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AI Solves 50-Year-Old Biology 'Grand Challenge' Decades Before Experts Predicted – ScienceAlert

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A long-standing and incredibly complex scientific problem concerning the structure and behaviour of proteins has been effectively solved by a new artificial intelligence (AI) system, scientists report.

DeepMind, the UK-based AI company, has wowed us for years with its parade of ever-advancing neural networks that continually trounce humans at complex games such as chess and Go.

All those incremental advancements were about much more than mastering recreational diversions, however.

In the background, DeepMind’s researchers were seeking to coax their AIs towards solving much more fundamentally important scientific puzzles – such as finding new ways to fight disease by predicting infinitesimal but vitally important aspects of human biology.

Now, with the latest version of their AlphaFold AI engine, they seem to have actually achieved this very ambitious goal – or at least gotten us closer than scientists ever have before.

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For about 50 years, researchers have strived to predict how proteins achieve their three-dimensional structure, and it’s not an easy problem to solve.

The astronomical number of potential configurations is so mind-bogglingly huge, in fact, that researchers postulated it would take longer than the age of the Universe to sample all the possible molecular arrangements.

Nonetheless, if we can solve this puzzle – known as the protein-folding problem – it would constitute a giant breakthrough in scientific capabilities, vastly accelerating research endeavours in things like drug discovery and modelling disease, and also leading to new applications far beyond health.

For that reason, despite the scale of the challenge, for decades researchers have been collaborating to make gains in developing solutions to the protein-folding problem.

A rigorous experiment called CASP (Critical Assessment of protein Structure Prediction) began in the 1990s, challenging scientists to devise systems capable of predicting the esoteric enigmas of protein folding.

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Now, in its third decade, the CASP experiment looks to have produced its most promising solution yet – with DeepMind’s AlphaFold delivering predictions of 3D protein structures with unprecedented accuracy.

“We have been stuck on this one problem – how do proteins fold up – for nearly 50 years,” says CASP co-founder John Moult from the University of Maryland.

“To see DeepMind produce a solution for this, having worked personally on this problem for so long and after so many stops and starts wondering if we’d ever get there, is a very special moment.”

In the experiment, DeepMind used a new deep learning architecture for AlphaFold that was able to interpret and compute the ‘spatial graph’ of 3D proteins, predicting the molecular structure underpinning their folded configuration.

The system, which was trained up by analysing a databank of approximately 170,000 protein structures, brought its unique skillset to this year’s CASP challenge, called CASP14, achieving a median score in its predictions of 92.4 GDT (Global Distance Test).

That’s above the ~90 GDT threshold that’s generally considered to be competitive with the same results obtained via experimental methods, and DeepMind says its predictions are only off by about 1.6 angstroms on average (about the width of an atom).

“I nearly fell off my chair when I saw these results,” says genomics researcher Ewan Birney from the European Molecular Biology Laboratory.

“I know how rigorous CASP is – it basically ensures that computational modelling must perform on the challenging task of ab initio protein folding. It was humbling to see that these models could do that so accurately. There will be many aspects to understand but this is a huge advance for science.”

It’s worth noting that the research has not yet been peer-reviewed, nor published in a scientific journal (although DeepMind’s researchers say that’s on the way).

Even so, experts who are familiar with the field are already recognising and applauding the breakthrough, even if the full report and detailed results are yet to be seen.

“This computational work represents a stunning advance on the protein-folding problem, a 50-year old grand challenge in biology,” says structural biologist Venki Ramakrishnan, president of the Royal Society.

“It has occurred decades before many people in the field would have predicted.”

The full findings are not yet published, but you can see the abstract for the research, “High Accuracy Protein Structure Prediction Using Deep Learning”, here, and find more information on CASP14 here.

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The Olduvai Gorge gives up two-million-year-old secrets – Varsity

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Few archaeological sites can claim to be famous, but the Olduvai Gorge in northern Tanzania is chief among them. With the word ‘olduvai’ coming from a misspelling of the Maasai word, ‘oldupai,’ a name for a plant that grows in the area, the fossil-rich region is famous for offering up some of the first evidence of fossil remains and stone tools used by early hominins, ancestors of today’s humans.

In the 1930s, Louis and Mary Leakey were working in Olduvai when they uncovered stone tools from early humans. Since then, it has become a popular archaeological site. The gorge lent an even older name — the Oldoway Gorge — to the paleolithic culture discovered there before the Abbevillian culture and, subsequently, their tools. Oldowan tools are often either large hammering stones or smaller, sharper flake stones used for cutting. They were used by precursors to modern Homo sapiens, such as Homo habilis.

