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Captain Underpants, BioBuilder and iGEM: Preparing Kids for the Biotech Century

Melvin’s Li’l Scientist Wristwatch had a built-in DNA extractor. Melvin inserted the filthy toenail into his watch and programmed a complete extraction procedure while the Turbo Toilet 2000 chased him back through town…

As Melvin ran screaming, his watch quickly pulverized and sonicated the toenail cells, removed their membrane lipids, proteins and RNA, and purified and isolate a single strand of Mr. Krupp’s DNA.

When Melvin reached his bedroom laboratory, he quickly fed the results into his Mecha-Computer, which identified themetallo-organic, “super-powered” substance and began replicating it in a saline gel solution. The gel percolated slowly as it oozed into a glass beaker.
      – Dav Pilkey, Captain Underpants and the Tyrannical Retaliation of the Turbo Toilet 2000 (2014)

Captain Underpants is not a name generally associated with biotechnology. Yet, this wildly successful (70 million copies sold worldwide) series of children’s novels may be the first exposure many children have to biotech. Probably, it won’t be their last.

Just a few years ago the idea that kids would interact with biotechnology might have been unthinkable: The costs associated with DNA sequencing and synthesis were astronomical and required expensive equipment and years of training. Practicing biotechnology in the classroom was literally out of reach.

However, with decreases in the cost of sequencing and synthesis outpacing Moore’s Law, and biotechnology and synthetic biology breakthroughs making the news nearly every day, it has become feasible to expose children to biotech practices. Indeed, it is essential they are exposed to and understand technologies that will play a fundamental role in solving many of the challenges the world faces today and tomorrow.

In contrast, kids are already being taught computer programming at younger and younger ages. In fact, seven EU countries including Britain, Bulgaria, Cyprus, Estonia, Finland, Greece and Lithuania have set up computer programming as a stand-along subject in their primary and middle schools. Programming languages such as Scratch teach their users the same skills that professional programmers use in their jobs.

Unfortunately, until now, this type of hands-on engagement has not existed for biotechnology.

This article considers is how and why small children might be given similar opportunities, as well as the impact of doing so.

Teaching Synthetic Biology in Middle and High Schools

Gel Electrophoresis (source: Huntington's Outreach Project for Education at Stanford)
Gel Electrophoresis (source: Huntington’s Outreach Project for Education at Stanford)

For the past decade, it’s become commonplace for high school students in biology and AP Biology course to use gel electrophoresis to separate DNA, RNA and proteins, and to learn how to add new genetic material to bacterial cells.

Nearly all teachers that teach the basics of genetic engineering use the same materials and teach the same set of experiments every year. Though these experiments introduce important laboratory techniques, they present a narrow range of experimental problems. In most cases, the laboratory experience ends when the experiment does and students are learning techniques rather than the inquiry or creativity that makes the practice of science exciting.

Earlier this year, Natalie Kuldell, Rachel Bernstein, Karen Ingram and Kathryn M. Hart published BioBuilder, a book-length series of open-access, modular, hands-on experiments designed to be easy to incorporate into high school classrooms and laboratories.

BioBuilder was developed at MIT in collaboration with award-winning high school teachers from across the country with the goal of teaching the foundational ideas of synthetic biology, as well as key aspects of biological engineering that researchers are using in their labs today. The aim was to enrich the way that biotechnology is being taught to middle and high school children.

Among the experiments that BioBuilder teaches are how to measure variants of an enzyme-generating genetic circuit, modeling “bacterial photography,” and building living systems that produce purple or green pigment.

The book and the experiments have been well received because are they easy to introduce into a typical high school biology curriculum (with little to no expense) and expose students to synthetic biology by teaching both science skills and the engineering-design process in the context of living systems.

High School and College Students Advance the Field at iGEM

Every year starting in 2004, high school, college and graduate students have competed in the International Genetically Engineered Machine (iGEM) competition. Student teams are given a kit of Lego-like biological parts from the Registry of Standard Biological Parts, work at their own schools over the summer, and design and build biological systems to solve real-world challenges. They compete in 15 tracks that now include art and design, energy labs, environment, health and medicine, and even policy and practice.

