Monthly Archives: October 2019
A new way of studying planets in other solar systems – by doing sort of an autopsy on planetary wreckage devoured by a type of star called a white dwarf – is showing that rocky worlds with geochemistry similar to Earth may be quite common in the cosmos. Researchers studied six white dwarfs whose strong gravitational pull had sucked in shredded remnants of planets and other rocky bodies that had been in orbit. This material, they found, was very much like that present in rocky planets such as Earth and Mars in our solar system. Given that Earth harbors an abundance of life, the findings offer the latest tantalizing evidence that planets similarly capable of hosting life exist in large numbers beyond our solar system.
“The more we find commonalities between planets made in our solar system and those around other stars, the more the odds are enhanced that the Earth is not unusual,” said Edward Young, a geochemistry and cosmochemistry professor at the University of California, Los Angeles (UCLA), who helped lead the study published in the journal Science. “The more Earth-like planets, the greater the odds for life as we understand it.”
The first planets beyond our solar system, called exoplanets, were spotted in the 1990s, but it has been tough for scientists to determine their composition. Studying white dwarfs offered a new avenue.
A white dwarf is the burned-out core of a sun-like star. In its death exoplanets, the star blows off its outer layer and the rest collapses, forming an extremely dense and relatively small entity that represents one of the universe’s densest forms of matter, exceeded only by neutron stars and black holes. Planets and other objects that once orbited it can be ejected into interstellar space. But if they stray near its immense gravitation field, they “will be shredded into dust, and that dust will begin to fall onto the star and sink out of sight,” said study lead author Alexandra Doyle, a UCLA graduate student in geochemistry and astrochemistry.
“This is where that ‘autopsy’ idea comes from,” Doyle added, noting that by observing the elements from the massacred planets and other objects inside the white dwarf scientists can understand their composition.
Andrew Anzalone was restless. It was late autumn of 2017. The year was winding down, and so was his MD/PhD program at Columbia. Trying to figure out what was next in his life, he’d taken to long walks in New York’s leaf-strewn West Village. One night as he paced up Hudson Street, his stomach filled with La Colombe coffee and his mind with Crispr gene editing papers, an idea began to bubble through the caffeine brume inside his brain. Crispr, for all its DNA-snipping precision, has always been best at breaking things. But if you want to replace a faulty gene with a healthy one, things get more complicated. In addition to programming a piece of guide RNA to tell Crispr where to cut, you have to provide a copy of the new DNA and then hope the cell’s repair machinery installs it correctly. Which, spoiler alert, it often doesn’t. Anzalone wondered if instead there was a way to combine those two pieces, so that one molecule told Crispr both where to make its changes and what edits to make. Inspired, he cinched his coat tighter and hurried home to his apartment in Chelsea, sketching and Googling late into the night to see how it might be done. A few months later, his idea found a home in the lab of David Liu, the Broad Institute chemist who’d recently developed a host of more surgical Crispr systems, known as base editors. Anzalone joined Liu’s lab in 2018, and together they began to engineer the Crispr creation glimpsed in the young post-doc’s imagination. After much trial and error, they wound up with something even more powerful. The system, which Liu’s lab has dubbed “prime editing,” can for the first time make virtually any alteration—additions, deletions, swapping any single letter for any other—without severing the DNA double helix.
“If Crispr-Cas9 is like scissors and base editors are like pencils, then you can think of prime editors to be like word processors,” Liu told reporters in a press briefing. Why is that a big deal? Because with such fine-tuned command of the genetic code, prime editing could, according to Liu’s calculations, correct around 89 per cent of the mutations that cause heritable human diseases. Working in human cell cultures, his lab has already used prime editors to fix the genetic glitches that cause sickle cell anemia, cystic fibrosis, and Tay-Sachs disease. Those are just three of more than 175 edits the group unveiled in a scientific article published in the journal Nature.