Now, an international research team comprised of scientists from around the world, including from U of T, have conducted a thorough search of the Olduvai Gorge and concluded that hominins were living and building tools in the site as early as two million years ago. Moreover, their continual occupation of the gorge, extending over a 235,000-year period, shows how early hominins could adapt to changing environments — a skill that might have aided in their expansion out of Eastern Africa.

A wide source of information

The researchers combed through a wide array of sources to reach their findings. They took samples from previously excavated fossils and tools and compared them against samples of pollen, plants, and charcoal from wildfires, which were all deposited into the soil millions of years ago. The result was a pattern of human activity in the same place across time.

The prehistoric Olduvai landscape contained a variety of environments, such as streams, floodplains, woody forest, dry steppe, and even patches of land covered by ash from volcanic activity. Early hominins were able to exploit all of these environments, partly by bringing materials they needed for tools with them. Some of the rocks used to make tools originated 12 kilometres from where they were found. Others were made using what was at hand.

However, it is not clear which hominin species made these tools, largely because no new fossils were found. One possible candidate is Homo habilis because their fossils have been excavated nearby.

Rethinking the past

Oldowan tools have been excavated in nearby Ethiopia dating back to 2.6 million years ago, so this study does not represent the earliest discovery of stone tools. But it does extend the timeline of the Olduvai Gorge specifically. Previously, the oldest use of tools in the region was dated to 1.85 million years ago, so these findings push that start point by about 150,000 years. 

Moreover, these new findings demonstrate that early hominins had a robust ability to adapt to new environments. Julio Mercader Florin, lead author and professor at the University of Calgary, wrote in The Conversation that “This is a clear sign that 2 million years ago humans were not constrained technologically and already had the capacity to expand geographic range.”

The researchers discovered that the tools used remained the same regardless of what environment they were found in. It might have been human adaptability, then, that enabled our ancestors to thrive in the Olduvai Gorge and beyond.

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Test fire of NASA's SLS moon rocket ends prematurely – CTV News

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NASA’s Space Launch System rocket ignited its four main engines Saturday on a test stand in Mississippi, but the engines shut down earlier than the agency planned.

The hot fire test was the last of eight tests that make up what NASA calls a “green run,” a series of ground tests aimed at ensuring the vehicle doesn’t have any major structural or engineering issues before it is put on a launch pad. The rocket is the most powerful launch vehicle the space agency has ever constructed.

The SLS was supposed to light its engines for about eight minutes, the length of time the engines will have to fire to propel the rocket on its orbital missions.

It’s not yet clear why the engines powered down after little more than a minute at NASA’s Stennis Space Center near Bay St. Louis, Mississippi. The test was still useful for gathering data and “teams are assessing the data on early engine shutdown,” the space agency tweeted.

During a Saturday night news conference, John Honeycutt, the SLS program manager, said NASA officials will go over the data gathered in the test to identify the issue.

“What we learned was — is that we didn’t have the pressurization valve modeled appropriately,” Honeycutt said.

Officials had hoped to run the test for at least 250 seconds, he said.

During the hot fire test, engineers “power up all the core stage systems, load more than 700,000 gallons of cryogenic, or supercold, propellant into the tanks and fire all four engines at the same time,” according to NASA.

It is unclear if another test will be needed before the rocket is shipped to Florida, the launch site where the rocket is expected to make its first journey into outer space.

Rick Gilbrech, director of the Stennis Space Center, said his site would need at least four to five days to prepare the fuel for another test if the rocket is ready. He and his team aren’t discouraged by Saturday’s test and are proud of what they’ve accomplished this year, especially during the Covid-19 pandemic, he said.

NASA administrator Jim Bridenstine said the test was “not a failure.”

“This is not a failure. This is a test, and we tested today in a way that is meaningful where we’re going to learn … we’re going to make adjustments, and we’re going to fly to the moon,” he said.

“This was a successful day. We didn’t get everything we wanted and yes we’re going to learn, we’re going to have to make adjustments,” he said. “But again, this is a test. And this is why we test.”

 

Yet another delay

 

SLS has been haunted by critiques of long delays and cost overruns, and with the premature end of the critical hot fire test, its launch may be delayed once again.

“We got lots of data that we’re going to go through and be able to sort through and get to a point where we can make determinations as to whether or not, you know, launching in 2021 is a possibility or not,” Bridenstine said.

The rocket is a key part of NASA’s Artemis lunar exploration program, which aims to send the first woman and next man to the moon by 2024. NASA officials also hope the SLS will be used to reach Mars and other “deep space destinations.”

SLS has been under development for a decade. Under the Obama administration, NASA was already planning to use SLS to take astronauts back to the moon by 2028, and that remained the plan until Vice President Mike Pence directed the space agency to drastically accelerate its timeline in 2019.

