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Archive for the ‘Human Genetics’ Category

FDA sends letters to 5 genetic testing companies

Friday, June 11th, 2010

It appears that the FDA sent letters to several different direct to consumer genetic testing companies. They are 23andme, Navigenics, DeCode, Illumina, and Knome, which provides whole genome sequencing. The FDA is claiming the tests must undergo approval as a medical device, but did not say anything about removing them from the market. The article also mentions that Pathway Genomics, the company producing the genetics tests that Walgreens considered selling in its stores, also received a letter.

Having recently received my 23andme results, I’m a little concerned by this statement:

Concern about the tests was also raised this week when 23andMe said that because of a laboratory mix-up, up to 96 customers might have received genetic information belonging to someone else.

I certainly hoped that they notified these customers of the potential error…

OpenPCR: DNA amplification for anyone

Thursday, June 10th, 2010

OpenPCR is a cool new project dedicated to building plans for an open source PCR machine. There’s not much inherently complicated about a PCR machine and it’s about time — a PCR machine built with $300 in parts using a modern software controller will likely be as powerful as any non-realtime PCR out there. Of course, the reagent pricing is what gets you.

Josh and Tito are raising money for this project using Kickstarter. $1024 gets them to build you a PCR machine, which is a reasonably good deal in the scheme of scientific equipment. I gave them $8, because I like stickers and already have a PCR machine that doesn’t exactly get a lot of use.

Singularity Summit 2010 in San Francisco to Explore Intelligence Augmentation

Monday, June 7th, 2010

Kevin: I’ve been volunteering for the Singularity Institute these last few months. Each year, the Singularity Institute hosts the Singularity Summit, a two-day conference in San Francisco this August that may be of interest to many of the readers of this blog.

Will it ever become possible to boost human intelligence using brain implants, or create an artificial intelligence smarter than Einstein? In a 1993 paper presented to NASA, science fiction author and mathematician Vernor Vinge called such a hypothetical event a “Singularity“, saying “From the human point of view this change will be a throwing away of all the previous rules, perhaps in the blink of an eye”. Vinge pointed out that intelligence enhancement could lead to “closing the loop” between intelligence and technology, creating a positive feedback effect.

This August 14-15, hundreds of AI researchers, robotics experts, philosophers, entrepreneurs, scientists, and interested laypeople will converge in San Francisco to address the Singularity and related issues at the only conference on the topic, the Singularity Summit. Experts in fields including animal intelligence, artificial intelligence, brain-computer interfacing, tissue regeneration, medical ethics, computational neurobiology, augmented reality, and more will share their latest research and explore its implications for the future of humanity.

“This year, the conference shifts to a focus on neuroscience, bioscience, cognitive enhancement, and other explorations of what Vernor Vinge called ‘intelligence amplification’ (IA) — the other route to the Singularity,” said Michael Vassar, president of the Singularity Institute, which is hosting the event.

Irene Pepperberg, author of “Alex & Me,” who has pushed the frontier of animal intelligence with her research on African Gray Parrots, will explore the ethical and practical implications of non-human intelligence enhancement and of the creation of new intelligent life less powerful than ourselves. Futurist-inventor Ray Kurzweil will discuss reverse-engineering the brain and his forthcoming book, How the Mind Works and How to Build One. Allan Synder, Director, Centre for the Mind at the University of Sydney, will explore the use of transcranial magnetic stimulation for the enhancement of narrow cognitive abilities. Joe Tsien will talk about the smarter rats and mice that he created by tuning the molecular substrate of the brain’s learning mechanism. Steve Mann, “the world’s first cyborg,” will demonstrate his latest geek-chic inventions: wearable computers now used by almost 100,000 people.

Other speakers will include magician-skeptic and MacArthur Genius Award winner James Randi; Gregory Stock (Redesigning Humans), former Director of the Program on Medicine, Technology, and Society at UCLA’s School of Public Health; Terry Sejnowski, Professor and Laboratory Head, Salk Institute Computational Neurobiology Laboratory, who believes we are just ten years away from being able to upload ourselves; Ellen Heber-Katz, Professor, Molecular and Cellular Oncogenesis Program at The Wistar Institute, who is investigating the molecular basis of wound regeneration in mutant mice, which can regenerate limbs, hearts, and spinal cords; Anita Goel, MD, physicist, and CEO of nanotechnology company Nanobiosym; and David Hanson, Founder & CEO, Hanson Robotics, who is creating the world’s most realistic humanoid robots.

You can watch videos from past summits and register at www.singularitysummit.com.

Dan Vorhaus, Attorney At Law, Legally Advises Medical Doctors Can Use 23andMe To Provide Medical Advice

Friday, May 28th, 2010

Daniel B. Vorhaus, Harvard Law School, J.D., editor of Genomics Law Report, and practicing attorney in North Carolina at Robinson, Bradshaw & Hinson, gives the following legal advice to Dr. Steven A. R. Murphy regarding possibility of using 23andMe in clinical practice. In the following quote, Dan Vorhaus advises Dr. Steven Murphy with “no ambiguity” that the 23andMe Terms of Service ”aren’t binding.”

@Andrew Evans is correct. Steve, the [23andMe] ToS aren’t binding on you. You do with the 23andMe data – and any other piece of information provided by one of your patients – what your professional judgment dictates. There’s no ambiguity there.

According to Dan Vorhaus, the 23andMe Terms of Service do not exclude its use for health ascertainment. He further implies that intended use for 23andMe service should be inferred from the contents of the test results themselves and not solely defined by the 23andMe Terms of Service.

There’s no ambiguity to me here, either. Here Dan Vorhaus has published what I consider to be written advice from a lawyer in his professional capacity to a medical doctor in response to a specific complaint regarding the legality of the application 23andMe service for use in health ascertainment or disease purposes in a clinical setting for medical application.

