Yesterday, U.S. Secretary of State Hillary Clinton announced the Open Book Project, a major initiative to make Open Educational Resourcesavailable in Arabic. There was a big launch program at the State Department, and some remarkable words from Mrs. Clinton: You can look around the world and see young adults in remote villages and towns huddling around a computer watching videotaped physics lessons by MIT professors. Top universities like Rice University are creating free online textbooks and saving students money in their studies. Science education websites like Khan Academy go viral. There are other examples, and these are all fruits of technological progress, but also of a commitment to make more learning materials open – free, open licensing for anyone to use, adapt, and share. (from the text of Mrs. Clinton’s remarks - emphasis at the end added by me) I was one of many people excited to see these kind of words. I’m always glad to see this kind of phrasing about copyright in the halls of government, because it indicates at least some understanding of the potential of open copyright licenses to create innovation. But then I started thinking more about it, and the uncritical acceptance of the project without a conversation about the politics of it started to bother me. I still think it’s a worthy, and wonderful project. But let’s unpack what we’re doing here, as a government. It seems to me that we are applying state power to create digital knowledge resources that (probably, maybe, definitely) subvert the attempts of both state and non-state (social, religious) actors to control the kind of educational materials available in the Arabic speaking world. That we are practicing, as statecraft, what Nils Gilman has called deviant globalization, using an open source approach. And that’s worth contemplating. I do not think that this is an embrace of open copyright because of philosophical shift in favor of openness. I think it’s a pragmatic piece of realpolitik - getting textbooks into a language and format where they can evade the controls imposed by actors whose interests are felt to be contrary to the US. The theory that more knowledge in more hands is better for the world is one I happen to subscribe to, and agree with, but let’s not pretend this isn’t an exercise of state power. It is far more like the Voice of America  (especially at its founding, when it was not required to provide “unbiased” news) than it is like Free Software. Note: I edited this post at the end with the bold text in the final sentence at the suggestion of Dave Clifford after it was first posted.

The White House has published a response to our We the People petition, commonly known as the OA Monday petition. I’ll have a longer post up once I’ve had time to thoroughly review the policy, but the multi-year campaign to turn the NIH public access policy into something that applied to the entire federal research system is over. I’d like to thank the White House, especially the Office of Science and Technology policy, for listening to us through the various RFIs and then finally to the petition. This is good policy. And it’s nice to see something substantive emerge from the We the People platform, too. To the squeals of the publishers, I say only this. Jobs will be created by open content. I personally built a company years ago on the open data published by the NIH. I’m looking forward to watching others build companies on the open literature that will emerge under this policy. And the fight’s not over - it won’t be until we have reuse rights, not just free downloads. But for now, let’s dance.  We won.

Now that I’ve had some time to process thenew White House public access policy, here’s a few thoughts. First and foremost, I think the policy is worth celebrating. This is something on which there is a difference of opinion. Mike Eisen is the most vocal and eloquent critic of the policy, and his post on the topic is essential reading whether you like his position or not. I disagree with Mike on the conclusion, but it’s worth examining why. And it’s not worth attacking him - indeed, attacking each other is a feature of the OA movement that sickens me. But I think his position comes more from a worldview where there is indeed real movement towards true OA (i.e., no embargo, open copyright licenses, and a total change of the publication industry via startups both non profit and for profit). Compared to that progress, the policy is like going back in time to when the NIH had no policy. But here’s the thing. That progress simply doesn’t exist in most of the other spaces where the US Government invests in research. It doesn’t exist in agriculture (100,000 papers per year which will be key to food supply and debunking bullshit claims about GMO food, for example), or defense, or trade, or patents, or space science, or energy. I wrote a paper with my dad on open access and energy policy (my dad is a climate change adaption scientist with a piece of the IPCC Nobel Prize) that opened my eyes to just how little of the energy literature is OA. If you look at the links in an IPCC report you’ll be shocked at how few you can read. None of the green, or gold, OA conversation has had a significant impact there at all. Compared to the world that exists there, a world that is not being wrenched open by change and entrepreneurs and repositories, this policy is indeed enormous progress. I don’t like the embargo entrenchment at 12 months. I don’t like the lack of reuse rights. I don’t like allowing linking into journal archives as opposed to centralized repositories. I don’t like the praise of the dying traditional publishing industry, but that’s pablum. So let’s be frank. This isn’t a strong open access policy. But that’s ok by me. Because it’s an enormous expansion of public access into spheres of research where it was essentially absent from the conversation. It creates a policy environment that tilts the field towards change, towards startups, towards publishers whose embrace to real Open Access becomes a competitive advantage over time - and it does so across an enormous swath of science. It re-creates the conditions built in the life sciences years ago in other sciences. I believe that’s what will advance open access fastest there. But let’s also not attack Mike, or others, who disagree. We need to be constantly reminded to strive for the most, and attacking one’s own critics is not a healthy sign of an open movement. This policy is not the end of our work in open access, or even the beginning of the end. But I do believe it’s at last the end of the beginning of the enormous change from closed publication of science to open publication of science. From now on it’s about how we implement access, not if. Hats off to everyone, and now get back to work, because we’re a long way from done. Time to focus our energy on Congress to finish the job.

