Tag Archives: biology

The Erector Set of the 21st Century

We have reached a critical point for creation. A few hot spots bloom with innovation, but for the most part, our youth sits at home with Mario Kart and first person shooter games. Science education consists of baking soda and vinegar volcanoes, and kids lose interest in any science before they even realize what it is. Instead of embracing technology, we have started to fear the exciting advance we’re making. Newspapers write articles about “Bio-Hackers running Imageloose, threatening our livelihoods, our children” yet, a mentally disturbed man can buy an AK-47 and we can’t even pass an assault weapon ban. The public fears the wrong things entirely; most can’t even accomplish the bio-catastrophes they dread. We regulate and restrict things in the name of protection, yet we these little labs are more likely to make a glow-in-the dark gold fish than a bio-weapon.

We should be convincing kids to play with science, to foster innovation from an early age. The US fast falls behind other countries, but we can help change that. A 6 year old can extract DNA from a strawberry, a 10 year old can try their first experiment with algae. High school and college students should be encouraged and able to test their ideas, but they can’t even order a plasmid online. We need to make simple, and safe biology tools more open and available. We have a safety ranking system for biology, so why is Bio Safety Level 1, “suitable for work involving well-characterized agents not known to consistently cause disease in healthy adult humans, and of minimal potential hazard to laboratory personnel and the environment”, so restricted? Biotech companies don’t even want to deliver simple things like buffers to DIYBio labs. They’re too worried about getting sued.

These materials need to be widely available! Biotech stands poised in the same boom potential as tech and computers 20 years ago, but the difference lies in those with computers versus those with plasmids. We are going to fall behind and lose the potential for innovation if people cannot interact with Biotech. I envision a world where I can go to Amazon, go to the Bio category, and order some plasmids to run my experiment.

As a high school student looking to test an award winning project idea, I spent months looking for a lab to test my idea. After more than 100 emails, and 20 meetings, I found an internship, but I still couldn’t test my idea. What about all the other people that have biology ideas? I got inspired to open a Seattle Bio-Hackerspace, HiveBio, with my co-director Bergen McMurrary. We want to help make biology more accessible to the community. Because E. coli is fun! We need the legislation to change. In the 20s 30s, kids built crystal radios, in the 50s and 60s they built models, my parents played with Erector sets. DIYBiology can be the Erector set of today, but we have to change the legislation to help it and give the youth of today a creative outlet that will propel our society to a better world.Image

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Hackerspace Update – The circle begins

Not to keep up with stereotypes or anything, but I’m super excited to see The Hobbit. Long long ago, in a land far far away, when I believed I wanted to be an actress, I debuted in a camp production of The Hobbit at age 10. I wore white fuzzy socks for Hobbit feet. It was most excellent.Image

But um, away from my nerdi- I mean coolness, and back to bio! There is exciting news on the Hackerspace front. When I visited Genspace, the NYC Hackerspace, a couple of weeks ago, they put me in contact with someone who had expressed interest in starting a Seattle Hackerspace. Bergen McMurray works at the Allen Insitute and is part of the Hackerbot meetups in Seattle. I sent her an email and opened her reply with some trepidation. Had she already started, and I’d been out of the “popular bio group”, and so hadn’t heard? Had she failed, harangued by angry Bacteria rights activists? (This is Seattle after all). But no! She had already found a space to rent in South Seattle, and had started to gather lab materials and search out funding. 

Right now, we are in the difficult processes  of finding free-ish lab equipment and funding. I will keep you updated on the process, and mean while…

“Got Milk?!”Oops, wrong slogan. “We Need You!” There we go.

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 We need a name for the Hackerspace. If you can remember back to high school science, you might recollect that scientists cannot name things. Look at Cummingtonite, a mineral named after Cummington, Massachusetts. Real original guys. Unfortunately, I am not blessed with naming prowess either. I named my two gray cats Foggy and Smoky (to be fair, I was nine.) Therefore, I need name suggestions for the lab. We want something interesting but so that you can tell that it’s about biology. Something in between “Seattle Hackerspace” and “Marigold Unicorn Space”. 

Au revoir,

Katriona

Visit to Genspace

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The Sterile Room at Genspace

I just returned from New York a couple of days ago. We got back at 12:30, though i wasn’t even sure we would get back that day. Due to extreme fog we were diverted to the Portland airport, where all the passengers, like middle school girls, huddled around whispering about what was to happen. When I heard in the telephone train that we weren’t going to get out until the next morning I almost needed resuscitation. My poor feet after 4 days of walking around New York could barely hold me up.

