Maiko and Kiyoshi Kurokawa photoblog Maiko and Kiyoshi Kurokawa
Wed, Dec 31 19:00 UTC

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One of the first words that I learned when I joined the Media Lab was "antidisciplinary." It was listed an a requirement in an ad seeking applicants for a new faculty position. Interdisciplinary work is when people from different disciplines work together. An antidisciplinary project isn't a sum of a bunch of disciplines but something entirely new - the word defies easy definition. But what it means to me is someone or something that doesn't fit within traditional academic discipline­­­-a field of study with its own particular words, frameworks, and methods. Most academics are judged by how many times they have published in prestigious, peer-reviewed journals. Peer review usually consists of the influential members of your field reviewing your work and deciding whether it is important and unique. This architecture often leads to a dynamic where researchers focus more on impressing a small number of experts in their own field than on taking the high risk of an unconventional approach. This dynamic reinforces the cliché of academics-learning more and more about less and less. It causes a hyper-specialization where people in different areas have a very difficult time collaborating-or even communicating-with people in different fields. For me, antidisciplinary research is akin to mathematician Stanislaw Ulam's famous observation that the study of non-linear physics is like the study of "non-elephant animals." Antidisciplinary is all about the non-elephant animals.

The Media Lab focuses on "uniqueness, impact and magic." What our students and faculty do should be unique. We shouldn't be doing something that someone else is doing. If someone else starts doing it, we should stop. Everything we do should have impact. Lastly, things should induce us to be passionate and should go beyond incremental thinking. "Magic" means that we take on projects that inspire us. In the Lifelong Kindergarten group, researchers often describe the "Four Ps of Creative Learning" as Projects, Peers, Passion and Play. Play is extremely important for creative learning. There is a great deal of research showing that rewards and pressure can motivate people to "produce," but creative learning and thinking requires the "space" that play creates. Pressure and rewards can often diminish that space, and thus, squash creative thinking.

The kind of scholars we are looking for at the Media Lab are people who don't fit in any existing discipline either because they are between--or simply beyond--disciplines. I often say that if you can do what you want to do in any other lab or department, you should go do it there. Only come to the Media Lab if there is nowhere else where you could do what you want to do. We are the home of the misfits-the antidisciplinarians.

When I think about the "space" that we've created, I like to think about a huge piece of paper that represents "all science." The disciplines are little black dots on this paper. The massive amounts of white space between the dots represent antidisciplinary space. Many people would like to play in this white space, but there is very little funding for this, and it's even harder to get a tenured positions without some sort of disciplinary anchor in one of the black dots.

As we engage in tackling harder and harder problems that require many fields and perspectives, the separation of disciplines appears to be causing more and more damage. The complex system that is the human body has become impossibly multi-disciplinary. We should really be working on "One Science," but instead we are a mosaic of different disciplines sometimes not even recognizing when we are looking at the same problem because our language is so different and microscopes are set so differently.

The Center for Extreme Bionics at the Media Lab--led by Hugh Herr, Ed Boyden, Joe Jacobson, and Bob Langer--utilizes everything from mechanical engineering to synthetic biology to neuroscience in its quest to eliminate a variety of disabilities. This disparate collection of disciplines would never fit in any traditional department or lab.

Media Lab co-founder Nicholas Negroponte famously coined a twist on the academic dictum that faculty must "publish or perish." Media Lab faculty, he said, must "demo or die." I have made a modification- "Deploy or die." I'd like all of the Lab's faculty and students thinking about how their work ultimately deploys in the world, and if they can deploy it themselves, even better.

I think this philosophy of working together on big projects will help bring researchers together across disciplines - creating a single science instead of fragmented disciplines. We will still need disciplines, but I think that it's time we focus on a higher mission and the changes needed in academia and research funding to allow more people to work in the wide-open white space between disciplines - the antidisciplinary space.

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Update: One of our faculty members pointed out that disciplines are more like broad swaths and that a lot of the most cited papers are the ones in the disruptive "antidisciplinary" spaces.

