DIY Bio: A Growing Movement Takes on Aging

· January 22, 2010

A movement is growing quietly, steadily, and with great speed. In basements, attics, garages, and living rooms, amateurs and professionals alike are moving steadily towards disparate though unified goals. They come home from work or school and transform into biologists: do-it-yourself biologists, to be exact.

DIYbiology (“DIYbio”) is a homegrown synthesis of software, hardware, and wetware. In the tradition of homebrew computing and in the spirit of the Make space (best typified by o‘Reilly‘s Make Magazine), these DIYers hack much more than software and electronics. These biohackers build their own laboratory equipment, write their own code (computer and genetic) and design their own biological systems. They engineer tissue, purify proteins, extract nucleic acids and alter the genome itself. Whereas typical laboratory experiments can run from tens-of-thousands to millions of dollars, many DIYers knowledge of these fields is so complete that the best among them design and conduct their own experiments at stunningly low costs. With adequate knowledge and ingenuity, DIYbiologists can build equipment and run experiments on a hobbyist‘s budget. As the movement evolves, cooperatives are also springing up where hobbyists are pooling resources and creating “hacker spaces” and clubs to further reduce costs, share knowledge and boost morale.

This movement, still embryonic, could become a monster — a proper rival to industry, government, and academic labs. The expertise needed to make serious breakthroughs on a regular basis at home hasn‘t yet reached a critical mass, but there are good reasons to believe that this day will soon come.

 

Software

Image courtesy: bioperl.orgDIYbio software has been around for a long time. Folding@home, which came out of Professor vinjay Pande‘s group at Stanford Chemistry Department in 2000, is designed to perform computationally intensive simulations of protein folding and other molecular dynamics. FAH, as it‘s known, is now considered the most powerful distributed computing cluster in the world. Open source software for bioinformatics, computational neuroscience, and computational biology is plentiful and continues to grow. On their own time, students, professors, entrepreneurs, and curious amateurs contribute to open source work that captures their interests. BioPerl and BioPython have hundreds of contributors and tens of thousands of users. Programs like GENESIS and NEURON have been downloaded by computational neuroscientists for over twenty years.

The software part is easy. The FOSS/OSS machine is well established, and has been successful for a long time. As the shift to open source software continues, computational biology will become even more accessible, and even more powerful. (Red Hat has recently asked the US Supreme Court to bar all software patents, submitting an amicus brief to the Supreme Court in the “Bilski case.” See Resources.)

Hardware

Biological research is expensive. Microscopes, pipetmen, PCR machines, polyacrylamide gels, synthesizers — basics for any molecular biology lab — run from hundreds to thousands of dollars apiece. Traditional experiments cost hundreds-of-thousands to millions of dollars to conduct. How can the hobbyist afford this equipment? Unless “Joe (or Jill) the DIYBiologist” is extremely wealthy, they can‘t. So instead of purchasing brand new equipment, DIYers like to find good deals at auction sites like eBay or Dovebid, refurbish discarded equipment from labs or biotech companies, or — more and more frequently — build it themselves.

Hardware hacking has a rich history, filled with geek heroes, and these skills are being turned towards the creation of biotech equipment. On the bleeding edge of it all, some DIYbiologists are applying their skills to h+ technologies. SENS researchers John Schloendorn, Tim Webb, and Kent Kemmish are conducting life-extension research for the SENS Foundation, building equipment for longevity research, saving thousands of dollars doing it themselves.

Stem cell extraction and manipulation, DIY prosthetics, DIY neural prosthetics, sensory enhancements, immune system testing, general tweaking of whatever system strikes the hobbyist‘s fancy.

The DIY SENS lab is headed by PhD candidate John Schloendorn. John is a last- year PhD student at Arizona State University. He volunteers full time for the SENS Foundation. Entering his lab was a mind-blowing experience. The ceilings were high, the lab itself was spacious and well-lit. It smelled of sawdust, the product of constructing the furniture on site. The equipment was handmade, but brilliantly so. Elegance and function were clear priorities. When a panel could be replaced with a tinted membrane, it was. When metal could be replaced by sanded wood, it was. The on-site laser was modified from a tattoo-removal system. Costs were down, but the technical skill involved in manufacturing was top notch.

