Hackaday Links: February 23, 2020

February 23, 2020 by Dan Maloney 19 Comments

If you think your data rates suck, take pity on New Horizons. The space probe, which gave us lovely pictures of the hapless one-time planet Pluto after its 2015 flyby, continued to plunge and explore other, smaller objects in the Kuiper belt. In January of 2019, New Horizons zipped by Kuiper belt object Arrokoth and buffered its findings on the spacecraft’s solid-state data recorders. The probe has been dribbling data back to Earth ever since at the rate of 1 to 2 kilobits per second, and now we have enough of that data to piece together a story of how planets may have formed in the early solar system. The planetary science is fascinating, but for our money, getting a probe to narrowly miss a 35-kilometer long object at a range of 6.5 billion km all while traveling at 51,500 km/h is pretty impressive. And if as expected it takes until September to retrieve all the data from the event at a speed worse than dialup rates, it’ll be worth the wait.

Speaking of space, if you’re at all interested in big data, you might want to consider putting your skills to work in the search for extraterrestrial intelligence. The Berkeley SETI Research Center has been feeding data from the Green Bank Telescope and their Automated Planet Finder into the public archive of Breakthrough Listen, a 10-year, $100 million initiative to scan the million closest stars in our galaxy as well as the 100 nearest galaxies for signs of intelligent life. They’re asking for help to analyze the torrents of data they’re accumulating, specifically by developing software and algorithms to process the data. They’ve set up a site to walk you through the basics and get you started. If you’re handy with Python and have an interest in astronomy, you should check it out.

Staying with the space theme, what’s the best way to get kids interested in space and electronics? Why, by launching a satellite designed to meme its way across the heavens, of course. The Mission for Education and Multimedia Engagement satellite, or MEMESat-1, is being planned for a February 2021 launch. The 1U cubesat will serve as an amateur radio repeater and slow-scan TV (SSTV) beacon that will beam down memes donated to the project and stored on radiation-hardened flash storage. In all seriousness, this seems like a great way to engage the generation that elevated the meme to a modern art form in a STEM project they might otherwise show little interest in.

It looks as though Linux might be getting a big boost as the government of South Korea announced that they’re switching 3.3 million PCs from Windows to Linux. It’s tempting to blame Microsoft’s recent dropping of Windows 7 support for the defenestration, but this sounds like a plan that’s been in the works for a while. No official word on which distro will be selected for the 780 billion won ($655 million) effort, which is said to be driven by ballooning software license costs and a desire to get out from under Microsoft’s thumb.

And finally, in perhaps the ickiest auction ever held, the “Davos Collection” headed to the auction block this week in New York. The items offered were all collected from the 2018 World Economic Forum in Davos, Switzerland, where the world’s elites gather to determine the fate of the 99.999%. Every item in the collection, ranging from utensils and glassware used at the many lavish meals to “sanitary items” disposed of by the billionaires, and even hair and fluid samples swabbed from restrooms, potentially holds a genetic treasure trove in the form of the DNA it takes to be in the elite. Or at least that’s the theory. There’s a whole “Boys from Brazil” vibe here that we find disquieting, and we flatly refuse to see how an auction where a used paper cup is offered for $8,000 went, but if you’d like to virtually browse through the ostensibly valuable trash of oligarchs, check out the auction catalog.

Hackaday Podcast 055: The Most Cyberpunk Synthesizer, Data In Your Cells, Bubbly In Your Printer, And The Dystopian Peepshow

February 21, 2020 by Mike Szczys 2 Comments

Hackaday editors Mike Szczys and Elliot Williams discuss the many great hacks of the past week. Just in case you missed the fact that we’re living in the cyberpunk future, you can now pop off your prosthetic hand and jack directly into a synthesizer. The robot headed for Mars has a flying drone in its belly. Now they’re putting foaming agent in filament to make it light and flexible. And did you ever wonder why those pinouts were so jumbled?

Take a look at the links below if you want to follow along, and as always tell us what you think about this episode in the comments!

Take a look at the links below if you want to follow along, and as always, tell us what you think about this episode in the comments!

Direct download (60 MB or so.)

Continue reading “Hackaday Podcast 055: The Most Cyberpunk Synthesizer, Data In Your Cells, Bubbly In Your Printer, And The Dystopian Peepshow” →

DNA Now Stands For Data And Knowledge Accumulation

February 18, 2020 by Bob Baddeley 33 Comments

Technology frequently looks at nature to make improvements in efficiency, and we may be nearing a new breakthrough in copying how nature stores data. Maybe some day your thumb drive will be your actual thumb. The entire works of Shakespeare could be stored in an infinite number of monkeys. DNA could become a data storage mechanism! With all the sensationalism surrounding this frontier, it seems like a dose of reality is in order.

The Potential for Greatness

The human genome, with 3 billion base pairs can store up to 750MB of data. In reality every cell has two sets of chromosomes, so nearly every human cell has 1.5GB of data shoved inside. You could pack 165 billion cells into the volume of a microSD card, which equates to 165 exobytes, and that’s if you keep all the overhead of the rest of the cell and not just the DNA. That’s without any kind of optimizing for data storage, too.

This kind of data density is far beyond our current digital storage capabilities. Storing nearly infinite data onto extremely small cells could change everything. Beyond the volume, there’s also the promise of longevity and replication, maintaining a permanent record that can’t get lost and is easily transferred (like medical records), and even an element of subterfuge or data transportation, as well as the ability to design self-replicating machines whose purpose is to disseminate information broadly.

