all the information, none of the junk | biotech • healthcare • life sciences

Allan Jones, the Force Behind Paul Allen’s Vision for Brain Science

Xconomy Seattle — 

Nowhere along his life journey did Allan Jones appear destined to do big things as a biotech CEO. He was born into a family of musicians, not scientists. He passed on a chance to go to the Ivy League, thinking it too stuffy. He doesn’t seek attention. He deflects credit to others. He’s short. When he walks into a room, no one thinks “here comes the Alpha Dog.”

Most improbably, when he started nine years ago as employee No. 2 at Paul Allen’s then-vague brain science project, he had experience as a biologist and project manager, but no training in neuroscience.

Yet Jones, 43, has emerged as the key behind-the-scenes operator who has taken Allen’s vision much further than most scientists thought possible when it started in 2003. The Seattle-based Allen Institute for Brain Science started revving up for even bigger things in March when Allen said he was committing another $300 million over the next four years to the nonprofit effort to push the frontiers of neuroscience.

The institute has now secured $500 million in support since the beginning, and is doubling in size to about 350 employees. It has recruited star talents in the past year from Caltech, Stanford University, and Harvard Medical School, who were drawn to the institute’s new initiatives to ask some tough questions about cognition, vision, and perception. It’s all part of the next step in the Allen Institute’s ongoing mission to accelerate scientists’ understanding of how the brain works.

Already, the Allen Institute has created functional maps of the wiring in the adult mouse brain, the developing mouse brain, spinal cords of mice and humans, and the human brain. All of those maps are out in the public domain for scientists to use freely. And while scientists were deeply skeptical about the value of such a resource in the early years, or whether it could really be built, the Allen Institute now gets 50,000 unique visitors a month who use it to study things like how the brain goes awry in diseases like schizophrenia and Alzheimer’s.

Paul Allen (left) with Allan Jones at a March press conference

“Allan has done a remarkable job of staying the course on a very long project,” says Stephen Friend, the founder and former CEO of Rosetta Inpharmatics, where Jones worked previously. “It’s about having staying power, being able to justify ways to keep it continuing, and allowing it to ripen so that it gained value that’s way beyond what people thought it might have.”

Marc Tessier-Lavigne, a member of the Allen Institute’s scientific advisory board and the president of Rockefeller University in New York, says Jones’ ability to see the big picture strategy and also follow through on tactical details has been essential to the institute’s growth. The low-key personal style also has played a part, in helping him recruit a team with myriad skills needed to create such a brain map.

“The great thing about Allan is he’s entirely focused on getting the job done,” Tessier-Lavigne says. “He has no need to be in the limelight, he just wants to get the smartest people together to think things through, to identify the best ideas, and then execute on them. He doesn’t care if ideas are his or someone else’s.”

Jones started on his journey in Wichita, KS. He grew up there the younger of two sons in a family of musicians. His dad was a professor at Wichita State University, his mother taught music in the public schools, and both played in the local symphony. Jones started playing the violin when he was five, and was serious about it all the way through high school, when he ended up as the second-ranked violin player in the state his senior year. He seldom plays anymore, he says.

As the valedictorian in a high school class of about 400 students, Jones had a lot of options on what to do besides music. He started showing interest in biology in high school. Coming from a small Midwestern city, he says the Ivy League schools turned him off as too stuffy. He looked for top schools that weren’t in that category or in California and settled on Duke University, without even making a campus visit, which he calls “an arbitrary decision.”

Once on campus in Durham, NC, Jones soon started becoming very focused on building a career in biology, and rolling up his sleeves in the lab. His freshman year, he recalls showing up at labs and eagerly inquiring about any jobs he could do, only to be turned away because he lacked experience. He persisted, finally getting a lab job his sophomore year, which gave him a management lesson he remembered later. “In any kind of team building, it’s so much more about attitude than it is about a skill set you can write down on paper. If somebody comes to you very eager to do something, that counts for a lot in my book,” Jones says.

While majoring in biology, he was drawn to much of what was happening outside the classroom, spending as much as 30 hours a week working on all kinds of lab tasks as an undergrad. Harvard University was an option for him for graduate school, but Jones says he was turned off by the attitude of the professors. It was the early 1990s, and he ended up looking for a place to pursue top-notch biology with a lifestyle more like that of his upbringing.

“After living as a poor undergrad, in shared housing, as much as I wanted to go to a good school, I also wanted a good quality of life,” Jones says. That led him to Washington University in St. Louis.

Wash U was then, and still remains, a hotbed of genetics research. Robert Waterston and Maynard Olson, two of the founders of the Human Genome Project, were on the faculty. “I basically watched the Genome Project being born there,” Jones says.

As a grad student, Jones was able to pursue his curiosity in everything from basic genetics to plant biology. He ended up focusing much of his time there on C. elegans, where he had a lot of freedom to build up diverse skills in the discovery of genes, cloning, sequencing of mutations, and developing antibodies to bind with proteins that were encoded by the genes.

He got his PhD in genetics and developmental biology in 1995, and moved on to a short stint as a postdoc at the University of Pennsylvania, studying plant biology. Jones grew discouraged by the lack of funding for the discipline, so he left for industry, in a small diagnostics startup near Philadelphia called Avitech. He recalls some “crazy” demanding work conditions, in which he’d regularly ride Amtrak to visit a collaborator at Johns Hopkins University with wet lab facilities the company lacked. But he was hooked. “I liked the discipline that you find in companies, and that you don’t find in academia,” Jones says.

