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DeepMind's AlphaFold Crosses Threshold in Solving Protein Riddle – BNN

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(Bloomberg) — DeepMind Technologies Ltd.’s protein analysis project swept a major international competition, in a step toward making the tool more widely available to scientists studying new drugs and diseases.

AlphaFold, which uses artificial intelligence to predict the structure of proteins, beat other researchers in the latest Critical Assessment of Structure Prediction competition. The event started in 1994 and is held every two years to accelerate research on the topic.

DeepMind became a subsidiary of Google after a 2014 acquisition and is best known for its gamer AI, teaching itself to beat Atari video games and defeating world-renowned Go players like Lee Sedol. The company’s ambition has been to develop AI that can be applied to broader problems, and it’s so far created systems to make Google’s data centers more energy efficient, identify eye disease from scans and generate human-sounding speech.

The task of determining the structures of proteins has been described as a project akin to mapping the genome. Different folds in a protein determine how it will interact with other molecules, and understanding them has implications for discovering how new diseases like Covid-19 invade our cells, designing enzymes to break down pollutants and improving crop yields.

“These algorithms are now becoming strong enough and powerful enough to be applicable to scientific problems,” DeepMind Chief Executive Officer Demis Hassabis said in a call with reporters. After four years of development “we have a system that’s accurate enough to actually have biological significance and relevance for biological researchers.”

DeepMind is now looking into ways of offering scientists access to the AlphaFold system in a “scalable way,” Hassabis said.

“Citizen Science”

CASP scientists analyzed the shape of amino acid sequences for a set of about 100 proteins. Competitors were given the sequences, and charged with predicting their shape. AlphaFold’s assessment lined up almost perfectly with the CASP analysis for two-thirds of the proteins, compared to about 10% from the other teams, and better than what DeepMind’s tool achieved two years ago

Hassabis said his inspiration for AlphaFold came from “citizen science” attempts to find unknown protein structures, like Foldit, which presented amateur volunteers with the problem in the form of a puzzle. In its first two years, the human gamers proved to be surprisingly good at solving the riddles, and ended up discovering a structure that had baffled scientists and designing a new enzyme that was later confirmed in the lab.

“Determining a single protein structure often required years of experimental effort,” said Janet Thornton, director emeritus of the European Bioinformatics Institute and one of the pioneers of using computational approaches to understanding protein structure. “A better understanding of protein structures and the ability to predict them using a computer means a better understanding of life, evolution and, of course, human health and disease.”

©2020 Bloomberg L.P.

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Tonight, Uranus will be on display for all to see – BGR – BGR

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  • Uranus isn’t the easiest planet to spot in the night sky, and most of the time we can’t see it at all, but tonight it’ll be a bit easier to spot the distant, frosty world.
  • NASA says that Uranus will be near Mars in the night sky, and if you have something like a nice pair of binoculars or, better yet, a telescope, you should be able to see it.
  • The planet, which is a pale blue and white, will appear tiny at such a distance, but it’s actually nearly 15 times more massive than Earth.

When you gaze up at the night sky you see plenty of stars, but can you pick out planets when you see them? Sometimes it’s possible to spot the likes of Jupiter and Mars without a telescope, but more often than not, folks with “average” eyes can’t tell much of a difference. Tonight, however, you might be able to catch a glimpse of Uranus, and all you should need is a decent pair of binoculars.

Uranus huge, blue, and stinky. It’s also one of the most interesting planets in our system, and it’s not often that we have guideposts in the sky in order to see it. This time around, Uranus will appear close to Mars in the sky, making it a bit easier to spot, especially if you have the hardware to zoom in a little closer.

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Tonight, Uranus will appear between our own Moon and Mars in the sky. It’ll be tiny and very faint, but it’ll be there, shining a pale blue and just waiting for someone to come visit in search of life.

“The distant, outer planet Uranus is too faint for most of us to see with the unaided eye, and it can be tough to locate in the sky without a computer-guided telescope,” NASA explains in its weekly skywatching tips post. “But Uranus can be located now right between the Moon and Mars.”

Uranus is strange and special for a variety of reasons. It’s very cold, which isn’t particularly unusual, but the planet happens to rotate on a 90-degree angle compared to the rest of the planets in our system. The theory is that something huge slammed into Uranus a long time ago, causing it to shift and ultimately rotate at an angle that doesn’t match up with its own orbit around the Sun.