Further, while Dan Vorhaus did not state so explicitly, I have implied as a layperson from this comment thread that Dan Vorhaus publicly advises 23andMe users to share 23andMe results with medical doctors to communicate clinically useful information for intended possible medical application in a clinical application despite the 23andMe Terms of Service which state that the 23andMe service “cannot be used for health ascertainment or disease purposes.”

Dan Vorhaus has published that the 23andMe Terms of Service are not binding.

Maybe I’m mistaken —but I’m just a layperson. I don’t see any ambiguity regarding how lawyer Dan Vorhaus has advised doctors that 23andMe can be used in the provision of medical advice within the professional capacity of licensed medical practice. Despite that the 23andMe Terms of Service explicitly forbids this use, Dan Vorhaus advises that these terms in the 23andMe contract are not binding in a medical setting when the test results are provided by a patient to a medical doctor.

23andMe is an egregious attack on civil liberties and I have yet to read a compelling argument otherwise. Freedom with Terms of Service like 23andMe’s is not freedom at all.

Note: I do understand that a third party is not necessarily bound to the 23andMe Terms of Service when presented with unsolicited information derived from the 23andMe service. However, I also understand that this 23andMe legal strategy is unethical because it distorts the law with a bad faith contract intended to evade regulation at the expense of public health and in favor of arbitrary federal enforcement at the expense of independent medical institutions and professionals.

Reference: 23andMe Terms of Service

3. Description of What the Services Are and Are Not: 23andMe Service Is For Research and Educational Use Only. We Do Not Provide Medical Advice, And The Services Cannot Be Used For Health Ascertainment or Disease Purposes

Please Stop Antagonizing the AMA

Wednesday, May 26th, 2010

The American Medical Association (AMA) has one real function:

To Defend the Language of Medical Procedures (CPT codes).

They have done this by regularly publishing standard definition, enforcing access to licensing, cooperation with Center for Medicare / Medicaid Services (CMS), and aggressively defending their copyrights and trademarks.

They do not do this by “reorganizing a community of doctors.”

Please stop antagonizing the AMA by accusing it of ineffectiveness and corruption. It’s not relevant if these accusations could be true because these accusations are self-fulfilling. Empty accusations of ineffectiveness pressures the AMA to raise even more dubious funding to further purchase its own overextension. Then, to medical doctors, the more an organization resembles a pharmaceutical campaign, the less they will believe that organization legitimately represents them. Every glossy brochure, every phone call, every fax, every campaign further alienates doctors.

Eventually, somebody will breach the CPT wall and decades of wisdom will be dumped into the digital sea of craven monsters. Think: Napster. Imagine a world where musicians could effectively print their own cash by recording music and selling it online. Napster utterly destroyed that dream.

Is that what you want? To bring down medical doctors down to your level where everything you make is valued only by what it costs for other people to take it from you? That’s bad.

If you want to help doctors “organize,” then apply for a $30k receptionist job at a medical office and, from there, use your skills and vision to organize their operations. That’s a start.

Meanwhile, if continue to call people “Beezlebub” casually enough in passing conversation, then somebody will eventually believe you. That’s bad. There’s no mercy for people whom other people think are evil.

Death And Taxes: CMS to IRS

Wednesday, May 19th, 2010

I hope this is a meme that sticks.

The American Center of Medicare and Medicaid Services (CMS) is not your friend any more than the American Internal Revenue Service (IRS).

CMS, like IRS, is charged with the grim duties of its office. They are not magic or Gods or evil or friendly. They are people with jobs. Jobs that they do. But know this: there is no civilian interaction with either CMS or IRS after which you’ll come home smiling.

Remember the movie “Meet Joe Black?” How did the screenplay writers depict Death himself? A noisy bully? A pedantic bureaucrat?

No. Death is already everywhere. He already knows everything. He has all the time and all the power in the universe, and he amuses himself by drifting about the highest pinacles of power in effortless bemusement punctuated by an occasional gesture of utter domination. (Except, arguably, over “the power of the human spirit,” —not that that’s going to make you any less dead or any less liable. Anthony Hopkins still died in that movie.)

CMS: The Death Office. Boring, boring, boring… BOOM! By the time you’re warned, it is too late, and in the meantime, Death had been watching you the entire time. You had simply chose to ignore Death because you had simply chose not to think about Death. Too scary. Yah, well now you’re too audited and too broke to do anything about it (or too dying and too broke to do anything about it, depending on your perspective).

Now, certain idiots in Silicon Valley think that 4chan “Internet is Serious Business” is a great big joke and that they can be invincible so long as they run around with their impossible powers like obnoxious children. Free! Free $44,000 from CMS! Just Sign Here!

Hey, this worked for Google, right? (no, but that’s what everybody thinks, so that’s what’s relevant)

The problem is that it’s not going to be the software vendors who will suffer the wrath of CMS. Or, they will, but the best nerds already expect to be kicked around —they basically build that into their business plans –you aren’t even a real Silicon Valley player until you can prove your creds by goading dumb jock powerful enough to kick at you. Meanwhile, the alpha nerds made their money, the bagmen kick down a few paper companies, and poof! Nerdswarm spores explode into the breeze —drift about, puff puff puff— until enough land in whatever new domain seems ripe enough for a whole new nerdswarm raiding party. These few hire their friends… The Great Nerd Cycle of Life begins anew. (that’s basically how I got to where I am, so yah, that’s basically how the technology industry works)

No, it’s not the guilty nerds who will suffer, its the most vulnerable doctors —and their patients— who don’t know yet not to blindly trust the alpha nerds and their blueshirt lackeys because, to doctors, they all look like harmless Best Buy kids with free cool toys and —oh hey! Free money from the government! Doctors can get behind “free money from the government” (especially when their own medical practice businesses are failing and their embarrassed to admit it)

Meanwhile, the real “muhaha’s” are left for the financier politocrats who don’t do the work and don’t care about the science but now have all the power because you idiots all bankrupted each other in a big “Who Is Most T Shirt Che Guevara” competition funded by increasingly “creative” loans and contracts gleefully doled out by Ambitious Young Men who also love to par-tay! and truly believe everything you do but who, regrettably *sad face*, had to include all that “boring legal boilerplate stuff” because otherwise their bosses would get all mad and, like, “Whatever, dude. Eat or be eaten… but not you. You’re a champ. A real go-getter.”