Wednesday featured a double-barreled shot by Nature Publishing Group across the bow of the Open Access conversation. First, an editorial unambiguously endorsing “gold” open access as the proper form of scholarly publishing. Second, a majority investment in Frontiers, a for-profit CC-BY scholarly publisher. I’m personally just as happy to see this as I was to see the OSTP policy expanding public access across all federal research. Let’s just say some of my friends were surprised at that.

Evgeny Morozov’s been on a tear lately, with articles about “solutionism” in Slate and the New York Times, and an absolute destruction of Gavin Newsom’s new book on networked politics. I’m torn by Evgeny’s work. I tend to agree with what I perceive is one of his basic ideas: our culture of deifying the application has a nasty side effect of reducing the perceived importance of political change: don’t bother actually risking anything to protest, just like the Facebook page about the protest. I really liked the concept about the rise of the choosing algorithm and its impact on creativity.  I have a soft spot for a truly well written negative book review. And I think it’s vital that those of us who self-identify as “open” advocates engage with his work, because I think he’s onto something in more cases than I’d like to admit. On a related note, I’ve been reading The Theory That Would Not Die recently. It’s a nice look at the waxing and waning of probability and inference over hundreds of years. When we’re in periods where we don’t know what we’re looking for - and it’s important to be as right as possible as fast as possible - then Bayes’ table becomes a vital tool in the kit. In World War II, that was cracking Enigma. Unfortunately now, most of its usage is social, mobile, commercial. It offers me rehab in Napa Valley when I buy wine online. But I worry that in burying the algorithm and the application and the game, to kill its overestimation in culture and in politics, he fails to appreciate the places where those tools are yet to be applied, but might bring real change. By real change, I mean epistemic change, a change in the way that we know we know something. Science is one of those places. Science has a problem related to, but different than, solutionism. I’d call it “sensorism” perhaps - the belief that because we can make a machine that senses things more finely, more completely, and in massive parallel, we’ll somehow come to a greater understanding of the underlying thing being studied. Sensorism is rife in the sciences. Pick a data generation task that used to be human centric and odds are someone is trying to automate and parallelize it (often via solutionism, oddly - there’s an app to generate that data). What’s missing is the epistemic transformation that makes the data emerging from sensors actually useful to make a scientific conclusion - or a policy decision supposedly based on a scientific consensus. One of the reasons I do “open” work is that I think, in the sciences, it’s a philosophical approach that is more likely to lead to that epistemic transformation. If we have more data available about a scientific problem like climate change, or cancer, then the odds of the algorithms figuring something out that is “true” but incomprehensible to us humans go up. Sam Arbesman has written about this nicely both in his book the Half Life of Facts and in another recent Slate article. I work for “open” not because “open” solves a specific scientific problem, but because it increases the overall probability of success in sensorism-driven science. Even if the odds of success themselves don’t change, increasing the sample size of attempts will increase the net number of successes. I have philosophical reasons for liking open as well, and those clearly cause me cognitive bias on the topic, but I deeply believe that the greatest value in open science is precisely the increased sample size of those looking. I also tend to think there’s a truly, deeply political element to enabling access to knowledge and science. I don’t think it’s openwashing (and you should read this paper recommended by Morozov on the topic) to say that letting individuals read science can have a real political impact. I look forward to reading Morozov’s new book this weekend at SXSW. It’ll be a bracing antidote to what I expect will be rampant solutionism. My panel is political - it’s about who owns the data these solutions create, and what rights and risks those solutions entail. It’ll get a lot less attendees than a product launch. And I hope Morozov engages with sensorism one of these days. It’d be fun to see what he does with it.

