
No title available
sheepfilms

★

祝日 / Permanent Vacation

if i look back, i am lost

roma★

titsay
art blog(derogatory)
h
todays bird

shark vs the universe
almost home

izzy's playlists!
Monterey Bay Aquarium

❣ Chile in a Photography ❣
🪼

PR's Tumblrdome
cherry valley forever
Sade Olutola
RMH

seen from Japan

seen from Malaysia

seen from Brunei
seen from Germany

seen from South Africa

seen from France
seen from Bulgaria
seen from United States
seen from United States
seen from United States
seen from United States
seen from United States
seen from United States
seen from United States
seen from United States
seen from United States
seen from United States
seen from United States
seen from Singapore
seen from United States
@del-fi
we are not responsible for nature
Smug, by Tony Smith. At Glenstone.
homily for my friends
I was lucky to officiate the wedding of my dear friends Kelsey and Ryan earlier this week. I wrote this little homily for them as part of the ceremony.
Photograph by the ever-awesome Eric Steuer
A wedding is a big day.
It’s the joining of two people. It’s the joining of their friends and families, and their friend-families. It’s a piece of minor theater. It’s a party. And more.
So take a moment and breathe it in. Weddings don’t happen often, especially between two people with a community like this. Let’s all savor the moment, that we are here today, in Toronto, with these two, chosen to be part of their big day.
A wedding is also two things we don’t often think about when we think about weddings.
Since we’re a legal crowd it would be remiss to ignore that a wedding is, most formally, a contract.
It’s a contract between two people to fight together against the tides of the world. It’s a contract to push through the hard times. A contract to celebrate the good times. Because when pain is shared, it is diminished, and when joy is shared, it is increased. A marriage is an agreement to share as deeply as it’s possible to share. As Dorothy Parker once noted, it’s an agreement to sit amid bowers of neuroses, and match psychoses. Marriage shares everything.
Since we’re all kind of about sharing here, let’s recognize and honor that commitment to share.
But a marriage is also about forming a new entity – a “we” that gains legal status in a wedding. It’s a status that people have fought and died for the right to have. This moment, now, we are all graced with the chance to watch that “we” come into being.
And those of us here, and others scattered through the world who couldn’t make it? It is our job to help raise that new entity. Because that new “we” comes into the world needing support. And that is one of the reasons we’ve got this ritual, handed down through time, in which a community comes together to watch that “we” be born. Because it’s also up to us to hold Ryan, Kelsey, and their “we” up when they are down. To share their pain to diminish it, and to share their joy to increase it.
We’re part of the “we” – and we should take that obligation to Ryan and Kelsey just as seriously as they take their vows to one another.
And what a joyous obligation that is.
Eulogy for my father
I wrote this two months ago, as my dad died on January 29. but attending yesterday’s climate march pushed me to post it publicly (dad was a co-laureate on the IPCC Nobel for his work on climate adaptation). This one’s for you, Dad.
Dad told me, a long time ago, that he didn’t want a funeral. That if he had anything, he wanted to have a party - that a good party was much cheaper than even a cheap casket. And that it better have good music, good food, and good drink, and it shouldn’t have any speeches.
Now, we’re violating that last request. Because he also told me, the same day, that these kinds of events are for the living. That what we hope to achieve at an event like this is to help us, not to help the deceased. To help us process the loss, to help us integrate the incredibly sudden, and completely final, absence of someone we loved into our new lives.
That was the day of his mom’s – my grandmother’s – funeral. I was in my mid twenties. I’d missed my maternal grandmother’s funeral, living in France at the time, and I never met any of my male grandparents, so that was the first time I had to confront a close death. He was trying to help me, even as he suffered. And those words have stuck with me to this day, and I’m going to try to honor him in this eulogy, but I’m also trying to pass along that gift of assistance. To help all of us through that process.
This was very hard to write. In the end, we realized that for a lot of people, Dad was a certain type of person. A work colleague, a husband, a parent, a friend. But not that many people knew all the sides of Dad. For a lot of reasons, he often kept those pieces separate from one another. But the thing about Dad is that the more you knew of him, the better it got. So I’m going to tell some stories about Dad, so that we can all walk out of here tonight with a more complete picture of him. So that we can integrate the fullness of him into our memories, and keep him there as we process his absence here on earth.
Uncle Dana just gave you a sense of what Dad was like as a big brother. And I have some sense of that time in his life as well. I loved to pester him with questions about where he came from, what shaped him. And he was usually elliptical – he’d answer personal questions with philosophy, most of the time. But I got enough out of him over the years, especially after I became a father as well, to tell you a few things.
First, he loved greenery. I mean, he loved it. He loved the mountains, and the woods. Hated the damn beach, but would do anything to spend summer weeks in Colorado in the high alpine forests, and he loved the green drive to the lab from west Knoxville. It bugged him that Middelbrook Pike got built up, because it took away from the absolutely all-surrounding green. I got him a little lit up on wine one night in Boston, early in my relationship with Carolina, and pushed him on it a little.