So, where is the state of the art in DNA data storage? There’s plenty of promise, but does it actually work?

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Art Imitates DNA

February 1, 2020 by Al Williams 8 Comments

It has recently been possible to pay a service a little bit of money and learn more about your own DNA. You might find out you really aren’t Italian after all or that you are more or less susceptible to some ailments. [Paul Klinger] had his DNA mapped and decided to make a sculpture representing his unique genetic code. The pictures are good, but the video below is even better.

The project requires a DNA sequencing, a 3D printer, and a Raspberry Pi Zero. Oh, you can probably guess you need a lot of RGB LEDs, too. Of course, the display doesn’t show the whole thing at one time — your DNA pattern scrolls across the double helix.

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Put The Power Of PCR In Your Pocket With This Open-Source Thermal Cycler

January 26, 2020 by Dan Maloney 23 Comments

When the first thermal cyclers for the polymerase chain reaction came out in the 1980s, they were as expensive as a market driven by grant money could make them. Things haven’t got much better over the years, largely shutting STEM classes and biohackers out of the PCR market. That may be about to change, though, if the €99.00 PocketPCR thermal cycler takes hold.

PCR amplifies DNA in a three-step process: denaturation, which melts double-stranded DNA into single strands; annealing, which lets small pieces of primer DNA bind to either side of the region of interest; and elongation, where the enzyme DNA polymerase zips along the single strands starting at the primer to replicate the DNA. The cycle repeats and copies of the original DNA accumulate exponentially. Like any thermal cycler, [Urs Gaudenz]’s PocketPCR automates those temperature shifts, using a combination of PCB-mounted heating elements and a cooling fan. The coils rapidly heat a reaction block up to the 99°C denaturation temperature, the fan brings that down to the 68°C needed for annealing, and then the temperature ramps back up to 72°C for elongation with thermostable DNA polymerase. PID loops keep the reaction temperature precisely controlled. The whole thing is, as the name suggests, small enough to fit in a pocket, and can either be purchased in kit form or scratch-built from the build files on GitHub.

We applaud [Urs]’ efforts to get the power of PCR into the hands of citizen scientists. Quick and dirty thermal cyclers are one thing, but Pocket PCR has a great fit and finish that makes it more accessible.

Thanks to [Abe Tusk] for the tip.

A Beginner’s Guide To X-Ray Crystallography

January 21, 2020 by Dan Maloney 6 Comments

In graduate school, I had a seminar course where one of the sections was about X-ray crystallography. I was excited, because being able to discern the three-dimensional structure of macromolecules just by shining X-rays on them seemed like magic to me. And thanks to a lackluster professor, after the section it remained just as much of a mystery.

If only I’d had [Steve Mould] as a teacher back then. His latest video does an outstanding job explaining X-ray crystallography by scaling up the problem considerably, using the longer wavelength of light and a macroscopic target. He begins with a review of diffraction patterns, those alternating light and dark bands of constructive and destructive interference that result when light shines on two closely spaced slits — the famous “Double-Slit Experiment” that showed light behaves both as a particle and as a wave and provided our first glimpse of quantum mechanics. [Steve] then doubled down on the double-slit, placing another pair of slits in the path of the first. This revealed a grid of spots rather than alternating bands, with the angle between axes dependent on the angle of the slit pairs to each other.

Shining a laser through a light bulb can reveal the structure of DNA 3-29 screenshot

$Photo_51_x-ray_diffraction_image$

Photograph 51, an X-ray crystallogram of the B-form of DNA, by Gosling and Franklin, 1952. Source: Wikipedia

To complete the demonstration, [Steve] then used diffraction to image the helical tungsten filament of an incandescent light bulb. Shining a laser through the helix resulted in a pattern bearing a striking resemblance to what’s probably the most famous X-ray crystallogram ever: [Rosalind Franklin]’s portrait of DNA. It all makes perfect sense, and it’s easy to see how the process works when scaled down both in terms of the target size and the wavelength of light used to probe it.

Hats off to [Steve] for making something that’s ordinarily complex so easily understandable, and for filling in a long-standing gap in my knowledge.

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A DNA-Based Computer Calculates Square Roots Up To 900

January 12, 2020 by Sharon Lin 20 Comments

While DNA-based computing may not be taking over silicon quite so soon, there is progress in the works. In a paper published by Small, researchers from the University of Rochester demonstrate a molecular computing system capable of calculating square roots of integers up to 900. The computer is built from synthetic biochemical logic gates using hybridization, a process where two strands of DNA join to form double-stranded DNA, and strand displacement reactions.

DNA-based circuits have already been shown to implement complex logic functions, but most existing circuits prior to the recent paper were unable to calculate square root operations. This required 4-bit binary numbers – the new prototype implements a 10-bit square root logic circuit, operating up to the decimal integer 900.

The computer uses 32 strands of DNA for storing and processing information. The process uses three modules, starting off with encoding a number on the DNA. Each combination is attached to a florescent marker, which changes signal during hybridization in the second module. The process for calculating the square root controls the signals, with the results deducted from the final color according to a threshold set in the third module.

We’re beginning to see the end of Moore’s Law approaching, with companies like Intel and AMD struggling to shrink transistors 10 nm wide. Nevertheless, with DNA molecules still about 10 time smaller than the best transistors today and DNA computing systems continuing to gain in sophistication, biochemical circuits could potentially be holding solutions to increasing the speed of computing beyond silicon computing.