Study: The genetic legacy of extreme exploitation in a polar vertebrate

Understanding the effects of human exploitation on the genetic composition of wild populations is important for predicting species persistence and adaptive potential. We therefore investigated the genetic legacy of large-scale commercial harvesting by reconstructing, on a global scale, the recent demographic history of the Antarctic fur seal (Arctocephalus gazella), a species that was hunted to the brink of extinction by 18th and 19th century sealers. Molecular genetic data from over 2,000 individuals sampled from all eight major breeding locations across the species’ circumpolar geographic distribution, show that at least four relict populations around Antarctica survived commercial hunting. coalescent simulations suggest that all of these populations experienced severe bottlenecks down to effective population sizes of around 150–200. Nevertheless, comparably high levels of neutral genetic variability were retained as these declines are unlikely to have been strong enough to deplete allelic richness by more than around 15%. These findings suggest that even dramatic short-term declines need not necessarily result in major losses of diversity, and explain the apparent contradiction between the high genetic diversity of this species and its extreme exploitation history.

Study: MIPT’s DREAM team makes semifinals of Amazon contest for AI developers

The DREAM team from the Moscow Institute of Physics and Technology has reached the semifinals of the Alexa Prize Socialbot Grand Challenge 3, an international university contest for conversational AI developers.

The goal of the challenge is to create advanced dialogue agents, or “socialbots,” for Amazon Alexa that will converse with users on popular topics and current events. Each participating team received a $250,000 research grant and access to other Amazon resources.

The DREAM team consists of undergraduate and graduate students from MIPT’s Neural Networks and Deep Learning Lab: Dilyara Baymurzina, Elena Ermakova, Idris Yusupov, Dmitry Karpov, The Anh Le, Denis Kuznetsov, Daniil Cherniavskii, and Yury Kuratov, the team leader.

“We became one of the six teams with the highest average ratings provided by Alexa users, securing a spot in the semifinals. We see this contest as a great opportunity to work on advanced AI technologies and develop something unique. As for our main goal, we are planning to make it to the finals and win,” said Kuratov. “The Alexa Prize Challenge provides a unique opportunity for researchers to test their hypotheses on actual user interactions rather than the static datasets that tend to be used in academia.”

During the quarterfinals, which took place from Feb. 3 to March 17, all Alexa users had the opportunity to interact with and rate eligible socialbots through the Alexa Prize Skill. Teams were selected by evaluating the socialbots on two key criteria: the user ratings after having a conversation with the bot and the average duration of the interaction session. Only six teams reached the semifinals. The MIPT team is the only one representing Russia. The final results of the contest are expected in May 2020

Study: Newly discovered enzyme “square dance”

How do you capture a cellular process that transpires in the blink of an eye? Biochemists at MIT have devised a way to trap and visualize a vital enzyme at the moment it becomes active — informing drug development and revealing how biological systems store and transfer energy.

The enzyme, ribonucleotide reductase (RNR), is responsible for converting RNA building blocks into DNA building blocks, in order to build new DNA strands and repair old ones. RNR is a target for anti-cancer therapies, as well as drugs that treat viral diseases like HIV/AIDS. But for decades, scientists struggled to determine how the enzyme is activated because it happens so quickly. Now, for the first time, researchers have trapped the enzyme in its active state and observed how the enzyme changes shape, bringing its two subunits closer together and transferring the energy needed to produce the building blocks for DNA assembly.

Before this study, many believed RNR’s two subunits came together and fit with perfect symmetry, like a key into a lock. “For 30 years, that’s what we thought,” says Catherine Drennan, an MIT professor of chemistry and biology and a Howard Hughes Medical Institute investigator. “But now, we can see the movement is much more elegant. The enzyme is actually performing a ‘molecular square dance,’ where different parts of the protein hook onto and swing around other parts. It’s really quite beautiful.”

Drennan and JoAnne Stubbe, professor emerita of chemistry and biology at MIT, are the senior authors on the study, which appeared in the journal Science on March 26. Former graduate student Gyunghoon “Kenny” Kang PhD ’19 is the lead author.

