DIYBio brand petri dishes!

We had our first DIYBio workshop in Broad Hall on the UCLA Campus over the weekend. The student community from both north and south campus were involved, which included art and science/math majors.

Romie Littrell started things off with a short presentation on the concept and history of DIYBio. His talk kicked off discussion focusing on the safety and security of biotechnology that is open to the public.

Romie (middle, blue) presents to DIYBio attendees.

Big discussion on safety and terrorism issues of biotechnology

The highlight of the workshop included an extraction of DNA from everyday food products, akin to the extraction of DNA from strawberries.

DNA from a cup of green tea!?

lysing cells through a syringe

Everyone is in awe

Looking for the nucleic acid precipitate

Homemade centrifuge

Other demos at the workshop included a sampling of a biological polymer made from cornstarch and other products found in every kitchen.  The red color and taste reminded me of Twizzlers.

Tor Nowlan and Max Belasco explain to us the elegance behind this!

DIY bio Los Angeles Workshop at UCLA! February 27th, 2010 from Kenneth Wei on Vimeo.

We had a diverse group of visitors throughout the workshop over 4 hrs.  Other than science and art professionals,  a lawyer and stay-at-home mother with toddler came to participate.

Check out our Flickr page for more pictures from this specific event.  Stay tuned for an exciting announcement in the coming weeks on the next workshop and the start of our long term project!

“I teach middle school math science and history for beginning ESL students. My students originate from all parts of the globe including Sudan, Peru, Mexico, Korea, and Japan. 80% of my students receive free or reduced lunches. Students often see subjects such as history and science as unrelated. In the community where my students live they often do not see the practical application of scientific methods in the work force. Additionally, the rich diversity of cultures makes the idea of interconnectedness especially important. Testing our mitochondrial DNA will allow my students to trace their haplogroups and trace their ancestors migrations out of Africa. We’ll be able to find common ancestors between us and tell the history of the human race. Using the lab equipment (the conical tubes, saline solution, and kit) students will process their own DNA using the same process anthropologists and forensic experts use, giving students a real connection to science in the work force. The DNA models and evolution charts will be used to explain the processes of population shifts and explain how we can use DNA to determine common ancestors. Your help will fund a project that connects science (through genetics), history, and math. Students will get training in DNA testing that is used by real scientists everyday. This project makes the vital concept of DNA tangible and gives my students the tools needed to access higher science subjects in high school. You will make it possible for my students to describe our common heritage as humans. My students need 9 pieces of DNA analysis equipment such as conical tubes, saline solution, DNA models, evolution charts, and a DNA Replication and Transcription Set.”

Check out some photos from the project: http://www.donorschoose.org/donors/proposal.html?id=341067&pmaId=264576&pmaHash=-507759220

There is a whole range of biology, biotech, and DNA related projects that you can contribute to on the Donors Choose website: http://www.donorschoose.org/

Tito

You may feel surprised to know that PLoS has web icons which you can display on your own web page!  Check it out, make your science blog or web notebooks “PLoS inside” to raise awareness of their efforts.  Here’s how:

To add this banner to your webpage, add this html code to your page: <a href=”http://www.plos.org”><img src=”http://www.plos.org/images/support_plos_100x157.jpg” alt=”I Support the Public Library of Science” width=”100″ height=”157″ border=”0″></a>

To add this banner to your webpage, add this html code to your page: <a href=”http://www.plos.org”><img src=”http://www.plos.org/images/join_plos.gif” alt=”Join the Public Library of Science” width=”140″ height=”80″ border=”0″></a>

To add this banner to your webpage, add this html code to your page: <a href=”http://www.plos.org”><img src=”http://www.plos.org/images/join_plos_banner.gif” alt=”Join the Public Library of Science” width=”600″ height=”119″ border=”0″></a>

Library Buttons and Banners

To add this banner to your webpage, add this html code to your page: <a href=”http://www.plos.org/journals/”><img src=”http://www.plos.org/images/banners/library_button.gif” alt=”I Support the Public Library of Science” width=”120″ height=”60″ border=”0″></a>

To add this banner to your webpage, add this html code to your page: <a href=”http://www.plos.org/journals/”><img src=”http://www.plos.org/images/banners/library_vert.gif” alt=”I Support the Public Library of Science” width=”120″ height=”240″ border=”0″></a>

To add this banner to your webpage, add this html code to your page: <a href=”http://www.plos.org/journals/”><img src=”http://www.plos.org/images/banners/library_banner.gif” alt=”I Support the Public Library of Science” width=”486″ height=”60″ border=”0″></a>

From their website: “We identified 95 different animal species.”

