Open-Source Biology And Biohacking Hack Chat

February 11, 2019 by Dan Maloney 16 Comments

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.

Simple, Low-Cost Rig Lets The Budding Biohacker Run DNA Gels

December 1, 2018 by Dan Maloney 12 Comments

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.

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Katrina Nguyen Automates Her Mice

November 29, 2018 by Dan Maloney 5 Comments

When embarking on a career in the life sciences, it seems like the choice of which model organism to study has more than a little to do with how it fits into the researcher’s life. I once had a professor who studied lobsters, ostensibly because they are a great model for many questions in cell biology; in actuality, he just really liked to eat lobster. Another colleague I worked with studied salt transport in shark rectal glands, not because he particularly liked harvesting said glands — makes the sharks a tad grumpy — but because he really liked spending each summer on the beach.

Not everyone gets to pick a fun or delicious model organism, though, and most biologists have had to deal with the rats and mice at some point. It’s hard to believe how needy these creatures can be in terms of care and feeding, and doubly so when feeding is part of the data you’re trying to collect from them. Graduate student Katrina Nguyen learned this the hard way, but rather than let her life be controlled by a bunch of rodents, she hacked a solution that not only improved her life, but also improved her science. She kindly dropped by the Hackaday Superconference to tell us all about how she automated her research.

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See Cells In A New Light With A DIY Fluorescence Microscope

November 21, 2018 by Dan Maloney 2 Comments

Ever since a Dutch businessman peered into the microscopic world through his brass and glass contraption in the 1600s, microscopy has had a long, rich history of DIY innovation. This DIY fluorescence microscope is another step along that DIY path that might just open up a powerful imaging technique to amateur scientists and biohackers.

In fluorescence microscopy, cells are treated with various fluorescent dyes that can be excited with light at one wavelength and emit light at another. But as [Jonathan Bumstead] points out, fluorescence microscopes are generally priced out of the range of biohackers. His homebrew scope levels the playing field a bit. The trick is to use 3D-printed parts to kit out commonly available digital cameras – a USB microscope, a DSLR, or even a smartphone camera. Excitation is provided by a ring of Nexopixel LEDs, while a movable rack holds a filter that blocks the excitation wavelength but allows the emission wavelength to pass through to the camera. He demonstrates the technique by staining some threads with fluorescent ink from a highlighter marker and placing them on a sheet of tissue paper; in conventional bright-field mode, the threads all but disappear into the background, but jump right out under fluorescence.

Ith’s true that the optics are not exactly lab quality, and the microscope is currently only set up to do reflectance imaging as opposed to the more typical transmissive mode where the light passes through the sample. That’s an easy fix, though, and reflectance mode is still useful. We’ve seen fluorescence microscopy get quite complex before, but this simple scope might be enough to get a biohacker started.

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Hacked Heating Instruments For The DIY Biology Lab

November 12, 2018 by Dan Maloney 4 Comments

[Justin] from The Thought Emporium takes on a common molecular biology problem with these homebrew heating instruments for the DIY biology lab.

The action at the molecular biology bench boils down to a few simple tasks: suck stuff, spit stuff, cool stuff, and heat stuff. Pipettes take care of the sucking and spitting, while ice buckets and refrigerators do the cooling. The heating, however, can be problematic; vessels of various sizes need to be accommodated at different, carefully controlled temperatures. It’s not uncommon to see dozens of different incubators, heat blocks, heat plates, and even walk-in environmental chambers in the typical lab, all acquired and maintained at great cost. It’s enough to discourage any would-be biohacker from starting a lab.

[Justin] knew It doesn’t need to be that way, though. So he tackled two common devices: the incubator and the heating block. The build used as many off-the-shelf components as possible, keeping costs down. The incubator is dead simple: an insulated plastic picnic cooler with a thermostatically controlled reptile heating pad. That proves to be more than serviceable up to 40°, at the high end of what most yeast and bacterial cultures require.

The heat block, used to heat small plastic reaction vessels called Eppendorf tubes, was a little more complicated to construct. Scrap heat sinks yielded aluminum stock, which despite going through a bit of a machinist’s nightmare on the drill press came out surprisingly nice. Heat for the block is provided by a commercial Peltier module and controller; it looks good up to 42°, a common temperature for heat-shocking yeast and tricking them into taking up foreign DNA.

We’re impressed with how cheaply [Justin] was able to throw together these instruments, and we’re looking forward to seeing how he utilizes them. He’s already biohacked himself, so seeing what happens to yeast and bacteria in his DIY lab should be interesting.

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Ask Hackaday: What Are Your Less Extreme Brain Hacks?

October 31, 2018 by Al Williams 51 Comments

Kahn — perhaps Star Trek’s best-hated villain — said: “Improve a mechanical device and you may double productivity, but improve man and you gain a thousandfold.” In fact, a lot of hacking effort goes into doing just that. Your phone has become an extension of your memory, for example. We use glasses, cameras, and hearing aids to shore up failing senses or even give us better senses than normal. But hacking your body — or someone else’s — has always been controversial. While putting an RFID chip in your finger is one thing, would you consider having a part of your brain removed? That sounds crazy, but apparently, there is a growing interest in having your amygdala removed.

To be clear: we think this is a terrible idea. The science is shaky, at best, and we certainly wouldn’t want to be among the first to try something so radical. But why is anyone even talking about it?

The amygdala is part of your brain that causes at least some of your fear and anxiety. Get rid of your amygdala, get rid of anxiety? What’s even stranger is this the procedure — an amygdalectomy — has been going on since the 1960s! Injections of oil and wax destroy the tissue and this treatment is used for some forms of epilepsy and to manage certain aggressive behavior problems in mentally ill patients. In modern times, the procedure is not very common although it appears that it does still occur in some places. But the technology to do it does exist. There have also been documented cases where people lose their amygdala from natural causes that gives us some clues of what life would be like without one.

However, it is hard to say if these people lost fear. Most of the surgical patients were already suffering from a variety of problems. There is some evidence that the naturally occurring amygdalaless patients experienced less fear in some situations, but may experience more fear in others. They also may have other problems such as difficulty understanding social cues or making eye contact. We’re not 100% sure what the amygdala does, even disregarding potential side effects.

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I Hear You Offer WiFi

September 22, 2018 by Brian McEvoy 13 Comments

We are swimming in radio transmissions from all around, and if you live above the ground floor, they are coming at you from below as well. Humans do not have a sensory organ for recognizing radio signals, but we have lots of hardware which can make sense of it. The chances are good that you are looking at one such device right now. [Frank Swain] has leaped from merely accepting the omnipresent signals from WiFi routers and portable devices to listening in on them. The audio signals are mere soundwaves, so he is not listening to every tweet and email password, merely a representation of the data’s presence. There is a sample below the break, and it sounds like a Geiger counter playing PIN•BOT.

We experience only the most minuscule sliver of information coming at us at any given moment. Machines to hack that gap are not had to find on these pages so [Frank] is in good company. Magnetosensory is a popular choice for people with a poor sense of direction. Echolocation is perfect for fans of Daredevil. Delivering new sensations could be easier than ever with high-resolution tactile displays. Detect some rather intimate data with ‘SHE BON.’

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