‘It’s the best job in the world’: Allan Jones reflects on his time at the Allen Institute

Allan Jones had worked for Paul G. Allen for three years before he met the Microsoft co-founder.

“I was just taking Paul around for a tour of the thing that he had been funding for the past several years. Paul is one of those people who just takes it in. You see him processing. I could see that there was excitement there,” Jones recalls. “It wasn’t that long of a meeting, but it was just sort of a thing like, ‘OK, this is good.’”

Jones would eventually go on to lead the Allen Institute, a nonprofit medical research organization known for its atlas of gene expression maps of mouse and human brains.

Jones announced in January that he would step down after 18 years with the Seattle-based institute, which was founded by Allen in 2003. There is an ongoing international search to replace him.

“It’s a bittersweet thing. It’s the best job in the world,” he said. “If I hadn’t been doing it for the last 18 years, I’d be first in line.”

After his successor takes the helm, Jones will join the institute’s board of directors and be named president emeritus. He plans to remain in his position this year until a replacement is found.

How did you get started with the institute? At the outset I wasn’t the leader. My first job title when I joined was research alliance manager, then I was promoted to project director and then a few years after that I was promoted to chief scientific officer. It was me and a chief operating officer that were leading the organization until 2010. That’s when I stepped in as CEO.

Why leave Merck? I had ambition and I knew that I had something more to do.

With Paul always asking “what’s next,” did you get the sense that the institute would be a long-term project? I think every step along the way was sort of an increase in confidence that this would be around for the long term. I’ve been convinced that Paul always had in mind that he wanted it to be, but I think there was always a sense that we need to keep delivering and not get complacent. We went from this initial project, which we did at breakneck speed and delivered in three years 20% under budget, which also served us well. Paul was like, “Well, let’s do more.” And I think this is a good thing for me.

What are some of your proudest moments? Certainly the Atlas project. We were truly a scrappy startup. It has had such legs and an impact on the field of brain science just as a resource. It’s hard not to point to that as being a really important moment.

How did you help take the institute from a scrappy startup to a functioning business? Before Paul’s passing, I really tried hard to get him to understand that we needed to be thinking about the institute in the long run and find a good business model for how we might honor the way he likes to tackle big problems in biology. The idea is we have these institutes, they’re between 75 and 100 people; they have big science focus in some interesting way. They’re resource bound, more or less $20 million to $25 million a year, and they have a time period in which they finish. It gives you this ability if you have more or less a sort of fixed endowment income that’s coming in, but you still have this ability to kind of recycle and go after new ideas.

What are some of the biggest challenges in biology in the coming years? I always used to say this to Paul, “You picked a great area for discovery because we know almost nothing about biology.” We still don’t know how the brain works, although through our efforts over the last 10 to 15 years, we’ve actually kind of nailed the parts list. If you need to understand why we don’t understand biology, look at Covid. There’s so many areas to work on. But the brain, we’re at the early stage.

What does it mean for businesses and therapeutics? Brain drugs are pretty much like the mechanic pouring oil on top of your engine hoping that some of it will get inside. That’s the sort of level at which we treat a lot of the brain disorders right now. That sort of precision medicine is coming down the pike.

Why step down now? If I had my druthers I probably would have done it earlier, but then when we hit crisis last year, I realized that was not going to be the time.

What’s next? I still have gas in the tank to go do something interesting. The fun part about even making these announcements is you suddenly get people pinging in, “Hey we should talk.”

Who’s reaching out? Oh, I’d rather not say. They’re fun opportunities. You do a job like this for 18 years and you have a pretty extensive network throughout everything from Washington, D.C., and government and (the National Institutes of Health) to people in pharma, biotech, academia and all different walks of science. I certainly will find some interesting ways to contribute.

Who should replace you? It’s a unique role in the sense that it’s not an academic position. It’s not like a provost, although someone who is maybe a provost at a major research university would be a great fit for the role. Someone who’s been running or has run one of the National Institutes of Health is a good example to look at. They’re not actively doing science or running lab. They’re looking and they’re thinking about science strategically for the long term. They have administrative and executive experience.

This interview has been edited for length and clarity.

About Allan Jones

What was something unique about Paul Allen? The thing I always loved about Paul, over the many years, he was never one that got all that impressed about what you delivered. He was much more interested about what’s next. I remember when we were barely finishing this first project for the mouse Atlas, and Paul was like, “When are we doing the human?”

Editor's note: Allan Jones' work history previously listed the incorrect name for a company. The correct company name is Rosetta Inpharmatics.