I remember my 24th birthday very clearly. It was 1990. I had just finished working as the associate to the executive producer on the film The Indian Runner. I was running a nightclub in the Roppongi district of Tokyo at the time together with my team fromThe Smart Bar in Chicago. Madonna had just released "Vogue," Chicago House music had evolved into Acid House and the rave scene was going strong. It was a fun and tumultuous time in the world and in my life.

I met Timothy Leary for the first time through a mutual friend, David Kubiak, the editor of The Kyoto Journal at the time. I remember being very excited about meeting Tim because the rave scene had caused a revival of many 1960s themes. I had been reading books about consciousness and the mind - trying to chart my own journey along a path where Timothy often appeared as a central figure. Most recently, I had read a book by Robert Anton Wilson called Cosmic Trigger in which the author first tells the reader that everything in the book is a lie, and then proceeds to weave a story about one of the most wonderfully elaborate conspiracy theories every described. In the book, Wilson explains that "23" is a magic number and also explains that Timothy Leary had received "transmissions" from aliens. I wasn't sure what to believe, if anything, but at the time, I was convinced that the world was full of secrets and I wanted in on them.

I remember standing with Tim at the main Roppongi crossing called "Almond's" at the time named after the venerable coffee shop on that corner where everyone met up on their way into town at night. As we stood there talking about the budding Cyberpunk scene and how it was unfolding in Japan, I remember explaining to Timothy that I had just turned 24 and that I had hoped something magical would happen when I was 23 since it was the "magic number." I also asked him about the "Starseed transmissions" described in Cosmic Trigger. I remember Timothy's laugh vividly, as he told me that the whole thing was a joke. He said that everything in that book as well as most of the stuff that those guys talked about was one big joke and that I shouldn't believe any of it. In one instant, Timothy, the guru of the particular shrine that I was worshiping, knocked me whirling off my path.

Later, Timothy told me another joke.

A bunch of hippies go to India looking for the meaning of life. They travel for years climbing mountains and looking everywhere for the guru who knew the answer. They finally find the guru who was said to know the meaning of life. They ask the guru, "What is the meaning of life?" The guru says, "Wet birds don't fly at night." The hippies say, "They don't?" The guru says, "Do they?"

This was one of the most important spiritual lessons that I ever learned. That evening, I took Timothy on a whirlwind tour of the Tokyo nightlife scene introducing him to the Japanese kids who he later called "The New Breed" - a new youth culture that was technically and culturally savvy and wanted to take over instead of drop out. Tim modified his "Tune in, Turn on, Drop Out" slogan to "Tune in, Turn on, Take Over." He recruited me as his God Son explaining to me that the role of a God Son was to teach the Godfather. We started writing a book together and did public events around this theme.

Timothy always told everyone to "Question authority and think for yourself." I remember after an event where he and I spoke, a bunch of kids came up to Tim and said, "so what should we do?!?!" and Tim shouted at them, "Think for yourself!!" What I realized as I spent time with Tim was that people wanted gurus and that the more you tried to explain that you weren't a guru, the more many people became convinced that you were in fact a guru and that they wanted in on the secret. People wanted "answers" and wanted to get to some kind of goal. The thing is, there is no answer and there is no goal. You don't "win."

Ever since being knocked off of my original "path to enlightenment" by Timothy Leary, I've dabbled in various spiritual and mindfulness investigations and pursuits with a curious but skeptical stance. In retrospect, I think that Timothy probably believed that there was a spiritual path, but that the particular version of the path that I was on and the naive way that I was thinking about it was best completely destroyed so that I could start again with a more questioning mind.

I've tried very hard to avoid the pull of gurus or being mistaken for some kind of guru myself. I've had many teachers and have tried a variety of meditation and mindfulness techniques, but I still consider myself a novice. I am very happy with my journey and with relative consistency, each year of my life brings more happiness and becomes more interesting and I thank Timothy for the trajectory correction at a key point in my life.

