P.C. Shannon

I’ve got two projects going in lab at the moment. One is the same thing I’ve been working on for a while: mining the structural data in AANT. You can read the paper describing the database (PubMed or PDF) for more background.

I have also been drafted, at least temporarily, by the selection facility to operate the Tecan robot workstation and do some aptamer selections. There’s a paper in review that describes the process. I’ll let you know when it gets published. Sadly, it doesn’t have my name on it.

Modern nanotechnology, such as it is, is concerned with producing materials on an atomic scale, such as fiber made from so-called “bucky balls.” Star trek fans and other afficionados of science fiction think of nanotechnology as it may some day exist — millions of microscopic machines (referred to as “nanites” or more accurately “assemblers”) pushing around individual atoms and molecules. Part of this scenario is that the assemblers are self-replicating, meaning they copy themselves using any available materials. This leads to the grey goo problem, wherein an out-of-control replication process reduces the Earth and everything on it to a mass of replicators (which look like nothing so much as grey goo).

K. Eric Drexler, the father of nanotechnology, recently published a paper refuting the grey goo danger. Basically, he says that even if we are someday able to make assemblers, it will be very difficult to make them self-replicating and there won’t be much need to do so. In fact, he says, the danger from military applications (i.e. nanotech weapons) is much greater. The problem with Drexler’s thesis is that he’s an engineer.

I mean no disrespect. In my experience, there are two camps of nano people, each with very different ideas of how the whole “assembler” idea will play out. On the one hand, you have the engineers, who are used to working with machines, so they expect that assemblers will be some sort of machine (a bioMEM in the jargon, which stands for biological micro-electromechanical machine, or something like that). On the other hand, there are the biologists, who work with cells all day and think that assemblers will be some sort of heavily engineered cell. After all, cells are just biological machines that have been programmed by nature to carry out specific tasks. Why couldn’t we just reprogram them?

It’s this biological notion of the assembler that Drexler ignores in his paper. It’s pretty much impossible that a bacteria, no matter how much you engineered it, could rearrange individual atoms in a molecule, so the massive, planet-wide grey goo problem isn’t a concern. However, I can easily envision a scenario where a biological assembler intended to clean your arteries of cholesterol grows out of control and quickly kills the patient. The crux of the problem is that while mechanical assemblers are manufactured, biological ones are necessarily self-replicating.

To control this problem of uncontrolled growth, we need multiple ways to permanently turn off the cell’s ability to replicate itself before it is administered to the patient. One solution is to knock out the replication genes in the genome and put them on a plasmid, then we would need a way to destroy the plasmid before setting the bugs loose on someone’s arteries. The cells should also have multiple metabolic dependencies (similar to the way the dinosaurs in Jurassic Park needed lysine in their diet) as well as susceptibility to multiple antibiotics.

The scientists in Michael Crichton’s novel thought they had their creations under control by making them dependent on a dietary amino acid. This was a single point of control and a single point of failure, which nature is often very good at overcoming. That’s why our biological assemblers need multiple points of control. The Jurassic Park scientists should have realized this, but I guess they weren’t very good scientists. Fortunately, they were also fictional.

In this Wired piece, Bruce Sterling agrees with my recurring theme that science in this country is in jeopardy. He makes the connection much more soundly than I have between the President’s fundamentalist beliefs and the erosion of this nation’s position as the worldwide leader in biomedical science. This reminds me of a point made by Chris Rock’s character Rufus, the thirteenth and only black apostle, in Kevin Smith’s film Dogma. Beliefs, Rufus says, are problematic; ideas are better. You can change an idea, you can have a wrong idea, but a belief is central and core, something you hold onto, something that defines who you are.

First, consider an example removed from Western theology and all of our prejudices that go along with it. Suppose you are an anthropologist studying a remote tribe in the Amazon jungle. Among this tribe’s mythology is the idea that women get pregnant by bathing in a particular pond at a certain time of day. There is a woman in the tribe who desperately wants to have children, and every day for a year, she bathes in the pond at the appropriate time, all to no avail. You decide to help this woman. Ignoring issues about cultural interference for the moment, what do you say to her?

Obviously our idea about heterosexual intercourse is a much better one because it works reliably and stands up under scientific testing. The tribe’s idea about the pond works inconsistently at best. We can say our idea is a fact. But you can’t just waltz up to the woman and boldly declare that she’s wrong in thinking what she does about the pool and that you magically have the right answer. She will cling to her belief and denounce you as a practitioner of dark magic. But if you offer her a way to save face, to incorporate your idea into her practices, then she will likely take your advice.

Similarly, we need to find a way to make science work with religion. To take a real and controversial example, considers Dr. W. David Hager, Bush’s recent appointee for reproductive health to the FDA. This doctor says that women should pray for relief from severe menstrual symptoms rather than receiving a prescription for the birth control pill. To me, this looks like the pond versus intercourse debate from the previous example. Certainly there’s no reason why women shouldn’t pray - and there is some evidence that prayer does help in some cases — but they should also be able to rely on known, proven facts, like the pill can relieve physical symptoms of menstruation (although it should be noted that the pill exacerbates emotional and psychological symptoms).

There’s no reason for Dr. Hager to not take this position - that the best remedy is a combination of prayer and medicine — except that he believes that prayer is the only solution. That’s fine for his private practice, but it seems negligent for a federal appointee, who sets policies and guidelines for doctors nationwide, to deviate so wildly from facts and standard medicine. I also think it’s negligent for the president to even appoint someone with such a position.

I have to admit, in all fairness to Dr. Hager, that my compromise position, one of both prayer and medicine, is constitutionally dubious. It seems like the ACLU may have something to say about a federal appointee advocating prayer. Of course, this caveat really applies to his present position as well.

In the end, science and religion must co-exist. Science under the control of religion is not science, and religion suppressed by science is dehumanizing. There is a wide middle ground. We just need some level-headed leadership to find it.

Here are two more pictures from Mary-Scott’s wedding festivities this weekend.