Life in the Lab | Southern Fried Science

Fun Science FRIEDay – Gut Enzyme Turns Blood Into Type O

Posted on November 16, 2018 by Kersey Sturdivant

The process of blood transfusions, started in the late 19th century and perfected in the early 20th century, were a big advancement in modern medicine and the treatment of human health. Part of the improvements in this procedure was the discovery of the various blood types in humans, and how that affects how the immune system responds to and “accepts” blood transfusions. Recently, researchers from the University of British Columbia may have found a reliable way to use a bacterial enzyme from the human gut to convert any type of blood into type O – which is compatible with nearly everyone.

Animation of red blood cells (Photo credit: meghanmecrazy)

Fun Science FRIEDay – Resurrection

Posted on August 3, 2018 by Kersey Sturdivant

Life has unbelievably complex and diverse strategies to ensure survival. Organisms are able to go dormant during unfavorable conditions, and resuscitate once the environment becomes ideal again. This can play out over relatively short time periods such as when animals hibernate, or over longer periods where organisms can go into stasis, e.g. reviving bacteria from 250 million year old salt crystals.

Researchers in Russia recently thawed out permafrost sediment frozen for the past 42,000 years, and revealed once frozen and now living nematodes. Yes you heard that correctly, worms birthed and subsequently frozen during the Pleistocene (42,000 years earlier) were just resurrected in the 21st century. Frankenstein, eat your heart out.

Eophasma jurasicum, a fossilized nematode. (Photo credit: Ghedoghedo)

Fun Science Holidays – The World’s Smallest Snowman

Posted on December 31, 2016 by Kersey Sturdivant

As 2016 winds to a close, and in the spirit of the holiday season behold the world’s smallest snowman, measuring in at 3 microns. To put that into perspective, the smallest grains of sands are approximately 60 microns.

Mini snowman, ~3 microns in height (Photo credit: Western Nanofabrication Facility)

This creation is the work of Canadian nanotechnologists from the Western Nanofabrication Facility. The snowman is made from three ~1 micron silica spheres stacked using electron beam lithography. The eyes and mouth were cut with a focused ion, beam while the arms and nose were sculpted with platinum.

Tiny snowman amongst other 1 micron silica spheres. (Photo credit: Western Nanofabrication Facility)

A cool feel good story to round off 2016 as we head into 2017. Happy New Year all!

Trading blue collars for scarlet robes, my working-class experience of academic life

Posted on June 9, 2016 by Michelle Jewell

More people are going to college, graduate school, and obtaining PhDs in STEM fields than ever before (Figure 1), and a growing minority of these PhD candidates are non-traditional or not white affluent males. While we celebrate this change, let us not forget that academia was built by – and for – the “traditional” student. My favourite analogy to explain this type of ingrown privilege is bicycles on USA streets. Bicycles are legally allowed to be on streets, some streets even have extra space just for bicycles, but streets were designed for automobiles. You may be allowed and, in some areas, encouraged to get on the street with your bicycle, but biking a street is going to be intrinsically more difficult than if you were driving a car.

Like Marconi and La Bamba in a city built on rock and roll, you will inevitably end up in situations that conflict with your way of life. You will not receive a warning before you stumble upon these bumps, and you will be judged by how quickly you accept traditional standards (if you can). I remember a conversation with traditional tenured and tenure-track scientists discussing proposals for a large grant scheme. One tenure-track scientist was lamenting the process of shopping for editors for his proposal. He talked about it freely, how there were two companies that charged different rates and he was in talks with one but that company felt a conflict of interest that he had worked with another rival editing company. The rest of the traditional scientists nodded in mutual understanding. Finding good, cheap editors to improve your work is hard. My working-class ethos was busy screaming inside my head. How can hiring someone to edit and improve written works that you will ultimately be rewarded for be so blithely acceptable? You’re not allowed to hire editors for any task throughout your training. You learn how to write from earning disappointing grades (or failing grant applications). You read more, you study written works, you develop a voice, and you try again. The results get better until you are at an appropriate level to move up another notch on the ladder, right? Not for traditionals.

Here are some more bizarre “traditional” customs you should expect if you are biking down the academic street:

Build your own BeagleBox 2!

Posted on May 9, 2016 by Andrew Thaler

A more comprehensive build guide, along with the 3D printer files, can be found in the BeagleBox GitHub Repository.

The BeagleBox 2 is a dirt-cheat, tough, versatile field computer built from 3D-printed parts, off-the-shelf hardware, and a single board computer. You can read all about it here: The BeagleBox 2: a dirt-cheap, tough-as-nails, 3D-printed, versatile field laptop.

