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image courtesy Condor Journeys and Adventures


February 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.

Chris 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.


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