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Monday, June 18, 2018

EHR Science update

My online pal Dr. Jerome Carter has resurfaced. He's been burrowed away for months working on what he calls "a monograph" (he'd asked me to be one of the pre-pub reviewers).

From his latest blog post:
…Clinical processes have many moving parts, and many of those parts are ad-hoc adaptations (workarounds) invented by process participants. Frequently, there is a significant difference between what should happen (formal process, as written in policy and procedure documentation) and what actually happens—even when no EHR is present. Process variations may be introduced by a number of factors. Variations created by those performing the process may or may not be a good idea. (After all, workarounds are not necessarily bad if the formal process is poorly designed.) Likewise, patients may introduce process variations, and those variations are actually good if they help to ensure each patient gets the care that is best for his/her situation.

The unavoidable reality is that clinical environments are inherently dynamic and messy, and when safety or quality issues arise, the underlying causes are likely to be multi-factorial. No two ICUs work the same, and primary care practices, even those under the auspices of the same organization, may vary.  So what does all of this mean? It means we need a more scientific way of describing, decomposing, and modeling clinical processes so that for any given process we understand what it actually accomplishes, how it affects patients and those who perform it, and what goes wrong.  The first stab at meeting all of these requirements is found in the two chapters currently in progress.

Matters of software usability and safety have also taken on a new light with this evolution in thinking on clinical processes. Software implementation adds new ways of performing tasks, disrupting existing clinical processes. The resulting disruptions are only partially understood because the original processes were probably incompletely understood and documented. Thus, addressing usability and safety issues requires both looking deeply into existing processes and their variations in addition to looking at software-specific issues. Stated another way, workarounds and disruptions that arise after EHR implementation are not likely arising in an otherwise orthodox process environment. The more probable case is that heterodoxy is already present and the EHR simply adds some of its own.
Further, the mistaken belief that orthodoxy ever prevailed likely results in many futile attempts to correct the problems that arise after implementation.

Usability testing, as now performed, does not have a well-defined method for capturing the nuances of clinical processes in a standard way. Further, usability research is itself not standardized across researchers and institutions. Since each care setting is different, usability findings in one setting may not apply well in another, even though they are ostensibly the same…
I really look forward to reading it.

I've posted on "workflow" many times, see, e.g., Clinical workflow: "YAWL," y'all?

Tangentially apropos, I've been poring over a massive book (849 pages) lately as a registered Springer "journalist online reviewer" It's way too expensive for my piss-ant budget.

You gotta be kidding.

(BTW, I got onto this book in the wake of hooking up with "The International Center for Information Ethics.")

I can peruse all of it via the cumbersome template interface, but cannot screen-scrape any excerpts. I can get at some non-firewalled summary info, though. to wit:
This handbook enumerates every aspect of incorporating moral and societal values into technology design, reflects the fact that the latter has moved on from strict functionality to become sensitive to moral and social values such as sustainability and accountability. Aimed at a broad readership that includes ethicists, policy makers and designers themselves, it proffers a detailed survey of how technological, and institutional, design must now reflect awareness of ethical factors such as sustainability, human well-being, privacy, democracy and justice, inclusivity, trust, accountability, and responsibility (both social and environmental). Edited by a trio of highly experienced academic philosophers with a specialized interest in the ethical dimensions of technology and human creativity, this syncretic handbook collates an array of published material and offers a studied, practical introduction to the field. The volume addresses myriad aspects at the intersection of technology design and ethics, enabling designers to adopt a constructive approach in anticipating, preventing, and resolving societal and ethical issues affecting their work. It covers underlying theory; discrete values such as democracy, human well-being, sustainability and justice; and application domains themselves, which include architecture, bio- and nanotechnology, and military hardware. As the first exhaustive survey of a field whose importance is characterized by almost exponential growth, it represents a compelling addition to a formerly atomized literature.

The design of new products, public utilities, and the built environment is traditionally seen as a process in which the moral values of users and society hardly play a role. The traditional view is that design is a technical and value-neutral task of developing artifacts that meet functional requirements formulated by clients and users. These clients and users may have their own moral and societal agendas, yet for engineers, these are just externalities to the design process. An entrenched view on architecture is that “star” architects and designers somehow manage to realize their aesthetic and social goals in their design, thus imposing their values rather than allowing users and society to obtain buildings and artifacts that meet user and societal values.
The table of contents via Mac graphical snips (Shift-Ctrl-Command-4, click-drag).

I am principally interested in implications for improving healthcare tech (e.g., EHR, mHealth UX) and intertwined privacy considerations.

Lots to consider. Stay tuned.


While we were up in Napa for Father's Day Brunch we heard this NPR/KQED segment while driving home.
City Arts and Lectures
The New Science Of Psychedelics With Michael Pollan

When Michael Pollan set out to research how LSD and psilocybin (the active ingredient in magic mushrooms) are being used to provide relief to people suffering from difficult-to-treat conditions such as depression, addiction and anxiety, he did not intend to write what is undoubtedly his most personal book. But upon discovering how these remarkable substances are improving the lives not only of the mentally ill but also of healthy people coming to grips with the challenges of everyday life, he decided to explore the landscape of the mind in the first person as well as the third. Thus began a singular adventure into the experience of various altered states of consciousness, along with a dive deep into both the latest brain science and the thriving underground community of psychedelic therapists. In “How to Change Your Mind: What the New Science of Psychedelics Teaches Us About Consciousness, Dying, Addiction, Depression, and Transcendence,” Pollan sifts the historical record to separate the truth about these mysterious drugs from the myths that have surrounded them since the Sixties, when a handful of psychedelic evangelists catalyzed a powerful backlash against what was then a promising field of research. Pollan’s other books include “Omnivore’s Dilemma,” “The Botany of Desire,” “Food Rules,” and “Cooked.”
They've not yet posted the audio. I will embed it as soon as it becomes available. I'm reading his book.


ICD-10 K40.90. Should be an interesting day.

More to come...

America is better than this?

My Father's Day...

But, hey, at least North Korea is no longer a nuclear threat.

Friday, June 15, 2018


Elizabeth Holmes indicted on wire fraud charges, steps down from Theranos

Theranos founder Elizabeth Holmes has been indicted on federal wire fraud charges, the office of the United States Attorney for the Northern District of California announced Friday.