Growth of iGEM participation 2004-2014 (Source: iGEM.org)
Growth of iGEM participation 2004-2014 (Source: iGEM.org)

In its first year, iGEM attracted five teams of students. This year’s Giant Jamboree took over Boston’s Hynes Convention Center, attracting 260 teams of college and high school students from around the world.

In the past, teams have designed a microbe to detect and kill a fungus that has been destroying the world’s banana supply.  The 2015 Grand Prize-winning team from Virgina’s College of William and Mary characterized the variability (or stochasticity) of gene expression for the most commonly used promoters in synthetic biology. Promoter regions of DNA initiate the first step of turning genomic information into proteins.

The most successful teams have even gone on to start companies based on their ideas. Among them, Ginkgo Bioworks, a Boston-based microorganism engineering company, competed in the first iGEM and recently raised nearly $50 million.

In a 2014 New Yorker article on iGEM, co-organizer Randy Rettberg commented,  “We used to say we just needed to educate people about the science… We said that if they understood it, they would accept it… [but] to create an environment where [these] students can live this future, what we really need to do is involve people.”

In a survey undertaken by the Oklahoma State University Department of Agriculture, it was found that as many as 80 percent of Americans support  “mandatory labels on foods containing DNA,” about the same number as support mandatory labelling of FMO foods “produced with genetic engineering.” This fundamental misunderstanding of DNA reflected a general lack of understanding of basic science. Giving children the opportunity to learn about biotechnology sooner can only be a good thing.

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[Thanks to Davis Endries, John Garrison, Natalie Kuldell, Taylor Hamman and Danielle Wilde for reading early drafts of this.]

Nag Nag Nag: Cabaret Voltaire vs Akufen’s (karaoke slam mix)

It’s been a while, a long while, since I’ve posted anything music related, so I offer up a contrast of sorts.

Here’s Cabaret Volataire‘s brilliant Nag Nag Nag from their 1980 Live at the YMCA album. Simple distorted guitars, bristling synthesizer electronics, this was early – but still danceable – industrial music no doubt inspired by the Cold War and Sheffield*’s urban decay.

Some 30 years later, Montreal’s Akufen remixes the song and aptly titles it the Karaoke Slam remix. When I email him to compliment him on the mix, Marc LeClair answers “musics just getting crazier and crazier.” Not sure I agree with his sentiment but I love the remix.

Enjoy.

* I didn’t know this but in researching Sheffield, I also learned the city spawned The Human League, Heaven 17, ABC, Clock DVA, and is home to the legendary Warp Records.

Biofabricate: Scientists + Artists Transform Materials, Manufacturing

This week, a group of artists, designers, and scientists will gather in New York City for the second annual Biofabricate conference.

They’ll be discussing the use of biological organisms to create new materials and transform manufacturing.

You might think a conference like this would attract only scientists, but surprisingly it is the often artists and designers in attendance who are pushing the limits of biotechnology.

I attended last year’s conference and asked Suzanne Lee, Biofabricate’s organizer, what would be different this year. Here is her preview:

“For one, we’re helping people think beyond 3-D printing with the use of living cells as substrates to build novel materials and systems,” said Lee. “For example, one of our presenting companies, BioBots, has developed a desktop bioprinter that can build three-dimensional living tissues from human cells. One hundred research institutions around the globe purchased that printer, but so did an art school. I believe that combination of scientists and artists-designers working separately and together are driving innovation in biofabrication.”


Pembient’s cultured rhino horns and elephant tusks aim to decrease illegal wildlife poaching – a $20 billion black market.

“We’ll also be looking at how engineered biology has the potential to replace animal products,” continued Lee. “Egg, milk, and meat produced in cell culture are less resource heavy and more sustainable, and Pembient’s cultured rhino horns and elephant tusks aim to stop illegal poaching.”

I’m looking forward to hearing more this week about our progress in using biology to advance materials science and manufacturing. Check back for my report next week.

Book Review: Ready Player One

Ready Player One Review is a geektastic nerdgasmIt’s 2044, the world’s a dystopian mess and people escape to, learn, live and work in a virtual world called OASIS (the followup to William Gibson’s cyberspace and Neal Stephenson’s metaverse).

At the start of the book, videogame designer James Halliday, the ultimate 1980s geek, leaves his vast fortune to the person who can find three magical keys (Easter eggs) hidden in the vast OASIS.