From KevinMD:

But – after I talked to an Apple employee, they informed me the 2009 American Recovery and Reinvestment Act of 2009 is one of the main reasons why Apple is trying to promote its platform for electronic medical record use – and one of the main reasons for the workshops.

Really? The best feature of the iPhone is that CMS is going to pay you to use it? That’s your pitch to doctors?

“Hey! Go Fuck with The Death Office! They’re giving out FREE MONEY! (sign here)”

Listen: most people already know that you can’t trust all doctors all the time. Why? Because you can’t trust all people all the time, and all doctors are people; therefore, you don’t double down any drug Whatever Clinic dumped into your purse to get you out the door because you saw it on television.

The same is true with technology. Use common sense! You are trusting these companies about which you know nothing with your most private and valuable information on the premise of what we already know to be a lie: Free $44k From CMS. Does it matter that from this lie that it doesn’t necessarily follow that the software vendor is untrustworthy? No, it does not follow necessarily, but then, neither does it necessarily follow that your ruin will be of Management Team Bagman at frothy Software Vendor Yesterday, or, much more likely but much less interesting, the simple bad business of giving away your only means of economically supporting your business to people you don’t know for free while meanwhile you refuse to address the most obvious flaws of your business including 1) you don’t understand technology 2) your business is utterly dependent on that technology 3) medical insurance stopped paying you and there’s nothing you can do about it (now).

Listen: if you make medical software, can’t you just made a reasonable product and sell it for regular money without all the gimmicks and stupid tricks? Is it really so hard to charge a fair price for a fair value? Come on. The iPhone itself is a great tool for a steal price because —with no additional “Applications”— it is already a cell phone and a pager that browses the web and downloads your email for a few hundred. Come on! That’s crazy voodoo magic. It’s wonderful! So, do you really have to also entertain these venture-funded campaigns to steal All The Medical Data in the World! (muhahaha) and then shuffle around all-bashful-like confused while they concoct troll-face excuses and Lawyer-To-The-Letter defenses to cover their own guilty-as-hell-but-too-smart-to-get-caught asses? Then what? Play or be played? Nerd rage on Twitter?

Go to hell.

There’s plenty of potential for great work in medicine without resorting to tricks. For example: you are going to die. So are all your friends! That sounds like a problem to me. Wouldn’t you like to credibly try and solve that problem rather than just blow about until you’re hired to push whatever stupid blueshirt tech fad you saw at the last bubblecon? I would. Hell, you can start all the back with “billing software” in medicine (yes, addition and subtraction) because —I can assure you from personal experience running an actual medical practice —doctors are not getting paid, and that’s bad —assuming you want anybody around in your country still in business who has dedicated their lives to understanding and healing the human body in a credible and responsible way? (Yes, you do.)

Yes, I think that DMV medicine is basically a given, but you people don’t have to exasperate it, and hey, maybe DMV medicine is not inevitable. Maybe I’m wrong, and the whole world will be singing koom-ba-yah because this “Free Universal Healthcare! (insurance)” thing actually worked out. Maybe Jesus will return to Earth and fix up the math of it with super Jew Plus Team America GO! chacha magic or whatever. And if I’m right and we (you) are all screwed, well, maybe now is the time to make friends with some private jet pilots (doctors) to discuss that other Plan B (your escape to the good private healthcare that’s going to be technically unlawful in a decade) because you’re not going to be able to do that so easily in twenty years standing in line to register your car and update your pharmacogenomic profile —especially if you’re already dead from hypertension complications or whatever because you thought this New Age stuff was the real deal and the DMV Clinic line was pretty long and it’s so boring and yah whatever smoking and drinking and fast food and soda really wasn’t that bad after all or at least you don’t care anymore so whatever.

Response to “Genomic Medicine: Lost”

Wednesday, May 19th, 2010

(in response to “Lost” by Steven Murphy)

I claim that you can’t expect results better than the ideal model by using that model.

I claim that it’s not enough to choose another ideal model that gives you answers that you like irrespective of reality. That method already exists; it’s called religion. Go to church.

I say that genomics is the best opportunity of which I’m aware to design and implement a better model of human medicine, but that the gravity and magnitude of this potential as it can be applied to each human individual to themselves has been so far squandered by people who —by all external appearances— had just wanted to throw parties for themselves.

