11, 2002 | My printed in China desk calendar tells me
that tomorrow is Abraham Lincoln's birthday. February 12th, is also
the first anniversary of the simultaneous release of the human genome
sequence by the publicly funded Human Genome initiative and by privately
owned Celera Genomics Corporation, and I think not coincidentally,
Charles Darwin's birthday. It's mine as well.
As the two rival teams were preparing to publicly put aside their
differences and jointly celebrate leading humanity into the postgenomic
era, I was in the upper right corner of Chile, high on edge of the
altiplano close to the borders of Peru and Bolivia, in the Aymara
village of Putre.
My friend Carlo, who managed the road crew upgrading Chile 11,
the main connection between landlocked Bolivia and Chile's Pacific
ports, left me to order lunch in a small family run restaurant while
he went to investigate a rock fall a few kilometers up the road.
I waited for Carlo and ate my Cazuela de vacuno, a traditional
Chilean soup of beef and vegetables. With each spoonful of Cazuela
I was unknowingly swallowing billions of toxic nanobots called Alpha-hemolysin
or alphaHL. AlphaHL is a protein mechanism made of just 293 amino
acids. It is an amazing naturally engineered molecular machine,
that automatically constructs very neat ultramicroscopic hexagonal
holes in cell membranes on contact. It is secreted by Staphylococcus
aureus, the tiny spherical bacteria of the common staff infection.
In short, I had food poisoning, and a few hours I would be violently
ill as my body tried to purge itself of the alphaHL nanotoxin.
I would discover about a month after my nanoillness that researchers
lead by David Deamer at the University of California, Santa Cruz,
have devised a method of analyzing DNA molecules that can rapidly
discriminate between nearly identical DNA strands. The technique,
based on the use alphaHL, may someday do essentially what the Human
Genome Initiative and Celera did in months with hundreds of millions
of dollars, in hours for hundreds of dollars. But for now, the ability
simply to distinguish individual DNA molecules in a mixed solution
is a notable achievement.
The instrument used to perform the analysis, called a nanopore
detector, is built around a membrane containing an alphaHL induced
nanopore which is just big enough for a single strand of DNA to
pass through. A voltage applied across the membrane generates an
ionic current and pulls the negatively charged DNA molecules through
the nanopore. A characteristic decrease in the current occurs when
a DNA molecule temporarily blocks the opening. Using machine learning
techniques, a computer program is "trained" to recognize
the signals generated by different DNA molecules. The detector is
able to analyze a mixed sample and indicate the proportions of each
type of molecule present in the sample.
"It's almost like the detector is tasting the solution, pulling
in one molecule at a time, spitting it out, sampling another molecule,
and it's doing this hundreds of times a second," Deamer said
in a university press release.
Right now, Deamer's lab and high-tech equipment maker Agilent are
working to construct what is hoped will become a $20,000 nanopore
DNA sequencer with single-base resolution that could decode an individual's
genome in 24 to 48 hours. Such a device would be the ultimate diagnostic
tool, allowing medical care to become truly personal for the first
time by allowing your doctor to know almost immediately your susceptibility
to specific diseases and your reaction to certain drugs.
There are larger implications however.
Rapid DNA sequencing will have a great impact on us because collecting
and comparing large numbers of individual genomes opens all human
physical and behavioral traits to rapid statistical attack. Such
statistical attacks on the functionality of our DNA will greatly
accelerate our understanding of ourselves and bring a future where
we control, for better or worse, every aspect of life. A future
that will include legitimate medical as well as behavioral and cosmetic
genetic manipulation and a whole host of changes yet unimagined.
Ingesting alphaHL made me very ill, and I have to admit, I feel
a little sick to my stomach just thinking about alphaHL and it's
implications for all of us.
McKinstry is a Canadian living in Chile where he operates
the world's largest optical telescope for the European
Southern Observatory. He is also the creator of the Mindpixel
Digital Mind Modeling Project, the world's largest AI effort.