One of my favorite users of CC-BY is Pratham Books in India. Pratham Books is a non-profit trust that publishes high quality books for children at affordable prices and in multiple Indian languages. They’ve shipped more than 7,000,000 books. They’ve got a beautiful post about their move from the Attribution-NonCommercial-ShareAlike (BY-NC-SA) CC license to the Attribution (BY) only license and the internal back story of the decision. What’s really fascinating isn’t just that they relicensed 400 books under BY, but that they only managed to post 173 of those books online at Scribd. The other 227 books were not posted. So we have a nice, natural study to analyze of the differences between openly licensed content that is in a stable, well used platform and content that isn’t. Some brief takeaways. Read their whole post to see the graphs. The sales of individual books available on Scribd don’t differ greatly than those that aren’t  - but they’re definitely not significantly lower. Cumulatively, the sales of Pratham books on Scribd appear to outsell those that don’t, though not totally outside the error margins. But again, they’re not lower. For cumulative sales data for CC books that were available on Scribd vs. CC books that were not available on Scribd, the former outsold the latter in almost a 3:1 ratio. \tightlist Let’s unpack point #3, because it’s fascinating. These are books that are available online, under the most liberal license offered by Creative Commons. You can one-click download and print them, or even send them off to be reprinted and sell them yourself. Yet the ones that are there radically outsell those (also liberally licensed books) that are in a more controlled technical environment. There’s a lot of money spent looking for ways to sell books and content on the web, to protect authors, to protect old revenue sources. Sometimes though, the best advertising for the content (and implicitly the author) is the content itself. And there is mounting evidence that at least some people will pay for the authentic version, whether it’s to get the physical artifact, to help the author, or simply because they want to. This is a tiny data point. What’d be great is if as these experiments happen, more publishers started to release the data as to the outcomes. We live in a world where we can’t even get a publisher to tell us the breakdowns in their revenues, how much they make off subscriptions and new content versus access to the back catalog. Data about where the money and the sales actually happen will drive far better policy than we have. If only the publishers would get that and start opening up some channels.

So, I have a commentary published in Nature this month about the importance of using a CC-BY license to achieve full open access. I requested the article be made freely available as part of my agreement with Nature, but they paywalled it anyway. It’s freely available now but not until after some embarrassing email and twitter hassling. I am not particularly mad at any of the parties involved. It just points out the power of the default switch being closed, and how hard it is, even when you’ve negotiated an agreement, to flip it to open. It points out the weakness of the author in negotiation with the journal. Maybe I’m the fool in the fool’s errand. Also, in the search for brevity that print journals enforce, I didn’t get to be as granular as I wanted. My quarrel is with the publishing industry’s attempt to write a new license and I have no wish to lump those with whom I have a philosophical disagreement with those OA advocates who sincerely dislike CC BY, like Heather Morrison or many in humanities, into the same pool. Anyway. Below are references for key points I make in the commentary. 1. Re: definitions of OA, see “Budapest Open Access Initiative” at http://www.opensocietyfoundations.org/openaccess, accessed 03/13/13 2. Re: restrictions in licensing, see Elsevier’s published contract with California Digital Libraries: ““Schedule 1.2(a) General Terms and Conditions ”RESTRICTIONS ON USAGE OF THE LICENSED PRODUCTS/ INTELLECTUAL PROPERTY RIGHTS” GTC1] “Subscriber shall not use spider or web-crawling or other software programs, routines, robots or other mechanized devices to continuously and automatically search and index any content accessed online under this Agreement. ”” online at http://www.google.com/url?q=http://orpheus-1.ucsd.edu/acq/license/cdlelsevier2004.pdf&usd=2&usg=ALhdy2_FmzOtI3JkKs-fJwirgig4WLA5fA, accessed 03/13/13 3. Re: “CC Plus,” see various comments in lectures at “FACT Seminar No. 1:  Licensing in an Open Access Environment: legal niceties, funder mandates and publishing challenges“ at http://www.stm-assoc.org/events/fact-seminar-no-1/?presentations, accessed 3/13/13 4. Re: CC BY, See “Creative Commons Attribution 3.0 Unported” (the “commons deed” with links to complete underlying license) at http://creativecommons.org/licenses/by/3.0/, accessed 3/13/13 5. Re: 70+ requirements, see “Public Policy Requirements, Objectives and Appropriation Mandates” at  http://grants.nih.gov/grants/policy/nihgps_2010/nihgps_ch4.htm, accessed 3/13/13 6. Re: community defintions of open things, see “Open Knowledge Definition” at http://opendefinition.org, accessed 03/13/13, and “Open Source Definition (Annotated) at http://opensource.org/osd-annotated, accessed 3/13/13 7. Re: license incompatibility, see “GPL-Incompatible Free Software Licenses” at   http://www.gnu.org/licenses/license-list.html#GPLIncompatibleLicenses 8. Re: decomposition of licensed elements and the CC licenseed Time Photo of the Year, see “Trapped Underground,” a CC-BY photograph of the London Bombing aftermath, available at http://en.wikipedia.org/wiki/File:Trapped_underground.jpg  accessed 3/13/13 9. Re: technical solutions to provenance, see “Source Attribution in RDF,” http://www.w3.org/2001/12/attributions/ accessed 3/13/13

