DailyDirt: Looking At The Human Genome

from the urls-we-dig-up dept

The human genome contains an incredible amount of information that we are only starting to parse. Sequencing large amounts of DNA is getting cheaper and faster, so it's only a matter of time before we'll be able to collect a vast amount of genetic information and connect it with practical medical diagnoses and treatments. Here are just a few projects working on decoding our genetic blueprints.

• The international ENCODE project has been looking at the human genome to try to figure out what all the nucleotides do. Less than 2% of the genome is used for making proteins, and we're just beginning to discover that about 80% of the genome is biologically active and isn't just "junk" DNA. [url]
• The Genographic Project is asking the general public to participate in a genome analysis experiment to gather a broad sampling of DNA data. The results will be anonymous (but they'll have your DNA...?) and dedicated to the public domain. [url]
• The 1000 Genomes Project currently claims to have the world's largest, most detailed catalog of human genetic variation. The database includes sequenced genomes from over 1,092 people and should help medical researchers develop tests for genetic diseases. [url]

If you'd like to read more awesome and interesting stuff, check out this unrelated (but not entirely random!) Techdirt post.

Filed Under: biology, biotechnology, dna, genome, human, medicine, science

Malaysian Government Backing Away From TPP Support: Worried About Locking Up Medicine

from the good-for-them dept

As the secretive Trans Pacific Partnership (TPP) negotiations move forward, it appears that some more members are expressing concerns. In the past, we'd noted that politicians in Chile were questioning what benefit there was to being locked into the US's rules. And, now, another TPP negotiating member, Malaysia, seems to be questioning the agreement. The report claims that the government is now against TPP, though the actual article really only highlights the (significant) concerns from Health Minister Datuk Seri Liow Tiong Lai, who claims that TPP "would be detrimental to the local medical industry."

"We are against the patent extension. According to the agreement, if a medicine is launched in the US, and then three years later it is launched in Malaysia, the patent would start from when it is launched here and not when it was launched earlier in the US," said Liow. "This is not fair."

The end result, he warns, is that the TPP would make healthcare less affordable to citizens of Malaysia. Hopefully he really does represent the views of the Malaysian government and they really are considering dropping out over this issue.

Filed Under: malaysia, medicine, patents, tpp

Protected To Death: How Medical Privacy Laws Helped Kill 25,000 People

from the still-feeling-safe? dept

Privacy. Everybody talks about it. Grandstanding politicians make plenty of loud noises in the general direction of the internet, disparaging it for turning your perusal of Kim Kardashian-related articles into targeted ads for breast enhancement surgery and Kanye West tickets. Of course, while these politicians are making all this noise about your privacy, they're quietly signing off on efforts allowing them to sneak in the backdoor and raid your browser history.

Putting the government in charge of your privacy has never been a great idea. When HIPAA was enacted, its privacy requirements greatly affected the medical community. Like many regulatory acts, HIPAA both raised costs (additional paperwork and other compliance factors) and lowered quality (negatively affecting retrospective research and curtailing proactive follow up care).

The true cost of all this additional paperwork, regulation and privacy is now coming to light. Via The Volokh Conspiracy comes the news that HIPAA's privacy requirements may have hampered research efforts that could have prevented an estimated 90,000 unnecessary heart attacks and 25,000 deaths.

Vioxx, the non-steroidal anti-inflammatory drug once prescribed for arthritis, was on the market for over five years before it was withdrawn from the market in 2004. Though a group of small-scale studies had found a correlation between Vioxx and increased risk of heart attack, the FDA did not have convincing evidence until it completed its own analysis of 1.4 million Kaiser Permanente HMO members. By the time Vioxx was pulled, it had caused between 88,000 and 139,000 unnecessary heart attacks, and 27,000-55,000 avoidable deaths.

Even the government's own regulators were stymied by HIPAA's privacy requirements, as was pointed out by Dr. Richard Platt, a drug risk researcher for the FDA:

The Vioxx debacle is a haunting illustration of the importance of large-scale data research. If researchers had had access to 7 million longitudinal patient record, a statistically significant relationship between Vioxx and heart attack would have been revealed in under three years. If researchers had had access to 100 million longitudinal patient records, the relationship would have been discovered in just three months. Of course, if public health researchers did post-market studies that looked for everything all the time, many of the results that look significant would be the product of random noise. But even if it took six months or one year to become confident in the results from a nation-wide health research database, tens of thousands of deaths may have been averted.