Additionally, the planet’s moons have been of interest to scientists for some time, mainly because they’re thought to be covered in ice that may hide liquid water beneath it. If that’s the case, those moons could harbor life in some form, but we wouldn’t know for sure until we actually went and checked it out.

In any case, Uranus will be in the sky tonight, and if you have a pair of binoculars or a telescope, you’ll have a great shot at seeing it. Assuming the weather cooperates, of course.

Mike Wehner has reported on technology and video games for the past decade, covering breaking news and trends in VR, wearables, smartphones, and future tech.

Most recently, Mike served as Tech Editor at The Daily Dot, and has been featured in USA Today, Time.com, and countless other web and print outlets. His love of
reporting is second only to his gaming addiction.

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Giant predatory worm's ancient fossil burrows discovered – CBC.ca

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Millions of years ago, giant predatory worms as long as an adult human terrorized the ocean. The fearsome creatures hid under the sea floor, waiting to seize unwitting prey with their slicing jaws and drag them underground to be consumed — like they do today, recently discovered fossils suggest.

The fossils are “very, very distinctive,” said Shahin Dashtgard, a professor of earth sciences at Simon Fraser University in Burnaby, B.C., who co-authored a new study describing them.

“They’re like nothing we’ve ever seen before in the rock record.”

The fossil burrow opening, left, is compared to a modern Bobbit worm burrow opening. The researchers found that the fossil and modern burrows were similar. (Paleoenvironntal Sediment Laboratory/National Taiwan University, Chutinun Mora)

Unlike traditional fossils that are usually formed from the hard parts of an animal’s body, such as its bones or shell, the worm fossils are “trace fossils” consisting of non-biological traces such as footprints or, in this case, a burrow. The fossils are described in a study published this week in the journal Scientific Reports.

Dashtgard noted that because worms have soft bodies, they’re rarely fossilized.

“So, the burrows they make is really the only record we have of what the ecosystem would look like and how diverse the ecosystem was.”

Evoke the monsters of science fiction

The researchers propose that the ancient worm was similar to the modern-day Bobbit worm or sand striker, a marine predator that lives in tropical and subtropical seas in the Indo-Pacific Region and grows up to three metres long. It hides in underground burrows with just its head exposed, striking and grabbing prey, such as fish or shellfish with sharp, scissor-like jaws and dragging them into its burrow.

Bobbit worms are named for the slicing ability of their jaws, which was likened to the slicing that abused wife Lorena Bobbit did to remove her husband’s penis in 1989. They have also been compared to sand crawling monsters in science fiction worlds such as Star Wars, Dune and Tremors.

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Bobbit worms and their relatives are thought to have existed for a very long time. Fossil jaws of what is thought to be the oldest Bobbit worm have been found in a 400 million year old rock formation in Ontario.

But because they’re soft, worms are rarely found in the fossil record.

That’s why researchers have begun looking for trace fossils of soft-bodied marine animals. Ludvig Löwemark, a professor of geosciences at National Taiwan University and Masakazu Nara, a professor of biological sciences at Kochi University in Japan, two co-authors of the study, were looking for trace fossils of another ancient animal when they came across something unusual in a 20 million-year-old sandstone formation in Taiwan.

Figuring out what it was became the project of Yu Yen Pan, a master’s student working with Löwemark who is now a PhD student at Simon Fraser University.

An animation shows how the trace fossil would have formed. (Yu Yen Pan)

Key piece of the puzzle

The rock where the fossils were originally found, Badouzi promontory, was an ancient continental shelf about 30 or 40 metres below the surface of the ocean, said Pan.  It was likely similar to the environment found off the coast of Taiwan today. Other fossil evidence shows that it was likely a coral reef populated by animals such as stingrays and other fish, sea urchins and crustaceans such as shrimp and lobsters.

The first fossils were mostly fragments left behind by erosion, so the researchers decided to look for similar fossils in another part of the same rock layer some distance away in an area called Yehliu Geopark.

It wasn’t long before Löwemark called Pan over. He had found a complete fossil,  starting with a funnel at the top that narrows to a cylindrical tube about three centimetres in diameter, descending straight into the ground for 70 or 80 centimetres, before bending horizontally into an L-shape, reaching a total length of about two metres

“We were super excited,” Pan recalled. “This really could help us to connect the puzzle together and make the story more complete.”

The top part of the fossil burrow, seen from the side, is funnel shaped, with feathery lines from the disturbance of the soil that’s thought to be caused by the worm pulling prey into the burrow. (Paleoenvironntal Sediment Laboratory/National Taiwan University)

In total, the researchers found 319 fossil specimens at the two sites. A chemical analysis of the fossils found they were high in iron, which is typical of burrows made by soft-bodied animals. That’s because they tend to stabilize their burrows with mucus that attracts microbes that enrich the sediment with iron.

