blog.nforget.com

If Neanderthals ever walk the earth again, the primordial ooze from which they will rise is an emulsion of oil, water, and DNA capture beads engineered in the laboratory of 454 Life Sciences in Branford, Connecticut. Over the past 4 years those beads have been gathering tiny fragments of DNA from samples of dissolved organic materials, including pieces of Neanderthal bone. Genetic sequences have given paleoanthropologists a new line of evidence for testing ideas about the biology of our closest extinct relative.

The first studies of Neanderthal DNA focused on the genetic sequences of mitochondria, the microscopic organelles that convert food to energy within cells. In 2005, however, 454 began a collaborative project with the Max Planck Institute in Leipzig, Germany, to sequence the full genetic code of a Neanderthal woman who died in Croatia’s Vindija cave 30,000 years ago. As the Neanderthal genome is painstakingly sequenced, the archaeologists and biologists who study it will be faced with an opportunity that seemed like science fiction just 10 years ago. They will be able to look at the genetic blueprint of humankind’s nearest relative and understand its biology as intimately as our own.

In addition to giving scientists the ability to answer questions about Neanderthals’ relationship to our own species—did we interbreed, are we separate species, who was smarter—the Neanderthal genome may be useful in researching medical treatments. Newly developed techniques could make cloning Neanderthal cells or body parts a reality within a few years. The ability to use the genes of extinct hominins is going to force the field of paleoanthropology into some unfamiliar ethical territory. There are still technical obstacles, but soon it could be possible to use that long-extinct genome to safely create a healthy, living Neanderthal clone. Should it be done?

Patrick House, writing in Slate, thinks he’s found the secret to success at the World Cup: high rates of Toxoplasma gondii infection.

What if I told you that last week I predicted all eight winners of a round of the World Cup? And that instead of rankings or divination all I did was look up how many people in each team’s home country had a tiny parasite lurking in their amygdalas? Would you believe me? A decade ago, Discover Magazine concluded that parasites ruled the world, and now I’m going to try to tell you that, at the very least, parasites rule the World Cup.

Olivia Judson—one of my favorite science writers—writes about Neanderthals:

The past comes to us in tantalizing fragments — a bone here, a footprint there. But of all the fragments yet discovered, perhaps none is so tantalizing as the one published in the journal Science last week: the Neanderthal genome.

Neanderthals have perplexed and intrigued us ever since the first bones were discovered in a cave in what is now Germany, in 1856. Who were they? Why did they vanish?

Everything Louis Brandy says in this article is true. If you haven’t read The Selfish Gene, you really should—especially if you are a programmer.

If you are anything like me (a programmer and general science nerd) and you haven’t read it, this is approximately what you’ll be thinking:

I understand evolution pretty well, and I don’t really need to read a book to understand evolution. Besides, evolution is kind of boring — the fittest survive, and pass on their genes, problem solved. I’d rather read about physics.

—me (and maybe you), before reading

Let me try to put into words how wrong this was. First, and foremost, this book made me realize how absolutely little I’ve actually thought about evolution, and how absolutely fascinating evolutionary biology is. This book is basically a series of mental experiments to explain the biological world through game theory. The organisms are playing a giant game, and those with the best strategies will survive. Please note that the “best” strategies often depend on what strategies everyone else is using. Therefore, a population will then tend towards evolutionary stable mixes of strategies. You will have repeated WTF moments as he makes the most unintuitive animal behaviors (ie, strategies) suddenly make perfect sense.

Second, let me say, that as a programmer, you have a VERY UNIQUE perspective that makes evolutionary biology (and the arguments in the book) extremely fascinating (more on this in a bit). Last, and maybe most importantly, for me, it is fairly safe to say that if I had read this book in high school, instead of recently, I’d probably have become an evolutionary biologist, and not a programmer. It was that interesting.

Jonah Lehrer writes about the neuroscience of sarcasm:

Sarcasm is a cognitive challenge. In order to get the sarcastic sentiment, we can’t simply decode the utterance, or decipher the literal meaning of the sentence. Instead, we have to understand the meaning of the words in their larger social context. For example, if it’s a beautiful day outside - the sun is shining, etc - and somebody states “What a nice day!,” there is no sarcasm; the sentence makes perfect sense. However, if the same statement is uttered on a rainy day, then there is a clear contradiction, which leads to an interpretation of sarcasm. (We typically exaggerate the expression of sarcastic statements, thus making it easier to pick up the verbal/social contradiction.) Psychologists refer to such utterances as an incongruent word-emotion situation.

In a thought-provoking article in Sunday’s (Feb 28th) New York Times Magazine, neuroscientist Jonah Lehrer asked whether Depression might have some adaptive value. He cites research showing that the “rumination cycle” of a depressed person might help certain kinds of cognition. For example, the term “depressive realism” describes a theory (supported by “several studies”) that depressed people “have a more accurate view of reality and are better at predicting future outcomes.”

Later in the article, he offers some other possible adaptive benefits of depression, including increased attention, better short term memory, improved creativity, and signalling of distress to others.

The capacity for intense focus, they note, relies in large part on a brain area called the left ventrolateral prefrontal cortex (VLPFC), which is located a few inches behind the forehead. While this area has been associated with a wide variety of mental talents, like conceptual knowledge and verb conjugation, it seems to be especially important for maintaining attention. Experiments show that neurons in the VLPFC must fire continuously to keep us on task so that we don’t become sidetracked by irrelevant information. Furthermore, deficits in the VLPFC have been associated with attention-deficit disorder.

Several studies found an increase in brain activity (as measured indirectly by blood flow) in the VLPFC of depressed patients. Most recently, a paper to be published next month by neuroscientists in China found a spike in “functional connectivity” between the lateral prefrontal cortex and other parts of the brain in depressed patients, with more severe depressions leading to more prefrontal activity. One explanation for this finding is that the hyperactive VLPFC underlies rumination, allowing people to stay focused on their problem. (Andrews and Thomson argue that this relentless fixation also explains the cognitive deficits of depressed subjects, as they are too busy thinking about their real-life problems to bother with an artificial lab exercise; their VLPFC can’t be bothered to care.) Human attention is a scarce resource — the neural effects of depression make sure the resource is efficiently allocated.

Not everyone buys this theory. Ronald Pies, M.D., has written a response called “The Myth of Depression’s Upside” in which he takes Lehrer to task for perpetuating dangerous myths about depression.

The notion that severe depression may bring forth good things reminds me of a lecture I once attended on “fire safety” in the hospital setting. We were shown a movie of a house that had burned down in such ferocious heat that a package of frozen muffin dough had been completely baked. “So, the house wasn’t a total loss!” quipped one of the world-weary attendees. Yes, of course—people can learn from their severe depressive episodes, but often at the cost of emotional and spiritual conflagration.