You probably wouldn’t believe me if I told you that all of the species displayed above were found in local supermarkets and homes in New York City. A feather from a duster yielded Ostrich DNA. A delicacy labeled “sturgeon caviar” instead turned out to be from the strange-looking Paddlefish. A popular Asian snack was revealed as Giant flying squid. Bison DNA was found in a dog biscuit.

>

We found DNA evidence all around us. We found DNA “name tags” in all kinds of human and pet foods including raw, cooked, dried, and processed items. We obtained DNA from dried soup mix, scrambled eggs, dog food, chicken McNuggets, hamburger, beef jerky, bologna, yogurt, cheese and even butter. By analyzing DNA, we traced tiny, unrecognizable bits of once-living things to their source.

We could identify animals from what they left behind in the environment. We found tell-tale DNA in dried-out horse manure in Central Park, a pigeon feather on the sidewalk and a shed snakeskin.

Good work! Website: http://phe.rockefeller.edu/barcode/dnahouse.html

PDF of samples and results: http://phe.rockefeller.edu/barcode/DNAHouse%20specimens,%20results.pdf

Bryan Bishop presented at the 2009 H+ Summit onopen source hardware and took copious notes. Here he presents some of his favorites:

Patri Friedman. Meeting him in person is like meeting with a living legend. Hell, he wrote the book on seasteading. His talk was short and to the point: let’s make startups for governments and ways of organizing people. You know how everyone says let a thousand flowers bloom? Same thing going on here, except he’s serious about it. The Seasteading Institute is a 501c3 non-profit organization dedicated to living on the high seas and promoting a diversity of ways of living and organizing groups of people. At the end of the talk he gave a shout-out to the DIY scene: 12 miles off the coast, there is no FDA. The talk was recorded and is somewhere here, and here’s the transcript. I didn’t catch the Q&A because I was up next! What a talk to follow.

Todd Huffman also talked (transcript). Todd organized BIL, the simple and free alternative to TEDtalks. Todd spoke about whole brain emulation and his startup, 3Scan. He showed some really amazing videos collected from his team back at TAMU running off of a knife-edge microscope. His plan is to slice and dice brain tissue so as to scan in details all the way down to mitochondrial positions in order to parameterize and seed emulations and simulations of brains.

Gregory Benford (transcript) also showed up and talked about personal genomics, or what he calls “nutrigenomics”. It turns out that he bought the original Methuselah flies. The Methuselah flies were super-longevity flies living well beyond average lifespans. With these flies he sequenced their genome and found particular up-promoted and down-regulated genes that might be causing the flies to live longer. The idea is to then synthesize custom pharmaceuticals that enable and disable gene regulation for different (but targeted) genes in the human body. Greg is really amazing in person, although maybe that’s just me being a fanboy for his scifi after all these years? At some point you go “wtf, I’m having a one-on-one with Gregory Benford!” (He was also at the Singularity Summit earlier this year.)

You should also check out Anselm Levskaya‘s talk on brain input/output projects, Dylan Morris, and Christine Peterson had some good suggestions for not dying.

And one final plug- there’s no transcript for me because I was presenting (!) on open source hardware (1, 2, 3).

hplusmag - winter 2009 - cover "Hi there, Ray"

Parijata Mackey wrote an article for the Winter 2009 h+ magazine about diybio titled “diybio: a growing movement takes on aging.” She provides an overview of diy -hardware, -software, and -wetware, and gives shoutouts to some of the projects listed at diybio.org/projects (man we gotta develop a better system for collecting projects).  Overall she provides an overview of where diybio came from and where it’s going in an optimistic manner consistent with h+. She also provides tantalizing interview coverage with John Schloendorn concerning his DIY SENS lab and biotech co-working space in the Bay Area.

Andrew Hessel wrote another article called “Why DIY Bio” in which he explains his vision, based on open source & synthetic biology principles, for a distributed, open anti-cancer research collective. He calls it Pink Army.

UPDATE: slashdotted on 26 Jan 2010.

