Trevor Bedford has written a cool simulation that illustrates basic ideas behind coalescent theory in Processing.js. It would be great for an intro to population genetics class.
Richard Conniff, of the blog Strange Behaviors and whom I’ve mentioned in the past, has a great five-part series on the connections between your mirobiome (the bacteria that live on and in you) and health. The whole thing is well worth a read, but here’s a snippet:
Blindly tinkering with the microbiome is, however, exactly what some researchers say we have been doing, willy-nilly, for more than 70 years, since the dawn of the antibiotic era. For Martin Blaser, a physician at New York University’s School of Medicine, one trend stands out: The typical child in the developed world now receives 10 to 20 courses of antibiotic treatment by the age of 18, often for conditions where these drugs do little or no good. “For two or three generations we’ve been under the illusion that there is no long-term cost to using antibiotics,” says Blaser, eyebrows rising over the tops of his wire-rimmed eyeglasses. It certainly hasn’t seemed like a cost for the child being treated, and only remotely for society at large (because excess use can lead to antibiotic resistance). But “you can’t have something this powerful,” says Blaser, “and change something as fundamental as our microbiome, at a critical time in development, and not have an effect.”
Though they have always known that antibiotics kill “good” bacteria as well as “bad,” doctors generally assumed the body’s microbial community was resilient enough to bounce back. But new studies show that the microbiome struggles to recover from repeated assaults, and may lose species permanently. Blaser suspects that diversity loss is cumulative, worsening from one generation to the next. He calls it “the disappearing microbiota hypothesis.” It’s like somebody played the piano solo with a two-by-four.
Along with the antibiotics, Blaser blames our obsession with cleanliness and antibacterial soaps and lotions. In addition, about 30 percent of American children are now born by Caesarean section. They start life without the microbiome they would normally have picked up passing through the mother’s birth canal, and some research suggests that this puts them at a disadvantage. Studies show that a diverse microbial community is essential to jump-start a baby’s immune system, establish a healthy digestive tract and even help shape the growing brain. Blaser doesn’t think it’s a coincidence that children now face an epidemic of medical disorders in all these areas, and that the surge in incidence tracks with an increase in Caesarean births and the introduction of powerful new antibiotics in the 1970s and ’80s.
“Here’s the point,” he says. “You have 10 or 12 diseases that are all going up dramatically, more or less in parallel—diabetes, obesity, asthma, food allergies, hay fever, eczema, celiac disease. They’re not going up 2 or 3 percent, they’re doubling and quadrupling. Each one may have a different cause. Or there could be one cause that’s providing the fuel, and my hypothesis is that it’s the disappearing microbiota.”
Here’s a snippet of an answer to the question of which is “better,” academia or the real world. Fieldwork seems to bring a lot of people into biological anthropology, so this bit by Bruce Lewenstein jumped out at me.
I’ve traveled to dozens of countries on someone else’s money, met the presidents of at least two countries, gotten private tours of some of the world’s great sites (and sights) from people with some of the deepest richest knowledge possible, given talks in some of the world’s most beautiful buildings, eaten in wonderful restaurants and homes at levels of quality and elegance far beyond what someone with my income would normally have access to. I count all that as “better.”