changed at least once a year while there. While Friend knew about Jones, the new recruit also didn’t make a huge impression on the CEO at the time. “When he showed up at Rosetta, you could look to his left and his right and there were such remarkable people that Allan was just another brilliant addition,” Friend says. He does recall Jones being confident, having a dry sense of humor, and showing signs as both a thinker and doer. “He was known as someone who could work independently, was able to execute, and often would come up with odd ideas,” Friend says, adding that they were unconventional, not stupid.
Jones was there for the Rosetta IPO, and the big acquisition by Merck. As exciting as it was for him, he knew it wasn’t going to last forever. He was the project manager for Rosetta’s plant biology collaboration with Monsanto. “I sort of read the writing on the wall that I didn’t want to be the project manager for the plant project inside a pharmaceutical company,” Jones says. He moved on to some other gene expression work inside Merck until 2003, but by then, he was settling down in Seattle, and preparing for the birth of his first son. His two boys are 9 and 7 now.
“Merck is great, but to move up there, you needed to be on the East Coast. That was clear,” Jones says. “We weren’t going to move to the East Coast. We liked being in Seattle.”
So Jones started networking in the community to figure out what his next opportunity might be in Seattle. He met with Mark Boguski, the former chief scientist of Rosetta, who was involved as the founding director of what was becoming the Allen Institute for Brain Science. (Friend says he personally pitched the idea of an open-source functional brain map to Allen, and introduced legendary biologist Jim Watson to Allen to help make the case.)
The effort was still very much a work in progress when Jones joined in April 2003. He started as a Vulcan employee, when the idea was for Allen to fund what amounted to a consortium of academic neuroscience centers around the U.S. About a month into Jones’ tenure, he recalls Allen nixing that idea on the grounds that it would be too tough to put all the pieces of the effort together at multiple sites. “Paul, to his credit and wisdom, said ‘No, I want something brick-and-mortar here in Seattle,’” Jones recalls.
Allen’s original commitment was to pour in $100 million to create a functional map of the wiring of the mouse brain. The team was asked to start from scratch, and create the map of mouse brain circuitry in three years. Jones knew it would be hard, but a worthy effort. “I love big science, taking things to scale trying to make a difference with things you can’t do in an individual lab,” Jones says. “The excitement was around being able to start from scratch. You don’t often get the ability to do that.”
The early days were frenetic and scary, as the pressure to deliver on time was intense, Jones says. Boguski, the founding leader, left within the first year. “Mark is a big thinker, but the implementation piece was a challenge,” Jones says.
Boguski’s departure created a leadership void, and Jones’ job was to fill it as senior director of operations. Jones had never had that much responsibility before. “I’m really glad the founders were willing to take a chance on me. We had already pushed it out there, and we needed to get moving forward. We were already building the team. It just needed more structure and organization,” he says.
The doubters’ and skeptics’ voices grew louder. From the start, scientists questioned why Allen was putting so much money into a new institute, rather than funding an existing center of excellence. People wondered how useful the data would be, and how open the Allen Institute would really be. And there were concerns about whether a hard-charging capitalist like the co-founder of Microsoft was really interested in giving away all this knowledge, or whether he really had some hidden business angle, attempting to get intellectual property that might lead to the next big Alzheimer’s drug.
Partly because there was so much pressure to meet deadlines, the institute kept its blinders on and didn’t collaborate much with outside groups in the early days. “There was a lot of skepticism,” Jones says. “Scientists are skeptics, that’s fine. We needed to deliver.”
By late 2004, the first major deadline was approaching, as the institute was supposed to deliver the first 10 percent of the mouse brain map. By this time, the group had grown to about 25-30 people who were
