Deep Woods PCR
by Paul Vanouse, 2011
|CONTEXT / BACKGROUND
To me, an encampment deep in the Canadian wilderness evoked a Romantic notion of exploration. In canonical Romantic exploration narratives, the journey into the unknown is often a vehicle for self-discovery as the external environs force an internal revelation. (e.g., Herman Melville's Ishmael in Moby Dick, Joseph Conrad’s Marlow in Heart of Darkness.)
The deep woods location also brought to mind, the idea of the “Pioneer”, and a slew of expedition writing of the colonial period, such as journals and historical accounts of Lewis and Clark.
|Invention of the “Polymerase
Reaction”, commonly referred to as “PCR”, has
romantic, mythic dimensions.
The Polymerase Chain Reaction is an elegant algorithmic process that allowed Kary Mullis to copy a small region of DNA billions of times, thereby “amplifying” a region, potentially to differentiate individuals. The first great patent of the biotechnological revolution profited Cetus and Roche corporations with the first billion dollar invention. For his discovery, Mullis, along with Michael Smith, was awarded the Nobel Prize in Chemistry in 1993.
|Within a few years, the entire process could be
performed by a PCR thermocycler, which partially black-boxed the
Algorithm became machine.
Kary Mullis epitomizes the scientific pioneer.
(1) He is a generalist, able to use and connect concepts outside his specific area of expertise. (2) He is a loner who some claim to have alienated others at the Cetus corporation where he worked. Varied accounts have Mullis threatening other workers.
(3) And lastly, he is credited with a big idea that was before its time that he doggedly pursued despite his other duties at the corporation.
PCR is also a technology of “self-discovery”, or less optimistically, authoritarian identification. PCR has replaced the original DNA Fingerprinting methods in many cases, including massive government DNA databases, such as the US FBI’s CODIS project.
|THE PERFORMANCE / TIMELINE:
My plan was to perform all phases of the “high-tech” PCR process in the unlikely setting of the deep-woods encampment.
I wanted to open up meanings of the PCR discovery/patent during the low-tech PCR experiment, a technologically anachronistic reenactment, in the heart of the national forest.
The performance conflated scientific pioneer with its expedition counterpart and probed the idea of “self-discovery” in its broadest sense.
|First, I incubated water from the famed natural
hotsprings of the Banff region hoping to discover living Thermus
Acquaticus bacteria in its warm, sulfuric waters. This
thermophilic organism produces an enzyme, generally referred to as Taq,
essential to PCR’s commercial effectiveness.
In 1989, Science Magazine dubbed Taq Polymerase the “molecule of the decade”. It was discovered in geysers at Yellowstone National Forest in the 1970s... and eventually commercialized for great monetary gain (but not for the national park).
My hunch of the bacteria’s presence proved correct, but incubation proved slow at the campsite as the available incubator couldn’t hold the 70 degree Celsius, ideal temperature for incubation, nor could it agitate the samples to facilitate their respiration and colony formation. Thus, the Taq enzyme used in the subsequent experiment wasn’t the same as that which I fished out. (Alas, I think this may be the basis of future “Out back PCR” endeavors.)
|I extracted my own DNA to underscore the slippage of
“exploration”. Also added to each tube is a mixture
of DNA primers, Taq enzyme, DNTPs and MgCl buffer solution.
Finally, the experiment could begin in pioneer fashion, without the PCR machine, but rather a campfire.
I needed to keep water buckets at very precise temperatures: 95, 65, 72 Celcius to allow the PCR amplification process to work correctly.
|The experiment required that I
“thermocycle”--switch DNA tubes between water buckets 120
times, or 40 cycles. I was simultaneously maintaining water
temperatures by adding wood to fire, shifting placement, etc. This
phase was the central focus of Deep Woods PCR and what I considered the
primary artistic and scientific challenge. It took hours.
Filmmakers, Zoot Derks and Jeanette Groenendaal, tirelessly document the event in its entirety. Angus Leech strums acoustic guitar and premieres his original composition “Thermocyclin’ ‘neath the moon.” All the fabulous artists and scientists from the BioARTCAMP also joined me in solidarity at the campfire for the all-night performance including Jennifer Willet, Tagny Duff, Marta De Menezes, Adam Zaretsky, Marie Pier Boucher, Kurt Illerbrun, Ian and Louise Chance Baxter, Bulent Mutus, Grant Yocom, Tokio Webster, Brit Wray, Jamie Ferguson, Dave Dowhaniuk and Kacie Auffret.
|During thermocycling, I attempt to channel Mullis. The fluorescent green raccoon in the adjacent image, played by Rafael Vanouse, repeatedly chants “amplify the source, not the signal.” The phrase refers to the genius of PCR for DNA analysis. Prior to PCR, scientists seeking to visually analyze DNA fragments needed to radioactively label target sequences and typically they sought better imaging apparatus or stronger radiation to enhance their dim images. Mullis, on the other hand, realizes that DNA regions could be amplified exponentially by successively initiating the DNA transcription process and thus greatly enhance any imaging or analytical process. In his autobiography, Mullis credits frequent LSD experimentation as central to his own personal and scientific development. He also describes a subsequent, enigmatic, deep-woods abduction by a flourescent, extra-terestrial raccoon who greets him with "Good evening, doctor".|
|Then we electrophoresed. To actually test if the
PCR process worked, we ran each of the samples in a dna gel
Success… The campfire PCR produced extremely dense banding. These results show me to be heterozygous for the PV92 Alu gene on chromosome 16, shown in columns 2-3 of the adjacent gel. This particular site is often used for genotyping, as there is a high degree of variation across our species.
In the four, center columns of the gel I have amplified two sites of the SLC24A5 gene, which is one of the human genes coding for skin color.
|CONCEPTUAL / REFLECTIONS
Just as context is a meaningful paratext in any cultural activity (such as an artistic performance) the context in which PCR is “invented” by Mullis is fundamental to its cultural meaning, economic value, and scientific merit.
When Mullis begins his exploration, there is a big problem. It has no purpose. The idea of duplicating a region of DNA exponentially is "cool", and "elegant" but of little use in research or industry. However, by the time he obtains publishable results, the technology is of great utility for Genetic Engineering (allowing one to duplicate a gene for transplant) and DNA Typing (allowing one to compare highly variable regions of DNA). Changing context turns a neat trick into an indispensible laboratory tool.
|Mullis’ “invention” occurs at the brink of the biotech era, while patent laws were being stretched as the private biotech corporation ascended over the university research laboratory. “Invention”, is used in quotes here as parts of the process had already been invented—the patents were contested by scientists who had developed these building blocks of the PCR process. However in the changing context of research science, Mullis’s unique "idea" would be worth billions. Unfortunately for Mullis, Cetus, the company where he had worked didn't realize PCR's implications and sold to Roche Pharmaceuticals. PR Newswire estimates that "the global PCR market is projected to reach around US$27.4 billion by 2015, with a Compounded Annual Growth Rate (CAGR) of 13.9% for the analysis period, 2009-2015."|
BioARTCAMP, organized by Jennifer Willet, in conjunction with the Banff Center, Alberta, Canada.
Jordan Dalton, University at Buffalo.
Katie Brown, Buffalo River Keepers.
Dancing Naked in the Mind Field, Kary Mullis, Vintage Press, 1998.
Making PCR: A Story of Biotechnology, Paul Rabinow, University of Chicago Press, 1996.
"Biotech in Court: A Legal Lesson on the Unity of Science" Kara Swanson, Social Studies of Science, 2007; 37; 357.
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