He told me that he lived for a long time in dry, dusty places, in a dry and dusty time after the Depression. He talked about being a night worker at the Ace Motel, a disreputable place on the south side of Oklahoma City, and the dust blowing constantly in the wind, he talked about Canyon Texas, he talked about building a cabin high on a mountaintop in Taos (the one thing he loved out of the dry, it seemed), and more. And then he said when he came to Tennessee for the first time, it was almost overwhelming how green it was. That it reminded him of Mason OH, which was the closest thing he had in his mind to “home” as a child, even though he never lived there. That it reminded him of spending a summer in a work camp in Switzerland, which had been an escape from other summers working as an elevator repairman, or at a Sears warehouse. That the simple pleasure of green was actually a piece of his decision to join the Lab back in the late 70s.
He wasn’t as purely rational as he liked to seem, you see. He was just good at hiding his emotions.
Another thing is that Dad was tough as hell. Physically and mentally. I’m guessing that a lot of his work colleagues saw the mental toughness, in his ability to produce work at a rate that seems almost impossible for one person. But it wasn’t just mental.
Dad went through college on an ROTC scholarship, which meant he had to muster into the regular Army on graduation to pay it back with service. He was not a typist, it’s safe to say – he joined the infantry as an officer, he went through Airborne school successfully, and then through Ranger school successfully. Five people died in the Ranger course he took – mostly through drowning while carrying heavy loads and dangerously deprived of sleep.
Dad didn’t like to talk about that experience much. I did get a great story out of him once though: each Ranger candidate was going to be assigned leadership of a commando unit once over the course of seven days, and if you made any mistakes when you were leading the unit, you washed out. Thanks to other candidates making mistakes, Dad got taken prisoner at one point, hogtied and his mouth filled with mud – this was in a swamp, and the regular army guys holding the high ground would get a week’s leave if they kept the Ranger candidates away. When he got his shot, he hadn’t slept in four days. But he was able to keep it together and they took the high ground.
What he talked about was how you could force your mind to override your body, to a certain extent. How that ability was something that distinguished success from failure all across life – to show up when others didn’t, to perform when others were tired, to perform under pressure when others cracked. How that ability came from practice, from willpower, and to a certain extent, from good luck – the luck to be physically and mentally stable. How if you had that luck, it was your job to use it.
We saw that throughout life with Dad, for things as simple as driving through the night to get to the beach. But it was very evident after he got sick. He fought through three surgeries, atrial fibrillation, multiple bouts with pneumonia, a stomach tube that constantly fell out and leaked gastric juices onto his skin, hospital-induced dementia, and indignities that I won’t go into in public. He lost his ability to speak, to eat, to drink – all things he loved desperately. And yet he fought on. He spent the last year of his life writing a new book, called Living With Climate Change, which will be published soon – the beginning of the prologue is in your programs. He finished it just a few weeks before his death.
A lot of people pretend to be tough. Dad taught us that really tough people don’t need to advertise. That you can figure out who they are just by watching and seeing – do they show up? Do they crack? Are they reliable?
Dad always showed up, and Dad didn’t crack. He was tough as nails. The old paratrooper fought and worked til the very damn end.
A third thing about Dad was that he could contain in his head an incredible number of ways to see. He could look at a problem and not be boxed in by one way of seeing it – he was the opposite of a lot of what we have in politics today, in that way, on either side.
When he wanted to learn about something, he would read everything he could get his hands on. He’d read the stuff that everyone read, but he’d also go to extremes to find other points of view, including ones he disagreed with. When I was young I learned my way around a library by helping him chase down books, papers, chapters, cartoons, you name it – and I learned at the same time that being able to hold several positions in my head at once meant I could see way more dimensions than people who got trained to hold one position.
This is the skill that let him see the long game, which let him marry complex theoretical work to real world implications. That’s what let him look at the Green Revolution in India – a revolution about food crops – and see a future world full of crises for energy and land and sustainability. That’s what let him look at climate change and immediately jump to thinking about what it meant for humans to adapt to that change. That’s what led him to think about how geography impacts terrorism, and a full decade of deep work with the Defense Department.
Because he didn’t want to just think about a single position and write a paper about it. He wanted to use his understanding to improve people’s lives. To anticipate problems and have solutions sitting, ready, when they were needed.
He would have cackled at the news in the past two weeks of the infrastructure failures at the Oroville Dam in California. That’s precisely the kind of thing he anticipated, the way that climate change meant normal things like droughts would get more extreme, and that the end of the drought would mean even more extreme rains, and that infrastructure built for non-extreme events would therefore fail in predictable ways that could be planned for. And he loved being right – it meant that he had stared through the problem and seen its bones.
Dad was also a deeply artistic guy. He channeled a lot of that into work – you can see it in his writing, especially his writing for broad audiences. But there was a deeper artistic sense in there, one that not everyone maybe knew about. He consumed more music and more books than anyone I’ve ever met – across a dizzying array of genres and styles. He read high literature and low literature, fancy books and dimestore mysteries. He loved latin jazz, bluegrass, new Orleans music, rock and roll, classical music, anything you could imagine.
