Start Up No.1851: AlphaFold predicts protein universe, data centres slow housing build, endemic monkeypox?, and more

The supply of secondhand pricey watches has suddenly boomed following the crypto crash. Coincidence? Vendors think not. CC-licensed photo by Seko Fotografía on Flickr.

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A selection of 9 links for you. Tickety-boo. I’m @charlesarthur on Twitter. Observations and links welcome.

‘The entire protein universe’: AI predicts shape of nearly every known protein • Nature

Ewen Callaway:


From now, determining the 3D shape of almost any protein known to science will be as simple as typing in a Google search.

Researchers have used AlphaFold — the revolutionary artificial-intelligence (AI) network — to predict the structures of more than 200 million proteins from some 1 million species, covering almost every known protein on the planet.

The data dump is freely available on a database set up by DeepMind, the London-based AI company, owned by Google, that developed AlphaFold, and the European Molecular Biology Laboratory’s European Bioinformatics Institute (EMBL–EBI), an intergovernmental organization near Cambridge, UK.

“Essentially you can think of it covering the entire protein universe,” DeepMind chief executive Demis Hassabis said at a press briefing. “We’re at the beginning of new era of digital biology.”

The 3D shape, or structure, of a protein is what determines its function in cells. Most drugs are designed using structural information, and the creation of accurate maps of proteins’ amino-acid arrangement is often the first step to making discoveries about how proteins work.

DeepMind developed the AlphaFold network using an AI technique called deep learning, and the AlphaFold database was launched a year ago with more than 350,000 structure predictions covering nearly every protein made by humans, mice and 19 other widely studied organisms. The catalogue has since swelled to around 1 million entries.

“We’re bracing ourselves for the release of this huge trove,” says Christine Orengo, a computational biologist at University College London, who has used the AlphaFold database to identify new families of proteins. “Having all the data predicted for us is just fantastic.”

This really is one of the great breakthroughs by AI, but it could take years for its effect to be felt in the outside world. Also, it’s 23TB for the entire database, which is going to mean lots of local storage (plus updates) or lots of pricey cloud storage.

Even so, in some ways this is as crucial as the first genome sequencing. Another British (DeepMind) success.
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Debt-ridden water giants at risk from rate rises • The Sunday Times

Jon Yeomans:


Net debt in the water sector topped £56bn last year, according to Ofwat. One of the most indebted firms, Thames Water, took steps to shore up its finances last month with the injection of £1.5bn of fresh equity from shareholders.

Last year, Southern Water was taken over by Australian bank Macquarie after coming close to bankruptcy. Last week, it became the first big water company to implement a hosepipe ban because of the dry conditions across England.

Scrutiny of [the UK’s 25] water companies has grown after a damning report by the Environment Agency earlier this month recommended that company directors be jailed if they fail to meet their responsibilities to clean up rivers. Emma Boyd, the agency’s chairwoman, said performance on pollution had “hit a new low”, adding: “Company directors let this happen. We plan to make it too painful for them to continue like this.”

The warning on rates comes as the Bank is this week expected to raise rates from 1.25% by as much as half a percentage point, as it seeks to tame inflation that is running at 9.4%.

Ofwat was granted new powers last year to enforce greater financial resilience in the water sector. It said its proposals on curbing payouts to water company owners “will reinforce the link between performance and dividends”. The proposals will remain open for consultation until September 29.

The regulator has already attracted strong resistance from water utilities after floating its ideas at the end of last year. In one response to the proposals, Thames Water warned that tighter rules on dividends could have “unintended consequences — by making it more challenging to attract equity” from investors.


Ofwat’s page on the (privatised in 1989) water companies financial resilience has a spreadsheet which is faintly worrying: gearing (the debt/equity ratio) averages 72%. For a monopoly that could be OK, except the rate they can charge is fixed, so rising interest rates mean a squeeze where they can’t raise costs: investment or dividends must slow.
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Housing development in England under threat as electricity capacity nears limits • Financial Times

George Hammond:


New housing development in London and the south-east of England is at risk as electricity networks near capacity and upgrades are stalled, according to experts, despite the UK government forecasting increased demand for power almost a decade ago.

Electricity demand has fallen in recent years as homes have become more efficient, but it is forecast to rise as drivers adopt electric vehicles and homeowners install heat pumps, placing additional demands on local networks.

Three boroughs in west London have paused development because there is no spare capacity for new connections to the electricity grid until 2035, the Financial Times reported on Thursday.

Experts on Friday warned the problem could spread as national efforts to hit net zero carbon emissions boost electricity consumption, unless networks are quickly upgraded to withstand extra demand.

“The truth is, the overall electricity system is creaking a bit,” said Guy Newey, formerly energy adviser to two Conservative business secretaries and now boss of Energy Systems Catapult, an independent research centre.

Warning that power outages were likely without upgrades, he added: “If we’re serious about net zero targets we have to build ahead of need, otherwise you’ll keep getting stories like west London.”


