So What Is Protein Folding, Anyway?

April 14, 2020 by Dan Maloney 26 Comments

The current COVID-19 pandemic is rife with problems that hackers have attacked with gusto. From 3D printed face shields and homebrew face masks to replacements for full-fledged mechanical ventilators, the outpouring of ideas has been inspirational and heartwarming. At the same time there have been many efforts in a different area: research aimed at fighting the virus itself.

Getting to the root of the problem seems to have the most potential for ending this pandemic and getting ahead of future ones, and that’s the “know your enemy” problem that the distributed computing effort known as Folding@Home aims to address. Millions of people have signed up to donate cycles from spare PCs and GPUs, and in the process have created the largest supercomputer in history.

But what exactly are all these exaFLOPS being used for? Why is protein folding something to direct so much computational might toward? What’s the biochemistry behind this, and why do proteins need to fold in the first place? Here’s a brief look at protein folding: what it is, how it happens, and why it’s important.

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John Horton Conway, Creator Of Conway’s Game Of Life, Has Died

April 13, 2020 by Mike Szczys 57 Comments

Programmers everywhere are familiar with Conway’s Game of Life: whether they’ve written a version themselves or simply seen the mesmerizing action resulting from the cellular automata, it’s a household name in all homes where code is spoken. On Saturday April 11th, 2020 its inventor and namesake, John Horton Conway passed away from COVID-19 at the age of 82.

Born in Liverpool, Conway received his PhD in mathematics in 1964 from Gonville and Caius College, Cambridge. He accepted a position at Sidney Sussex College, Cambridge which he held until joining the faculty of Princeton University in 1987. A brilliant mathematician, he received numerous awards and was well known for his work in combinatorial game theory, group theory, and theoretical physics.

Many readers will be familiar with his Doomsday algorithm which can be used to deduce the day of the week for any given date in your head. But by far the rockstar mathematics moment of developing Conway’s Game of Life in 1970 cements him a perpetual place of legend in computing lore. His original work on the concept used pencil and paper as the computing revolution had yet to make digital resources easily available, even to mathematics researchers like Conway.

The game uses an infinite grid of squares where all of the edges of the grid wrap around. Four simple rules (which can be boiled down to three if you’re clever) determine which cells live and which cells die during each frame of the “game”. The only parameters that are needed are the number and position of living cells at the start of the game, and the delay between each game frame. But the effect of this simplicity is not to be understated. The game can be coded by a novice — and it’s become a common challenge in University course work. Small errors, or intentional tweaks, in the implementation have profound effects on behavior of the game. And the effect on the person programming it for the first time can be long lasting. You could call it a mathematics gateway drug, grabbing the curiosity of the unsuspecting mind and pulling it down the rabbit hole of advanced mathematics discovery.

We’d love to celebrate his life by hearing your own stories of programming the Game of Life in the comments below. If you haven’t yet had the pleasure, now’s a great time to take on the challenge.

[Game of Life example shown in this article is John Conway’s Game of Life – 1.0 written in Python by Nick Jarvis and Nick Wayne]

Will 2020 (Finally) Be The Year Of Electronic Paper?

April 13, 2020 by Tom Nardi 85 Comments

These days paper is being phased out whenever possible, and while we’re still far from being a completely digital society, the last decade or two has seen a huge reduction in the amount of paper the average person deals with on a daily basis. At the very least, we seem a lot closer to a future without the printed page than we are flying cars or any of the other concepts we generally associate with the far-flung future.

That said, there’s still something undeniably appealing about reading on paper. The idea of squirting ink on a piece of thin wood might seem increasingly archaic to us, but it sure does look nice when you hold it in your hand. Which is exactly why so much effort has been put into recreating the look of printed paper in electronic form; we all love the experience of paper, but the traditional execution doesn’t align itself particularly well with modern sensibilities.

Of course electronic “eReaders”, most notably the Kindle line from Amazon, have gone a long way towards making this a reality. At least for reading books, anyway. But what about magazines, newspapers, or even the lowly notebook we keep by the bench to jot down measurements or ideas? A PDF datasheet, with graphics where the grey tones matter? Being able to carry a whole bookshelf worth of novels in your bag is incredible, but despite what science fiction has promised us since 2001: A Space Odyssey, we’re still consuming plenty of media off of dead trees.

But that might be changing soon. This year will see the release of two tablets that promise to deliver an experience much closer to reading and writing on traditional paper than anything we’ve seen previously. They certainly aren’t cheap, and it’s too early to tell how much is just hype, but these devices could end up being an important step towards the paperless future we’ve been dreaming of.

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Three Years Of HardwareX: Where Are They Now?

April 13, 2020 by Orlando Hoilett 8 Comments

After three years of online publications, HardwareX may have solidified itself as an academic journal for open-source hardware. We originally wrote about HardwareX back in 2016. At the time, HardwareX hadn’t even published its first issue and only begun soliciting manuscripts. Now after three years of publishing, six issues as of October 2019 (with the seventh scheduled for April 2020), and an impact factor of 4.33, it’s fair to say that Elsevier’s push into open-access publications is on a path to success.