The work “has a strong potential to change the way we edit cells and be transformative,” says Gaétan Burgio, a geneticist at the Australian National University who was not involved in the work, in an email. He was especially impressed at the range of changes prime editing makes possible, including adding up to 44 DNA letters and deleting up to 80. “Overall, the editing efficiency and the versatility shown in this paper are remarkable.”
Today’s commercial aircraft are typically manufactured in sections, often in different locations — wings at one factory, fuselage sections at another, tail components somewhere else — and then flown to a central plant in huge cargo planes for final assembly. But what if the final assembly was the only assembly, with the whole plane built out of a large array of tiny identical pieces, all put together by an army of tiny robots? That’s the vision that graduate student Benjamin Jenett, working with Professor Neil Gershenfeld in MIT’s Center for Bits and Atoms (CBA), has been pursuing as his doctoral thesis work. It’s now reached the point that prototype versions of such robots can assemble small structures and even work together as a team to build up a larger assemblies. The new work appears in the October issue of the IEEE Robotics and Automation Letters, in a paper by Jenett, Gershenfeld, fellow graduate student Amira Abdel-Rahman, and CBA alumnus Kenneth Cheung SM ’07, PhD ’12, who is now at NASA’s Ames Research Center, where he leads the ARMADAS project to design a lunar base that could be built with robotic assembly.
“This paper is a treat,” says Aaron Becker, an associate professor of electrical and computer engineering at the University of Houston, who was not associated with this work. “It combines top-notch mechanical design with jaw-dropping demonstrations, new robotic hardware, and a simulation suite with over 100,000 elements,” he says. “What’s at the heart of this is a new kind of robotics, that we call relative robots,” Gershenfeld says. Historically, he explains, there have been two broad categories of robotics — ones made out of expensive custom components that are carefully optimized for particular applications such as factory assembly, and ones made from inexpensive mass-produced modules with much lower performance. The new robots, however, are an alternative to both. They’re much simpler than the former, while much more capable than the latter, and they have the potential to revolutionize the production of large-scale systems, from airplanes to bridges to entire buildings.
Researchers in UC Santa Barbara/Google scientist John Martinis’ group have made good on their claim to quantum supremacy. Using 53 entangled quantum bits (“qubits”), their Sycamore computer has taken on — and solved — a problem considered intractable for classical computers.
“A computation that would take 10,000 years on a classical supercomputer took 200 seconds on our quantum computer,” said Brooks Foxen, a graduate student researcher in the Martinis Group. “It is likely that the classical simulation time, currently estimated at 10,000 years, will be reduced by improved classical hardware and algorithms, but, since we are currently 1.5 billion times faster, we feel comfortable laying claim to this achievement.”
The feat is outlined in a paper in the journal Nature.
The milestone comes after roughly two decades of quantum computing research conducted by Martinis and his group, from the development of a single superconducting qubit to systems including architectures of 72 and, with Sycamore, 54 qubits (one didn’t perform) that take advantage of the both awe-inspiring and bizarre properties of quantum mechanics.
“The algorithm was chosen to emphasize the strengths of the quantum computer by leveraging the natural dynamics of the device,” said Ben Chiaro, another graduate student researcher in the Martinis Group. That is, the researchers wanted to test the computer’s ability to hold and rapidly manipulate a vast amount of complex, unstructured data.
“We basically wanted to produce an entangled state involving all of our qubits as quickly as we can,” Foxen said, “and so we settled on a sequence of operations that produced a complicated superposition state that, when measured, returned output (“bitstring”) with a probability determined by the specific sequence of operations used to prepare that particular superposition.” The exercise, which was to verify that the circuit’s output correspond to the sequence used to prepare the state, sampled the quantum circuit a million times in just a few minutes, exploring all possibilities — before the system could lose its quantum coherence. “We performed a fixed set of operations that entangles 53 qubits into a complex superposition state,” Chiaro explained. “This superposition state encodes the probability distribution. For the quantum computer, preparing this superposition state is accomplished by applying a sequence of tens of control pulses to each qubit in a matter of microseconds. We can prepare and then sample from this distribution by measuring the qubits a million times in 200 seconds.” “For classical computers, it is much more difficult to compute the outcome of these operations because it requires computing the probability of being in any one of the 2^53 possible states, where the 53 comes from the number of qubits — the exponential scaling is why people are interested in quantum computing to begin with,” Foxen said. “This is done by matrix multiplication, which is expensive for classical computers as the matrices become large.”