All proteins, including RNR, are composed of fundamental units known as amino acids. For over a decade, Stubbe’s lab has been experimenting with substituting RNR’s natural amino acids for synthetic ones. In doing so, the lab realized they could trap the enzyme in its active state and slow down its return to normal. However, it wasn’t until the Drennan lab gained access to a key technological advancement — cryo-electron microscopy — that they could snap high-resolution images of these “trapped” enzymes from the Stubbe lab and get a closer look.

“We really hadn’t done any cryo-electron microscopy at the point that we actively started trying to do the impossible: get the structure of RNR in its active state,” Drennan says. “I can’t believe it worked; I’m still pinching myself.”

The combination of these techniques allowed the team to visualize the complex molecular dance that allows the enzyme to transport the catalytic “firepower” from one subunit to the next, in order to generate DNA building blocks. This firepower is derived from a highly reactive unpaired electron (a radical), which must be carefully controlled to prevent damage to the enzyme.

According to Drennan, the team “wanted to see how RNR does the equivalent of playing with fire without getting burned.”

First author Kang says slowing down the radical transfer allowed them to observe parts of the enzyme no one had been able to see before in full. “Before this study, we knew this molecular dance was happening, but we’d never seen the dance in action,” he says. “But now that we have a structure for RNR in its active state, we have a much better idea about how the different components of the enzyme are moving and interacting in order to transfer the radical across long distances.”

Although this molecular dance brings the subunits together, there is still considerable distance between them: The radical must travel 35-40 angstroms from the first subunit to the second. This journey is roughly 10 times farther than the average radical transfer, according to Drennan. The radical must then travel back to its starting place and be stored safely, all within a fraction of a second before the enzyme returns to its normal conformation.

Because RNR is a target for drugs treating cancer and certain viruses, knowing its active-state structure could help researchers devise more effective treatments. Understanding the enzyme’s active state could also provide insight into biological electron transport for applications like biofuels. Drennan and Kang hope their study will encourage others to capture fleeting cellular events that have been difficult to observe in the past.

“We may need to reassess decades of past results,” Drennan says. “This study could open more questions than it answers; it’s more of a beginning than an end.”

Report: Tips to make the most of NBN, internet services

NBN performance will vary during the current rise in social distancing and working from home, Flinders University expert Dr Paul-Gardner Stephens says.

Delivery speed and service reliability will differ based on internet provider and technology: Fibre to the Premises (FTTP), copper (FTTN), cable TV coaxial networks, fixed wireless, or satellite.

IT and software engineering senior lecturer Dr Paul Gardner-Stephen says if you’re on FTTP or FTTN, there is no significant structural bottleneck because the NBN (National Broadband Network) can increase the feed on your line, and the limitation will instead be in your ‘garden hose’ that connects to your home or business.

But the situation is more difficult for those Australians using a cable TV cable, fixed wireless or satellite because everyone in a particular area is connected to the same ‘sprinkler’.

“While someone could try to turn the sprinkler this way or that so that someone gets wetter than someone else, there is only so much water to go around, and so if there are too many people near the sprinkler, they will each get less water,” Dr Gardner-Stephens says.

“That’s because there is a limited amount of usage to go around with these technologies (usually because of limited frequencies), and if there are too many people ‘contending’ for access, then each of them will get less.

“While in some cases the NBN can ‘turn up the sprinkler’ a bit, this may not be enough to really help. This is particularly a problem in areas that were originally planned to get FTTN, but were moved to fixed wireless, or worse, to satellite.”

Satellite users are also particularly vulnerable, because unlike fixed wireless towers, where more can be built in areas of need, building an extra half a satellite is really expensive and takes a really long time.

“Some areas of Queensland and New South Wales in particular seem to be approaching this situation, where the part of the satellite that looks in their direction is much fuller than was originally planned, and might be at risk of getting overloaded under increased load due to COVID-19 having everyone working from home.

“However in many other parts of the state and country, this is not a problem. For example, where I am based in the Northern Flinders Ranges, we are able to get the advertised 25mbit/sec (or very close to it) during the working day, and even in the evenings.

Study: Mesoamerican copper smelting technology aided colonial weaponry

When Spanish invaders arrived in the Americas, they were generally able to subjugate the local peoples thanks, in part, to their superior weaponry and technology. But archeological evidence indicates that, in at least one crucial respect, the Spaniards were quite dependent on an older indigenous technology in parts of Mesoamerica (today’s Mexico, Guatemala, Belize, and Honduras).