But how could it be that west London, which has all sorts of space to its west, could be struggling?


In Hillingdon, Ealing and Hounslow, the network has come under strain far faster than expected because a series of data centres, which can consume as much energy as thousands of homes, have been connected.

According to the Energy Networks Association, which represents network operators, the volume of new requests for connections from data centres in the past two years alone has equalled the entire area’s electricity demand.


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Axie Infinity has left Filipino gamers despondent and in debt • TIME

Andrew Chow and Chad De Guzman:


amerson Orias was working as a line cook last year in the rural Philippines when his friend told him he could make way more money playing a new video game.

Orias was earning about 4,000 pesos a month (about $80, a little less than half the national minimum wage) making takoyaki—Japanese octopus balls. His friend told him he and others were pocketing up to $600 a month playing Axie Infinity, a game fueled by cryptocurrency and NFTs.

Orias, now 26, desperately needed an escape hatch from his financial woes: his mother had had a stroke and required medication, and electricity and grocery bills were stacking up. So he plunged into Axie, doing battle with cartoon monsters for hours deep into the night. He soon began earning cryptocurrency, which he converted into pesos, allowing him to take better care of his mother and his home. At the same time, thousands of young people in the Philippines were jumping headlong into the game. For a brief moment at the peak of crypto’s astonishing 2021 boom, these young Filipino players were fulfilling a longtime dream of crypto’s most ardent evangelists: that “play-to-earn” blockchain games like Axie could lead the way to a more equitable, opportunity-rich global economy.

Fourteen months later, most Filipino players, including Orias, have exited the game nursing anger and anxiety—and, in some cases, thousands of dollars down. Orias grew to hate playing the game. It was boring and stressful, he says, a common refrain among the dozen players TIME interviewed for this story. “I felt fatigued all the time. I became more aggressive in every aspect of my life,” he says.


Data point:


The game initially made a huge impact in the Philippines. At one point, players there made up 40% of the game’s user base.


An indenturing scheme developed inside the Philippines, which is what created the indebtedness. Same as so many schemes for earning money or whatever in games.
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It may be too late to stop monkeypox becoming endemic in the US and Europe • Daily Beast

David Axe:


Monkeypox is spreading fast all over the world, especially in the United States and Europe. With cases doubling every two weeks or so, there’s a growing risk that monkeypox will become a permanent problem in countries where, before, outbreaks were rare and small.

The pox is, in other words, close to becoming endemic in a lot of new places. If that happens, it might become very difficult to eradicate. Monkeypox, which causes a fever and rash and is fatal in a very small number of cases, will become yet another disease that people have to worry about all the time.

For the pox, there are two paths to endemicity. If the virus infects enough people fast enough to outpace authorities’ efforts to trace transmission and vaccinate at-risk individuals, it might become endemic in people. “We are getting close to this already,” James Lawler, an infectious disease expert at the University of Nebraska Medical Center, told The Daily Beast.

The good news with this kind of endemicity is that it doesn’t have to be permanent. Reversing human endemicity is hard, yes—but it’s possible. “If it’s just spreading in humans it can be controlled—eventually—through vaccination and natural immunity,” Amesh Adalja, a public health expert at the Johns Hopkins Center for Health Security, told The Daily Beast.

But monkeypox was originally a “zoonotic” animal virus. It circulates in rodent and monkey species in West and Central Africa, where outbreaks in the human population are frequent.

If the pox finds a home in some animal species in North America or Europe—say, squirrels, rats, or prairie dogs—it’ll be all but impossible to eradicate regionally.


This other article says it has 50 mutations, far more than you’d expect for its type. Possibly it’s an example of immune escape from immunocompromised hosts, as we’ve seen with SARS-Cov-2. (Thank G for the links.)
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The crypto market collapse has flooded the luxury watches from brands like Rolex • Bloomberg

Andy Hoffman:


The collapse in cryptocurrencies is easing supply of the most sought after watches on the second-hand market, depressing prices for hard-to get-Patek Philippe and Rolex models.

The supply of trophy watches such as the Rolex Daytona or Patek Nautilus 5711A “is now much larger,” online-watch trading platform Chrono24 said in an emailed statement. 

The recent swoon in cryptocurrency valuations “has directly impacted pricing of luxury watches from brands like Rolex and Patek Philippe,” said the company, which is based in Karlsruhe, Germany, and has more than half a million watches listed for sale on its website.

The price decline for the most sought after models is the latest indication that the once soaring second-hand luxury watch market is starting to lose pace. Surging valuations for crypto currencies had minted a new class of luxury buyers, leading to an unprecedented price increase for models particularly from brands like Rolex, Audemars Piguet and Patek. Now that many digital tokens have been hammered, these consumers are going into reverse.


