Open-Source Biology And Biohacking Hack Chat

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.

join-hack-chatOur 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.

Hacked Heating Instruments For The DIY Biology Lab

[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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Arachnid Ale Uses Yeast To Make Spider Silk

Many people who read Hackaday hold the title of “Webmaster” but [The Thought Emporium] is after slightly different credentials with the same title. He aims to modify a strain of yeast to produce spider silk. Charlotte’s Web didn’t go into great detail about the different types of silk that a spider can produce, but the video and screencap after the break give a rundown of how spiders make different types of silk, and that each species of spider makes a unique silk. For this experiment, the desired silk is “beta sheets” which the video explains are hard and strong.

Some of the points mentioned in the video rely on things previously mentioned in other videos, but if you are the type of person excited by genetic modifications or using modified yeast to produce something made by another lifeform, you will probably be just fine. This is one of the most technical videos made by [The Thought Emporium] as he goes into the mechanisms of the modifications he will be making to the yeast. It sounds like a lot of work and the financial benefit of being able to produce spider silk affordably could be great, but in true hacker form, the procedure and results will be made freely available.

For some background into this hacker’s mind, check out how he has hacked his own lactose intolerance and even produced graphene through electrochemical exfoliation.

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Raspberry Pi Tracks Starter Fermentation For Optimized Sourdough

Those of you who’ve never had a real sourdough have never had real bread. Good food fights back a little when you eat it, and a proper sourdough, with its crispy crust and tangy center, certainly fits the bill. Sourdough aficionados, your humble writer included, all have recipes that we pretend are ancient family secrets while in reality we’re all just guessing. Sourdough is partly science, partly art, but mostly delicious black magic.

In an effort to demystify his sourdough process, [Justin Lam] has gone digital with this image processing sourdough starter monitor. Sourdough breads are leavened not by the addition of brewers yeast (Saccharomyces cerevisiae), but by the inclusion of a starter,  a vibrant ecosystem of wild yeasts that is carefully nurtured, sometimes for years. Like any other living thing, it needs to be fed, a task that should happen at the point of maximum fermentation. Rather than guess when this might be, [Justin] used a Raspberry Pi Zero and PiCam to capture a time-lapse video of the starter as the beasties within give off their CO₂, thus expanding it up inside its container. A little Python does the work of thresholding and finding the top of the starter as it rises, allowing [Justin] to plot height of the starter over time. He found that peak height, and therefore peak fermentation, occurs about six hours after feeding. He has used his data to better inform his feeding schedule and to learn how best to revive neglected starters.

Surprisingly, this isn’t the first time we’ve discussed sourdough here. It seems that someone uses Git for iterative sourdough recipe development, and we once featured a foundry made from a pyrolyzed loaf of sourdough.

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Breadboarding: Git For A/B Testing Actual Bread

We will be the first to admit, we like to use Git for a lot of things that are probably off the beaten path. But now thanks to [hendricius] you can find out how to make your own bread on GitHub. Let’s get one thing straight. This isn’t the breadmaker fad from a while back, although we are surprised we don’t see more hacked together breadmakers with Internet connectivity. This is old-fashioned bread baking with a bowl, some ingredients, and an oven or another heat source.

You might think this is just using Git as a repository for recipes, but it is more than that. According to [hendricius]:

Learn how to master the art of baking the programmer way. If you love programming, you will also enjoy breaking some bread. A/B test, iterate and ultimately become a self-taught baker. This repository is dedicated to becoming your bread manifesto with useful tricks and hacks. Furthermore, the goal is to illustrate how easy making bread is and that you can get started today without expensive tools.

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The Biohacking Movement And Open Source Insulin

In March of 2014, I knew my eight year old daughter was sick. Once borderline overweight, she was now skeletally thin and fading away from us. A pre-dawn ambulance ride to the hospital gave us the devastating news – our daughter had Type 1 diabetes, and would be dependent on insulin injections for the rest of her life.

This news hit me particularly hard. I’ve always been a preparedness-minded kind of guy, and I’ve worked to free myself and my family from as many of the systems of support as possible. As I sat in the dark of the Pediatric ICU watching my daughter slowly come back to us, I contemplated how tied to the medical system I had just become. She was going to need a constant supply of expensive insulin, doled out by a medical insurance system that doesn’t understand that a 90-day supply of life-saving medicine is a joke to a guy who stocks a year supply of toilet paper. Plus I had recently read an apocalyptic novel where a father watches his 12-year old diabetic daughter slip into a coma as the last of her now-unobtainable insulin went bad in an off-grid world. I swore to myself that I’d never let this happen, and set about trying to find ways to make my own insulin, just in case.

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That’s Not Beer! A Biofuel Fermentation Controller Project

biofuel-fermentation-controller

Any home brewer will recognize the setup pictured above as a temperature controlled fermentation chamber. They wouldn’t be wrong either. But you’re not going to drink what results. This project is aimed at providing a temperature controlled environment for fermenting biofuel.

[Benjamin Havey] and [Michael Abed] built the controller as their final project in his microprocessor class. The idea is to monitor and control the mini-refrigerator so that the strain of Saccharomyces Cerevisiae yeast produce as much ethanol as possible. An MSP430 microcontroller was used. It monitors a thermister with its analog to digital converter and drives a solid state relay to switch mains power to the fridge. At 41 degrees Fahrenheit this is down below what most lager yeasts want (which is usually in the low fifties). But the nice thing about using a microcontroller is you can set a schedule with different stages if you find a program that gives the yeast the best environment but requires more than one temperature level.

Who knew all that beer making was getting you ready to produce alternative fuels?