Scientists Map the Brain, Gene by Gene

Wired has an interesting article, Scientists Map the Brain, Gene by Gene (warning, there's a pretty gross picture at the top of the page). Paul Allen started an institute who's mission is to map the human brain and make the data publicly available at brain-map.org. They've already been working on mapping the mouse brain and are now moving on to mapping it at various developmental ages. They're also working on the human brain.

"To achieve this, the Allen Institute reimagined the scientific process. There was no grand hypothesis, or even a semblance of theory. The researchers just wanted the data, and, given the amount needed, it quickly became apparent that the work couldn't be done by hand. So, shortly after the institute was founded in 2003, Jones and his team started thinking about how to industrialize the experimental process. While modern science remains, for the most part, a field of artisans—scientists performing their own experiments at their own benches—the atlas required a high-throughput model, in which everything would be done on an efficient assembly line. Thanks to a team of new laboratory robots, what would have taken a thousand technicians several years can now be accomplished in less than 20 months. The institute can produce more than a terabyte of data per day. (In comparison, the 3 billion base pairs in the human genome can fit in a text file that's only 3 gigabytes.) And the project is just getting started."

"Over several days, Allen asked the neuroscientists to imagine a way to move their field forward dramatically. "I wanted them to think big," he says. "Like the Human Genome Project, only for the brain." Some advocated focusing on a single disease, like Alzheimer's. Others argued for more investment in brain imaging technology. But a consensus emerged that what neuroscience most needed was a map, a vast atlas of gene expression that would reconcile the field's disparate experimental approaches. It's not that scientists don't know a lot about the brain—it's that they have no idea how it all fits together."

They had to create some robotic systems to dissect the brains, takes microscopic pictures, do genetic analysis and then create software tools to manage the huge amount of data and make it searchable.

"One unexpected—even disheartening—aspect of the Allen Institute's effort is that although its scientists have barely begun their work, early data sets have already demonstrated that the flesh in our head is far more complicated than anyone previously imagined.The brain might look homogenous to the naked eye, but it's actually filled with an array of cell types, each of which expresses a distinct set of genes depending on its precise location...But the atlas has revealed a startling genetic diversity; different slabs of cortex are defined by entirely different sets of genes."

"Scientists at the institute are just starting to grapple with the seemingly infinite regress of the brain, in which every new level of detail reveals yet another level. "You can't help but be intimidated by the complexity of it all," Jones says. "Just when you think you're getting a handle on it, you realize that you haven't even scratched the surface." This is the bleak part of working at the Allen Institute: What you mostly discover is that the mind remains an immense mystery. We don't even know what we don't know.""