I think if he’d been a little more willing to risk himself he’d have been a lot more of an artist. He had perfect pitch (if he hadn’t gotten stuck playing trombone he might have stuck with performing). And he was an incredible writer. He wrote a small history of his family tree for Lisa and me nearly twenty years ago and it’s full of just incredible sentences, like this one about a small town called Pikeville KY, where they lived when he was young:
“I remember Saturday movies, (with suspenseful serials, sort of young-male-oriented-soap-operas), sledding in wintertime, coal fires in the fireplace in the winter, Christmas time in the local Presbyterian church (the minister’s daughter was my fourth-grade girlfriend!), Kentucky basketball on the radio, and the taste of honeysuckle.”
That’s the way a writer remembers a place. I wish he’d written more about non work things. He told me once that he wanted to write novels but was afraid of being as honest as he’d need to be for them to be good.
He loved fine dining – for the past 25 years, he reveled in taking me and Lisa out to dinner in DC and elsewhere, always showing up with detailed ideas and research on restaurants, dishes, even routes for the taxicabs. He loved to eat. Losing that ability was one of the great insults of the past three years. And boy did he love wine. He’d be glad we have it tonight. Some of my best memories with dad involve food and wine, and I’m deeply sad that Noah won’t get to know him that way as he grows up. It’s weird to think I’ll play that role for him, because Dad played it so well.
He was incredible with kids. He was a very physical grand-dad – down on the floor, rolling around, playing the fool, doing anything for a laugh. One of his favorite yearly traditions was to spend November collecting details about what everyone was into that year, and assembling incredibly personal stockings for each of us on the couch, full of personal touches. He spent a hundred hours a year on it, easily.
Now, he wasn’t perfect. He was human, and no human is perfect. I won’t dwell on his flaws, but I will say that God help you if you got in the way of his trips to WalMart. He’d start snorting – he always did that when he was good and mad – sounding like a congested dragon. And his very toughness and emotions could sometimes blind him a little bit to the struggles that characterize our own lived experiences – he told me that himself once.
But that toughness was on the balance something that was a good trait for Dad. It carried him through the fight with cancer. He was always grateful to his care team – Dr Carlson, Dr Stephenson, Dr Locasio, Dr Mancini, just to name a few – and the entire universe of everyone who supported him as he tried to find his way back from the abyss of summer 2014. Even in the hospital, stripped of his ability to speak or eat or drink, he would grab the white board to ask a nurse how he or she was doing in writing.
OK, I’m pretty sure that if he’s somewhere watching, he’s making the dragon breathing. He didn’t want long speeches, or a funeral. He wanted a party with live music and I’m now officially in the way. So I’ll wrap up.
I don’t know how Dad would have felt about this. I hope he would have liked it. But, as I said at the start, he also told me these events are about the living. We retell the story of the one we have lost, and fit our own stories into that story, as part of how we process and integrate their loss into our ongoing lives. And in that memory, we can keep a piece of them alive, in us, by connecting our stories to their stories. By telling those stories over time, looking at those photographs, watching those videos, eating those foods, reliving the memories.
So thanks to all of you for coming. Don’t stop telling stories about Dad. Don’t stop looking at photos, or watching videos, or eating those foods. Because as long as you keep him alive in your mind and your heart, he’s not gone. And that’s the best possible way for us to honor him – to say his name, and to live like he lived.
Failures of imagination
I spent most of this week at Health Datapalooza, the big annual event that brings the health IT industry and the health IT feds together here in Washington DC. It was as wonky and startupy as ever, and I’m ever-grateful to Academy Health for letting me be a part of it.
As is usual, I was going on about informed consent and ethics and the idea that we don’t have to toss those two things over the side to get innovation out of health IT, especially health IT that moves closer and closer to the citizen. But I felt alone a lot. Many folks didn’t even want to use the word citizen, preferring “consumer” or “user” instead. There was a sense among quite a few people I spoke with that privacy was a problem to be gotten rid of, sand in the gears of the soon-to-be-realized brave new health world.
And that bugs me a lot.
We gave away our shot at an ethical consumer technology world a while ago. We don’t have to give this one away.
The failure is evident every time I see a story about an amazing technology. Design a robot that can unfold inside a kid’s stomach to get swallowed batteries out? DONE. Design software that respects privacy? WHOA SLOW DOWN THERE BUDDY.
This failure of imagination is the most significant threat to health privacy - the idea that because we threw it away in the software stacks that we have to throw it away in the health stacks.
It’s a failure that comes from entrepreneurs, who don’t see the opportunity in treating people like citizens with rights instead of potential customers to be targeted. It’s also a failure that comes from investors who can’t imagine a business model other than “data is oil” - with no thought to the network effects of treating human beings literally as oil wells (without even the grace to share mineral rights - my Texan family would never stand for that).
Imagine bigger, folks. Try integrating ethics into your design. Try thinking of participant-centric as meaning “inviolable rights” rather than “targeting for purchase.” You might be surprised to find that ethical designs work really well, and that you don’t have to treat a human being like an oil well to innovate in health IT.
Hey, this tumblr is still here!
Fund the Prize - ALS DREAM Challenge
I don't often ask y'all for financial support. But this is important.
My employer, Sage Bionetworks, is partnering with Prize4Life and the DREAM project to run a computational challenge in ALS.
