Search the KHIT Blog

Saturday, November 28, 2015

Getting a handle on the costs of care

I'm on sort of a blog hiatus at the moment. My wife and I are celebrating our 35th wedding anniversary in a cabin above Gatlinburg, TN in the Smokies. Lying low, doing a good bit a reading and talking with my best friend of nearly 42 years.

We'll be back in California Tuesday night.

Saw this bit of news last night.

Hit the lower right corner "expand" icon next to the arrow.

NY Times article on the topic: What Are a Hospital’s Costs? Utah System Is Trying to Learn
SALT LAKE CITY — Only in the world of medicine would Dr. Vivian Lee’s question have seemed radical. She wanted to know: What do the goods and services provided by the hospital system where she is chief executive actually cost?

Most businesses know the cost of everything that goes into producing what they sell — essential information for setting prices. Medicine is different. Hospitals know what they are paid by insurers, but it bears little relationship to their costs...

More to come...

Monday, November 16, 2015

On "Big Data" and "the spaces that live between facts"

Up next, in considerable triangulating detail, as is my customary M.O. I just finished reading it. Highly recommended. Finally, I make get closer to the heart of this woolly, elusive "art of medicine" thing.

"The advent of new medical technologies will not diminish bias. They will amplify it. More human arbitration and interpretation will be needed to make sense of studies—and thus more biases will be introduced. Big data is [sic] not the solution to the bias problem; it is merely a source of more subtle (or even bigger) biases.

...The greatest clinicians who I know seem to have a sixth sense for biases. They understand, almost instinctively, when prior bits of scattered knowledge apply to their patients— but, more important, when they don’t apply to their patients. They understand the importance of data and trials and randomized studies, but are thoughtful enough to resist their seductions. What doctors really hunt is bias."

Mukherjee, Siddhartha (2015-10-13). The Laws of Medicine: Field Notes from an Uncertain Science (TED Books) (Kindle Locations 612-620). Simon & Schuster/ TED. Kindle Edition.
"[H]uman decision making, and, particularly, decision making in the face of uncertain, inaccurate, and imperfect information, remains absolutely vital to the life of medicine. There is no way around it. “The [political] revolution will not be tweeted,” wrote Malcolm Gladwell. Well, the medical revolution will not be algorithmized." [Mukherjee, op cit, Kindle Locations 664-666].
"The medical revolution will not be algorithmized."

A half-million physicians laboring under the still-contentious, workflow-obstructive Meaningful Use compliance requirements nod their head in unison at that.


A strong intuition is much more powerful than a weak test.

“Normals” teach us rules; “outliers” teach us laws.

For every perfect medical experiment, there is a perfect human bias.

Again, an excellent, rather quick read. I studied it closely in about a half-day.

"The still-contentious, workflow-obstructive Meaningful Use compliance requirements"

While this blog began in 2010 amid the outset of my REC tenure with the Meaningful Use initiative and necessarily had a core focus on Health IT and proximate interrelated subjects subjects such as workflow (including "process QI"), UX (including the gamut of "human factors"), ePHI privacy/security, and the continuing misnomer "interoperability," I have always ranged further afield into the broader (and also inextricably interrelated) issues that necessarily come to bear on clinical effectiveness, e.g., organizational cultural issues, clinical pedagogy (and "how doctors think"), the socioeconomic "upstream," the market (including intellectual property, and the "shards" of care delivery), "artificial intelligence," and the rapidly maturing applied "omics" field.

On health IT per se, it's always worth studying the excellent, voluminous work of Dr. Jerome Carter at EHR Science:
A Usability Conundrum: Whether it is EHRs or Hospital Gowns, One Size Never Fits All…

Building clinical care systems that intimately support clinical work has to begin with the acknowledgement that clinicians perform many tasks within the context of a patient encounter, and those tasks very in type, number, and sequence. Everyone knows this. So, one might ask, if this is common knowledge, why are there so many problems with EHR usability? The answer is very simple. EHR systems are designed to be one-size-fits-all.

One-size-fits-all (OSFA) is such a fundamental precept of EHR design that no one even questions it. Instead, there is a pursuit of every possible means of fixing EHR systems, while allowing them to remain OSFA. Why? Because it is a design assumption carried over from past software design/development limitations.   Achieving the highest possible level of usability requires dumping deeply-ingrained OSFA thinking.

