Seriously: “Beach said people become infected when they wade through shallow water and stir up the bottom. If someone allows water to shoot up the nose—say, by doing a somersault in chest-deep water—the amoeba can latch onto the olfactory nerve. The amoeba destroys tissue as it makes its way up into the brain, where it continues the damage, ‘basically feeding on the brain cells,’ Beach said.” [via Yahoo/AP]
Ok, I’m gonna crank the nerdliness up to 11…
This video shows what I love about biology: there’s all this really amazing, incredible stuff going on inside your body all the time. The most basic business of life itself is a miracle. I find it all fascinating. In fact, I’m such a nerd that this video almost brought a tear to my eye. There’s also a full-length version available.
Last week, I gave a presentation on my current research. My brief introduction ended with comments that are a mantra to many grad students: “…which will hopefully be my dissertation project.” The talk went well enough—the audience was just other grad students—and I got a lot of good feedback. At the start of the question-and-answer period, one of the girls raised her hand and asked, “Do you have a hypothesis?”
An organism’s metabolome is all of its metabolites and metabolic processes—in other words, all of the chemicals that come out of it (like urea, carbon dioxide, and progesterone) and all of the biochemical reactions that produce those compounds. It’s one of those words that scientists concocted out of thin air because they fancy themselves clever lexicographers. But it’s a powerful concept and one of the keys to the future of personalized medicine.
Popular Mechanics gave a “Breakthrough Award” to MIT researchers who reprogrammed a virus to instead form a tiny, tiny battery anode. The researchers, lead by Dr. Angela Belcher, used the bacteriophage M13, which is a workhorse of molecular biology to incorporate cobalt oxide and gold, forming a nanowire. M13 grows in a tight cylindrical spiral, and I suspect that the scientists exploited this property in convincing the virus to grow a nanowire. As Popular Mechanics recognized with their award, this is a very interesting development.
Wired News is reporting on an international team of scientists that is developing a microrobot small enough to swim through arteries and the heart. They hope that the robot, as small as two human hairs, will be able to perform microsurgeries on cranial arteries and other areas that are beyond the reach of catheters. This both refutes and supports my notion that nanotechnology will have to draw inspiration from biology rather than our everyday macroscale world.
One the one hand, this contradicts what I said last night about micromechanical approaches not being viable, because, if they can get this robot to work, it obviously will be viable. On the other hand, it very much agrees with my assertions:
“People have tried various techniques, including electromagnetic motors,” [team leader] James Friend said. “But at this scale, electromagnetic motors become impractical because the magnetic fields become so weak.”
Instead of trying to scale down common mechanical systems, like an electromagnetic motor, Friend and his team are building piezoelectric motors, which operate on different principles.
Moreover, the new design doesn’t use propellers:
The microrobot’s design is based on the E. coli bacterium, complete with flagella that will propel it through the body.
As nanotechnology moves from hype to actual products, we will see that most successful designs use new techniques developed for the nanoscale and draw on knowledge from biology.
Researchers at MIT and the University of Hong Kong describe how peptides can self-assemble to control bleeding from surgical wounds. From Nature Nanotechnology:
The key to the success of this particular peptide is that it is water soluble and can be easily delivered by a syringe. Furthermore, self-assembly of the peptides is triggered by the ionic environment of the blood, and when broken down, the amino acid building blocks of the hydrogel can be used by the body to repair the injury.
This a great advance, thanks to nanotechnology. It can save lives on the battlefield or in accidents by stopping bleeding before the wounded are transported to the hospital. I think the other important thing here is that this is a clever application of biology rather than some sort of micromechanical approach. I think I’ve said this before—I think a lot of the important nanotech innovations are going to come from adapting biology, which already operates on the nanoscale, rather than trying to scale down macroscale machines. This is one example of that.
A new exhibit at the Oslo Natural History Museum showcases examples of homosexual behavior throughout the animal kingdom. Geir Soeli explained the motivation behind the exhibit:
“As homosexual people are often confronted with the argument that their way of living is against the principles of nature, we thought that … as a scientific institution, we could at least show that this is not true … You can think whatever you want about homosexuals but you cannot use that argument because it is very natural, it’s very common in animal kingdom.”