You may remember ALS from this summer's insanely viral Ice Bucket Challenge. If you took the challenge but never donated, here's a good chance to do so. And you'll know exactly where your money is going, unlike most donations!
We are trying to raise $37,000 in prize money. We'll use the funds to set up prizes to be won in a challenge format. We'll ask brilliant minds from around the world to develop computational tools that predict why it is some ALS patients live longer than others, and to figure out why symptoms are so different for some patients than others. 100% of your prize money will go to Fund the Prize.
This isn't particularly risky, because we know it works - it's been done before. In the first ALS DREAM Challenge, a data analyst from a marketing company, who had no life sciences training, shared the lead prize with a lawyer and statistics professor from Stanford University. Their innovative tools were published in Nature Biotechnology and outperformed the estimates of more than 12 expert clinicians of ALS. The first Challenge's outputs will allow future clinical trials to be run with 20% fewer patients and reduce costs by at least $6 million per trial.
If we knew which body parts would be affected and how quickly motor and neurological functions might deteriorate, and the reasons why some people's progression is different from other ALS patients, families could make clearer decisions about how to live their lives at each stage. This kind of knowledge would also help to target clinical trials on ALS sub-groups, advancing new treatments or a cure faster and more cheaply.
The innovator that develops the best software-based mathematical model to stratify and predict these ALS sub-groups will receive the prize your donation supports.
Take a few minutes and support the Fund The Prize project for ALS DREAM Challenges.
Nature's Shareware Moment
So, Nature said a thing about public access tonight. Everything is free to read* they say.
But there's an asterisk, pesky and persistent, next to read. And it's a big one.
The asterisk is that you can't do anything but read the document, and you have to download use their proprietary reader software in order to read the document, and you have to hope that someone who has a subscription or is a journalist is kind enough to share a link to the document that you want to read, and if you try to do anything other than look at the document passively on a screen you're basically gonna get sued for copyright infringement.
I got contacted in advance for my take, and I really did think long and hard on this. I wanted to be impressed. I wanted to believe in it. I wanted to be courteous, to find common ground. And I am certainly pleased they included the backfile of old papers in their strategy, a longtime gripe of mine.
But I can't praise. I just can't.
The ability to beg for a link, to be opened in a closed ecosystem that literally disables core functions on your device like "print" and "screenshot"...that's not an advance. It's a canonization of a system that privileges the wealthy academic. It's a canonization of a system that says it's ok to pay for documents while simultaneously losing all rights. It's a canonization of a system that says a small number of companies not only do control the world's knowledge, but should control all the world's knowledge.
Think about it. The people who are allowed to share the link are people who have paid enormous sums for the literature...yet they can't send you something you're even allowed to print on a crappy deskjet.
The right to index the literature so we can have scholarly search that doesn't totally suck? Not here. The right to cross-reference the literature to databases? Absent. The right to start companies that can outdo the famous publishers on both of these fronts? Explicitly forbidden.
And we need those rights. As Dave Clifford noted...
@wilbanks There's no reason a computer would ever need to read a pdf instead of a human. *Counts the # of publications last year.* Oh wait.
— Dave Clifford (@DCDave)
December 2, 2014
So let's do count that number. How many papers do get published? How long would it take to read them all, with no rights to get help from computers? Jason Priem has a handy chart for us.
That's, conservatively, 100 articles per hour per day with no sleep ever to process a year's worth of text...four years ago.
The lack of rights to re-process the literature is why science literature search sucks so very badly. We need computer assistance to process it, because the scope is beyond any one person's mind. And open access would immediately create a market segment ripe for investment and competition.
It's perhaps the biggest functional argument for open access in my mind. It's a place where value can literally be created overnight. And it's impossible under this announcement.
Apple's iTunes is explicitly referenced in the article above. What's not referenced is that this is what iTunes used to be, not the iTunes we have today. iTunes used to be full of technological protection measures that are still messing up people's music collections five years after Apple stopped protecting files.
Think about it. Even Apple doesn't lock you down to read-only.
Attaching digital locks to the files wasn't good enough for consumers of music. Yet we are to accept it for, quite literally, the canon of western scientific knowledge?
Well, I guess it's progress, because it shows we've made enough noise to force a massive player into what they think is a massive change. But open access, this is not.
UPDATE: Richard van Noorden notes that you don't have to download the software to read in the browser view. I've updated the third paragraph to note that, with a strikethrough my original text. I've also edited for clarity a bit, and included a sentence about the policy's access to the backfile of literature in the fourth paragraph.
Informed Consent, Post-Snowden
We blew our chance to build a data world that truly empowers individuals already with consumer data and surveillance. We screwed it up well and good. We let the argument be that functionality - features, free stuff - is a solid, ethical, and most of all, normal trade for data that describes us in intimate detail. We let the companies that create that functionality use that intimate detail to sift our mail for us, to recommend sweaters to us, to share with the surveillance state and watch us.
But we haven't yet blown that chance with health. Health data is frustratingly illiquid, a truth that frustrates so many attempts to bring consumer level functionality to the health care system, especially here in the USA.