Holmes and former Theranos COO and president Ramesh "Sunny" Balwani allegedly engaged in a multi-million dollar scheme to defraud investors, as well as a scheme to defraud doctors and patients, according to a release from the US Attorney's office.

Holmes and Balwani are charged with two counts of conspiracy to commit wire fraud and nine counts of wire fraud. The indictments happened Thursday and were unsealed on Friday. If convicted, they each face a maximum sentence of 20 years in prison and a fine of $250,000, plus restitution for each count of wire fraud and each conspiracy count, according to the US Attorney's office…
See my prior post "Holmes and Balwani should be indicted."


Elizabeth Holmes founded Theranos in 2003 when she was 19 years old. At its height, the company reached a valuation of over $9 billion on the strength of its promise that it had revolutionized the blood-testing industry. Friday, an unraveling that began in October 2015 with a series of Wall Street Journal articles accelerated, as Holmes and her colleague Ramesh “Sunny” Balwani were indicted on multiple counts of fraud. Holmes has also stepped down as CEO.

The indictment, which comprises 11 counts, alleges that Theranos misled both investors—one of whom sent Theranos nearly $100 million in a single wire transfer October 31, 2014—and doctors and patients with its promises of a blood test that delivered quick results with a single finger-prick, rather than the more demanding requirements of conventional methods.

“Holmes and Balwani devised a scheme to defraud doctors and patients, through advertisements and marketing materials, through explicit and implicit claims concerning Theranos’s ability to provide accurate, fast, reliable, and cheap blood tests and test results, and through omissions concerning the limits of and problems with Theranos’s technologies,” the indictment reads…

Holmes has been held up as the ultimate symbol of Silicon Valley’s “fake it til you make it” culture, and for good reason. But the reason the Theranos saga has resonated so deeply, and that Holmes and Balwani face such serious charges now, is that the scandal also transcends the typical tech hype cycle. Theranos wasn’t promising a better juicer, or a shift in the human resources paradigm. It had a direct effect on medical diagnoses: The indictment alleges that Holmes and Balwani knowingly passed along test results that were inaccurate and unreliable. You can’t move fast and break things when those things are human lives...
Felix Salmon at Slate:
Elizabeth Holmes Deserves Prison, but Her Indictment Won’t Make Silicon Valley Any Less Reckless

The long-awaited criminal complaint has now arrived, and Elizabeth Holmes, the founder of medical-tech startup Theranos, has been indicted on two counts of conspiracy to commit wire fraud and nine counts of wire fraud. The charges could send her to prison for as long as 20 years; given the sums of money involved, and the utter lack of remorse that she has shown as her company has imploded in scandal, there’s every reason to expect that if she’s found guilty, her sentence will be at the upper end of that range.

None of this is problematic in the slightest. If you’ve read John Carreyrou’s book about Theranos, you will almost certainly think that Holmes, along with her co-defendant Sunny Balwani, very much deserves anything that’s coming to them. After all, she didn’t just waste investors’ money. Hers was a health-care company, and her fraud—claiming that her finger-prick blood-testing technology worked when it largely didn’t, leading to tens of thousands of voided test results—endangered people’s lives.

But while it’s good that Holmes and Balwani are being prosecuted, there’s another message being sent here by the U.S. Attorney’s Office in the northern district of California. Which is, implicitly: If you’re a startup and you’re not in the highly regulated health-care industry, then you probably can continue to embrace Silicon Valley’s fake-it-till-you-make-it ethos without fear of criminal prosecution…
Not sure I agree about sentencing severity for Holmes.

Maybe Balwani, though (do I really need to spell it out?).

More to come...

Tuesday, June 12, 2018

Omics update: microbiome implications for clinical care

I've addressed the broad topic of "Omics" sciences and technologies a number of times in prior posts. On a personal level, earlier in the year, an article in Science Magazine spoke to issues in cancer therapies that seem to be adversely impacted by gut microbiota bearing certain genetic profiles. I found it of particular interest, given that they gave the example of attenuating or neutralizing microbiome impacts on the Folfirinox chemo that my (now late) daughter was undergoing.

More stuff to have to know and consider.

Just saw a book review in a new issue of Science.
Probing the Microbial

Angela Douglas is an internationally recognized expert on symbiosis, with a number of foundational texts to her name (1, 2). In her new book, Fundamentals of Microbiome Science, Douglas synthetizes data from the burgeoning field of microbiome science in eight highly informative chapters. Topics include the origins of the animal microbiome, what we know about the microbiome's interactions with the immune system, hints at how microbes drive animal behavior, and how the gut microbiota are involved in gut-brain communication. The book also clearly delineates the influence of the microbiome in determining human health and disease.

The microbiome revolution is expanding at breakneck speed and moving from “the study of correlation to causation and mechanism.” For example, mice lacking the leptin gene, which regulates satiety, consume more food and become obese. When the microbiota of obese mice are transferred to lean mice, the mice eventually become obese.

The reciprocal mechanisms involved in the interactions between the immune system and the microbiota are just beginning to be understood. In mammals, for example, the production of immunoglobulin A prevents contact of the microbiota with the epithelial cells of the gut, thus impeding microbe access to internal organs. Other innate immune effectors, including antimicrobial peptides, lectins, and certain enzymes, complement this effect, but many other factors (e.g., age of host, sex, and genotype) could also influence the outcome. The immune system can thus promote, tolerate, or inhibit the composition of the microbiota. In contrast, the microbiota can “promote or dampen immune system function,” and the effects of microbial products on the regulation of immune effectors have been implicated in this process…

This one is heavy duty.

This book is about animal microbiomes: the microorganisms that inhabit the body of animals, including humans, and keep their animal hosts healthy. In recent years, animal microbiomes have become a hot topic in the life sciences. Academic, commercial, and funding institutions are investing in major microbiome research centers and funding initiatives; microbiomes are the topic of special issues in journals, conference symposia, and new undergraduate and graduate courses; microbiomes have twice been a Science journal “breakthrough of the year” (in 2011 and 2013); and the US National Microbiome Initiative was announced from the White House in May 2016. Why all the excitement about microbiomes? The reasons are twofold: microbiome science provides a radically different way to understand animals, and it offers the promise of novel therapies, especially for human health…

1.4. Scope of This Book

The realization that every animal is colonized by microorganisms that can shape its health and well-being is transforming our understanding of animal biology. The purpose of this book is to provide some initial explanations and hypotheses of the underlying animal-microbial interactions. For this, we need multiple disciplinary perspectives.