So Mendeley got bought by Elsevier. And there was much teeth-gnashing. I won’t link to it but it spawned two solid hashtags: #mendelsevier and #mendelete. I have a Mendeley account, but never used it other than to test the system against Zotero, which is what  I use to track my own work. So I am not affected by this but I’ve been a bit stunned by the depth of the anger against Mendeley. I’ve waited to write this to try and understand it. Part of it, I assume, is just Elsevier rage. Danah Boyd has summarized why Elsevier is rage-worthy nicely in her post on the acquisition. But the greater part feels like the anger over what many seem to think is a broken promise made by Mendeley to be an “open” company. I don’t feel that way. I never thought Mendeley was an open company. I thought they were deploying a strategic approach to openness by exposing their data under CC-BY, but I always thought that openness wasn’t the point of the company. It’s why I didn’t use the product and why I wasn’t surprised, shocked, or saddened by the acquisition. It’s got me thinking though about companies and “open” - and what matters in deciding whether or not to use a product from a company claiming that mantle. For me it boils down to where the openness lives in a company. There’s a lot of ways to slice this, but a simple one would be: is the “open” part of the revenue model or is it part of the market acquisition strategy? If the former, like BioMed Central, I have a lot more faith that an acquisition will not destroy the openness, because “open” is part of the way that the company makes money. But the open access part of Mendeley to me always appeared to be a customer acquisition strategy. It appealed to the OA folks, it appealed to developers, and it never affected any monetization or revenues. There were always visible choices by management to hedge their open bets, as Jason Hoyt has laid out. And that makes it a risky bet to think they’ll stick with it now that they have access to a massively larger customer base while inside a company with traditional antipathy towards openness. Again, I’m not mad. I either avoid, from a professional basis, companies built on closure, or I mitigate my expectations of them and do a lot of backing up. Because at some point unless the revenues come from open, the customer acquisition strategy of openness will be deprecated. If it isn’t, then the management of the company will be replaced with managers who are willing to shut things down to make money. Always, always, always examine claims made by companies about openness. I’m not the world’s biggest Evgeny Morozov supporter, but he’s right to examine the way that the words “open” and “sharing” and “free” get co-opted. Facebook lets you share! It’s free, and always will be! Look the gift horse in the mouth. And if the revenue model of a startup isn’t built on open, then feel free to use the tool. But don’t get emotionally invested, or dependent, no matter how seductive the rhetoric may be. Because at some point your use and attention and content will be monetized, probably in a way that bothers you.

I got a lot of good responses to my post yesterday about Mendeley’s acquisition by Elsevier. But a theme emerged that I didn’t intend to emerge, which was the idea that because I pegged Mendeley’s investment in open access as a customer acquisition strategy that it made it insincere. That was most definitely not the point. Remember that half the time I’m a senior fellow in entrepreneurship at the Kauffman Foundation. We study startups and support entrepreneurs. I can tell you that using openness as a customer acquisition strategy is something I think is a smart move, especially the way that Mendeley did it. As a quick reminder for those who’ve never started a company, they need to acquire customers or they go out of business (as mine did, because mine didn’t). If you don’t have a strategy to do that, you’ll fail. By selecting open, and fully committing to it, as a strategy, Mendeley helped the Open Access world enormously over the past four years. What they’ve done creates a solid track record in OA, a serious and provable one. They didn’t do this for evil reasons, or in anything close to an insincere way. And by doing it they advanced the movement. We can, and should, thank them. That’s why the anger stunned me, as I mentioned yesterday. They hired a community manager (William Gunn) personally and professionally dedicated to OA, and let him run. I know, respect, and believe deeply in William and his commitment. That’s not an insincere company move. Their data’s under CC-BY. That’s not insincere. I made a crack about allowing the database to be downloaded and reposted, and immediately heard back from William that I could go for it. That’s not insincere. They ran the binary battle with PLoS (I was a judge!). That’s not insincere. They backed the Access2Research petition, immediately. That’s not insincere. My point wasn’t to gleefully give Mendeley the finger and say, you were closed all along, or to say, you were just using us to get customers. Every startup needs customers, and if you don’t realize that you’re kind of being a dick to the people in the startup. Mendeley’s making a meaningful commitment to open as a customer acquisition strategy was innovative, and important, and advanced the cause of open access to the scholarly literature. My point was deeper. It was that because the openness was not tied to revenue, it could be removed now that the product didn’t need an innovative customer acquisition strategy. It’s tied to a massive customer base now. Open can be discarded. When it’s part of the revenue model, it can’t be discarded nearly as easily. And in my experience, if open *can* be discarded, it usually *is* discarded when monetization becomes the priority. I hope that I’m wrong.