My frustration is that the leaders of “genomics medicine” were unworthy —which I claim by evidence including:

  • their lack of quantitative results as measured in unhealthy people made healthy
  • their failure to lead their teams and companies over even a few years
  • sometimes even outright abandonment or exile which I can only interpret as shear cowardice or perhaps weakness but nonetheless was at the expense of the domain and those invested in it
  • demonstrable commercial gluttony of pricing the market for genomic tests and services far below the sustainable cost to provide them
  • demonstrable civil gluttony of abusing permissive public health regulations and academic endorsement until law enforcement is forced to interviene (e.g. FDA)
  • demonstrable intellectual gluttony of abusing academic endorsements including those by Stanford, Harvard, Yale, Oxford, and Google which were justified as “experimental” until the community was forced to publish work which has humiliated even the endorsement of the theoretical substance of these “experiments”
  • demonstrable publicity gluttony of abusing the trust of media institutions including the New York Times and Time magazine to broadcast bombastic declarations of the future which were then held against them when they were found to be absurd which has substantially damaged both the credibility and the morale of these institutions —particularly regarding their participation in this domain

I claim that the continued entertainment of the residual sophistry propping the myth failed leader’s success and their obnoxious superstitions is an obstruction, a distraction, and an insult, and I think that the people at fault are not the majority of the domain leaders themselves who are probably all too acutely aware of their own failures, but the crowds of teaming enthusiastic groupies who had believed the original mythology on the cheap but now will not be constructively disabused otherwise for a reasonable expense because it is more difficult to unlearn an identity than it is to adopt a new identity and because of a residual interest by this leadership to not publicly flagellate itself at its own expense and pride. These people are largely worthless excluding their unconditional support or cooperation which will no longer be readily available due to the abuses I described. It is my advice that this mess be labeled “DTC Genomics,” publicly mocked, cast away, and then relaunched under some other label which actually is the same people in the same domain doing the same work but without the negative connotation of “whatever was bad about the last time” which will be labeled as “DTC.”

People fail, but fail honestly, accept responsibility, and learn from your mistakes. No yoga happy fun time go team A for Æffort bullshit is going to get code written or diseases cured. This isn’t China; but it’s not the Special Olympics either.

Dr. Steven Murphy expresses another frustration which is that he knows that the best of what is already available in medicine has not been already widely applied before new methods are being explored. I agree, but I don’t think that is relevant to exploratory genomic medical application like as in the Lancet paper because that was not the intent of the paper and that would not have changed its conclusions or relevance. I also think that Steve conflates his general frustration with the politics of the domain with his frustration of its substance, and that this weakness (ie he’s a shitty writer and a sloppy debater) makes his arguments read like incoherent rants when in demonstrable reality he knows more about the successful application of genomic medicine at an individual patient level appropriate to expect in common practice because he actually regularly achieves this in his daily work as opposed to merely publishing theories about such application with experience limited to practice within City Of God like enclaves of a world class medicine institution. Being a shitty writer and a sloppy debater is irrelevant to Steve’s excellence as a medical doctor and is unlikely to necessarily prevent him from improving these skills given practice and relevant corrective exposure.

Sam R. Riley Wants To Tell You About Practice Fusion

Monday, May 17th, 2010

Sam R. Riley follows me around the Internet, including to the comments of The Last Psychiatrist, defending Practice Fusion and attacking me. I assume from the contents of his comments that he would like to draw more attention to me and my opinions about Practice Fusion.

Very well. However, it is good manners to move unrelated discussion to your own website, and so I have done this.

My comment (excluding extraneous details):


My ire derives from that this technotronic bamboozling continues be abused to con vulnerable _doctors_ (and by proxy, their patients) into poor decisions with dire future ethical hazards. For example: http://www.practicefusion.com.

Practice Fusions’s “business plan” is to provide a “free EMR” which will store all your patient’s billing and medical information and then sell that information to marketers for advertising. In exchange, the doctor gets “$45,000 free money” from Medicare, plus “free EMR software service.”

Now, if you had to fill out a grubby paper forms in a dingy office as advertised on TV so that your doctor could sell your demographics to some aggressive “outside agency” to “pay his bills,” that would be outrageous.

And yet, that is exactly what is happening here with Practice Fusion and —I promise you— other “social media” web 2.0 applications which are coming. Because they use a flashy website and not paper forms, and because they advertise online rather on television, we don’t make the ethical connection.

It’s funny: people think it’s the patients who need to be protected. Oh no. No no no. I can assure you, it’s the _doctors_ who need protecting, because patients don’t make decisions —doctors do— and doctors are going broke because many medical insurers are bankrupt and continue to simply miss minimum payments with a barrage of lame excuses and evasion.

No no, I don’t think “other” people entrusted to me are “retarded.” I think that the human condition _universally_ is “retarded,” and I include both myself, doctors, and patients as humans. That’s what tortures me.

Sam Riley’s response:

My Yates,

I was very surprised when reading your comments, particularly at your hostile tone, as I am a Practice Fusion user and have been for some time now. From my experience the product and it’s functionality have been top notch, and the support from their team has been a class act. The e-prescribing feature and lab integration features are excellent – and every time I log into the product there seems to be more functionality available to me. In the past I used to use eclinicalworks at a hospital I worked at and it was a terribly unfriendly application. The screens were hostile and non-intuitive and the application was always freezing and slowing down our interaction with patients.

I was concerned about data sales when registering for Practice Fusion and discussed this with my account manager, as well as actually read the user agreement when registering – and made sure that they do not sell physician or patient information. I even received a letter from the CEO stating this.

After reading your other blog posts, I was disappointing to see that you are not even a doctor, nor are you qualified to make a recommendation on an Electronic Health Record. Your endorsement to use google docs as an EHR in not only illegal but almost blasphemous, as this product is not even HIPAA compliant. Your juvenile youtube video about 23andme was particularly telling about your professionalism, or lack there of. Other readers can see what I am referring to here: http://www.youtube.com/watch#!v=euO3-h9_jdQ&feature=related

When you graduate school, finish your residence, start practicing medicine, or even reach puberty, you might be a reliable source to recommend how to practice medicine and what tools to use, but until then, you’re just a little social medial weasel attempting to get his 15 minutes of fame.

PS – why did you reject my comment on your blog? Are you afraid of a little debate?