Scientific American Oct 1953 - Evolution in Bacteria

DIYbio aims to be “the institution for the amateur,” developing and providing access to all of the resources a professional might have and an amateur might want, such as equipment, protocols, access to literature, etc. And we are collectively doing so in a distributed fashion right now.

But we are also doing something more, something that will occur slowly, over long time-scales. We are helping lay the foundations for cultural shift. We are laying the foundations for broad, deep, domestic understanding of science and technology.

We are proving that the cultural barriers to practice science in general, and biotechnology in particular, are imaginary. We are proving this by doing it ourselves. We are building a familiarity with the practice and product of science and slowly demonstrating that it can be a cultural activity like musicianship or cooking or solving sudoku puzzles. We are domesticating biotechnology.

As Sophia Roosth recently pointed out, we are proving that “the biological is not something cordoned-off in labs, but something quotidian, personal, and apprehensible,” that we are “intentionally destabilizing what it means to ‘do science’.”

Why is the domestication of biotechnology important? Listen to how W. Brian Arthur begins his recent book, The Nature of Technology:

We are attuned in the deepest parts of our being to nature, to our original surroundings and our original condition as humankind. We have a familiarity with nature, a reliance on it that comes from three million years of at-homeness with it. We trust nature. When we happen upon a technology such as stemcell regenerative therapy, we experience hope. But we also immediately ask how natural this technology is. And so we are caught between two huge and unconscious forces: Our deepest hope as humans lies in technology; but our deepest trust lies in nature. These forces are like tectonic plates grinding inexorably into each other in one long, slow collision. The collision is not new, but more than anything else it is defining our era. Technology is steadily creating the dominant issues and upheavals of our time. We are moving from an era where machines enhanced the natural—speeded our movements, saved our sweat, stitched our clothing—to one that brings in technologies that resemble or replace the natural—genetic engineering, artificial intelligence, medical devices implanted in our bodies. As we learn to use these technologies, we are moving from using nature to intervening directly within nature. And so the story of this century will be about the clash between what technology offers and what we feel comfortable with.

By domesticating biotechnology, we are helping society temper its natural mistrust of technology.

DIYbio is just one stone in this cultural foundation, set next to other DIY communities and Citizen Science projects and part of the broader resurgence of DIY culture championed by publications such as MAKE, President Obama, and perhaps the forebears of the internet itself.

Sophia Roosth, a doctoral student at MIT, presented a talk at The Kennedy School of Government STS seminar series on 9 Nov 2009 called “Crafting the Biological: Open-Sourcing Life Science, from Synthetic Biology to Garage Biotech.“

It’s a fantastic talk.  Sophia has been engaged in non-institutional biology at least since 2003, when she worked for Natalie Jeremijenko on the singular art / activist Biotech Hobbyist Magazine, and in her talk she presents her anthropological insight into DIYbio, richly contextualizing the social causes and effects of the movement.

Sophia talks about the practice of biology in terms of Knowing and Making. For DIYbiologists, she says:

“Knowing means a personal sort of knowledge, in which quotidian biologies like human bodies or the organisms you might encounter in a produce stand, for example, may be explored and modified. And Making is less about following engineering principles than it is about tinkering and making do, which I claim [DIYbiologists] do to destabilize what counts as legitimate scientific practice.” “Biology, Knowing, and Making, are all concepts up for grabs at this moment in the life sciences (and in this talk). If what historian Philip Pauly called the ‘engineering ideal for biology‘ unfolded in the 20th century within institutionally-sanctioned spaces, then in the 21st we are witnessing synthetic biologists and self-described biohackers recasting the bioengineering project as malleable and explicitly domestic. Think of the personal computing revolution, but for biology.”

And that’s all in the first 5 minutes! Check it out. It’s great. (mp3)

Then you pull out your iPhone, magnify the sample 100 x and snag a photo. Doesn’t look like anything familiar but…

Maybe #diybio on Twitter would know?

“#diybio, I’m at the salt flats outside San Francisco. Any idea if I’m looking at something like red tide, or is this just algae?” – DIYbioGuy, N 37^o 50′ 55.5” – W 121^o 55′ 53.0”

Fellow citizen scientists take interest…

“@DIYbioGuy — Those algae look active, and wow look at the chambers on that Foraminifera! It looks like it may be ornamenting itself. #diybio” – wreinhardt

Make this happen — a portable, web-enabled 100x microscope that plugs into an iPhone. The purpose of this article is to document my attempt. To be sure, I had an idea and I tried it out. I did not refine the idea or do very much planning. In place of refining the idea, I used lots of tape. I also didn’t get very far.