How did OSFA become so entrenched in EHR designs? Here are the main reasons.

Poor choice of design metaphor
Paper charts are the inspiration for current EHR systems. Charts are OSFA. No clinician was allowed to customize the chart to fit his/her personal work habits or information needs. Every hospital or practice has strict rules about chart organization and use. There are legal rules that dictate how charts must be stored and what they must contain. There is an entire profession dedicated to charts. Charts are designed to be standardized information repositories; they are not designed to aid in care delivery. Paper charts are a means to an end, and I have never heard anyone gush over how wonderful a paper chart was or how it made their lives so much better. However, since paper charts are (were) a fact of life, one simply adapted to them, like it or not...
I'd certainly be interested in Dr. Mukherjee's take on HIT.

  1. Listen
  2. Look
  3. Palpate
  4. Empathize
Hmmm... how about "5. Sympathize"? Maybe that would be a stretch sometimes.

None of that is original with me, and, of course, I am no clinician. But, these are core takeaways from my long and deep study here, and they certainly cohere with "The Laws of Medicine." Some dot-connecting will ensue shortly.
I recall an interesting conversation early on during my REC tenure. Keith Parker, my nominal "boss" (who I'd interviewed and helped hire during my 2nd stint with HealthInsight during the DOQ-IT era in 2005) is a retired Special Forces medic. We were talking "SOAP" stuff one day in his office, and he started in on me, sizing me up (I'd not been feeling well), walking me through his take on the mostly "Subjective" component of the "Assessment" -- his reflexive process of in-the-exigent-field-circumstances evaluation: "Listen, Look, Palpate, Empathize." Keith was/is as clinically adept in that regard as any physician I've ever met. Probably goes in large measure to his high-stakes military background and experience.
Again, it's not just about EHR "structured data." It's also about "the spaces that live between facts."


apropos of the topic, from THCB:
First, we Devalued Doctors; Now, Technology Struggles to Replace Them

...I realized there was something that seemed a little sad about the idea of developing extensive market analytics and fancy digital engagement tools to simulate what the best doctors have done for years – deeply know their patients and suggest treatments informed by this understanding.

Instead, it seems, we’ve slashed the time physicians get to spend with patients, protocolized and algorithmitized almost every moment of this brief encounter, and insisted the balance of time is used for point-and-click data entry and perhaps a rushed dictation.  We’ve industrialized the physician-doctor encounter – the process and the paperwork — but eviscerated the human relationship; it’s value, unable to translate easily to an excel spreadsheet, was discounted and dismissed...

ERRATUM: px transcript

What if, in addition to / in lieu of Dragon-enabled transcription along with standard EHR structured data keyboard and mouse-click input, we had audio and/or video recordings of HIPAA-protected clinical encounters?

My new Harper's came in the mail today.

Shit Talkers

From an audio recording entered as evidence in a 2014 lawsuit filed by a man identified as D.B., who claims that he inadvertently recorded his colonoscopy on his cell phone. Tiffany Ingham and Soloman Shah were the anesthesiologist and the gastroenterologist who performed the procedure. In June, a jury awarded D.B. $500,000 in damages.