I do agree that free, advertising-supported Google Docs and Gmail is not appropriate for medicine. That is why I advocate purchasing a license from Google to resolve the relevant privacy and ethical issues which would otherwise disqualifies these service from medical use.

I’m not qualified to comment about blasphemy.

John Dolan on Aging and the Horrifying Conclusion of GWAS

Sunday, May 16th, 2010

Behold! The ideal reference human.

The eXile Guide to Aging

Look down at your hand. Flex the tendons, watch them ripple under the skin. What a nice design! So silent and quick. That’s what they never get in these cyborg movies: the fact that a really good design doesn’t whirr and clank. It’s silent and quick, like bodies are. Like yours. Yours, these sinews; and that long, stretchable leg, genital toy, brave shoulders, stubborn toes, a zoo of perfect forms and all yours for the price of admission.

There’s only one little flaw: you are trapped in the body of a dying animal…

There’s been a mistake. Someone screwed up the design, with malicious intent. Can you sue Darwin? Can you negotiate an exit from this dying animal? Apparently not. What are we, mere medieval peasants, serfs? Absolutely.

Read this. Digest it.

Now, consider the conclusion of “Clinical assessment incorporating a personal genome” [Lancet 2010; 375: 1525–35]

Important limitations remain in our ability to comprehensively integrate genetic information into clinical care. For example, a comprehensive database of rare mutations is needed. Since risk estimates change as studies are completed, a continually updated pipeline is necessary. There are imperfections in all human genomes published to date—false positive and false negative SNP calls, incomplete measurement of structural variation, and little direct haplotype data. Finally, gene-environment interactions are challenging to quantify and have been little studied.

Really? And what are these “important limitations?”

  • “database” not “comprehensive” “enough”
  • “imperfections” in “published” data
  • “challenging to quantify”

OK. Skip ahead two decades. We’ve done more studies, our models have improved, and our data is more complete.

Prediction: This same paper will be published in two decades with the following conclusions:

  • “database” not “comprehensive” “enough”
  • “imperfections” in “published” data
  • “challenging to quantify”

Why? For once in medicine, the disappointing conclusion is not because the clinical application was sloppy. This is excellent data analyzed by excellent people using excellent methods. The problem with this paper is the premise —first paragraph, first sentence:

the clinical translation of genetic risk estimates remains unclear

No! The clinical translation of genetic risk estimates remains clearly to be what we already know about human medicine:

THE REFERENCE HUMAN AGES AND DIES IN LESS THAN 100 YEARS. DEVIANTS FROM THE REFERENCE HUMAN FARE EVEN WORSE.

The conclusion of GWAS is right there, in your face, cold and ugly. You’re an animal, animals die, and there’s nothing you can learn about yourself to change that.

There is no “silver bullet” in software, and there’s no silver bullet in medicine, because there is no particular feature you can correct or understand about the human body to achieve a clinical expectation of “perfect health” because that hypothesis is nonsensical.

Life is not the movie Avatar. The Nature Tree doesn’t love you, and you won’t live forever if you can always remember your yoga mat and buy fresh groceries at Whole Foods. Disease is not a human flaw, it is a human feature, and a disease-free human would not be human as we understand humans to be. It is an insane, desperate superstition to believe that if only we can “purge all unnatural toxins” or “fix all diseases” or “learn everything about our bodies” that we’ll live in “good health” forever. No, you won’t, and you’ll be dead before you can tell anybody that you didn’t.

All existing medical science from antiquity to present confirms this conclusion, and I am unaware of any credible counter example —which I consider to include a living adult human who is casually indistinguishable from middle age, but who is actually over 150 years old.

I’m not discouraging research or clinical application of genomics. I’m saying that the ideal human is not good enough if your premise includes an expectation of superhuman health.

Why Was Pathway Targeted for FDA Enforcement and Not 23andMe?

Saturday, May 15th, 2010

In response to Dan Vorhaus, Of Drugstores and Devices: Parsing the FDA’s Evolving DTC “Policy”

Perhaps Pathway has been targeted for regulatory enforcement not because of a particular of “substance”, but because of a particular of enforcement itself: it is easier to physically enforce containment than it is to ideologically enforce cooperation.

I do believe that location is relevant to FDA enforcement because American federal government agencies police the “location” of the geographic United States and not the substance of ideas as universal abstractions.

However, I do agree that I think that the “discretion of enforcement” has been crudely applied. I too would prefer that this “regulatory discussion” began with an official publication describing enforcement policy rather than a quote in the popular press.

But, perhaps the attitude of many people is that while they too prefer a “regulatory discussion,” they do not deign themselves to participate in “block faction conflicts.” In that case, enforcement is not about “substance”: who started what in medical genomics. It’s all about “location”: expedient slum clearance without lame excuses and backtalk from the denizens of DTC Genomics.

Indeed: how do you host a good faith, civilized conversation about “genomics in public health” with the sort of rabble who sells Tay-Sachs, BRCA, and drug metabolism diagnostics as “Not for diagnostic use” from a blimp over booze with celebrities; who call themselves “revolutionaries” and you “the evil empire” and then publicly mock your inaction to stop them?

I disagree with Steven Murphy that the regulatory agencies should have been included in the first place. I think that the FDA should have never have been engaged at all.

Ideally, people would be trusted to order their own medical tests reasonably, and medical test providers would be trusted to govern themselves sincerely. But no. A certain cabal and their trashy scheme to “seize the future of entrepreneurship” has ruined this future for everybody.

So, I think that Pathway has been selected for FDA enforcement not because of any particular about Pathway’s genetic test itself, but because Pathway was a vulnerable target in an already targeted domain, and it’s easier to start with a one easy win as precedence for future enforcement policy than it is to try to police all possible targets simultaneously.