Enter one Wade Watts, an 18-year old living in the Oklahoma City “stacks” of trailers upon trailers left behind by people migrating to the cities. Compared to the other egg hunters (“gunters”), the poverty-born Wade is at a disadvantage and can’t travel OASIS. But what he lacks in finances he more than makes up in his knowledge of 1980s pop culture, and videogames skills. As a result, he finds the first key and starts the race that will continue until all three keys are discovered.

The quest is a blast. There are allies and enemies, a romance and an overload of 1980s nostalgia. I read it laughing aloud along the way, handed it to my son Alejandro, who enjoyed it, then I reread it. It’s a total blast.

(24.100)

Your Founder Is Crazy, Isn’t He? (Part 1)

Is your founder crazy? Insane? Bonkers? How can you tell?At the beginning of the week, the Founder swore he’d have me back on payroll by the end of the month. It’d been six weeks since any of us had been paid.

“What about the options?” I asked.

“I’ll take care of those by the end of the week,” he answered. It was the same answer I’d heard every month for a year – the length of time I’d been working there.

That whole week, my other co-workers were in a bad mood and nothing seemed to go right. It wasn’t one thing that had put us in a bad mood – it was a series of little things: The tone of voice the founder took when asking about a client, how he disappeared from the office for a week, how he wouldn’t return phone calls.

Yet I continued to hold out. We continued to hold out. Just a few months earlier, we had all believed in the company we were building. We believed in the founder and we would have followed him into any battle.

My hand, my right hand – my writing hand – was sore and bothering me. Every little thing pissed me off and I was yelling at my kids and my wife all the time.

The next day, the CFO called, “There’s something I need to tell you… I feel super shitty about this but every other week I have to release the funds.”

“What funds?”

“The funds to pay the president. The president is still getting paid.” The CFO told me he’d had a conversation with the Founder who admitted he had to continue to pay the President so he wouldn’t get distracted.

“Distracted from what?” I asked. “Isn’t a startup CEO, a startup president supposed to feel the same pain as his team?”

“You know the founder hasn’t taken a salary in years. He hadn’t paid his mortgage until the investors stepped in. They almost turned off his lights.”

I was sitting alone in the conference room. The President, the one guy who was getting paid in the company, was down the hall in a shared office. Presumably on the phone.

I felt my stomach rise into my mouth. I no longer felt comfortable there.

“I can’t talk about this any more,” I told the CFO. I hung up and left.

I almost vomited in the elevator down.

I took the subway home, tasting my sour stomach the whole way, praying I wouldn’t become one of those people that vomited and caused a medical emergency shutting down the entire Brooklyn-bound F-train line. I had a sense that drowning in alcohol might help but my stomach was so wrecked I knew it would only make things worse. No matter how much I imagined I’d drink I knew alcohol couldn’t drown away the anger and erase the disappointment.

When I got home, Alejandro was there to greet me. I mentioned that my hands and stomach were hurting because of the stress.

“How is that even possible?” he asked. Only an innocent fourteen-year could ask such a question.

I explained that stress can manifest in your body, that you can feel the fight that happened before you walked into a room. At that moment, the stress was manifest in my stomach and the part of my body I used to make my living. He looked at me like I was crazy and I realized that I was but didn’t have to be.

The next day I didn’t go back.

(23.100)

The Pool at 4 A.M.

The Pool at 4AM

My father’s pool is, was, and always will be –– all skaters agree –– absurd. The pale blue surface is very hard, durable, very fast, and sentient. The coping is a great grindable bullnose. The shape is a perfect kidney, just under nine-feet deep. To ride the pool from one lip to the other across the deep end, a skater must roll no more than three seconds (I know, I’ve timed it) but to measure this distance in time is folly. It should be measured in synapses fired, neurochemicals released, DNA unwinding from histones and proteins synthesized while calculating your next move, the one you’ll make when you hit that coping.

Its name is YinYangles, not because of the Chinese philosophy of yin-yang or yin and yang which describes the interconnectedness and interdependence of the natural world. (Truthbetold, we’re not so keen on cheap Chinese knockoff paper decks and those living wheels that die much too soon. And fans of their red paper currency we are not.) No, YinYangles is some HighIQ’s joke about the mathematical reduction of the perfect transitions into evolving y-angles and it stuck much to the amusement of dumbshits who don’t understand math and nostalgize the days of lifeless petroleum-based wheels and static, concrete bowls.