We start with evolutionary history in chapter 2. The propensity of animals to associate with microorganisms has ancient roots, derived from both the predisposition of all eukaryotes to participate in associations and, likewise, the tendency of many bacteria to interact with different organisms, often to mutual benefit. Chapter 2 outlines the patterns of these interactions, especially in taxa related to animals and basal animal groups. Interactions are mediated by chemical exchange, enhancing access to energy and nutrients and providing chemical information that enables the interacting organisms to anticipate and respond adaptively to environmental conditions. Many of these core interactions were firmly established in the ancestor of animals. The multicellular condition of animals, sophisticated immunological function of even basal animals, and key animal innovations, including the polarized epithelium and the gut, play important roles in shaping the pattern of animal-microbial interactions.

Although all animals are associated with microorganisms, we know more about the microbiome of humans than any other animal. Chapter 3 addresses current understanding of the role of the microbiome in human health. Studies of the microbiology of humans combined with experimental analyses of model animals are revealing complex problems—and some solutions. The complexity lies in the great diversity of microorganisms within each individual human, as well as considerable among-individual variation; and the importance of the microbiome is reinforced by the increasing evidence for microbial involvement in some diseases, especially metabolic and immunological dysfunctions. Western lifestyles, including diet and antibiotic treatment, have been argued to contribute to the incidence of microbiome-associated diseases, with opportunities for microbiological restoration by microbial therapies.

Our understanding of interactions between animals and the microbiome is most developed in relation to the immune system, and this is the focus of chapter 4. It is now apparent that animal immune system is a key regulator of the abundance and composition of the microbiota, and that immunological function is strongly regulated by the composition and activities of the microbiome. The immune system cannot be understood fully except in the context of the microbiology of the animal. Furthermore, this highly interactive system is overlain by microbial-mediated protective functions, essentially comprising a second immune system.

Chapter 5 investigates the role of the microbiome in shaping animal, including human, behavior. It has long been known that pathogens can drive animal behavior, and there is now increasing evidence that resident microorganisms can have similar, although often more subtle, effects. Research has focused primarily on three aspects of animal behavior: feeding behavior, chemical communication among animals, especially in relation to social interactions, and the mental well-being of mammals, including humans. As chapter 5 makes clear, this topic has attracted tremendous levels of interest, but fewer definitive data.

The impacts of animal-associated microorganisms on host health and their interactions with the immune system and nervous system of animals (chapters 3–5) have one overriding theme in common: that these interactions are complex, with multiple interacting variables. This complexity can often appear to defy comprehension. Chapter 6 discusses the ecological approaches that have the potential to solve many of these problems of complexity. Treating the animal as an ecosystem, we can ask multiple questions: what are the ecological processes that shape the composition and diversity of microbial communities, and how do these properties of the microbial communities influence overall function of the ecosystem? Research on complex microbiomes, especially in the animal gut, as well as one-host-one-symbiont systems are revealing the role of interactions among microorganisms and interactions between the microorganisms and host in shaping the diversity of the microbiome. Furthermore, the response of individual taxa and interactions can influence the stability of communities to external perturbations, ranging from the bleaching susceptibility of shallow-water corals to the gut microbiota composition of humans administered with antibiotics.

In chapter 7, the evolutionary consequences of animal-microbial associations are considered. There is a general expectation that the fitness of both animal and microbial partners is enhanced by these associations largely through the reciprocal exchange of services. Nevertheless, hosts can exploit their microbial partners, and there are indications that animals can be addicted to their microbial partners. At a broader scale, this chapter investigates how these associations affect the rate and pattern of evolutionary diversification of the microbial and animal partners. In addition to evidence for coevolutionary interactions and facilitation of horizontal gene transfer, various studies point to a direct role of microbiota in interrupting gene flow and speciation by both prezygotic and postzygotic processes.

Finally, chapter 8 addresses the implications of the microbiology of animals and some key priorities for future research. It is now abundantly clear that the microbiome has pervasive effects on the physiological and developmental systems of animals and the resultant animal phenotype. One of the big biological questions in the life sciences today concerns how the phenotype of an animal maps onto its genotype and the underlying physiological and developmental mechanisms. The answers to this question will require the integration of the microbiome with the traditional animal-only explanations of animal function. As this book illustrates, the technologies and concepts to achieve this intellectual transformation of animal biology are largely in place. Why is this integration of disciplines needed? Beyond the fundamental priority to understand and explain, the microbiome offers important, but currently untapped, routes to promote human health and to mitigate and manage some of the damaging effects of human activities on our environment.

Douglas, Angela (2018-05-14T23:58:59). Fundamentals of Microbiome Science: How Microbes Shape Animal Biology (Kindle Locations, 114-121, 333-386). Princeton University Press. Kindle Edition.
Downstream from the research science, we'll likely see another "omics" subspecialty dealing with the microbiome and its implications for front-line clinical care. Docs in the "productivity treadmill" exam rooms will neither have the expertise nor the time to ruminate on these details directly.


Of course, this stuff will inevitably bring us back around to Health IT, specifically "AI." Specifically, recall my prior "There IS no Precision Medicine without AI."


Recall my prior post "Holmes and Balwani should be indicted." An interview by Vanity Fair's Nick Bilton with "Bad Blood" author John Carryrou.
Silicon Valley is notoriously full of founders who exaggerate, intentionally lie to the media, and dupe investors, and even Congress. But there are few stories that rival the fraud behind Theranos, the blood-testing company once worth $10 billion, and now worth nothing. John Carreyrou, author of a new book, "Bad Blood," joins us to explain how the company's CEO, Elizabeth Holmes, defrauded everyone who came into her orbit, how she might still end up behind bars, and he answers the question on everyone's mind: Is Holmes a sociopath?
"According to Carreyrou, Holmes is currently waltzing around Silicon Valley, meeting with investors, hoping to raise money for an entirely new start-up idea. (My mouth dropped when I heard that, too.)"

More to come...

Sunday, June 10, 2018

A very sad loss: Anthony Bourdain, RIP

I only watched his show every now and then. But, I've been binge-watching the CNN back-to-back tribute episodes this weekend. Very sad that we've lost him. Suicidal depression, man, terrible.


Wednesday, June 6, 2018

Factfulness: Hans Rosling's new book.