At least as troubling as the fact that several thousand deaths could have been prevented if HIPAA's restrictions and terms had not been so limiting is the fact that the privacy stipulations were put into place based on a faulty premise and the Dept. of Health and Human Services' misplaced confidence in the erroneous results.

The premise, as demonstrated by Massachusetts graduate student Latayna Sweeney, was that patient reidentification was possible using only voter registration records and Massachusetts Group Insurance Commission's (GIC) anonymized records. Sweeney was able to reidentify Governor Weld using voter record information, including birth date, name, address, zip code and sex and cross-referencing it with GIC's data. But, as Info/Law points out, Sweeney made a couple of errors, not the least of which was conflating two different terms:

Latanya Sweeney used census data to estimate that 87% of the population has a unique combination of 5-digit zip code, birthdate, and gender, and implied that the same sort of attack, using voter registration records or other public files. Phillip Golle's replication corrected the figure to 63%, though that's hardly comforting. But these uniqueness statistics are rather misleading. There is an important difference between distinguishability and identifiability. Distinguishability is a necessary condition to conduct the sort of matching attack that Ohm describes, but it is not sufficient. Latanya Sweeney conflated the two when she suggested that a unique individual can be identified by linking the unique combination of attributes to public records-voter registration records, e.g.. But public records are never complete. We know, for example, that a significant portion of the population is not registered to vote. How was Sweeney so sure that there was not another man who shared Gov. Weld's birth date and zip code who was not registered to vote?

Not only was the data set incomplete, but it was overly simplistic and off by a large margin:

Daniel Barth-Jones has recently uploaded a fascinating new article that revisits the famous Gov. Weld reidentification. To start with, Sweeney's estimate of the Cambridge population is way off. There were nearly 100,000 people living in Cambridge at the time of the William Weld attack. This should have been the first hint that Sweeney's methodology was overly simple. She reported a population of 54,000 because that is the number of Cambridge residents who were registered to vote. Sweeney used these records as if they described the entire population.

By comparing Sweeney's count of Cambridge voter registrants with U.S. Census records, Barth-Jones confirmed that many voting-age adults in Cambridge (about 35%) were not registered to vote. In William Weld's case, the census data show that approximately 174 men living in Weld's zip code were Weld's age. We don't know their precise birth dates, but we can calculate that the chance another man living in Weld's zip code shared his birthdate was about 35%. This is quite important all on its own to illustrate the difference between identifiability and distinguishability. Most of those 174 men had a unique combination of birth date, gender, and zip code, but each one of them was quite likely-35% likely-to be non-unique.

Sweeney presumably used the voter registration records to rule out the possibility that some of these 174 Cambridge men shared Gov. Weld's birth date. But even if Sweeney did indeed confirm that no other registered voter shared Weld's gender, zip, and birth date, she could not have been sure about the 50 or so Cambridge residents who were Weld's age and were not registered to vote. Thus, at best, Weld's chance of having a unique birth date, zip code, and gender combination is 87%. Put differently, the chance that Latanya Sweeney's matching attack would have been wrong using these three variables alone was 13%- much worse than traditional 5% statistical confidence.

Despite these erroneous assumptions based on incomplete data, the Dept. of Health and Human Services stated the study had shown that "97 percent of the individuals in Cambridge whose data appeared in a database which contained only their nine digit ZIP code and birth date could be identified with certainty." This completely ignores the fact that over a third of the population wouldn't even show up on the list.

But bad data and faulty research have never stopped governmental "progress." The threat of reidentification is low and any attacks remain purely speculative. But while bad regulations have a tendency to be able to weather even the toughest criticism without making the slightest concessions, HIPAA has one thing most bad regulations don't, as Info/Law points out: "a body count."

Filed Under: fda, hipaa, hmo, medicine

DailyDirt: Death Ain't So Simple

from the urls-we-dig-up dept

Medical technology is making progress all the time, and with that progress comes new ethical questions. One of the big issues that we may need to deal with soon is determining who is really dead (or when to stop resuscitating). Growing new organs isn't quite a reliable technology, so until we can re-grow our own organs, we're not immortals. But we're not dead yet....