Last year, in an email exchange, Pierre Omidyar, an old friend from my short stint at Tufts University, mentioned that I should look up Tenzin Priyadarshi. Tenzin runs the Dalai Lama Center at MIT and when we met, we decided we should teach a class together. Remembering the adage that the best way to learn is to teach, I jumped on the opportunity to teach a class where I could learn more about mindfulness and work on my practice.

Tenzin and I decided to call the class "Principles of Awareness".

What is awareness? Is self-awareness a "default" state or is it cultivated? Can it improve performance and wellbeing? What role does technology play in promoting or hindering awareness? Is there an ethical framework for our capacity to be aware? Can self-awareness be linked to happiness? The course will be set in an experiential learning environment where students/ participants will explore various theories and methodologies around awareness. Students will be required to keep an open lab book documenting methods and evaluations. Students will present their findings and observations regularly during class sessions. The final project will consist of evaluating various tools, techniques, and interfaces around awareness targeted towards "performance" and "wellbeing."

Class meetings (virtual and real) will consist of practice, lectures, and discussions with invited speakers/experts. Some of the talks will be open to the public. And the practice will range from meditation to hacking.

The first class last Wednesday was fascinating. We had a wide range of students, some students had never meditated, some engaged in regular prayer (a form of meditation) and others were experienced in many forms of mindfulness practice. In the conversation about awareness, Tenzin and I talked a lot about meditation. One of the students asked me, "so what's the 'there' you keep referring to?" I realized that I used "there" to refer to the "place" that you get to when you meditate - the place where you connect to true nature and depending on your skill and style of meditation, "there" can be a place of bliss. "There" can also be "enlightenment". Tenzin quickly jumped in and explained that we should not focus on getting "there" because everyone will want to get "there" and that wasn't the point.

I totally agree. One of the best comments I've heard about Qi Gong, a form of Chinese energy movement and meditation is that you shouldn't be goal oriented. You can't "win" at Qi Gong. The purpose wasn't to get better, although you will, but that the purpose was just the practice. I find the exact same thing about meditation. The point is not to "win" against yourself or anyone else. I find that even writing this blog post smacks of boastfulness and "know-it-all-ness" which is so not the point of the exercise. One will get better at any form of practice the more you do it and feeling good about progress isn't a bad thing, but the whole point of mindfulness and meditation is being present in the "Now" and NOT being goal oriented, egotistical or focused on the future or the past.

I find it off-putting to hear people boast about their meditation practice and in the past, I've mostly only talked about meditation and mindfulness with small groups of people where we were sharing our own experiences. However, now that I'm "teaching" a class about awareness where I'm asking my students to share all of their experiences as well as keeping an open log of their experiences, I thought I should share as well.

I hope to be posting more updates in the coming weeks about some of my experimentation and observations.

I first heard about Synbiota at SXSWi this year, when they won an Accelerator Award. According to the announcement, "Synbiota is a virtual collaboration site that connects scientists, researchers, universities and others from around the world to solve complex problems using genetic engineering." That week they announced the world's first Massive Open Online Science (MOOS) event. Called #ScienceHack, hundreds of researchers from around the globe (some as clueless as us!) would use a new "wetware" kit to produce prohibitively expensive medicine at a fraction of the price.

A month later I got this email:

From: Connor Dickie
To: Joi Ito
Cc: Kim de Mora
Date: Apr 17, 2014, at 11:12
Subject: ML alumni wins SXSW prize for SynBio startup & Invitation to #ScienceHack

"I'm writing to invite you to participate in #ScienceHack, our distributed science effort to make real medicine for just a fraction of current costs using Synthetic Biology and the Synbiota platform. O'Reilly Radar recently called #ScienceHack the most ambitious distributed science project, and knowing your interest in biotech, I thought I'd reach out to you with a cool opportunity to learn with us.