In addition to his own experiments, Schloendorn is building an incubator (no pun intended) for DIYbio engineers who work on fighting death.

Schloendorn tells me that working by ourselves might only take us so far, but thinks it‘s a great place to start (many successful discoveries and businesses were founded in someone‘s garage). He believes that being a DIYer doesn‘t mean you must “go it alone,” but can include cooperation and teamwork. He cautions that since time and effort are limited, DIYers must choose carefully what they‘re going to work on and do that which is most important for them. His personal priority is to solve parts of the aging question, and he‘d obviously like many other DIYers to take up this challenge. “I wanted to make a dent in the suffering and death caused by aging. It seemed like the SENS people were the smartest, most resourceful and best organized among those ambitious enough. Of course, there are also DIYers with no ambitions to save the world, who are content to ‘make yogurt glow‘ in the basement for their own personal satisfaction.”

The DIYbio community has a high-traffic mailing list, where projects are discussed, designs shared, and questions asked or answered. The community has worked on dozens of DIY designs: gel electrophoresis techniques, PCR machines, alternative dyes and gels, light microscopes, and DNA extraction techniques. All of them focus on enabling cheap and effective science.

Wetware

DNAThe most popular conception of wetware is the genome — the language of life, the ultimate hackable code. Genetic engineering and (more recently) synthetic biology are the hallmarks of this effort. Synthetic biology takes genetic engineering and builds it into a scalable engineering framework. It is the synthesis of complex, biologically-based (or inspired) systems that display functions that do not exist in nature. In synthetic biology, genetic code is abstracted into chunks, colloquially known as biological “parts.” These parts allow us to build increasingly complex systems: putting several parts together creates a “device” that is regulated by start codons, stop codons, restriction sites, and similar coding regions known as “features.” (Visit MIT‘s Standard Registry of Biological Parts for more detailed information, and tutorials on how to make your own biological part.)

These parts are primarily designed by undergraduates competing in the International Genetically Engineered Machine (iGEM) competition, the largest student synthetic biology symposium. At the beginning of the summer, student teams are given a kit of biological parts from the Registry of Standard Biological Parts. Working at their own schools over the summer, they use these parts, and new parts of their own design, to build biological systems and operate them in living cells.

Randy Rettberg, director of the iGEM competition, says that iGEM is addressing the question: “Can simple biological systems be built from standard, interchangeable parts and operated in living cells? Or is biology just too complicated to be engineered in this way?” The broader goals of iGEM include enabling the systematic engineering of biology, promoting the open and transparent development of tools for engineering biology, and helping to construct a society that can productively apply biological technology.

If this sounds suspiciously like a front for DIYbio, that‘s probably because it is. In addition to attracting the brightest young minds to the critical field of molecular biology, many of the founders of iGEM, including Drew Endy at Stanford, Tom Knight at MIT, and DIYbio-rep Mac Cowell are heavily involved in or supportive of the DIYbio community. The recent introduction of iGEM teams unaffiliated with universities (“DIYgem”) is a step towards an inclusive community, allowing anyone with the brain and the drive to participate at the level of academics.

So many seeking, Around lampposts of today, Change is on the wind. — Unknown

Mainstream science is increasingly friendly to DIYbio. DIYbiologist Jason Bobe works on George Church‘s Personal Genome Project (PGP), which shares and supports DIYbio‘s drive to make human genome data available for anyone to use.

How to get involved

Join the DIYbio mailing list (see Resources). Anyone can join and it‘s the best way to begin your involvement with DIYbio. You‘ll want to check out their DIYbio forums, which are growing rapidly. You can also find a local group there and connect with like-minded DIYers. Have a look around the DIYbio.org site, which lists some of the current projects:

BioWeatherMaps: “Self-Assembly Required”
Flash mobs meet consumer-generated science in the new DIYbio initiative Flashlabs, where they‘ll be pulling-off a new large-scale collaborative science project annually for amateurs and enthusiasts worldwide. Case in point — the BioWeatherMap initiative is a "global, grassroots, distributed environmental sensing effort aimed at answering some very basic questions about the geographic and temporal distribution patterns of microbial life."