• An adapted excerpt from "The Undead" by Dick Teresi discusses how the definition of death has evolved with medical technology. People used to call it death when the heart stopped beating... but they don't do that anymore. [url]
• Brain dead people are being harvested for their organs, but these folks might not be as dead as you'd think. Billy Crystal might call these patients "mostly dead" -- and revive them for true love.... [url]
• Facebook encouraged over 100,000 users to register as organ donors recently. However, there's still a large unfilled need for more donors -- would getting more Facebook "likes" be a good incentive for live donors? [url]
• To discover other biological curiosities, check out what's currently floating around the StumbleUpon universe. [url]  

By the way, StumbleUpon can recommend some good Techdirt articles, too.

Filed Under: billy crystal, death, dick teresi, ethics, medicine, organ donor
Companies: facebook

DailyDirt: Open Source Robots

from the urls-we-dig-up dept

Robots are getting better and better at performing simple repetitive tasks that most people think are fairly easy to perform. But if you're not paying attention to robot developments, you might have missed some robots that have been taught to do a few more impressive feats. Here are some examples of open source robots that we might want to keep an eye on.

• An open source robot surgeon called Raven is making some impressive progress in the field of medicine. However, its advancements could be threatened by the makers of the da Vinci Surgical System -- and various patents on robot surgery procedures. [url]
• PhillieBot is a one-armed robo-pitcher designed by engineers at Penn that threw a ceremonial opening pitch for an MLB game. The creators credit the open source robot operating system (ROS), but also admit that their robot won't be competing with human pitchers any time soon. [url]
• In 2010, Willow Garage modified its open source PR2 robot to do a laundry task -- successfully folding towels neatly. The towels don't have to be a specific size or color, but it does take some patience to wait for a pile of towels to be completed. [url]
• To discover more interesting robotics-related content, check out what's currently floating around the StumbleUpon universe. [url]  

By the way, StumbleUpon can recommend some good Techdirt articles, too.

Filed Under: baseball, laundry, medicine, open source, philliebot, pitcher, pr2, raven, robots, ros, surgeon
Companies: willow garage

DailyDirt: Cures To Whatever Ails You...

from the urls-we-dig-up dept

Medicine has improved a lot over the years, but there are still plenty of treatments out there that aren't based on evidence that they actually work. Some modern snake oils are backed up by technobabble worthy of a Star Trek episode, and others just appeal to "common sense" for justification. Here are a few quick links on some "reliable" medical treatments.

• This TEDtalk points out how to identify bad medical science through publication bias. If you flip a coin a hundred times and ignore half of the times it comes up tails, then maybe you're not doing something right. [url]
• Buying cocaine without a prescription was once commonplace -- to cure all sorts of maladies, like "flatulence, colic, hysteria, hypochondria, back pain, muscle aches"... Whenever there's fun, there's always coca-cola..? [url]
• Neuroscience could point to more effective treatments for various addictions and improve the success rate for rehab clinics. They tried to make me go to rehab, I said, "No, no, no..." [url]
• To find more interesting stuff on health-related topics, check out what's currently in the StumbleUpon archives. [url]  

By the way, StumbleUpon can recommend some good Techdirt articles, too.

Filed Under: addiction, cocaine, medicine, neuroscience, publication bias, rehab, treatments

Doctors Against Patients Having Direct Access To Test Results

from the too-much-information-access-makes-the-gatekeepers-angry dept

The title of this article is a tad melodramatic, claiming "Big Brother doctors say patients don't need to see their imaging test results," but the conclusion from a study of a small sample set of radiologists and referring physicians is that these medical professionals are against empowering their patients with their own information.

This isn't too surprising knowing that the entire healthcare system is wrought with ill-conceived ideas against efficient and ready access to patient health records.

Physicians with a "Big Brother" mindset apparently think people having imaging tests are incapable of dealing with the outcomes without suffering from so much anxiety they must be protected from seeing the results.

It's not clear exactly that this attitude is akin to an Orwellian state, rather than simply an elitist mindset.  Many "experts" feel that people outside of their field have no business reviewing their work (look at the commenters on Techdirt who claim others should not comment on music/patents/laws/newspapers if they aren't a musician/inventor/lawyer/journalist).

The attitude of these physicians is just one reason of a whole host as to why the healthcare system is one of the last industries holding out against the IT revolution.  The argument that patients will freak out being exposed to the core information that leads to diagnoses is ridiculous.  If someone is going to be overly anxious, it isn't because they have information; they'll be anxious because they have symptoms and a diagnosis, but little-to-no information.  They'll be anxious because the medical industry is unwilling to have a two-way conversation with the patient themselves.