Boeing was contracted in 2012 to build SLS’s main components, and the rocket was originally expected to start flying in December 2017. But Boeing has been blasted in several government oversight reports for “poor performance,” costly schedule slips and ballooning expenses. That made SLS a touchy political talking point, and many in the space industry remain suspicious that a 2024 moon landing is possible.

At one point, Bridenstine reportedly considered skipping the green run test to expedite SLS’s development. But more recently he has asserted that the tests are essential to ensuring the rocket is safe enough to carry humans into space and to work out any potential engineering problems before attempting an orbital launching.

Bridenstine is expected to step down when President-elect Joe Biden is inaugurated next week. It’s not clear if NASA will stick with the 2024 timeline under the new administration, though the official Democratic platform calls for “continuity” in NASA’s space programs between presidential administrations.

The SLS rocket stands taller than the Statue of Liberty and has about 15% more thrust at liftoff than the Saturn V rockets that powered the Apollo missions about 50 years ago.

NASA’s Artemis I mission is expected to launch by the end of 2021 with two test flights around the moon without astronauts.

A crewed test mission, Artemis II, is set to launch in 2023 in preparation to have the Artemis III mission return astronauts to the surface of the moon in 2024 for the first time since the 1970s.

Artemis is named after the Greek goddess of the moon and is the twin sister of Apollo, which was name NASA used for the missions and spacecraft that first took Americans to the moon in 1969.

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US: NASA cuts short ground test of its giant moon rocket – Al Jazeera English

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US space agency NASA ignited all four engines of its giant Space Launch System (SLS) for the first time on Saturday, but the “hot fire” test ended much earlier than expected.

Mounted in a test facility at NASA’s Stennis Space Center in the state of Mississippi, the SLS’s 65-metre-tall (212-foot) core stage roared to life at 4:27pm local time (22:27 GMT) and burned for more than a minute before the exercise was aborted.

The test was supposed to last for eight minutes to simulate the rocket’s climb to orbit.

NASA said in a statement that its teams were “assessing the data to determine what caused the early shutdown”.

The fiery show on Saturday is a vital step for the space agency and its top SLS contractor, Boeing, before the SLS’s planned debut launch later this year.

The success of that unmanned mission, called “Artemis I”, will set the stage for the first landing on the Moon by humans since the Apollo 17 mission in 1972. US President Donald Trump has pushed for that trip – which will also see the first woman on the Moon – to take place by 2024.

‘Important milestone’

It was unclear whether Boeing and NASA would have to repeat Saturday’s test, a prospect that could push the SLS’s debut launch into 2022.

Speaking to reporters following the test, SLS Program Manager John Honeycut said it was hard to detect what exactly went wrong. He said they had seen a flash in a thermal protection blanket on one of the engines and were analysing the data.

And despite the test being cut short, NASA Administrator Jim Bridenstine said the firing of the RS-25 engines had provided valuable information for the planned missions.

“I know not everybody is feeling as happy as we otherwise could because we wanted to get eight minutes of a hot fire and we got over a minute, but I just want to remind people where we’ve been and where we’re going and what an important milestone this is,” he told reporters.

He added: “We got lots of data that we’re going to be able to sort through,” to determine if a do-over is needed and whether a November 2021 debut launch date is still possible.

In addition to Artemis I, two other missions are planned. The first mission will test the SLS and an unmanned Orion spacecraft, while Artemis II will take astronauts around the Moon in 2023 but it will not land. Astronauts will only be sent to the Moon during the third mission in 2024.

The SLS, in its configuration for Artemis I, will stand 98 metres (322 feet), taller than the Statue of Liberty, and is more powerful than the Saturn V rockets used in the Apollo missions.

The rocket is now three years behind schedule and nearly $3bn over budget.

Critics have long argued for NASA to retire the rocket’s shuttle-era core technologies, which have launch costs of $1bn or more per mission, in favour of newer commercial alternatives that promise lower costs.

By comparison, it costs as little as $90m to fly the massive, but less powerful, Falcon Heavy rocket designed and manufactured by Elon Musk’s SpaceX, and some $350m per launch for United Launch Alliance’s legacy Delta IV Heavy.

While newer, more reusable rockets from both companies – SpaceX’s Starship and United Launch Alliance’s Vulcan – promise heavier lift capacity than the Falcon Heavy or Delta IV Heavy, potentially at a lower cost, SLS backers have argued it would take two or more launches on those rockets to launch what the SLS could carry in a single mission.

NASA’s eventual goal is to establish an Artemis Base Camp on the Moon before the end of the decade, an ambitious plan that would require tens of billions of dollars in funding and a green light from President-elect Joe Biden and Congress.

A manned return to the Moon is the first part of the Artemis programme to set up a long-term colony and test technologies for a crewed mission to Mars in the 2030s

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