Our bowl is the best in the land, every skater rips – a not-so-secret interaction of YinYangle’s intelligence with your own. At this pool every skater’s a legend – an Alva, a Burnquist, a Hawk, a Sheckler, a Way, every fan’s a teaching critic, every biohacker’s an angel investor and every punkDJ’s Kanye himself. To assure the sentient being understood the subtle energies of the sexes and the problem-solving skills of today’s vertical gene-rippers, my father’s genius was to feed the bowl the fearlessness of the male and female skaters who first skated it and the collective intelligence of the bio-engineers and genome hackers who worked in the deep end ceaselessly. Those who do not ride can bask in the glow of the bowl’s subtle energies. I was the only one who thought himself crippled.

(22.100 After Bartheleme. Previously published in Three Pool Rhumba)

Why I Write (Or How I Started Writing)

“Two hundred years of American technology has unwittingly created a massive cement playground of unlimited potential. But it was the minds of 11 year old that could see that potential.”
– C.R. Stecyk

My first stories were skateboarding stories inspired by C. R. Stecyk‘s Skateboarder Magazine articles, his fabrication and chronicling of the Dogtown’s Z-boys’ adventures. As a sheltered kid turned skateboard geek growing up 60 miles away from Santa Monica, I was blown away by the exploits of the Z-boys and the skaters that became my heros. But I also devoured and dissected the stories and began “borrowing” his openings (which I would later learn he’d borrowed from Raymond Chandler or Dashiell Hammett or Hunter S. Thompson), then wrote my own skateboarding procedurals.

My main character was a teenage private eye, asked to solve some mystery or another, find a missing person. Criss-crossing Southern California in a hot-rodded Volkswagen Transporter, blasting Led Zepplin and Ted Nugent, and (later) punk rock along the way, the stories inevitably climaxed with the arrival at an empty backyard swimming pool or hidden ditch that begged to be ridden. After an epic skate session, he’d solve the mystery and arrive home in time for dinner.

20. How To Clone A Dragon 2 | Can We Bioengineer Dragons?

You have to bioengineer a dragon before you can clone a dragon.

[For Part 1 of this series on How to Clone* a Dragon, click here.]

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In the first of her two part post on How to Bioengineer a Dragon, Keira Havens, of Revolution Bioengineering, argues that there should be a compelling reason to modify a living organism to create a dragon. She points out that “it is unlikely that bioengineering will be the quick and inexpensive way of accomplishing your goal” of personal transportation. Which is true, if you’re looking to create a new form of transportation.

In the end of her post, she concludes the top reason to bioengineer a dragon is “because they’re cool.”

I respectfully disagree.

While I’m more in the school of possibility and am very closely watching George Church’s Wooly Mammoth revival, I think there is a more compelling reason to bioengineer a dragon.

In describing the reasons to bring back the Wooly Mammoth, Church’s team list three reasons they are pursuing their bioengineering experiement:

  1. As an ecosystems approach to confront climate change
  2. Because ancient DNA holds secrets that impact modern biology and medicine
  3. [Cloning a mammoth] is the future of large mammal conservation

In the past year, Church’s team has inserted mammoth DNA into the cells of living elephant cell cultures. But they are a long way off from cloning a mammoth, just as we are a long way off from cloning a dragon.

So, why clone a dragon?

Not because they’re cool.

Though I do believe the creation of a complex organism like a dragon – a flying lizard able to breath fire and is intelligent enough to understand and respond to commands – is extremely cool. However, I don’t think that’s enough of a reason.

Back in 2006, The Economist reported the efforts of GeneDupe, a company purported to be cloning dragons. While the GeneDupe story turned out to be an April Fool’s Day joke (that the Economist fell for 😉 ), the story hit upon the real reason to create a dragon: for business.

Biotech pets, new animals that never existed before will create new markets. And why not? Dragons will part of that market, as will revived and extinct animals and new chimeras.

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Here’s a conversation on GoogleGroups that Revolution Bioengineering lead scientist Nikolai Braun and Keira Havens participated in early in 2015. And here’s the best answer from a Yahoo! Answers on whether a dragon could be created using synthetic biology.