And, my friends, in this story you have a history of this entire movement. First they ignore you. Then they ridicule you. And then they attack you and want to burn you. And then they build monuments to you. Although the substance of the above quote is usually attributed to Gandhi, there’s no record that he actually said it. The quote above is by Nicholas Klein, a labor activist, from 1918. I don’t include it as an example of attribution decay. I use it as a frame for where we are in the open access world right now. We’ve had a good run. We got the NIH public access mandate. We got the petition to 25,000 signatures. We got the presidential directive extending the NIH policy across the entire federal government. We got multiple examples of open access publishers into sustainable revenue models. But changing the default from closed to open was always going to involve a phase where those whose revenue models depend on closed really brought the guns out against us. And we’re there now. There’s Wiley, wallowing in the mud and smearing Public Library of Science’s peer review credentials under the charade of a survey of authors. There’s Elsevier, proposing a novel license for STM publishers and somehow magically being part of a Netaction “bad legislation” coalition that attacks all open access bills, while denying any knowledge of it (no story coverage, but some conversations on Alicia Wise’s twitter feed). (UPDATE May 24 2013: Times Higher Education UK has a story in which Elsevier sort of distances themselves from Netaction) There’s crocodile tears covering the emergence of scammy open access journals, none of which mentions the long-time existence of scammy closed access journals. This is not surprising, as so many of the large, “authoritative and important” publishers make money by publishing scammy journals - anyone remember the Merck-Elsevier scammy bone journal? Still waiting to see someone mention that in the same breath. Then there’s the systemic disadvantage we have as advocates once policies move into implementation phase. The meetings last week at the National Academies are a great example of why it’s so hard to change the system. I had to travel 3 of the 4 days for work, and the fourth day I was in meetings all day that made it impossible for me to attend, or to speak. We have day jobs, us advocates. But the publishing industry we’re fighting against has no other job. They can hire people who have only the responsibility of making sure the open policies are implemented in the least open way. They can saturate every meeting in DC with hired guns, and claim it as evidence that the public supports them. But it’s not about being depressed, or complaining. It’s a sign that we’re finally getting close to the bone. We’re enough of a threat not to be ignored, or ridiculed. We’re gonna get hit, and we’re gonna get hit hard. We have to keep reminding the world that this isn’t about protecting a dinosaur business model, this fight. It’s not about scammy journals, which exist no matter how they get paid for. It’s not about who has the most lobbying money in DC. It’s not about new licenses, or sleazy survey language. It’s about letting entrepreneurs build businesses on top of open content. It’s about kids building cancer tests on open content. It’s about you and me being able to read what our tax dollars paid for. Don’t let the FUD and mudslinging get in the way of that message, ever. We have to keep getting up. We have to keep fighting back. Because in the end, we’re on the right side of history. And once we get through this phase we get to the good part, where they build a monument to Heather Joseph and Peter Suber and Mike Eisen and all the heroes of open access.

My notes for the panel today at Health Datapalooza. I’ll come back later and add links, fix typos, and so forth… Why consumer access to data is important - because data is a digital representation of us. and it’s increasingly being used to affect our real-world services, their costs, their benefits. - we’re increasingly able to generate data that used to be the exclusive space of the clinical system. genomes are just part of it. health data is in everything. Facebook cups, keyboards, iPhones, google’s next phone. - but it’s faulty at worst, and incomplete at best. if we can’t access it, we can’t tell how and where it’s incomplete or wrong. Use cases and potential applications for consumer access to data - send to app provider to interpret data and help me make better choices about my care. - send to app provider to interpret data and help me make better lifestyle choices (ideally not a panopticon of health provider, ATT, and government - but a decentralized, competitive market) that’s what this event is mainly concerned with. but there’s more. - extract the “real” clinical data (compared to the “dry” data from phones etc) from the record. needs a lot of normalization etc but it starts to paint a longitudinal phenotype of me and my life. mapped to my genome, in large in sample sizes, we can start to correlate lifestyle and medical treatment outcomes to individual genomic variation. Current state of consumer access to data - raw in every sense of the word. most folks aren’t exactly aware of the things we here are aware of. - most of the data collection is happening in zones like mobile and social where we have no positive rights to privacy, like health, and where the entire system depends on designing awareness of the data (and its ownership) out of the hands of us as citizens. - in health, access to data is hamstrung by a combination of rapidly advancing technology and slowly (that’s a nice way of putting it) adapting law. - we just moved here from Oakland. when i wanted my son’s immunization records to get him into his new child care center here in DC, the provider couldn’t fax them to me because they were afraid it violated hipaa. but it would have been legal to hire a TaskRabbit - total stranger - to go pick them up, take them to Kinkos, and fax them to me. - that’s insane. we’re not being protected. we’re not getting access at the rate or in the form that we need yet. it’s getting better, but it’s still slow. and we’re less willing to tolerate it, because we’ve been trained to expect more from our institutions by good technology. Where we have to go next / role of Blue Button+ - the hard part is that most of us, when handed a file of data, don’t know what to do with it. i downloaded my genotype, my fitbit data. No idea what to do with it. compared to my “medical record” in PDF, which is computationally useless but human readable. - the investment in BB will pay off best when I have the right to direct my file to someone who can do something with it, for whatever reasons i choose. whether to run an app that makes sense of the data or to donate the data to research. - BB+ is a great example of this. It allows for both market solutions (banks!) to emerge and for pre-competitive or public private solutions to emerge where we can donate data, or share it conditionally. - i’m looking forward to pushing Sage Bionetworks, the non profit where I work, to be one of the first certified recipients of BB+ precisely to enable the non-market reuse of health records data.