TIFFANY INGHAM: All right. This medicine is going to start making you feel a little drowsy and relaxed.
D.B.: Pretty much instantly?
INGHAM: Quickly, yeah. Once Dr. Shah comes in, I’ll make you go all the way to sleep.
D.B.: What’s the medication?
INGHAM: The one that I just gave you? It’s called midazolam. There you go.
D.B.: I used to want to be a surgeon in high school.
INGHAM: What kind of work do you do now?
D.B.: I’m an attorney.
INGHAM: That’s kind of a big switch.
D.B.: I couldn’t take the sight of blood.
INGHAM: Well, you probably made a good career choice there.
D.B.: Yeah. There’s little chance that I will remember this, right? Maybe this part.
INGHAM: It can make your memory a little fuzzy, so you may not recall too much of it.
D.B.: Am I going to remember the procedure?
INGHAM: No, you’ll be unconscious.
[SOLOMAN SHAH enters.]
D.B.: Hey, is that Dr. Shah? How are you, my friend?
SOLOMAN SHAH: Good, good. All right, we’re gonna get started shortly.
[D.B. goes under.]
INGHAM: I don’t think this prep’s going to be so hot. That’s my impression of this gentleman. Is that a clog? Did he clog it up with his crappy prep?
ASSISTANT: Do you need a towel, Dr. Ingham?
SHAH: You’re going to need more than a towel.
INGHAM: On his pre-op form, he has, as his only medication, gabapentin. And I’m like, “Why are you taking gabapentin?” “Well, I went to a dermatologist. I have this irritation on my penis.”
SHAH: Right. That’s a little too much information.
INGHAM: I said, “I don’t think that you should go back to that dermatologist. If you’re having issues in that area, you should see your urologist.”
SHAH: I told him that already! He’s seen two urologists. He told me. I said, “You need to follow up with your urologist.”
INGHAM: He’s crazy.
SHAH: And he keeps mentioning it like it’s the first time he’s ever talked to anyone about it. I’m like, “Sir, you’ve seen two urologists. What are you telling me for?”
INGHAM: I don’t know. Most men I know, if they have the problem with that area of the body, they are in a doctor’s office the next day.
SHAH: And also, don’t mention it to me. I’m not interested.
INGHAM: Exactly. And then he went on and on about it.
SHAH: One nice thing about being a specialist is I don’t deal with that crap.
INGHAM: One nice thing about being an anesthesiologist is making people shut the hell up.
SHAH: That’s why I didn’t become a fricking urologist. Because I didn’t want to put wires in people’s penises all day.
INGHAM: I would make bank as a urologist because (a) I’m a pretty girl, so all the Viagra-seeking dudes would want to see me, and (b) all the ladies whose vaginas have fallen out after their babies would want to come see me, too.
SHAH: I’m going to get a chair. Because it’s going to take me a couple hours to suction all this out of him.
INGHAM: Big shocker. I just knew it. As soon as he said, “No, it’s not clear,” I’m like, “Well, is there solid material?” “Well, yes, there is, it’s dark brown.”
SHAH: Let me guess, does he work for the Justice Department or CIA?
INGHAM: He’s a lawyer, for somebody.
SHAH: The most kooky people that I know work for the Justice Department or the CIA. Or they’re lawyers.
INGHAM: Amazing. I mean, I have anxiety and nervousness, but he’s over the top. You gotta calm down. You’re gonna have a heart attack at forty.
SHAH: Why is it always the last colon of the day that’s like this? Doesn’t he know that I want to go to lunch? His frickin’ colon is slow as molasses.
INGHAM: Put some gloves on. That’s a soupy-doupy-poopy prep.
ASSISTANT: Not to mention a penile rash.
INGHAM: Just make sure you’re gowned up. Don’t want you to accidentally rub against it and get some syphilis or something.
SHAH: That would be bad. That would be real bad.
INGHAM: If you didn’t rub up against the penis, then you should be all right.
ASSISTANT: I did, I did.
SHAH: Well, as long as it’s not Ebola, you’re okay.
INGHAM: It’s penis Ebola. The gabapentin will fix it. . . . Sir, the word I want to use to describe you is not appropriate for this venue.
SHAH: So, Vicky, so you’re going to go talk to this patient afterward, right?
ASSISTANT: [Laughs] Suuure.
INGHAM: You’re going to have to have a timer go off or, like, a fake page. “Dr. Shah, you’re needed urgently in the office.” I’ve done the fake page before. . . . Who will be the lucky nurse who gets him? It’s lunchtime. It could be anyone. Round and round we go. Wheel of annoying patients. Where will it land? Nobody knows. . . . I feel bad. I shouldn’t be so mean. . . . I’m going to mark “hemorrhoids” even though we don’t see them and probably won’t. I’m just going to take a shot in the dark. And I’m writing it “H.O.R.” in capital letters.
Lordy. Now a matter of public record. How's that for "mHealth"?