Aside: Isn’t this what Fancy School is for? You go to Fancy School to learn how to act civilized, and in exchange, you are given the power and the discretion to operate in society beyond what is otherwise tolerated. You don’t actually have to be civilized. (That’s for sucker overachieving middle class types who try too hard and don’t know better.) You just have to not flaunt yourselves in public and embarrass everybody.

This sounds like a fair deal to me: in exchange for not insulting everybody with your trashy “non-medical” Tay-Sachs, BRCA Breast Cancer, and drug metabolism medical tests which you push on the public as a goofy toys while you play T-Shirt Che Guevara, you don’t have to suffer the indignity of arbitrary FDA beat cop interrogations for whichever of your hoodies happen to be most conveniently “available” and then having to list your home address, driver’s license, and the contact information of your “current or most recent employer” for “future reference.”

(But Andrew, 23andMe and Pathway are completely different companies!)

Yah. Uh huh. Yah. Wrong neighborhood. Cops don’t care. You all look the same. Name, address, license and registration? Sign here, please.

23andMe Now Diagnoses Fatal Tay-Sachs Disease

Wednesday, May 12th, 2010

Exhibit: Patient: Andrew Yates “Tay-Sachs Disease | 23andMe Established Research Report” (negative/negative)

A deleterious mutation of the HEXA gene is by definition a diagnosis of Tay-Sachs disease (homozygous or compound heterozygous) or Tay-Sachs carrier (heterozygous).

Regarding 23andMe’s medical laboratory test commercially advertised by 23andMe to the public as “Tay-Sachs Disease | 23andMe Established Research Report”, (“Report”) 23andMe publishes the following Claim:

Intended for research and educational purposes. Not for diagnostic use.

My complaint, as a human subject of this Report, is that 23andMe provides no distinction —other than the Claim itself— to justify why this Report is not for diagnostic use when the contents of the Report itself are sufficient for diagnostic use by the definition of a diagnosis of Tay-Sachs disease and of Tay-Sachs carrier status.

Thus, I claim that the negligence of 23andMe to justify its Claim endangers my safety as I myself am unable to reconcile this apparent contradiction without this distinguishing information which 23andMe withholds from me and thus I am unable to best act to protect my health and the health of my potential children.

===

They are making medical claims. We don’t know whether the test works and whether patients are taking actions that could put them in jeopardy based on the test.

Alberto Gutierrez, Director of the FDA’s Office of In Vitro Diagnostic Device Evaluation and Safety, 2010

Indeed.

Gattaca: “The Matrix” of Genomics

Tuesday, May 11th, 2010

Gattaca is as much about genomics is The Matrix is about informatics —which is to say: nothing and everything.

NOTHING because YOU LEARN NOTHING ABOUT EITHER FROM THE MOVIE. You actually understand less about the subject than you did before the movie because now domain language has been conflated with the cinematic affect of the movie. After 106 minutes of the world’s most sophisticated propaganda, your squishy mammal brain leaves that theatre with strong opinions, high confidence, and a grab bag of superstitions superficially identical to the language of the actual science, but entirely inapplicable to representing physical reality.

Wearing a trenchcoat and calling yourself a hacker does not write software. Supporting awareness and calling yourself an ethicist does not cure diseases.

EVERYTHING because EVERYBODY UNDERSTANDS BOTH FROM THE MOVIE. You left that theatre with all the right passion, confidence, and signals: congratulations, you are now perfectly sociologically equipped to infect the collective domain understanding with noise. Go forth! Even if you yourself don’t watch the movie, other people did, and they now understand you by it.

And, I don’t mean “everybody except you because you know better.” I mean “everybody especially you because you know better.” For example, you will learn more about Gattaca reading this post than you will about genomics. You’ll learn more about The Matrix than genomics from this post. You think that because you “know better” that you’re immune from your own humanity? No! Personally, the best I can cope is by some tortured parody. I know that Pepsi is terrible for me. I know that I’m being manipulated to want it despite my own interests. Yet, somehow, I’ll be wandering around the Stop-n-Shop, and magically a Pepsi product has appeared in my hand. At least a tortured hostility sometimes results in me successfully rejecting the impulse. It works better than arrogant rationalization.

“Hmph, I’m wise to this game, so like a good American, I’ll completely overlook that I’ve completely complied with all the objectives of the propaganda while applying my intelligence to rationalize the propaganda’s success invisible to me because I prefer to understand myself as the sort of person who is too sophisticated to be affected by such crude manipulation. ”

See, let’s watch how well rationalization doesn’t work. I’ll now spend the rest of this post infecting you with all ideas Gattaca because we’re all just too clever to be affected by such things.

For example, after I mocked Steve Dickman at Boston Biotech Watch for presenting the Gattaca movie poster as credible expert commentary about medical testing company Counsyl, commenter John cleverly searched the Think Gene archives. The Gattaca Movie Poster is ubiquitous in hack genomic commentary. Think Gene is hack genomic commentary. Surely, I must have posted the poster myself… Yes!

But ah ha!

“For example, when you are an astronaut assigned to critical mission in space, you had better not have a 90% chance of dying of a heart attack during the mission. Oh… I guess the scene where Vincent dies in space and the mission is aborted at the cost of decades and trillions… was cut.”

John responds:

That’s what I thought when I watched it. It’s a risk. Do we want to take a risk in order to give someone the chance to fulfill a dream or to prove to people that they can meet their dreams? Once something becomes an objective fact, it’s hard to ignore it. The fact that Vincent faked his physical training and checkups, in the movie, demonstrates that the scriptwriters for the movie apparently felt that those processes are unnecessary. Ok, so I guess NASA should no longer do them since Gattaca says so?