I have long liked the statistical data visualization work of (the now sadly late) Hans Rosling.

My wife informed me of his recent book this morning.

I ordered the hardcopy via my Amazon Prime. Will probably also get the Kindle edition, once I clear some of my current huge reading pile.

This is painful for me to read:
When he was 20, in 1968, doctors told Rosling that there was something wrong with his liver and as a consequence he stopped drinking alcohol. In 1989, Rosling was diagnosed with hepatitis C. Over the years this progressed and Rosling developed liver cirrhosis. In the beginning of 2013 he was in early stages of liver failure. However, at the same time new hepatitis C drugs were released and Rosling went to Japan to buy the drugs needed to cure the infection. He expressed concerns in the media over the restricted use of the new drugs due to high costs, stating that it is a crime not to give every person with hepatitis C access to the drugs.

A year after being diagnosed with pancreatic cancer, Rosling died in Sweden on 7 February, 2017 at the age of 68.
Pancreatic cancer, ugh.


The never-ending book pile accrual.

Stay tuned.

More to come...

Sunday, June 3, 2018

Dr. Atul Gawande commencement address, UCLA Medical School, June 1st 2018

As reported by The New Yorker:

"I want to start with a story. One night, on my surgery rotation, during my third year of medical school, I followed my chief resident into the trauma bay in the emergency department. We’d been summoned to see a prisoner who’d swallowed half a razor blade and slashed his left wrist with the corner of the crimp on a toothpaste tube. He was about thirty, built like a boxer, with a tattooed neck, hands shackled to the gurney, and gauze around his left wrist showing bright crimson seeping through.

The first thing out of his mouth was a creepy comment about the chief resident, an Asian-American woman. I won’t say what he said. Just know he managed in only a few words to be racist, sexist, and utterly menacing to her. She turned on her heels, handed me the clipboard, and said, “He’s all yours.”

I looked at the two policemen with him to see what they were going to do. I don’t know what I expected. That they’d yell at him? Beat him? But they only looked at me impassively, maybe slightly amused. He was all mine.
So what now?

Graduates, wherever you go from here, and whatever you do, you will be tested. And the test will be about your ability to hold onto your principles. The foundational principle of medicine, going back centuries, is that all lives are of equal worth.
This is a radical idea, one ultimately inscribed in our nation’s founding documents: we are all created equal and should be respected as such. I do not think it a mere coincidence that among the fifty-six founding fathers who signed the declaration of our independence was a physician, Dr. Benjamin Rush. He was a committed revolutionary and abolitionist precisely because of his belief in the principle.

We in medicine do not always live up to that principle. History has been about the struggle to close the gap between the aspiration and the reality. But when that gap is exposed—when it turns out that some people get worse or no treatment because of their lack of money, lack of connections, background, darker skin pigment, or additional X chromosome—we are at least ashamed about it. We believe a C.E.O. and a cabbie with the same heart disease deserve the same chance at survival.
Hospitals are one of the very few places left where you encounter the whole span of society. Walking the halls, you begin to understand that the average American is someone who has a high-school education and thirty thousand dollars a year in per-capita earnings, out of which thirty per cent goes to taxes and another thirty per cent to housing and health-care costs. (These Americans are also told, by the way, that people like them, the majority of the population, have no future in a knowledge economy, because, hey, what can anyone do about it, anyway?) Working in health care, you also know, more than most, that we incarcerate more people than any other economically developed country; that thirty per cent of adults carry a criminal arrest record; that seven million people are currently incarcerated, on parole, or on probation; and that a massive and troubling proportion of all of them are mentally ill or black.

Most people don’t have this broad vantage. We all occupy our own bubbles. Trust in others, even our neighbors, is at an historic low. Much of society has become like an airplane boarding line, with different rights and privileges for zones one to ninety-seven, depending on your wealth, frequent-flier miles, credit rating, and S.A.T. scores; and many of those in line think—though no one likes to admit it—that they deserve what they have more than the others behind them. Then the boarding agent catches some people from zone eighty-four jumping ahead of the people in zone fifty-seven, and all hell breaks loose.

Insisting that people are equally worthy of respect is an especially challenging idea today. In medicine, you see people who are troublesome in every way: the complainer, the person with the unfriendly tone, the unwitting bigot, the guy who, as they say, makes “poor life choices.” People can be untrustworthy, even scary. When they’re an actual threat—as the inmate was for my chief resident—you have to walk away. But you will also see lots of people whom you might have written off prove generous, caring, resourceful, brilliant. You don’t have to like or trust everyone to believe their lives are worth preserving.

We’ve divided the world into us versus them—an ever-shrinking population of good people against bad ones. But it’s not a dichotomy. People can be doers of good in many circumstances. And they can be doers of bad in others. It’s true of all of us. We are not sufficiently described by the best thing we have ever done, nor are we sufficiently described by the worst thing we have ever done. We are all of it.

Regarding people as having lives of equal worth means recognizing each as having a common core of humanity. Without being open to their humanity, it is impossible to provide good care to people—to insure, for instance, that you’ve given them enough anesthetic before doing a procedure. To see their humanity, you must put yourself in their shoes. That requires a willingness to ask people what it’s like in those shoes. It requires curiosity about others and the world beyond your boarding zone.

We are in a dangerous moment because every kind of curiosity is under attack—scientific curiosity, journalistic curiosity, artistic curiosity, cultural curiosity. This is what happens when the abiding emotions have become anger and fear. Underneath that anger and fear are often legitimate feelings of being ignored and unheard—a sense, for many, that others don’t care what it’s like in their shoes. So why offer curiosity to anyone else?

Once we lose the desire to understand—to be surprised, to listen and bear witness—we lose our humanity. Among the most important capacities that you take with you today is your curiosity. You must guard it, for curiosity is the beginning of empathy. When others say that someone is evil or crazy, or even a hero or an angel, they are usually trying to shut off curiosity. Don’t let them. We are all capable of heroic and of evil things. No one and nothing that you encounter in your life and career will be simply heroic or evil. Virtue is a capacity. It can always be lost or gained. That potential is why all of our lives are of equal worth.

In medicine, you are asked to open yourself to others’ lives and perspectives—to people as well as to circumstances you do not and perhaps will not understand. This is part of what I love most about this profession. It aims to sustain bedrock values that matter across all of society.