Let’s build one!

The Brain of the BeagleBox 2

The BeagleBox 2: a dirt-cheap, tough-as-nails, 3D-printed, versatile field laptop.

Posted on May 9, 2016 by Andrew Thaler

The BeagleBox 2

Last year, as part of Oceanography for Everyone, we debuted the BeagleBox, a small, cheap, tough, basic field computer powered by a BeagleBone Black. The first BeagleBox didn’t promise much, it was designed for basic field work and, most importantly, to be cheap enough that researchers (particularly grad students) wouldn’t be too worried about damaging it. It wasn’t designed to be your only computer but to replace your more valuable computer when participating in fieldwork.

In the last year, the single board computer landscape has changed, with new systems running off tiny, powerful 64bit ARM chips. One of the first of this new breed of SCB to hit the market was the massively Kickstarted, and rocky-launching Pine64. I received my 1GB Pine64 late last week, and immediately set to work redesigning the BeagleBox to house this larger board (and correct for some other annoyances in the original design). So here it is, an even beefier, cheaper, tougher field machine.

Yes, it will run an OpenROV. It will not run it well.

A 3D-printable, drone and ROV-mountable, water sampler

Posted on August 10, 2015 by Andrew Thaler

The Niskin bottle, a seemingly simple tube designed to take water samples at discrete depths, is one of the most important tools of oceanography. Coupled with a CTD, an array of Niskin bottles fit into the rosette, a Voltron-esque amalgamation of everything an oceanographer needs to profile the ocean. Niskin bottles are neither cheap nor particularly easy to use. A commercial rosette requires a decent-sized winch to launch and recover, which means you need a vessel and a crew to deploy. For Rogue Ecologist and citizen scientists, getting a high-quality, discrete water sample is a perpetual challenge. With tools like the OpenROV and the soon-to-be-completed EcoDrone, I wanted a Niskin bottle that was light weight and capable of being mounted on both underwater robots and quadcopters with ease.

Until now.

After a few months of brainstorming and planning, I sat down this Friday and began building a 3D printable Niskin bottle that could be hand deployed or mounted on an OpenROV or drone. While this version is designed around a 1.25 inch acrylic tube, the trigger mechanism can be expanded to fit any size pipe. The trigger is driven by a waterproof servo developed by the good folks over at OpenROV. Everything else can either be purchased off-the-shelf or printed on you home 3D printer. Later this month, I’ll be taking my prototypes out on the RV Blue Heron for field testing in Lake Superior.

Bill of Materials Read More

Graduate minions vs masterminds

Posted on July 30, 2015 by Chris Parsons

The other day I overheard an academic tell an upcoming graduate student that they should pick a PhD project by finding an advisor who already had a project set up and who had funding and that they should do research where the funding was rather than where their interests lay. This was so totally contrary to my PhD experience it left me reeling.

Build a dirt cheap, tough-as-nails field computer in a Pelican case

Posted on July 21, 2015 by Andrew Thaler

For and updated version of the BeagleBox, please go here: The BeagleBox 2: a dirt-cheap, tough-as-nails, 3D-printed, versatile field laptop.

Fieldwork is tough. You’re in the elements, facing wind, rain, and salt spray, sometime on an open boat far out in the Atlantic. You and your gear takes a beating. But you’re out there because there’s science that need to get done.

But your equipment is controlled via computer, and your data entry mandates a computer, which means your precious laptop needs to come with you. For graduate students and early career scientists, this can be a dilemma. I’ve see the calculations happen as my colleagues prepare for the field–do I take my one and only computer out into the field and risk damaging it, or do I leave it brute-force my way through sampling without it. That is, if they’re lucky enough to have alternative methods they can employ. For some gear, there’s no choice but to take the computer.

This equation is, counter-intuitively, getting worse. Our sensors, sampling devices, and scanners are getting cheaper and lighter. Rather than buying a $20,000 piece of equipment, you can get a $20 chip, but there’s a trade off, and the trade off is that chip based systems rely on external processing power, they need a general computer, and that means your laptop is coming with you.

I don’t like going out on the water with my laptop. Losing it would be frustrating and time consuming. It’s tough, but it’s not tough-as-nails. And it’s definitely not cheap.

So I tapped into the wealth of Maker experience I’ve accumulated over the last few years and build a new one, using a single board computer, some extra peripherals, and a 3D printer. And I shoved the whole thing into a Pelican case. Say hello to the BeagleBox, a dirt cheap, tough-as-nails field computer for about $200.