The invaders needed copper for their artillery, as well as for coins, kettles, and pans, but they lacked the knowledge and skills to produce the metal. Even Spain at that time had not produced the metal domestically for centuries, relying on imports from central Europe. In Mesoamerica they had to depend on local smelters, furnace builders, and miners to produce the essential material. Those skilled workers, in turn, were able to bargain for exemption from the taxes levied on the other indigenous people.

This dependence continued for at least a century, and perhaps as long as two centuries or more, according to new findings published in the journal Latin American Antiquity, in a paper by Dorothy Hosler, professor of archeology and ancient technology at MIT, and Johan Garcia Zaidua, a researcher at the University of Porto, in Portugal.

The research, at the site of El Manchón, in Mexico, made use of information gleaned from more than four centuries worth of archeological features and artifacts excavated by Hosler and her crew over multiple years of fieldwork, as well as from lab work and historical archives in Portugal, Spain, and Mexico analyzed by Garcia.

El Manchón, a large and remote settlement, initially displayed no evidence of Spanish presence. The site consisted of three steep sectors, two of which displayed long house foundations, some with interior rooms and religious sanctuaries, patios, and a configuration that was conceptually Mesoamerican but unrelated to any known ethnic groups such as the Aztec. In between the two was an area that contained mounds of slag (the nonmetallic material that separates out during smelting from the pure metal, which floats to the surface).

The Spanish invaders urgently needed enormous quantities of copper and tin to make the bronze for their cannons and other armaments, Hosler says, and this is documented in the historical and archival records. But “they didn’t know how to smelt,” she says, whereas archaeological data suggest the indigenous people had already been smelting copper at this settlement for several hundred years, mostly to make ritual or ceremonial materials such as bells and amulets. These artisans were highly skilled, and in Guerrero and elsewhere had been producing complex alloys including copper-silver, copper-arsenic, and copper-tin for hundreds of years, working on a small scale using blowpipes and crucibles to smelt the copper and other ores.

But the Spanish desperately reqired large quantities of copper and tin, and in consultation with indigenous smelters introduced some European technology into the process. Hosler and her colleagues excavated an enigmatic feature that consisted of two parallel courses of stones leading toward a large cake of slag in the smelting area. They identified this as the remains of a thus-far-undocumented hybrid type of closed furnace design, powered by a modified hand-held European bellows. A small regional museum in highland Guerrero illustrates just such a hybrid furnace design, including the modified European-introduced bellows system, capable of producing large volumes of copper. But no actual remains of such furnaces had previously been found.

The period when this site was occupied spanned from about 1240 to 1680, Hosler says, and may have extended to both earlier and later times.

The Guerrero site, which Hosler excavated over four field seasons before work had to be suspended because of local drug cartel activity, contains large heaps of copper slag, built up over centuries of intensive use. But it took a combination of the physical evidence, analysis of the ore and slags, the archaeological feature in the the smelting area, the archival work, and reconstruction drawing to enable identification of the centuries of interdependence of the two populations in this remote outpost.

Earlier studies of the composition of the slag at the site, by Hosler and some of her students, revealed that it had formed at a temperature of 1150 degrees Celsius, which could not have been achieved with just the blowpipe system and would have required bellows. That helps to confirm the continued operation of the site long into the colonial period, Hosler says.

Years of work went into trying to find ways to date the different deposits of slag at the site. The team also tried archaeomagnetic data but found that the method was not effective for the materials in that particular region of Mexico. But the written historical record proved key to making sense of the wide range of dates, which reflected centuries of use of the site.

Documents sent back to Spain in the early colonial period described the availability of the locally produced copper, and the colonists’ successful tests of using it to cast bronze artillery pieces. Documents also described the bargains made by the indigenous producers to gain economic privileges for their people, based on their specialized metallurgical knowledge.

“We know from documents that the Europeans figured out that the only way they could smelt copper was to collaborate with the indigenous people who were already doing it,” Hosler says. “They had to cut deals with the indigenous smelters.”

Hosler says that “what’s so interesting to me is that we were able to use traditional archeological methods and data from materials analysis as well as ethnographic data” from the furnace in a museum in the area, “and historical and archival material from 16th century archives in Portugal, Spain, and Mexico, then to put all the data from these distinct disciplines together into an explanation that is absolutely solid.”