According to the new paper, the researchers used a method called cross-entropy benchmarking to compare the quantum circuit’s bitstring to its “corresponding ideal probability computed via simulation on a classical computer” to ascertain that the quantum computer was working correctly. “We made a lot of design choices in the development of our processor that are really advantageous,” said Chiaro. Among these advantages, he said, are the ability to experimentally tune the parameters of the individual qubits as well as their interactions.
A team at King’s College London looked at data from London, Birmingham, Bristol, Derby, Liverpool, Manchester, Nottingham, Oxford and Southampton. They calculated days with above average pollution levels would see an extra 124 cardiac arrests over the year. NHS England boss Simon Stevens said it was evidence of “a health emergency“. The figure is based on ambulance call data and does not count heart attacks suffered by patients already in hospital. It points to significant short-term health risks caused by air pollution, on top of contributing to almost 500,000 premature deaths in Europe every year.
On days with high pollution levels, across the nine cities in total, they calculated that there would be a total of 231 additional hospital admissions for stroke, with an extra 193 children and adults taken to hospital for asthma treatment. Dr Heather Walton, of King’s College London’s Environmental Research Group, said air pollution reduction policies concentrated in the main on effects connected to life expectancy. “However, health studies show clear links with a much wider range of health effects,” she added.
In London, high-pollution days would see an extra 87 cardiac arrests per year, an extra 144 strokes, and 74 children and 33 adults ending up in hospital with asthma-related issues. In Birmingham the figure would be 12 more out-of-hospital cardiac arrests, 27 additional admissions for stroke and 26 more for asthma. Bristol, Liverpool, Manchester, Nottingham, Oxford and Southampton would see between two and six more out-of-hospital heart attacks and up to 14 extra hospital admissions for both stroke and asthma. Only in Derby would there be no apparent increase.
Among the long-term risks associated with high pollution levels are stunted lung growth and low birth weight. The King’s College research also suggests cutting air pollution by a fifth would decrease incidents of lung cancer by between 5% and 7% across the nine cities surveyed. Mr Stevens said: “It’s clear that the climate emergency is in fact also a health emergency. “Since these avoidable deaths are happening now – not in 2025 or 2050 – together we need to act now.”
The figures were published ahead of Wednesday’s International Clean Air Summit hosted by Mayor of London Sadiq Khan and the UK100 network of local government leaders.
Eye drops that can reverse poor vision? It may sound like science fiction, but one Israeli company is aiming to bring this product to market. The drops passed their Phase 2b clinical trial earlier this month, meaning they’ve proven to improve farsightedness, the inability to see or read nearby objects, and are highly tolerable.
Although results have yet to be released, Israel-based Orasis, Pharmaceuticals, revealed details last week about the latest results of the Phase 2b study for their CSF-1 eye drops. The drops offer temporary relief reversal of farsightedness. Their effects can be felt quickly, although they only last for a few hours.
The study was based on results from 166 participants across several research centers in the U.S. and designed to test both the efficacy and safety of the product. According to Elad Kedar, CEO of Orasis, results are extremely positive.
“We are very encouraged by the results,” said Kedar. “The results were great not only on the efficacy endpoints, but also on the safety and tolerability, so we are moving as quickly as possible into Phase 3.”
According to Kedar, the drops are made from chemicals already existing in eye medication for other treatments. In addition, the concentrations used in the eye drops are far lower than those already used for current eye treatment. In trials, patients improved their eyesight by three eye chart lines, which is the FDA requirement for eyesight studies, according to Kedar.