Human Brain Mapping color charges

A few years ago, I had the pleasure of in Seattle, and the scientist next to me is in a hurry: His specimen—this fragile cortex—is falling apart. Dying, the gray matter turns acidic and begins to eat away at itself; nucleic acids unravel, cell membranes dissolve. He takes a thin, sterilized knife and slices into the tissue with disconcerting ease. I’m reminded of Jell-O and guillotines and the meat counter at the supermarket. He saws repeatedly until the brain is reduced to a series of thin slabs, which are then photographed and rushed to a freezer. All that remains is a pool of blood, like the scene of a crime.

Behind all the gore there’s a profound purpose: The scientists here are mapping the brain. And while conventional brain maps describe distinct anatomical areas, like the frontal lobes and the hippocampus—many of which were first outlined in the 19th century—the Allen Brain Atlas seeks to describe the cortex at the level of specific genes and individual neurons. Slices of tissue containing billions of brain cells will be analyzed to see which snippets of DNA are turned on in each cell.

If the institute succeeds, its maps will help scientists decipher the function of the thousands of genes that help produce the human brain. (Although the Human Genome Project was completed more than five years ago, scientists still have little idea which genes are used to make the brain, let alone where in the brain they are expressed.) For the first time, it will be possible to understand how such a complex object is assembled from a basic four-letter code.

“The maps of the brain we currently have are like those antique maps people used to draw of the New World, ” says Allan Jones, chief scientific officer at the Allen Institute. “We can see the crude outlines of the structure, but we have no idea what’s happening on the inside.” Jones is in charge of making sure the atlas gets finished. He wears starched button-up shirts and crisply pleated khakis, and he looks like the kind of guy who has a drawer full of bow ties. “Studying the brain now is like trying to navigate a vast city without any driving instructions, ” he says. “You don’t know where you are, and you have no idea how to find what you’re looking for.”

Yesterday, the Allen Institute announced that their human brain map is complete. Here, for instance, is a 3-D snapshot of all the locations in the brain where the Prozac’s biochemical target is expressed. Researchers can click on each dot and see which genes are expressed in those specific areas, in addition to the underlying biochemistry:

Allan Jones, the CEO of the Institute, was kind enough to answer a few questions about how the map was created and what it means.

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