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After Paul Allen Co-Founded Microsoft, He Changed Brain Science Forever

Microsoft co-founder Paul Allen, who died Monday, made his fortune from software that ran computer brains.

But Allen's own passion was for the human brain.

"The human brain works in, so far, mysterious and wondrous ways that are completely different than the ways that computers calculate," he told NPR during an interview in 2003. "Things like appetite or emotion, how do those function in the brain?"

The occasion of that interview was Allen's $100 million gift of "seed money" to launch the Allen Institute for Brain Science in Seattle. The institute's initial goal was to create a detailed online atlas of gene expression in the mouse brain, a job the institute's scientists completed in just three years.

But that turned out to be just the beginning of Allen's scientific ambitions. He would go on to give hundreds of millions more to the Allen Institute, which now has nearly 500 employees and has become a powerhouse in the world of brain research.

In 2011, the institute completed an online atlas that allowed scientists around the world to see which genes were turned on or off in any area of the human brain. Then the institute began the daunting task of identifying every type of cell in the brain – scientists believe there are thousands.

By 2013, when President Barack Obama announced his BRAIN Initiative, the Allen Institute had become a prominent player in brain research. The White House recognized this by inviting the Institute's CEO, Allan Jones, to the ceremony.

And throughout the institute's rise, Paul Allen was an active presence, not just a distant funder.

For example, Allen played an important role in luring the neuroscientist Christof Koch from a tenured position at Caltech to become the institute's chief scientific officer in 2011.

And Allen made it clear he wanted the institute's scientists to take chances and make an impact, says Koch, who is now the institute's chief scientist and president.

"He challenged us: Think big, what is it that we could do to move the needle that couldn't be done with universities," Koch says.

So the institute set out to avoid the university model, in which relatively small labs work independently under the direction of a senior scientist and rarely share results. Instead, Koch says, the Allen Institute has "hundreds of people working closely together and accepting common standards and putting all the data out there" for anyone to use.

And Koch is following Allen's admonition to think big.

Among the ambitious goals Koch is pursuing is figuring out how the brain creates consciousness, a subject that fascinated Allen.

This effort, like the one that produced the human brain atlas, is beginning with studies of mice. And already it has produced some results.

In 2016, an Allen Institute team that included Koch was able to monitor the activity of about 18,000 neurons in mice as they watched Touch of Evil, an Orson Welles film. The data from that experiment are available online so other scientists can study it.

That sort of research is an important part of Paul Allen's legacy. And his commitment to understanding the brain has created an unusual sort of loyalty among many scientists.

Koch, for example, got a tattoo of the cerebral cortex of a mouse on his left bicep. It was his way of showing Allen and his colleagues at the institute that he shared their determination to figure out the brain.

"I thought you should show your commitment on your body," Koch says. "So that's what I did."

Allen reaffirmed his own loyalty to his institute in 2012, when he pledged another $300 million to pursue new projects.

"We have only begun to scratch the surface of the complex problems inherent in figuring out ... the brain's inner workings," he said during the announcement ceremony. "Our dream is to one day uncover the essence of what makes us human."

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Jon Hamilton is a correspondent for NPR's Science Desk. Currently he focuses on neuroscience and health risks.