This book is about information, imperfection, uncertainty, and the future of medicine. When I began medical school in the fall of 1995, the curriculum seemed perfectly congruent to the requirements of the discipline: I studied cell biology, anatomy, physiology, pathology, and pharmacology. By the end of the four years, I could list the five branches of the facial nerve, the chemical reactions that metabolize proteins in cells, and parts of the human body that I did not even know I possessed. I felt poised to begin practicing real medicine. But as I advanced through my training— becoming an intern, then a resident, a fellow in oncology, and then an attending doctor treating patients with cancer— I found that a crucial piece of my education was missing. Yes, I needed the principles of cell biology to understand why, say, a platelet transfusion lasts only two weeks in most patients (platelets live in the body for only about two weeks). Anatomy helped me recall why a man had woken up from a surgical procedure with his entire lower body paralyzed (an unusual artery that supplies the lower spinal cord had become blocked by a clot, resulting in a “stroke” of the spinal cord, not the brain). An equation from pharmacology reminded me why one antibiotic was dosed four times a day while its close molecular cousin was given only once a day (the two chemicals decay at different rates in the body). 

But all this information could, I soon realized, be looked up in a book or found by a single click on the Web. The information that was missing was what to do with information— especially when the data was imperfect, incomplete, or uncertain. Was it appropriate to treat a forty-year-old woman with acute leukemia with an aggressive bone-marrow transplant if her health was declining rapidly? At first glance, textbooks and published clinical trials gave you an answer. In this instance standard wisdom held that patients with declining health and performance should not be given a transplant. But what if that answer did not apply to this woman, with this history, in this particular crisis? What if the leukemia itself was causing the rapid decline? If she asked about her prognosis, I could certainly quote a survival rate pulled from a trial— but what if she was an outlier? 

My medical education had taught me plenty of facts, but little about the spaces that live between facts. I could write a thesis on the physiology of vision. But I had no way to look through the fabric of confabulation spun by a man with severe lung disease who was prescribed “home oxygen,” but gave a false address out of embarrassment because he had no “home.” (The next morning, I got an irate phone call from the company that had attempted delivery of three canisters— to a Boston storefront that sold auto parts.) 

I had never expected medicine to be such a lawless, uncertain world. I wondered if the compulsive naming of parts, diseases, and chemical reactions— frenulum, otitis, glycolysis— was a mechanism invented by doctors to defend themselves against a largely unknowable sphere of knowledge. The profusion of facts obscured a deeper and more significant problem: the reconciliation between knowledge (certain, fixed, perfect, concrete) and clinical wisdom (uncertain, fluid, imperfect, abstract). 

This book began as a means for me to discover tools that might guide me through a reconciliation between these two spheres of knowledge. The “laws of medicine,” as I describe them in this book, are really laws of uncertainty, imprecision, and incompleteness. They apply equally to all disciplines of knowledge where these forces come into play. They are laws of imperfection. 
The stories in this book are of real people and cases, but I have changed names and identities and altered some contexts and diagnoses. The conversations were not recorded verbatim, but have been paraphrased from my memory. Some situations, tests, and trials have also been changed to maintain the anonymity of patients and doctors. [The Laws of Medicine, Kindle Locations 56-88].
Sciences have laws— statements of truth based on repeated experimental observations that describe some universal or generalizable attributes of nature. Physics is replete with such laws. Some are powerful and general, such as the law of gravitation, which describes the force of attraction between two bodies with mass anywhere in the universe. Others apply to specific conditions, such as Ohm’s law, which only holds true for certain kinds of electrical circuits. In every case, however, a law distills a relationship between observable phenomena that remains true across multiple circumstances and multiple conditions. Laws are rules that nature must live by. 

There are fewer laws in chemistry. Biology is the most lawless of the three basic sciences: there are few rules to begin with, and even fewer rules that are universal. Living creatures must, of course, obey the fundamental rules of physics and chemistry, but life often exists on the margins and in the interstices of these laws, bending them to their near-breaking limit. Even the elephant cannot violate the laws of thermodynamics— although its trunk, surely, must rank as one of the most peculiar means to move matter using energy. 

But does the “youngest science” have laws? It seems like an odd preoccupation now, but I spent much of my medical residency seeking the laws of medicine. The criteria were simple: a “law” had to distill some universal guiding principle of medicine into a statement of truth. The law could not be borrowed from biology or chemistry; it had to be specific to the practice of medicine. In 1978, in a mordantly acerbic book called The House of God, the writer Samuel Shem had proposed “thirteen laws of medicine” (an example: “Law 12: if the radiology resident and the intern both see a lesion on an X-ray, then the lesion cannot be there”). But the laws that I was seeking were not attempts to skewer medical culture or highlight its perversities à la Shem; I was genuinely interested in rules, or principles, that applied to the practice of medicine at large. 