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*BTW, I know, “to clone” means to make an identical biological copy. To clone a dragon implies someone has already done the hard work of bioengineering this complex organism. In a future post, I’ll describe why I chose the word “clone” versus “bioengineer.”

(20.100)

Why I Keep A Journal

Why I Keep A JournalI’ve been keeping a journal for more than 25 years. I should say “mostly keeping a journal” because there have been periods of time where I haven’t written in a journal regularly – though probably, I was writing just not in a journal.

At the pace of one page per day, that’d come to 9,132 pages or some 2,283,000 words. I’m sure I’ve written five times that.

My father suggested I keep a journal of a Eurail trip I was taking after college. Since I knew I’d be spending time alone on trains, in foreign cities, and since I wanted to write professionally, I started writing in a blue lab notebook back in mid-1980s and pretty much never stopped.

If you want to keep a journal, you need a notebook.Keeping a journal became a habit pretty quickly. It’s not something I think about, I just write. (Unlike blogging which I do in fits and starts and am much more self-conscious about.)

I wonder how much that particular point in my life – my early 20s – motivated the writing. I’d just finished my formal education, hadn’t written much more than school papers and a few stories, and knew the only way I was going to become an author was to write. How much was motivated by being in that funny place between graduation and still trying to figure out who I was and what I would do. And how much was motivated by my father’s suggestion that I keep a journal.

Over the years, the journal became my the place where I’ve documented my marriage, the birth and growth of my three sons, my life in Brooklyn, and the ebb and flow of my businesses. It’s where I’ve given thanks for the blessings that fill my life, admitted my jealousies, fears, and shortcomings, celebrated successes and worked out anger and conflicts. I’ve also explored ideas for businesses, stories, novels and articles, analyzed dreams, made predictions, lamented the loss of friends and money, mourned the death of ideas that I’d finally grown out of, confessed and complained complained complained all in the confines of the written page.

The journal has taken many forms. From the blue-covered lab notebook to soft-cover oversized lab notebook, spiral-bound and hard-bound blank-paged sketch books, and loose leaf sheets of paper from companies that changed names or went out of business, canary-colored legal pads, to black-, green-, mango-covered Moleskines decorated with skateboard brand, band and random decals, I’ve written everywhere I’ve lived my life: in dens, kitchens, bedrooms, dining rooms, offices, hotel rooms, on boats, in trains, on planes, in cars. In every city I’ve lived in and visited in North and Central America and brief visits to Europe. It would be rare to find me without some kind of journal to write with.

I have tried keeping a journal on a computer, used Penzu for a couple of years, even have a secret email account that I will on occasion send notes to, but I prefer writing on paper, mostly with a fountain pen (a Lamy 2000).

Keeping a Journal with a Lamy 2000 fountain pen

The poet, Allen Ginsberg, founder and frequent lecturer at The Naropa Institute, warned me that the wrong ink, particularly ballpoint pen ink would destroy the paper. He also warned me that my journal would accumulate and that at some point, if I was diligent with my writing, I’d have to contend with quantity. It’s true, I have several plastic containers in my basement, a suitcase in an attic, and a shelf of my most recent scribblings in my bedroom.

(I’ll continue this post later.)

(19.100)

Book Review: The Dog Stars

The Dog Stars by Peter Heller

I’m not a fan of post-apocalyptic fiction though I’ve read more than a lifetime’s worth and I get why it is popular: We live in a world of uncertainty and great post-apocalyptic stories give us the hope that we can survive the worse of times.

Peter Heller’s brilliant The Dog Stars gives us the story of loss, survival, and love in a United States decimated by a pandemic flu. The main character, Hig, shares his life with his dog Jasper, and Bangley, his gun-loving misanthropic neighbor. Hig spends days flying above their little outpost in Northern Colorado in a Cessna, patrolling their small expanse of land. He hikes into the Rockies to hunt and fish. While Hig and Bangley kill intruders with ease, their losses are significant because their world is empty and silent, and survival forces them to keep their guard up.

Heller’s writing is a treat and he has real talent for describing nature, ratcheting up the tension, and delivering a very satisfying story.

(18.100)