Movie Encoded in DNA is the First Step Toward Datalogging with Living Cells

While DNA is a reasonably good storage medium, it’s not particularly fast, cheap, or convenient to read and write to.

What if living cells could simplify that by recording useful data into their own DNA for later analysis? At Harvard Medical School, scientists are working towards this goal by using CRISPR to encode and retrieve a short video in bacterial cells.

CRISPR is part of the immune system of many bacteria, and works by storing sequences of viral DNA in a specific location to identify and eliminate viral infections. As a tool for genetic engineering, it’s cheaper and has fewer drawbacks than previous techniques.

Besides generating living rickrolls and DMCA violations, what is this good for? Cheap, self-replicating sensors. [Seth Shipman], part of the team of scientists at Harvard, explains in an interview below a number of possible applications. His focus is engineering cells to act as a noninvasive data acquisition tool to study neurobiology, for example by using engineered neurons to record their developmental history.

It’s possible to see how this technique can be used more broadly and outside an academic context. Presently, biosensors generally use electric or fluorescent transducers to relay a detection event. By recording data over time in the DNA of living cells, biosensors could become much cheaper and contain intrinsic datalogging. Possible applications could include long-term metabolite (e.g. glucose) monitors, chemical detectors, and quality control.

It’s worth noting that this technique is only at the proof of concept stage. Data was recorded and retrieved manually by the scientists into the bacterial genome with 90% accuracy, demonstrating that if cells can be engineered to record data themselves, accuracy and capacity are high enough for practical applications.

That being said, if anyone is working on a MEncoder or ffmpeg command line option for this, let us know in the comments.

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Practical IoT Cryptography on the Espressif ESP8266

The Espressif ESP8266 chipset makes three-dollar ‘Internet of Things’ development boards an economic reality. According to the popular automatic firmware-building site nodeMCU-builds, in the last 60 days there have been 13,341 custom firmware builds for that platform. Of those, only 19% have SSL support, and 10% include the cryptography module.

We’re often critical of the lack of security in the IoT sector, and frequently cover botnets and other attacks, but will we hold our projects to the same standards we demand? Will we stop at identifying the problem, or can we be part of the solution?

This article will focus on applying AES encryption and hash authorization functions to the MQTT protocol using the popular ESP8266 chip running NodeMCU firmware. Our purpose is not to provide a copy/paste panacea, but to go through the process step by step, identifying challenges and solutions along the way. The result is a system that’s end-to-end encrypted and authenticated, preventing eavesdropping along the way, and spoofing of valid data, without relying on SSL.

We’re aware that there are also more powerful platforms that can easily support SSL (e.g. Raspberry Pi, Orange Pi, FriendlyARM), but let’s start with the cheapest hardware most of us have lying around, and a protocol suitable for many of our projects. AES is something you could implement on an AVR if you needed to.

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Game Boy Mod Uses Raspberry Pi Compute Module 3

[inches] wanted the power of a Raspberry Pi 3 in a form factor closer to the Pi Zero for a Game Boy mod. This led him to design a custom PCB to interface with one of the less popular items in the Raspberry Pi line: the Compute Module 3. A hardware comparison between the three platforms is available here.

After correcting some minor issues, it booted correctly on the first try. The final result is slightly larger than a Raspberry Pi Zero, but significantly smaller than the Raspberry Pi 3, and fits perfectly inside the Game Boy for a clean build.

The Raspberry Pi Zero remains difficult to source in some parts of the world and can cost nearly as much as the more powerful CM3 (e.g. in Southeast Asia). If you’re comfortable making a breakout board and benefit from the added computing power, it’s a reasonable option when it needs to be small.

Worth noting is that the Raspberry Pi Foundation does sell an open-source development kit for the CM3 that has been used in some projects, but the retail cost is relatively high compared to a Raspberry Pi 3. Smaller but less feature-rich breakout boards like the one by [inches] make the CM3 more accessible.

Thanks to [Lou Hannoe] for the tip.

 

 

Energy Harvesting Wristwatch Uses a Versatile Photodiode

There’s some interesting technology bundled into this energy harvesting wristwatch. While energy harvesting timepieces (called automatic watches) have been around for nearly 240 years, [bobricius] has used parts and methods that are more easily transferable to other projects.

Unlike early mechanical systems, this design uses the versatile BPW34 PIN photodiode (PDF warning). PIN photodiodes differ from ordinary PN diodes in that there’s a layer of undoped ‘intrinsic’ silicon separating the P and N doped layers. This reduces the utility of the diode as a rectifier, while allowing for higher quantum efficiency and switching speed.

They are typically used in the telecommunications industry, but have a number of interesting ‘off label’ applications. For example, the BPW34 can be used as a solid-state particle detector (although for detecting alpha particles you’re better off with something in a TO-5 package such as the Hamamatsu S1223-01). The fast response speed means you can send data with lasers or ambient light at high frequencies – a fun use for an LED lighting system or scrap DVD-RW laser.

Some common solar panels are essentially large PIN photodiodes. These are the brownish panels that you’ll find in a solar-powered calculator, or one of those eternally waving golden plastic neko shrines. They specifically offer excellent low-light performance, which is the basis of the energy harvesting used in this project.

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Attack on the Clones: A Review of Two Common ESP8266 Mini D1 Boards

ESP8266-based development boards have proliferated rapidly. One favorite, the WEMOS Mini-D1 is frequently imitated and sold without any branding. As these boards continue to ship to hobbyists and retailers around the world, we thought it might be interesting to conduct a little experiment.

There are a few ESP8266 development boards available, and the most popular seem to be the NodeMCU ‘Amica’ board. Of course, there are dozens of other alternatives including the WiFiMCU, Sparkfun’s ESP8266 Thing, and Adafruit’s HUZZAH ESP8266. Given that, why is this review limited to the Mini D1 boards? Because the Mini D1 is the cheapest. Or was, until it was cloned.

We took a look at some of these ‘clone’ boards to figure out the differences, find out if they work as intended, and perhaps most importantly, are these clone boards shipped out reliably. What are the results? Check that out below.

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Conflict Escalates Between Brilliant Rat and 555 Timer

After [Casey Connor] captured and relocated a number of unwanted rodents in his home using commercially available live traps, he was presented with a problem: a rat had learned to avoid them.

In an epic, and adorable, conflict caught on video (and embedded below),  he documents the  designs used and how the rat escaped them by either recognizing the trap, or sheer agility. We can only tip our hat to the determination of both parties.

All the trap mechanisms are based on a 555 monostable solenoid triggering circuit that ensures that a pulse of sufficient duration is sent to the solenoid to trigger the trap correctly. This way even intermittent contacts will trigger the trap rather than just causing the solenoid to twitch without fully actuating. This is the same technique used to debounce a switch using a 555 timer.

A Raspberry Pi Zero detects motion using an IR camera to film the interesting parts. This is also a good indicator for when you’ve trapped your quarry – if you’re trying be humane then leaving it in a trap for days is counterproductive.

With the time and effort we spend building better and more complex rodent traps, we sometimes wonder who has cleverly trapped whom.

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