Of course, these would not be laws like those of physics or chemistry. If medicine is a science at all, it is a much softer science. There is gravity in medicine, although it cannot be captured by Newton’s equations. There is a half-life of grief, even if there is no instrument designed to measure it. The laws of medicine would not be described through equations, constants, or numbers. My search for the laws was not an attempt to codify or reduce the discipline into grand universals. Rather, I imagined them as guiding rules that a young doctor might teach himself as he navigates a profession that seems, at first glance, overwhelmingly unnavigable. The project began lightly— but it eventually produced some of the most serious thinking that I have ever done around the basic tenets of my discipline. [ibid, Kindle Locations 182-202]
While grounded in scientific thinking (soon to likely be amplified in truly "transformative" measure by the application of the "omics"), an effective "art of medicine" goes materially to adroit tactical heuristic analytic reasoning grounded in empathy. ("Listen, Look, Palpate, Empathize"). Creative, synergistic leaps of expert imagination. The "care" part of "health care." The meditative "slow medicine" of "God's Hotel."

The "care" part of "health care."

I guess it's worth noting that neurologist Antonio Damasio, in "Descarte's Error," points out that "reason versus emotion" is a false dichotomy. One has to care about reasoning.

More to come...

Sunday, November 15, 2015

Shards writ large

"Shards," indeed.

Below, one of my 2004 shots of the Eiffel Tower, at dusk.

We were in Paris for the finish of le Tour that year, joyfully shlepping those very arrondissements proximate to the attacks. Below, a couple of blocks from our hotel.

If this nihilist tragedy isn't a "population health" catastrophe (along with other recent equally gruesome atrocities that weren't accorded 24/7 worldwide press coverage), I don't know what qualifies. Acute care medical services certainly got their workout this weekend. And, given the large number of people still hospitalized with serious to critical wounds and injuries, the frantic medical work will continue apace.

Below, a map of the current Middle Eastern states' diaspora.

The heated social media and news site commentary rhetoric across the weekend has been rife with xenophobic, genocidal "bomb-them-all-back-to-their-beloved-7th-Century" exhortations. Eliminationist allusions to the entire Middle East turned into a "glass parking lot" fly off the trolls' keyboards with abandon.

We're talking about 23% of humanity, the proportion of world population identifying as "Muslim" (~1.7 of 7.3 billion people on earth).

The politicians are elbowing each other aside to be seen as the "toughest." Ted Cruz advocates ramping up U.S. airstrikes and quit worrying about civilian casualties. Donald Trump advocates forcibly shutting down mosques in the U.S. Jeb Bush says only "Christian" refugees should be admitted into  the U.S. The governor of Alabama declares that no Syrian refugees will be permitted in his state.

Update: dozens of other states have chimed in to cite the same bans.

Ben Carson, in addition to calling for legislation barring Syrian refugees, advocates resuming full-scale U.S. military operations in Iraq (to demonstrate "leadership") and going to war with Russia if necessary over a U.S.-imposed no-fly zone over Syria.

And so it goes.


More to come...

Wednesday, November 11, 2015

Shards of health care -- the Nuke the Donald update

"Shards of health care" update. Yesterday (Nov. 10th) I finished my two months of prostate cancer Calypso IMRT tx, 45 daily M-F sessions in all.

I jokingly named my tumor 'The Donald." Now that's he's been "nuked," perhaps I should henceforth refer to him as "Ben."

Staff gave me a "Certificate of Completion" yesterday after I finished tx.

I could not recommend this oncology facility more highly. They exemplify the phrase "patient-centered, team-base care." My prognosis is excellent. I've seen a lot of misery every day during my treks to the clinic. My cancer is relatively trivial in comparison, and the outright "cure" literature for my circumstance is in the "98-99%" range. My radiation oncologist said unequivocally, "you're not gonna die from prostate cancer." I turn 70 in February, so it's likely gonna be something else that gets me. My consulting radiation oncologist at Stanford had told me "you've got another 20 years." Well, my late dad died at 92, my mom, just shy of 90 (and her sister, my aunt Edna, recently passed at 91), so, yeah, perhaps. I just have to do what I can to make them 20 good years (which they were not for my parents).