Participation is easy - I'll ship you one of our "Violacein Factory" wetware kits, and connect you with Kim de Mora at iGEM HQ (CC'd) who is not only interested to build one of the kits, but also has the required wet lab skills. It will take about an hour and a half for the in-silico design and build of the actual DNA part. Kim would handle the incubation etc. You would then come back to his lab in about 5 days to look at the results.

We recently built a Violacein Factory kit here in Canada, and more recently at Genspace in NYC, and everyone learned a bunch and helped us make significant advances towards our goal of an optimized violacein-producing organism.

I'll be in Boston/Cambridge on the 27th-through-30th as part of a Canadian trade delegation, and will have some time to meet you and chat about the opportunity in person if it interests you.

With regards,

Connor Dickie
http://alumni.media.mit.edu/~connord/

I knew about iGEM. It was the spinout from MIT that brought high school and college students together to hack DNA much in the same way that robot competitions bring together kids interested in robots to hack and learn and compete. What's amazing is that iGEM, now bringing together over two thousand students at their Jamboree, takes the state of the art of synthetic biology and brings it to the masses.

Violacein is a natural purple compound made by Chromobacterium violaceum, a bacteria that is found in the soil in the tropics such as the Amazon. Violacein is created by the bacteria as a natural defense against amoebic creatures that try to eat it and is viewed as a potential anti-parasitic. It also appears to show promise as a treatment for cancer. The problem is that it currently costs $356,000 per gram because of the difficulty of harvesting it in the wild.

An opportunity to learn synthetic biology through doing it (my favorite way to learn) was too good to turn down so I immediately accepted the challenge. I started by taking the required safety courses for playing with recombinant DNA : General Biosafety for Researchers, check. Bloodborne Pathogens: Researchers, check. Hepatitis Information form, check. General Chemical Hygiene (web) and Managing Hazardous Waste (web). Check and check.

Then I started hunting for a place to do the actual work. That turned out to be a bit more of a challenge. Although the kit and process provided by Synbiota were basically safe and non-toxic, work with recombinant DNA and bacteria required a proper wet lab at MIT which are in short supply and used for more important things than the Media Lab director messing around with street bio.

After discussing with the team and looking at what we needed, we decided that my kitchen would be the least disruptive place to do the work.

On July 27, the Synbiota team and Kim from iGEM gathered at my house with a rag tag team of researchers from the Media Lab and elsewhere to work on the Violacein Factory #Sciencehack. We started with a briefing on what we were actually doing.

Our mission was to be one of the hundreds of teams participating in trying to innovate on developing the most effective method of synthesizing Violacein using synthetic biology.

Scientists have determined the metabolic pathway in Chromobacterium violaceum that converts tryptophan, a common amino acid, into violacein. This pathway involves five enzymes and various genetic sequences for their production. These "parts" of genetic code can be positioned differently in the DNA molecule and each combination has different attributes and tradeoffs - the optimal sequence and combination being currently unknown.

The #ScienceHack Violacein Factory Kit co-designed with Genomikon which develops synthetic biology kits, had vials of all of the various genetic "parts" and the other materials needed to assemble these parts into a plasmid. According to Synbiota:

This Kit includes everything you need except:

• pipettes, nitrile gloves, petri dishes, PCR tubes, lab coats (for the full biotech experience, but any ol' trench coat will do!)
• ice buckets and ice
• 42 C water bath with epi tube floaty blanket
• 37 C incubator

All the above can be found around the house, from online suppliers, at your local university lab store, or in a friendly scientist's stash.

Kim from iGEM brought everything from the iGEM lab. He walked us through the kitchen version of the protocol for using all of the equipment safely.

Synbiota, in addition to putting together this amazing #ScienceHack project has developed a suite of online tools to publish and share lab books online (I guess I don't need that fancy paper notebook I bought!), design DNA using a very nice graphical interface and provide researchers with a whole suite of tools to do synthetic biology as a community. Everything was very well designed and worked well.

First, I created an account on the Synbiota website and logged into our notebook. Justin explained the violacein pathway and explained how we can use the online gene editor, GENtle3, (video) to design the gene sequence online.