But the work of preserving those values is hard. When I began my story, I made a point of not telling you the inmate’s crime, although one of the policemen told me. I wasn’t sure whether it’d change how open you’d be to putting yourself in my shoes as I wrestled with what to do.

The man’s vital signs were normal. He had no abdominal tenderness. An X-ray showed the razor hadn’t perforated his gastrointestinal tract. I put on gloves and unwrapped his blood-soaked dressing. I held pressure. He’d made numerous slashes but none deep enough to reach an artery. I’d heard that inmates sometimes swallowed blades wrapped in cellophane or inflicted wounds on themselves that, though not life-threatening, were severe enough to get them time out of prison. This man had done both.

I tried to summon enough curiosity to wonder what it had taken to push him over that edge, but I couldn’t. I only saw a bully. As I reluctantly set about suturing together the long strips of skin on his forearm, he kept up a stream of invective: about the hospital, the policemen, the inexpert job I was doing. I don’t do well when I feel humiliated. I had the urge to tell him to shut up and be a little appreciative. I thought about abandoning him.

But he’d controlled himself enough to hold still for my ministrations. And I suddenly remembered a lesson a professor had taught about brain function. When people speak, they aren’t just expressing their ideas; they are, even more, expressing their emotions. And it’s the emotions that they really want heard. So I stopped listening to the man’s words and tried to listen for the emotions.

“You seem really angry and like you feel disrespected,” I said.

“Yes,” he said. “I am. I am angry and disrespected.”

His voice changed. He told me that I have no idea what it was like inside. He’d been in solitary for two years straight. His eyes began to water. He calmed down. I did, too. For the next hour, I just sewed and listened, trying to hear the feelings behind his words.

I didn’t understand him or like him. But all it took to see his humanity—to be able to treat him—was to supply that tiny bit of openness and curiosity.

Graduates, you have studied for thousands of hours on end. You will be licensed to make diagnoses and prescribe an armament of drugs and procedures. Most of all, you will be given trust to see human beings at their most vulnerable and serve them. That trust is earned because of your values, your commitment to serving all as equals, and your openness to people’s humanity. The renewal of these values is why we’re all so grateful to be here—and so grateful that you will carry those values on, beyond us.""
"...You will be given trust to see human beings at their most vulnerable and serve them. That trust is earned because of your values, your commitment to serving all as equals, and your openness to people’s humanity." 
 Empathy. Not a synonym for "sympathy." More on that to come.

After reading that address I thought immediately of Dr. Rachel Pearson (@HumanitiesMD), whose book is also a must-read.


Thursday, May 31, 2018

Update on our favorite whipping boy, the EHR

From Trump's "failing NY Times" (I finally ponied up and subscribed, along with forking over at WaPo):

There are times when the diagnosis announces itself as the patient walks in, because the body is, among other things, a text. I’m thinking of the icy hand, coarse dry skin, hoarse voice, puffy face, sluggish demeanor and hourglass swelling in the neck — signs of a thyroid that’s running out of gas. This afternoon the person before me in my office isn’t a patient but a young physician; still, the clinical gaze doesn’t turn off, and I diagnose existential despair.

Let’s not call this intuition — an unfashionable term in our algorithmic world, although there is more to intuition than you think (or less than you think), because it is a subconscious application of a heuristic that can be surprisingly accurate. This physician, whose gender I withhold in the interest of anonymity and because the disease is gender-neutral, is burned out in what should be the honeymoon of a career. Over the years, I have come to recognize discrete passages in a medical life, not unlike in Shakespeare’s “Seven Ages of Man” — we have our med-school equivalent of “the whining schoolboy with his satchel and shining morning face” and the associate professor “jealous in honor, sudden and quick in quarrel.” But what I see in my colleague is disillusionment, and it has come too early, and I am seeing too much of it.

Does this physician recall sitting before me as an idealistic first-year medical student, keen to take the world in for repairs? It was during those preclinical years that the class learned to use the stethoscope, the ophthalmoscope and the tendon hammer, to percuss the body, sounding out its hollows, the territorial boundaries of lung and liver. After the preclinical come the two clinical years, though I think of those phases these days as precynical and cynical. When students arrive on the wards full time, white coats packed with the aforementioned instruments, measuring tape, tuning fork, flashlight and Snellen eye chart, they are shocked to find that the focus on the ward doesn’t revolve around the patients but around the computers lining the bunkers where students, residents and attending physicians spend the majority of their time, backs to one another. All dialogue among them and other hospital staff members — every order, every lab request and result — must pass through this electronic portal, even if the person whose inbox you are about to overload is seated next to you.

In America today, the patient in the hospital bed is just the icon, a place holder for the real patient who is not in the bed but in the computer. That virtual entity gets all our attention. Old-fashioned “bedside” rounds conducted by the attending physician too often take place nowhere near the bed but have become “card flip” rounds (a holdover from the days when we jotted down patient details on an index card) conducted in the bunker, seated, discussing the patient’s fever, the low sodium, the abnormal liver-function tests, the low ejection fraction, the one of three blood cultures with coagulase negative staph that is most likely a contaminant, the CT scan reporting an adrenal “incidentaloma” that now begets an endocrinology consult and measurements of serum cortisol.

The living, breathing source of the data and images we juggle, meanwhile, is in the bed and left wondering: Where is everyone? What are they doing? Hello! It’s my body, you know!…

My young colleague slumping in the chair in my office survived the student years, then three years of internship and residency and is now a full-time practitioner and teacher. The despair I hear comes from being the highest-paid clerical worker in the hospital: For every one hour we spend cumulatively with patients, studies have shown, we spend nearly two hours on our primitive Electronic Health Records, or “E.H.R.s,” and another hour or two during sacred personal time. But we are to blame. We let this happen to our trainees, to ourselves.

How we salivated at the idea of searchable records, of being able to graph fever trends, or white blood counts, or share records at a keystroke with another institution — “interoperability”! — and trash the fax machine. If every hospital were connected, we would have a monster database, Big Data that’s truly big and that would allow us to spot trends in disease so much earlier and determine best practice and predict complications. But we didn’t quite get that when, as part of the American Recovery and Reinvestment Act of 2009, $35 billion was eventually steered toward making medicine paperless.