But the same structural barriers to data liquidity that are so frustrating have given us a gift, the gift of time. Time has revealed exactly how abusive "data liquidity" can be when it's controlled completely by large corporations, by an app economy that uses design to make us think as little as possible about the tradeoffs involved with our data. If we already had it in health, do you think it'd be any more individually empowering?
We have a chance to do it right.
We have a chance to build a health system from the inside out around mobile devices, around commodity prices for clinical data, around cheap DNA sequences, around electronic health records owned by the individual rather than the health care Borg.
It's no small irony that we can use the very same devices that have been revealed to relentlessly surveil us without agency to relentlessly surveil ourselves for health and pool that data to advance our collective understanding of health. And it's going to happen, one way or another. There's too much money at stake.
But the choices that get made in what we measure, and how we measure, encode our politics. We can measure depression with the secondary measure of movement, for example. Do we take in GPS data? If we do, do we measure the latitude and longitude all the time, or the percentage change from a single point over the course of the day, which in turn is deleted every day? One of those choices is more exploitative than the other. Choosing one is a clear proof of how we think about the individual's rights.
Doing research this way involves risks. Some of those risks we know: disclosure, loss of privacy, risk of re-identification, discrimination, bullying. Some of them we don't. But clinical study has never been without risk. Informed consent exists because we believe that "normal" people are capable of balancing the risks of a study against its benefits, and exercising their agency to decide to join or not.
We can't transition to a new kind of science based on individual engagement if we don't agitate for people's rights to share their data. We won't be able to do that until we start to loudly and regularly proclaim, basically, that people can - should - must - be trusted to process complex concepts about research and make an informed choice to participate.
Right now we run informed consent as a zero sum choice, a form written by a doctor, edited by a lawyer and a committee, no agency at all besides yes or no. The forms are typically long, filled with boilerplate that limits the liability of the organizations involved, and ban re-use of the data. Generally, we allow clinical research to treat the individual involved like a piece of land on which valuable oil sits waiting to be extracted and piped away. That's what the participant gets to slog through, and it has a predictable impact.
That's unacceptable. We have an entire industry devoted to making complex things engaging, as long as those complex things make it easier to purchase goods and services. We need apply the same design tools towards the illustration of complex concepts like de-identification, risks of data disclosure, and benefits of data sharing and collaborative analysis.
We need a visual language for the concepts of informed consent and research. We need technical frameworks that encode the agency of the individual: return results to participants, allow them to connect with the researchers, to connect with other participants. We need new norms and structures that impose obligations on data users: to be good stewards, to respect clinical study as partnership with real people, to be trustable.
We can do much of this with good informed consent. Informed consent is a vector into the entire engagement of people in research, and it's uniquely a vector that helps the open society world compared to the corporate world.
And that's another reason to do not just act on this chance, but to act quickly: if we wait until the health care behemoths get to it, we can expect informed consent to get road-graded down to a one-click. And that'd be a damn shame.
(derived in part from a talk given at the Broad Institute yesterday)
Participant Centered Consent Toolkit - Coming Soon
Coming soon, stay tuned...
The participant centered consent (PCC) toolkit is just about ready for its first release next month at Sage Bionetworks.
The toolkit is built for people who are designing clinical studies and who wish to make their informed consent user-centered, rather than document-centered. It contains the building blocks of a visual, interactive approach to informed consent. The PCC toolkit lets its users create visual summaries of consent forms, mapped to key underlying text, for use in software or print.
The goal of the PCC toolkit is to transform the concept of consent from a signature on a legal form to a process that engages participants, and to allow as many people as possible to engage in consented studies.
We'll be providing several elements in the toolkit.
a visual dictionary for informed consent - icons that represent the ways that data might be gathered or used;
workflows for visual informed consent - a set of designs and patterns that can map an informed consent document to the visual dictionary, for use in various consent interactions;
sample clinical documents - a template informed consent form and instances of toolkit as implemented in a successful IRB filing for an observational clinical study;
implementation support - step by step instructions on how to use the toolkit, a sample piece of workflow softare, detailed FAQs, and more.
The PCC toolkit will be licensed to the commons and will be usable in any context, by any user, for any purpose, as long as attribution is provided back to Sage Bionetworks. The EDM Forum was a key supporter of the toolkit, and essential to its development.
More to come. We're excited. You can check out a recent presentation to see an example of the toolkit in action - start on slide 21.
Update on PLC 2.0
I've been quiet on the Portable Legal Consent front for a bit, but there's enough going on that it feels like time to make a public update on where we've been, where we are, and where we're going.
First, the study we've been running at Sage Bionetworks - the Self-Contributed Cohort - has yielded a lot of data. I've got a chapter in the Privacy, Big Data, and the Public Good book coming out later this year that goes into some detail, and we'll be preparing a paper for peer-review later in the year as well. The short version is:
Deploying interaction design is incredibly effective at increasing informedness in an e-consent context. We can get levels of informedness, even on complex concepts, that can outstrip traditional methods of consent. That's the good news.
Most people do not yet have enough data about themselves, or good enough data, to feed computational modeling processes that generate insights. Despite all the advances of patient-centered research, direct-to-consumer genomics, electronic medical records, and more, the data simply aren't yet rich and clean enough to make the big data analytics tools really sing in a citizen-contributed cohort. That's the bad news.
