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Sensemaker: Biology’s breakthrough

Thursday 10 December 2020

What just happened


Long stories short

  • Brexit negotiations have been extended to Sunday but both sides say “large gaps” remain between their positions (more below). 
  • A prototype of Elon Musk’s SpaceX Starship exploded on landing after a six-minute test flight.
  • Britain signed a free trade agreement with Singapore that mirrors an existing one negotiated by the EU. 

Biology’s breakthrough

Last week’s announcement by DeepMind that it had worked out how to predict the structure of proteins with an algorithm is still sending ripples of excitement through the world of science – and industry, and environmentalism. One expert on plastic-eating enzymes told Tortoise he was so excited when the news broke that he couldn’t sleep all night. 

So, to recap. It can take months and sometimes years for biologists to accurately determine protein’s shapes, but they stick at it because structural models help scientists understand how proteins work, which in turn helps them solve problems and develop new drugs and technologies. 

How to speed that process up? By using AI. DeepMind, based in London but now owned by Google, last week announced the success of what it calls the AlphaFold2 system, which uses AI-powered modelling to predict how proteins fold, producing in hours extraordinary 3D models that look like party streamers. The company patted itself on the back for its “solution to a 50-year-old grand challenge in biology”.

The announcement was based on results from DeepMind’s participation in the Critical Assessment of protein Structure Prediction (CASP) programme, which has been encouraging research groups to develop predictive technologies since the 1990s. The groups test their tech on sequences of amino acids from recently discovered protein structures. The testing is done blind. They don’t have access to the structures beforehand, but their predictions are compared with the actual shape once they’ve produced a result. 

DeepMind’s predictions were incredibly accurate. A CASP insider told us he was “blown away” by AlphaFold’s results. In fact there was speculation about whether there’d been cheating.

Is it that exciting? Yes. Our sleepless enzyme researcher is Exhibit A here, but the ability to produce highly accurate models within hours – instead of waiting for models based on difficult, expensive methods like x-ray crystallography – should be revolutionary. 

Where?

  • Plastic waste: a few years ago, biotech researchers in Japan found an enzyme that can break down PET plastics – which, left to themselves, take at least 450 years to start decomposing. Other researchers are seeking to improve on that naturally-occurring enzyme by engineering versions that can work faster. AlphaFold could hugely accelerate this research. 
  • Drug discovery: Coupling DeepMind’s protein structure predictions with databases of drug-candidate chemicals should radically speed up drug discovery and design. Professor John Moult, chairman of CASP, anticipates new treatments for cancer and tropical diseases within five years. The Motley Fool reports that AlphaFold has already modelled in half an hour the shape of one bacterial protein that the Max Planck Institute in Germany had been working on for more than a decade. 
  • Biotechnology: the ability to predict structures for proteins not found in nature – for example, enzymes that are good at capturing CO2 from the environment – could make possible a new generation of climate enzyme engineering.

There’s always a caveat. Two years ago, DeepMind tested the first version of AlphaFold. Scientists were excited about it then but it took the company a year to release a paper about it and even then it released only a portion of the code that made it work. Will Google be more open to sharing the software this time round? Last week’s announcement said it was “exploring how best to provide broader access to the system”. AlphaFold has such enormous potential, it would be dismal if Google decided to treat it as just another piece of proprietary software.  


Wealth investment, fairness, prosperity

Oil money
Kuwait is in a tight spot. A general decline in the oil price and an additional Covid-induced slump mean that it’s forecasting a deficit of 40 per cent of GDP this year, according to the FT (£). Kuwait’s parliament is hesitant to draw down on the country’s $550 billion sovereign wealth fund and is blocking legislation which would allow it to lean on global debt markets to ease its liquidity problem. Few places on earth show quite as vividly as Kuwait that being rich doesn’t necessarily spare you from the curse of resource-dependency. It is baffling, though, that in their so-far half-hearted attempts at diversification the gulf states haven’t looked more seriously at their other big resource. Solar, anyone? 


New things technology, science, engineering

No more abuse
PornHub, the adult video streaming site, will change its rules to ban content uploads from unverified users following an investigation by the NYT ($) which found that searches on the site returned user-generated videos of child abuse, rape, revenge porn and spy camera footage filmed without consent. Campaigners have been raising this issue for years. In the past, PornHub has responded to claims that it profits from images of abuse by pointing to its “non-consensual content removal system”. Now Visa and Mastercard – two prominent financial partners of MindGeek, PornHub’s parent company – say they’re investigating the NYT’s allegations, and PornHub is taking action at last. Better late than never. 


Our planet environment, natural resources, geopolitics

Bugs’ lives
So-called charismatic animals such as bears, lynx and wolves attract far more money than imperilled invertebrates. Recent analysis of the EU’s Life programme, which finances conservation efforts, found that between 1992 and 2018 vertebrates received €970 million of funding compared with €150 million for invertebrates. Two species – wolves and bears – received €80 million between them. That’s a problem if you care about biodiversity. A 2017 study found that even in protected areas of Germany, populations of flying insects had declined by 75 per cent over three decades. Plumage and pelts are more appealing than worms and beetles but insects are an essential part of the life cycles of other plants and animals as pollinators and food sources. So spare a thought for the ugly endangered: they matter too. 


The 100-year life health, education, living, public polic

Taking flight
Aviation is still on life support because of Covid, and especially because of quarantine rules that have halted virtually all transatlantic flights. Overall, air traffic is projected to be down by 66 per cent this year. But there may be a solution to the quarantine conundrum. The first “Covid-tested” transatlantic flight since the start of the pandemic arrived in Rome from New York on Wednesday. The 100 passengers on the Alitalia flight had to show a negative Covid test taken within 48 hours of departure to be allowed on board. They had to change their masks every four hours in flight, and take another test on arrival in Italy. All tested negative, allowing them to waive Italy’s two-week quarantine period. These flights aren’t for fun – only essential travel to Italy is permitted – but if Italian officials get comfortable with the new routine holiday trips could resume in the new year. 


Belonging identity, society, beliefs, countries

Back from Brussels 
Last night Boris Johnson dined with EU commission president Ursula von der Leyen in Brussels in a last-ditch attempt to make a Brexit deal. After three hours of “lively” and “frank” (read: tempestuous) talks about the outstanding issues – fisheries, governance and the level playing field requirements on competition and regulation – Johnson did not come away with a deal, but he did get an extension of the deadline to Sunday, at which point “a firm decision should be taken about the future of the talks”.  

Thanks for reading, and do share this around. 

Ella Hill
@_EllaHill

Photographs Getty Images