Going forward post-Calypso tx, I will simply have PSA tests every three months for a couple of years, starting in mid December, and an annual DRE.

Not much in the way of "shards" news to report, given that I've maxed out on my BCBS calendar year 2015 OOP. But, we've been advised to lose the Blue Cross/HSA coverage and go straight Medicare with a Part-B supp, so, we have to quickly look into all of that and enroll. For one thing, it turns out that my wife's company (Gilbane, where we get our coverage) is "self-insuring" (we'd not known that), with the hapless, obstructive BCBS/RI serving merely as the Plan Administrator. Gilbane's "loss experience" this year has been quite high, and employees have been notified of major pending premium increases for 2016. Between our premiums and my OOP, we're out more than $10k this year.

We'll see. Stay tuned.

Time to get caught up on health IT developments and the gamut of health policy stuff I'm behind on. I'm really tired, which was to be expected. I anticipate that that will wane across the next few weeks.

Over at Science Based Medicine, a new book came to my attention yesterday. Bought it and have just begun reading.

This Book Won’t Cure Your Cancer, But It Will Help You Think More Clearly About It

Gideon Burrows has an inoperable brain cancer that is slow growing but is inevitably going to kill him. He has written a remarkable book about his experience, This Book Won’t Cure Your Cancer. A professional wordsmith, he is able to describe his experience of illness so vividly that the reader enters into his life, feels what he feels, and shares his suspense about what the next scan or doctor’s visit will reveal. Along with him, we suffer through the panic and fear, the chaos, the agonies of delays and uncertainty, the unpleasant hospital environment, and specialists with poor bedside manners. We follow him through difficult decisions about how to share the bad news with friends, relatives, and his young children; and we understand why this engenders guilt feelings. The story is as engaging as a detective story; we can hardly wait to see what the next scan will show and how the story of his illness will play out. It puts a human face on the cancer experience, and it would be valuable for that alone, but it is much more. The gradually unfolding episodes of his personal story are interwoven with what amounts to a primer on how to think critically about science-based medicine vs. alternative treatments. I can’t recommend this book highly enough.

Untrustworthy information

When people are diagnosed with cancer, they are vulnerable and desperate. They look for information and are likely to find cookbooks, miracle stories, alternative medicine, and “forbidden cancer cures.” Their friends bombard them with advice. Most of those sources “offer hope to people when they need it most, but have earned no right to do so..."
That all rings so true to me. Recall my "One in Three" essay.
One in three
The statistics (of which I had been blissfully unaware despite having recently worked as a Medicare analyst) reveal that one in three of us will at some point come to deal with cancer, either as a patient, or as an immediate family member of one. Cancer is a disease of such subliminal dread as to induce an ongoing denial while we are healthy and not having direct contact with a cancer sufferer. We'd just as soon not think about it, thank you.

But when cancer does appear, the impact is frequently devastating for all involved. For too many, a diagnosis of cancer comes late in the progression of the disease, leaving the afflicted with limited and problematic therapeutic options and their loved ones with a feeling of being endlessly "behind the curve" also awash in often conflicting information and emotions, groping desperately for the means of survival and healing. Such has indeed been our case for the past year and a half. I have come to learn more than I ever wanted to know about this insidious disease that so frustrates the finest minds in medical science. It is a frustration that fuels a thriving and fervent -- but often naive and irresponsible --"alternative healing" industry whose wildly varying methods and claims must also be individually evaluated in the quest for the tools of a loved one's survival and healing...
I also finished this excellent book, and will be reporting on it ASAP.

"Two leaders in the field of genetics—a bioethicist-health lawyer and an obstetrician-gynecologist geneticist—answer the most pressing questions about the application of new genetics to our universal medicine and what personalized medicine means for individual healthcare.

Breakthroughs in genetic research are changing modern medicine and pharmaceuticals. But what are these changes and how do they affect our individual care? Genomic Messages examines these groundbreaking changes and the questions they raise: What kind of specific medical innovation do we have to look forward to now and tomorrow? How will this “flood” of genetic messages change our lives, our interaction with our physicians and our healthcare system?