Big news today: the Supreme Court has ruled that naturally occurring genes are not patentable. This is a Big Fucking Deal, as Joe Biden might say. But it’s not as complete a victory as it may seem on the surface. The ruling explicitly excludes cDNA, and notes that the case didn’t address methods, applications of knowledge, synthetic DNA, or alterations of gene sequences that do occur in nature*. Lots of room to negotiate privatization there - indeed, that sentence could be the next “by means of a computer program” in patent law, though it doesn’t have to be so. This is a ruling that resets the default to unpatentable, as Mike Eisen rightly pointed out on twitter. That’s why it’s big. But it doesn’t close the door, at all, on lots of patents in and around DNA*. That’s why the biotech stock index is up today*. I’m actually not nearly as interested in those parts of the ruling though. What this means for me is more that the biggest barrier to building a commons of mutations with diagnostic potential is gone: the inability of DTC sequencing companies like 23andme to reveal the status of its customers to its customers because of patents. The companies that rely on these patents now have to move to trade secret approaches, as Myriad already has done, and the thing about trade secrets is…we can compete with them. What the patents did was make it impossible, illegal, for us to build commons-based competition. They were enforcers on trade secrecy. Those enforcers are gone. We can now go straight to the citizen and say, get yourself genotyped, and donate your data to science. At Sage Bionetworks, my non-profit employer, we’ve built a system that allows precisely that. It’s called Portable Consent, and we’ve got a study called the Self-Contributed Cohort for Common Genomics Research. You can enroll and donate your data in less than ten minutes, start to finish. So go get yourself genotyped. Download your data. And donate it to science. Let’s stop fighting companies that privatize, and start competing with them. Note: edited post at 12:15PM EST for clarification of a few points. Those sentences carry asterisks at the end.

Today is the White House’s Champions of Change event celebrating Open Science. You can watch and join in at 1PM US Eastern time today. But on this day, I wanted to remind everyone that “open” is a word that comes with history and, more importantly, with meaning. It’s not a word that someone can take and sprinkle on their work and claim without understanding the history and the meaning. If someone does that, they are going to get bullshit called on them - like the Yale-Medtronic supposedly open data agreement, which is anything but open. So let’s get this clear. Just because you’re making something available that wasn’t previously available doesn’t qualify as open. Just because you’re reducing the transaction costs of access to something doesn’t qualify as open. Just because you’re involving more people than before doesn’t qualify as open. Open means that there is no prejudice against any kind of user, anywhere, any time. Open means that commercial use is allowed, in advance. Open means that new works, new research, new products are allowed, in advance. Open means following the Open Definition. Here’s the Definition. It’s short and sweet. “A piece of data or content is open if anyone is free to use, reuse, and redistribute it — subject only, at most, to the requirement to attribute and/or share-alike.” The reason for a definition is so that the word open actually means something. Open is a great word. But it has to mean something for it to mean anything. And it’s hard to meet this definition. It means you can’t be granular, or differential, or non-commercial, or academics only, or only for some kinds of uses in science and not for other kinds of uses. It means a bright line test that a project either meets or doesn’t meet. The Yale-Medtronic example is a classic case of misappropriation of the word open. It’s anything but. Yet there goes the science establishment trumpeting it as such. If “open” is going to mean something in science the way it means something in culture and in software, those of us who’ve spent years toiling in the trenches have to collectively examine, carefully, every claim to open science. And we have to speak truth to power, to hold those who would claim openness as their mantle to the definitions and call them out when they fail to meet them. Otherwise, the nascent open science movement will suffocate under the weight of semi-open science, content that is segregated by incompatible and overly restrictive licenses, data that comes with complex terms of use, service, field of use restrictions, and patents that pop up out of the blue when open projects attempt to scale. Being open - really open - is hard to do. It doesn’t give the people what they want. As Bob Young noted in his keynote at this year’s Sage Congress, what people wanted out of Red Hat software was for it to run Microsoft Office. He didn’t give them that. He gave them what they needed, which was the right and the power to control their own operating systems. And people thought he was crazy for not giving them what they wanted, for not compromising on open, right up until Red Hat was so successful that everyone agreed it had been obvious all along that open was the smart choice. It wasn’t easy being open in software, then. It isn’t easy now in science. But the value comes over the long term from the decision of a small set of people being unreasonably committed to making true public goods. Today’s event is a small but pivotal step in recognizing those people, and in carrying those true public goods forward.

