Crowdsourcing the Brain

Traditionally, the study of the brain was organized somewhat like an archipelago. Neuroscientists would inhabit their own island or peninsula of the brain, and see little reason to venture elsewhere.

Molecular neuroscientists, who study how DNA and RNA function in the brain, didn’t share their work with cognitive specialists who study how psychological and cognitive functions are produced by the brain, for example.

But there has been an awakening to the idea that brains of humans and mammals should be studied like the complex, and interrelated systems that they are. Neuroscientists realized that they had to start collaborating across disciplines and sharing their data if they wanted to make advances in their own field.

However, this realization came with a conundrum: Researchers in the modern era have come up with so many different ways to obtain data — microscopes, MRI machines, super-charged computers — that they’ve literally compiled more data than they know how to share.

“There are thousands of instruments all delivering new forms of data — torrents of data — at all levels of biology,” said Mark Ellisman, a University of California, San Diego neuroscientist who is world renowned for redefining the patterning of cells in the nervous system. “We are swamped.”

Ellisman and his UCSD colleagues have devised a solution: crowdsource a brain. And this week they unveiled their years-long project — the Whole Brain Catalog — at the annual convention of the Society for Neuroscience, the largest gathering of brain experts in the world.

The roughly $10 million project, funded by a gift from Gateway co-founder and San Diego resident Ted Waitt and National Institutes of Health grants, is envisioned an open source venue that hopefully will host all the information available on the mouse brain. They use a mouse brain because it is the most commonly studied noggin in the world, and used in a vast majority of research involving human brain disease.

Anyone, researcher or layperson, with something useful to add to the catalog can do so, and there will be a Wikipedia-like policing of the data. “It will be a place where tens of thousands of researchers will come together to assemble this brain, something no single laboratory could do,” Ellisman said.

The hope is that it will vastly speed up the understanding of how the brain works and goes awry in diseases such as Alzheimer’s and Parkinson’s, as well as inspire a new generation of artificial intelligence.

The molecular neuroscientist, for example, will have an abundance of data at the cellular level that he can upload to the site and then integrate with genetic data uploaded by a neurogeneticist. This new view could lead the researcher to a better understanding of how brain structures change through age and disease.

“A thousand people may be working in an area, and you might not know 990 of them, but you are learning from them,” said Bill Mobley, the chairman of UCSD’s neurosciences department, who got a tour of the catalog at this week’s conference.

Mobley said he has no doubt that it will change how he researches his specialty, which is the connection between Down syndrome and Alzheimer’s. All people with Down syndrome, if they live long enough, will develop Alzheimer’s. But, he said, there is not a great understanding of why.

In another realm, the brain is an extremely efficient user of energy, and better understanding it from systemic standpoint will help scientists learn how to make smart machines that operate on little power.

The program’s screen has a Google Earth-like feel to it. The right-hand side of the screen is dominated by a 3D representation of the mouse brain, and on the left are navigation tools that allow you to zoom deep into the brain and then back out, similar to how Google Earth allows you to go from a shot of the whole world to one showing your street.

But spend some time with the Whole Brain Catalog, and Google Earth might seem simplistic.

“If you want to understand, in Google Earth terms, how all the cells in mouse brain connect it would be roughly equivalent to looking at the entire continent of North America and being able to read the writing on the license plates on all the cars in the entire continent at the same time,” Ellisman said.

The various layers allow you to go from a wide shot of the brain down to the cellular level in a couple clicks. Type in a brain structure in the search box, such as the hippocampus, and it will take you to the seahorse-shaped structure and allow you to examine it from all angles.

The catalog is among a handful of online brain modeling efforts in the works. One is being run by fellow UCSD researcher Jacopo Annese, who runs the university’s Brain Observatory. Annese this year took possession of the brain of famous amnesiac H.M., who died last December.

Later this year, Annese and his team will begin slicing the brain into 3,000 fraction-of-a-millimeter thin sections that can be placed on oversized microscope slides and scanned into a computer. Ultimately, the researchers will construct the first ever three-dimensional, high-resolution digital map of a complete human brain.

“Everyone’s goal is to eventually build a model that shows how the brain is connected,” Annese said.

Ellisman compares the work being done now in neuroscience to the Lewis & Clark expedition of 200 years ago.

“When they set out, there were a few trails blazed, but they often had to follow rivers to the unknown,” he said. “For the brains of different animals we have quite a bit of information on some scales, but there is also a lot of wilderness.”

Please contact David Washburn directly at david.washburn@voiceofsandiego.org and follow him on Twitter: twitter.com/davidwash. And set the tone of the debate with a letter to the editor.