I spend a lot of time ranting on about openness, and a lot of that time I am preaching to a choir or people who believe in openness at a deep enough level that they don’t think about the why of it. It’s just accepted that open = good in some epistemic sense. And that’s nice in a lot of ways. It’s nice to be able to just talk about good stuff and not make basic arguments. But I arrived at openness from a different place than a lot of my compatriots. I didn’t arrive at it from a political freedom perspective like the founders of the free software movement did, although I now embrace the political. I didn’t arrive at it from a horror at copyright expansionism like the founders of Creative Commons did, although I now share that horror. Nor did I arrive at openness after experiencing the misery of scholarly publishing models like the founders of the Public Library of Science did, although I now know that same misery. I arrived at it after getting my nose bashed in by biology. I started a company about thirteen years ago, based on some work I did in university epistemology and semantics, whose entire premise was that we knew enough about biology that if we simply converted that knowledge to formal ontologies and then used common identifiers to connect those ontologies into networks, we’d discover some basic laws of biology that were implicit in the knowledge but invisible to us because of format problems. Was I ever wrong. But I was wrong in a way that is a leitmotiffor people entering biology from other fields, whether technologists or philosophers, whether naive twentysomethings like me or successful Silicon Valley executives: I bought into reductionism.

Tomorrow, my dad will be honored at Trinity University in San Antonio as a distinguished alumnus. We’re flying the whole family down to celebrate with him, but I wanted to take a moment to celebrate him here. Since I live on the web most of the time, and few of you know his story, I wanted to tell it. The Trinity blurb is remarkably apt and pithy: His occupation is hard to describe: mainly a scientist - at the intersections of the social and environmental sciences - but also a research program manager, provider of technical assistance, and institution-builder - with one foot in the world of research and one foot in the world of practice. That’s about right. I remember learning the words “sustainable development” from him around the time he taught me to swing a baseball bat, which means late 1970s. My dad drew me into libraries in the 1980s, where I made first contact with networked computer systems, as I helped him find books and images for speeches he gave. His work picnics were places where I stepped on the feet of people who dated back to the Manhattan Project, which is part of being a national labs kid at a place like Oak Ridge. My dad has gotten a lot of notice in his own fields, but the biggest thing, the thing that makes others realize that he’s a pretty towering guy, is when the Nobel committee formally recognized him as a co-laureate in the 2007 Peace Prize shared by the IPCC and Vice President Gore. Hiscareer is remarkable, and he’s not showing any signs of stopping.

Guest post by Carolina Rossini (@carolinarossini)

I’m more than 20 years away from my last math classes. And though I spent my startup experience around some very smart mathematical types, I didn’t learn enough at any point to actually use data in models, make models, or otherwise become one of those “big data” types you read about…well, fucking everywhere. But I did learn a healthy dose of respect for what data, and math, when put together by the right people, are capable of. And since signing up with Sage Bionetworks, first as a Board member, and more recently as a member of the management team, I’ve learned a lot about what data can do now that processors, storage, bandwidth, and sequencing are all brutally cheap. The key is, as per @DCDave, to reset your expectations. Cheap, plentiful data changes the epistemology of fields. It did so in baseball, which went from trusting a scout’s “gut” instinct to an intensely data driven science. It did so in weather. This year, it did so in politics. But it’s very hard to reset your expectations when you’re at the top of a traditional industry. The punditocracy’s dismissive handwaving towards Nate Silver is all I can think of when I go to traditional events on science and health these days.

Olin Hyde noted a nifty survey on patient control of electronic health record information the other day. But he interpreted it in a dour way, at least for my own worldview of openness. Here’s his tweet: Bad news for #opendata advocated by @wilbanks “@berniemd31: Study: Patients Want To Control #EHR Information - bit.ly/ToOglB” — Olin Hyde (@olinhyde) November 29, 2012 The article talks about how patients want control over the privacy of their data, so I can see why this is an easy interpretation to make. You’re a patient, someone tells you how much crap is happening with your data, and your gut reaction is to protect it. Makes sense.

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.

My TED Global talk from yesterday has generated attention, as I’d hoped. I want to clear up one point from an otherwise excellent summary of the talk from the TED blog. The title of the talk could well have been the “unintended consequences” of informed consent. I’m not criticizing the idea that we should be informed before we join medical studies - indeed, in the talk, I note that this is a beautiful invention of society, something we should be proud of. My problem is that we’ve joined the idea of being informed with an idea of privacy  that is creating a drag on innovation. That prevents reuse of data without extensive permissions. That makes it hard to donate your data to science. Consent to Research is about untangling the two. It’s built on informed consent, not an attack on it. Because the reality is that privacy and consent have become entwined, and are used by researchers who are competitive, or just plain lazy or arrogant about our ability to understand data about our own bodies, to keep their data secret. Just as free software is a hack built on copyright, open consent is a hack built on informed consent. Simple as that.

Re-reading Holy Fire by  Bruce Sterling. It’s probably been a decade since I first read it, and it is remarkably fresh and relevant - a fate few futurist books can claim fifteen years after publications. It’s got great bits on all sorts of things. Gerontocracy. The crudity and just plain boneheadedness of what we think of as “modern” medicine. Love. Art. Transformation. I teared up reading the description of the emotion of holy fire as something Mia, the main character, sees as she looks at a young girl, and how it was an emotion she felt on looking at her daughter. It’s what I feel when I see my son raise his arms on our little patio, water coursing over him from a gardening bucket. It’s a fantastic book. Since I work on privacy these days I’m completely obsessed by the novel’s approach towards privacy. Everyone’s medical information is online to all. Everything, to everybody. Sterling posits a generation burned by a decade of plagues, preferring total transparency to the alternatives. And it’s very plausible. However, it’s not an all or nothing world. It gives us perhaps the idea that what we need is not a monolithic approach to privacy. Maybe we need a new epistemics of privacy - where not all data is the same, and not all things need be shared. There’s a little exchange in the front of the book that sums it up perfectly. “I’m not asking you what networks they’re accessing,” Mia explained. “I just want to know a little about their personal lives.” “Oh, okay, no problem,” Stuart said, relieved. Heh. I’m going back and re-reading Distraction next. As I recall there’s some lovely near-future biohacking in it, as well as great Louisiana dystopia-fiction. Pick up a copy at Amazon.

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.

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.

Lee Dirks died yesterday with his wife in a car accident in Peru. They leave two daughters behind. Lee worked in Microsoft Research, where he was a large force in the open access world. He was also a very good friend. Someone I trusted to talk to in confidence. Someone I called the first day I changed jobs. When his name was on the agenda, flying twelve hours in a cramped plane to a mediocre hotel in an impossible time zone was a lot more fun. We’d have 30 minute work calls that ran 80 minutes to talk about balancing fatherhood and the travel schedules we shared. We drank together, cussed out our favorite sports teams together, complained about mediocre mexican food together. We sent each other pictures of our kids. And we’ve spent more than one night talking about some awesome place one of us heard about. Nowhere near the mediocre hotel, just a place you can reach in an poorly maintained cab, on a road with crumbling features, that great local version of the overrun tourist attraction with no crowds and the best food stall. Nearly every time that ride is ok. Sometimes something goes wrong but it always ends as a minor thing, a sideswipe, a funny story to tell at the next bar night. But I guess it doesn’t always. This ending sucks. Lee deserved, more than most I know, to go out fat and happy with a smile on his face. He was a mensch. I’m going to miss him fiercely.

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.

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.