Report: Restricting civil liberties amid COVID-19 pandemic

In the past week alone, the spread of COVID-19 has caused federal and state governments to take measures that would have seemed extreme just weeks earlier: shutdowns of businesses, closing of borders, and curtailing of large gatherings. By Friday, one in five Americans had been asked by state and local officials in places like California, New York, and Illinois to stay home. Under most circumstances, this might be seen as an attack on civil liberties.

Yet there are moments in history when the normal rules don’t apply, and two of Harvard’s legal experts suggest that we are now living in such a time. While Harvard Law School faculty members Charles Fried and Nancy Gertner agree that the coronavirus situation is distressing on numerous levels, both say the restriction on individual freedom is largely appropriate for the circumstance.

Beneficial Professor of Law Charles Fried characterizes this as a “black swan event,” one without modern precedent. “Most people are worrying about restrictions on meetings — that’s freedom of association. And about being made to stay in one place, which I suppose is a restriction on liberty. But none of these liberties is absolute; they can all be abrogated for compelling grounds. And in this case the compelling ground is the public health emergency.”

This, he says, calls for unique measures to be taken. “So much about this is unique: the extreme danger, the unpredictability, the fact that it is everywhere. Maybe the situation after 9/11 is comparable, when there were sleeper cells all over. But even that was much more focused; this is widely dispersed in all 50 states.”

He says it’s also unlikely that anyone would have a case against the government for loss of business. “I don’t think you could demand compensation, because the government didn’t put you out of business; circumstances did. And it’s not a permanent deprivation if you go out of business.”

A murkier issue, Fried says, is the place of free speech at a time when false information — such as the incorrect self-test guides being shared on social media — can be especially harmful. But any effort to police falsehoods online would be particularly hard to enforce. “It seems to me that certain information can be dangerously false — say, if someone is told on social media that they are not allowed to go to an emergency room when they are. But what exactly can you do about that? You could direct Facebook to scan for things like that, but it’s hard to see where you could effectively target the maker of the false statement itself. There would have to be some kind of statute, and it’s hard to see what that statute would look like. To me, the liberties of getting where you want to go are less concerning than the potential for disinformation and rumor-mongering.”

Nancy Gertner, senior lecturer on law and a retired federal judge, suggests we may be seeing stronger restrictions in days to come. “The premise for any quarantine would be a public health emergency, and the limits of that aren’t clear. Clearly, state and local governments have the authority to declare an emergency and take steps to mitigate that. The federal government has more limited powers, but it can address transportation between the states and international travel. How far could they go? ‘Who knows?’ is the answer. Could they tell people to stay in their homes given the nature of this virus? Probably.”

Study: Machine-learning approach could improve lung cancer screening

A machine-learning method that can identify patients with early-stage lung cancer is described in Nature this week. The approach detects tumour-derived DNA in blood samples — so-called liquid biopsies — and may help to increase the adoption of screening for high-risk individuals.

The recommended mode of screening for lung cancer in high-risk individuals is CT scanning, which has been shown to reduce lung cancer-related deaths. However, uptake is low owing to factors such as high costs, limited screening programmes and concerns with false positives; around 5% of eligible individuals undergo such screening in the United States. Blood tests are an attractive alternative means of cancer detection, although most liquid biopsy studies focus on monitoring patients with advanced disease, who may have higher levels of tumour-related DNA markers than early-stage patients.

Maximilian Diehn and colleagues optimize an existing sequencing method for assessing circulating tumour DNA (ctDNA). They improve the recovery of DNA and identify alterations that may serve as useful markers of disease. Using this method the authors show that although ctDNA is present in only very low levels in early-stage lung cancers, it is a strong prognostic marker. They go on to use these data to refine a machine-learning method for predicting the presence of lung-cancer-derived DNA in blood samples. This technique discriminates early-stage lung cancer patients from risk-matched controls in an initial sample of 104 patients with early stage non-small cell lung cancer and 56 matched controls, which was confirmed in an independent validation cohort of 46 cases and 48 controls.

Report: California has been passing tough animal welfare laws

For more than a decade, foie gras producers have been fighting to stop California from banning foie gras.

Their argument: that some states imposing different, higher animal welfare standards violates the commerce clause of the US Constitution (which leaves the regulation of interstate commerce up to the federal government), or alternately violates federal laws about the production of poultry products.

