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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.

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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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SpaceX launch marks 300th successful booster landing – Phys.org

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Credit: Unsplash/CC0 Public Domain

SpaceX sent up the 30th launch from the Space Coast for the year on the evening of April 23, a mission that also featured the company’s 300th successful booster recovery.

A Falcon 9 rocket carrying 23 of SpaceX’s Starlink internet satellites blasted off at 6:17 p.m. Eastern time from Cape Canaveral Space Force Station’s Space Launch Complex 40.

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The first-stage booster set a milestone of the 300th time a Falcon 9 or Falcon Heavy booster made a successful recovery landing, and the 270th time SpaceX has reflown a booster.

This particular booster made its ninth trip to space, a resume that includes one human spaceflight, Crew-6. It made its latest recovery landing downrange on the droneship Just Read the Instructions in the Atlantic Ocean.

The company’s first successful booster recovery came in December 2015, and it has not had a failed booster landing since February 2021.

The current record holder for flights flew 11 days ago making its 20th trip off the .

SpaceX has been responsible for all but two of the launches this year from either Kennedy Space Center or Cape Canaveral with United Launch Alliance having launched the other two.

SpaceX could knock out more launches before the end of the month, putting the Space Coast on pace to hit more than 90 by the end of the year, but the rate of launches by SpaceX is also set to pick up for the remainder of the year with some turnaround times at the Cape’s SLC-40 coming in less than three days.

That could amp up frequency so the Space Coast could surpass 100 launches before the end of the year, with the majority coming from SpaceX. It hosted 72 launches in 2023.

More launches from ULA are on tap as well, though, including the May 6 launch atop an Atlas V rocket of the Boeing CST-100 Starliner with a pair of NASA astronauts to the International Space Station.

ULA is also preparing for the second launch ever of its new Vulcan Centaur rocket, which recently received its second Blue Origin BE-4 engine and is just waiting on the payload, Sierra Space’s Dream Chaser spacecraft, to make its way to the Space Coast.

Blue Origin has its own it wants to launch this year as well, with New Glenn making its debut as early as September, according to SLD 45’s range manifest.

2024 Orlando Sentinel. Distributed by Tribune Content Agency, LLC.

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SpaceX launch marks 300th successful booster landing (2024, April 24)
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Wildlife Wednesday: loons are suffering as water clarity diminishes – Canadian Geographic

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The common loon, that icon of northern wilderness, is under threat from climate change due to declining water clarity. Published earlier this month in the journal Ecology, a study conducted by biologists from Chapman University and Rensselaer Polytechnic Institute in the U.S. has demonstrated the first clear evidence of an effect of climate change on this species whose distinct call is so tied to the soundscape of Canada’s lakes and wetlands.

Through the course of their research, the scientists found that July rainfall results in reduced July water clarify in loon territories in Northern Wisconsin. In turn, this makes it difficult for adult loons to find and capture their prey — mainly small fish — underwater, meaning they are unable to meet their chicks’ metabolic needs. Undernourished, the chicks face higher mortality rates. The consistent foraging techniques used by loons across their range means this impact is likely echoed wherever they are found — from Alaska to Canada to Iceland.

The researchers used Landsat imagery to find that there has been a 25-year consistent decline in water clarity, and during this period, body weights of adult loon and chicks alike have also declined. With July being the month of most rapid growth in young loons, the study also pinpointed water clarity in July as being the greatest predictor of loon body weight. 

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One explanation for why heavier rainfall leads to reduced water clarity is the rain might carry dissolved organic matter into lakes from adjacent streams and shoreline areas. Lawn fertilizers, pet waste and septic system leaks may also be to blame.

The researchers, led by Chapman University professor Walter Piper, hope to use these insights to further conservation efforts for this bird Piper describes as both “so beloved and so poorly understood.”

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Giant prehistoric salmon had tusk-like teeth for defence, building nests

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The artwork and publicity materials showcasing a giant salmon that lived five million years ago were ready to go to promote a new exhibit, when the discovery of two fossilized skulls immediately changed what researchers knew about the fish.

Initial fossil discoveries of the 2.7-metre-long salmon in Oregon in the 1970s were incomplete and had led researchers to mistakenly suggest the fish had fang-like teeth.

It was dubbed the “sabre-toothed salmon” and became a kind of mascot for the Museum of Natural and Cultural History at the University of Oregon, says researcher Edward Davis.

But then came discovery of two skulls in 2014.

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Davis, a member of the team that found the skulls, says it wasn’t until they got back to the lab that he realized the significance of the discovery that has led to the renaming of the fish in a new, peer-reviewed study.

“There were these two skulls staring at me with sideways teeth,” says Davis, an associate professor in the department of earth sciences at the university.

In that position, the tusk-like teeth could not have been used for biting, he says.

“That was definitely a surprising moment,” says Davis, who serves as director of the Condon Fossil Collection at the university’s Museum of Natural and Cultural History.

“I realized that all of the artwork and all of the publicity materials and bumper stickers and buttons and T-shirts we had just made two months prior, for the new exhibit, were all out of date,” he says with a laugh.

Davis is co-author of the new study in the journal PLOS One, which renames the giant fish the “spike-toothed salmon.”

It says the salmon used the tusk-like spikes for building nests to spawn, and as defence mechanisms against predators and other salmon.

The salmon lived about five million years ago at a time when Earth was transitioning from warmer to relatively cooler conditions, Davis says.

It’s hard to know exactly why the relatives of today’s sockeye went extinct, but Davis says the cooler conditions would have affected the productivity of the Pacific Ocean and the amount of rain feeding rivers that served as their spawning areas.

Another co-author, Brian Sidlauskas, says a fish the size of the spike-toothed salmon must have been targeted by predators such as killer whales or sharks.

“I like to think … it’s almost like a sledgehammer, these salmon swinging their head back and forth in order to fend off things that might want to feast on them,” he says.

Sidlauskas says analysis by the lead author of the paper, Kerin Claeson, found both male and female salmon had the “multi-functional” spike-tooth feature.

“That’s part of our reason for hypothesizing that this tooth is multi-functional … It could easily be for digging out nests,” he says.

“Think about how big the (nest) would have to be for an animal of this size, and then carving it out in what’s probably pretty shallow water; and so having an extra digging tool attached to your head could be really useful.”

Sidlauskas says the giant salmon help researchers understand the boundaries of what’s possible with the evolution of salmon, but they also capture the human imagination and a sense of wonder about what’s possible on Earth.

“I think it helps us value a little more what we do still have, or I hope that it does. That animal is no longer with us, but it is a product of the same biosphere that sustains us.”

This report by The Canadian Press was first published April 24, 2024.

Brenna Owen, The Canadian Press

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