Never have understood the desire to have a super-pricey watch. They’re not just premium, as in well-made; they’re super-expensive but without any further functionality than others. And of course less functionality than a smartwatch, which you could upgrade multiple times for the price of one of those. Feel free to point me to someone explaining this.
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Meta officially cuts funding for US news publishers • Axios

Sara Fischer:


Meta on Tuesday began telling its news partners in the US that the company no longer plans to pay publishers for their content to run on Facebook’s News Tab, sources tell Axios.

As the company moves forward with sweeping changes to the Facebook experience, news has become less of a priority.

Meta’s VP of media partnerships, Campbell Brown, told staffers the company was shifting resources away from its news products to support more creative initiatives, the Wall Street Journal reported.

Facebook brokered a slew of three-year deals with publishers in 2019. At the time, the company was ramping up its investment in news and hired journalists to help direct publisher traffic to its new tab for news.

The deals were worth roughly $105m in the US, sources told Axios. In addition to that, the company spent around $90m on news videos for the company’s video tab called “Watch.”

“A lot has changed since we signed deals three years ago to test bringing additional news links to Facebook News in the US. Most people do not come to Facebook for news, and as a business it doesn’t make sense to over-invest in areas that don’t align with user preferences,” a Facebook spokesperson told Axios.


Back and forth it goes: Facebook does like news, it doesn’t like news, although it loves video more and more (until it pauses and doesn’t because friends and family users don’t make much video). It’s like a slow-motion abusive relationship.
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The dirty carbon secret behind solid state memory drives • Discover Magazine


Swamit Tannu at University of Wisconsin in Madison and Prashant Nair at the University of British Columbia in Vancouver have measured the carbon footprint per gigabyte of these devices across their entire lifetimes and, unexpectedly, it turns out that SSDs are significantly dirtier. “Compared to SSDs, the embodied [carbon] cost of HDDs is at least an order of magnitude lower,” say the researchers.

Tannu and Nair come to their conclusion by adding up the amount of carbon emitted throughout the estimated 10-year lifespans of these devices. This includes the carbon emitted during manufacture, during operation, for transportation and for disposal.

The carbon emitted during operation is straightforward to calculate. To read and write data, HDDs consume 4.2 Watts versus 1.3W for SSDs. The researchers calculate that a 1 terabyte HDD emits the equivalent of 159 kilograms of carbon dioxide during a 10-year operating lifespan. By comparison, a 1 terabyte SSD emits just 49.2 kg over 10 years.

But SSDs are significantly more carbon intensive to manufacture. That’s because the chip fabrication facilities for SSDs operate at extreme temperatures and pressures that are energy intensive to maintain. And bigger memories require more chips, which increases the footprint accordingly.

All this adds up to a significant carbon footprint for SSD manufacture. Tannu and Nair calculate that manufacturing a 1 terabyte SSD emits the equivalent of 320 kg of carbon dioxide. By comparison, a similar HDD emits just 40 kg.

So the lifetime footprint for a 1 terabyte SSD is 369.2 kg of carbon dioxide equivalent versus 199 kg for an HDD. So HDDs are much cleaner.

That’s a counterintuitive result with important implications. At the very least, it suggests that computer manufacturers and cloud data storage operators should reconsider the way they use SSDs and HDDs.


I suspect the cloud companies (at the least) won’t, because the operation output is so low. Manufacturing output is, as so often, someone else’s problem – the manufacturer’s?
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Astrobiologists suggest the Earth itself may be an intelligent entity • Futurism

Tony Ho Tran:


A group of researchers have posed a fascinating — and downright mind bending — thought experiment: If a planet like Earth can be “alive,” can it also have a mind of its own?

The team published a paper exploring this question in the International Journal of Astrobiology. In it, they present the idea of “planetary intelligence,” which describes the collective knowledge and cognition of an entire planet.

…The researchers point to evidence that underground networks of fungi can communicate to suggest that large-scale networks of life could form a vast invisible intelligence that profoundly alters the condition of the entire planet.

One of the primary species driving that change at the moment, they point out, are humans — and currently, from the climate to the plastic crisis, we may well be irrevocably changing the environmental balance.

“We don’t yet have the ability to communally respond in the best interests of the planet,” Adam Frank, professor of physics at the University of Rochester and coauthor of the paper, said in a press release about the paper. 

The researchers believe that such thought experiments can help humans to understand their impact on the Earth and serve as a guide on how to better it. Interestingly, they also believe that it could aid in the search for aliens too.

“We’re saying the only technological civilizations we may ever see — the ones we should expect to see — are the ones that didn’t kill themselves, meaning they must have reached the stage of a true planetary intelligence,” Frank said. 


So it’s “may” as in “could be”. All very Solaris, isn’t it?
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• Why do social networks drive us a little mad?
• Why does angry content seem to dominate what we see?
• How much of a role do algorithms play in affecting what we see and do online?
• What can we do about it?
• Did Facebook have any inkling of what was coming in Myanmar in 2016?

Read Social Warming, my latest book, and find answers – and more.

Errata, corrigenda and ai no corrida: none notified

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