A thoughtful and useful report on the Aaron Swartz tragedy

This (http://swartz-report.mit.edu/docs/report-to-the-president.pdf) is a report that Professor Abelson helped author on the behalf of MIT. It is chock full of lessons for education institutions, libraries and the larger academic ecosystem, including the ancillary industries. Although section V is focused on questions for MIT, many of those same questions will find wider resonance.

Epidemic or epiphenomenon?

A number of crowd-sourced infection monitors such as FluNearYou (by our own Dr. J. Brownstein) have reported an apparent upsurge in influenza-like illnesses over the last week. The CDC has not yet reported the same trend. If the CDC then confirms this early warning, it will represent a transition from proof of principle of the citizen as health monitor (see here and here) to general public health utility. If not, then we may be witnessing an outbreak of hypochondria.

Take this ontology and shove it. Or, why classification matters.

I was recently called out by one of my colleagues for saying that ontologies were boring, this despite my own doctoral work on knowledge representation. Motivating my glib comment was an image of a group of pasty-faced individuals gathered around a large boardroom table and discussing which angel fit on which pin. Events from this past weekend are a reminder why such glibness is not helpful.

The American Psychiatric Association has just approved a set of updates, revisions and changes to the reference manual (DSM5) used to diagnose mental disorders. Among the changes are those redefining the inclusion and exclusion criteria for autistic disorders. By changing which children are classified as having an autistic disorder, parents will be made to feel more or less comfortable having a child carrying the diagnosis. Just as importantly, insurance companies and school programs might shift their criteria that determine which child and family gets what kind of support and at what cost. In the near term, clinical trials for the treatment of autism may not include the same patients as they would have prior to this retaxonomization.

So, are ontologies boring? Perhaps. But they certainly belong to the class of hugely important societal constructs.

Hat tip: David Osterbur.

Hungry for DNA Games?

Thirty teams world-wide are apparently hungry enough and willing to contribute to making genomic medicine possible. Their efforts will help reduce to practice a game that to date is only within reach of star teams. May the odds be ever in our favor.

Mad Men and Mad Nerds

Should we enable the following conversation between any website and your web browser (e.g. Safari, Internet Explorer, Firefox, Chrome)?

Your web browser: "Hello website potentiallyInteresting.com."

Website: "Hello web browser."

Your web browser: "Dear Website, please do not track who I am. Do not even try to remember that I came to visit you."

Website: "You mean you don't want me to track you even if though you did not switch on all your privacy controls such as switching off acceptance of 'cookie' files?"

Your web browser: "That's right. You are an upstanding website and when I say to you 'DNT:1" that means that I don't want you to track me. That's what the user who controls me wants."

Website: "I certainly am upstanding and I respect your statement of the user's wishes. Consider this whole visit forgotten."

Your web browser: "Thanks for your understanding."

Website: "Do I know you?"

It turns out that there is a great deal of controversy about these five characters: DNT:1. On the one side are the user advocates who argue that websites should honor the do not track directive. One the other side are the companies who fund large parts of the web infrastructure because of the advertising revenues (~70 billion) that are generated by being able to track the traffic of users across their Internet properties. These companies now wonder where their investments will go if few users allow their websites to track them. Their concerns are not misplaced. After all, how many of us would choose to keep commercial breaks on broadcast television if all we had to do is to flip a switch? Of course, those same companies could choose to have the following alternative ending to the above conversation:

Website: "I certainly am upstanding and I respect your statement of the user's wishes. But we have to pay the bills. If you will not allow tracking, I just cannot show you my contents. Sorry."

Your web browser: "OK then. I'll let my user know that she has to allow tracking if she wants to see your contents."

Website: "I will be waiting. But don't expect me to recognize you."

Ultimately, the debate is going to turn on the valuation that the public places on its autonomy and privacy relative to the broadest access to web content. For those of us in the arts, sciences or businesses of curation of the various forms of knowledge and data, the outcome of this multi-billion dollar debate will affect our work for decades to come.

Hat tip: Ben Adida

City as organism

This video from Geneva, Switzerland is a beautiful instance of the repurposing of data. Shown are the data flows between cell phones across the city over night and day. This glimpse of the interactions over time also suggests new frontiers in real-time epidemiology. What if these (anonymized) data could be tagged with symptoms (e.g. cough, sneeze) could we track the spread of infections? Public health would then start to look a lot more like intensive care medicine, providing real-time monitoring of cities or nations (taking the "pulse" of the population, evaluating the activity and coherence of its "neural" activity). Will there be a new research and medical discipline that fuses the sciences of population ecology and population health? And should populations be empowered to forego such intensive study?

(Hat tip: Joshua Parker).

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Ville Vivante from Interactive Things on Vimeo.

p.s. As a someone who grew up in Geneva, I was quite surprised to see a lot of activity at 2 AM. Is this the consequence of the Swiss work ethic?