My A.T.M. card is amazing: I can get cash and account details all over America and beyond. Yet I can’t reliably get a patient record from across town, let alone from a hospital in the same state, even if both places use the same brand of E.H.R., for reasons that are only partly explained by software that has been customized for each site. This is not like sending around a standard Word file. And so, too often the record comes by fax.

What the E.H.R. has done is help reduce medication errors; it is a wonderful gathering place for laboratory and imaging information; the notes are always legible. But the leading E.H.R.s were never built with any understanding of the rituals of care or the user experience of physicians or nurses. A clinician will make roughly 4,000 keyboard clicks during a busy 10-hour emergency-room shift. In the process, our daily progress notes have become bloated cut-and-paste monsters that are inaccurate and hard to wade through. A half-page, handwritten progress note of the paper era might in a few lines tell you what a physician really thought. (A neurosurgeon I once worked with in Tennessee would fill half the page with the words “DOING WELL” in turquoise ink, followed by his signature. If he deviated from that, I knew he was very worried and knew to call him.) But now, with a few keystrokes, you can populate your note with all the listed diagnoses, all the medications, all the labs, all the radiology reports, pages and pages of these, as well as enough “smart phrases” — “.EXT2” might spit out “Extremities-2+ pedal edema, normal pulses” — to allow you to swear you personally examined the patient from head to foot and personally took all the elements of the history, personally did a physical exam separate from the admitting physician that would put Sir William Osler to shame, all of which make it possible to bill at the highest level for that encounter (“upcoding”)...
"For every one hour we spend cumulatively with patients, studies have shown, we spend nearly two hours on our primitive Electronic Health Records..."

I'm still having trouble believing that. It is, however, an empirical matter, vague "studies have shown" anecdotes aside. (See, e.g., my 2014 riff on data-mining the EHR security logs for workflow analytics.)

Read the entire NY Times piece.

apropos, see a couple of my prior posts: "Are structured data the enemy of  health care quality?" and "Clinical cognition in the digital age."

And, of course, we musn't forget English major @Healthcare_Kate's swell "EHRs are a dying technology."

The NY Times article headline cites 'Machine Learning." But, I've noted possible "reproducibility problems."

Finally (for now). see my post "Fix the EHR?" Of course, but how about fixing the clinical process workflows?


Five weeks since my daughter died. Still seems like last night. Sigh...

Next up for me? The SAVR px. Just thrilled. Meeting with my Primary and my Cardiologist tomorrow, then the Cardiac Surgeon next Tuesday. I had a coronary angiogram done. Negative for blockages, so I'm looking at "just" a straight aortic valve job.

BTW, Danielle's former employer has launched the Danielle L. Gladd Scholarship Fund in her honor and memory. I just contributed.


Another cautionary tale regarding medical charts, this one having zilch to do with keystrokes and mouse clicks.
Your Medical Chart Might be Biased. Here’s What Doctors Should Do About It.
Racial disparities in health outcomes are complicated, but this is one place to start.

…A recent paper caught my eye because it captured one of the more subtle aspects of the brew: how we write about patients in the chart. Mary Catherine Beach and her colleagues at Johns Hopkins University were curious about whether our choice of language transmits bias from one medical professional to another. The researchers created a hypothetical case of an African American man with sickle cell disease, a condition that typically requires opiate medications for control of painful flares. They wrote two versions of the medical chart, one with neutral language and one with language—taken from real charts—that could be viewed as more stigmatizing. Medical students and residents were randomized to read one of the charts and then asked about their attitude toward the patient and how much pain medication they would prescribe.

Those trainees who read the chart with the more stigmatizing language exhibited more negative attitudes toward the patient and elected to give less aggressive pain treatment. This result is probably not surprising—we know that black patients tend to receive lower rates of pain treatment. But what is intriguing is how subtle the differences in language were between the two charts. In the first chart, the patient was described as a “28-year old man with sickle cell disease” and in the second chart as a “28-year old sickle cell patient.” Before the symptoms occurred the patient “spent yesterday afternoon with friends” versus “was hanging out with friends outside McDonalds.”

For the physical examination, the doctor observed in the first chart that the patient “is in obvious distress,” and in the second that the patient “appears to be in distress.” A nursing note in the first chart reported that the patient “is not tolerating the oxygen mask and still has 10/10 pain,” and in the second chart that the patient “refuses to wear his oxygen mask and is insisting that his pain is ‘still a 10.’ ”

The descriptions in the second chart weren’t necessarily inaccurate, but together they subtly paint the patient as a less reliable person, someone who perhaps is trying to game the system for drugs. According to Beach, this type of language not only discredits the patient’s report of pain, but highlights details that reinforce negative stereotypes. Medical charts are the primary means of communication among medical professionals, so this sort of language covertly signals to other members of the team that this is a ‘low class’ person who isn’t trustworthy or deserving.

As soon as Beach put it this way, I could see that our supposedly objective medical records contain racially laden dog whistles of the sort that we regularly decry in political speech. In the last two years we’ve gotten more adept at noticing and calling out references to inner cities, illegal aliens, international bankers, Sharia law, and locker-room talk, but we doctors like to think that we treat all our patients equally. We would never think of ourselves as racist or marginalizing. Yet, it’s there in our language…
Seriously doubt that digital "AI/NLU" (Natural Language Understanding) tech portends any help there.

I love Dr. Ofri's work, and have cited her many times.

Numerous relevant Danielle Ofri articles up on Slate, btw.

I'd like to know what Rachel Pearson ("@HumanitiesMD") thinks about the foregoing. I keep bugging her about wanting to read her Doctoral Dissertation, to no avail as yet. "You must be the only person in the country who wants to read it."
Summary of Dissertation:

Objectivity is an epistemological virtue that physicians aspire to embody in our practice. Historians and philosophers have pointed out that objectivity is culturally specific: it varies with time, place, and profession. In pre-clinical training, physicians learn to honor a scientific version of objectivity, in which the self is understood primarily as a potential source of error and “scientific selves” seeks to eradicate the pernicious influence of the self from scientific data. In practice, however, this research identifies that medical objectivity is distinct from scientific objectivity. This dissertation examines memoirs of medical training to understand how physician trainees learn, experience, and use objectivity...
All part of a piece, 'eh?

More to come...

Friday, May 25, 2018

Holmes and Balwani should be indicted

I finished John Carryrou's riveting Theranos expose´ book Bad Blood in short order.

I closely studied every word from cover to cover. It is now awash in Kindle yellow highlighter and bookmarks.

