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.
Data exfiltration via side channel attacks can be a fascinating topic. It is easy to forget that there are so many different ways that electronic devices affect the physical world other than their intended purpose. And creative security researchers like to play around with these side-effects for ‘fun and profit’.
Engineers at the University of California have devised a way to analyse exactly what a DNA synthesizer is doing by recording the sound that the machine makes with a relatively low-budget microphone, such as the one on a smart phone. The recorded sound is then processed using algorithms trained to discern the different noises that a particular machine makes and translates the audio into the combination of DNA building blocks the synthesizer is generating.
Although they focused on a particular brand of DNA Synthesizers, in which the acoustics allowed them to spy on the building process, others might be vulnerable also.
In the case of the DNA synthesizer, acoustics revealed everything. Noises made by the machine differed depending on which DNA building block—the nucleotides Adenine (A), Guanine (G), Cytosine (C), or Thymine (T)—it was synthesizing. That made it easy for algorithms trained on that machine’s sound signatures to identify which nucleotides were being printed and in what order.
Acoustic snooping is not something new, several interesting techniques have been shown in the past that raise, arguably, more serious security concerns. Back in 2004, a neural network was used to analyse the sound produced by computer keyboards and keypads used on telephones and automated teller machines (ATMs) to recognize the keys being pressed.
You don’t have to rush and sound proof your DIY DNA Synthesizer room just yet as there are probably more practical ways to steal the genome of your alien-cat hybrid, but for multi-million dollar biotech companies with a equally well funded adversaries and a healthy paranoia about industrial espionage, this is an ear-opener.
We written about other data exfiltration methods and side channels and this one, realistic scenario or not, it’s another cool audio snooping proof of concept.
If you are a science fiction fan, you are probably aware of one of the genre’s oddest dichotomies. A lot of science fiction is concerned about if a robot, alien, or whatever is a person. However — sometimes in the same story — finding life is as easy as asking the science officer with a fancy tricorder. If you go to Mars and meet Marvin, it is pretty clear he’s alive, but faced with a bunch of organic molecules, the task is a bit harder. Now it is going to get harder still because Cornell scientists have created a material that has an artificial metabolism and checks quite a few boxes of what we associate with life. You can read the entire paper if you want more detail.
Three of the things people look for to classify something as alive is that it has a metabolism, self-arranges, and reproduces. There are other characteristics, depending on who you ask, but those three are pretty crucial.
Continue reading “Forget Artificial Intelligence; Think Artificial Life”
Although it isn’t very real-world practical, researchers at Cal Tech have produced a DNA-based programmable computer. Spectrum reports that the system executes programs using a set of instructions written in DNA using six bits. Like any programmable computer, this one can execute many programs, but so far they have run 21 different programs.
Using DNA for computation isn’t new — your body does it all the time. But, in general, DNA computers were akin to some logic gates that would do one set of things, not a general-purpose reprogrammable computer.
DNA has two parts composed of four different chemicals — you can think of each part as a ladder cut vertically down the middle with each “rung” being one of the four chemicals. Each part will try to pair up with a part that has a complementary set of rungs. The researchers created DNA strands to act like logic gates that have two inputs and two outputs. They combine five of these gates to create a layer with six inputs and six outputs. A program contains a stack of these six-bit layers.
Continue reading “DNA Computers Are In The Lab Now”
Join us on Wednesday at noon Pacific time for the open-source biology and biohacking Hack Chat!
Justin Atkin‘s name might not ring a bell, but you’ve probably seen his popular YouTube channel The Thought Emporium, devoted to regular doses of open source science. Justin’s interests span a wide range, literally from the heavens above to the microscopic world.
His current interest is to genetically modify yeast to produce spider silk, and to perhaps even use the yeast for brewing beer. He and the Thought Emporium team have been busy building out a complete DIY biology lab to support the effort, and have been conducting a variety of test experiments along the way.
Please join us for this Hack Chat, in which we’ll cover:
- The how’s and why’s of yeast genetic engineering;
- What it takes to set up an effective biology lab from scratch;
- An update on the current status of the spider-silk yeast project; and
- Where the open-source biology field is, and where it’s going.
You are, of course, encouraged to add your own questions to the discussion. You can do that by leaving a comment on the Open-Source Biology and Biohacking Hack Chat event page and we’ll put that in the queue for the Hack Chat discussion.
Our Hack Chats are live community events on the Hackaday.io Hack Chat group messaging. This week we’ll be sitting down on Wednesday, February 13, at noon, Pacific time. If time zones have got you down, we have a handy time zone converter.
Click that speech bubble to the right, and you’ll be taken directly to the Hack Chat group on Hackaday.io. You don’t have to wait until Wednesday; join whenever you want and you can see what the community is talking about.
We use a lot of voltmeters and we bet you do too. We have some big bench meters and some panel meters and even some tiny pocket-sized meters. But biological researchers at the University of Chicago and Northwestern University have even smaller ones. They’ve worked out a way to use a DNA-based fluorescent reporter to indicate the voltage across cellular membranes.
We don’t know much about biology, but apparently measuring the voltage on the membrane around a cell is easy, but measuring the voltages across membranes inside the cell isn’t. Previous work disrupted cells and measured potentials on isolated organelles.
The indicator — called Voltair — can target specific parts of a cell and includes a reference indicator so that a ratiometric measurement is possible. In fact, there are three main parts to the 38-base pair DNA duplex. One module contains a voltage-sensing dye that fluoresces in a way that indicates voltage. The second module is a reference dye that allows researchers to judge the voltage level. The final module identifies where the probe should attach.
Continue reading “Tiny Voltmeter Uses DNA”
We all the know the basic components for building out an electronics lab: breadboards, bench power supply, a selection of components, a multimeter, and maybe an oscilloscope. But what exactly do you need when you’re setting up a biohacking lab?
That’s the question that [Justin] from The Thought Emporium is trying to answer with a series of videos where he does exactly that – build a molecular biology lab from scratch. In the current installment, [Justin] covers the basics of agarose gel electrophoresis, arguably the fundamental skill for aspiring bio-geeks. Electrophoresis is simply using an electric field to separate a population of macromolecules, like nucleic acids and proteins, based on their sizes. [Justin] covers the basics, from building a rig for running agarose gels to pouring the gels to doing the actual separation and documenting the results. Commercial grade gear for the job is priced to squeeze the most money out of a grant as possible, but his stuff is built on the cheap, from dollar-store drawer organizers and other odd bits. It all works, and it saves a ton of money that can be put into the things that make more sense to buy, like fluorescent DNA stain for visualizing the bands; we’re heartened to see that the potent carcinogen ethidium bromide that we used back in the day is no longer used for this.
We’re really intrigued with [Justin]’s bio lab buildout, and it inspires us to do the same here. This and other videos in the series, like his small incubators built on the cheap, will go a long way to helping others get into biohacking.
Continue reading “Simple, Low-Cost Rig Lets The Budding Biohacker Run DNA Gels”