SKDB: “Apt-Get for Real Stuff (Hardware)”
Skdb is a free and open source hardware package management system. The idea is to let the user “make” a project by using all of the packaged hardware out on the web, so that the wheel isn‘t reinvented every time a new project is started. The package includes milling machines, gel boxes, semiconductor manufacturing processes, fabratories, robot armies, wetlab protocols… everything. At the moment, they‘re working on OpenCASCADE integration. Package maintainers from the DIYbio and open manufacturing communities assist others in bringing in projects into the system.

Smartlab: “Taking the Work out of Benchwork”
Project Smartlab is aiming to build hardware to augment the benchtop science experience. This includes automatic data logging instruments with painless electronic lab book integration, video streaming with “instant replay” features for those “did-I-just-pipette-that-into-the-wrong-tube” moments, and interactive protocol libraries that guide new scientists and the scientifically enthusiastic alike through tricky protocols.

The Pearl Gel Box: “A Built-In Transilluminator and Casting Box for $199!”
Want to get a jump start in DIYbio? The gel electrophoresis box is a basic tool for any DIYbiologist — and they‘re making kits so you can build your own. The Pearl Gel Box is cutting edge, open-source, and cheap. The participants in this project have created a professional grade gel box, available fully assembled or as free design documents. Plus, they want you to design new features like a built-in light filter or a mount for your digital cam.

Image courtesy: diybio.orgThis is a mere glimpse into the vast undertaking that is DIYbio. Most DIYers work independently on projects that have significant personal meaning. Tyson Anderson, a specialist in the US Army, was struck by the lack of technological infrastructure during his time in Afghanistan. Anderson, a transhumanist as well as a DIYbiologist, was trying to discuss the implications of the Singularity with the friends he had made there. He realized it was difficult to conceive of a technological paradise in a world with limited electricity. He looked to DIYbio to make a difference, and is now engineering bioluminescent yeast to construct sugar-powered lamps for his friends in Afghanistan.

Because there is much overlap between the DIYbio and transhumanist communities, it‘s not surprising that many emerging projects focus on both. DIY-SENS is only the tip of the iceberg. DIYh+ is a fusion of DIYbio and h+, coordinating projects that allow willing individuals to experiment with practical human enhancement. Example projects include supplement/ exercise regimens, DIY-tDCS, DIY-EEG, and the personal harvesting of stem cells. From the group description: “This group is a friendly cross between DIYbio and Open Source Medicine, with a dash of the ImmInst (Immortality Institute) forums [see Resources]. It‘s the slightly edgier half of OSM. The community, ideally, should strive to foster an open and safe way for responsible adults to learn about do-it-yourself human enhancement. We do not believe in limiting the use of medical technology to therapy.”

It‘s not just enhancement technology that can benefit from DIYbiology. As the popular distrust of doctors grows, people will want to understand and monitor their own body. Likewise, as personalized medicine becomes a reality, we will probably see a rise in the number of hobbyists who treat their own bodies as machines to be worked on — like a radio or a car — branching out from personalized genomics to things like DIY stem cell extraction and manipulation, DIY prosthetics, DIY neural prosthetics and sensory enhancements (infrared vision, anyone?), immune system testing, and general tweaking of whatever system strikes the hobbyist‘s fancy. This hacker‘s paradise has not yet come to pass, but it is, perhaps, our exciting future.

The road to true DIYbiology will not be easy. It‘s not a magic bullet. It will probably not produce the next Bill Gates, at least not for a long time. Biology is hard, messy, and failure is more common than success. The knowledge required takes time and effort to acquire, and even then, so-called textbook knowledge is being revised almost daily. Many are attracted by the glamour of it all. They‘re drawn to the romance of being a wetware hacker — the existential thrill of tweaking life itself. They tend to become quickly disappointed by the slow, tedious, difficult path they face.