Click to enlarge

It is infuriating.

The latest hardcopy issue of my AAAS Science Magazine showed up in my mailbox yesterday. Among the book reviews:
A biotech company’s blood test proves too good to be true
By Jennifer Couzin-Frankel

In the opening pages of Bad Blood, the chief financial officer for the blood-testing company Theranos meets with his boss, Elizabeth Holmes, a charismatic 20-something Stanford University dropout, and warns her that the company must stop lying to its investors. Holmes’s expression turns icy. She informs him that he’s not a team player. Then she fires him on the spot.

Variations on this story recur throughout this engrossing new book by John Carreyrou, the Wall Street Journal reporter whose articles—guided by dozens of frightened but determined sources—brought down Theranos. The fraud that fooled everyone from Walgreens to U.S. statesmen is almost too fantastical to be believed. Holmes, vindictive and paranoid, and the company’s number two, Ramesh “Sunny” Balwani, a bully almost 20 years her senior with whom she was in a romantic relationship, are pitted against employees frantic that patients will be harmed by a technology that doesn’t work.

Holmes dreamed up Theranos in 2004, while at Stanford. She had recently completed an internship at the Genome Institute of Singapore, where she tested patient samples for the severe acute respiratory syndrome (SARS) virus that had devastated Asia. Determined to transform the clunky testing technology, Holmes imagined an arm patch that would diagnose and treat medical conditions. This morphed into Theranos testing devices, which she claimed could run hundreds of tests on a few drops of blood.

It was a remarkable idea. There was just one problem: Scientists and engineers at Theranos couldn’t produce reliable results, at least not in the time frame demanded. That didn’t stop Holmes and Balwani from raking in hundreds of millions of investor dollars or from deploying the error-prone machines for use on unsuspecting patients…
Science Magazine book reviews typically take the obligatory "Praise-Criticism-Praise" format.

Not this one.

See my many prior posts on Theranos here.

In addition to the tsunami of civil litigation that will surely henceforth consume the lives of Elizabeth Holmes and her thuggish co-conspirator Sunny Balwani, these two should be criminally indicted. John Carryrou's book overflows with comprehensively vetted elements of probable cause for charges of egregious felony fraud.
...[O]n March 14, 2018, the Securities and Exchange Commission charged Theranos, Holmes, and Balwani with conducting “an elaborate, years-long fraud.” To resolve the agency’s civil charges, Holmes was forced to relinquish her voting control over the company, give back a big chunk of her stock, and pay a $ 500,000 penalty. She also agreed to be barred from being an officer or director in a public company for ten years. Unable to reach a settlement with Balwani, the SEC sued him in federal court in California. In the meantime, the criminal investigation continued to gather steam. As of this writing, criminal indictments of both Holmes and Balwani on charges of lying to investors and federal officials seem a distinct possibility.

Carreyrou, John. Bad Blood: Secrets and Lies in a Silicon Valley Startup (p. 341). Knopf Doubleday Publishing Group. Kindle Edition.
An important book, IMO. Reads like a suspense novel. Great job, sir.


CBS "60 Minutes: The Theranos Deception."
John Carreyrou: She [Elizabeth Holmes] is a pathological liar. She wanted to be a -- celebrated tech entrepreneur. She wanted to be rich and famous. And she wouldn't let anything get in the way of that.
Norah O'Donnell: What kind of job did the board do in holding Holmes accountable?
John Carreyrou: This is one of the most epic failures in corporate governance in the annals of American capitalism. They did nothing to verify that her scientific claims were true...
Watch all of it. Read the book.

BTW, random note. Google "Naked Capitalism Horan Uber" and bring a Snickers (you'll be a while; a book's worth of accrued analysis). They make the Theranos fraud look like relative chump change. They're trying to hang on and blow enough smoke long enough to IPO their way out of their multi-billion dollar mess (they lost about $4.5 billion in 2017) and foist their intractable losses onto the markets (meaning, in part, into your retirement funds).


Another "Holy Shit" book. Just started it. Yikes.

ALMOST two decades ago, when I wrote the preface to my book Causality (2000), I made a rather daring remark that friends advised me to tone down. “Causality has undergone a major transformation,” I wrote, “from a concept shrouded in mystery into a mathematical object with well-defined semantics and well-founded logic. Paradoxes and controversies have been resolved, slippery concepts have been explicated, and practical problems relying on causal information that long were regarded as either metaphysical or unmanageable can now be solved using elementary mathematics. Put simply, causality has been mathematized.”

Reading this passage today, I feel I was somewhat shortsighted. What I described as a “transformation” turned out to be a “revolution” that has changed the thinking in many of the sciences. Many now call it “the Causal Revolution,” and the excitement that it has generated in research circles is spilling over to education and applications. I believe the time is ripe to share it with a broader audience.

This book strives to fulfill a three-pronged mission: first, to lay before you in nonmathematical language the intellectual content of the Causal Revolution and how it is affecting our lives as well as our future; second, to share with you some of the heroic journeys, both successful and failed, that scientists have embarked on when confronted by critical cause-effect questions.

Finally, returning the Causal Revolution to its womb in artificial intelligence, I aim to describe to you how robots can be constructed that learn to communicate in our mother tongue— the language of cause and effect. This new generation of robots should explain to us why things happened, why they responded the way they did, and why nature operates one way and not another. More ambitiously, they should also teach us about ourselves: why our mind clicks the way it does and what it means to think rationally about cause and effect, credit and regret, intent and responsibility…

Pearl, Judea; Mackenzie, Dana. The Book of Why: The New Science of Cause and Effect (Kindle Locations 47-61). Basic Books. Kindle Edition.
This one is gonna be fun. Stay tuned. From the Atlantic interview article: Pearl sees it, the field of AI got mired in probabilistic associations. These days, headlines tout the latest breakthroughs in machine learning and neural networks. We read about computers that can master ancient games and drive cars. Pearl is underwhelmed. As he sees it, the state of the art in artificial intelligence today is merely a souped-up version of what machines could already do a generation ago: find hidden regularities in a large set of data. “All the impressive achievements of deep learning amount to just curve fitting,” he said recently...
"If I could sum up the message of this book in one pithy phrase, it would be that you are smarter than your data. Data do not understand causes and effects; humans do."
In short, being unreflectively "data-driven" (that fashionable tech cliche) is a both naive and a cop-out. (Note: some of this will surely go -- at least tangentially --  to the "information ethics" topic of my prior post.)

