Dirk Knemeyer

The Digital Life #167: Open Science

Episode Summary

On The Digital Life this week, we embark on the first in a special series of episodes put together in conjunction with our friends at the GET Conference, on the cutting edge of research science and technology.

The GET Conference is on the front lines of the open science movement, seeking to make scientific research and data accessible to both professionals and citizens.

In this episode we explore the topic of open science through interviews with Brian Bot and John Wilbanks of Sage Bionetworks, Alexander Wait Zaranek from the Personal Genome Project and Curoverse, and Tim Errington from the Center of Open Science.

Jon F.: Welcome to Episode 167 of The Digital Life, a show about our insights into the future of design and technology. I’m your host Jon Follett.

This week on the podcast we’ll embark on the first in a special series of episodes put together in conjunction with our friends at the GET Conference on the cutting edge of research science and technology.

In this week’s episode we’re exploring the topic of open science, with interviews with Brian Bot and Jon Wilbanks of Sage Bionetworks, Alexander Wait Zaranek from the Personal Genome Project and Curoverse, and Tim Errington from the Center of Open Science.

The GET Conference is on the front lines of the open science movement seeks to make scientific research and data accessible to both professionals and citizens.

We’ll start with our interview with Brian Bot and Jon Wilbanks describing their endeavors at Sage Bionetworks.

Brian: I’m Brian Bot at Sage Bionetworks. I’m a Principal Scientist and Community Manager there.

John: John Willbanks. I’m the Chief Commons Officer at Sage Bionetworks.

Dirk: That’s great. Tell us a little bit about what Sage Bionetworks does.

John: We’re a nonprofit organization that tries to do two things. One is to bring some of the same capacity increase in scientific analysis that we’ve seen in software development over the past fifteen, twenty years. Reusable architectures, community development, some of the opensource culture that you see where if you want to build a website, you don’t have to scratch anymore. If you want to build an app, you don’t have to start from scratch. There’s frameworks. In science it’s not like that. People start from scratch almost every time. We host a set of technical platforms that make it possible to do this large-scale collaborative community science.

Dirk: That’s great. What’s the genesis of your company and your philosophy? When did it get started, what was the motivation behind it, and what has the evolution looked like?

John: We were founded in 2009 as a nonprofit spinning out of Merck Pharmaceuticals. It was the Rosetta informatics unit at Merck, which was looking at large-scale associations between genetic variation and observed health, more or less. When it became clear that lots more work was needed, lots more time was needed, lots more sample size was needed, Merck decided to spin it out into a nonprofit which became Sage Bionetworks.

Since then, we’ve sort of had these twin philosophies that we want to bring some of these methodology changes, these collaborative methodology changes, and then the political aspect, which is creating large enough pools of open data that you don’t have to go rent data from companies if you want to start doing innovative science.

Dirk: How do you settle on the pools of data to include? Are you just openly inclusive or is there an editing/vetting process? What does that look like?

Brian: Yeah. We tend to focus on areas where incentives need to be aligned and there needs to be a neutral arbiter than can step in and provide guidance to disparate parties. We have a number of examples where we’re working with funding agencies as well as academics and pharmaceutical companies as well. The key is to focus on areas where it makes sense for all of those groups to be working with one another. That oftentimes ends up being in the pre-competitive space in drug development, is one example, where pharmaceutical industry might be interested in cost sharing early on. They’re actually very, very interested in making data broadly available, such that they can compete later on. They can crowd source, if you will, the target discovery aspects of it, but later in the stage when the targets are developed, they can compete to develop drugs against those targets.

John: Another example would be we work with a bunch of groups in colo-rectal cancer. This was something where we sort of assembled the group. Some of our scientists noticed that multiple papers were published in one year in different journals, each of which claimed to have the canonical genetic sub-typing for colo-rectal cancer, but of course, all of them had different sub-types because they had different samples, they had different populations, and they were using different math. The idea was let’s go talk to all of them and ask them, “What if you pooled all of your data, so that only people who contributed data could see it and then each of you could run your math on the pooled data and see how it looks at scale. Then as neutral arbiters, right, we will help build a consensus analysis that uses the best pieces of every algorithm on all of the data.” After we get the first four groups I think nine more petitioned to join, right, because then they didn’t want to get left out. That’s a place where you have alignment because it’s an area where no one has large enough samples and the methods are early enough that there’s a real value just pooling it and doing consensus stuff. If they were worried that we were literally their competitor, they wouldn’t trust us to be Switzerland.

Dirk: You’ve mentioned a few times the openness, the open philosophy, and how you’re doing business that way. You’re a nonprofit but still doing business in a certain way. You’re a spin off of Merck. Usually companies the size of Merck are not driven by openness in quite the same way. Has openness always been something that’s core to what you’re doing from inception or is that something that you’ve developed overtime?

John: It’s been since inception, and I think it’s one of the reasons they were willing to spin us out. We actually have a presentation on the website which is a presentation that our founder made to the Merck board of directors before the spin out, basically advocating for a giant Wikipedia of open human genomes. You can go look at the presentation that was made and then their reaction was, “That’s nice. You can take that and make it a nonprofit.” They were very generous in the spin out. They helped staff, transition, they gave assets. It wasn’t just a trivial thing. They actually put some work into it. From the very beginning of the orb, the idea was that openness and collaboration … Openness was the political, collaboration was the methodology. Those two things together were going to be more powerful than either one alone.

Jon F.: Next, we’ll hear from Tim Errington from the Center for Open Science.

Tim: I’m Tim Errington, I’m from the Center for Open Science.

Dirk: Excellent. What kind of work are you doing at the Center for Open Science?