Yes! Of all possible occupations, “interplanetary astronaut” is probably the MOST appropriate occupation for exhaustive medical screening. It’s even more appropriate than “olympic athlete.” If you have a heart attack on the 100 meter butterfly —that’s annoying. If you have a heart attack on the the 1,000,000,000 meter  —that’s also annoying, but also, while the world’s most incompetent doctor humors your angina as “indigestion,” you were supposed to be piloting the world’s largest ballistic missile to Saturn. The “triumph of the human spirit” is not going to help you pump your blood at 10Gs, and I generally prefer my world’s largest ballistic missiles to be piloted by people generally healthy enough to prevent them from exploding over… well, so don’t explode at all.

Also, the inspirational quote? “I never saved anything for the swim back.” Translation: “suicidal.” Olympic swimmer: good attitude. Pilot of world’s largest ballistic missile: bad attitude.

Why can’t Vincent be a navigator and not an astronaut? Or get his heart fixed?

Further, I am entirely unable to practically distinguish a common RFID employee identification badge —which every NASA-like facility already uses— and the “DNA test” used in Gattaca. Even a driver’s license works better than those crappy DNA scans —they include a color, high resolution photograph of your face.

And when Vincent is hired by a prestigious firm solely by his “profile” before the hiring manager even meets him… what, that’s never happened to a Stanford graduate? Come on.

We wish the real world was as lenient or dramatic as Gattaca’s. In real life, some prig threatened by Vincent’s ambition would have reported Vincent to Human Resources for something as lame as a resume mis-reference and —strictly per the employee handbook— Vincent would be transferred or fired because he wouldn’t have the political connections with management as the “mysterious, gifted outsider” to make an exception.

Video: Google Enterprise to Outsource Medical Administration

Sunday, May 9th, 2010

This is a video of my sister, Katie Yates, at the University of Toledo, Ohio describing how she uses Google Enterprise and Apple iPhone to remotely manage the administrative functions of my medical practice in Connecticut.

Katie will be joining me at Google I/O next week in San Francisco.

Brawndo: Still Mutilating Thirst, Still Not Yet Sold at the Stop-n-Shop Pharmacy

Sunday, May 9th, 2010

Brawndo: It has electrolytes!

Brawndo: it’s what plants crave

“Go Get Me A Brawndo” Speech

Lunch Meeting regarding labor dispute over Brawndos

(These videos are from this summer)

Various Whiteboards on Solid State Medical Operations

Friday, May 7th, 2010

This was from when I tried to “prove” to Steve that “you can’t just write stuff on scraps of paper.”

Basically, the conclusion of this conversation was (as Steve will attest), “your egghead airforce crap is all ‘lazers and shit,’ but here on the ground I have a wall of bodies here beating down the door and every dumbshit chuck-a-chuck two bits to an NPI is gunning down every open phone line to get me to sign something or read something and then refuses to pay me and meanwhile I have two infant children and people in the hospital, so get this fucking billing out. I can’t just type this into a computer, patients hate that, and I’m dying here.” But as you can see from previous posts, Steve and I have mutually made some progress.

Basically: I’ll trust you that this shit works… if you trust me to give me the shit that actually works now.

This was “why you can’t just throw a nurse at it.” There was another board where I showed that every staff member you add that isn’t a provider themselves adds overhead downstream of the actual event which accumulates exponentially per unit medical provided. The idea here was that it greatly mattered in medicine how easy it was to enter the data into the iPhone because there was an inflection point where technology just required too much attention and the doctor has to revert to paper, and that if you can’t reliably overcome that activation energy of attention, then all your computer systems are worthless.

Haha, this was from when I taught Steve binary; I think because he asked something about “why 128 ASCII characters?” or something like that, so I made him figure it out over the course of the day. This was also a bad day; I remember some real estate agent had tried to sell Steve a “great unfinished property in an upcoming neighborhood” in the cold rain, and over subsequent lunch with the agent at Greenwich Hospital, I told the agent to his face that his property was a “knock down piece of shit” and then listed the construction and neighborhood flaws I had noticed, and then I scolded him for wasting my time. So this hotshot thirty something blueshirt is sitting there while some kid in a t-shirt deconstructs his entire psyche over salads. This agent now tries to avoid me —for some reason— when he tries to pitch Steve other real estate opportunities.

===

My goal is to build a “solid state” medical office. The idea is that if everything in “one unit doctor” can be represented by a graph of [web addresses] (emails, HTTP requests, ICD, CPT, and medical keyword addressing), and that this “one unit doctor” itself operates at a profit independently, that one could then continue to add doctors to the system without incurring the overhead which currently keeps medicine local while “solving medicine” as we currently know it via graph analysis.

This is hard to do in practice.

I’m posting some of my ideas because frankly: I need more help because I’m tapped on activation energy running both the office and my personal life which, as a preview, here’s how I spent today:

  • Woke up in a hotel to “engineering” demanding to know from behind me door if “my floor is damp.” Why am I in a hotel? Yes. Is my floor damp? Not that I noticed, but considering that yesterday the problem was “the fire alarms keep going off because ‘they’re drawing too much power in the conference room’, this was an improvement. I bet you that this hotel costs more per day than a mortgage for a house.
  • Waited for an hour to get expensive salad. Tried to connect to Internet.
  • Waited for an hour to get a car pickup.
  • While in the hotel lobby waiting for said car, had to track down the contact information for a patient on my iPhone internet, call several times from three different phones while in the hotel lobby trying to get past the patient’s family’s screen of “telephone calls are always solicitors and debit collectors”, and inform irate “member of the family who handles persistant phone calls” that the patient had an INR of [GO TO THE EMERGENCY ROOM, NOW] to “GO TO THE EMERGENCY ROOM, NOW.”
  • Car took me to other side of town to car rental agency, car agency refused to rent me a car without a credit card because a debit card is not acceptable by “Connecticut law?” The girl at the desk at this dank car depot wanted me to produce paystubs and home utility bills “like, from the Internet or something.” I told her no. Car drove me back to hotel.
  • Called another car, $20 cab ride to office; it is now 3pm.
  • Started doing work, but then an elderly patient wandered into the office because I forgot to lock the door and I scheduled an appointment for her and talked with her about “life.”
  • Locked door.
  • Wrote these posts.

