Microsoft co-founder Paul Allen is giving $300 million to fund new brain research at the institute he founded in 2003. It's his largest single philanthropic gift.

Share story

Microsoft co-founder Paul Allen is digging deep to explore one of the most complex structures in the universe: the brain.

Allen on Wednesday announced $300 million in funding for an ambitious project to unravel the workings of an organ that has been studied for more than a century, yet remains largely a black box. The gift to the Seattle-based Allen Institute for Brain Science is the local billionaire’s largest single philanthropic donation.

The money will allow the institute to double its staff and bring an arsenal of new techniques to bear on the cerebral cortex — the gray matter that is the seat of higher intelligence — in a systematic way that no other lab has attempted.

“We believe that this project has the potential to revolutionize our understanding of the mammalian brain,” Allen Institute scientists wrote in the March 22 issue of the journal Nature.

The grant brings Allen’s total funding for the institute to half a billion dollars — one of the richest infusions of private cash to the field of biomedical research. It also reflects his long-standing fascination with the computer in our heads.

“If you start out as a programmer — I did in high school — the brain works in a completely unknown and different fashion than computers do, and it’s amazingly complex,” Allen said Wednesday. “So there is really no greater challenge with potentially huge impact than understanding how brains work.”

And he has a personal reason as well for his interest in brain research: His mother has Alzheimer’s disease, he said. “I want to see cures of those things brought forward for the benefit of everybody.”

Nino Ramirez, director of the Center for Integrative Brain Research at Seattle Children’s Research Institute, predicts the initiative will raise Seattle’s profile as a center of brain research.

“It’s like an Amazon or Microsoft for neuroscience,” he said.

But even for one of the world’s richest men, tackling the human brain in all its complexity remains an impossible dream. So the new project will focus on the mouse. More specifically, it will seek to tease out in unprecedented detail how the mouse sees — the way the eye sends signals to the brain, the way the brain processes those signals into images, and even the way the animal responds to those images.

Vision as “entry point”

Though the focus is on vision, the mouse’s ability to process information and react to its environment also draws on higher brain functions such as perception, consciousness and decision-making.

“We’re focusing on vision because it’s a good entry point,” said institute CEO Allan Jones. “But the goal isn’t to understand vision, but to understand how the brain works.”

The human brain is a thousand times more complex than the mouse brain, but the basic building blocks are the same, Jones pointed out. Insights from the mouse could increase understanding of Alzheimer’s disease, epilepsy and other brain disorders.

In a related project, the scientists also plan to compile an encyclopedia of the hundreds of types of cells that make up the human brain, and develop ways to grow them in the lab. By culturing cells from healthy people and people with conditions such as autism, it should be possible to pinpoint the differences.

“The hope is that by understanding the mechanism, we will be able to come up with cures eventually,” Ramirez said. “But in order to understand the mechanism, you need to attack the brain at all different levels, and that is what this project will do.”

More than 10,000 labs around the world are engaged in brain research, yet most of the fundamental questions remain unanswered, said Dr. R. Clay Reid, who will relinquish his neurobiology professorship at Harvard to join the Allen Institute this summer.

For example, scientists have known for decades about brain regions that allow animals to see the difference between vertical and horizontal lines, but they still don’t know how they work.

“The reason we’re still arguing about it is that we don’t have enough data,” Reid said.

With 180 scientists, technicians and other staff — which will grow to about 350 over the next few years — the Allen Institute can focus an enormous amount of intellectual firepower on the visual systems in the mouse brain. The time is ripe for such an assault thanks to new techniques that allow scientists to go beyond vague maps of brain activity and zero in on specific neurons, Reid said.

Using fluorescent tags and genetic tricks, it’s now possible to cause brain cells in living animals to light up when specific neural circuits are activated. “We can peer inside a mouse brain and track the activity of a thousand neurons by watching them flash on and off,” he said.

Scientists can also manipulate the brain by using laser pulses to activate or quiet neurons. New microscopic methods are capable of tracing the tangle of connections between neurons that are crucial to brain function.

The scientists hope to translate what they learn about the brain into a computer model — a kind of silicone version of one portion of the brain.

Unique approach

A university lab would never be able to muster the manpower, equipment or time to focus on one brain area in such an intense and coordinated way, Reid said. Nor would the federal government fund such a project. That’s why he decided to make the leap to Seattle.

“This is completely new,” he said. “It could never have been done anywhere else.”

Larry Squire, professor of neuroscience at the University of California, San Diego and San Diego Veterans Administration Medical Center, agrees that the approach is unique. “I think it’s very promising,” he said. In order to treat human-brain disorders, a deeper understanding of brain function is crucial, he said.

Allen founded his brain institute in 2003, with $100 million. It is best known for developing human- and mouse-brain maps that show which genes are switched on and off. The information is so valuable to researchers around the world that the website logs nearly 50,000 unique visitors a month.

As with the brain maps, all the data and methods from the new project will be freely available.

Allen’s $300 million commitment will cover the first four years of a 10-year project, Jones explained. The institute will look for other sources of money to make up the difference — something it has been trying to do since its creation, with limited success. Allen remains the major funder, contributing more than 80 percent of the money to keep the institute running, Jones said.

Allen joined his former colleague Bill Gates in pledging to give away most of his fortune, and there are some indications he’s picking up the pace of donations.

With a fortune estimated at $14.2 billion by Forbes Magazine, Allen ranked third on the Chronicle of Philanthropy’s list of the most generous Americans in 2011 — up from 31 the previous year. His donations totaled $373 million, most of which he gave as an endowment to the Paul G. Allen Family foundation.

Gates wasn’t included in the ranking, because his 2011 donations were based on pledges made in previous years.

Seattle Times staff reporter Brier Dudley contributed to this story.

Sandi Doughton: 206-464-2491 or