To give you a bit of background, HardwareX aims to promote the reproducibility of scientific work by giving researchers an avenue to publish all the hardware and software hacks that often get buried in traditional manuscripts. The format of HardwareX articles is a bit different than most academic journals. HardwareX articles look more like project pages similar to Hackaday.io. (Maybe we inspired them a bit? Who knows.)

It’s a bold attempt on Elsevier’s part because although open-access is held as an ideal scenario for scientific work, such efforts often come under quite a bit of scrutiny in the academic community. Don’t ask us. We can’t relate.

Either way, we genuinely wish Elsevier all the best and will keep our eyes on HardwareX. Maybe some of our readers should consider publishing their projects in HardwareX.

COVID-19 And The State Of The Climate

April 10, 2020 by Zoe Skyforest 48 Comments

The novel coronavirus sweeping the globe has led governments to institute widespread quarantines to stem the spread. Many industries have slowed production or shutdown entirely, and economic activity has slowed to a crawl. This has naturally led to a sudden reduction in greenhouse gas emissions. But how great will the effect be, and will it buy us any real time?

On The Ground

Nitrogen dioxide levels in China have dropped sharply with the reduction in industrial activity due to COVID-19. Image source: NASA

In the wake of COVID-19, good news stories have sprung up as people look for a silver lining. Unfortunately, these stories aren’t always true. There aren’t dolphins in the waters of Venice, though the water has cleared due to reduced boat activity. And drunken elephants did not begin roaming the mountains of China.

Despite this, there have been notable reductions in emissions in several areas due to government-mandated lockdowns. Northern Italy is seeing a much lower concentration of nitrogen dioxide, likely due to reduced industrial and vehicular activity. Carbon monoxide levels have similarly dropped in New York, while China has seen its carbon emissions temporarily drop by a full 25%.

On the surface of it, these are all promising numbers. Many are cautiously optimistic that this could be a major development to help stave off the worst of climate change for a little longer. Nonetheless, it’s early days yet, and what happens after the crisis passes is just as important as what’s happening now.

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This Week In Security: Zoom (Really This Time), Fingerprints, And Bloatware

April 10, 2020 by Jonathan Bennett 9 Comments

You were promised Zoom news last week, but due to a late night of writing, that story was delayed to this week. So what’s the deal with Zoom? Google, SpaceX, and even the government of Taiwan and the US Senate have banned Zoom. You may remember our coverage of Zoom from nearly a year ago, when Apple forcibly removed the Zoom service from countless machines. The realities of COVID-19 have brought about an explosion of popularity for Zoom, but also a renewed critical eye on the platform’s security.

“Zoombombing”, joining a Zoom meeting uninvited, made national headlines as a result of a few high profile incidents. The US DOJ even released a statement about it. Those incidents seem to have been a result of Zoom default settings: no meeting passwords, no “waiting room”, and meeting IDs that persist indefinitely. A troll could simply search google for Zoom links, and try connecting to them until finding an active meeting. Ars ran a great article on how to avoid getting zoombombed (thanks to Sheldon for pointing this out last week).

There is another wrinkle to the Zoom story. Zoom is technically an American company, but its Chinese roots put it in a precarious situation. Recently it’s been reported that encryption keying is routed through infrastructure in China, even though the calling parties are elsewhere. In some cases, call data itself goes through Chinese infrastructure, though that was labeled as a temporary bug. Zoom was also advertising its meetings as having end-to-end encryption. That claim was investigated, and discovered to be false. All meetings get decrypted at Zoom servers, and could theoretically be viewed by Zoom staff. Continue reading “This Week In Security: Zoom (Really This Time), Fingerprints, And Bloatware” →

No Windshield? No Problem, Says McLaren

April 9, 2020 by Kristina Panos 79 Comments

All the best sports cars look like they’re moving when they’re just sitting there, and the lines on McLaren’s newest limited-edition plaything redefine that look of speed standing still. Maybe it’s the sneering headlights or the streamlined, reverse-1966 Batmobile styling. Whatever it is, the 804-horsepower two-seater project Elva looks like it’s leaping off the line into the future.

But this future is free from the last thing we’d expect to see removed from any vehicle, especially a $1.7 million supercar — the windshield. Now that the headphone jack has been deemed expendable, it seems that nothing is sacred. The Elva is already a permanent convertible with no windows.

Though McLaren didn’t start this weird and windowless fire, the Elva is meant to fan the flames of futurism. She joins the ranks of a few windshield-free models from Ferrari, Mercedes-Benz, and Aston Martin. In the other guy’s cars, you’ll need a helmet above 30MPH unless you love the thunderous sounds of air buffeting and blown-out hair. It’s a young idea with a few bugs to work out.

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