So yah, could use a little help… and unless you’re into the unemployed-if-not-now-then-soon mortgage derivative finance blueshirt scene… not really much of a culture here in Connecticut that doesn’t make you want to go all Tyler Durtin all the time.

In software, I’m currently writing authenticated robots to navigate insurer websites for Google App Engine. (I’ll share my code so far at Google I/O for anybody into Python Google App Engine.) This is hard because insurance is not in the business of telling you how to bill them for money. Also, this is hard because of the organic profitability of incompetence and a culture of “typing is for secretaries.” This is also hard because I can’t effectively do data entry and write software to do the data entry at the same time from the back of a cab.

The Raw Facts about Counsyl

Friday, May 7th, 2010

Counsyl Genetics: The Truth

Oh… the “raw facts” about Counsyl are already freely available in a well documented scientific paper hosted at Nature Biotechnology which precisely describes Counsyl’s medical genomic testing product and its intended application. A layperson’s summary of Counsyl is, oh… already freely available on Counsyl’s website.

What did you expect? A movie poster?

(Andrew, don’t you have something intelligent to say about Counsyl?)

No, because:

  • I’m not Counsyl
  • All the relevant information about Counsyl is already freely available
  • Oh… you can JUST BUY THE STUPID THING YOURSELF ON THE COUNSYL WEBSITE RIGHT NOW and… IT’S EXACTLY AS DESCRIBED which is a BORING MAIL ORDER MEDICAL TEST WHICH COSTS A FEW HUNDRED DOLLARS. Since Counsyl neither ports your existing library of sega genesis games so that you can smugly reminisce how easy it always really was beat Sonic the Hedgehog now that you’re almost thirty nor downsamples your favorite top 40 RnB tunz into twenty second loops on your mobile even though you have purposely selected from five to ten years ago so that you can feel ironic because you’re “hip” to the “whole thing,” I don’t know how Counsyl is of any general interest … unless there is a movie poster?… no, no movie poster. so… tldr; go away

I have no idea what else I’m supposed to say. I think that the Counsyl product as it is now is a finished product, I think that everybody should get one, but I think that the Counsyl engineers should find something else to do because I can assure you —from personal experience— that the Counsyl website —by the simple virtues that it A) exists and B) usually works— is already better and easier than anything else I have to use in my medical office. My problem is that EVERYBODY ELSE in medicine is so horrible, and that we at the medical office only have a limited amount of attention we can levy per patient, so preventative medicine beyond “stop smoking” and “lose weight” and “you are going to die; here’s a thing that probably preventativizes that; you can pick it up at the pharmacy counter next to the cigarette case inside the box store that had to add a second soda isle —plus checkout coolers— to accomodate all the new flavors energy drinks because bulk soda which already had its own double sided isle”

…is effectively noise.

Google Calendar Overhead Waiting Room Display

Friday, May 7th, 2010


Simple: Google Enterprise calendar, HTML view. The entire system including the solid wood cabinet cost about a couple thousand dollars. Aside: I have not read all of Unix Power Tools or Unix Networking, so don’t think I’m a Unix genius. I just know basic stuff like how to open a port and manually read and write HTTP headers. I did read War Nerd. So far, nobody I’ve noticed has complained about that book, though sometimes I mark up books that I don’t like, and last week, a patient exclaimed to Steve that he knew the author of the book I had defaced! But it was OK, because he thought she was a “such a snob,” so he thought that was hilarious. So sometimes, Greenwich Connecticut is OK. There’s nothing that can bring people of all cultures together faster than a mutual hatred for stuck up snob impostors. I told the patient: “yah, that’s why I like computers. They don’t lie.” I don’t think he liked that answer, but whatever.


This computer was originally my desktop computer purchased for me by Paul Charlton of Mountain View, CA. So if you’re out there… hey, Paul. You can have you computer back, but I broke the system fan sensor so you have to press F2 twice to bypass the BIOS warning.


This is how the waiting room is arranged from the entrance; the calendar display is immediately to the left.

I had bought the drawers from Ethan Allen across the street. I had somehow convinced the Ethan Allen people that it was OK to move the piece across Highway 1 on a dolly directly into my office lol. This was from this summer.

Remote Medical Video Monitoring on iPad and iPhone

Friday, May 7th, 2010




iPhone video not shown; it works similar to the iPad.

We do not record in the exam rooms.

Conversations are recorded using iPhone voice recorder. This is usually for “business use” not for “patient use” because the culture here in Greenwich / Stamford is to lie about everything and later intimidate people into silent conformance so as not to “disturb the tidy.” Basically, imagine the movie Atonement, include the variety of accents and corrosive duplicity of inherited wealth, but subtract beauty, costumes, and wealth, and set the movie in the year 2010 next to a Dunkin Donuts in a smog cloud: that is urban southwestern Connecticut.

Funny Pictures from This Year Building the Medical Practice

Thursday, May 6th, 2010


Andrew with a baby.


Steven with a computer.

Apple And Google Team Up To Launch Revolutionary Mobile Health System

Saturday, May 1st, 2010

No, just kidding. This is just a toy iPad and a $10 Google enterprise account.