[ExI] DIYbio on O'Reilly & New Scientist
kanzure at gmail.com
Fri Jan 9 15:01:27 UTC 2009
On Fri, Jan 9, 2009 at 8:13 AM, Jim H <gahaga at gmail.com> wrote:
07 January 2009 by Phil McKenna, Boston
KATHERINE AULL's laboratory in Cambridge, Massachusetts, lacks a few
mod cons. "Down here I have a thermocycler I bought on eBay for 59
bucks," she says, pulling out a large, box-shaped device she uses to
copy short strands of DNA. "The rest is just home brew," she adds,
pointing to a centrifuge made out of a power drill and plastic food
container, and a styrofoam incubator warmed with a heating pad
normally used in terrariums.
In fact, Aull's lab is a closet less than 1 square metre in size in
the shared apartment she lives in. Yet amid the piles of clothes she
recently concocted vials of an entirely new genetically modified
Aull, who works as a synthetic biologist for a biotech company by day,
created her home lab after hearing about a contest on the science
fiction website io9.com for "mad scientists with homebrew closet labs,
grassroots geneticists, and garage genome hackers".
After two months of tinkering, she engineered a microbe that she says
is capable of performing simple logic operations, which could be the
forerunner to basic biological computers. "Biology is wet, squishy and
imprecise. It drives engineers insane," Aull says. "This would allow
us to take the noise out of biology."
One amateur biologist engineered a microbe she says is capable of
simple logic operations
Despite her success, Aull was edged out of first place in the
competition by Vijaykumar Meli, a graduate student at the National
Centre for Plant Genome Research in New Delhi, India, who designed
bacteria that could help rice plants process nitrogen more
efficiently, reducing fertiliser use.
The competition is part of a do-it-yourself movement that hopes to
spark a revolution in biotechnology. It is based on the emerging field
of synthetic biology, which uses genes and other cell components as
the building blocks for new organisms or devices. The movement is
trying to open up this field to anyone with a passion for tweaking DNA
in their spare time - from biologists to software engineers to people
who just like it as a hobby. The hope is that encouraging a wider mix
of people to take part could lead to advances that would not happen
otherwise, just as tinkering by the Homebrew Computer Club hackers of
the 1970s spawned the first personal computers.
"Biology is becoming less of a science and more of a technology," says
Mackenzie Cowell, co-founder of the group DIYbio, which aims to be an
"Institution for the Amateur", providing scientists with resources
akin to those found in academia or industry. "There will be more
opportunity for people who didn't spend up to seven years getting a
PhD in the field," he says.
Meredith Patterson, a software engineer in San Francisco, is one such
amateur. She is engineering fluorescent yoghurt by zapping bacteria
with a $40 ultrasonic jewellery cleaner she set up in her kitchen. The
sound waves create pores in the bacteria's cell walls which stay open
for long enough for Patterson to insert genes that code for green
fluorescent proteins she bought from a biological supply company.
You might say that making glow-in-the-dark yoghurt is an end in
itself, but Patterson has a serious goal in mind: to engineer bacteria
that light up in the presence of melamine, the industrial chemical
recently found in infant formula in China, which injured hundreds of
children and killed at least six. At present, the principal test for
the toxin is chromatography, an expensive laboratory procedure. "Here
is a problem that was difficult to solve by conventional means,"
Patterson says. "People should have an inexpensive and portable test
to make sure their food is safe, but no lab was working on this, so I
said let's do it ourselves."
Patterson took up DIY biology as a hobby after doing some
bioinformatics work for a biotech company. "Biology is an interesting
puzzle. I learned the informatics tools to solve those puzzles, now
I'm interested in taking that to the next level and producing novel
organisms to solve problems," she says.
It's not hard to get in on the act either. Patterson uses resources
such as openwetware.org for research, and found the best growth medium
for yoghurt bacteria in a 1950s edition of a dairy science journal.
"Knowing how to do research helps, but the barrier for entry is pretty
low," she says.
DIYbio, which so far has around 20 active participants, held its first
meeting in Cambridge, MA, in May 2008. Amateurs were invited to
extract DNA for analysis from apples, oatmeal and their own saliva,
and learned how to make gel boxes and dyes - essential tools for
Is it a good idea, though, to encourage "freelance" researchers to
experiment with DNA, however well-intentioned they may be? Not
everyone thinks so. Inexperienced hackers could pose a significant
public health threat, warns Richard Ebright, a biochemist at Rutgers
University in Piscataway, New Jersey. "Without any oversight from an
institution, colleagues or peers, the probability that a cataclysmic
entity might be constructed by someone unaware of known cautions is
significant," he says.
The greatest potential danger, he says, is that someone might
intentionally synthesise or recreate deadly pathogens like the 1918
flu strain, which killed an estimated 40 million people worldwide.
"That is on the edge of being within the technical capabilities of
someone working outside the laboratory environment."
In response to such fears and in anticipation of calls for the group
to be shut down, DIYbio has begun policing itself. Cowell says there
is now "a self-imposed moratorium on 'wetwork'", or all synthetic
biology experiments, until researchers can show that what they are
doing is safe. For the moment, the group is focusing on DNA
fingerprinting projects, with the analysis carried out by commercial
labs, rather than manipulating genetic information themselves.
The first such project is BioWeatherMap, a plot of the different
microbes, or "bioweather", to be found on street crossing buttons.
Over the next few months DIYbio hopes to mobilise amateur scientists
in Boston, San Francisco, Seattle and other cities to send in swab
samples from their nearest street corner. A commercial lab will then
sequence the microbes they find and DIYbio will post the results
online with the help of mapping software such as Google Maps.
"I think this is a perfect opportunity for high-school biology classes
to get exposed to genomics, sequencing and microbiology," says DIYbio
co-founder Jason Bobe, who expects to find hundreds or even thousands
of different species living on each crosswalk button.
Ultimately, Cowell hopes to set up a public lab where group members
can safely conduct experiments of the kind Aull managed in her closet.
In this he has the surprising support of George Church, a synthetic
biology researcher at Harvard University who in 2004 published a paper
claiming that the consequences of synthetic DNA misuse could be more
severe than chemical and nuclear weapons. He now says: "The world has
an energy crisis and a healthcare crisis that synthetic biology can
help solve; we need to go out and do it and the more people working on
this, the better."
Church argues that licensing and monitoring would-be DIY biologists is
better than alienating them. "It's going to happen anyway; you can
make it go underground or you can try to shape it," he says.
Church has agreed to act as an adviser to DIYbio, which will give the
group greater academic oversight and could allow it to resume
experimental work with less fear of being shut down.
As for Aull, she is coming out of the closet with plans to help DIYbio
set up protocols for safe lab practices. She says she will donate her
thermocycler to the group if it is able to secure a public lab and
she's also planning to carry out further work on her microbe to
confirm it really is performing logic operations.
Based on her own experiences of DIY biology, including its
limitations, she says warnings of the dangers are overblown. "It's
like a baby that just rolled over for the first time and his aunt is
crying because she doesn't have anything to wear to his wedding."
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