been applied to other species and may have medical uses in generating cells that could repair tissues damaged by injury or disease.

Summary: the epigenome and the ENCODE project – the “Large Hadron Collider” of Biology

Whereas the term “genome” refers to the entire DNA sequence of an organism (three billion letters of it for humans), the epigenome refers to the entire pattern of epigenetic modifications across all genes, including methyl DNA tags, methyl histone tags, acetyl histone tags and other chemical tags that we have not mentioned, in each cell type of an organism. This represents an almost unimaginable amount of information, dwarfing even the human genome project. Nevertheless, knowledge of the epigenome is essential to fully answer some of the biggest questions in biology such as: how do we develop from a ball of identical cells into a whole organism? why do we age? and how can we better understand diseases such as cancer? Not surprisingly then, epigenetics and the epigenome is a big area of research. Some of the research in this field is encompassed by the ENCODE (Encyclopedia of DNA Elements) project, an ongoing venture to identify patterns of epigenetic tags in many different types of cells for the entire human genome (http://genome.ucsc.edu/ENCODE/). The ENCODE project is sometimes likened to the Large Hadron Collider or LHC in Switzerland. The LHC is the largest piece of scientific equipment ever built and the experiments physicist conduct with it aim to probe the fundamental details of the matter that makes up our Universe. Although biologists don’t have (or need) such a spectacular piece of kit for their research, the effort to examine the intricacy of the human epigenome has been likened to the LHC project because of its scale, complexity and the amount of information being created.

Epigenetic errors

Epigenetics is an area where our scientific knowledge is rapidly increasing. One thing that scientists have discovered is that epigenetic errors are common in diseases such as cancer and in ageing cells.  As a result, scientists are developing medicines that target faulty epigenomes and one of the first examples is the use of HDAC inhibitors, similar to the compound found in royal jelly. From the study of strange patterns of inheritance such as genetic imprinting, the yellow/agouti Avy mouse, the all-female tortoiseshell cat population and other related phenomena biologists have uncovered a whole new layer of information that lies “on top” of the DNA sequence of our genes. These new discoveries explain these previous puzzling observations, but also have great potential for new understanding and treatments for human disease.

Further Reading:

  • Bird, Adrian. ’Epigenetics. Instant Expert No. 29’, New Scientist, 5th January 2013, No. 2898.
  • Carey, Nessa. ‘The Epigenetics Revolution: How Modern Biology is Rewriting Our Understanding of Genetics, Disease and Inheritance’. Publisher: Icon Books. Paperback 1st March 2012. ISBN-10: 1848313470. RRP Price £9-99.

 

Mars Methane Mystery

Curiosity’s Mars Methane Mystery Continues

Updated at 5 p.m. PDT (8 p.m. EDT) on June 24, 2019:

Curiosity’s team conducted a follow-on methane experiment this past weekend. The results came down early Monday morning: The methane levels have sharply decreased, with less than 1 part per billion by volume detected. That’s a value close to the background levels Curiosity sees all the time.

The finding suggests last week’s methane detection — the largest amount of the gas Curiosity has ever found — was one of the transient methane plumes that have been observed in the past. While scientists have observed the background levels rise and fall seasonally, they haven’t found a pattern in the occurrence of these transient plumes.

“The methane mystery continues,” said Ashwin Vasavada, Curiosity’s project scientist at NASA’s Jet Propulsion Laboratory in Pasadena, California. “We’re more motivated than ever to keep measuring and put our brains together to figure out how methane behaves in the Martian atmosphere.”

Curiosity doesn’t have instruments that can definitively say whether the source of the methane is biological or geological. A clearer understanding of these plumes, combined with coordinated measurements from other missions, could help scientists determine where they’re located on Mars.

Curiosity’s most recent methane findings will be announced during a livestream of the 5 p.m. PDT / 8 p.m. EDT NASA Town Hall at AbSciCon 2019, an astrobiology science conference happening in Bellevue, Washington. Watch the plenary broadcast at:

https://connect.agu.org/abscicon/home

This week, NASA’s Curiosity Mars rover found a surprising result: the largest amount of methane ever measured during the mission — about 21 parts per billion units by volume (ppbv). One ppbv means that if you take a volume of air on Mars, one billionth of the volume of air is methane.

The finding came from the rover’s Sample Analysis at Mars (SAM) tunable laser spectrometer. It’s exciting because microbial life is an important source of methane on Earth, but methane can also be created through interactions between rocks and water.

Curiosity doesn’t have instruments that can definitively say what the source of the methane is, or even if it’s coming from a local source within Gale Crater or elsewhere on the planet.

“With our current measurements, we have no way of telling if the methane source is biology or geology, or even ancient or modern,” said SAM Principal Investigator Paul Mahaffy of NASA’s Goddard Spaceflight Center in Greenbelt, Maryland.

The Curiosity team has detected methane many times over the course of the mission. Previous papers have documented how background levels of the gas seem to rise and fall seasonally. They’ve also noted sudden spikes of methane, but the science team knows very little about how long these transient plumes last or why they’re different from the seasonal patterns.

The SAM team organized a different experiment for this weekend to gather more information on what might be a transient plume. Whatever they find — even if it’s an absence of methane — will add context to the recent measurement.

Curiosity’s scientists need time to analyze these clues and conduct many more methane observations. They also need time to collaborate with other science teams, including those with the European Space Agency’s Trace Gas Orbiter, which has been in its science orbit for a little over a year without detecting any methane. Combining observations from the surface and from orbit could help scientists locate sources of the gas on the planet and understand how long it lasts in the Martian atmosphere. That might explain why the Trace Gas Orbiter’s and Curiosity’s methane observations have been so different.

Andrew Good
Jet Propulsion Laboratory, Pasadena, Calif.