The fact that the tunnel was L-shaped also suggested that it was made by a soft-bodied animal, as such animals can’t dig too deep before the ground gets too hard and compacted for them to continue, and they need to start digging horizontally.

The burrows were different in size and shape from burrows made from other animals, such as eels or razor clams. 

But when the researchers compared the fossil burrows to the burrows of modern Bobbit worms, which inhabit modern ecosystems not much different from those that the fossil was found in, they appeared very similar.

Dashtgard suggests that means the worms have been living in a similar environment for quite a long time — about 20 million years.

‘Feathery footprint’ from Taiwan

The researchers named their new fossil Pennichnus formosae. The first part of the name refers to the feathery (“penna” in Latin) “footprint” (“ichnus” in Latin) left in the top “funnel” of the burrow by the way the sediments were disturbed when the animal pulled its prey inside. “Formosae” after Formosa, a former name for Taiwan, honours the place it was found, 

Pan said the fossil is notable because it provides clues about hunting behaviour of an ancient invertebrate, something that is quite rare.

The study coauthors included, from left, Shahin Dashtgard, Ludvig Lowemark, Yu Yen Pan and Masakazu Nara, standing on right. (Paleoenvironmental Sediment Laboratory/National Taiwan University)

David Rudkin was one of the researchers who studied the Ontario Bobbit worm jaw fossils but was not involved in the trace fossil study. Rudkin, a retired assistant curator at the Royal Ontario Museum and a retired lecturer at the University of Toronto, said while he isn’t an expert in trace fossils, he found the interpretation in the new study “pretty convincing.”

“The kicker, of course, would be finding a direct association in the form of either ‘jaw’ elements or soft-body bits within the burrows, left after the animal died in place,” he said in an email.

Unfortunately, the conditions that preserve burrows and those that preserve bodies tend to be quite different, so they’re rarely found together, he said. 

“Under the circumstances,” he said, “I think the authors have done a nice job of making the case for these being Bobbit burrows!”

This is an artistic reconstruction of Websteroprion amrstrongi, a Bobbit worm that lived 400 million years ago in Ontario. Its fossil jaws were discovered and reported by a team of researchers that included David Rudkin at the Royal Ontario Museum in Toronto. (James Ormiston)

More burrows likely to be found

Murray Gingras is professor at the University of Alberta who studies traces made by modern animals and compares them to the fossil record. He wasn’t involved in the new study but has gone to Australia to study the burrows of modern Bobbit worms as part of his own research.

One challenge with trace fossils, he said, is that many animals can make very similar traces and figuring out which one any given trace came from requires some interpretation. But in this case, he thinks the researchers’ interpretation is reasonable and well argued.

“I think it’s a fun discovery,” he said. 

He said he’s surprised such fossil burrows haven’t been found before given how widespread Bobbit worms are and how conspicuous their burrows are.

He suspects that many more will be found now that other researchers know what to look for, and that will help uncover the animals’ movements and distribution over the past 20 million years.

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SpaceX opens up Starlink internet beta program to eligible Canadians – MobileSyrup

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Starlink has opened up its beta program to more people, as the website now lets you sign up immediately if your location is eligible.

Reddit users have discovered that if you live in an eligible area, you are now able to sign up for the beta program and purchase the necessary equipment. Prior to this, you could only take part in the beta if you received an email invite from Starlink.

“Enter your email and service address below to participate in Starlink’s beta program. If service is not yet available in your area, we will notify you when it becomes available,” the website reads.

To check if you’re eligible for the beta program, you just need to head to the Starlink website and enter your home address. You’ll then be notified if you’re eligible for the program right away, after which you can place an order for the hardware package.

If your location is not eligible for the program, you can sign up to be notified of future beta opportunities in your area.

In terms of pricing, Starlink internet costs $129 per month in Canada and the equipment costs $649. Some Canadians who are already part of the beta have reported welcome improvements in connectivity.

Starlink aims to leverage an extensive network of hundreds of low-Earth-orbit (LEO) satellites to provide high-speed internet across parts of the U.S. and Canada. SpaceX recently launched its 17th batch of Starlink satellites, putting the total Starlink constellation size at almost 1,000.

Image credit: Starlink 

Source: Reddit Via: Tesla North 

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