[ExI] H+ Magazine: DIYbio - Growing movement takes on aging

[Bryan Bishop]

Hey all, did anyone catch this one popping up in the news?

DIYbio: Growing movement takes on aging
http://hplusmagazine.com/articles/bio/diy-bio-growing-movement-takes-aging

Also showing up on:
http://science.slashdot.org/story/10/01/26/165254/Open-Source-Software-Meets-Do-It-Yourself-Biology
http://www.reddit.com/r/Cryptogon/comments/aufme/diy_bio_a_growing_movement_takes_on_aging_h/
http://news.ycombinator.com/item?id=1081033
http://futurismic.com/2010/01/27/garage-ribofunk-redux-diy-biohacking-gaining-popularity/

Here's some of the more interesting comments:

http://science.slashdot.org/comments.pl?sid=1525022&cid=30907022
"Many of these biology experiments require very expensive machines,
such as microarray machines, as mentioned by the article. I don't know
if purchasing refurbished machines is a wise choice since we don't
want data quality to be compromised. Also, don't forget about service
plans when the machines break or producing inconsistent output. Not to
mention various reagents, other chemicals, and supplies such as
microarray chips that make the experiment yields high quality data.
These easily reach hundreds of dollars a piece. Also, purchasing such
chemicals will get you labeled as a terrorist.

Another issue is gathering the samples. If you're collecting yeast,
that would be simple. Arabidopsis, other small plants, mice, or other
small animals, you probably need quite some space. Humans? That won't
be simple at all. You have to clear privacy issues, getting the
research review board to sign papers, etc. Sample collection alone can
cost you lots of money and time. You can always resort to publicly
available data. But chances are that you won't be able to impress
scientists much for going that route. Also, most of the important
discoveries are already done on this data. Most likely, all you can do
is to confirm existing results or to provide some tangential
additional info."

Someone replied:
http://science.slashdot.org/comments.pl?sid=1525022&cid=30907562
"Sure some of the more exotic equipment will, probably, still be out
of the hands of DIYers. However, one of the things that this movement
is known for is designing home-made versions of some of the expensive
lab-grade equipment (such as 30k+ rpm centerfuges from Dremels;
digital optical microscopes from an optical scope and a webcam; home
built electron microscopes; etc.) which, actually, work. Pair that
with their willingness to publish their, individual, projects as
step-by-step instructions and share all their info as a community and
I think it's completely possible that their communal capabilities will
ramp up, relatively, quickly. A similar effect can be seen in the,
long existing, amateur astronomy community and the DIY CNC community."

http://science.slashdot.org/comments.pl?sid=1525022&cid=30907092
"Downloading computational biology software, that you have no idea how
to use, makes you a molecular biologist, the same way that downloading
finite element analysis software that you don't know how to use, makes
you a mechanical engineer, downloading a SPICE simulator that you
don't know how to use, makes you an electrical engineer, or
downloading Pr0n that you can't re-enact makes you a sex expert. At
least the Pr0n is easier to apply than a FEM or SPICE package, it
being a "pictorial diagram", the disadvantage being that it requires a
member of the appropriate sex (and species!) to re-enact."

and someone replied: "Sure. And downloading an IDE you have no idea
how to use doesn't make you a programmer, either. But it can certainly
be a good first step in that direction. Knowing how to use those tools
properly is part of what a (molecular biologist|mechanical
engineer|electrical engineer) does, so if you're interested in doing
that, you'll want to learn. The way to learn something complex is to
see it, fumble around with it, make some mistakes, figure out what
caused them, take a look at the documentation, mess up again, take
another look, and so on. How will you ever start that process without
first getting your hands on the tool?"

Red means break here
http://science.slashdot.org/comments.pl?sid=1525022&cid=30908560 "I'm
a mechanical engineer who uses finite element analysis every day.
These days are numbered. Every year something new comes out that makes
it even easier and more idiot-proof, heading towards the point where
really anyone COULD do it. Red = "breaks here". "Would you like to use
the Analysis Assistant?" The distinction between the expert and the
automated amateur is diminishing. Remember when you needed to know
HTML to have a web page? It's only now getting started with DIY
biology, but just wait... the progress since last time might not be
obvious, but it's happening."

There was a really awesome point-by-point breakdown of a naysayer's
issues with diybio:
http://science.slashdot.org/comments.pl?sid=1525022&cid=30909342

So, yeah, very interesting feedback from the community. Article goes
something like this:

"""
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

DIYbio software has been around for a long time. Folding at 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 technology 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.

“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.
""""

- Bryan
http://heybryan.org/
1 512 203 0507