Hobbyist biology is still in its infancy, and it will take a great deal of work before it reaches its potential. Few are more skeptical than DIYbiologists themselves. But many see no choice. Squabbles over sponsorship, intellectual property, and cumbersome regulations often prevent progress along more conventional lines. An anonymous DIYbiologist puts it this way: “universities charge far more than the experiments really cost, and bureaucratic rules constantly retard real progress.” Questions of IP and ownership can hamstring innovation in industry, while concerns for national security prevent real information sharing in government science. Large, unwieldy bureaucracies and regulatory agencies find it difficult to keep pace with the breakneck speed of technological progress. Thought-monopolies make it unwise to promote new ideas while waiting for tenure, despite the fact that many central dogmas of biology change. Individuals willing to intelligently circumvent convention may find themselves stumbling into uncharted areas of biology where they may make new discoveries.

Sleep Remaining Indicator Minimalist Clock. Photo credit: blog.makezine.com

Indeed, it is only in the last century that biology has become an unreachable part of the academic-corporate-government machine. History‘s naturalists, from Darwin to Mendel, are the true fathers of DIYbiology. They shared the spirit of discovery and scientific ingenuity and the drive to “figure it out yourself.” No one told Isaac Newton to discover the laws of classical mechanics, and you can bet he was never given calculus homework. Einstein‘s life would have been respectable if he hadn‘t spent a silent decade questioning the nature of spacetime. They were driven by the simple need to know, and they would not be stopped by the incidental truth that no one had figured it out before. DIYbiology is perhaps a reemergence of this basic curiosity, applied to the study of life.

As technologyl advances, let us study the workings of the cell the same way Newton may have studied the effects of gravity. Who wouldn‘t want to know? Who can resist a peek at the mechanisms of our own existence? DIYbio may be young, but it is a symptom of our species‘ unbreakable curiosity. We will know these secrets too, someday.

Bio“For me, chemistry represented an indefinite cloud of future potentialities which enveloped my life to come in black volutes torn by fiery flashes, like those which had hidden Mount Sinai. Like Moses, from that cloud I expected my law, the principle of order in me, around me, and in the world. I would watch the buds swell in spring, the mica glint in the granite, my own hands, and I would say to myself: I will understand this, too, I will understand everything.” —Primo Levi

Without a lab supervisor to guide them, DIYbiologists must take a carefully disciplined (and perhaps more genuine) approach to science. DIYbio has the potential to revive a noble tradition of pure scientific curiosity, with a modern, engineering twist. If you want to get something done, some day it really will be possible to do it yourself.

Parijata Mackey is the Chief Science Officer of Humanity + and a senior at the University of Chicago, interested in applying synthetic biology, stem cell therapies, computational neuroscience, and DIYbio to life-extension and increased healthspan.

12 Responses

  1. Richard says:

    This article refers to a Reference section. Where is it?

  2. Anonymous says:

    Don’t forget R/Bioconductor! Not only is R free, but there are thousands of available Bioconductor packages ready for out-of-the-box use.

    Also consider Cytoscape and or EGAN for graph visualization of established and experimental bio-knowledge.

    http://www.bioconductor.org/
    http://www.cytoscape.org/
    http://akt.ucsf.edu/EGAN/

    (full disclosure – I work on EGAN)

  3. JTP says:

    BioRuby is also maturing nicely
    http://www.bioruby.org/

  4. Richard says:

    A great place to get biomed equipment on the cheap is GSA Auctions . com. You can, at times, find the most amazing lab equipment for less tha 300 dollars.

  5. Anonymous says:

    Another step on the road to the Brave New World

  6. Yeah, man. Looks pretty cool. I LOVE little experiments like this! Keep up the good work.

  7. Renton Innes says:

    Try starting folding protein to see what life is all about thus far molecular scale first…

    http://www.fold.it

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