Let's bring genome-scale sequencing into the clinic—safely and responsibly

Children's Hospital Boston today announced the launch of the CLARITY Challenge, a $25,000 competition intended to advance standards for genomic analysis and interpretation and the reporting of clear, actionable results to clinicians and patients. The competition marks the first time a healthcare institution has sent out a broad call for the development of consistent and clear ways of applying genomic insights to everyday pediatric and adult patient care.

CLARITY (Children’s Leadership Award for the Reliable Interpretation and appropriate Transmission of Your genomic information) competitors will be tasked with discovering the unknown genetic basis of the disorders faced by three pediatric patients and, in the process, create best practices for interpreting and presenting genomic sequence results to patients and their families and physicians in meaningful ways that can help guide healthcare decisions.

Ancestral betrayal

We share many things with our ancestors, including a fraction of their genetic code. This genetic link to the past has further invigorated an already large industry and hobby in the exploration of genealogy and historical provenance. This piece from today's news, shows how these same records can be used to leverage your ancestors to identify you. In this instance, a murder suspect is potentially fingered by his ancestors from the Mayflower.

Hat tip: Ben Reis

Weighty searches

Billions of Google searches may seem to be evanescent, ephemeral, electronic abstractions but this article suggests that they leave a weighty, grimy residue. The company’s electrical consumption (mostly the data centers) is said to create a carbon footprint of one million five hundred thousand tons in a single year. That is possibly much less than the footprint left by the car/bus trips and phone calls that have been made unnecessary by web searches. But it does suggest that search engines that will be better (i.e provide the sought for answer in fewer searches) will also be greener, even without more efficient computational hardware.

Holding our breath for this diabetes risk

A recent study exemplifies the leverage that can be obtained from mining existing, public data sets to further our national healthcare agenda. As described by the NY Times, our colleague John Brownstein obtained data from the Centers for Disease Control and Prevention (CDC) and U.S. Environmental Protection Agency (EPA) and found a consistent relationship between the amount of air pollution (particulate matter in the air) and population risk for diabetes (after correcting for the usual suspects such as income and ethnicity). This and other large-scale populations studies such as the one we recently reported by Atul Butte suggest that we might be insufficiently including the larger environment in our study of the diabetic plague that has afflicted us.

It also suggests that we have insufficiently taken advantage of freely available public data to pursue relevant and timely medical research.

What does a Harvard Medical or School of Public Health student think when she first tours the library?

Circulation and reference staff gave tours and orientations to the incoming medical and public health students and just wrote down every question that the students asked. The students volunteered these questions, and they were not prompted. The word cloud below represents their questions. It will be interesting to see if this cloud will change with time for this group. (Hat tip Wendy Brown)

Do you get to read your own genetic data?

My distinguished colleague Patrick Taylor and genetics/bioethics researchers Wylie Burke and Laura Beskow engaged in an interesting debate that can be listened to at TheScientist.

Let our data go

In principle we have access to our own healthcare data. In practice, it is frequently laborious, costly and at least inconvenient and sometimes impossible. In that context as noted by my colleague Keith Strier, we have some good news from the federal government.

In the very first PCHRI conference, when I facilitated the business section, one of the few truly memorable take-aways for me was coming to the conclusion that what we really needed was a “download” button on EHRs. It seemed so simple, but unachievable. Yet, here we are, the first major public initiative to install a download button. It’s nice to see if come full circle.

http://govhealthit.com/newsitem.aspx?nid=73961

Perhaps the government will mandate that all developers and vendors of electronic health records must follow suit.

What about the environment?

Hundreds of millions of dollars have been spent on comparing the frequencies of genetic variants in disease-afflicted and control populations to suss out the genetic basis of diseases, common or rare. The results for diseases with diabetes have been mixed which despite the high concordance of this disease in identical twins raises yet again the question of the role of the environment in the etiology of diabetes. Of course, we know that the inherited component of diabetes risk is contingent on environmental factors (notably diet) but these are much harder to quantify and moreover there is a universe of environmental risks that is potentially much larger than the entirety of the genome. So how to go about capturing more of the environmental risk as it pertains to real human beings (as opposed to petri dish or rodent studies)?

Atul Butte at Stanford shows us how, through the lens of informatics, systematic approaches can be taken to understand the environmentally-borne determinants of our disease burden. He leverages one of the most admirable public national studies of US citizens, the NHANES study. Butte and colleagues performed analyses analoguously to genome wide association studies but instead examined each of the chemicals (e.g. pesticides, heavy metals, vitamin metabolites) measured in the urine and blood of the members of the NHANES groups comparing cases of diabetes vs. controls. As summarized in the figure below, after comparing multiple groups they found a consistent increased risk of diabetes with PCB and pesticide derivatives and a decreased risk with some carotene derivatives (related to vitamin A). Although, just as for their genome-wide analogues, the results of this Environment Wide Association Study (EWAS) should be taken with due caution, they add to a growing array of methodologies that provide a complement to conventional randomized and controlled studies.