Tim: The Center for Open Science, we’re a non-profit organization that its mission is to increase the openness, reproducibility, and integrity of scientific research across all disciplines. We do that through three main activities. Infrastructure, technology development, building a tool to a lot of researchers to collaborate. Document share, so essentially a scholarly commons that’s free and open source. We do community activity, that’s working with different stakeholders in the community, so journal, funders, researchers, to try to align our practices with our values, our ideals. Basically trying to shift that incentive structure to reward open practices, reward reproducible practices.

Then the area that I lead at the Center for Open Science, which is metascience research, so research on research. Right now we do that, currently looking at previous research. Reproducibility studies. We just finished one last year in psychology, where we replicated a hundred different psychology studies. I’m leading one currently right now in pre-clinical cancer biology research, where we’re trying to directly replicate previously published research to better understand the challenges that are associated with that and actually what’s our replicability rate.

Dirk: Yeah, I think the word, and when I think of this conference and the people we’ve spoken with, that most captures the zeitgeist is “openness.”

Tim: Yes.

Dirk: I’m curious … This is obviously a bubble. Is it a bubble that is reflective of the greater scientific community in the areas you’re participating in, or are you the exception? Certainly in the for profit technology world, openness is the exception. A few people are really behind, but most companies are still very closed. What does it look like in your scientific communities?

Tim: Yeah, that’s a great question. I think you’re right in the sense that it’s a bit of a bubble. It’s very much a bubble. It’s definitely more the exception than the rule. A lot of that’s because there’s no incentive for it. It’s got to be a culture that brings it out and it’s got to be a system that rewards you when you do it. We don’t see that right now. Right now, our present culture rewards us for flashy big discoveries that get us the big papers. Those papers don’t have to be open, those papers don’t have to be reproducible. They just have to be the big story, and then that gets you the grant, gets you the promotion and then it cycles. There’s not really a reward for it.

I think one thing is that you can still embody open principles by doing your research transparently, even if it’s closed. We try to make sure that … We’ve heard this here at the conference, the same thing. You respect that private-public workflow. You respect the fact that you can’t always share something, or maybe someone is just not ready to share that, but you should still make sure that you’re embodying those open principles throughout it. Hopefully, you can start to have those incentives or have that ability to just say, “Maybe this one time I’ll share and see what happens.” I think there’s a lot of culture of “I’m afraid somebody’s going to take my idea, and they’re going to get the credit instead of I get the credit.” I think if you can play with that in this public-private setting, allow the individual, the researcher, to try it out, hopefully the culture says, it’s okay, it’s not going to happen.

Until then, I think still remembering that there’s open practices in what we do anyways, whether you never share it, we can’t forget that.

Jon F.: We’ll wind up this episode with some thoughts from Alexander Wait Zaranek of the Personal Genome Project and Curoverse on the importance of open science and its benefits.
Alexander: Yeah. I’m Alexander Wait Zaranek. Everybody calls me Sasha. I’m a co founder of the Harvard Personal Genome Project and the chief scientist at a start up called Curoverse.

I am a co-founder of Curoverse and we’re a free software business. All of the software we write is free and open source software. You don’t have to pay us anything to use it. We have venture capital backing and our investors really believe that there is an interesting and really large business here, but I think that one of the most important mechanisms to ensuring that everyone gets to participate in these technical benefits is the support internationally of free and open source software and more broadly free knowledge standards. Things like Wikipedia is an example of a free knowledge artifact. What can then happen is that the wealthiest organizations in society pay a lot of the initial development costs for this free software and free knowledge, but because there are no strings attached, much poorer places can follow on and adapt that software to their needs and if they cannot afford the price points that are charged in the more wealthy clients, then that’s okay because they can just proceed at their own pace.

There is a natural equilibrium that is achieved. What tends to happen today, without this kind of mechanism is that these technologies stay proprietary because it’s the only way to get investors to pay for them. Then customers that would never buy the technology just get left out. There’s no point of restricting people who are never going to pay for the thing from not having. I mean, if you can make the business model work, then … Software and free knowledge, I think, is the sort of core to doing this kind of redistribution and I think that I’m quite pleased with my contribution to the Global Alliance for Genomics and Health, which is a standards organization very similar to the World Wide Web consortium here in Boston. That’s kind of help make the internet possible. That organization is really trying to build these kinds of standards and we’re really working with them to ensure that all of their standards are implemented in commercially supported free software. Very long answer, but I do think that that is a part of, maybe even a core part, of the solution, to making sure that people don’t get left out.

Dirk: That was a wonderful answer and I’m glad to hear it because as I’ve gotten older I’ve become very cynical that the people with the money and the power will forever disadvantage the rest of us.

Alexander: Well, we have some say in the matter so we should take advantage… we should put our work in achieving that.

Dirk: Amen, amen, brother.

Jon F.: Listeners remember that while you’re listening to the show, you can follow along with the things that we’re mentioning here in real time. Just head over to thedigitalife.com, that’s just one “L” in The Digital Life, and go to the page for this episode. We’ve included links to pretty much everything mentioned by everybody. It’s a rich information resource to take advantage while you’re listening, or afterward if you’re trying to remember something that you liked. You can find The Digital Life on iTunes, Soundcloud, Sticher Player FM, and Google Play. If you want to follow us outside of the show, you can follow me on Twitter, at @JonFollett. That’s J-O-N F-O-L-L-E-T-T. Of course, the whole show is brought to you by Involution Studios. Which you can check at goinvo.com. That’s G-O-I-N-V-O.com. Dirk.

Dirk: You can follow me on Twitter at @DKnemeyer. That’s @D-K-N-E-M-E-Y-E-R. Thanks so much for listening.

Jon: That’s it for episode 167, of The Digital Life. For Dirk Knemeyer. I’m Jon Follett, and we’ll see you next time.

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