Lots of stuff trumping blogging right now. TCGA Pan-Cancer analysis published. BRIDGE funded. ImpactStory funded. Giving a ton of talks, and a few big publications coming in the next few months. Be right back.

Just a quick note to put out a thought. I’ve done a lot of work with informed consent, and am one of the people pushing the idea that in its current form it isn’t serving our needs as a society, as patients, as scientists, as people. That’s pretty much the whole point of my TED talk. And I’m a supporter of projects like Reg4All, which embrace fair information services practices as their basis. There’s a real role to play for that approach, especially in aggregate level data, or in recruitment of people for studies that will in turn require informed consent. But I am noticing a disturbing trend in the conversation around consent, one that I intend to combat fiercely, which is the idea that informed consent itself is the problem. I don’t think it is. I think it’s the way we do it that’s a problem. When it’s used as a shield against patient involvement, or as an excuse to deny people their data, that’s a problem. When people don’t understand the forms and are rushed through the process, that’s a problem. When data can’t be integrated into larger and larger studies because of consent, that’s a problem. But the idea that we should be informed about the risks and benefits to ourselves and society before we decide to share our data? I don’t think that’s a problem that needs disrupting. We need to embrace better design for informed consent. We need to bring it into the 21st century, to make it compatible with distributed computing, with large-scale mathematics, with the internet. That’s clear. None of these problems, together or collectively, mean we should treat the issue of consenting people into research as a simple transaction cost. It’s not about reducing the “friction” of “participation” to a few clicks here or there. If we treat informed consent as a transaction cost to be minimized or eliminated, we may solve the problems of data liquidity. But data liquidity, as we’ve seen in national security, social media, and more, doesn’t always come alongside beneficence, justice, and respect for people. That’s the point of informed consent, not liquidity of data. Health data is one of the only places where informed consent - not just simple clicking - is part of our cultural heritage. I think that’s a feature, and not a bug. If we can’t find a way to balance informed consent, and its ethical heritage, with data liquidity, that failure is on us.

I’ve been following the 23andme saga with dread and fascination and frustration since it hit earlier in the week. If you’re not up to date, David Dobbs has the canonical collection of stories to get you there. This is a post about business models and culture clashes. It’s long. I should also start by disclosing that my former non profit project received funding from Anne Wojcicki’s philanthropic foundation, that I hold some shares in small startups that could benefit from the success of direct to consumer genomics (though not in 23andme) and that I now work at a non profit that is premised on the idea that personal access to data will fundamentally change research. My 23andme data is online for all to download. So I could personally benefit if 23andme survives and thrives, and I personally admire Anne and her work, even when I criticize some of the choices she makes. It’s hard as hell to be a CEO and she deserves credit for icebreaking, vision, and perserverance. That said, I am deeply frustrated by the simplistic narrative of OMG FDA BIG GUBBERMINT SILENCING DARING ENTREPRENEUR. It’s not that simple. 23andme has been trying to bring a technology business model, and a bayesian data culture, to the genetics world for six years. Both of those were gambles. And I think the problem they’re in right now is a direct consequence of those gambles not paying off yet. First, by a technology business model, I mean the idea that you go get all the users you can get by giving your service away for free and figure out a way to make money later. This is no different than social networks business models. Facebook, Twitter, Instagram, Snapchat - all of them started with this concept of acquiring the most users and then working out a model for revenue. And all of them converged on advertising, because for all the promises of the new network, selling people sweaters worked better than anything else. As a business model for genetics though, it’s different, because your cost isn’t just distributing an app and paying Amazon cloud fees. 23andme has been selling their direct-to-consumer genotyping kits for six years now, always at a deep discount to their actual price. They exacerbated that financial model when they dropped the monthly subscription requirement last year. If they can’t find a way to make money soon, they’re going to wind up in the pets.com box - you can’t sell a dollar for fifty cents and expect to make money on volume. I would guess that the hope was that population genetics would yield a business model that wasn’t regulated. If you could get enough people in the door, then your internal analysis could inform efforts at pharma, at insurance companies, and more - without ever having to market your spit kits as medical devices in the regular business model. Their push to hit a million users indicate this remains a goal. But since they’re not doing that yet, it seems they’re not at the magic number. That means going the traditional route, which is to develop and rigorously validate a test, get it approved by the FDA, and then market it at an incredible markup. That’s what 23andme tried to do in this run. They invited the FDA in the front door, and at least so far, haven’t been very good about serving them tea. We’ll find out more about why later. But I posit the data culture that permeates technology companies is at the root of the frosty relationship between the FDA and 23andme. It makes it very hard to pivot from a model based on loss leadership and data mining to one based on regulatory submission. That “traditional” submission to the FDA would be of a very specific kind of analysis based on randomized controlled trials. It is designed to keep bad things from happening to people, not to make sure good things happen to people. As one of my favorite papers lays out, parachutes would not receive FDA approval as a gravity-resisting device. Modern tech culture doesn’t work that way. Bayes’ rule is about probability. It’s a different way of knowing that you know something, and it’s one in which there is far more tolerance for uncertainty than the FDA is accustomed to. And there’s been statements by FDA officials that they are deeply uncomfortable with that. Note in particular Janet Woodcock’s statement that causal inference needs a “level of rigor” - and the date in late April. It’s right before 23andme cut off communication with the FDA. The FDA isn’t saying that 23andme needs to shut down, or stop giving people data, or stop providing spit kits. It’s saying their causal inference doesn’t hit the level of rigor that allows it to pursue a technology business model in the health regulatory space. That’s a gamble 23andme was always taking, that the FDA wouldn’t know how to regulate it in time for it to make money. It’s not an overreach, or a screw job on patients. It’s just business. And I hope this isn’t the end of it. We need DTC screening. It helped me. It’ll help many others. But until the FDA learns how to deal with Bayes’s rule and its discomforts - and until DTC companies figure out a business model that isn’t based on massive loss leadership - we’re going to keep coming back to this clash of culture and business models. Both sides need to make some changes if we’re going to avoid doing this over, and over, and over.