More to come...

Wednesday, May 23, 2018

"The International Center for Information Ethics?"

Gradually trying to start moving on after losing my daughter. The house is now quiet and empty except for Cheryl and I, after a crazy busy week.

Got a new (promptly reciprocated) Twitter Follow:

Given that my grad degree is in "Ethics and Policy Studies" (an interdisciplinary mashup of PolySci, Econ, applied Philosophy, and Jurisprudence, etc), I am innately attracted to this area. I joined. We shall see.
The International Center for Information Ethics (ICIE) is an academic community dedicated to the advancement of the field of information ethics. It offers a platform for an intercultural exchange of ideas and information regarding worldwide teaching and research in the field. ICIE provides an opportunity for community and for collaboration between colleagues practicing and teaching in the field. It provides news regarding ongoing activities by various organizations involved in the shared goals of information ethics…

Digital Ethics concerns itself with human and digital interactions, including decisions made by humans while interacting with the digital, as well as those decisions made by the digital interacting with humans. Digital Ethics includes, in order of appearance into the field, Computer Ethics, Cyberethics, and AIethics. It places a focus on ethical issues pertaining to such things as software reliability and honesty, artificial intelligence, computer crime, digital transparency and e-commerce. The origins of Digital Ethics are found in the adoption of ethical concerns into Computer Science, as influenced by Norbert Wiener's 1948 Cybernetics.

Media Ethics concerns itself with ethical practice in journalism and information dissemination, and includes issues as diverse as conflicts of interest, source transparency, fairness, fake news, and information accuracy. It aims to represent the best interests of the public through impartiality and balance, recognizing and addressing bias, and strives to respect individual privacy while demanding corporate and government transperency. Media Ethics makes explicit that journalism and media play a large part in shaping worldviews in society and as such demands a responsibility and personal commitment on the part of the journalist.

Alongside ethical considerations for Computer Science, the field of Information Ethics was first encapsulated under the ethical practices of Libraries and Information Science in the late 1980’s and early 1990’s. Library Ethics focuses on issues of privacy, censorship, access to information, intellectual freedom and social responsibility. It addresses copyright, fair use, and best practices for collection development. While Library Ethics originates, in the professional sense, in 19th-century librarianship, it finds its origins in a tradition of information ethics that stretches back to ancient Greece.

Intercultural Information Ethics considers perspectives on information dissemination, ICTs and digital culture from the point of view of both globalization and localization. It provides an account of information culture as originating from all cultures, envisaged through comparative philosophies such as Buddhist and western-influenced information ethics traditions to African Ubuntu and Japanese Shinto ethics traditions in ICTs. In its applied sense, Intercultural Information Ethics strives to move beyond the presumed biases of western and greek-influenced ethical foundations for the field of Information Ethics to include globally diverse information ethics traditions. Philosophically, it endeavors to bridge a notable chasm in the field of information ethics, namely the foundational divide between information ecology and hermeneutics.

Bioinformation Ethics explores issues of information pertaining to technologies in the field of biology and medicine. Traditional concerns in Bioethics such as abortion, organ donation, euthanasia, and cloning form the basis of Bioinfomation Ethics, but are supplemented by questions regarding the influence of digital and information & communication technologies. Bioinformation Ethics addresses rights to biological identity, the use of DNA and fingerprints, the dissemination of biomedical information and equal rights to insurance and bank loans based on genetics.

Business Information Ethics is the convergence of two separate fields of applied ethics, those being Information Ethics and Business Ethics. Business Information Ethics addresses informational considerations of the dissemination of goods and services, including information as a commodity, and provides ethical guidance in the analysis of the use of goods and services, including discourse on the impact they have on society. Business Information Ethics also addresses concerns for journal and information management, and includes the subfield of Organisational Information Ethics, as represented by the Centre for Business Information Ethics (CBIE).

“An important aspect of today's understanding of Ethics concerns issues of individual and social responsibility with regard to the impact of our choices in light of the influence of science and technology. While information and communication technologies open doors to new technological and scientific possibilities, they also act as a catalyst to an unprecedented encounter with otherness, ensuring through digital mediums the en masse collision of hitherto closed ethical systems and cultural worldviews."
-- Rafael Capurro
Yeah. It resonates.

apropos, see my prior post "Artificial intelligence and ethics." See also "The old internet of data, the new internet of things and "Big Data," and the evolving internet of YOU."

Stay tuned.


Also trying to get back on pace with my reading. I'm buried. Just a couple of new ones (I have about a dozen piled up):

I've had a good recurrent go at the massive fraud of Theranos (John Carreyrou's topic in his newly released book). Thus far a compelling "page turner." They've probably already sold movie rights.

More on Michael Pollan and Judea Pearl.

Three others I've recently started:


BTW, speaking of "AI" and "Ethics," see
How the Enlightenment Ends
Philosophically, intellectually—in every way—human society is unprepared for the rise of artificial intelligence.
Henry Kissinger, no less.
...If AI learns exponentially faster than humans, we must expect it to accelerate, also exponentially, the trial-and-error process by which human decisions are generally made: to make mistakes faster and of greater magnitude than humans do. It may be impossible to temper those mistakes, as researchers in AI often suggest, by including in a program caveats requiring “ethical” or “reasonable” outcomes. Entire academic disciplines have arisen out of humanity’s inability to agree upon how to define these terms. Should AI therefore become their arbiter?...
Yeah. One of my grad school profs observed one day that "it is often erroneously claimed that the Nazis 'had no ethics.' They most certainly did -- an aggressive ethos of murderous elimination."


A fashionable (overhyped?) area of AI of late is "NLP" (Natural Language Processing). Within that topical area is the subfield "NLU" (Natural Language Understanding). Notwithstanding its obvious extant (if circumscribed) utility -- e.g., "Siri" --, I have concerns. See my prior post "Assuming / Despite / If / Then / Therefore / Else..." Could AI do "argument analysis?"

It seems rather obvious to me that one foundational element of "Information Ethics" is that of the accuracy of information (in particular information comprising "arguments") -- i.e. rationality in pursuit of truths. If you don't have that, all you have is "noise."

I'd be rather skeptical of trying to sanguinely delegate such tasks to "NLU."

More to come...