They haven’t met with much success in court. While one federal judge overturned the foie gras ban in 2015, that decision was later overturned by the Ninth Circuit, and the ban went back into effect when the Supreme Court declined to hear the case last year. The courts have also struck down trickery such as restaurants giving away foie gras with purchase of an expensive tasting menu. After that, foie gras advocates sued again — and last week, the courts found against them again.

The latest ruling reaffirms that the federal government doesn’t have the authority to stop states from imposing their own animal welfare requirements. And while foie gras is a tiny fraction of animal farming, the ruling has implications for more expansive welfare laws, too.

Lots of states want to regulate animal cruelty. The courts are mostly agreeing they can.
In the past decade, voters in lots of states have imposed various animal welfare-related restrictions on the meat, dairy, and egg products sold in their state. The biggest of those was California’s Proposition 12, which bans the sale of meat and eggs from caged animals. It followed on the heels of a similar 2016 Massachusetts law, as well as foie gras bans in California and New York City; battery cage bans in Michigan, Ohio, Rhode Island, and Washington; and bans on gestation crates for pregnant pigs in Arizona, California, Colorado, Florida, Maine, Michigan, Ohio, Oregon, and Rhode Island.

After many of these laws were approved, meat industry groups sued, in some cases joined by other states. Their justification? No state ought to be allowed to impose any animal welfare standard above the standards set forward by the federal government. Laws like these, they argued, impede interstate commerce. (The states argued that they had standing to sue because their residents, as well as state institutions like prisons, would pay higher prices for animal products whose production was changed to be compatible with animal welfare laws.)

If that argument were to succeed in court, it wouldn’t just mean that foie gras could be served in California. It would effectively mean that a core strategy of the movement against animal cruelty in factory farming — slowly convincing voters, state by state, that specific practices are unethical and should be banned — was impossible.

Instead, any fight to reduce cruelty in animal agriculture would have to happen in Congress, which is much more favorable territory for factory farms and their lobbyings. While voters have overwhelmingly supported laws to reduce animal cruelty, legislators have been distinctly more inclined to drag their feet. The last major federal bill targeting farm animal welfare was introduced in 2010, and it never passed.

So it’d be a big victory for factory farms if they were able to ban states from considering their own animal welfare restriction and take the fight to the more favorable territory of Congress.

But courts haven’t been persuaded.

What the court had to say about California’s much-contested foie gras ban
California’s foie gras ban passed in 2004, but the state phased it in gradually; foie gras wasn’t fully prohibited until 2012. Then producers sued. In 2015, the ban was overturned by a federal judge who found California was unconstitutionally attempting to override federal poultry law. Foie gras returned to restaurants. The state appealed to the Ninth Circuit, which ruled 3-0 in 2017 that the lower court had erred in overturning the ban. Foie gras advocates appealed again, this time to the Supreme Court, but early last year, the Supreme Court declined to hear the case, making the Ninth Circuit’s decision final.

Some people thought that would be the end of the foie gras legal fight. Instead, the plaintiffs sued again. The US District Court for the Central District of California seemed unimpressed to be revisiting the issue. It ruled in favor of the ban, complaining that the plaintiffs had presented “substantially the same challenges they brought up in the first case.”

The plaintiffs said in a statement they intend to appeal the ruling again.

The decision “affirms that state lawmakers and governors have a right to set standards for humane treatment, if they choose to do so,” Kitty Block, CEO of the Humane Society, wrote.

That’s a big deal because the vast majority of animals raised for food in the US are now factory farmed, often in horrific conditions. And while the majority of Americans still eat meat and aren’t ready to go vegetarian, most of them oppose the conditions on factory farms and in slaughterhouses, and most of them support animal cruelty measures when they get the chance to vote on them. Those laws not only improve conditions for billions of animals but also offer a route toward a world without factory farming. If one state can figure out how to ban cruel conditions while still offering the food its citizens love (perhaps by leaning heavily on plant-based and cell-cultivated meat options), then similar laws will have the chance to sweep the rest of the nation.

At their best, America’s states function as laboratories of democracy that test policies so other states can learn from them and adopt the best ones. Permitting that kind of experimentation here will help bring about the end of animal cruelty much sooner.