23andme has an API. They announced it in a talk called “Own Your Data” - which i thoroughly recommend. And they back it up in terms of your actual genotype on their website. You can download your SNPs, and upload them (as I have in multiple places). They also provide on their site interpretations of the genotype. Those interpretations are what make the data useful to us as patients. They’re at the center of the FDA-23andme battle, which isn’t the point of this post. I can’t download and export my interpretations the way I can download and export my genotype, and that seems a missed opportunity. It’s directly supported in the API, which features the elements at the bottom of the post. So, I hereby pledge to give $500 to the first person who makes a web application that works in Firefox, and lets me log into 23andme and download my health and ancestry data into a structured file (CSV at least - no text files). The app must have its source code on github, and be licensed under an FSF approved free software license. The app must work not just for me, but for four more testers. It must pass a security review to make sure it’s not leaking passwords. The file should contain my genomic and health data, not my user data or my ancestry data. “First” will be judged by twitter timestamp - send me a message if you have a submission. I know $500 isn’t a lot. If I could code, I would. But I suck at it. This is out of my own pocket. I’ll also promise to give just incredible amounts of attribution, acclaim, and more. It’s a chance to get known too. It’s part of my “stop complaining and do useful stuff” resolution. If no one bites, I’ll post this as a claimable job somewhere else. User\label{user} GET /user GET /names GET, POST /profile_picture GET, PUT, POST /publish GET, PATCH, POST /introduction \tightlist Genetics\label{genetics} GET /genotypes GET /genomes \tightlist Ancestry\label{ancestry} GET /haplogroups GET /ancestry GET /neanderthal GET, PATCH /relatives \tightlist Health\label{health} GET /risks GET /carriers GET /drug_responses GET /traits \tightlist

Well, that didn’t take long. Less than seven hours after I posted a request and reward for a 23andme app, I had two submissions. Beau Gunderson and Eric Jain (who turn out to be friends) both submitted short programs that fulfilled my request. The winning version is at Beau’s site. First, a little context. The point of this wasn’t to create a consumer experience, so don’t go to the link and expect one. It’s a download tool, no more and no less. But it didn’t exist before and now it does. What you will get if you click the link is the ability to store local copies of your genotype and health results. You will have to accept conditions to execute the app. Read them carefully before you do so. I am not sure if the 20 user limit is concurrent or total, and the tool may break at some point if it’s the latter until it goes through account review. This is alpha software, caveat emptor, you should probably wait to use it until lots of other people do, and so forth. I generated a zip file and downloaded it, for reference’s sake. Second, let’s thank 23andme for supplying the API and enabling the health GET commands. They didn’t have to do that at all, much less make it so easy to do. This doesn’t get done in seven hours without clean API design. Credit where it is deserved. More reason to hope they can get data into the FDA that gets approved and they keep DTC genomics economically accessible. Third, we now have the challenge of integrating the output into a Blue Button format, so it can benefit from the ecosystem of applications emerging there. I’m not sure I can pull that off in a twitter challenge but we’ll see - at least we’ve moved to the next step of the process. More in a bit. I’m going to wire this into a few places over the next week and think about it some more. This was both wonderful and unexpected in the best way. Thanks to everyone who joined the conversation and to 23andme for making the API available.