Cellscope demo at Critter Salon (SF)

Inspiration: A few weeks ago at the CRITTER Salon in downtown San Francisco, I talked with Amy from UC Berkley about a project called “CellScope“.  Their mission — diagnosing diseases in remote areas by hooking a simple microscope up to a cell phone. Snag an image, and send it off to some professions for diagnosis of sickle cell and TB, and other diseases.

I love the idea, I dislike squinting into microscopes (and maybe you do to?). Though I won’t be diagnosing diseases, a portable, web-enabled microscope would be very useful. Extending this project to connect to an iPhone seemed like the obvious choice, so I gave it a shot.

Day 1 – I bought a RadioShack pocket scope tonight. Lining up the microscope with my iPhone while trying to focus was a disaster. I needed to mount the microscope to something flat.

Using the packaging, a whole bunch of tape, and a butter knife for stability, I mounted the microscope to the cardboard. Then I got the microscope to line up with my iPhone’s camera – and snagged this picture of a quarter. It’s pretty tedious to get the scope aligned with the camera, so I called it a night after nabbing a cool picture of the threads from the green Foo Camp shirt I was wearing.

My t-shirt through the Radioshack pocket scope + iPhone

Day 2 – When I returned home after work, I was inspired to make a more permanent mount that wouldn’t go out of alignment as easy. I had a package of moldable plastic beads lying around from Maker Fair. The beads melt in boiling water, forming a big malleable blob. You mold the blob to whatever shape you desire and when it cools, it’s hard plastic. This stuff was great, and you can re-heat and reform it too. After my first attempt at molding a mount, I discovered the problem wasn’t just the mounting. The precise alignment needed between the scope and the phone was too much, I estimate about 1/16″ difference would cause the image on the microscope to move outside of the iPhone’s sight.

Stabilizing the pocket scope

Over the next few days, I attempted to enlarge  the image using eyeglasses from a Dollar store, and other types of magnifying lenses, none of which helped. At this point, I had a good understanding for the challenges ahead. I wrote Amy back to see what a copy of the Cellscope would cost, but the parts she suggested were about $300. I decided to let the project settle and moved on to something else. Then I met the Hackteria team…

Turning a $20 webcam into a 200x USB microscope

At the DIYbio + iGEM meeting last week at MIT, a team from Hackteria (Bangalore) showed us how it’s done. Mac brought a $20 USB webcam to the meeting for us to hack. Basically just unscrew the case, flip the little lens around, and there you have it, a 200x USB microscope. Of course, focusing is still a manual process and somewhat tricky.

Above: A video from Hackteria’s USB webcam project

Summary: Overall, I went through a lot of crummy ideas to get to some ok ones. Many of my best “discoveries” were simply stumbling upon the great work of others, like the Cellscope and Hackteria! Turning a USB webcam into a microscope is great for innovation in low cost labs. The next step is mobility – hooking one of these up to an iPhone, either through the USB port or just relying on the built in camera. Check out the Hackteria blogpost, here.

Challenges: A portable iPhone microscope

1. Low cost magnification  – solved

• USB webcam or Manual pocket scope

1. Digitizing and recording images — getting there

• Standard desktop software for USB webcam
• unknown for pocketscope + iPhone

1. Connecting a USB webcam to an iPhone  – ??

2. Obtaining and positioning the sample — ??

• This is the most challenging part of the project. How would you use an iPhone microscope? Do you want to keep it in your pocket? If you want to look at a leaf, how do you hold the scope + sample so that they stay in focus? Do you need to keep slides with you as well, in order to quickly mount your sample?

After reading this, you might get the initiative to try building something of your own. Go for it! Fail fast. Fail frequently!

I’ve started a discussion in the DIYbio Forums, and would love to hear about your thoughts, ideas, and progress!

– Tito Jankowski is a founder of Pearl Biotech. His interests include building better hardware for biology.

Sources – Hackteria: DIY USB microscope Instructables: 30 minute USB microscope Critter Salon CellScope

Doing the infamous dna extraction

If you’re in the Boston area, drop by the Cambridge Science Festival between noon and 4:00pm this Saturday, April 25, to visit the DIYbio table! We’ll be in the tent at the opening Science Carnival – see the Cambridge Science Festival’s schedule for details.