Adding Some Herbs to Open Databases

"Harnessing the Crowd to Make Better Drugs: Merck’s Friend Nails Down $5M to Propel New Open Source Era"

Friend, 54, is leaving his high-profile job as Merck’s senior vice president of cancer research, after having nailed down $5 million in anonymous donations to pursue this vision at a nonprofit organization getting started in Seattle called Sage.

Sage is built on the premise that vast networks of genes get perturbed, or thrown off-kilter, in complex diseases like cancer, diabetes, and obesity. Scientists can’t just pick one faulty gene or protein and make a magic bullet to shut it down. But what if researchers around the world capturing genomic profiles on patients could get all of their data to talk to each other through a free, open database? A researcher in Seattle looking at how all 35,000 genes in breast cancer patients are dialed on or off at a certain stage of illness might be able to make critical comparisons by stacking results up against a deeper and broader data pool that integrates clinical, genetic, and other molecular data from peers in, say, San Francisco, New Haven, CT, or anywhere else.

Some big names have signed on for the early incubating phase. Besides the full-time efforts of Friend and Schadt, the Sage board includes Nobel Laureate Lee Hartwell of the Fred Hutchinson Cancer Research Center; Paul Ramsey dean of the School of Medicine at the University of Washington; Richard Lifton, the chairman of genetics at Yale University; and Hans Wigzell, director emeritus of Sweden’s Karolinska Institute. For insight into how to apply lessons from the open-source computing world, the board has brought on John Wilbanks, the vice president of science at the San Francisco-based Creative Commons.

As with any far-out vision, plenty of things can derail it along the way. What if researchers use different gene analysis machines, from Affymetrix, Illumina, or Applied Biosystems? How will Sage reconcile differences in how experiments are designed by different scientists? How will researchers be enticed to let go of their precious data, currently stored on password-protected hard drives and servers? How will Sage manage the intellectual property that arises from the database? Why would companies want to participate and run the risk of putting valuable proprietary data out in public? How will this get financed?

Some of these things Friend can answer, and some still need to be worked out. Software is already making it possible to manage differences between the various instruments scientists use, and deal with the differences in experimental design, Friend says.

Who Holds the Power?

On Monday I went and saw John Wilbanks talk on "Publishing in Today`s Environment" (I can't seem to find a decent URL but a good overview of some of the topics discussed is "The Open Access Interviews: John Wilbanks"). I didn't take many notes but a few things have stuck with me:

• Libraries providing a role as repositories of data (both public and private).


• The idea of "free as in puppy" in relation to digital curation - a great metaphor. When someone gives you a puppy it is initially free but the upkeep of it is anything but.


• The Queensland Government has its own Creative Commons initiative and the Australian Government is following suite.


• There's a power struggle occurring between researchers and publishers to make data, papers and the like freely available. The power used to be on the side of publishers but as the producers band together (by country, university, faculty and so on) the power is going back to them.


• Creative Commons are continuing to fight, in cunning ways, to get back to decent copyright law.

The kind of behavior that publishers have exhibited appears to be on the way out and seems to be going the other way. This is where databases interoperate with each other, papers can link to the original data, and tools, data and papers are all part of an integrated experience. The linking and integration of papers and other artifacts seems to be a one way process, it's hard to imagine a developer, scientist, arts graduate or anyone else spending huge amounts of money and time finally wresting control from one bunch of people only to tie it to another.

This leads to the T-Mobile G1 announcement. The announcement was very underwhelming - guys speaking for the first 10-15 minutes saying what a wonderful job they had done and the guy talking about how good an experience the phone was at playing Pacman. The more intersting part is the open platform. Much like the publishing area the ability to have open access will be a massive differentiator. It reminded me a bit about the discussion on how AOL, Prodigy and the other closed networks quickly died when faced with the open web:

By contrast, the proprietary networks of CompuServe, AOL, Prodigy, and Minitel were out beating the bushes for content, arranging to provide it through the straightforward economic model of being paid by people who would spend connect time browsing it. If anything, we would expect the proprietary networks to offer more, and for a while they did. But they also had a natural desire to act as gatekeepers—to validate anything appearing on their network, to cut individual deals for revenue sharing with their content providers, and to keep their customers from affecting the network’s technology. These tendencies meant that their rates of growth and differentiation were slow.

The closed versus open network is not quite the whole picture with respect to the iPhone versus Android. While there is competition between iTunes versus Amazon, Streetview versus normal Google Maps and there will be other content battles, I don't think that's the source of the real innovation. I think it's probably the technical innovation that the online providers couldn't match that was decisive and will be for phones:

The software driving these communities was stagnant: subscribers who were both interested in the communities’ content and technically minded had few outlets through which to contribute technical improvements to the way the communities were built. Instead, any improvements were orchestrated centrally. As the initial offerings of the proprietary networks plateaued, the Internet saw developments in technology that in turn led to developments in content and ultimately in social and economic interaction: the Web and Web sites, online shopping, peer-to-peer networking, wikis, and blogs.

Is developing on an iPhone going to lead to more technical innovation over Android? Does the ability to have open source code on Android beat the Apple NDAs?

Apple will probably recognize that it's the developers that will ultimately have the power but like publishing it depends on the actions of both parties. At the moment both of these new phone platforms are a little limited - the ability for people to innovate on iPhones using iTunes, Mail is out but it doesn't seem terribly better for Android (being DRM free is a good start though). If history is any guide, it would seem to favor open development over closed.

Update: Similar more succinct explanation.

Update: No Pragamatic book due to NDA - the outrage!