If we want the kind of prediction engines in use by Amazon or Facebook or Google, which we use to figure out why drugs work in arthritis, generate insights for personalized cancer therapy, predict Alzheimers progression, and more...we need the kind of rich, clean data that comes out of structured study.
Clinical studies are the best structured place at the moment to get rich, clean data about individuals to feed computational reuse.
Given these results, we have turned the revision of PLC towards the study itself. We have been working in partnership with the Electronic Data Methods (EDM) Forum as a Collaborative Methods Project. The EDM Forum is funded by the Alliance for Healthcare Research and Quality and is a multi-year project to build capacity for networks of actors working in health care.
We conducted a series of interviews under the EDM's guidance earlier this year as part of an in-depth interaction design process. We talked to giant clinical systems, hospital surgical centers, patient-powered networks, clinical data networks, patient advocates, and more. And to get to the million patients I've always wanted under PLC and make their data actionable for computation, we need to infuse PLC into clinical studies. This creates a requirement for decentralized approaches, which fits nicely with most of my underlying beliefs about networks (they are either dominated by a dictator at the center, or they're built at the edges by lots of people using standardized tools - take a guess with my preference!).
Clinical studies happen locally, and their protocols and consent forms are approved locally. Think of it as thousands of little pieces of software - legal code - that don't interoperate. Thus, PLC 2.0 is not "one consent form to rule them all." It is instead designed to make it easy for those writing the thousands of little pieces of legal code to add on functionality: getting the data from the study into the cloud for secondary reuse, and empowering patients to receive and transmit a copy of the data about them to other parties. It's akin to a software developer's kit, but for legal code.
The beta of PLC 2.0 (which we're calling the PLC toolkit) will be released in the fall of 2014. The toolkit isn’t going to contain any technology in this release. It’s instead a set of text documents containing consent language for various classes of data, wireframes for those classes of data, implementation guidelines for investigators running studies, and educational materials for institutional review boards. Supported data modules include mobile devices, wearable sensors, electronic medical records, labs data, and genetic sequences. All the files will be available under the CC-BY 4.0 license, so they'll be infinitely reusable by all parties for all uses as long as we get attribution.
I expect to see a few mobile applications using the toolkit as part of Sage's BRIDGE project and partnerships coming out this fall. And we are conducting private alpha testing now and welcome anyone who wants to get involved and review - email me for details.
In the interim, here's a teaser that I showed publicly at the last EDM forum meeting. It's the dashboard that sits inside mobile applications and manages a participant's ongoing consent inside a clinical study. This is the kind of wireframe we're designing.
Thoughts on Goetz's The Remedy
I've been devouring The Remedy by Thomas Goetz since it came out last week and finished it on a series of long flights this week.
It's a lucid, accessible popular science book. It's primarily about two men - Robert Koch and Arthur Conan Doyle - engaged in a debate over whether a tuberculosis cure was indeed a cure or not. If you're even a little interested in the late 1800s, popular science, the origins of Sherlock Holmes, or the emergence of medicine as a science you'll probably enjoy it.
For me though, I was most struck by the first few chapters and the remarkably clear unfolding of how certain moments in scientific time can be moments of massive and rapid change. Goetz traces how Koch, a country doctor in Germany with big dreams, integrated theoretical, methodological, and technological breakthroughs to become one of the most famous scientists in the world.
This integration of breakthroughs fascinated me. The theoretical breakthrough was germ theory, and Koch didn't invent it. It had spent decades burbling from the fringes of science towards the mainstream but was still well on the outside. It threatened the theories of the famous, eminence-based scientific system. And it hadn't been demonstrably proven. But it was a powerful enough theory that despite the shutout, it continued to develop, quietly, on the edges.
The methodological breakthrough was Koch's. He figured out how to use pure cultures (the Four Postulates) to determine the cause of infectious disease. In so doing he helped cement germ theory as a cornerstone of modern science and medicine.
The technological breakthroughs laid out in the book may be my favorite part. I knew about the emergence of germ theory, I knew vaguely of the four postulates, but I had no idea of the kind of rapid, on-the-fly invention that the emergence of the culture-based methodology spurred. It is straight out of Eric Von Hippel.
The example that sticks with me from the book is such a simple one on the surface: the petri dish full of agar. But it arrived after Koch began culturing anthrax in the aqueous humor of a cow's eye between glass, moving to gelatin on plates, moving to agar on the advice of a jam-savvy scientist's wife, finally to round plates with upraised edges. This kind of evolution of technology to support methodology to support theory is packed onto most every page of the first few chapters and just blew me away.
I'm fairly convinced that this is a pattern we're in the middle of right now. What struck me reading The Remedy was that I think we can identify the methods and the technologies - sequencing, causal statistical analysis, self-tracking, all the stuff that is on the bingo card of a "Big Data" conference attendee.
But I wonder what the theory is. Goetz clearly makes the point that scientific progress is only obvious in retrospect. In the moment, it's messy, competitive, sometimes downright personally nasty (the Pasteur-Koch animosity is epic!). The methods can seem so much more obvious in the moment than the theory.