We will miss our book-filled bookshelves (at least for a while)

This article on the proliferation of incompatible electronic book formats and digital rights management (DRM) standards for book content is a stark reminder that much of what is digital is incompletely archived, if at all. This is particularly the case for our personal collections. I have some favorite novels and text books which I can still pick off my shelves in my office months or decades after I first purchased them. Until that unlikely day that all digital books are sold without DRM or that one DRM/encoding is adopted by all electronic book vendors, I will have to hope against hope that the vendor of the e-book I also use will remain in business. Otherwise, I will have to regularly repurchase all the books I purchased in electronic form every few years. Or just reread those older and less evanescent paper-based books.

What the Tell-Tale Heart Tells Us About Healthcare

At the end of his short story, Edgar Allen Poe's haunted murderous protagonist lets loose in front of the unsuspecting police officers:

"Villains!" I shrieked, "dissemble no more! I admit the deed! -- tear up the planks! -- here, here! -- it is the beating of his hideous heart!"

It is this story that inspired the title of a paper we published a few years ago on how we could detect the increase (and subsequent decrease) of myocardial infarctions coincident with the rise and fall of the use of Vioxx. This investigation relied solely on the informational byproducts of healthcare delivery. This weekend a Senate report on the risk of Avandia and what was known by GSK came to light. This resonated because we had recently published an article in Diabetes Care about the rapid identification of an increased risk of myocardial infarction with Avandia in patients with diabetes mellitus as compared to other drugs, even drugs in the same class, such as Pioglitazone. Whereas the current headlines are about what the pharmaceutical company knew or dissimulated, there is a broader question that needs addressing: Should every healthcare system not be instrumented so that the clinical leaders of these systems should know whether there are unexpected changes in the risks and health status of their patient populations?

Often, the state of clinical practice is compared unfavorably to the practice of commercial air travel, but what remains underemphasized is that as a system, we are flying blind. There is no local, regional or national air-traffic-controller-equivalent for the healthcare system. Should not the local hospital, and Department of Public Health be the first to know if there is about to be a local health collision or crash? Should not such local surveillance systems run in parallel to regional and national systems? Do we not need multi-level redundancy and open communication to avoid tens of thousands of unnecessary deaths? Further, even as the federal government becomes more aware of the need of such instrumentation, we all expect that our local healthcare systems and health authorities should know of any untoward health trends. Perhaps healthcare systems will start to compete on being able to provide timely and localized health trend data to their customers. Unfortunately right now, the major investments in such health market intelligence is to the payors (i.e. the insurers) who quite reasonably want to know what are the local risks, performance and trends for each of their contracts. Will it take regulation or market competition to make such data extraction and return to patients a matter of course? Let's hope we do not have to wait for a post-mortem Poe'esque orgy of recrimination to find out.

No iTunes-equivalent for Google

Google and the Authors Guild and the Association of American Publishers had hoped to create a one-stop shop for a wide array of published works. The Department of Justice has just ruled that the current proposal does not pass muster. Whether or not this helps or hinders dissemination or scholarship appears to be a matter of some controversy.

Who are the right practictioners of medicine?

This report from Haiti is a reminder that doctors are not always the answer to a healthcare need. We might be well-served by a national discussion of what are the properties of healthcare practitioners that we believe we are seeking to maximize and whether these are well matched to our needs as a society and as patients. It is a discussion which will also inform budgets.

Positive Peer Pressure

Can we use Internet-borne viral messages to counter biological viruses? Our very own Ben Reis is recognized by HHS Secretary Kathleen Sebelius for his Facebook application:

The “I’m a Flu Fighter” Facebook application takes users through four steps. In the first step, “Choose My Character,” users choose between a superhero, a doctor, a virus behind bars, or a cartoon syringe to represent themselves as a flu fighter. Then, users set their status by sharing whether they got the flu vaccine or plan to, and how it was (Could be better, Fine, Good, Great!). Next, users can send invites to their friends challenging them to get vaccinated. Lastly, users are taken to a page with resources about flu such as the flu vaccine locater. The visibility of users’ information as Flu Fighters is controlled by users through their privacy settings.

Screening to distraction: Greater focus on the incidentalome

Last week, Gina Kolata of the New York Times summarized a growing controversy around the value of some of the types of medical screening tests currently employed.The salutory effect of this and related articles is a growing awareness of the tradeoff between increased sensitivity and specificity. It also is a shot across the bow as we contemplate the growth in the number of incidental findings that are going to occur as we test hundreds if not thousands of genetic variants today and in the future. Also, today, Gina Kolata reviewed how little we know about diseases as extensively studied as cancer. Some of them do disappear. Do these spontaneously regressed tumors contribute to the surprisingly high false positive rates for screening?