Groundbreaking and provocative, Genomic Messages fuses the often conflicting worlds of medicine and law to provide information and insight that will impact the health choices of every one of us, from how medicine is practiced to concepts of privacy, confidentiality, and informed consent. Ultimately, it reveals how genetic information is changing how we think about ourselves, our health, and our future."
apropos of the topic, I read this in my New Yorker yesterday.

The Gene Hackers
A powerful new technology enables us to manipulate our DNA more easily than ever before.


At thirty-four, Feng Zhang is the youngest member of the core faculty at the Broad Institute of Harvard and M.I.T. He is also among the most accomplished. In 1999, while still a high-school student, in Des Moines, Zhang found a structural protein capable of preventing retroviruses like H.I.V. from infecting human cells. The project earned him third place in the Intel Science Talent Search, and he applied the fifty thousand dollars in prize money toward tuition at Harvard, where he studied chemistry and physics. By the time he received his doctorate, from Stanford, in 2009, he had shifted gears, helping to create optogenetics, a powerful new discipline that enables scientists to use light to study the behavior of individual neurons.

Zhang decided to become a biological engineer, forging tools to repair the broken genes that are responsible for many of humanity’s most intractable afflictions. The following year, he returned to Harvard, as a member of the Society of Fellows, and became the first scientist to use a modular set of proteins, called TALEs, to control the genes of a mammal. “Imagine being able to manipulate a specific region of DNA . . . almost as easily as correcting a typo,” one molecular biologist wrote, referring to TALEs, which stands for transcription activator-like effectors. He concluded that although such an advance “will probably never happen,” the new technology was as close as scientists might get.

Having already helped assemble two critical constituents of the genetic toolbox used in thousands of labs throughout the world, Zhang was invited, at the age of twenty-nine, to create his own research team at the Broad. One day soon after his arrival, he attended a meeting during which one of his colleagues mentioned that he had encountered a curious region of DNA in some bacteria he had been studying. He referred to it as a CRISPR sequence.

“I had never heard that word,” Zhang told me recently as we sat in his office, which looks out across the Charles River and Beacon Hill. Zhang has a perfectly round face, its shape accentuated by rectangular wire-rimmed glasses and a bowl cut. “So I went to Google just to see what was there,” he said. Zhang read every paper he could; five years later, he still seemed surprised by what he found. CRISPR, he learned, was a strange cluster of DNA sequences that could recognize invading viruses, deploy a special enzyme to chop them into pieces, and use the viral shards that remained to form a rudimentary immune system. The sequences, identical strings of nucleotides that could be read the same way backward and forward, looked like Morse code, a series of dashes punctuated by an occasional dot. The system had an awkward name—clustered regularly interspaced short palindromic repeats—but a memorable acronym.

CRISPR has two components. The first is essentially a cellular scalpel that cuts DNA. The other consists of RNA, the molecule most often used to transmit biological information throughout the genome. It serves as a guide, leading the scalpel on a search past thousands of genes until it finds and fixes itself to the precise string of nucleotides it needs to cut. It has been clear at least since Louis Pasteur did some of his earliest experiments into the germ theory of disease, in the nineteenth century, that the immune systems of humans and other vertebrates are capable of adapting to new threats. But few scientists had considered the possibility that single bacterial cells could defend themselves in the same way. The day after Zhang heard about CRISPR, he flew to Florida for a genetics conference. Rather than attend the meetings, however, he stayed in his hotel room and kept Googling. “I just sat there reading every paper on CRISPR I could find,” he said. “The more I read, the harder it was to contain my excitement.”

It didn’t take Zhang or other scientists long to realize that, if nature could turn these molecules into the genetic equivalent of a global positioning system, so could we. Researchers soon learned how to create synthetic versions of the RNA guides and program them to deliver their cargo to virtually any cell. Once the enzyme locks onto the matching DNA sequence, it can cut and paste nucleotides with the precision we have come to expect from the search-and-replace function of a word processor. “This was a finding of mind-boggling importance,” Zhang told me. “And it set off a cascade of experiments that have transformed genetic research...”
Very interesting piece. Read all of it.

Some of my prior posts on the myriad "Omics" issues are here, here, and here.