I do what I do in the belief, naive though it may be, that the breakthrough methods and technologies of the last 20 years are on the edge of allowing us to prove or disprove new theories about the causation of chronic disease, as Koch's time did about infectious disease. And it seems obvious in retrospect that germs would emerge as the causative theory. But at the time, it wasn't. Just like it wasn't obvious that ulcers were caused by infection.
So what are the theories of chronic disease that are going to be embarrassingly obvious? What are even the candidates? I wonder.
Is It Research? Or Is It Connecting To People?
(disclosure: This post is about Jane McGonigal. I've met Jane in person twice, and we follow each other on twitter. we have spent about 10 minutes total in each others' company - we are friendly, though we don't know each other well.)
Jane McGonigal, a well-known gamer and advocate for the good that games can bring to people's health, put up a webpage recently. It's titled "Play, don't replay!" and it's intended to broadcast the existence of a study that established a small, but statistically significant, connection between playing games like Tetris and easing post-traumatic stress disorder.
It's a neat theory. I spent some time in treatment for traumatic stress disorder and looked into eye-movement desensitization and reprocessing as a therapeutic intervention, and there is some real evidence that EMDR works. It makes intuitive sense to me that games, especially ones that inspire a visual twitch like Tetris, could trigger some of the same effects.
Jane came under some withering criticism for putting up the page. Much of it is gaslighting and I won't link to it. The criticism that interests me comes from Brendan Keogh, who lists himself as a PhD Candidate in Game Studies at RMIT University in Australia, and who called the page "shockingly unethical and irresponsible."
Here's the thing. What's ethical or responsible depends on where you live, where you work, and what your goals are. What's ethical is changing on us, in real time, thanks to social media. And charging that someone is shockingly unethical and irresponsible, as Brendan did, is serious stuff. It's about the worst thing you can say in academia (perhaps only plagiarism is worse).
But here's the thing. It's not clear to me that the page constitutes research under U.S. law. I can't see anything on the page that says the point of the page is "a systematic investigation . . . designed to develop or contribute to generalizable knowledge" - which is what our laws define as research. It's not systematic. It's not promising to publish results. So the law's ambiguous to me here.
And it's really important, this definition. Because the whole point of the criticism seems to be about research ethics (as opposed to, say, Aristotle's Ethics). So whether or not this is research is really relevant to its ethics.
Besides governing law, institutions control for their own liability, which means that Game Studies researchers would probably have to get institutional review for something like this even if it's not research under the law. But Jane doesn't work at a research institution, which means she's not subject to institutional review. If this had been a Huffington Post piece promoting the article and asking for people to leave their experience in the comments, it wouldn't be much different.
Now it's entirely fair to question that Jane should have taken some more time to think about whether or not she's covered, if this is human subjects research, if she should get independent review. If her internet stature imposes an obligation. I think that would have been smart, and I'll come back to that later in this post. But that's the thing. It's arguable.
And arguable is a long way from "shockingly unethical."
Reading the piece it feels like there was a pre-existing allergic reaction to the "games evangelism industry" that colored the reaction to the page in question. The first version of the piece even added an Upworthy twist to the page's description of "one simple technique" by converting it to "one simple trick" (this may be an example of priming).
I have run into this allergic reaction for years in the "harder" sciences (biology especially). There is a real distaste for connecting directly to people via social media, a distaste that I believe has at least some origins in ethics training. I'd imagine Brendan has had ethics drummed into him by his university (likely the Australian version of research ethics, which does seem to have a larger idea of research than US law).
Research ethics require us to get informed consent, assess risks and benefits, and perform selection of subjects - none of which are explicit in Play, don't replay. And as someone who works nearly full time on informed consent, that does nag at my senses. I'd like to see more of those elements drawn in, more of a sense of responsibility incorporated.
But I can't get past the idea that this isn't clearly research. It's talking to people. And the internet has changed the way we talk to people. Talking to people over twitter reaches more people than a clinical trial if you're Jane. When Amanda Palmer has a twitter chat about sexual violence, it reaches several orders of magnitude more people than a sexual violence research study.
That reach itself doesn't make it a study.
I also can't get past the idea that this isn't clearly not-research either. There's enough dancing near the creation of knowledge that, with the right eyes, one could say this is a page that should have been reviewed by an ethics committee.
I would love to have seen both parties do something different here.
I think Brendan's accusation of shocking unethical irresponsible behavior ignores local context about what is research and where research ethics kick in. If you're going to criticize someone's ethics, you must first attempt to understand their context. I see no evidence of that in the criticism, and that bothers me.
I also think Jane's page brushes close enough to research that she should have run it past someone (not me, someone who does social science and social media) to get an ethical review. I do not think it's unethical, though.
The real reason I think she should run it by ethical review is because of her reach. I think that reach imposes an obligation, an obligation that has never existed the way it now exists.
There is a real possibility for abuse in this space by those who have social reach. Indeed I think this possibility is part of the criticism leveled by Brendan, as he repeatedly notes that he believes in her good intentions. The shockingness here is not attributed to intention, which is an interesting point of intersection. Jane could be a leader in how to use social reach ethically. I would love to see her do it - there's not a lot of candidates who could do it better than she could.