But back to the far more interesting matter of New York and visiting Genspace. If you don’t know about Genspace, it’s the first Biotech Hackerspace. It’s set up in a loft in Brooklyn. They run classes and offer lab space and advice, like most Hackerspaces, it started out in the corner of a different ex-Google run Hackerspace. Joseph Jackson from Biocurious and my friend Cindy Wu helped set up a meeting with Ellen Jorgensen, one of the PHD heads. Genspace is pretty small, taking up about 1/4 of the top floor of the loft. It has a computer room with a big table, then a sterile room closed off by glass for bacteria, and a workbench area

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A look at Genspace. It ends after the book shelf. You can’t see the computer/ reading area from here. But the glass at the left is the Bacteria Room, and the benches to the right are work area.

Me and Ellen talked about Hackerspaces in General and she gave me some quality advice about starting and running one. She told me that a Hackerspace needs:

  1. Someone with Lab Experience to be there in operating hours (12-8 pm). Seems pretty obvious, but I actually hadn’t quite realized it. Generally good to make sure no one’s creating genetically engineered bunnies. Yes they could be benign Bunnicula like creatures (Please tell me you’ve read Bunnicula!), but in case they weren’t, I think death by bunny would be a bad way to go. I mean how pathetic would that be to have on your gravestone. You’d be known as the sucker that got beat up by a bunny rabbit forever.
  2. A person with authority who knows what they’re doing. 
  3. 1-2 people to devote all their time and coordinate with an expert. Because really, who needs a social life? I’m in the IB program in highs chool so social interaction just seems to foreign. I’ve come to the point where not having any work is stressful, because I must be forgetting something! So this part will work wonderfully for me.
  4. Someone to give and teach introductory classes. Anyone out there with biology experience looking for a karma boost or spare cash? The Holiday season tends to inspire both needs as we tell too cheery colleagues that “No, you can’t pull of that elf outfit” and mom’s candle turns out “to cost how much?!”.
  5. Create and atmosphere with support and fun social environment. Hmmm. Maybe I’ll have to do slightly more than advertising free pizza…
  6. Must have a Science Advisory Board to give opinions on tough questions. Like, “We probably shouldn’t let this girl genetically modify her boyfriend to want to watch less video games. Right?”
  7. The space must have non-absorbant floors for bacteria. hadn’t thought of that one, but good point. The neighbors would probably get unhappy if their ceilings started to glow. I mean, I would think it was great. But I’ve found not everyone shares my view of mixing synthetic biology and interior decorating.

She also highly recommend having Workshops to have funding. 

Seeing Genspace and meeting Ellen was really cool and definitely made me inspired about a Hackerspace in Seattle. I’m enclosing some pictures, so enjoy. And if anyone has lab equipment they don’t need. Well, post a comment and I’d be happy to pick it up!

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Genspace work area

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One shot of the Computer area

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The other side of the computer reading area. This is the other boundary of Genspace

Luciferase

Firefly luciferase

Firefly Luciferase is one of several fluorescent proteins. Other common ones are Green Fluorescent Protein, Renilla Luciferase, and Bacterial Luciferase.

Firefly luciferase catalyzes the oxidation of luciferin, the substrate in fireflies that makes them light up. The oxidation of luciferin, which is when oxygen is fused with the luciferin, happens in two steps. First the luciferin bonds with Mg2and ATP to create luciferyl adenylate and PPi (Pyrophosphate). Then the luciferyl adenylate reacts with diatomic oxygen to create oxyluciferin, AMP, and light.

Luciferase is interesting because of its compact two-part domain structure. The active site of luciferase is thought to be located in the cleft between the C and N-terminuses (Fig. 5). The C-terminus is the smaller part of luciferase, and it has the free carboxyl group. The larger N-terminus has the free amine group. During the reaction, luciferase undergoes a reversible conformational change, where the cleft between the C and N-terminus close up. This prevents water from entering the reaction and hydrolyzing one of the reactants.[1]

Protein Structure of Firefly Luciferase

Protein Structure of Firefly Luciferase

 

In the theorized interaction that I modeled, the two very separate domains of luciferase are very important to the interaction. Because they split easily into the two separate terminuses, it allows my idea for a split catalyst genetic-specific biocatalyst. The recombination of the two domains is central to the idea and dependent on the two very separate domains.


[1] Conti, Elena, Peter Brick, and Nick P Franks. “Crystal structure of firefly luciferase throws light on a superfamily of adenylate-forming enzymes.” Structure 4.3 (1996): 287-298. Print.