No more 30 oz of daily Calypso prep water intake. What a relief.


My reaction to a THCB post entitled "Interoperability: Faster Than We Think – An Interview with Ed Park"
“The most useful thing that meaningful use did from an interop standpoint was to standardize all the data dictionaries.”

That is simply not true. Standard nomenclatures/vocabularies are not the same as “standard data dictionaries,” which come at the EHR architectural RDBMS metadata level. Data dictionaries continue to differ from one vendor to another. Because ONC never bothered to study the extent of the differences — by, say, requiring the submission of the database dictionaries as a condition of the MU certification application — we simply still don’t know the magnitude of the variability.

The other thing Mr. Park leaves out of the IEEE interop definition clause “without special effort on the part of the customer.” By “defining interoperability down,” we really could simply declare victory and go home, given that virtually all mainstream EHRs have report-writing functionality that can burp out PDF and XML documents to send as secure attachments — i.e., “data exchange,” materially differing little from faxes.


“…the next advances in interoperability from a technical perspective will not and cannot be legislated. One of the analogies for interoperability, which I find to be a useful starting point, is the thread to a light socket. So everyone got together and decided that there’s one way to build a light socket and everyone conforms to that. Or that there’s one thread to a fire hydrant. That’s a famous example. “If everyone just standardizes the way that hoses connect to fire hydrants then we could have saved that city.” That’s a standard way of looking at interop…”

“Will not be legislated.” Yeah, I buy that. But not the “cannot be” assertion; that’s a choice we’ve made. And, just to be clear, I’m not arguing that the feds would have to derive and publish a data dictionary standard themselves. But, WHERE is the Consensus Standards-Bodies “convening” leadership here? I see a lot of endless talk and slick 4-color 10 Year Plan report-writing, but little else.

We missed the boat on that window of opportunity, I suppose. And, to be sure, there are myriad functional “industry consensus standards” out there across the breadth of industries and technologies. And, to riff on your “socket” analogy, if ONC promulgated an “interop standard” for household electricity, today you’d likely go to Lowe’s to choose from more than 2,000 sizes and shapes of “Stage 2 Certified 120 VAC 15 amp” wall sockets.

Maybe APIs will be the HIT interop panacea. Maybe. I certainly hope so. But citing social media and other online consumer-facing interfaces obscures the reality that the typical incumbent ONC certified ambulatory EHR houses about 4,000 dictionary-defined variables within the schema, not a dozen or two.

More to come...

Thursday, November 5, 2015

Google Ventures on investing in the healthcare space

Interesting interview.

I have no idea why the the embedded iFrame came out so small here. There are no end-user adjustable parameters in the underlying iFrame html code. 

Link to the original Bloomberg article here. Alternatively, you can also click the little 4-arrows "expand-to-full-screen" icon in the lower right corner of the video (hover over that area).

Pretty harsh assessment of Theranos commences at 03:30. Recall my prior coverage of the Theranos controversy here, here, and here.

Lots of other stuff to report on: MU, Interop, ICD-10, AHRQ, Theranos (the gift that keeps giving), more Omics stuff, etc. Maybe after I get back from RadOnco. I'm getting short. Only 4 Calypso IMRT tx sessions left out of the 45. I finish next Tuesday, the 10th. I'm a bit behind. Took some time out to go the Minnesota for my Grandson's final home football game at St. Olaf (he's a senior).


From The Neurologica Blog:
The Ben Carson Contradiction

By all accounts, Ben Carson is a brilliant pediatric neurosurgeon. He was the Director of Pediatric Neurosurgery at Johns Hopkins Hospital until he retired, and received the Presidential Medal of Freedom for his surgical achievements...
Carson is also evidence that people who hold extreme or anti-scientific beliefs are not necessarily stupid. Belief in pseudoscience and the paranormal is not about general intelligence. It is about the human tendency to form and maintain beliefs for a variety of social, cultural, and personal reasons...
What we can conclude about Carson is that he is not systematically following a valid intellectual process in forming his beliefs. He has no problem dismissing the opinion of experts and scientists, and substituting his own poorly-informed hunches. Obviously this is a disturbing trait in someone running for high office.
So much for the "transfer of training" argument. Dr. Carson is a one-man refutation.

More to come...