Why medicine needs scirate.com

Defenders of the traditional publishing model for medicine say that health-related claims need to be vetted by a referee process. But there are heavy costs. In quantum information, one might know the proof of a theorem (e.g. the Quantum Reverse Shannon Theorem) for years without publishing it. But one would rarely publish using data that is itself secret. Unfortunately, this is the norm in public health. It’s ironic that the solution to the 100-year-old Poincaré conjecture was posted on arxiv.org and rapidly verified, while research on fast-moving epidemics like H5N1 (bird flu) is
delayed so that scientists who control grants can establish priority.
All this is old news. But what I hadn’t realized is that the rest of science needs not only arxiv.org, but also scirate.com. Here is a recent and amazing, but disturbingly common, example of scientific fraud. A series of papers were published with seemingly impressive results, huge and expensive clinical trials were planned based on these papers, while other researchers were privately having trouble replicating the results, or even making sense of the plots. But when they raised their concerns, here’s what happened (emphasis added):

In light of all this, the NCI expressed its concern about what was going on to Duke University’s administrators. In October 2009, officials from the university arranged for an external review of the work of Dr Potti and Dr Nevins, and temporarily halted the three trials. The review committee, however, had access only to material supplied by the researchers themselves, and was not presented with either the NCI’s exact concerns or the problems discovered by the team at the Anderson centre. The committee found no problems, and the three trials began enrolling patients again in February 2010.

As with the Schön affair, there were almost comically many lies, including a fake “Rhodes scholarship in Australia” (which you haven’t heard of because it doesn’t exist) on one of the researcher’s CVs. But what if they lied only slightly more cautiously?
By contrast, with scirate.com, refutations of mistaken papers can be quickly crowdsourced. If you know non-quantum scientists, go forth and spread the open-science gospel!

Fighting tuberculosis with BB84

Tuberculosis (TB) has been with humans for millenia, infects 1 in 3 people worldwide and kills almost 2 million people per year.  BB84 is everyone’s favorite information-theoretically secure key expansion system, and is secure at bit error rates up to at least 12.9%.  So what’s the connection?
TB is treatable, but the treatment involves taking multiple antibiotics daily for 6-9 months (or up to 24 months for drug-resistant strains).  The drugs have painful side effects (think chemotherapy) and most TB symptoms go away after a few months, so it can be hard for people to be motivated to complete the course.  In poor countries, where TB is most common, doctors are in short supply, and have little time for counseling about side effects, or patients might not have access to doctors, and just buy as many pills as they can afford from a pharmacist.  But when people stop treatment early, TB can return in a drug-resistant form, of which the scariest is XDR-TB.
As a result, the WHO-recommended treatment is DOTS (directly observed treatment, short course), in which a health worker watches the patient take all of their pills.  This is effective, though proving this is hard, and implementation is difficult.  The community health workers monitoring patients are paid little or nothing, are often unmonitored, and spend their time in the houses of people with active TB, often without good masks.  So absenteeism and low morale can be problems.  Patients also can find it condescending, disempowering, and stigmatizing, since neighbors can notice the daily community-health-worker visits.
One ingenious alternative is called X out TB.  Patients are given a device that dispenses a strip of paper once every 24 hours.  If a patient is taking their antibiotics, then peeing on the paper will cause a chemical reaction (with a metabolite of the drugs) that reveals a code, which patients send to the local clinic by SMS.  As a result, the clinic can remotely monitor which patients are reliably taking their pills.  Patients in turn are given a reward (cell phone minutes have been popular) for taking their pills every day.
This system seems to be working well in trials, but the presence of the dispenser means that batteries are necessary, and security considerations arise. For example, one could try to open the dispenser up, to save a jar of urine and keep dipping strips in it after stopping the pills, or even to pour urine inside the dispenser. Imagine that the unfortunate TB patient is actually Eve, who has a dark determination to cheat the system, even at the expense of her own health.
Fortunately, BB84 has already provided an elegant, if not entirely practical, solution to this problem.  The dispenser can be replaced by a numbered series of strips, and the bottle of pills needs to be replaced by a similarly numbered blister pack (for simplicity, the two could be packaged together). On day i, the patient takes pill i and several hours later, pees on strip i. The twist is that there are two types of strips—let’s call them X and Z—and two types of pills, which we will also call X and Z.  These appear the same visually, but have different chemical properties.  Peeing on an X strip after taking an X pill will reveal the code, as will peeing on a Z strip after taking a Z pill.  But if the strip type doesn’t match the pill type, or there are metabolites from both pill types present, then the code will be irrevocably destroyed.
For a patient following instructions, the pill on day i will always match the strip on day i, and so all of the codes will be properly revealed.  But any attempt to reveal codes without matching up pills and strips properly (e.g. peeing on all the strips at once) will inevitably destroy half the codes.  The threshold for rewards could be set at something like 90-95%, which is safely out of range of any cheating strategy, but hopefully high enough to prevent resistance.
This scheme has its flaws.  For example, a patient could get a friend to take the pills for them (although this friend would probably suffer the same side effects).  The metabolites might not clear the system quickly enough, in which case honest patients would still invalidate strips sometimes when an X strip/pill is followed by a Z strip/pill or vice versa.  While the original X-out TB approach relied on using metabolites of common TB medications, the BB84 approach would probably want to use pharmacologically inactive additives, and I don’t know if drugs exist that are FDA-approved and have the necessary properties. On the other hand, this enables the additive to have a half-life much shorter than the medicine.  And of course, patients generally want to get better, and are likely to take their pills when given even mild encouragement, monitoring and counselling.  So information-theoretic security might be more than is strictly necessary here.
Can anyone else think of other applications of BB84?  Or other ways to stop TB?

A Curmudgeon's and Improv's Guide to Outliers: Introduction

So I picked up Malcolm Gladwell’s newest book Outliers: The Story of Success the other day, as I’m sure many of you will be doing on your next trip to the airport (where stands of Gladwell’s hardcover book, marked down thirty percent, block your every exit through the already cramped airport bookstores.) Gladwell’s books are fun, but I find myself often disagreeing with his analysis, so I thought it would be entertaining to take my time reading his latest and jot down my thoughts as I progress. Well “entertaining” in that “holy shit dude you are pedantic” sort of way. Note that I really do like Gladwell’s books, and indeed for me, reading with critical eyes is exactly the reason I like his books. Ah, the life of a curmudgeonly pedant, revealed before your eyes, here on these there intertubes!
To balance things out, I’ve also included some thoughts from the improv part of my brain: the part that takes ideas at more than face value and tries to run with them.
SPOILER ALERT: Dude, I can’t talk about the book without giving away what the book is about, so if you don’t want the book’s main ideas to be spoiled, don’t continue reading.
IDIOT ALERT: I’m in no way qualified in most of the fields Gladwell will touch on, so please, a grain of salt, before you start complaining about my ignorance. Yes I’m an idiot, please tell me why!
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