There are many examples of this elitism when it comes to sourcing and analysis of information. Why is it that experts fail to recognize that more points of view have a greater opportunity for catching errors and bringing different perspectives to the forefront?  In addition, bringing the patients into the conversation gets them involved in their own health stories, leading to many long term benefits and ultimately lower healthcare costs.  But maybe this is another one of the reasons the healthcare industry is unwilling to change?

Filed Under: doctors, health, medicine

Open Sourcing A Disease Diagnosis

from the with-enough-eyes,-all-biological-bugs-are-shallow dept

If you follow Larry Lessig on Twitter, you noticed that all day Monday he was putting messages on Twitter about how "JZ" was sick and was trying to "open source" his diagnosis. This pointed to a blog that only referred to "JZ" as "Z" and had some basic info on the symptoms of "the patient." There were a series of blog posts, detailing some of the details of the sickness, tests that had been done, and some of the general questions that the doctors were trying to zone in on. It even included a list of possible diagnoses, crossing out the ones that had been ruled out. Relatively quickly, two separate readers came up with an obscure medical journal article from South Korea from 1994 "about heptatic mega-hemagionas and FUOs," which apparently quite accurately described the situation.

It didn't take long for people to realize that the JZ was Harvard professor Jonathan Zittrain, and once revealed, he put up a blog post of his own clarifying the situation, noting that they no longer needed help with the diagnosis, and everything sounds fine (what they diagnosed sounds treatable). He especially wanted to downplay the situation, and not create too much concern for his well-being or the need for any immediate help. The original blog where the details were being shared was taken down, and it now just points to Zittrain's own explanation.

It's great to hear that this worked out, and so rather than worrying about Jonathan, I thought it was interesting to think about this aspect of "open sourcing" a diagnosis. Obviously, when it comes to medical info, there are always serious privacy concerns, but this definitely does seem like a case where when there's confusion, more eyes and more brains can help. I'm reminded of the silly complaint often lodged against Wikipedia, that people wouldn't want brain surgery done by "a crowd," but by an expert. But, as has been noted over and over again, that presumes the crowd includes no experts, and that the real experts won't quickly establish themselves as such. On top of that, it ignores that once you have many different people -- some experts, some not -- you may get obscure or different perspectives that help lead to the important nugget of info you were seeking out, such as a medical journal article from Korea in 1994.

All this has me wondering if there's an opportunity out there for the medical profession to make more use of something like this, with patient consent, obviously. I know doctors converse informally all the time, but opening up some aspects of the diagnosis could be interesting. Of course, I also don't know how often situations like this occur, where the diagnosis is obscure enought that additional help might be useful, but it seems like an area that has possibilities.

Filed Under: confidentiality, crowd sourcing, jonathan zittrain, larry lessig, medicine

The Doctr Is In

from the housecalls-by-IM dept

Back in the day, when you were sick, you would call the doctor, and they make a house call to diagnose your condition and provide care. In this modern age of managed care, where doctors are evaluated on the volume of patients that they are able to process, house calls are now but a distant memory. Now, Dr. Jay Parkinson, a Brooklyn doctor, brought the house call back -- but it's been updated for the times. Parkinson has started a new medical practice that centers around instant messenger, email and house calls. During regular business hours, he is available to his patients for online medical consultations. Dr. Parkinson then pays the patient a house call only if it is really necessary (you get two included house calls in the fee), but most issues can be addressed virtually. This is not surprising since studies confirm that online chat with your doctor is nearly as effective as an in-person visit. Specializing in young adults age 18 to 40 without traditional health insurance, this approach could teach a few things to the health care industry. Of course, what he's doing is really similar to what many nurse practitioners do, so you could see him scaling his practice by employing a staff of nurse practitioners who answer IMs and emails, and then escalating qualifying issues to doctors and specialists. A second interesting point about Parkinson's plan is that since all of his clients are very price conscious (since they're paying out of pocket), he actively shops around for the best value specialists to send his clients to. In the age of copayments and insurance, you very rarely see much price comparison shopping in health care. As we've discussed here before, the current health care system is beset with problems, so it's encouraging to see a differentiated spur some excitement (and competition) in a very homogeneous marketplace.

Filed Under: doctors, im, medicine