Avitech ended up running out of money. The CEO, Chris Earl, ended up going to work for billionaire investor George Soros, who was an early investor in Kirkland, WA-based Rosetta Inpharmatics. Earl introduced Jones to Rosetta CEO Stephen Friend, and Jones liked what he heard—he flew out to Seattle to join the company as employee No. 56 in August 1998. Rosetta, which ended up being bought by Merck for more than $600 million in 2001, was fast emerging as a hothouse for scientific talent.

“I learned a lot about bringing in great talent to different disciplines, rather than try to get a lot of utility players and people who are jacks of all trades,” Jones says. “We knew that if you want to study data, go get a physicist. If you want to do engineering, get a serious engineer, don’t mess around.”

Jones moved around the organization a lot, and his job title 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 working on all the behind-the-scenes work needed for such an effort. Standard operating procedures needed to be developed for bringing in samples, and slicing them up for staining in the lab. Informatics systems needed to built specially for the task, robots needed to be set up to automate as much of the process as possible, and user-friendly interfaces had to be developed to help scientists make use of the resource.

There were all-night marathon work sessions heading into December 2004. Jones recalls one terrifying moment, in which a hard disk failed, and another when the software development team came down with the flu.

“We knew we had a good plan in place, and knew we had risk points,” Jones says. “You always have your doubts, you have your dark days. But the team here was quite motivated to show we could do it.”

The team met its goal. That was an important milestone, and gave the team confidence it could scale up what was started, and keep hitting its deadlines.

Tessier-Lavigne recalls the scientific advisory board having its doubts about whether the team could truly deliver on the full mouse brain by its deadline in 2006, but Jones walked through the timeline step-by-step, insisting that the team could still meet that goal. They did. “The first 10 percent was the hardest. Then you’re scaling on your processes,” Jones says. The full adult mouse brain, the developing mouse brain, and the mouse spinal cord were built on similar templates, as the team honed its process.

The next big challenge was the human brain, which required most every piece of technology to be redeveloped, Jones says. While the mouse is a good model system because of its genetic similarity to human brains, a hemisphere of a human brain is far too big to fit on a standard 1-inch by 3-inch microscope slide. The Allen Institute needed to switch to bigger 6×8-inch slides and find some way to scan slides that big—which are too big for off-the-shelf scanners, Jones says.

Plus, since good human brain tissue is hard to find, the institute would have to be very judicious with every sample it got, getting the most information possible. That meant it couldn’t use the original gene-by-gene mapping technique from the mouse brain—known as in situ hybridization—because then it would probably only be able to show functional mapping of a couple hundred genes, not enough to be useful for scientists, Jones says.

So the decision was made to use another platform, a microarray technology from Agilent Technologies, in which the brain tissue was analyzed to see which genes in the full human brain were active and which weren’t. (For a more in-depth look at how the Allen Institute creates these brain maps, watch Jones give this TED talk).

Over the years, Jones and Allen have developed a close working relationship, as the billionaire personally remains engaged in the institute’s work and attends all of the scientific advisory board meetings. The founder isn’t a neuroscientist, but he works hard to educate himself, speak the language, and keep the scientists on their toes. “That’s why it’s great to work with Paul Allen,” Jones says. “When you’re just getting going with momentum on a project, he’s already thinking about the next thing.”

Jones says he’s enjoyed the past couple years, seeing scientists at conferences who now thank him and his team for creating the resource. “The perception has gone from ‘who are these guys?’ to ‘we love your data.’ That’s really rewarding to get from the field,” Jones says.

Now the Allen Institute is extending its ambitions even further. In March, Jones said the institute hopes to complete its sixth human brain map by the end of this year. The new $300 million commitment will go toward building a variety of research tools that Allen said will help explore what makes us human.

As chief scientific officer Christof Koch put it, one of the efforts will be to “exhaustively identify, catalog, record, and intervene in the cognitive networks underlying visual perception, visual behavior, and visual consciousness in the mouse.” And that’s only part of what’s being built.

As the institute has grown, Jones has a new set of management challenges to deal with. It’s expanded into three buildings in Fremont, which makes it tougher to collaborate, and has prompted the search for new space. There are cultural issues too, as academic scientists often revel in exploring their own ideas and getting glory in publications, not through toiling on big projects that put data in the open. Jones talks about the need to find top-notch talents who are willing to be team players.

No one can say what discoveries will come from the various brain maps, but the founder has made clear that he wants to see medical progress, at least partly because his recently deceased mother had Alzheimer’s.

It’s also too early to say what kind of medical progress might eventually be traced back to the resource created by the Allen Institute. But one thing is for sure—the credit will probably go to someone else, not the low-key scientific manager and his team who built the resource. And Jones says he’s fine with that. When I asked what he does outside of work, he laughed, saying he’ll have time for hobbies when he’s older—for now all he has time for is work and family activities.

“I want to look back 10 years from now and say ‘Look at the great team we built, and look at what we were able to accomplish.’” Jones says. “It’s always been an interesting thing, having me as CEO. I’m not a big ‘sales-y’ person, a get-out-there kind of person. I’m not that person. That’s fine. It’s about achieving the mission.”