But in the general context...the line between "just talking to people" and "doing research" is dissolving.
We never had to even deal with that line. It was there because only credentialed researchers could hit scale in talking to people. They could raise money, they had structures to recruit. Now Jane's got the structures to recruit, and it's costless to contact. Now talking-to-people can brush right up against the edge of doing-research, with all the attendant ethical questions swept up into the engine, with none of the systems functioning and none of the people talking to each other about the real problem.
We need to have a serious conversation about what the dissolution of that line between research and conversation means. Research has much to teach conversation. But - and this is essential - conversations at scale have much to teach research. I would submit that conversations at scale are simultaneously the most powerful form of research that we have yet invented and a form of research that is totally outside our ethics, because it is so new.
This needs to be a two-way street if traditional, university-oriented research wants to survive. Because conversations at scale are going to eat it alive if the academy tries to pick the wrong fight.
Open As A Service
The Synapse software we run at Sage Bionetworks is open source software.
That's a statement that has a certain set of expectations that we provide you, the user, with some serious powers: you can download the code from github under the Apache 2.0 License, you can grab our bug tracker. We've invested in developer documentation.
That's what "open source" means. You can get our code. You can change our code. You can redistribute those changes. You can sell our software and never tell us or send us a check. There is an Open Source Definition that spells this all out clearly, arrived at via community consensus, and long used to adjudicate claims of open source-ness.
There's a rub, though. The definition is based on the distribution terms of the software - the legal tools that wrap around the code and govern its use and reuse. And we comply with all those terms.
But Synapse has been built from the bottom up as a cloud-based service, Our users love that aspect. Our developers develop for that. And that creates a very interesting conundrum. We run a product that is clearly, legally, technically open source. But the definitions that govern our ability to make that claim about a piece of software don't reach anywhere into the operations of that software - the way that we run it.
This has big long-term implications. It's thus possible to market an organization as an open source software organization, yet to architect a radically closed service built on it. It's not what we do at Sage, or where we're going, but it's something that we have learned, almost by accident, that's entirely doable. The Free Software Foundation has written about some elements of the relation between services and freedoms. But there's not a roadmap for an organization that wants to run an open service for free.
We need to watch out for for Fauxpen Source here. Not everyone can stand up an Amazon instance and run a cloud service, even if they've got the license rights to do so. Not everyone has steady internet. Not everyone will pay attention to the details when they see an open source stamp. Not everyone will pay for open services.
And costs are a big part of the rub. Open source in the old technology model is inherently scalable at a fairly low cost other than the costs of development, which can be either paid or volunteer. The usage of the software doesn't add much cost. If everyone is downloading and running code locally, then you don't need a big budget for users and their usage. In a service context, our costs scale with our users - maybe linearly, but given that we store genomes and genome sequencing is cheaper every day, maybe exponentially.
Open as a service is where we're going. But no one has a map yet. If anyone's got ideas, please get in touch.
Larry Page, TED, and Pooling Our Medical Data
I'm sitting in the Vancouver airport winging home from TED 2014. It's still going on, but I only had a day pass for yesterday as we gathered DNA samples for the soft launch of the Resilience Project (a collaboration between Sage Bionetoworks and Mount Sinai).
I don't often take DNA swabs, but when I do, I kneel on the floor and furiously barcode TED attendees DNA swabs. Elissa Levin, Stephen Friend, Lesa Mitchell, Diana Friend. Not pictured: Linda Avey, who was on the floor with me.
Thanks, TED (and especially Priscilla, the ever-gracious speaker concierge) for letting us launch our project!
As we were decompressing, Charlie Rose started interviewing Larry Page. It was a very wide-ranging interview, but the part that stuck out to me was Page's desire to have a massive pool of medical records available for research purposes.
This is obviously near and dear to my heart, and to many others. TechCrunch picked up on it and was gracious enough to quote me in their coverage.
But it was the phrasing that stuck like a splinter in my brain. At no point was this mass of records about the people referenced by those records. It was as if the data had no relation to the people other than as grist for a vast mill, something to be turned into insights that only then would help people. There was a desire for total disconnect between the medical records and the very real, very human beings whose cholesterol and hemorrhoids were described therein.
This is often done in the name of protecting the privacy of those people. But as we've seen, anonymization of records doesn't mean the records are anonymous in the hands of skilled attackers.
I think the real reason is that it's just easier. It solves for the privacy laws, if not the privacy problems, and it lets those analyzing the data treat it as an economic and computational resource without moral dimensions. I don't blame a company for taking that stance. It's easier.
Easier isn't always the answer. My own TED talk, from 2012, was about looking into the mirror and making informed consent the centerpiece of pooling medical data.
We can do this. It's what underpinned the first version of the Portable Legal Consent study. It's underpinning the Resilience Project. It's underpinning the Bridge platform at Sage.
But it won't happen - we won't do it - if fall into the trap of thinking about "50,000,000 anonymized records."
One medical record is a person. 50 million is a statistic. It's a lot easier to toss moral and ethical concerns away when the numbers get big. But no matter how many records we have, each one came from a person. And she deserves a voice, a consent, an engagement, with the research she empowers.