There are two examples of homosexual behavior in animals that I’m familiar with. One is bonobos, a species of primate closely related to humans. They use sex the way chimps use violence—which is to say, as one of their main forms of social interaction. The second example is when male rats are overcrowded in a cage, although that seems to explain what happens in prisons more than normal homosexuality. So it was interesting to read about other examples, especially from non-primates. As Soeli said, homosexuality is very normal.
Recently I was watching the ST:TNG episode “Genesis“. The science in this episode is all on the level of the Heisenberg compensator, which is to say, laughably bad. (Someone did point out once that a Heisenberg compensator doesn’t necessarily mean one can determine both a particle’s speed and position, it just compensates for the fact that you can’t.) But Dr. Crusher’s estimation of the number of genes in the human genome was pretty accurate, at least for 1994.
Estimations of the number of genes make for an amusing measure of scientific progress. I’ve heard that in the 60’s, the number was estimated in the millions. According to Star Trek, it was down to 100,000 by the mid-nineties. (It’s also interesting to note that at that time, the Human Genome Project would have been considered to be only a third of the way into it’s fifteen year lifespan, but it actually finished in 2001, four years ahead of schedule, because the technology improved so drastically during the project.) I noticed recently that my genetics textbook, which was probably written in 2001, estimates the genome to be between 40,000 and 60,000. The current estimate is much more like 27,000.
For comparison’s sake, the fruit fly Drosophila melanogaster has about 12,000 genes. The bacterium E. coli, which is famous for killing people at Jack in the Box but also thrives in your intestines, has about 3000 genes.
We’re far more than twice as complex as a fruit fly, or nine times as complex as a lowly bacterium. Clearly there are other mechanisms that contribute to complexity, so that it doesn’t scale linearly with gene number. We already know about several, but we’re also finding new ones.
The picture is somewhat more complicated because the idea of a gene has changed over time, and, in my opinion, is fairly nebulous. The word “gene” actually has two different meanings, even in the halls of science. In one sense, it means “allele.” Alleles are different types (or flavors) of one gene. So when someone says, “he has the gene for sickle cell anemia,” they really mean he has the allele for it. The average person has the non-sickle cell allele.
The other meaning is “locus,” which is the physical position of the gene in the genome. You might hear, for example, that the gene for color blindness is on the X-chromosome, which really means that the locus is there.
When we talk about how many genes there are in the genome, we’re really talking about loci and not alleles. Some of the recent discoveries about gene regulation—the mechanisms that make us so much more complex than fruit flies even though we only have about twice as many genes—turn traditional notions about these mechanisms on their ear. They may even require another revision to the number of genes in the human genome.
Ok, I don’t actually hate science, but I certainly feel that way sometimes when doing experiments. Here’s an example. In my system, I have some RNA (an aptamer, in fact) that has been labeled with a fluorescent dye. I also have a shorter piece of DNA that is complimentary to the aptamer, so it will bind to the aptamer. The DNA is labeled with a quencher that prevents the dye from emitting its signal. Basically, when the DNA is present, the aptamer doesn’t glow, and when the DNA is absent, it does glow.
At least, that’s the way it should work. In some of my experiments, the more DNA I added, the brighter the aptamer glowed. This is the exact opposite of what should happen. It’s like the TV turning off when you press the on switch, only you can’t blame it on faulty wiring. Maybe it’s more like water flowing uphill, since these are basic physical properties of matter we’re talking about.
Nonetheless, it’s very frustrating. Fortunately, that project was canceled recently, due in part to the confounding results I was getting.
I’ve been having some trouble getting back on track with my other projects. I’m not sure why, exactly. Sometimes simply having to do something makes it unappealing, no matter how interesting it might be if it weren’t a requirement.
But in the last few days, I’ve felt really on top of things. I’ve been very productive. I worked on my mountain bike and have gone on a few short rides. I’ve taken care of various projects around the house. I’ve even made some progress on my main research project. Hopefully, I can keep things on track and maintain my forward momentum.
Plus, I always have Piled Higher and Deeper to console me in any event.