Report: 200-MW CCA solar project comes online in California

Peninsula Clean Energy this month began providing more solar power to California’s San Mateo County from the 200-MW utility-scale Wright Solar Project located in the nearby Central Valley.

“This is actual new steel in the ground that will send more clean and affordable power to our customers,” Peninsula Clean Energy CEO Jan Pepper said. “As a leader among CCAs in California and nationwide, we are proving that aggressive movement toward 100 percent carbon-free power can be both environmentally and economically beneficial. Wright Solar is just the beginning of what is possible for providing good jobs and strong economic benefits to areas such as Merced County in California’s Central Valley.”

Peninsula Clean Energy has an exclusive 25-year power purchase agreement with Wright Solar Park LLC to buy all of the facility’s electricity to power more than 100,000 San Mateo County homes.

The solar facility was constructed by Swinerton Renewable Energy with roughly 400 union workers from the surrounding areas that were hired as part of a five-union project labor agreement. That agreement was a result of Peninsula Clean Energy’s workforce policy requirements developed in consultation with local building trades and other unions.

“This project illustrates the vast potential that solar and other renewable generation can have in Merced County and Central California, from new construction jobs to millions of dollars in new tax revenues,” said Lloyd Pareira, chairman of the Merced County Board of Supervisors.

“The Wright Solar Project showcases how local hires can complete a project in an amazing timeframe and provide a huge economic stimulus to the surrounding community,” said Bobby Stutzman, business manager at International Brotherhood of Electrical Workers Local 684. “This is also one of those projects that will transcend construction and can be used by the building trades and other unions as a model for future labor agreements.”

Laborers, electricians, iron workers, carpenters, operators and engineers — many from the Bakersfield and Fresno areas — joined forces to install roughly 650,000 solar panels and accompanying equipment in only 11 months.

The Wright project is owned by Centaurus Renewable Energy and the construction and operations are managed by Clēnera.

The project adds to an escalating trend of new development spearheaded by CCAs that is advancing clean energy, economic development and green jobs throughout California and elsewhere. California’s 19 CCAs have on average added roughly 1,000 MW annually in long-term renewable energy purchase agreements, and are expected to make long-term investments in more than 10,000 MW of new clean energy resources and energy storage by 2030.

That includes a joint solicitation in November from Peninsula Clean Energy and three other Bay Area CCAs for the installation of more than 30 MW of battery storage to 6,000 homes and hundreds of businesses, adding a clean and resilient backstop to areas hit by PG&E power shutoffs.

Trump Iran attack injuries, “I heard that they had headaches”

Trump Iran attack injuries, “I heard that they had headaches”.

President Trump on Wednesday minimized the injuries of several U.S. service members who suffered concussions during an Iranian missile attack on two Iraqi bases that house American personnel.

“I heard that they had headaches and a couple of other things, but I would say and I can report that it’s not very serious,” Trump told reporters at a press conference in Davos, Switzerland.

“I don’t consider them very serious injuries relative to other injuries that I’ve seen,” he continued. “I’ve seen what Iran has done with their roadside bombs to our troops. … I’ve seen people that were horribly, horribly injured in that area, in that war.”

“No, I do not consider that to be bad injuries, no,” he added, referring to the soldiers who were taken for treatment last week.

The president declared earlier this month that there were no casualties after Iran fired missiles at the bases housing U.S. forces on Jan. 8. But the Pentagon last week revealed 11 U.S. troops were evacuated from Iraq and taken to hospitals in Germany and Kuwait for treatment for concussions suffered during attack on Al Asad Air Base.

The Associated Press reported Tuesday night that additional U.S. troops were flown to Germany for closer evaluation for similar injuries, though the exact number was not known.

The Iranian missile attack came as a direct response to a U.S. drone strike that killed top Iranian Gen. Qassem Soleimani. The two countries appeared to step back from the brink of military conflict after the attacks, though tensions remain.

The Trump administration has faced intense pressure from lawmakers in both parties about its justification for the strike that killed Soleimani. Secretary of State Mike Pompeo initially said the general posed an “imminent threat” to American lives, and Trump later said he was targeting four U.S. embassies. But officials have struggled to defend both explanations.

The House passed a resolution earlier this month to rein in Trump’s war powers with regards to Iran, and a similar Senate resolution appears to have the votes needed to pass.