In GENtle3, we were able to drag and drop any of the genetic parts that came in the kit into our sequence and as long as we followed the basic rules of which parts could be connected to each other. The sequence I designed was Anc-ABEDDDC-Cap, where A, B, C, D, E represent the enzymes that make up the violacein metabolic pathway. (Visit the sequence tab in the Sciencehack project to view this and other designed sequences.)

The sequence had to start with the Anchor--Origin-X' part because that was the part that was attached to the magnetic bead. One of the keys to being able to do all of this amazing work in a kitchen had to do with this innovation.

In the kit were tiny sub-micron magnetic beads with the anchor part - a strand of DNA attached to it. What this meant is that we could use a small but very strong external magnet held to the side of the container - the epi tube - to pull all of the genetic material we were working with to the side of the epi tube allowing us to insert and extract liquids from the container using pipettes while leaving our working material secured to the container.

What we needed to do after designing our sequence was to assemble it. We did this putting the beads in a epi tube, adding a "wash", removing the wash, adding a genetic part from a color coded tube that corresponded with the next link in our design, adding the T4 DNA ligase, the "genetic glue" to attach that new part to the strand on the bead, removing the excess material, washing again, and then repeating until we had added each part in order to the bead. Theoretically, we should now have a long strands of DNA attached to each bead representing our version of the DNA sequence (plasmid) that we designed.

The last step was to use a buffer to remove the bead from the strands and we had a little drop of genetic material that when inserted into a living bacteria should create all of the enzymes necessary to produce violacein from tryptophan.

The next step was what was called "transformation" which is the process that takes our plasmid and inserts it into a bacteria, in our caseE. coli. The "competent" E. coli designed for easier transfection were created at iGEM. The process we used for transformation was called "heat shock" which involved adding our genetic material to a salt solution with the E. coli and then rapidly heating it which caused the genetic material to be absorbed into the E. coli. The device used for heating, I noticed, had a sticker from the "MIT Property Equipment Office" on it. Definitely a bit punk rock. After the "shock" we added liquid material with nutrients and minerals that "rebooted" the E. coli, waking it up and preparing it to be incubated for execution of the DNA code we just inserted.

The E. coli were then spread onto petri dishes with Jello-like "food" as well as an antibiotic, chloramphenicol. The chloramphenicol would kill all other bacteria on the dish except our own because we had cleverly included a chloramphenicol resistance building genetic part in our sequence.

We then sent the petri dishes back to iGEM for incubation. The results were not perfect, but none-the-less, it looks like violacein and other molecules from the pathway were created (some other got different colours). The images of my petri dish show a kind of blackish zig-zag smear which are billions of bacteria producing metabolites because the executed DNA I designed and created. At this point I don't know for sure whether violacein was created - I need to do more verification and experimentation, but for a first go at building a complex metabolic pathway, not too shabby. Something else that is cool, is that my intended DNA design was very long, 12,000 base pairs, the next #ScienceHack step is to verify that the entire code I designed was actually assembled properly. We shared our designs, protocols and procedures with the rest of the teams. The next step was to look at the work of the other teams and try to find out what we could improve and try again.

In two half days of work, we were able to do in our kitchen what would have been Nobel Prize winning work a decade ago. We designed a sequence of genes, actually assembled the genes and then injected them into a bacteria and rebooted the bacteria.

Also, unlike traditional labs where one team would do the work and publish a paper and then other teams would try to replicate the work, we worked as one large team of parallel labs sharing our work as we went along, iterating, innovating and discussing.

I think that there is a good chance that one of the hundreds of teams will discover an efficient way of synthesizing, extracting, and purifying violacein and that soon we will have something that will probably initially look something like a homebrew beer brewing contraption producing the extremely rare compound for researchers with instructions on how anyone can build one of these violacein factories.

--

Disclosure : After this experience, I was so excited that I donated to iGEM and decided to invest in Synbiota.

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